Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_007509924.1 R2APBS1_RS07500 long-chain fatty acid--CoA ligase
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_000230695.2:WP_007509924.1 Length = 561 Score = 148 bits (374), Expect = 5e-40 Identities = 143/517 (27%), Positives = 218/517 (42%), Gaps = 68/517 (13%) Query: 59 LGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV- 117 L + G ++++ PNV Q F AG ++ N AR + L S ++ I V Sbjct: 71 LKLGKGDRIALMMPNVLQYPIALFGALRAGLVVVNTNPMYTARELKHQLEDSGARAIVVL 130 Query: 118 -------DHLSRDLILEAIAL--------FPKQAPVPRLVFMADESESGNSSELGKEFFC 162 H+ + ++ + FPK A + ++ + F Sbjct: 131 DNFAATLQHVVAETHVQHVITTGIGDLLGFPKGALINFVLKHVKKMVPAFDLPQAVRF-- 188 Query: 163 SYKDLIDRGDPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGV 222 +D + RG + D L YT GTT KG + H + + + G Sbjct: 189 --RDALARGAAHPLQPVTLGHDDIAFLQYTGGTTGVAKGAMLTHGNMVANMLQAAAWIGT 246 Query: 223 ----PKQPVYLWTLPMFH-----ANGWSYPWGMAAVGGTN-ICLRKFDSEIIYDMIKRHG 272 P + V + LP++H ANG + +GG N + D +++ G Sbjct: 247 ELVTPGEEVIITALPLYHIFSLTANGLVF----MRLGGLNWLITNPRDMPGFVKELRKSG 302 Query: 273 VTHMCGAPVVLNMLSNAPGSEPLKTTVQIMTAGA--PPPSAVLFRTESL-GFAVSHGYGL 329 T + G + N L N PG L + +T G AV R + + G ++ YGL Sbjct: 303 FTALTGVNTLFNGLLNTPGFSELDFSKLHLTLGGGMAVQRAVAERWKKVTGCTLAEAYGL 362 Query: 330 TETAGLV-VSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAV-KRDGST 387 TET+ V ++ KE+N I + P T A+ DG Sbjct: 363 TETSPAVCINPLDLKEYNG---------------------SIGLPVPSTNVAIWSEDGKP 401 Query: 388 L-----GEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDV 442 L GE+++ G VM GY P+ TAK + ADGW +TGD+ M +GY I DR KD+ Sbjct: 402 LPVGEVGELMVHGPQVMKGYWNRPDETAKVLGADGWLHTGDIAKMDVNGYFYIVDRKKDM 461 Query: 443 IISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIV 502 I+ G N+ EVE + +HP +LE A V PDE GE FV K TE+ + Sbjct: 462 ILVSGFNVYPNEVEDAVMAHPGVLEVAAVGVPDEHSGEVVKLFVVRK---DPNLTEEALK 518 Query: 503 EYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539 ++CR L Y PK + F++ LPK++ GK+ + LRD Sbjct: 519 QFCRENLTGYKRPKLIEFRDSLPKSNVGKILRRELRD 555 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: 736 Number of extensions: 33 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: 561 Length adjustment: 36 Effective length of query: 520 Effective length of database: 525 Effective search space: 273000 Effective search space used: 273000 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