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

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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources