GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamH in Azospirillum brasilense Sp245

Align Benzoyl-CoA reductase electron transfer protein, putative (characterized, see rationale)
to candidate AZOBR_RS31940 AZOBR_RS31940 NADH-quinone oxidoreductase subunit F

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS31940 AZOBR_RS31940 NADH-quinone
           oxidoreductase subunit F
          Length = 561

 Score =  298 bits (763), Expect = 4e-85
 Identities = 175/526 (33%), Positives = 270/526 (51%), Gaps = 60/526 (11%)

Query: 23  PTKPCISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYP 82
           P    + VC    C  +G  +++     EL+   +  +V      C G C   P V I  
Sbjct: 94  PPPVTVRVCDSLSCCMAGGEKLL----DELKAADMGPDVRVVRAPCMGACHNAPAVAI-- 147

Query: 83  EGICYLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSE 142
                             H + E   V+ ++       T       +P Y          
Sbjct: 148 -----------------GHALHENATVESVVTAVKNGETHP----QLPTYV--------- 177

Query: 143 NLRLDSKSMDDYLAIGGYSALSKVLFQMTP-EDVMGEIKKSNLRGRGGGGFPAWRKWEES 201
                  S++ Y A GGY  L+  L    P +D++G+++ +NLRG GG GFP  RKW   
Sbjct: 178 -------SLEQYKAEGGYRLLADCLTGNVPVDDILGKLEGANLRGLGGAGFPTGRKWRFV 230

Query: 202 RNAPDPIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYP 261
           R+ P P + + VN DEG+PG F DR  +E +PH  LEG++IGA+ V A + +IY+R EYP
Sbjct: 231 RHEPGP-RLMAVNGDEGEPGTFKDRYYLENDPHRFLEGMLIGAWVVEATDVYIYLRDEYP 289

Query: 262 LAVENINLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEP 321
              E +   I    + G  G           + +  GAGA++CGE SA++ ++EG+ G P
Sbjct: 290 HIREVLEHEIAAVEKAGLAGHT--------RIHLRRGAGAYICGEESAMLESIEGKRGLP 341

Query: 322 RPKYIHTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKIT 381
           R K    +V G++  P+++NNVET   +  I+ KGADW+ S+G  G  G + +S+ G + 
Sbjct: 342 RHKPPFPSVVGLFGRPTLINNVETLFWIRDILEKGADWWGSHGRNGRKGLRSYSVSGHVK 401

Query: 382 NTGLVEVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKA 441
           + G+   P GVT+R++I +  GG+  G   K    GG SGG +P +M D+P+DF  L + 
Sbjct: 402 DPGVKLAPAGVTIRELIDEYCGGMADGHTLKGYLPGGASGGILPASMDDIPLDFGTLEQH 461

Query: 442 GSMMGSGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGK 501
           G  +GS  ++V+ +   M  + R  +DF +DESCG+CTPCR G  + +A++      K  
Sbjct: 462 GCFIGSAAVVVLSDQDDMRKVVRNLLDFFEDESCGQCTPCRVGTEKAVALI------KQP 515

Query: 502 EGDIELLEELAESTG-AALCALGKSAPNPVLSTIRYFRDEYEAHIR 546
             D  LL ELA   G A++C LG++A NP+ S +++FRD+    +R
Sbjct: 516 VWDEPLLTELARLMGTASICGLGQAAMNPLKSALKHFRDDLRGEVR 561


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: 944
Number of extensions: 54
Number of successful extensions: 5
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: 561
Length adjustment: 37
Effective length of query: 598
Effective length of database: 524
Effective search space:   313352
Effective search space used:   313352
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 paper from 2022 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