Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate SMc04095 SMc04095 acyl-COA synthetase
Query= BRENDA::A0A0G2K047 (683 letters) >FitnessBrowser__Smeli:SMc04095 Length = 635 Score = 677 bits (1747), Expect = 0.0 Identities = 325/627 (51%), Positives = 438/627 (69%), Gaps = 6/627 (0%) Query: 58 YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117 Y +AA DP FW AA I W+K + E WF +G+ N C+N +DRH+ Sbjct: 5 YSEVYAAWKTDPHGFWADAASAIDWFKRPERIFEPAGGTYGHWFPDGVTNTCHNCLDRHV 64 Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177 E G+G+++A IYDSPVT ISY ++L V +A + K GV KGD ++IYMPMIPQA Sbjct: 65 EAGRGEQLAFIYDSPVTGRIERISYADLLADVKAMAAIYRKLGVDKGDRIIIYMPMIPQA 124 Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237 AMLA ARIGA+HS++FGGFA+ EL+ RID + K+VV+AS G+EPGR V Y PLL++A Sbjct: 125 AIAMLAAARIGAVHSVVFGGFAANELAMRIDDCQAKIVVSASCGLEPGRTVAYKPLLDQA 184 Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKA----QSHDCVPVLSEHPLYIL 293 + HKP R LIY R +M ++SGRD+D+ E +A A + C PV S PLY+L Sbjct: 185 IETASHKPARCLIYQR-DMLAAEMVSGRDIDFAEALAAARDAGEEASCTPVASTDPLYVL 243 Query: 294 YTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLL 353 YTSGTTG PKGVVR GG+ V L W+M +G+ G+V+WAASD+GWVVGHSYI YGPLL Sbjct: 244 YTSGTTGQPKGVVRDNGGHMVALRWSMEHFFGVNAGDVFWAASDIGWVVGHSYIVYGPLL 303 Query: 354 HGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTR 413 +G T+VL+EGKPVGTPD G Y+RV++E GVA +FTAPTA+RAIR++DP AA +Y L+R Sbjct: 304 NGCTSVLFEGKPVGTPDPGTYWRVISERGVAVMFTAPTALRAIRKEDPEAAHAGRYDLSR 363 Query: 414 FKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGK 473 F+ L++AGER D +T+ W+++ +VPV+DHWWQTETG P+ + +GLG G Sbjct: 364 FRALYLAGERADPDTIRWAERALKVPVIDHWWQTETGWPVAGNPLGLGLLPV-KYGSPAV 422 Query: 474 CVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 533 +PGY+V ++DD ++ +LGN+V+KLPLPPG LW F Y E++PG+Y T Sbjct: 423 PLPGYDVQVVDDAGHPVETGTLGNVVIKLPLPPGCLPTLWNADHRFHAAYLEEYPGFYKT 482 Query: 534 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHV 593 DAGY+DE+GY+++M+R DD+INVAGHR+S GA+EE SH V +CAV+G DPLKG V Sbjct: 483 ADAGYVDEDGYIFIMARTDDIINVAGHRLSTGAMEEVCASHPDVAECAVIGIADPLKGQV 542 Query: 594 PLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSA 653 P V+ +V+ E++ +E+V VR+ IGPVAAFR AV VK+LPKTRSGKI RST+ Sbjct: 543 PAGFLVINANVSRETEEIEKEVVGLVRERIGPVAAFRTAVCVKRLPKTRSGKILRSTIQK 602 Query: 654 LVNGKPYKVTPTIEDPSIFGHIEEVLK 680 +++ +P+ + TI+DP+I I E+L+ Sbjct: 603 IIDRQPWTMPATIDDPAILDEITELLR 629 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: 1360 Number of extensions: 71 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: 635 Length adjustment: 38 Effective length of query: 645 Effective length of database: 597 Effective search space: 385065 Effective search space used: 385065 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