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 RR42_RS13560 RR42_RS13560 propionyl-CoA synthetase
Query= SwissProt::Q9H6R3 (686 letters) >FitnessBrowser__Cup4G11:RR42_RS13560 Length = 630 Score = 510 bits (1314), Expect = e-149 Identities = 279/634 (44%), Positives = 395/634 (62%), Gaps = 29/634 (4%) Query: 67 AASVTDPERFWGKAAEQISWYKPWTKTLENKHSPSTRWFVEGMLNICYNAVDRHIENGKG 126 A S++DPE FW + A +I W P+ L++ P TRWFV G N+C+NAVDRH+ + Sbjct: 9 ARSLSDPEGFWAEQARRIDWETPFDTVLDDSRPPFTRWFVGGRTNLCHNAVDRHLAE-RA 67 Query: 127 DKIAIIYDSPVTNTKATFTYKEVLEQVSKLAGVLVKHGIKKGDTVVIYMPMIPQAMYTML 186 D+ A+IY S T T++Y E+ ++V+++A +L + G+ KGD V+IYMPMIP+A + ML Sbjct: 68 DQAALIYVSTETGQHRTYSYAELHDEVNRMAAILQQLGVVKGDRVLIYMPMIPEAAFAML 127 Query: 187 ACARIGAIHSLIFGGFASKELSSRIDHVKPKVVVTASFGIEPGRRVEYVPLVEEALKIGQ 246 ACARIGAIHS++FGGFAS L++RID +P+V+V+A G G+ V Y PL++EA+K+ Sbjct: 128 ACARIGAIHSVVFGGFASVSLAARIDDAQPRVIVSADAGSRAGKVVPYKPLLDEAVKLAT 187 Query: 247 HKPDKILIYNRPNMEAVPLAPGRDLD---WDEEMAKAQSHDCVPVLSEHPLYILYTSGTT 303 HKP+++L+ +R + + L PGRD D W E + A+ C + S P Y+LYTSGTT Sbjct: 188 HKPERVLLVDR-QLSPMTLTPGRDEDYGAWRERVGAARV-PCAWLESSEPSYVLYTSGTT 245 Query: 304 GLPKGVIRPTGGYAVMLHWSMSSIYGLQPGEVWWAASDLGWVVGHSYICYGPLLHGNTTV 363 G PKGV R TGGYAV L SM I+ + G+ +++SD+GWVVGHSYI YGPLL G T+ Sbjct: 246 GKPKGVQRDTGGYAVALAASMEYIFCGKAGDTMFSSSDIGWVVGHSYIIYGPLLAGMATI 305 Query: 364 LYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFV 423 +YEG P+ PD G ++++ ++ V +F+APTAIR +++QDP A +Y L+ + LF+ Sbjct: 306 MYEGTPI-RPDGGILWQLVEQYHVNIMFSAPTAIRVLKKQDP--AWLTRYDLSSLRLLFL 362 Query: 424 AGERCDVETLEWSKNVFRVPVLDHWWQTETGSPITASCVGLGNSKTPPP---GQAGKSVP 480 AGE D T W + PV+D++WQTETG PI A GL P P G G V Sbjct: 363 AGEPLDEPTASWIQQGIGKPVVDNYWQTETGWPIIAIQRGL----DPLPAKLGSPGVPVY 418 Query: 481 GYNVMILDDNMQKLKARC----LGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPG--Y 534 GY++ I+D + A C G + + PLPPG + +W + E F Y+ PG Sbjct: 419 GYDLKIID---EATGAECPPGQKGVVAIDGPLPPGCMTTVWGDDERFVKTYWSGVPGRRC 475 Query: 535 YDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESILSHGTVADCAVVGKEDPLK 594 Y T D G DE+GY++++ R DDVINVAGHR+ IEESI SH VA+ AVVG D LK Sbjct: 476 YSTFDWGVQDEDGYIFILGRTDDVINVAGHRLGTREIEESISSHPAVAEVAVVGVHDALK 535 Query: 595 GHVPLALCVLR---KDINATEEQVLE-EIVKHVRQNIGPVAAFRNAVFVKQLPKTRSGKI 650 G +A ++R + + VLE +++K V Q +G VA FV LPKTRSGK+ Sbjct: 536 GQAAMAFVIVRDAGRTATQADRLVLEGDVMKTVDQQLGAVARPARVFFVNALPKTRSGKL 595 Query: 651 PRSALSAIVNGKPYKITSTIEDPSIFGHVEEMLK 684 R A+ A+ G+ +TIEDP+ ++ ++ Sbjct: 596 LRRAMQAVAEGRDPGDLTTIEDPTALAQLQAAMQ 629 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: 1130 Number of extensions: 61 Number of successful extensions: 8 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: 630 Length adjustment: 38 Effective length of query: 648 Effective length of database: 592 Effective search space: 383616 Effective search space used: 383616 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