Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate 7024497 Shewana3_1675 AMP-dependent synthetase and ligase (RefSeq)
Query= BRENDA::A0A0G2K047 (683 letters) >FitnessBrowser__ANA3:7024497 Length = 640 Score = 666 bits (1718), Expect = 0.0 Identities = 326/631 (51%), Positives = 438/631 (69%), Gaps = 6/631 (0%) Query: 49 LTTSSGGGEYKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNI 108 L T +G ++T S+A+ + FW +AA+ + W P + L+ P WF +G LN Sbjct: 5 LMTDAGQQLHQT----SIANKQAFWQQAAKALDWVTPSKQILDESEAPFYHWFSDGELNT 60 Query: 109 CYNAIDRHIENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVV 168 CYNA+DRH+ G+G++IAI Y SPVT+T+ +I+Y+E+ QV++LAG L GV KGD VV Sbjct: 61 CYNAVDRHVLAGRGEQIAIHYVSPVTETEYSITYRELQAQVARLAGYLQSVGVAKGDRVV 120 Query: 169 IYMPMIPQAIYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKV 228 IYMPM+P+ YAMLACARIGAIHS++FGGFA+ EL+TRI+ KPK+V++AS GIEP V Sbjct: 121 IYMPMVPETAYAMLACARIGAIHSVVFGGFAANELATRINDAKPKLVMSASCGIEPSGVV 180 Query: 229 EYMPLLEEALRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKAQSHDCVPVLSEH 288 Y PLL++AL HK + LI NRP E + +GRD DW+ + + S DCV V + Sbjct: 181 PYKPLLDKALNEAVHKVEHCLILNRPQYE-AQMQAGRDKDWQTALCTSDSADCVTVKATD 239 Query: 289 PLYILYTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYIC 348 PLY+LYTSGTTG PKGVVR GG+AV L W+M++IY + G+V+WAASD+GWVVGHSYI Sbjct: 240 PLYVLYTSGTTGQPKGVVRDNGGHAVALAWSMANIYDIAQGDVFWAASDVGWVVGHSYIV 299 Query: 349 YGPLLHGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQ 408 YGPLL G TT+LYEGKPVGTPD GA++R +A++ V + FTAPTAIRAI+++DP Sbjct: 300 YGPLLVGATTLLYEGKPVGTPDPGAFWRTIAKYRVKSFFTAPTAIRAIKREDPDGEFILG 359 Query: 409 YSLTRFKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPP 468 L+ K +F+AGERCD +TL W++ PV+DHWWQTETG P+ A+ +G+ Sbjct: 360 VDLSCLKNVFLAGERCDPDTLHWAEAKLHKPVIDHWWQTETGWPVAANLMGVAPIAV-KA 418 Query: 469 GQAGKCVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFP 528 G G+ VPGY V ++D+ K+ A GN+V+KLPLPPG + LW+N + ++ Y +P Sbjct: 419 GSPGRPVPGYEVDVVDELGAKVAANVSGNVVIKLPLPPGTLTTLWQNNKRYQDSYLSMYP 478 Query: 529 GYYDTMDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDP 588 GYY T DAGYMDE+GYLY+MSR+DD+INVAGHR+S G EE + H V + AV+G +D Sbjct: 479 GYYLTGDAGYMDEDGYLYIMSRIDDIINVAGHRLSTGRFEEVLCQHPDVAEAAVIGVDDK 538 Query: 589 LKGHVPLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPR 648 LKG VPL L VLKK V T+E++ ++++ VRQ IGPVA+FR +++LPKTRSGKI R Sbjct: 539 LKGQVPLGLVVLKKGVTITDEELHKQLIALVRQEIGPVASFRLVSAIQKLPKTRSGKILR 598 Query: 649 STLSALVNGKPYKVTPTIEDPSIFGHIEEVL 679 T+ + + + Y TIEDP + L Sbjct: 599 GTMRKIADNQQYTAPATIEDPQTLDLVRTTL 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: 1235 Number of extensions: 52 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: 640 Length adjustment: 38 Effective length of query: 645 Effective length of database: 602 Effective search space: 388290 Effective search space used: 388290 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