Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_016552585.1 RGCCGE502_RS02470 long-chain fatty acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_000298315.2:WP_016552585.1 Length = 566 Score = 149 bits (376), Expect = 3e-40 Identities = 157/563 (27%), Positives = 240/563 (42%), Gaps = 82/563 (14%) Query: 20 LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79 LE++ Y + T+ + T+ + +A+ + S+G+E G V+V+ PNV Q Sbjct: 41 LEKSCARYANRTAFSSMGKTLTYGALESQTRKIAAWLQSIGLEKGDRVAVMMPNVLQNPV 100 Query: 80 LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVP 139 + + AG ++ VN R + L S +K IFV LE A +Q V Sbjct: 101 AVYGILRAGFVVVNVNPLYTPRELEHQLRDSGAKAIFV--------LENFARTVEQVLVK 152 Query: 140 ---RLVFMADESESGNSSELGKEFFC----------------SYKDLIDRG-DPDFKWVM 179 R V + E + L ++K ++ G K Sbjct: 153 TDVRHVVVTSLGEMLGAKGLIVNLLVRRVKKLVPSWSIPQHKTFKQVLGEGAGKSLKPAS 212 Query: 180 PKSEWDPMILNYTSGTTSSPKGVVHCHRGIFI--MTVDSLIDWGVPKQPV-----YLWTL 232 K + D L YT GTT KG V HR + + ++ + K+P +L L Sbjct: 213 LKGD-DIAFLQYTGGTTGIAKGAVLTHRNLLSNKLQLELWLQSAFDKKPRPEVLNFLCAL 271 Query: 233 PMFHANGWSYPWGMA-AVGGTNICLRKFDSEIIYDMIKRHG---VTHMCGAPVVLNMLSN 288 P++H + M ++G NI + + I ++K G V G + N L N Sbjct: 272 PLYHIFALTVNSLMGMSLGAHNILVA--NPRDIPALVKEFGKVKVHIFPGLNTLFNALMN 329 Query: 289 APGSEPLKTTVQIMTAGA----PPPSAVLFRTESLGFAVSHGYGLTETAGLVVSCAWKKE 344 L + +M+ G P A + + G ++ GYGL+ET+ Sbjct: 330 NADFAKLDFSNIVMSLGGGMAVQRPVAERWM-KITGSHITEGYGLSETS----------- 377 Query: 345 WNHLPATERARLKSRQGVGTV----MQTKIDVVDPVTGAAVKRDGSTL-----GEVVLRG 395 P R S + G++ T++D+ D DG++L GE+ +RG Sbjct: 378 ----PVATANRFDSAEFTGSIGLPLPSTELDIRD--------EDGNSLPLGEIGEICIRG 425 Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455 VM GY PE TA+ MT+DG+F +GD+G M GY +I DR KD+I+ G N+ E+ Sbjct: 426 PQVMAGYWNKPEETARVMTSDGYFRSGDMGFMDARGYTKIVDRKKDMILVSGFNVYPNEI 485 Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVP 515 E + HP ILEAA V PD GE FV K TE ++ +C + L Y P Sbjct: 486 EEVAAMHPGILEAAAVGIPDGHSGEAVKLFVVRKDPAL---TEADVKAHCAANLTNYKRP 542 Query: 516 KTVVFKEELPKTSTGKVQKFILR 538 + V F+ ELPKT GK+ + LR Sbjct: 543 RFVEFRTELPKTPVGKILRKDLR 565 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: 744 Number of extensions: 37 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 566 Length adjustment: 36 Effective length of query: 520 Effective length of database: 530 Effective search space: 275600 Effective search space used: 275600 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 Sep 24 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