GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011383893.1
          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:

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