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_011384423.1 AMB_RS10200 4-hydroxybenzoyl-CoA reductase subunit alpha

Query= SwissProt::O33819
         (769 letters)



>NCBI__GCF_000009985.1:WP_011384423.1
          Length = 769

 Score = 1421 bits (3679), Expect = 0.0
 Identities = 709/768 (92%), Positives = 747/768 (97%)

Query: 1   MSPKLPQHGTVGVRTPLVDGVEKVTGKAKYTADIAAPDALVGRILRSPHAHARILAIDTS 60
           MSPK P++GTVG RTPLVDGVEKVTGKAKYTADIAAP ALVGRILRSP AHARI++IDTS
Sbjct: 1   MSPKFPKNGTVGARTPLVDGVEKVTGKAKYTADIAAPGALVGRILRSPVAHARIISIDTS 60

Query: 61  AAEALEGVIAVCTGAETPVPFGVLPIAENEYPLARDKVRYRGDPVAAVAAIDEVTAEKAL 120
           AAEAL+GV AVCTGAETPVP+GVLPIAENEYPLARDKVRYRGDPVAAVAA+DE+TAE+AL
Sbjct: 61  AAEALDGVYAVCTGAETPVPYGVLPIAENEYPLARDKVRYRGDPVAAVAAVDELTAEQAL 120

Query: 121 ALIKVDYEVLPAYMTPKAAMKAGAIALHDDKPNNILREVHAEFGDVAAAFAEADLIREKT 180
            LIKV+YEVLPAYMTPKAAMK GAIALHDDKPNN+LREVHAEFGDV AAF EA+LIREK 
Sbjct: 121 NLIKVEYEVLPAYMTPKAAMKEGAIALHDDKPNNVLREVHAEFGDVEAAFGEAELIREKV 180

Query: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240
           YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF
Sbjct: 181 YTFAEVNHVHMELNATLAEYDPVRDMLTLNTTTQVPYYVHLKVAACLQMDSARIRVIKPF 240

Query: 241 LGGGFGARTEGLHFEIIAGLLARKAKGTVRLLQTREETFIAHRGRPWTEVKMKIGLKKDG 300
           LGGGFGARTE LHFEIIAGLLARKAKGTV+L+QTREETFIAHRGRPWTEVKMKIGL +DG
Sbjct: 241 LGGGFGARTECLHFEIIAGLLARKAKGTVKLVQTREETFIAHRGRPWTEVKMKIGLMRDG 300

Query: 301 KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH 360
           KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH
Sbjct: 301 KIAALALEATQAGGAYAGYGIITILYTGALMHGLYHIPAIKHDAWRVYTNTPPCGAMRGH 360

Query: 361 GTVDTRAAFEALLTEMGEELGIDSLKIRQINMLPQIPYVTMYAQRVMSYGVPECLEKVKA 420
           GTVDTRAAFEALLTEMGEELGIDSL IRQ NMLPQIPY TMYAQ+VMSYGVPECLEKVKA
Sbjct: 361 GTVDTRAAFEALLTEMGEELGIDSLDIRQRNMLPQIPYTTMYAQKVMSYGVPECLEKVKA 420

Query: 421 ASGWEERKGKLPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD 480
           ASGW ERKGK+PKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD
Sbjct: 421 ASGWAERKGKMPKGRGLGIALSHFVSGTSTPKHWTGEPHATVNLKLDFDGGITLLTGAAD 480

Query: 481 IGQGSNTMASQVAAEVLGVRLSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL 540
           IGQGSNTMA+QVAAEVLGVR+SRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL
Sbjct: 481 IGQGSNTMATQVAAEVLGVRMSRIRVISADSALTPKDNGSYSSRVTFMVGNASISAAEEL 540

Query: 541 KGVLVKAAAKKLDAREEDIEVIDEMFMVSGSQDPGLSFQEVVKAAMVDSGTITVKGTYTC 600
           K +LVKAAAKKLDAREEDIEVIDE+FMV+GSQDPGL+FQEVVKAA++D+GTITVKGT+TC
Sbjct: 541 KAILVKAAAKKLDAREEDIEVIDEVFMVAGSQDPGLTFQEVVKAALIDTGTITVKGTFTC 600

Query: 601 PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGKVTAHKVWVAVDVGKALNPLAVE 660
           PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITG+VTAHKVWVAVDVGKALNPLAVE
Sbjct: 601 PTEFQGDKKIRGSAIGATMGFCYAAQVVEASVDEITGRVTAHKVWVAVDVGKALNPLAVE 660

Query: 661 GQTQGGVWMGMGQALSEETVYDNGRMVHGNILDYRVPTIVESPDIEVIIVESMDPNGPFG 720
           GQTQGGVWMGMGQALSEET +D+G+M+HGNILDYRVPT+ ESPDIEV+IVES+DPNGPFG
Sbjct: 661 GQTQGGVWMGMGQALSEETRWDDGKMMHGNILDYRVPTMAESPDIEVMIVESLDPNGPFG 720

Query: 721 AKEASEGMLAGFLPAIHEAVYEAVGVRATDFPLSPDRITELLDAKEAA 768
           AKEASEGMLAGFLPA+HEAVYEAVGVR+T FPLSP+ ITELLDAKEAA
Sbjct: 721 AKEASEGMLAGFLPAVHEAVYEAVGVRSTKFPLSPETITELLDAKEAA 768


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: 1806
Number of extensions: 57
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 769
Length of database: 769
Length adjustment: 41
Effective length of query: 728
Effective length of database: 728
Effective search space:   529984
Effective search space used:   529984
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: 55 (25.8 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