Alignments for a candidate for acs in Acidovorax caeni R-24608

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Acidovorax caeni R-24608

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_054256857.1 BN2503_RS11775 propionate--CoA ligase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_001298675.1:WP_054256857.1
          Length = 630

 Score =  486 bits (1250), Expect = e-141
 Identities = 261/632 (41%), Positives = 376/632 (59%), Gaps = 16/632 (2%)

Query: 62  YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121
           Y      S+ + + FW + A  I W  P  +  +  + P  +WFV G  N+C+NAVDRH+
Sbjct: 4   YADFHRRSIDERDAFWAEQARLIDWQTPPQQVCDYSNPPFAKWFVGGTTNLCHNAVDRHL 63

Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181
              +G + A++  S  TNT+  ++Y E+ ++V ++A  L   G+K+GD V+IYMPMI +A
Sbjct: 64  A-ARGQQNALVAISTETNTERAYSYAELHQEVQRMAACLQALGVKQGDRVLIYMPMIAEA 122

Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241
            + MLAC RIGAIHS++FGGFAS  L++RI+  +P V+V+A  G   G+ V Y PL+++A
Sbjct: 123 AFAMLACTRIGAIHSVVFGGFASSSLATRIEDAQPVVIVSADAGSRGGKVVPYKPLLDDA 182

Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSH--DCVPVLSEHPLYILYT 299
           +++  HKP  +L+ NR  +    L  GRD DW    A        CV + S  P Y LYT
Sbjct: 183 IELSAHKPAAVLMVNR-GLAPASLRAGRDHDWATLRASHMDTLVPCVWIESTQPSYTLYT 241

Query: 300 SGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHG 359
           SGTTG PKGV R TGGY V L  SM  I+   PG+ ++  SD+GWVVGHSYI YGPL+ G
Sbjct: 242 SGTTGKPKGVQRDTGGYTVALASSMRHIFQGNPGDTYFCTSDIGWVVGHSYIIYGPLIAG 301

Query: 360 NTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFK 419
            TT+LYEG P+  PDAG ++ ++ ++ V  +F+APTA+R +++QDP  A   +Y ++  K
Sbjct: 302 MTTILYEGLPI-RPDAGIWWSIVEKYKVTHMFSAPTAVRVLKKQDP--AYLSKYDISSLK 358

Query: 420 TLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSV 479
            L++AGE  D  T  W      VP++D++WQTETG PI   C G+   +    G  GK+V
Sbjct: 359 ALWLAGEPLDEPTATWISGALNVPIIDNYWQTETGWPILTLCNGV-EQQPSRFGSPGKAV 417

Query: 480 PGYNVMILDD--NMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPG--YY 535
            GYNV ++D+    +       G + ++ PLPPG    +W++ + F + Y++  PG   Y
Sbjct: 418 YGYNVKLIDEATGEELTVPNQKGVVAIEGPLPPGCLQTVWRDDDRFVNTYWKSIPGRLIY 477

Query: 536 DTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKG 595
            T D G  D +GY +++ R DDVINVAGHR+    IEE I SH  +A+ AVVG  D LKG
Sbjct: 478 STFDWGIRDADGYYFILGRTDDVINVAGHRLGTREIEECISSHANIAEVAVVGVADQLKG 537

Query: 596 HVPLALCVLRKDINATEEQ---VLE-EIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIP 651
            V LA  V R        +    LE E++K V   +G VA      FV  LPKTRSGK+ 
Sbjct: 538 QVALAFAVPRNTTGLETPEARAALEAEVMKVVDGQLGAVARPARVHFVTVLPKTRSGKLL 597

Query: 652 RSALSAIVNGKPYKITSTIEDPSIFGHVEEML 683
           R AL A+   +     +T+EDP+    +++++
Sbjct: 598 RRALQAVAERRDPGDLTTMEDPAALQQIKDLI 629


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: 1097
Number of extensions: 62
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: 630
Length adjustment: 38
Effective length of query: 648
Effective length of database: 592
Effective search space:   383616
Effective search space used:   383616
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.

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Steps (tab-delimited)
Rules (tab-delimited)
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 2024 update 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