Alignments for a candidate for hcl in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for hcl in Sedimenticola selenatireducens DSM 17993

Align 3-hydroxybenzoate--CoA/4-hydroxybenzoate--CoA ligase; 3-hydroxybenzoyl-CoA synthetase; EC 6.2.1.27; EC 6.2.1.37 (characterized)
to candidate WP_051302719.1 A3GO_RS24835 benzoate-CoA ligase family protein

Query= SwissProt::Q9AJS8
         (523 letters)



>NCBI__GCF_000428045.1:WP_051302719.1
          Length = 536

 Score =  522 bits (1344), Expect = e-152
 Identities = 253/519 (48%), Positives = 357/519 (68%), Gaps = 4/519 (0%)

Query: 3   EQLQPQQSMNAADEIIGRPLAQGLGEQTAMLCAERSITYRELDAATNRHGNALRAHGVGK 62
           E+  P  +MNA +E+IG  L++GL +QTA++   +S+TY ELD   NR+ +ALR  GV +
Sbjct: 6   ERYFPSGAMNAVEELIGPALSKGLEQQTALIGDTKSLTYGELDLLVNRYSDALRTAGVVR 65

Query: 63  GDRVLFLMDDSPELVAAYLGTLRIGAVAVALNVRLAPRDVLYVIQDSACRLLYIDAEFLH 122
            +RVLF+++DSP+ VAAYLG + +GAV++A NVR A +D+L+VI+DS C +L IDA +L 
Sbjct: 66  ENRVLFMLNDSPDFVAAYLGAMHMGAVSIAFNVRSAAKDLLFVIEDSNCTMLVIDAAYLP 125

Query: 123 LYQQIAGELEQPPQVVVRGD-EAPAPAIIAFKHFLDGQAATLESVQVAPDDVAYWLYSSG 181
           +Y QIA  ++ P +VVV GD E   P + +F   ++  A    +++V+PDD+A+W+Y+SG
Sbjct: 126 IYLQIADRIKHPLKVVVDGDYEGDLPTLGSF---VESGATRSPALKVSPDDMAFWVYTSG 182

Query: 182 TTGRPKAVMHAHRSVLIADRLEREYFGIKPGDRVFTTSKMFFGWSLGHSLMGGLQCGATV 241
           TTG PKA +H H  V+IAD   RE  G++PGDR+F+TSK+FF ++LGHSL+GGL+  AT+
Sbjct: 183 TTGTPKAAVHLHHDVIIADLHMRENLGVEPGDRIFSTSKLFFAYALGHSLLGGLRSCATI 242

Query: 242 IVAPGWPDAERVMATAARHRPTILFSTPVMYRNLLREGAGESAAMRDIRHFVSAGEKLPE 301
           I+   WPDA  +     RH+P ++FS P +YRNLLR+G  ++A  + +R +VSAGEKLP 
Sbjct: 243 ILTKQWPDAAAIAELIRRHQPDLVFSVPTLYRNLLRDGVADTAPFKSVRVYVSAGEKLPV 302

Query: 302 NIGQQWLDTFGIPITEGIGASETVFLFLCARPDAYRIGSCGKRVPWAEVRLLDELGNEIT 361
            +  QW    G PI EGIG SET+FL++      +R GSCGK VPWAE++L+DE    I+
Sbjct: 303 KLFDQWRLATGRPILEGIGTSETLFLYVTNSIKQFRSGSCGKPVPWAEIKLMDESEQAIS 362

Query: 362 TPDTPGLIAIRMASQFVGYWKLPETTEKALRDGWYYPGDMFSFDADGFWYHNGRADDMLK 421
           T +TPG + +RM S    YW   + + K+    WY  GDMF  D DG+WYH GR D+MLK
Sbjct: 363 TTETPGQLWVRMPSVADRYWNRQDQSRKSFHGHWYKTGDMFRVDEDGWWYHLGRGDEMLK 422

Query: 422 ISGQWVSPGEIESCASAVPGIAEAVVVAVPNDDGLTRLTLFIVPEDPSASQQKLSEAWMT 481
           ISGQWVSP EIE+CA  VPG+  A V+   N+D L R  LF+VP+        L++    
Sbjct: 423 ISGQWVSPAEIEACALTVPGVEAAAVIGYSNEDSLVRSALFVVPQQRGTDDDMLADKIRQ 482

Query: 482 TLRGTLSIYKCPRTIQFLEELPRTATGKVQKYRLRDMLQ 520
            L  TLSIYKCPR I+ ++E+P TA+GK+QKY+LR++L+
Sbjct: 483 ALIQTLSIYKCPRIIRLVDEMPCTASGKMQKYKLRELLR 521


Lambda     K      H
   0.321    0.137    0.417 

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: 822
Number of extensions: 43
Number of successful extensions: 3
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: 523
Length of database: 536
Length adjustment: 35
Effective length of query: 488
Effective length of database: 501
Effective search space:   244488
Effective search space used:   244488
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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