Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 5210124 Shew_2568 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A0A0G2K047 (683 letters) >FitnessBrowser__PV4:5210124 Length = 662 Score = 673 bits (1736), Expect = 0.0 Identities = 323/608 (53%), Positives = 432/608 (71%), Gaps = 8/608 (1%) Query: 65 SVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHIENGQGDK 124 S+ +P FWG+AA ++W K + + L++ P WF G LN CYNA+DRH+E G+G++ Sbjct: 40 SIDNPNAFWGEAAGALAWDKTFERVLDDSQAPMYRWFSGGQLNTCYNAVDRHVEAGRGEQ 99 Query: 125 IAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQAIYAMLAC 184 +AI Y SP+T T+ I+Y E+ QVS+LAG + QGV KGD V+IYMPM+P+ YAMLAC Sbjct: 100 VAIQYVSPITGTEYGITYNELQAQVSRLAGYMASQGVVKGDRVIIYMPMVPETAYAMLAC 159 Query: 185 ARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEALRIGQHK 244 AR+GAIHS++FGGFA+ EL+TRID PK++++AS G+EP V Y PLL++AL HK Sbjct: 160 ARLGAIHSVVFGGFAANELATRIDDATPKMILSASCGVEPSGVVAYKPLLDDALEQASHK 219 Query: 245 PDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEHPLYILYTSGTTGLPKG 304 ++ +I NRP ++ L+ GRD+DW+ MA A + +C V + PLYILYTSGTTG PKG Sbjct: 220 VEQCVILNRPQLQ-ADLVDGRDVDWQGAMADAPNIECQTVEATDPLYILYTSGTTGQPKG 278 Query: 305 VVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLLHGNTTVLYEGK 364 VVR GG+AV L W+M IY + PG+V+WAASD+GWVVGHSYI YGPLL G TTVL+EGK Sbjct: 279 VVRDNGGHAVALAWSMKHIYDIDPGDVFWAASDVGWVVGHSYIVYGPLLVGATTVLFEGK 338 Query: 365 PVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTRFKTLFVAGERC 424 PVGTPD G ++R +A++ V + FTAPTAIRAI++ DP K L+ TLF+AGERC Sbjct: 339 PVGTPDPGIFWRTIAKYNVKSFFTAPTAIRAIKRDDPEGDYLKDVDLSCLGTLFLAGERC 398 Query: 425 DVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAG---KCVPGYNVM 481 D +TL W+++ PV+DHWWQTETG P+ A+ +G P P +AG K VPGY+V Sbjct: 399 DPDTLHWAEQQLDKPVIDHWWQTETGWPVAANLMG----TAPVPVKAGSPAKAVPGYDVQ 454 Query: 482 ILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDTMDAGYMDE 541 +LD+ + GN+V+KLPLPPG + LW+N+ +K Y +PGYY T DAGYMDE Sbjct: 455 VLDEMGDVVAPDQSGNVVIKLPLPPGTLATLWQNEGRYKESYLSMYPGYYLTGDAGYMDE 514 Query: 542 EGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHVPLALCVLK 601 +GYLY+MSR+DD+INVAGHR+S G EE + H V + AV+G +D LKG VPL L VLK Sbjct: 515 DGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHEAVAEAAVIGVDDKLKGQVPLGLVVLK 574 Query: 602 KDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSALVNGKPYK 661 K + ++EQ+ +E++ VR+ IGPVAAF+ V +LPKTRSGKI R T+ + + + +K Sbjct: 575 KGCDLSDEQLYKELIALVREQIGPVAAFKLVSAVPKLPKTRSGKILRGTMRKIADNQEFK 634 Query: 662 VTPTIEDP 669 + TIEDP Sbjct: 635 MPATIEDP 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: 1348 Number of extensions: 54 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: 662 Length adjustment: 39 Effective length of query: 644 Effective length of database: 623 Effective search space: 401212 Effective search space used: 401212 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