Web document 3.8. Alignment of odorant-binding proteins

 

The accession numbers of rat and bovine odorant-binding proteins are NP_620258 and P07435.
This document includes:
1. The sequences of rat and bovine OBP.

2. EBI Needle global alignment

3. Result of a blastp search (March, 2007) using rat OBP as a query against the nr database restricted to human. The best match is shown.

4. The human protein in the fasta format
5. Result of a global alignment between the rat and human proteins.

 

1. The sequences of rat and bovine OBP.

 

>gi|20302101|ref|NP_620258.1| odorant binding protein I f [Rattus norvegicus]
MVKFLLIVLALGVSCAHHENLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKII
FNVKLDSECQTHTVVGQKHEDGRYTTDYSGRNYFHVLKKTDDIIFFHNVNVDESGRRQCDLVAGKREDLN
KAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ

 

>gi|129022|sp|P07435|OBP_BOVIN Odorant-binding protein (OBP) (Olfactory mucosa pyrazine-binding protein)
AQEEEAEQNLSELSGPWRTVYIGSTNPEKIQENGPFRTYFRELVFDDEKGTVDFYFSVKRDGKWKNVHVK
ATKQDDGTYVADYEGQNVFKIVSLSRTHLVAHNINVDKHGQTTELTELFVKLNVEDEDLEKFWKLTEDKG
IDKKNVVNFLENEDHPHPE

 

2. EBI Needle global alignment

 

########################################
# Program:  needle
# Rundate:  Sun Mar 25 12:05:00 2007
# Align_format: srspair
# Report_file: /ebi/extserv/old-work/needle-20070325-12045723908366.output
########################################
 
#=======================================
#
# Aligned_sequences: 2
# 1: EMBOSS_001
# 2: EMBOSS_001
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 179
# Identity:      53/179 (29.6%)
# Similarity:    80/179 (44.7%)
# Gaps:          27/179 (15.1%)
# Score: 216.0
# 
#
#=======================================
 
EMBOSS_001         1 MVKFLLIVLALGVSCAHHENLDISPSEVNGDWRTLYIVADNVEKVAEGGS     50
                                    |..|..:.:.||::|.|||:||.:.|.||:.|.|.
EMBOSS_001         1                AQEEEAEQNLSELSGPWRTVYIGSTNPEKIQENGP     35
 
EMBOSS_001        51 LRAYFQHMECGDECQELKIIFNVKLDSECQTHTVVGQKHEDGRYTTDYSG    100
                     .|.||:.:...||...:...|:||.|.:.:...|...|.:||.|..||.|
EMBOSS_001        36 FRTYFRELVFDDEKGTVDFYFSVKRDGKWKNVHVKATKQDDGTYVADYEG     85
 
EMBOSS_001       101 RNYFHVLKKTDDIIFFHNVNVDESGR--RQCDLVAG---KREDLNKAQKQ    145
                     :|.|.::..:...:..||:|||:.|:  ...:|...   :.|||.|..|.
EMBOSS_001        86 QNVFKIVSLSRTHLVAHNINVDKHGQTTELTELFVKLNVEDEDLEKFWKL    135
 
EMBOSS_001       146 ELRKLAEEYNIPN--ENTQHLVPTDTCNQ    172
                     ...|..::.|:.|  ||..|..|.     
EMBOSS_001       136 TEDKGIDKKNVVNFLENEDHPHPE         159

 

 

3. Result of a blastp search (March, 2007) using rat OBP as a query against the nr database restricted to human. The best match is shown.

 

>gi|119570938|gb|EAW50553.1|  hCG1795014 [Homo sapiens]
Length=181
 
 Score = 53.1 bits (126),  Expect = 3e-07, Method: Composition-based stats.
 Identities = 42/155 (27%), Positives = 74/155 (47%), Gaps = 9/155 (5%)
 
Query  20   NLDISPSEVNGDWRTLYIVADNVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSEC  79
            N D+S  +++G+W ++ + +D  EK+ E GS+R + +H+   D      + F  KL+  C
Sbjct  27   NFDLS--KISGEWYSVLLASDCREKIEEDGSMRVFVKHI---DYLGNSSLTF--KLNGNC  79
 
Query  80   QTHTVVGQKHEDGRY-TTDYSGRNYFHVLKKT-DDIIFFHNVNVDESGRRQCDLVAGKRE  137
                +  +  E     +TDY+G N   +L+   D+ I+F+N N+          +  +  
Sbjct  80   TEINLACKPTEKNAICSTDYNGLNVIDILETDYDNYIYFYNKNIKNGETFLMLELYVRTP  139
 
Query  138  DLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ  172
            D++   K+   K  EE+ I  EN   L   D C Q
Sbjct  140  DVSSQLKERFVKYCEEHGIDKENIFDLTKVDRCLQ  174

 

4. The human protein in the fasta format:

>gi|119570938|gb|EAW50553.1| hCG1795014 [Homo sapiens]
MMLLLLCLGLTLVCAQEEENNDAVTSNFDLSKISGEWYSVLLASDCREKIEEDGSMRVFVKHIDYLGNSS
LTFKLNGNCTEINLACKPTEKNAICSTDYNGLNVIDILETDYDNYIYFYNKNIKNGETFLMLELYVRTPD
VSSQLKERFVKYCEEHGIDKENIFDLTKVDRCLQARDEGAA

 

5. Result of a global alignment between the rat and human proteins.

 

# Aligned_sequences: 2
# 1: EMBOSS_001
# 2: EMBOSS_001
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 193
# Identity:      50/193 (25.9%)
# Similarity:    91/193 (47.2%)
# Gaps:          33/193 (17.1%)
# Score: 175.5
# 
#
#=======================================
 
EMBOSS_001         1 MVKFLLIVLALGVS--CAHHE--------NLDISPSEVNGDWRTLYIVAD     40
                        .:|::|.||::  ||..|        |.|:  |:::|:|.::.:.:|
EMBOSS_001         1    MMLLLLCLGLTLVCAQEEENNDAVTSNFDL--SKISGEWYSVLLASD     45
 
EMBOSS_001        41 NVEKVAEGGSLRAYFQHMECGDECQELKIIFNVKLDSEC-QTHTVVGQKH     89
                     ..||:.|.||:|.:.:|:   |......:.|  ||:..| :.:.......
EMBOSS_001        46 CREKIEEDGSMRVFVKHI---DYLGNSSLTF--KLNGNCTEINLACKPTE     90
 
EMBOSS_001        90 EDGRYTTDYSGRNYFHVLKKT-DDIIFFHNVNVDESGRR--QCDLVAGKR    136
                     ::...:|||:|.|...:|:.. |:.|:|:|.|: ::|..  ..:|.. :.
EMBOSS_001        91 KNAICSTDYNGLNVIDILETDYDNYIYFYNKNI-KNGETFLMLELYV-RT    138
 
EMBOSS_001       137 EDLNKAQKQELRKLAEEYNIPNENTQHLVPTDTCNQ           172
                     .|::...|:...|..||:.|..||...|...|.|.|       
EMBOSS_001       139 PDVSSQLKERFVKYCEEHGIDKENIFDLTKVDRCLQARDEGAA    181