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_041766327.1 PING_RS09720 acetate--CoA ligase
Query= SwissProt::Q9H6R3 (686 letters) >NCBI__GCF_000015285.1:WP_041766327.1 Length = 629 Score = 630 bits (1625), Expect = 0.0 Identities = 304/627 (48%), Positives = 426/627 (67%), Gaps = 6/627 (0%) Query: 60 SEYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDR 119 S Y+ F + DP FW + A+ I W+K K L + WF +G +N Y A+D Sbjct: 4 SAYQNEFNRAKNDPLTFWQEQAKAIEWFKFPEKILSKDENGIDSWFADGQMNTAYLALDY 63 Query: 120 HIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIP 179 H+ NG+GD+ A+IYDSPV+ K +TYKE+ + V++ AG+L G+ KGD V+IYMPMI Sbjct: 64 HVLNGRGDQTALIYDSPVSGKKQQYTYKELTDHVARTAGMLADLGVVKGDRVIIYMPMIA 123 Query: 180 QAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVE 239 +++ MLACAR+GA+HS++FGGFA EL RI+ +PKV++TAS GIE + + Y+PL+ Sbjct: 124 ESVMAMLACARLGAVHSVVFGGFAPNELVIRIEDAEPKVIMTASCGIEVKKIIPYMPLIN 183 Query: 240 EALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYT 299 +A+ + KP +++ R A L RD+DW E++A + HDCVPV PLYILYT Sbjct: 184 KAMADSRFKPKNVVVLQRDEYPA-ELTENRDIDWAEQVAISAPHDCVPVSGRDPLYILYT 242 Query: 300 SGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHG 359 SGTTG PKGV+R GG+AV L +SMS+IY +PG+V+WAASD+GWVVGHSYI Y PL+HG Sbjct: 243 SGTTGKPKGVVRENGGHAVALKYSMSTIYDAKPGDVYWAASDVGWVVGHSYIVYAPLIHG 302 Query: 360 NTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFK 419 TT+LYEGKPV TPD GA++RV E+ V LF+APTA RAI+++DP L KQY + + Sbjct: 303 CTTILYEGKPVRTPDPGAFWRVCEEYKVNILFSAPTAFRAIKKEDPEGELIKQYKMPDLR 362 Query: 420 TLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPP--PGQAGK 477 T+F+AGER D TLEW ++ +PV+DHWWQTETG I+ + +GL +T P PG + K Sbjct: 363 TIFMAGERLDPPTLEWVQSKTHLPVIDHWWQTETGWAISGNPLGL---ETFPLKPGSSTK 419 Query: 478 SVPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 537 VPG+ V ILD+ + L G IV+K PLPPG + +W++ E F+ Y +FPGYY + Sbjct: 420 PVPGFQVDILDEAGEPLPPNTQGYIVIKCPLPPGCLTTVWRHHERFQSGYLTQFPGYYVS 479 Query: 538 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHV 597 D GY+D++GYL+VM R+DDVINVAGHR+S G +EE + H VA+CAV+G D LKG + Sbjct: 480 GDGGYIDDDGYLFVMGRIDDVINVAGHRLSTGEMEEVLGGHPDVAECAVIGAHDELKGQM 539 Query: 598 PLALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSA 657 P+ VL+ + + V +E+++ +R +IG VA+ + + V +LPKTRSGK+ R + Sbjct: 540 PIGFVVLKDGHYSVDGNVEKELIQKIRDDIGAVASLKRVLVVNRLPKTRSGKVLRRTIKQ 599 Query: 658 IVNGKPYKITSTIEDPSIFGHVEEMLK 684 + +G+ Y + STI+DPS +E L+ Sbjct: 600 VADGEQYTMPSTIDDPSSITEIESALQ 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: 1274 Number of extensions: 64 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: 629 Length adjustment: 38 Effective length of query: 648 Effective length of database: 591 Effective search space: 382968 Effective search space used: 382968 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.
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:
Otherwise, a candidate is "medium confidence" if either:
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:
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:
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