Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_009763407.1 MICLODRAFT_RS18895 propionyl-CoA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_000262405.1:WP_009763407.1 Length = 637 Score = 682 bits (1760), Expect = 0.0 Identities = 330/627 (52%), Positives = 439/627 (70%), Gaps = 7/627 (1%) Query: 58 YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117 Y +A +ADP FW +AA +I W +P + WFV N CYNA+DRH+ Sbjct: 8 YHEVYAGWMADPAGFWERAAREIDWIRPAETVFDRDAGIYGRWFVGAECNTCYNAVDRHV 67 Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177 +G + AIIYDSPVT TK +I+Y E+ ++V+ LA VL GV KGD VVIYMPMIP+ Sbjct: 68 AT-RGGQAAIIYDSPVTGTKRSITYAELRDEVATLAAVLQDMGVTKGDRVVIYMPMIPET 126 Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237 +AMLACARIGAIHS++FGGFA+KEL+TRID KPKV+++AS GIE R + Y PLL+EA Sbjct: 127 SFAMLACARIGAIHSVVFGGFAAKELATRIDDAKPKVILSASCGIEGARVIPYKPLLDEA 186 Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHD----CVPVLSEHPLYIL 293 + + KP+ L++ RP + L+ GRD DW + +A+A+ D CVPV + PLY+L Sbjct: 187 IALSSFKPEACLVFQRPQLA-CALVEGRDRDWADAVAEAKVEDRRAECVPVAATDPLYVL 245 Query: 294 YTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLL 353 YTSGTTG+PKGVVR GG+ V L W+M +G+KPGEV+WAASD+GWVVGHSYI YGPLL Sbjct: 246 YTSGTTGIPKGVVRDNGGHMVALKWSMEHFFGVKPGEVFWAASDVGWVVGHSYIVYGPLL 305 Query: 354 HGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTR 413 HG T VLYEGKPVGTPDAGAY+RV+++HGV LFTAPTA RAI+++DP A L ++Y L+ Sbjct: 306 HGCTAVLYEGKPVGTPDAGAYWRVISDHGVVTLFTAPTAFRAIKKEDPKAELLRKYDLSS 365 Query: 414 FKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGK 473 F+ LF+AGER D +T++W++ + +VPV+DHWWQTETG P+ + +GLG + G Sbjct: 366 FRALFLAGERADPDTVKWAEDILQVPVIDHWWQTETGWPVAGNPLGLG-ALPVKHGSPTV 424 Query: 474 CVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 533 +PGY + +LD+ + + ++G IV+KLPLPPGA LW+ E F+ Y +PGYY+T Sbjct: 425 PMPGYVLEVLDEGGKPVAPNTMGAIVIKLPLPPGALPTLWQADERFRESYLSVYPGYYNT 484 Query: 534 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHV 593 DAGY+DE+GY++VM R DD+INVAGHR+S G +EE + SH V +CAV+G +D LKG V Sbjct: 485 SDAGYLDEDGYIWVMGRTDDIINVAGHRLSTGGMEEVLASHPAVAECAVIGVKDALKGEV 544 Query: 594 PLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSA 653 P VLK ++ E + E+V VR IGPVAAF+ A+ V +LPKTRSGKI R T+ Sbjct: 545 PCGFVVLKSGIDRPPETIEAELVALVRDRIGPVAAFKLAITVARLPKTRSGKILRGTMKK 604 Query: 654 LVNGKPYKVTPTIEDPSIFGHIEEVLK 680 + +G + TI+DP I I + L+ Sbjct: 605 IADGDTWSTPATIDDPMILSEIGDALR 631 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: 1376 Number of extensions: 76 Number of successful extensions: 6 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: 637 Length adjustment: 38 Effective length of query: 645 Effective length of database: 599 Effective search space: 386355 Effective search space used: 386355 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