Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_012277976.1 SHAL_RS15005 propionyl-CoA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_000019185.1:WP_012277976.1 Length = 634 Score = 672 bits (1735), Expect = 0.0 Identities = 322/617 (52%), Positives = 431/617 (69%), Gaps = 2/617 (0%) Query: 63 AASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQG 122 A S+ PE FW +AA QI W+ PW L++ P WF G LN CYNA+DRH++ G+G Sbjct: 10 AKSINQPEAFWAEAASQIDWFSPWNNVLDDSEAPFYHWFKGGKLNTCYNAVDRHVDAGRG 69 Query: 123 DKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAML 182 D+IA+ Y SPVTD + ISY+E+L QVS+LAG + GVKKGD VVIYMPM+P+ +AML Sbjct: 70 DQIALQYVSPVTDVEYGISYRELLAQVSRLAGYMDSIGVKKGDRVVIYMPMVPETAFAML 129 Query: 183 ACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQ 242 ACARIGAIHS++FGGFA+ EL+TRI+ KPK++++AS GIEP + Y PLL+ AL Sbjct: 130 ACARIGAIHSVVFGGFAANELATRINDAKPKLILSASCGIEPSGIIPYKPLLDAALDQAT 189 Query: 243 HKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLP 302 HK D L+ NR +E L GRD+DW+ +A A + DC P+ + PLYILYTSGTTG P Sbjct: 190 HKVDHCLVLNRGQLE-AELFPGRDIDWQAAVAAAPNIDCQPLDATDPLYILYTSGTTGQP 248 Query: 303 KGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYE 362 KGVVR GG+AV L W+M IY + G+V+WAASD+GWVVGHSYI YGPLL G T++LYE Sbjct: 249 KGVVRDNGGHAVALAWSMKHIYDINAGDVFWAASDVGWVVGHSYIVYGPLLVGATSILYE 308 Query: 363 GKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGE 422 GKP+GTPD GA++R +A++ V + FTAPTAIRAI++ DP + L+ K +F+AGE Sbjct: 309 GKPIGTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKRDDPHGDYLEGVDLSCLKNVFLAGE 368 Query: 423 RCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPGYNVMI 482 RCD +TL W++ + PV+DHWWQTETG P+ A+ +G + G VPGY + + Sbjct: 369 RCDPDTLHWTEGKLKKPVIDHWWQTETGWPVAANLMGYAPVEI-KAGSPALAVPGYQIEV 427 Query: 483 LDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDEE 542 +D +++A GN+V+KLPLPPG + LW+N++ ++ Y +PGYY T DAGY DE+ Sbjct: 428 VDVMGDEVEANESGNVVIKLPLPPGTLTTLWQNEQRYQDSYLSMYPGYYLTGDAGYKDED 487 Query: 543 GYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLKK 602 GYLY+MSR+DD+INVAGHR+S G EE + H V + AV+G +D LKG VPL L VLKK Sbjct: 488 GYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVKDVLKGQVPLGLVVLKK 547 Query: 603 DVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYKV 662 V+ ++ + ++++ VRQ IGPVA+FR V++LPKTRSGKI R T+ + + + Y V Sbjct: 548 GVSLNDDDLNQQLMSLVRQEIGPVASFRLVSAVQKLPKTRSGKILRGTMRNIADNQSYNV 607 Query: 663 TPTIEDPSIFGHIEEVL 679 TIEDP+ + L Sbjct: 608 PATIEDPATLDIVRNTL 624 Lambda K H 0.318 0.136 0.421 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: 1276 Number of extensions: 59 Number of successful extensions: 4 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: 683 Length of database: 634 Length adjustment: 38 Effective length of query: 645 Effective length of database: 596 Effective search space: 384420 Effective search space used: 384420 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