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 Acyl-CoA synthetase short-chain family member 3, mitochondrial; Acetate--CoA ligase 3; Acyl-CoA synthetase short-chain family member 3; Propionate--CoA ligase; EC 6.2.1.1; EC 6.2.1.17 (characterized)
to candidate WP_068168785.1 HTA01S_RS07630 propionate--CoA ligase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_001592305.1:WP_068168785.1
          Length = 633

 Score =  516 bits (1329), Expect = e-150
 Identities = 272/635 (42%), Positives = 400/635 (62%), Gaps = 22/635 (3%)

Query: 62  YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121
           Y      S+ + + FW + A+ + W+KP+ +     + P  RWF  G+ N+C+NAVDRH+
Sbjct: 7   YTEFHRRSIEERDAFWAEQAQLVDWHKPFDRVCNYDNPPFARWFEGGLTNLCHNAVDRHL 66

Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181
           ++ + D+ A+I+ S  T+T+ T+ ++E+  +V ++A +L   G+KKGD V+IYMPMIPQA
Sbjct: 67  KD-RADQNALIFVSTETDTEKTYNFRELHAEVQRMAAILQAQGVKKGDRVLIYMPMIPQA 125

Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241
            + MLACAR+GAIHS++FGGFAS  L+SRI+   P V+V+A  G   G+ VEY PL++EA
Sbjct: 126 AFAMLACARVGAIHSVVFGGFASHSLASRIEDASPVVIVSADAGSRGGKVVEYKPLLDEA 185

Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSH--DCVPVLSEHPLYILYT 299
           +++  HKP K+++ +R  + A     GRD+D+  E AK       C  V + HP Y LYT
Sbjct: 186 IRLSAHKPQKVVMVDR-GLAAFDAVEGRDVDYAAERAKHMDTVVPCEWVDATHPSYTLYT 244

Query: 300 SGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHG 359
           SGTTG PKGV R TGGYAV L  SM  IY  +PGE +++ SD+GWVVGHSYI YGPL+ G
Sbjct: 245 SGTTGKPKGVQRDTGGYAVALAASMKHIYMGEPGETYFSTSDIGWVVGHSYIIYGPLIGG 304

Query: 360 NTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFK 419
             T++YEG P+  PDAG ++ ++ ++ V+ +F+APTA+R +++ D  ++  K+Y ++  K
Sbjct: 305 MATIMYEGLPI-RPDAGIWWSLVEKYKVSVMFSAPTAVRVLKKYD--SSFIKKYDISSLK 361

Query: 420 TLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPP---GQAG 476
            LF+AGE  D  T +W       P++D++WQTETG PI A C    N   P P   G  G
Sbjct: 362 ALFLAGEPLDEPTAQWISGELGKPIVDNYWQTETGWPILAIC----NGVEPAPSKFGSPG 417

Query: 477 KSVPGYNVMILDDNM-QKLK-ARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPG- 533
           K+V GY+V +LDD   ++LK +   G + V+ PLPPG    +W + E F   Y+   PG 
Sbjct: 418 KAVYGYDVKLLDDQSGEELKGSNQKGVVAVEGPLPPGCMQTIWGDDERFVKTYWSSVPGK 477

Query: 534 -YYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDP 592
             Y T D G  D +GY +++ R DDVINVAGHR+    IEESI SH  +A+ AVVG  D 
Sbjct: 478 MVYSTFDWGIRDADGYYFILGRTDDVINVAGHRLGTREIEESISSHPRIAEVAVVGVADQ 537

Query: 593 LKGHVPLALCVLRKDINATEE----QVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSG 648
           LKG V +A  V++     T++    ++  E++K V + +G VA      FV  LPKTRSG
Sbjct: 538 LKGQVAMAFAVVKDASLLTDDAARLKLEGEVMKLVDEQLGAVARPARVRFVSILPKTRSG 597

Query: 649 KIPRSALSAIVNGKPYKITSTIEDPSIFGHVEEML 683
           K+ R A+ A+  G+     +T++DP+    ++++L
Sbjct: 598 KLLRRAIQAVCEGRDPGDLTTMDDPAALQQIKDLL 632


Lambda     K      H
   0.318    0.136    0.422 

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: 1121
Number of extensions: 64
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: 686
Length of database: 633
Length adjustment: 38
Effective length of query: 648
Effective length of database: 595
Effective search space:   385560
Effective search space used:   385560
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: 54 (25.4 bits)

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

Downloads

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

Related tools

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