GapMind for catabolism of small carbon sources

 

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

Align 4-hydroxybenzoyl-CoA reductase subunit alpha; 4-HBCR subunit alpha; EC 1.3.7.9 (characterized)
to candidate WP_011383893.1 AMB_RS07490 aldehyde oxidase

Query= SwissProt::O33819
         (769 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383893.1 AMB_RS07490 aldehyde
           oxidase
          Length = 913

 Score =  353 bits (906), Expect = e-101
 Identities = 254/778 (32%), Positives = 386/778 (49%), Gaps = 42/778 (5%)

Query: 3   PKLPQHGT-VGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTSA 61
           P +P+ G+ VG R   +DG ++V G   Y  D+  PD L+ R++RSPH HAR    D +A
Sbjct: 156 PVVPEAGSSVGTRLRRLDGRQRVDGSEIYGDDVCPPDCLLVRVIRSPHPHARFTIGDLTA 215

Query: 62  AE-ALEGVIAVCTGAETPVP--FGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEK 118
              A  G++ V T A+ P    F V+P  E++   A   VRYRG+ VAAV    +     
Sbjct: 216 LRVAYPGIVQVLTAADVPGINLFSVIPGMEDQPAFAEGLVRYRGEAVAAVVMEADTNDIF 275

Query: 119 ALALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIRE 178
             A   V +EVL   ++ + A  A A+ LH  +P NIL     + GD+   +A+A  + E
Sbjct: 276 QDADFPVLWEVLEPALSMEQATAADAVLLHAKRPGNILVRGFVQKGDLDLHWAKAAQVVE 335

Query: 179 KTYTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIK 238
            ++T   V H ++E  A  A    V D + +   TQ PY     VAA + +   ++R+I 
Sbjct: 336 DSFTTGFVEHAYIEPEAGYARR--VGDTIEIYACTQAPYMDRDSVAAIMALPPEQVRIIP 393

Query: 239 PFLGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKK 298
             +GGGFG + + +  +    L A      VR L TR E+  +   R    +  ++G   
Sbjct: 394 TAVGGGFGGKLD-VSLQPYVALAAWSLGRPVRCLYTRTESMASSTKRHPAAITARVGAGA 452

Query: 299 DGKIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMR 358
           DGK+ A+  +     GAYA +G            G Y IPA++     ++TN PP GA R
Sbjct: 453 DGKLTAMEFDGDFNTGAYASWGPTVANRVPVHCSGPYFIPALRARTRAIHTNNPPSGAFR 512

Query: 359 GHGTVDTRAAFEALLTEMGEELGIDSLKIRQINMLP--------QIPYVTMYAQRVMSYG 410
           G G      A E+L  ++ ++LG+D L+ R+IN +         QI   ++  Q      
Sbjct: 513 GFGIPQASIAQESLFDQLADKLGLDRLEFRRINAITAGQPTATGQILTASVGQQACFDAL 572

Query: 411 VPECLEKVKAASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDG 470
           VP   E + AA  +    G   + RG+G+A   +  G ++  +      +T+ + L  DG
Sbjct: 573 VPRWQEALAAAEAFNRTAGD--RRRGVGVAGMWYGCGNTSMSN-----PSTIRVALRADG 625

Query: 471 GITLLTGAADIGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVG 530
            + L  GA DIGQGSNT+ +Q+ A+ LG+ + +  ++  D+ALT     + +SR TF+ G
Sbjct: 626 AVVLFQGAVDIGQGSNTVITQICADALGIEIGKFTLVMGDTALTADAGKTSASRQTFVSG 685

Query: 531 NASISAAEELKGVLVKAAAKKLDAREEDIEVIDEMFMVS-GSQDPGLSFQEVVKAAMVDS 589
            AS  A  +L+  +++      D+R   + +   +  VS G+    +  Q + +    D 
Sbjct: 686 RASQLAGLDLRDKILRMVNAGADSR---LSLDGSILCVSDGADTHQIDLQSLARDQ--DG 740

Query: 590 GTITVKGTYTCPTEFQGDKKIRGSAIG---ATMGFCYAAQVVEASVDEITGKVTAHKVWV 646
             +  +GT+  PTE     K+  +  G   AT GF   AQ+ E  VD   G V   K+  
Sbjct: 741 LVMDGEGTFDPPTE-----KLDANGQGIPYATYGF--GAQMAEVEVDTALGTVKVLKIIA 793

Query: 647 AVDVGKALNPLAVEGQTQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIE 706
           A DVG+A+NP+ +EGQ +GG+  G+G AL EE  Y  GR    N+ DY +PT  + P IE
Sbjct: 794 AHDVGRAINPMLLEGQIEGGIAQGLGLALMEE--YIQGRT--ENLHDYLIPTAGDIPPIE 849

Query: 707 VIIVESMDPNGPFGAKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDA 764
            II+E  +P GPFGAK   E  L    PAI  A+  A GV     P +PDR+   + A
Sbjct: 850 TIIIEDAEPLGPFGAKGIGEQALIPTAPAILGAIRHATGVTIRQVPATPDRVRAAIRA 907


Lambda     K      H
   0.317    0.134    0.386 

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: 1372
Number of extensions: 56
Number of successful extensions: 9
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: 769
Length of database: 913
Length adjustment: 42
Effective length of query: 727
Effective length of database: 871
Effective search space:   633217
Effective search space used:   633217
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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 preprint 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