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_091290483.1 BLV57_RS18395 propionyl-CoA synthetase
Query= SwissProt::Q9H6R3 (686 letters) >NCBI__GCF_900107045.1:WP_091290483.1 Length = 625 Score = 675 bits (1742), Expect = 0.0 Identities = 330/624 (52%), Positives = 439/624 (70%), Gaps = 3/624 (0%) Query: 61 EYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRH 120 +Y S+ DPE FW +AAE I W + T+ L++ +P RWF +G LN NA+DRH Sbjct: 3 DYAEAHRRSLEDPEGFWLEAAEAIDWSRKPTRALDDSGAPLYRWFPDGELNTSVNALDRH 62 Query: 121 IENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQ 180 ++ G+G++ A+I+DSPVT FTY E+L +V++ AG L + KG+ V+IYMPM+P+ Sbjct: 63 VQAGRGERTALIWDSPVTGQTRRFTYAELLYEVTRFAGALASLHVDKGERVIIYMPMVPE 122 Query: 181 AMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEE 240 A+ MLACAR+GA+HS++FGGFA KEL++R+D KP+V+V AS GIEP R VEY P+++E Sbjct: 123 AVIAMLACARLGAVHSVVFGGFAPKELAARVDDAKPRVIVAASCGIEPTRTVEYKPIIDE 182 Query: 241 ALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTS 300 AL + H+PD+++I R +A RD+DW+E + A VPV + PLYILYTS Sbjct: 183 ALAMSAHQPDRVVILQRDRHKAE--LGERDVDWNELIEHAPPAQAVPVAATDPLYILYTS 240 Query: 301 GTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGN 360 GTTG PKGV+R TGG+AV L WSMS+IY +QPG+VWW ASD+GWVVGHSYI Y PLL G Sbjct: 241 GTTGKPKGVVRDTGGHAVALAWSMSAIYDIQPGDVWWTASDVGWVVGHSYIVYAPLLVGA 300 Query: 361 TTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKT 420 T+VLYEGKPVGTPDAGA++RV+AEHGV ALFTAPTA+RAI++ DP A +Y L+RF+T Sbjct: 301 TSVLYEGKPVGTPDAGAFWRVIAEHGVKALFTAPTALRAIKKVDPEAKELAKYDLSRFQT 360 Query: 421 LFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVP 480 LF+AGER D ET W+ PV+DHWWQTETG PI A+ GL PG A K VP Sbjct: 361 LFMAGERLDPETYHWASEHLGTPVIDHWWQTETGWPIAANPRGL-EPMPVKPGSATKPVP 419 Query: 481 GYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDA 540 G++V ILD + + A G I +KLPLPPG+ LW + E +K Y ++ GYY T D+ Sbjct: 420 GWDVRILDQAGESVPAGREGAIAIKLPLPPGSLPTLWGDDERYKETYLSRYDGYYLTGDS 479 Query: 541 GYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLA 600 GY+DE+GYL+VM R DDVINVAGHR+S G++E + SH VA+CAV+G +D LKG +P Sbjct: 480 GYLDEDGYLFVMGRTDDVINVAGHRLSTGSMEAVLASHPAVAECAVIGVKDQLKGQLPRG 539 Query: 601 LCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVN 660 L VL+ + TE + E+V VR++IGPVAAF++ V+ LPKTRSGKI R + I + Sbjct: 540 LVVLKAGVEVTEADLKAELVALVRRDIGPVAAFKDVSIVEALPKTRSGKILRKTMRGIAD 599 Query: 661 GKPYKITSTIEDPSIFGHVEEMLK 684 G+ + STIED S+ ++ +L+ Sbjct: 600 GRDEAVPSTIEDASVLEALKVVLR 623 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: 1219 Number of extensions: 57 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: 625 Length adjustment: 38 Effective length of query: 648 Effective length of database: 587 Effective search space: 380376 Effective search space used: 380376 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