Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_011384701.1 AMB_RS11645 propionyl-CoA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_000009985.1:WP_011384701.1 Length = 638 Score = 708 bits (1828), Expect = 0.0 Identities = 338/623 (54%), Positives = 447/623 (71%), Gaps = 2/623 (0%) Query: 58 YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117 Y+ + S+ DPE FWG+AA++I WYK W K L++ P WFV N CYNA+DRH+ Sbjct: 5 YQQAYEKSLKDPEGFWGEAAKEIHWYKTWDKVLDDSKKPFYRWFVGAETNTCYNAVDRHV 64 Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177 E G+G + AIIYDSPVT TK ISY E+ +QVS+LAG + GV KGD V++YMPM+P+A Sbjct: 65 EQGRGAQTAIIYDSPVTSTKRKISYDELKDQVSRLAGAMAALGVAKGDRVLLYMPMVPEA 124 Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237 + MLA AR+GAIHS++FGGFA EL+TRI+ KPKV+++AS GIE R + Y P+L+EA Sbjct: 125 VVGMLAVARLGAIHSVVFGGFAPAELATRINDAKPKVILSASCGIEGSRVIAYKPMLDEA 184 Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSG 297 + + +HKP ++ RP V +G DLDW E AKA+ DCVPVL+ PLYILYTSG Sbjct: 185 IALSEHKPGHTIMLQRPQSVAVMDKAG-DLDWTEVCAKAKPADCVPVLATDPLYILYTSG 243 Query: 298 TTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNT 357 TTG PKGVVR GG+ V L W+M +Y +KPGEV+WAASD+GWVVGHSYICY PLL+G+T Sbjct: 244 TTGQPKGVVRDNGGHMVALMWSMKYVYDIKPGEVFWAASDVGWVVGHSYICYAPLLNGST 303 Query: 358 TVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTL 417 TV+YEGKPVGTPDAGA++R+++E+ +A+LFTAPTA RAI+++DP L K+Y LT F+ L Sbjct: 304 TVVYEGKPVGTPDAGAFWRMISEYKMASLFTAPTAFRAIKREDPNGELLKKYDLTGFRAL 363 Query: 418 FVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGKCVPG 477 F+AGER D +T+ W+++ +VPV+DHWWQTETG I A+C+GL + PG K VPG Sbjct: 364 FLAGERSDPDTINWAREKLKVPVVDHWWQTETGWAIAANCLGL-HEFPIKPGSPTKPVPG 422 Query: 478 YNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAG 537 + + +LD+ Q +A +G++VV+LPLPPGA LW + Y+ +FPG Y T DAG Sbjct: 423 WGLEVLDEGHQPCEAGKVGSLVVRLPLPPGALLTLWNADQRCIDSYYSEFPGCYKTADAG 482 Query: 538 YMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLAL 597 +DE+GY Y+MSR DD+INVAGHR+S G +EE + SH V +CAV+G D LKG +PL Sbjct: 483 MIDEDGYAYIMSRTDDIINVAGHRLSTGGMEEVLASHPDVAECAVIGVADQLKGQLPLGF 542 Query: 598 CVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNG 657 LK V +QV+ E+VK VR+ IGPVAAF+ V +LPKTRSGKI R T+ + + Sbjct: 543 ICLKAGVTKPHDQVIAEVVKLVREKIGPVAAFKTCTVVNRLPKTRSGKILRGTMQKIADN 602 Query: 658 KPYKVTPTIEDPSIFGHIEEVLK 680 + +K+ TI+DPSI I E L+ Sbjct: 603 QDFKMPATIDDPSILDEIGESLE 625 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: 1339 Number of extensions: 61 Number of successful extensions: 3 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: 638 Length adjustment: 38 Effective length of query: 645 Effective length of database: 600 Effective search space: 387000 Effective search space used: 387000 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