Alignments for a candidate for acs in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Beijerinckia indica ATCC 9039

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_012383621.1 BIND_RS03160 propionyl-CoA synthetase

Query= SwissProt::Q9H6R3
         (686 letters)



>NCBI__GCF_000019845.1:WP_012383621.1
          Length = 643

 Score =  683 bits (1763), Expect = 0.0
 Identities = 325/614 (52%), Positives = 429/614 (69%), Gaps = 2/614 (0%)

Query: 66  FAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGK 125
           + AS+ DPE FW  AA  + W KP+ + L++++ P  RWF  G LNICYNA+DRH+  G 
Sbjct: 15  YRASLDDPEGFWSAAAAALEWQKPYDRALDSRNPPFYRWFPGGQLNICYNALDRHVAAGH 74

Query: 126 GDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTM 185
           GD+ A+I+DSPVT T   FTY E+ E V+  AG L   G+  GD VVIYMPM+P+A+ TM
Sbjct: 75  GDRTALIHDSPVTGTVRNFTYAELTEAVAHFAGALAHLGVAHGDRVVIYMPMVPEAVITM 134

Query: 186 LACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIG 245
           LACARIGA+HS++FGGFA+ EL+ RID  KPKV+V+AS GI+  + + Y  L++ A++I 
Sbjct: 135 LACARIGAVHSVVFGGFAANELAKRIDDAKPKVIVSASCGIDGSKLIPYKTLLDAAIEIS 194

Query: 246 QHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSGTTGL 305
              P   +I  RP M A PL P RD+DW + +AK+ +  C   L+  PLYILY+SGTTG 
Sbjct: 195 SAPPTHCIILQRP-MLAAPLTPHRDVDWHDVLAKSIAVPCASTLATDPLYILYSSGTTGA 253

Query: 306 PKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLY 365
           PKGV+R  GGYAV LHWSMS+IY + PGEV+WAASD+GW VGHSY  YGPLL G TT+LY
Sbjct: 254 PKGVVRDHGGYAVALHWSMSNIYAIAPGEVFWAASDIGWAVGHSYTVYGPLLQGCTTLLY 313

Query: 366 EGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAG 425
           EGKPVGTP+AGA++RV+ +H V  LFTAPT  RAIRQQDP A   K+  L  F+TLF+AG
Sbjct: 314 EGKPVGTPNAGAFWRVIRQHAVNVLFTAPTTFRAIRQQDPDATFLKEAPLGDFRTLFLAG 373

Query: 426 ERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPGYNVM 485
           ERCD  TL W++    VPV+DHWWQTETG PI A+C+G+       PG  G++VPG+ + 
Sbjct: 374 ERCDPSTLAWAQAQLNVPVIDHWWQTETGWPIAANCLGISQMPV-KPGSVGRAVPGWQID 432

Query: 486 ILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDE 545
           +LD +   +    +GN+V+KLPLPPG+ + LW   + F   Y   FPGYY T DAG++DE
Sbjct: 433 VLDFDQNPVPPGTIGNLVIKLPLPPGSLTTLWNADQRFVESYMVDFPGYYQTGDAGFIDE 492

Query: 546 EGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLALCVLR 605
           +GY+YVM+R DDVINVA HR+S GA+EE +  H  VA+CAV+G  D L+G +P+ L VL+
Sbjct: 493 DGYIYVMARTDDVINVAAHRLSTGAMEEVVAEHPAVAECAVIGVADELRGQIPVGLIVLK 552

Query: 606 KDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNGKPYK 665
            +       +  EI++ VR  IG VA+F++ + V  LPKTRSGKI R +L AI  G+   
Sbjct: 553 ANYTDDCTLIEGEIIELVRNRIGAVASFKHVLVVAGLPKTRSGKILRRSLRAIAEGQEIA 612

Query: 666 ITSTIEDPSIFGHV 679
           I +TI+DP++   +
Sbjct: 613 IPATIDDPAVLDEI 626


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: 1273
Number of extensions: 59
Number of successful extensions: 3
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: 643
Length adjustment: 38
Effective length of query: 648
Effective length of database: 605
Effective search space:   392040
Effective search space used:   392040
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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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
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