Align 2-methylpropanoate--CoA ligase CCL4; HlCCL4; 2-methylbutanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase
Query= SwissProt::M4IQQ5 (556 letters) >FitnessBrowser__Dyella79:N515DRAFT_1417 Length = 562 Score = 141 bits (356), Expect = 6e-38 Identities = 115/383 (30%), Positives = 174/383 (45%), Gaps = 49/383 (12%) Query: 185 DPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDW----GVPKQPVYLWTLPMFH---- 236 D L YT GTT KG + H G + + W P + V + LP++H Sbjct: 208 DLAFLQYTGGTTGVAKGAMLSH-GNMVANMLQAGAWIGTNAKPGEEVIITALPLYHIFSL 266 Query: 237 -ANGWSYPWGMAAVGGTN-ICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEP 294 ANG + +GG N + D +K+ T + G + N L N PG Sbjct: 267 TANGLVF----TRLGGLNWLITNPRDMPGFVKELKKSRFTALTGVNTLFNGLLNTPGFAE 322 Query: 295 LKTTVQIMTAGA--PPPSAVLFRTESL-GFAVSHGYGLTETA-GLVVSCAWKKEWNHLPA 350 + + ++ G AV R + + G ++ YGLTET+ ++ K++N Sbjct: 323 VDFSRLHLSLGGGMAVQRAVAERWKKVTGVTLAEAYGLTETSPAACINPLDLKDYN---- 378 Query: 351 TERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGST------LGEVVLRGGSVMLGYLK 404 + I + P T A+ + S +GE++++G VM GY K Sbjct: 379 -----------------SSIGLPIPSTDVAIWSEDSQPLPIGEVGELMVKGPQVMQGYWK 421 Query: 405 DPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPD 464 P+ TAK + ADGW +TGD+ M +GY+ I DR KD+I+ G N+ EVE I+ +HP Sbjct: 422 RPDETAKVLGADGWLHTGDIARMDANGYVYIVDRKKDMILVSGFNVYPNEVEDIVMTHPG 481 Query: 465 ILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEEL 524 + E A V PDE GE FV K T + + E+CR L Y PK + F++ L Sbjct: 482 VAEVAAVGVPDEHSGEVVKLFVVRK---DPNLTVEALKEFCRENLTGYKRPKLIEFRDAL 538 Query: 525 PKTSTGKVQKFILRDMARGMGSA 547 PK++ GK+ + LRD + A Sbjct: 539 PKSNVGKILRRELRDEKKAASPA 561 Lambda K H 0.319 0.135 0.412 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: 728 Number of extensions: 34 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: 556 Length of database: 562 Length adjustment: 36 Effective length of query: 520 Effective length of database: 526 Effective search space: 273520 Effective search space used: 273520 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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