Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8499484 DvMF_0256 AMP-dependent synthetase and ligase (RefSeq)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__Miya:8499484 Length = 583 Score = 175 bits (443), Expect = 5e-48 Identities = 145/542 (26%), Positives = 240/542 (44%), Gaps = 43/542 (7%) Query: 20 LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79 L+RAA T++ + ++++ + +A+++ + G+ G VS++ PN+PQ Sbjct: 35 LDRAAERTPRRTAIAFRNYRISYAKLRQLAEVMAANLRAQGVRRGDKVSIMLPNLPQTVI 94 Query: 80 LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVP 139 +AV AG ++ N + + +H S ++ + ++ DL+ I ++ + Sbjct: 95 AFWAVLKAGGVVVMTNPLYMEKELVHQIHDSGARFM----IALDLVWPKIEPLREKLGID 150 Query: 140 RL-----------------VFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKS 182 + F A + +K L+ +G Sbjct: 151 KYFLTRIGDGLAFPLNFLYAFKAKREGTWRELPFDGRHVLPWKTLL-KGKVRHSTTTCNP 209 Query: 183 EWDPMILNYTSGTTSSPKGVV--HCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGW 240 D +L YT GTT KGV+ H + + + + +++ +L +P FH G Sbjct: 210 TEDLAVLQYTGGTTGISKGVMLTHHNMSVNVQQITTILGDARDMDHCFLGLMPYFHVYGL 269 Query: 241 SYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKT 297 + + A+ T + ++ + I++H T GAP + L G L + Sbjct: 270 TTCLTLPTALAATIVPFPRYVPRDVLVGIQKHKPTIFPGAPSIYISLMQQKEVGDYDLTS 329 Query: 298 TVQIMTAGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARL 356 ++ AP P + R L G V G+GLTE + + HL Sbjct: 330 IRYCISGSAPMPVEHIKRFRELTGAQVIEGFGLTEASPVT----------HLNPIHGVSK 379 Query: 357 KSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTAD 416 G+ T+ +VD G V +GE+++RG VM GY P+ TA ++ + Sbjct: 380 TGSIGI-PFPDTEARIVDMEVGQ-VPLPAGKVGELIIRGPQVMKGYWNRPDETANTLR-N 436 Query: 417 GWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDE 476 GW YTGD+ +M DGY I DR KD+ + GG N+ E++ +L+ HP I EA V P Sbjct: 437 GWLYTGDIAIMDEDGYFTIVDRKKDMFLVGGYNVYPREIDEVLHEHPKIKEAVTVGVPHP 496 Query: 477 FWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFI 536 GE AFV +K G +K T+ E+V +CR KL Y VPK V F+++LPKT GKV + I Sbjct: 497 TRGEMIKAFVVVKPG--EKLTKAEVVAHCREKLASYKVPKQVEFRDDLPKTVVGKVLRRI 554 Query: 537 LR 538 LR Sbjct: 555 LR 556 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: 791 Number of extensions: 50 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: 583 Length adjustment: 36 Effective length of query: 520 Effective length of database: 547 Effective search space: 284440 Effective search space used: 284440 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