Web document 5.9. Results of the hmmsearch program of HMMER using a set of bacterial and fungal globins as a query (HMM file 02.hmm) and searching a database of human RefSeq proteins (downloaded from the ftp site linked on the home page of NCBI).

Note that there is only one database match (with an E value of 7.1).

 

 

hmmsearch - search a sequence database with a profile HMM

HMMER 2.3.2 (Oct 2003)

Copyright (C) 1992-2003 HHMI/Washington University School of Medicine

Freely distributed under the GNU General Public License (GPL)

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

HMM file:                   02.hmm [globins_bactfungal_]

Sequence database:          human.protein.faa

per-sequence score cutoff:  [none]

per-domain score cutoff:    [none]

per-sequence Eval cutoff:   <= 10       

per-domain Eval cutoff:     [none]

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

 

Query HMM:   globins_bactfungal_

Accession:   [none]

Description: [none]

  [HMM has been calibrated; E-values are empirical estimates]

 

Scores for complete sequences (score includes all domains):

Sequence                         Description            Score    E-value  N

--------                         -----------            -----    ------- ---

gi|27436879|ref|NP_775104.1|     armadillo repeat con  -102.4        7.1   1

 

Parsed for domains:

Sequence                         Domain  seq-f seq-t    hmm-f hmm-t      score  E-value

--------                         ------- ----- -----    ----- -----      -----  -------

gi|27436879|ref|NP_775104.1|       1/1     384   582 ..     1   599 []  -102.4      7.1

 

Alignments of top-scoring domains:

gi|27436879|ref|NP_775104.1|: domain 1 of 1, from 384 to 582: score -102.4, E = 7.1

                   *->MtSgnvhttkPLtpeqvqiilnsSSiGPVDNLKiNERPGSHDHSmRS

                       t+++                ++  i P  NL              

  gi|2743687   384    TTCNP---------ANANAAAEADGIDPLINL--------------- 406 

 

                   EmSSKNassptlpeaiSRSEGSVYQVKiDRGdspnteGFDFKVNARDLLL

                    +SSK +++ + +                                    

  gi|2743687   407 -LSSKRDGAIANA------------------------------------- 418 

 

                   LRmSWDiLLREYLTPKELKVFQALLYSNKHiTSTERPYLNTAPDGmiSKT

                                                                     

  gi|2743687     - -------------------------------------------------- -   

 

                   iDPTARPRKTKQRDNDNKVDgtlLteqFYdnmlaadPELepfFnetkqkv

                                       +t Lt     nm  ++P+           

  gi|2743687   419 --------------------ATVLT-----NMAMQEPLRL---------- 433 

 

                   rrqPrilakaLlayakNienlgpLldfvkkiasKHvgLqvKpehYpivGk

                                   Ni+n   + + ++ + s                

  gi|2743687   434 ----------------NIQNHDIMHAIISPLRS----------------- 450 

 

                   aLletmqellGdaLtlElidAWatAYsnLAnlmItaEadlYaeApWtgFr

                                                An  ++  a+          

  gi|2743687   451 -----------------------------ANTVVQSKAA----------- 460 

 

                   dFrVtkvqrEcseVkSlYltPvdGkplPepkRGQYLarrvDaePslPgea

                                                      La+          +a

  gi|2743687   461 -----------------------------------LAVTA--------TA 467 

 

                   yelvggEasiRempkefYyRisvrkllGLNPAEPGAKAHPglvslhlhgr

                    ++              ++R  +r   GL           +lv+l +  

  gi|2743687   468 CDV--------------EARTELRNSGGLE----------PLVELLRS-K 492 

 

                   wdnsgdklkvspPcGdFvyesseflvglLgGgqgyrgrhGHPrLrarHmp

                   +d+++                   +++++ +g+ ++ +           

  gi|2743687   493 NDEVRKHA---------------SWAVMVCAGDELTAN------------ 515 

 

                   lgideamrdqWLtcmlsaiEarltpaAg.ravrflhPslrtadsrafgkl

                      +   ++      l ++E++  +  g+r+ +f++         a +kl

  gi|2743687   516 ---ELCRLG-----ALDILEEVNVS--GtRKNKFSE--------AAYNKL 547 

 

                   lm.slkipygqqQVPTNKiPTlklteFtStekkgedydlidaiaprtlda

                   l ++l ++y q+                                     

  gi|2743687   548 LNnNLSLKYSQT-------------------------------------- 559 

 

                   eDLdlIspeddgyllGprgymtdvadylrnrgveDrvKlelFGptAQQKN

                              gyl           ++++n g  D   +    p+    

  gi|2743687   560 -----------GYLS---------SSNIINDGFYDYGRI---NPG----- 581 

 

