GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bamB in Magnetospirillum magneticum AMB-1

Align Benzoyl-CoA reductase, putative (characterized, see rationale)
to candidate WP_011385299.1 AMB_RS14710 aldehyde ferredoxin oxidoreductase

Query= uniprot:Q39TV8
         (653 letters)



>lcl|NCBI__GCF_000009985.1:WP_011385299.1 AMB_RS14710 aldehyde
           ferredoxin oxidoreductase
          Length = 616

 Score =  173 bits (438), Expect = 2e-47
 Identities = 137/422 (32%), Positives = 191/422 (45%), Gaps = 24/422 (5%)

Query: 6   TGYVLEVDLTKGSIERVATDPRDTELYLGGLGTNAKILWDRVPPEVEPFSPENLLIFAAG 65
           TG  L +DLT GS++    +      YLG  G   K   + V P+V+P SP N +IF  G
Sbjct: 4   TGKFLRIDLTNGSVKTEELNRAWARQYLGQRGLATKYFAEEVDPKVDPLSPANKMIFTTG 63

Query: 66  LLCGTPATGCNRTIVSTVSPQTKLMAFSMMGGFWAPELKYAGYDKIIFRGKSPELVYLYI 125
            L GT A+   R  V T  P T  +A S  GGF+  ELK AG+D II  G+SP+ VYL I
Sbjct: 64  PLTGTAASTGGRYSVVTKGPLTNCIACSNSGGFFGNELKNAGWDMIIVEGRSPKPVYLSI 123

Query: 126 NNDKVEIRDASHLKGKGAIETAEIIKKELNEPRAQVAAIGKAGENRVFYASIEQG-RSSA 184
            N+ VEIRDA+   GK   ET   +K    +P  +VA IG AGE  V YA I      +A
Sbjct: 124 ENETVEIRDAAEFWGKTVWETENGLKARHQDPMLRVATIGAAGEKGVLYACIVNDLHRAA 183

Query: 185 SRGGIGAVMGDKGLKAVVVRGTKDLCVAKPEEYIGLCNEVLDYIKHREENPIPDVMPILA 244
            R G+GAVMG K LKA+ VRGT+ + V  P+ +I      ++  K   +N +      L 
Sbjct: 184 GRSGVGAVMGSKNLKAIAVRGTRGVTVKDPDRFI---KATIEQKKVLADNAVTG--QGLP 238

Query: 245 GLGSPQEMKVHDEKWHTENFNWGNARTRRKDFWTDEVSHAWEKTMDKARTRLI-SCYNCP 303
             G+   M V +E       N+   +       + E  H    T  KA      +C+ C 
Sbjct: 239 KYGTQVLMNVINEIGAMPTRNFKEVQFEGAHKISAEAMHEPRATDGKANLATNGACFGCT 298

Query: 304 MKCG-------ATISMEGLPTYMMKCFTKLTYTMAAYSDLDFGLRIAQKAT-------EY 349
           + CG          S+   P Y  +    + Y  A     D G+   +  T       E+
Sbjct: 299 IACGRISRMDPGHFSITSRPQY-KEPSGGVEYEAAWAMGSDCGVDDLEACTFANFMCNEH 357

Query: 350 GLDGFSAPQVMAFAFELLEKGILKDSDFPG--LPEGNEERFFYLLDKIVNRDGIGDILAN 407
           G+D  S    +A A E+ E G++      G  L  G+ E    + +     +G G  L  
Sbjct: 358 GIDPISFGSTLAAAMEMFEMGVITKEQTGGVELKFGSAEALVKMAELTGKGEGFGLELGQ 417

Query: 408 GT 409
           G+
Sbjct: 418 GS 419



 Score = 49.7 bits (117), Expect = 4e-10
 Identities = 36/95 (37%), Positives = 46/95 (48%), Gaps = 11/95 (11%)

Query: 552 PKFIAAGAGIEMDTEKLKKAAKRYRTLVRAFNIRRGMRRVDEQPPANHWKNRFPE----- 606
           P+  AA  G E   E L +  +R  TL R FN+  GM   D+  P    K+         
Sbjct: 523 PQIDAACEG-EWTPEILLEVGERIWTLERQFNLAAGMTAADDTLPKRLLKDAAKTGPAKG 581

Query: 607 ----LEKELLDSYYKLKGWNDDGIPTKETLDDLGL 637
               LEK +L  YY+L+GW  DG+PT ETL  L L
Sbjct: 582 LTSGLEK-MLPEYYQLRGWTTDGVPTTETLKRLQL 615


Lambda     K      H
   0.319    0.138    0.425 

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: 904
Number of extensions: 46
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 653
Length of database: 616
Length adjustment: 38
Effective length of query: 615
Effective length of database: 578
Effective search space:   355470
Effective search space used:   355470
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: 54 (25.4 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