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_086509797.1 BZY95_RS10010 propionyl-CoA synthetase
Query= SwissProt::Q9H6R3 (686 letters) >NCBI__GCF_002151265.1:WP_086509797.1 Length = 636 Score = 638 bits (1645), Expect = 0.0 Identities = 309/626 (49%), Positives = 420/626 (67%), Gaps = 9/626 (1%) Query: 62 YKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHI 121 YK F S+ P+ FW A +I W+ P LE RW+ +G LN+C+ A+D H+ Sbjct: 4 YKNEFQRSIEQPQSFWADQARRIPWFTPPKTILEYDEQGHARWYTDGELNLCHAALDHHV 63 Query: 122 ENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQA 181 + G+GD+ AI +DSPVT K T TY+E+ ++V+ AG L G++KGD VVIYMPM+P+A Sbjct: 64 DQGRGDQPAIYWDSPVTGGKRTLTYREMRDEVALFAGALEGLGVEKGDRVVIYMPMVPEA 123 Query: 182 MYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEA 241 + M ACAR+GA+HS++FGGFA EL+ RID KPKVVV AS G+E R + Y P + A Sbjct: 124 LVAMYACARLGAVHSVVFGGFAPHELAVRIDDAKPKVVVAASCGVEIDRVIAYQPNIAAA 183 Query: 242 LKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSG 301 +++ +HKPD IY + + L P RDLDW E + A+ DCVPV PLY+LYTSG Sbjct: 184 IELSEHKPDAC-IYLQRQQQLAELGP-RDLDWSELLESAEPADCVPVKGSDPLYVLYTSG 241 Query: 302 TTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNT 361 TTG PKGV+R T GYAV LH+SM +IY + PG+V+++ASD+GWVVGHSYI Y PLL G T Sbjct: 242 TTGKPKGVVRDTAGYAVALHYSMETIYDVAPGDVFFSASDVGWVVGHSYIVYAPLLRGCT 301 Query: 362 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 421 TV+YEGKPV TPDAGA++R+++++ V + FTAPTA RAI+++DP L +QY ++ K L Sbjct: 302 TVVYEGKPVKTPDAGAFWRLISQYRVKSFFTAPTAFRAIKKEDPDGILLQQYDISCLKAL 361 Query: 422 FVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKS--- 478 ++AGER D T W ++ VPV+DHWWQTETG PI A+ GL P P +AG + Sbjct: 362 YLAGERLDPPTFHWLDDLLDVPVIDHWWQTETGWPIAANLQGL----EPMPTKAGSATVP 417 Query: 479 VPGYNVMILDDNMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTM 538 VPG+NV IL+ ++ G++V+K P+PPG G+W + + F Y FPGYY T Sbjct: 418 VPGFNVQILNREGEQAAPMEQGSVVIKQPMPPGCLIGVWGDPQRFHSAYMAAFPGYYLTG 477 Query: 539 DAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVP 598 D GY DE+GYL++M R DDVINVAGHR+S G +EE + +H VA+CAV+G D LKG +P Sbjct: 478 DGGYFDEQGYLFIMGRTDDVINVAGHRLSTGEMEEVVGAHRAVAECAVIGIHDALKGQIP 537 Query: 599 LALCVLRKDINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAI 658 + L + + + E + E++ VR+ IGP+A F+ + V +LPKTRSGKI R L I Sbjct: 538 VGLVIPKDGFDGDEVALENELIALVREKIGPIACFKQVLVVNRLPKTRSGKILRKLLRNI 597 Query: 659 VNGKPYKITSTIEDPSIFGHVEEMLK 684 +GK Y + STI+DP+ V E +K Sbjct: 598 ADGKEYGVPSTIDDPASLQDVHEAMK 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: 1205 Number of extensions: 52 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: 636 Length adjustment: 38 Effective length of query: 648 Effective length of database: 598 Effective search space: 387504 Effective search space used: 387504 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