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 Ac3H11_2208 Propionate--CoA ligase (EC 6.2.1.17)
Query= SwissProt::Q9H6R3 (686 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2208 Length = 633 Score = 501 bits (1290), Expect = e-146 Identities = 271/635 (42%), Positives = 388/635 (61%), Gaps = 18/635 (2%) Query: 60 SEYKTHFAASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDR 119 S Y + S+ + FW + A+ I W P + + + P +WFV G N+C+NAVDR Sbjct: 5 STYADFYRQSIDHRDAFWSEQAQLIDWKTPPQQVCDYSNPPFAKWFVGGTTNLCHNAVDR 64 Query: 120 HIENGKGDKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIP 179 H+ + + A++ S T+T+ ++++ E+ +V ++A VL G+KKGD V+IYMPMI Sbjct: 65 HLAT-RASQAALVAISTETDTERSYSFAELHAEVQRMAAVLQSLGVKKGDRVLIYMPMIA 123 Query: 180 QAMYTMLACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVE 239 +A + MLAC RIGA+HS++FGGFAS L+SRI+ +P VV+A G G+ V Y PL++ Sbjct: 124 EAAFAMLACVRIGALHSVVFGGFASGSLASRIEDSEPVAVVSADAGSRGGKVVPYKPLLD 183 Query: 240 EALKIGQHKPDKILIYNRPNMEAVPLAPGRDLDWDEEMAKAQSHDCVP---VLSEHPLYI 296 EA+ + +HKP +L+ NR + + L PGRD W + + + VP V S HP Y Sbjct: 184 EAIALSKHKPAAVLMVNR-GLAPMHLQPGRDHAW-ASLREQHLNTVVPCEWVDSTHPSYT 241 Query: 297 LYTSGTTGLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPL 356 LYTSGTTG PKGV R TGGYAV L SM I+ QPGEV++A SD+GWVVGHSYI YGPL Sbjct: 242 LYTSGTTGKPKGVQRDTGGYAVALAASMKHIFDAQPGEVYFATSDIGWVVGHSYIIYGPL 301 Query: 357 LHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLT 416 L G TT++YEG P+ PDAG ++ ++ ++ V +F+APTA+R +++QDP A QY++ Sbjct: 302 LAGMTTIMYEGLPI-RPDAGVWWSIVEKYQVTHMFSAPTAVRVLKKQDP--AFLTQYNVK 358 Query: 417 RFKTLFVAGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPPGQAG 476 K L++AGE D T W +P++D++WQTETG PI A G+ + G G Sbjct: 359 SLKALWLAGEPVDEPTARWIGAALNIPIIDNYWQTETGWPILAVANGI-EANAARWGSPG 417 Query: 477 KSVPGYNVMILDD--NMQKLKARCLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPG- 533 K+V GY+V +LD+ + A G + ++ PLPPG +W++ F + Y++ PG Sbjct: 418 KAVYGYHVKLLDEATGEELTGANQKGVVAIEGPLPPGCMQTVWRDDARFVNTYWKSIPGR 477 Query: 534 -YYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDP 592 Y T D G D +GY +++ R DDVINVAGHR+ IEESI SH +A+ AVVG D Sbjct: 478 LIYSTFDWGIRDADGYHFILGRTDDVINVAGHRLGTREIEESIASHPNIAEVAVVGVADS 537 Query: 593 LKGHVPLALCVLRK----DINATEEQVLEEIVKHVRQNIGPVAAFRNAVFVKQLPKTRSG 648 LKG V +A V R D +A ++ E++K V +G VA FV LPKTRSG Sbjct: 538 LKGQVAMAFAVARDASGLDSDAARLKLEGEVMKQVDSQLGAVARPSRVYFVSVLPKTRSG 597 Query: 649 KIPRSALSAIVNGKPYKITSTIEDPSIFGHVEEML 683 K+ R AL A+ + +T+EDP+ V+E++ Sbjct: 598 KLLRRALQAVAERRDPGDLTTMEDPAALQQVKELV 632 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: 1081 Number of extensions: 52 Number of successful extensions: 9 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: 633 Length adjustment: 38 Effective length of query: 648 Effective length of database: 595 Effective search space: 385560 Effective search space used: 385560 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:
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