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_RS14955 AZOBR_RS14955 formate dehydrogenase subunit beta

Query= uniprot:Q39TW5
         (635 letters)



>FitnessBrowser__azobra:AZOBR_RS14955
          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:

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