                   Ceiv<-*

                         

  gi|2743687   582 ---T    582 

 

 

Histogram of all scores:

score    obs    exp  (one = represents 24 sequences)

-----    ---    ---

<-207      4      -|=                                                          

 -207      0      0|                                                          

 -206      1      0|=                                                         

 -205      0      0|                                                          

 -204      1      0|=                                                         

 -203      0      0|                                                          

 -202      1      0|=                                                         

 -201      1      0|=                                                         

 -200      2      0|=                                                         

 -199      3      0|=                                                         

 -198      1      0|=                                                          

 -197      1      0|=                                                         

 -196      6      0|=                                                         

 -195      2      0|=                                                          

 -194     12      0|=                                                         

 -193     12      0|=                                                         

 -192      6      0|=                                                          

 -191     12      0|=                                                         

 -190     11      0|=                                                         

 -189     18      0|=                                                         

 -188     18      0|=                                                         

 -187     21      0|=                                                         

 -186     26      0|==                                                        

 -185     33      0|==                                                        

 -184     25      0|==                                                        

 -183     35      0|==                                                        

 -182     43      0|==                                                         

 -181     45      0|==                                                        

 -180     36      0|==                                                        

 -179     51      0|===                                                        

 -178     46      0|==                                                        

 -177     65      0|===                                                       

 -176     64      0|===                                                        

 -175     92      0|====                                                      

 -174     98      0|=====                                                     

 -173    109      0|=====                                                     

 -172    105      0|=====                                                     

 -171    132      0|======                                                    

 -170    129      0|======                                                    

 -169    169      0|========                                                  

 -168    144      0|======                                                    

 -167    163      0|=======                                                   

 -166    186      0|========                                                   

 -165    249      0|===========                                               

 -164    218      0|==========                                                

 -163    281      0|============                                               

 -162    269      0|============                                              

 -161    322      0|==============                                            

 -160    359      0|===============                                            

 -159    420      0|==================                                        

 -158    426      0|==================                                        

 -157    460      0|====================                                      

 -156    512      0|======================                                    

 -155    606      0|==========================                                

 -154    606      0|==========================                                

 -153    702      0|==============================                            

 -152    769      3|*================================                         

 -151    853     19|*===================================                      

 -150    838     74|===*===============================                       

 -149    950    210|========*===============================                  

 -148   1031    468|===================*=======================               

 -147   1069    855|===================================*=========             

 -146   1185   1330|==================================================     *  

 -145   1127   1819|===============================================           *

 -144   1198   2241|==================================================        *

 -143   1296   2539|======================================================    *

 -142   1328   2690|========================================================  *

 -141   1399   2698|==========================================================*

 -140   1329   2591|========================================================  *

 -139   1251   2403|=====================================================     *

 -138   1302   2166|=======================================================   *

 -137   1122   1908|===============================================           *

 -136   1052   1651|============================================              *

 -135    937   1407|========================================                  *

 -134    918   1186|=======================================          *        

 -133    815    990|==================================       *                

 -132    723    820|===============================   *                       

 -131    656    675|============================*                              

 -130    525    553|====================== *                                  

 -129    541    451|==================*====                                   

 -128    424    367|===============*==                                         

 -127    356    298|============*==                                           

 -126    266    241|==========*=                                              

 -125    230    195|========*=                                                

 -124    183    157|======*=                                                  

 -123    118    127|=====*                                                    

 -122    114    102|====*                                                     

 -121     77     82|===*                                                      

 -120    100     66|==*==                                                     

 -119     63     53|==*                                                       

 -118     43     42|=*                                                         

 -117     33     34|=*                                                        

 -116     21     27|=*                                                        

 -115     18     22|*                                                          

 -114     15     17|*                                                         

 -113      8     14|*                                                         

 -112     12     11|*                                                          

 -111      7      9|*                                                         

 -110      1      7|*                                                         

 -109      2      5|*                                                         

 -108      0      4|*                                                         

 -107      2      3|*                                                         

 -106      1      3|*                                                         

 -105      0      2|*                                                         

 -104      1      2|*                                                         

 -103      1      1|*                                                         

 

 

% Statistical details of theoretical EVD fit:

              mu =  -140.9514

          lambda =     0.2193

chi-sq statistic = 52071.7383

  P(chi-square)  =          0

 

Total sequences searched: 33669

 

Whole sequence top hits:

tophits_s report:

     Total hits:           67

     Satisfying E cutoff:  1

     Total memory:         21K

 

Domain top hits:

tophits_s report:

     Total hits:           67

     Satisfying E cutoff:  67

     Total memory:         150K