Web document 3.6. Example of global and local alignment.

 

Contents of this document:

1. Sequences in the fasta format

2. Global alignment using the needle program at EBI

3. Local alignment from a blastp search using the E. coli protein as a query.

 

 

1. Sequences in the fasta format

 

>gi|16130477|ref|NP_417047.1| fused nitric oxide dioxygenase/dihydropteridine reductase 2 [Escherichia coli K12]
MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNAIAAYASNIEN
LPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPGQEVLDAWGKAYGVLANVFINREAEIYN
ENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGGAVAEYRPGQYLGVWLKPEGFPHQEIRQYSLTR
KPDGKGYRIAVKREEGGQVSNWLHNHANVGDVVKLVAPAGDFFMAVADDTPVTLISAGVGQTPMLAMLDT
LAKAGHTAQVNWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGLMDLSKLEG
AFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGPHKVL

 

>gi|6321673|ref|NP_011750.1| Nitric oxide oxidoreductase, flavohemoglobin involved in nitric oxide detoxification; plays a role in the oxidative and nitrosative stress responses [Saccharomyces cerevisiae]
MLAEKTRSIIKATVPVLEQQGTVITRTFYKNMLTEHTELLNIFNRTNQKVGAQPNALATTVLAAAKNIDD
LSVLMDHVKQIGHKHRALQIKPEHYPIVGEYLLKAIKEVLGDAATPEIINAWGEAYQAIADIFITVEKKM
YEEALWPGWKPFDITAKEYVASDIVEFTVKPKFGSGIELESLPITPGQYITVNTHPIRQENQYDALRHYS
LCSASTKNGLRFAVKMEAARENFPAGLVSEYLHKDAKVGDEIKLSAPAGDFAINKELIHQNEVPLVLLSS
GVGVTPLLAMLEEQVKCNPNRPIYWIQSSYDEKTQAFKKHVDELLAECANVDKIIVHTDTEPLINAAFLK
EKSPAHADVYTCGSLAFMQAMIGHLKELEHRDDMIHYEPFGPKMSTVQV

 

2. Global alignment using the needle program at EBI

 

########################################
# Program:  needle
# Rundate:  Tue Mar 13 10:48:31 2007
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/needle-20070313-10483068446418.output
########################################
 
#=======================================
#
# Aligned_sequences: 2
# 1: NP_417047.1
# 2: NP_011750.1
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 423
# Identity:     145/423 (34.3%)
# Similarity:   210/423 (49.6%)
# Gaps:          51/423 (12.1%)
# Score: 579.0
# 
#
#=======================================
 
NP_417047.1        1 MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRN     50
                     ||..:|.:.:|||:|:|.:.|..:|..||..|.|.:.||..|||.:||:.
NP_011750.1        1 MLAEKTRSIIKATVPVLEQQGTVITRTFYKNMLTEHTELLNIFNRTNQKV     50
 
NP_417047.1       51 GDQREALFNAIAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGE    100
                     |.|..||...:.|.|.||::|..|:..|::|..||.:.|||||.|.||||
NP_011750.1       51 GAQPNALATTVLAAAKNIDDLSVLMDHVKQIGHKHRALQIKPEHYPIVGE    100
 
NP_417047.1      101 HLLATLDEMFSPG--QEVLDAWGKAYGVLANVFINREAEIYNENASKAGG    148
                     :||..:.|:....  .|:::|||:||..:|::||..|.::|.|..     
NP_011750.1      101 YLLKAIKEVLGDAATPEIINAWGEAYQAIADIFITVEKKMYEEAL-----    145
 
NP_417047.1      149 WEGTRDFRIVAKTPRSALITSFELEPVDGGAV----AEYRPGQYLGVWLK    194
                     |.|.:.|.|.||...::.|..|.::|..|..:    ....||||:.|...
NP_011750.1      146 WPGWKPFDITAKEYVASDIVEFTVKPKFGSGIELESLPITPGQYITVNTH    195
 
NP_417047.1      195 P--EGFPHQEIRQYSLTRKPDGKGYRIAVKRE------EGGQVSNWLHNH    236
                     |  :...:..:|.|||.......|.|.|||.|      ..|.||.:||..
NP_011750.1      196 PIRQENQYDALRHYSLCSASTKNGLRFAVKMEAARENFPAGLVSEYLHKD    245
 
