GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011385299.1
          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:

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