GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Pseudomonas fluorescens FW300-N2E2

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate Pf6N2E2_1468 NAD-dependent formate dehydrogenase beta subunit

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1468 NAD-dependent formate
           dehydrogenase beta subunit
          Length = 519

 Score =  335 bits (860), Expect = 2e-96
 Identities = 194/511 (37%), Positives = 289/511 (56%), Gaps = 21/511 (4%)

Query: 38  ASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEGIC--YLKVKPEDV 95
           A GA +V  A   E E   L   V    T   G     P+V +   G+   +  V P DV
Sbjct: 14  AVGADKVADALALEAERRQLPLTVLR--TSSRGLYWLEPLVELESAGVRLGFGPVTPADV 71

Query: 96  PEIVSHTIKEKKVVDRLLYEDPATGTRALRESD-IPFYKNQQRNILSENLRLDSKSMDDY 154
           P ++             L  DP +   AL   + IP+ K+QQR + +        S+DDY
Sbjct: 72  PGLLD-----------ALTGDPGSHPLALGPVEAIPYLKSQQRLLFARAGITQPLSLDDY 120

Query: 155 LAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPDPIKYVIVN 214
            A GG+  L++ + QM   DV+  +  S LRGRGG  FPA  KW   R+A    KYV+ N
Sbjct: 121 RAQGGFQGLARSI-QMDGADVVASVLDSGLRGRGGAAFPAGIKWRTVRDAVGAQKYVVCN 179

Query: 215 ADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVENINLAIRQA 274
           ADEGD G F DR L+EG+P  ++EG+II   AVGA  G+IYVR EYP A+  +N A+R A
Sbjct: 180 ADEGDSGTFADRMLMEGDPFLLIEGMIIAGLAVGATMGYIYVRSEYPAAISTLNDALRIA 239

Query: 275 SERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYIHTAVKGVW 334
            + G++G ++ GSG  F ++V +GAGA++CGE +AL+ +LEG+ G  R K    A++G++
Sbjct: 240 RDAGYLGANVSGSGRTFDIEVRVGAGAYICGEETALLESLEGKRGTVRAKPPLPAIQGLF 299

Query: 335 DHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLVEVPMGVTL 394
             P++++NV T A+V  I+ KGA ++  +G   S GT  F L G +   GLVE   G++L
Sbjct: 300 GLPTLVHNVVTLASVPIILEKGAQFYRDFGMGRSLGTMPFQLAGNVRQGGLVERAFGLSL 359

Query: 395 RDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMGSGGMIVMD 454
           R+++   GGG   G+  KA Q GGP G  +P +  D P+D++     G+M+G GG++V D
Sbjct: 360 RELVEGYGGGTASGRPLKAAQVGGPLGAWVPPSQFDTPLDYEAFAAMGAMLGHGGVVVAD 419

Query: 455 EDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRI---TVGKGKEGDIELLEEL 511
           +   M  +AR+ + F  +ESCGKCTPCR G  + + V+ R+   T    ++    LL++L
Sbjct: 420 DSLDMAQMARFALQFCAEESCGKCTPCRIGSTRGVEVVDRLIASTEAGARQEQALLLQDL 479

Query: 512 AESTG-AALCALGKSAPNPVLSTIRYFRDEY 541
            ++    +LCALG     PV S +++F  ++
Sbjct: 480 CDTLQYGSLCALGGMTSYPVASALKHFPADF 510


Lambda     K      H
   0.319    0.138    0.420 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 790
Number of extensions: 44
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 635
Length of database: 519
Length adjustment: 36
Effective length of query: 599
Effective length of database: 483
Effective search space:   289317
Effective search space used:   289317
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory