GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS31940
          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.

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 (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:

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