Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate WP_101589101.1 BJEO58_RS08245 acetate--CoA ligase
Query= BRENDA::A0A0G2K047 (683 letters) >NCBI__GCF_900169175.1:WP_101589101.1 Length = 645 Score = 587 bits (1513), Expect = e-172 Identities = 301/645 (46%), Positives = 415/645 (64%), Gaps = 18/645 (2%) Query: 50 TTSSGGGEYKTHFAA----SVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGM 105 +TS+ E +AA + DP FW AA+ I W P ++ L++ P WF +G Sbjct: 3 STSAAHDEAPRTYAAVARSAADDPASFWLGAAQAIDWVTPPSRALDDANAPIYRWFPDGT 62 Query: 106 LNICYNAIDRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGD 165 LN+C NA+DRH+E G GD++A++YDSPVTDT ++ + ++VS+ A L +G+ KGD Sbjct: 63 LNVCANALDRHVEMGSGDRVALVYDSPVTDTVREYTFTALRDEVSRFARALADRGITKGD 122 Query: 166 TVVIYMPMIPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPG 225 VVIYMPM+P+A AMLACAR+GA+HS++FGGFA+ EL+ RID ++PK V+++S GIE Sbjct: 123 RVVIYMPMVPEATIAMLACARLGAVHSVVFGGFAANELAVRIDDLQPKAVISSSCGIEKT 182 Query: 226 RKVEYMPLLEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKA-QSHDCVPV 284 R +EY PLL+EALRI P+ ++ R + L G DLD+ + +A D V V Sbjct: 183 RIIEYKPLLDEALRIATAGPEFSVVVQR-EQHRAELQEGFDLDYADLLASTPDGIDPVTV 241 Query: 285 LSEHPLYILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGH 344 + PLY+LYTSGTTG PKG++R GGYAV L W+M +++GL+PG+ + ASD+GWVVGH Sbjct: 242 QATDPLYVLYTSGTTGRPKGILRDAGGYAVALQWSMGNLFGLQPGDTMFTASDVGWVVGH 301 Query: 345 SYICYGPLLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAA 404 SYI Y PLL G TTVLYEGKPVGTPDA A++RV+ +H V FTAPTA+R IR++DP A Sbjct: 302 SYIVYAPLLAGVTTVLYEGKPVGTPDASAFYRVMDQHDVNVFFTAPTAMRVIRKEDPDAE 361 Query: 405 LGKQYSLTRFKTLFVAGERCDVETLEWSKKVFR------VPVLDHWWQTETGSPITASCI 458 + L+ + +F+AGER D +T EW+ +PV+D+WWQTETG PI A+ + Sbjct: 362 HARAADLSALRAVFLAGERLDPDTYEWTTATMAEATGRDIPVVDNWWQTETGWPIAANPL 421 Query: 459 GLGNSKTP-PPGQAGKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQE 517 G+ + P G PGY + ++D ++A + G I+ LPLPPG + +W + E Sbjct: 422 GI--ERLPLKAGSPTVPTPGYRLRVVDPAGNDVRAGTEGLILADLPLPPGTMASIWGDDE 479 Query: 518 AFKHLYFEKFPGYYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTV 577 F Y F G Y T D+GY+DE+GY++VM R DDVINV+GHR+S G +E ++ SH V Sbjct: 480 RFVSTYLSTFEGTYLTGDSGYLDEDGYVFVMGRTDDVINVSGHRLSTGVLEAAIASHPAV 539 Query: 578 TDCAVVGKEDPLKGHVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQ 637 T+CAV+G D G P A VL +A E V +E+V VR+ +GPVAA R V Sbjct: 540 TECAVIGVHDETSGQSPRAFVVLSP--SADPEMVPQELVALVRREVGPVAALRRVDVVDA 597 Query: 638 LPKTRSGKIPRSTLSALVNGKPYKVTP-TIEDPSIFGHIEEVLKQ 681 LPKTRSGKI R T+ + +G+ V P TIEDPS+ + L + Sbjct: 598 LPKTRSGKILRKTMRQISDGEADVVVPSTIEDPSVLDAMRTALSR 642 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: 1184 Number of extensions: 59 Number of successful extensions: 5 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: 645 Length adjustment: 38 Effective length of query: 645 Effective length of database: 607 Effective search space: 391515 Effective search space used: 391515 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