Alignments for a candidate for acs in Hydrogenophaga taeniospiralis NBRC 102512

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Hydrogenophaga taeniospiralis NBRC 102512

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_068168254.1 HTA01S_RS06610 acetate--CoA ligase

Query= SwissProt::P39062
         (572 letters)



>NCBI__GCF_001592305.1:WP_068168254.1
          Length = 587

 Score =  525 bits (1351), Expect = e-153
 Identities = 270/569 (47%), Positives = 362/569 (63%), Gaps = 14/569 (2%)

Query: 14  NLKNYEETYRHFDWAEAEKHFSWHETGK-LNAAYEAIDRHAESFRKNKVALYY--KDAKR 70
           NL +Y+ T   F W EAE+       G  LN A+EA+DRH    R +K A+ +  K  +R
Sbjct: 17  NLSDYDATVAGFSWQEAERQLDGLPGGAGLNIAHEAVDRHVLHGRGHKTAIRWLGKSGER 76

Query: 71  DEKYTFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLF 130
            E +++ ++   +N+  + L   G V  G+RVFI M R PELY  +LGA+K   +  PLF
Sbjct: 77  RE-FSYLDLARATNQFAHALEHLG-VRPGERVFILMGRLPELYVALLGALKARCVVTPLF 134

Query: 131 EAFMEGAVKDRLENSEAKVVVTTPELLERIPVD---KLPHLQHVFVVGGEAESGTNIINY 187
            AF    +  R E  +A+V+VTTPEL +R   D   +LP L+HV V G        +  +
Sbjct: 135 SAFGPEPIATRAEMGDARVLVTTPELYQRKVQDLRERLPGLRHVIVAGAVPSDEGGVHPW 194

Query: 188 DEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLKEE 247
                  ST   I   D +   LLH+TSG+TG PKG +HVH A++    TG++ LDL ++
Sbjct: 195 GALVSPASTTYTIAPTDPESMALLHFTSGTTGRPKGAVHVHAAVLAHMVTGRYALDLHDD 254

Query: 248 DIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPTAF 307
           D++WCTADPGWVTGT YGI AP + G TNV+V   F  ++WYG +E+  V++WY+APTA 
Sbjct: 255 DVFWCTADPGWVTGTSYGIIAPLVCGVTNVVVEAEFDAQTWYGVLERERVSIWYTAPTAI 314

Query: 308 RMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQLIC 367
           RM+M  G E     DL++LR + SVGEPLNPE + WG + F    HD WW TETG  ++ 
Sbjct: 315 RMMMKLGAEALKGVDLSALRFMASVGEPLNPEAVVWGLEAFGLPFHDNWWQTETGGIMVS 374

Query: 368 NYPCMDIKPGSMGKPIPGVEAAIVDNQGNE-----LPPYRMGNLAIKKGWPSMMHTIWNN 422
           NY  MDI+PGSMGKP+PG+ AA+V   G+        P   G LA++  WPSMM    + 
Sbjct: 375 NYLAMDIRPGSMGKPLPGIVAAVVRRTGSGHVEAITAPDVDGELALRAPWPSMMRGYLHE 434

Query: 423 PEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHPAI 482
            E+Y   F+  GWY++GD    D EGY+WF GR DDVI +SG  +GPFEVES L+EHPA+
Sbjct: 435 DERYRKCFV-DGWYLTGDLVRRDAEGYYWFVGRADDVIKSSGHLIGPFEVESALMEHPAV 493

Query: 483 AEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKDKL 542
           AEAGVIG PDP+ GE++KAF+AL+ G E S+ L+ E+    ++ L A  AP++I+F+D L
Sbjct: 494 AEAGVIGIPDPMAGEVVKAFVALKPGHEASEALRRELLGHARKRLGAAVAPKQIDFRDNL 553

Query: 543 PKTRSGKIMRRVLKAWELNLPAGDLSTME 571
           PKTRSGKIMRR+LKA EL LP GDLST+E
Sbjct: 554 PKTRSGKIMRRLLKARELGLPEGDLSTLE 582


Lambda     K      H
   0.318    0.136    0.425 

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: 1064
Number of extensions: 44
Number of successful extensions: 6
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: 572
Length of database: 587
Length adjustment: 36
Effective length of query: 536
Effective length of database: 551
Effective search space:   295336
Effective search space used:   295336
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: 53 (25.0 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)
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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