GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Pseudomonas fluorescens FW300-N2E3

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AO353_15695 AO353_15695 formate dehydrogenase

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15695 AO353_15695 formate
           dehydrogenase
          Length = 519

 Score =  319 bits (818), Expect = 2e-91
 Identities = 187/523 (35%), Positives = 287/523 (54%), Gaps = 26/523 (4%)

Query: 26  PCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIV-MIYPEG 84
           PC S+       A GA EV  A  T+     L  ++    T   G     P++ M  P+G
Sbjct: 7   PCDSLAR-----AVGADEVAVALATQARERNLPLDLQR--TSSRGLYWLEPLLEMDTPQG 59

Query: 85  -ICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALR-ESDIPFYKNQQRNILSE 142
            I +  +   DVP ++             L  +P+    AL    ++P+ K+QQR + + 
Sbjct: 60  RIGFGPLTAADVPSLLD-----------ALQGEPSAHPLALGLVEELPYLKSQQRLLFAR 108

Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESR 202
                  S+DDY A GG+  L++ +  +  E     +  S LRGRGG  FPA  KW   R
Sbjct: 109 AGITRPLSLDDYRAHGGFEGLTQAI-ALGGEQTATAVFDSGLRGRGGAAFPAGIKWRTVR 167

Query: 203 NAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPL 262
                 KY++ NADEGD G F DR L+EG+P  ++EG+ I    VGA  G+IYVR EYP 
Sbjct: 168 GTQAAQKYIVCNADEGDSGTFADRMLMEGDPFLLIEGMAIAGITVGASYGYIYVRSEYPQ 227

Query: 263 AVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPR 322
           AV  +  A+  A   G++G ++ GSG  F ++V +GAGA++CGE +AL+ +LEG+ G  R
Sbjct: 228 AVATLREALDIARAAGYLGANVGGSGLAFDMEVRVGAGAYICGEETALLDSLEGKRGIVR 287

Query: 323 PKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITN 382
            K    A++G++  P++++NV T A+V  I+ KGA ++  YG   S GT  F L G + +
Sbjct: 288 AKPPIPALQGLFGLPTLVHNVLTLASVPMIMAKGAQFYRDYGMGRSLGTMPFQLAGNVRH 347

Query: 383 TGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAG 442
            GLVE   G+TLR+++ + GGG   G+  KA Q GGP G  +P    D P+D++     G
Sbjct: 348 GGLVERAFGLTLRELVEEYGGGTASGRPLKAAQVGGPLGAWVPPGQFDTPLDYEAFAAIG 407

Query: 443 SMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVG---K 499
           +M+G GG++V D+   M  +AR+ + F  +ESCGKCTPCR G  + + V+ R+       
Sbjct: 408 AMLGHGGVVVADDSLDMAHMARFAMQFCAEESCGKCTPCRIGSTRGVEVIDRLLAAPDQS 467

Query: 500 GKEGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEY 541
            ++  + +L++L ++    +LCALG     PV+S ++YF  ++
Sbjct: 468 SRDEQVIILKDLCDTLQYGSLCALGGMTSYPVVSALKYFPADF 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: 827
Number of extensions: 42
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.

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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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