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_RS14955 AZOBR_RS14955 formate dehydrogenase subunit beta

Query= uniprot:Q39TW5
         (635 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS14955 AZOBR_RS14955 formate
           dehydrogenase subunit beta
          Length = 521

 Score =  333 bits (854), Expect = 1e-95
 Identities = 192/516 (37%), Positives = 291/516 (56%), Gaps = 14/516 (2%)

Query: 28  ISVCAGAGCLASGAAEVIAAFKTELEFHGLTTEVNTKGTGCPGFCERGPIVMIYPEG-IC 86
           I V   A  L+ GA E  AA + E    G+   +   G+    + E   + +  PEG + 
Sbjct: 8   IYVPRDAAALSVGADETAAAIRAEATKRGIPLRIVRNGSRGMLWLET-LVEVETPEGRVA 66

Query: 87  YLKVKPEDVPEIVSHTIKEKKVVDRLLYEDPATGTRALRESDIPFYKNQQRNILSENLRL 146
           Y  V  EDV  +      E    D  L          L E  IP++  Q+R   +    +
Sbjct: 67  YGPVMAEDVAGLFDAGFLEG--ADHAL-------AHGLTEK-IPYFAKQERLTFARCGII 116

Query: 147 DSKSMDDYLAIGGYSALSKVLFQMTPEDVMGEIKKSNLRGRGGGGFPAWRKWEESRNAPD 206
           D  S++DY   GG+  L + L  MTP +++ E+ +S LRGRGG GFP   KW    NA  
Sbjct: 117 DPLSVEDYRLHGGFRGLERAL-AMTPAEIVTEVTESGLRGRGGAGFPTGIKWNTVLNAKA 175

Query: 207 PIKYVIVNADEGDPGAFMDRALIEGNPHSILEGLIIGAYAVGAHEGFIYVRQEYPLAVEN 266
             KY+  NADEGD G F DR ++EG+P  ++EG+ I A AVGA EG+IY+R EYP AV  
Sbjct: 176 DQKYICCNADEGDSGTFADRMIMEGDPFCLIEGMTIAAIAVGATEGYIYIRSEYPHAVAT 235

Query: 267 INLAIRQASERGFVGKDILGSGFDFTVKVHMGAGAFVCGESSALMTALEGRAGEPRPKYI 326
           +  AIR A +  ++G +I G+G  F + V +GAGA++CGE ++++ +LEG+ G  R K  
Sbjct: 236 MREAIRLAYDEKWLGDEIHGTGHRFHLDVRVGAGAYICGEETSMLESLEGKRGTVRAKPP 295

Query: 327 HTAVKGVWDHPSVLNNVETWANVTQIITKGADWFTSYGTAGSTGTKIFSLVGKITNTGLV 386
             A++G++  P+++NNV +  +V  I+ KGA+ +  +G   S GT  F L G I + G+V
Sbjct: 296 LPALEGLFGKPTIVNNVLSLTSVPIILDKGANHYRDFGVGRSRGTLAFQLAGNIKHGGIV 355

Query: 387 EVPMGVTLRDIITKVGGGIPGGKKFKAVQTGGPSGGCIPEAMLDLPVDFDELTKAGSMMG 446
           E   GVTL +++ + GGG   G+  +AVQ GGP G  +P ++ +LP D++      +M+G
Sbjct: 356 EKAFGVTLHELLYEFGGGTITGRPIRAVQAGGPLGAYLPPSLFELPKDYEAFAAVEAMVG 415

Query: 447 SGGMIVMDEDTCMVDIARYFIDFLKDESCGKCTPCREGIRQMLAVLTRITVGKGKEGDIE 506
            GG++V D+   M   AR+ ++F   ESCGKCTPCR G  + + V+  I  G+  + +I 
Sbjct: 416 HGGIVVFDDSVDMARQARFAMEFCAAESCGKCTPCRIGAVRGVEVMDNIIAGEKVQANIT 475

Query: 507 LLEELAE-STGAALCALGKSAPNPVLSTIRYFRDEY 541
           LL +L E  T  +LCA+G   P PV S +++F +++
Sbjct: 476 LLNDLCEVMTDGSLCAMGGMTPIPVRSALKHFPEDF 511


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: 868
Number of extensions: 58
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: 521
Length adjustment: 36
Effective length of query: 599
Effective length of database: 485
Effective search space:   290515
Effective search space used:   290515
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