Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 206897 DVU1453 long-chain-fatty-acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >MicrobesOnline__882:206897 Length = 564 Score = 177 bits (450), Expect = 7e-49 Identities = 153/542 (28%), Positives = 246/542 (45%), Gaps = 41/542 (7%) Query: 19 FLERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMY 78 FL+ AA + T++++ ++++ A+++ + G+ G VSV+ PNVPQ Sbjct: 25 FLDEAAERHPKQTAIIFRNYKVSYAKLRLLAERFAANLRAQGVLPGDRVSVMLPNVPQAI 84 Query: 79 ELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPV 138 + + AG + N + + +H S ++ + ++ DL+ I + + Sbjct: 85 IAFWGLLKAGCTVVMTNPLYMEKELVHQIHDSGAEYM----IALDLVWPKIEPLRDRLGI 140 Query: 139 PRLVFMADESESGNSSELGKEFFC----SYKDLIDRGDPDFKW--VMPKSEW------DP 186 + G L F +++D+ G+ W + K E +P Sbjct: 141 RKFFITRISDALGFPLNLLYRFKAKREGTWRDVPFDGETVIPWKTLFKKKEGYSAKVENP 200 Query: 187 M----ILNYTSGTTSSPKGVV--HCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGW 240 +L YT GTT KGV+ H + + + + +++ + +L +P FH G Sbjct: 201 REALALLQYTGGTTGISKGVMLTHYNLSVNVQQIKAILGESTRMRHTFLGLMPYFHVYGL 260 Query: 241 SYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKT 297 + + A+G T I ++ + I +H T GAP + L G LK+ Sbjct: 261 TTCLTLPTALGATIIPFPRYVPRDVLVGIDKHKPTIFPGAPSIYISLMQQKDVGEFDLKS 320 Query: 298 TVQIMTAGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARL 356 ++ AP P + R L G V G+GLTE + + HL + Sbjct: 321 IKYCISGSAPMPLEHIRRFHELTGAQVIEGFGLTEASPVT----------HLNPIHGVQK 370 Query: 357 KSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTAD 416 GV T+ VVD G G +GE+++RG VM GYL P+ TA ++ + Sbjct: 371 PGSIGV-PFPDTEARVVDMEVGLVPLPPGK-IGELIIRGPQVMQGYLNRPDETANTLR-N 427 Query: 417 GWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDE 476 GW YTGD+ M DGY I DR KD+II GG N+ E++ +L+ HP + EA V P Sbjct: 428 GWLYTGDIATMDEDGYFFIVDRKKDMIIVGGYNVYPREIDEVLHEHPKVKEAVTVGVPHA 487 Query: 477 FWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFI 536 GE A++ ++G+ K T+ EIV +CR +L Y VPK V F+ ELPKT GKV + I Sbjct: 488 TRGEIIKAYIVPREGV--KLTKAEIVAHCREQLANYKVPKQVEFRNELPKTIVGKVLRRI 545 Query: 537 LR 538 LR Sbjct: 546 LR 547 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: 811 Number of extensions: 51 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 556 Length of database: 564 Length adjustment: 36 Effective length of query: 520 Effective length of database: 528 Effective search space: 274560 Effective search space used: 274560 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 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