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 6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq)
Query= SwissProt::Q9H6R3 (686 letters) >lcl|FitnessBrowser__SB2B:6937194 Sama_1364 acyl-coenzyme A synthetase/AMP-(fatty) acid ligase (RefSeq) Length = 644 Score = 660 bits (1702), Expect = 0.0 Identities = 315/612 (51%), Positives = 425/612 (69%), Gaps = 2/612 (0%) Query: 72 DPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKGDKIAI 131 +PE++W KAA+ + W+K + L++ +P RW+ +G +N CYNA+DR ++ G+G + A Sbjct: 25 NPEQYWRKAADMVDWHKAPSTILDSSQAPLYRWYTDGEINTCYNALDRQVDAGRGSQTAF 84 Query: 132 IYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTMLACARI 191 Y SPVT T+ + +Y E L QV +LAG+L G+ KGD VVIYMPM+P+ Y MLACARI Sbjct: 85 HYVSPVTETEYSISYTECLAQVKRLAGLLKAQGVNKGDRVVIYMPMVPETAYAMLACARI 144 Query: 192 GAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQHKPDK 251 GAIHS++FGGFA+ EL+SRI+ KP +V++AS G+EP V Y PL++ AL HK K Sbjct: 145 GAIHSVVFGGFAANELASRINDAKPVMVLSASCGVEPSGVVAYKPLLDAALAQASHKVSK 204 Query: 252 ILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKGVIR 311 LI RP EA + PGRDLDW E +A A D VPV + PLY+LYTSGTTG PKGV+R Sbjct: 205 CLILQRPQYEAA-MTPGRDLDWQESVASAADADWVPVKATDPLYVLYTSGTTGQPKGVVR 263 Query: 312 PTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGKPVG 371 GG+AV L WSM +Y ++PG+ +WAASD+GWVVGHSYI YGPL+ G T+VLYEGKPVG Sbjct: 264 DNGGHAVALAWSMRYLYDIEPGDTFWAASDVGWVVGHSYIVYGPLIAGATSVLYEGKPVG 323 Query: 372 TPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERCDVE 431 TPDAGA++R + ++GV + FTAPTAIRAI+++DP + +L K +F+AGERCD + Sbjct: 324 TPDAGAFWRTIKKYGVKSFFTAPTAIRAIKREDPEGFFCRNTNLDCLKQMFLAGERCDPD 383 Query: 432 TLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAGKSVPGYNVMILDDNM 491 TL W++ + PV+DHWWQTETG P+ ++ +G+ PG + VPGY V ++D+ Sbjct: 384 TLLWAQEMLGKPVIDHWWQTETGWPVASNLMGIAQMPI-KPGSPARPVPGYQVDVVDEAG 442 Query: 492 QKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEEGYLYV 551 + A GN+V++LPLPPG LW+N + + Y +P Y T DAGYMDE+GYLY+ Sbjct: 443 NSVGAGEYGNVVIRLPLPPGTLPTLWQNDKRYIDSYLSMYPDCYLTGDAGYMDEDGYLYI 502 Query: 552 MSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLKGHVPLALCVLRKDINAT 611 MSR+DDVINVAGHR+S G EE + H VA+ AV+G ED LKG VPL L VL+ ++ T Sbjct: 503 MSRIDDVINVAGHRLSTGRFEEVLCQHPAVAEAAVIGVEDKLKGQVPLGLVVLKNGVDIT 562 Query: 612 EEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKIPRSALSAIVNGKPYKITSTIE 671 +EQ+ +E+V VR IGPVAAF+ + +LPKTRSGKI R+ + I + + Y + +TIE Sbjct: 563 DEQLNKELVALVRSEIGPVAAFKLVSAIPKLPKTRSGKILRATMRKIADNQEYSVPATIE 622 Query: 672 DPSIFGHVEEML 683 DP+ V L Sbjct: 623 DPATLELVRNTL 634 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: 1250 Number of extensions: 60 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 686 Length of database: 644 Length adjustment: 38 Effective length of query: 648 Effective length of database: 606 Effective search space: 392688 Effective search space used: 392688 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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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