NP_417047.1      237 ANVGDVVKLVAPAGDFF----MAVADDTPVTLISAGVGQTPMLAMLDTLA    282
                     |.|||.:||.||||||.    :...::.|:.|:|:|||.||:||||:...
NP_011750.1      246 AKVGDEIKLSAPAGDFAINKELIHQNEVPLVLLSSGVGVTPLLAMLEEQV    295
 
NP_417047.1      283 KAGHTAQVNWFHAAENGDVHAFADEVKEL---GQSLPRFTAHTWYRQPSE    329
                     |......:.|..::.:....||...|.||   ..::.:...||       
NP_011750.1      296 KCNPNRPIYWIQSSYDEKTQAFKKHVDELLAECANVDKIIVHT-------    338
 
NP_417047.1      330 ADRAKGQFDSEGLMD---LSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLV    376
                             |:|.|::   |.:...|.:|    .|.||.:.|||.....|.
NP_011750.1      339 --------DTEPLINAAFLKEKSPAHAD----VYTCGSLAFMQAMIGHLK    376
 
NP_417047.1      377 DLGVKQENIHYECFGPHKVL       396
                     :|..:.:.||||.|||....   
NP_011750.1      377 ELEHRDDMIHYEPFGPKMSTVQV    399
 
 
#---------------------------------------
#---------------------------------------

 

 

 

3. Local alignment from a blastp search using the E. coli protein as a query:

 

>gi|6321673|ref|NP_011750.1| Nitric oxide oxidoreductase, flavohemoglobin involved in nitric 
oxide detoxification; plays a role in the oxidative and nitrosative 
stress responses; Yhb1p [Saccharomyces cerevisiae]
Length=399
 
 Score =  210 bits (535),  Expect = 6e-54, Method: Composition-based stats.
 Identities = 143/410 (34%), Positives = 208/410 (50%), Gaps = 36/410 (8%)
 
Query  1    MLDAQTIATVKATIPLLVETGPKLTAHFYDRMFTHNPELKEIFNMSNQRNGDQREALFNA  60
            ML  +T + +KAT+P+L + G  +T  FY  M T + EL  IFN +NQ+ G Q  AL   
Sbjct  1    MLAEKTRSIIKATVPVLEQQGTVITRTFYKNMLTEHTELLNIFNRTNQKVGAQPNALATT  60
 
Query  61   IAAYASNIENLPALLPAVEKIAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPGQ--EVLD  118
            + A A NI++L  L+  V++I  KH + QIKPE Y IVGE+LL  + E+       E+++
Sbjct  61   VLAAAKNIDDLSVLMDHVKQIGHKHRALQIKPEHYPIVGEYLLKAIKEVLGDAATPEIIN  120
 
Query  119  AWGKAYGVLANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGG  178
            AWG+AY  +A++FI  E ++Y E       W G + F I AK   ++ I  F ++P  G 
Sbjct  121  AWGEAYQAIADIFITVEKKMYEEAL-----WPGWKPFDITAKEYVASDIVEFTVKPKFGS  175
 
Query  179  AVA----EYRPGQYLGVWLKP--EGFPHQEIRQYSLTRKPDGKGYRIAVKREE------G  226
             +        PGQY+ V   P  +   +  +R YSL       G R AVK E        
Sbjct  176  GIELESLPITPGQYITVNTHPIRQENQYDALRHYSLCSASTKNGLRFAVKMEAARENFPA  235
 
Query  227  GQVSNWLHNHANVGDVVKLVAPAGDFF----MAVADDTPVTLISAGVGQTPMLAMLDTLA  282
            G VS +LH  A VGD +KL APAGDF     +   ++ P+ L+S+GVG TP+LAML+   
Sbjct  236  GLVSEYLHKDAKVGDEIKLSAPAGDFAINKELIHQNEVPLVLLSSGVGVTPLLAMLEEQV  295
 
Query  283  KAGHTAQVNWFHAAENGDVHAFADEVKELGQSLPRFTAHTWYRQPSEADRAKGQFDSEGL  342
            K      + W  ++ +    AF   V EL              + +  D+     D+E L
Sbjct  296  KCNPNRPIYWIQSSYDEKTQAFKKHVDEL------------LAECANVDKIIVHTDTEPL  343
 
Query  343  MDLSKLEGAFSDPTMQFYLCGPVGFMQFTAKQLVDLGVKQENIHYECFGP  392
            ++ + L+   S      Y CG + FMQ     L +L  + + IHYE FGP
Sbjct  344  INAAFLKEK-SPAHADVYTCGSLAFMQAMIGHLKELEHRDDMIHYEPFGP  392