Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate Pf6N2E2_3244 Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)
Query= SwissProt::M4IS88 (568 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3244 Length = 560 Score = 204 bits (519), Expect = 8e-57 Identities = 163/540 (30%), Positives = 261/540 (48%), Gaps = 40/540 (7%) Query: 36 TRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIGLGSTVAVIAPNVPALYEAHFAVPMAG 95 TR + Y++ R + A+ L + G TVAV+ + E FA+PM G Sbjct: 33 TREIIYRDQLRYSYPTLIERVARLANVLTEAGVKAGDTVAVMDWDSHRYLECMFAIPMIG 92 Query: 96 AVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFFSLAEEALKILAQESKSHYKPPLLVVI 155 AV++ +N+RL+ I + + H+ V+V+ EF L + L K+ LL+ Sbjct: 93 AVIHTINVRLSPEQIVYTMNHAEDRFVLVNSEFVGLYQAIAGHLTTVDKT-----LLLTD 147 Query: 156 GDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDWKPPEDEWQSISLGYTSGTTASPKGVV 215 E KT E G EYE+ L P +D++ DE + YT+GTT +PKGV Sbjct: 148 LPE----KTAELPNLVG--EYEQLLAAAAPTYDFQD-FDENSVATTFYTTGTTGNPKGVY 200 Query: 216 LSHRGAYLMSLSASVVWG-------INEGAIYLWTLPMFHCNGWCYTWGMAAFCGTNICL 268 +HR L ++ + + G + +Y+ PMFH + WG+ + T + L Sbjct: 201 FTHRQLVLHTMGVATIMGAIDSVRLLGTNDVYMPITPMFHV----HAWGLP-YVATMLGL 255 Query: 269 RQV-----TAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIPLPHLVHVMTAGAAP 323 +QV + + K VT P +L ++NA + ++ G+A Sbjct: 256 KQVYPGRYDPEFLVQLWRKEKVTFSHCVPTILQMVLNAKGAQDTDFGGW--KIVIGGSAL 313 Query: 324 PPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQARLNAR--QGVRYIA 381 S+ A +G ++ YG+SET GP CA E + + + R R GV Sbjct: 314 NRSLYEAAKARGIQLTAAYGMSET-GPLVSCAHLNE-ELMAGSEDERTTYRIKAGVPGPL 371 Query: 382 LEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFADGWFHSGDLAVK 441 +E +VDT+ + +PADG T GE+V+R + +GY P+ E +A GW H+GD+A Sbjct: 372 VEAA-IVDTEG-RFLPADGETQGELVLRAPWLTEGYFNEPQKGAELWAGGWLHTGDVATL 429 Query: 442 HPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPDERWGESPCAFVT 501 G+I+I+DR KD+I +GGE ISSL++E+ + H AV EV+VV PD +WGE P A + Sbjct: 430 DNMGFIDIRDRIKDVIKTGGEWISSLDLEDLISRHVAVREVAVVGIPDPQWGERPFALLV 489 Query: 502 LKPNIDKSNEQVLAEDIIKFCKSKMPAYW-VPKSV-VFGPLPKTATGKIQKHVLRAKAKE 559 ++ + + L E + F + + W +P + + +PKT+ GK+ K +R E Sbjct: 490 VREG-HEIGARELKEHLKPFVELGHLSKWAIPSQIALVTEIPKTSVGKLDKKRIRVDITE 548 Lambda K H 0.318 0.134 0.415 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: 741 Number of extensions: 31 Number of successful extensions: 6 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: 568 Length of database: 560 Length adjustment: 36 Effective length of query: 532 Effective length of database: 524 Effective search space: 278768 Effective search space used: 278768 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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