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 3607285 Dshi_0700 AMP-dependent synthetase and ligase (RefSeq)
Query= SwissProt::M4IQQ5 (556 letters) >FitnessBrowser__Dino:3607285 Length = 505 Score = 156 bits (395), Expect = 2e-42 Identities = 145/496 (29%), Positives = 219/496 (44%), Gaps = 45/496 (9%) Query: 52 LASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILNAVNLRLDARTISILLHHSE 111 + +++++ G+ G + V N + + + GA +N +L R + +L +E Sbjct: 40 IGAALSARGLGKGDRIGVFMKNSTDYLRVLYGIWWCGAAAIPINSKLHPREAAWILSDAE 99 Query: 112 SKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRG 171 + L V + + EA AP V S+ G+ Sbjct: 100 AALCLVTPDLAEGLAEA-------APDCACVVTG-------SAAFGEMLAA--------- 136 Query: 172 DPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWG-VPKQPVYLW 230 P + ++ D L YTSGTT PKGV+ + MT+ +D V Q L+ Sbjct: 137 -PPMAAPVARASGDLAWLFYTSGTTGKPKGVMMSFATLTAMTLSYFVDVDEVTAQDAILY 195 Query: 231 TLPMFHANGWSYPWGMAAVGGTNICLRK--FDSEIIYDMIKRHGVTHMCGAPVVLNML-- 286 + PM H G Y + G ++ FD I+D+ + + AP ++ + Sbjct: 196 SAPMSHGAG-VYNFMHVLRGARHVVPESGGFDPAEIFDLAREMRQVSLFAAPTMVRRMID 254 Query: 287 ---SNAPGSEPLKTTVQIMTAGAPPPSA-VLFRTESLGFAVSHGYGLTETAGLVVSCAWK 342 + + +KT I+ AG P A ++ E LG YG E + + + Sbjct: 255 VAKARGDTGDGIKT---IVYAGGPMYLADIIEAVEVLGDRFVQVYGQGEYPMSITALSRA 311 Query: 343 KEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGY 402 + +ARL S VG V QT DV G T GE+ +RG +MLGY Sbjct: 312 DVSDRSHPDWQARLAS---VG-VAQTISDVAILDAEGRPVPPGET-GEIAVRGAGLMLGY 366 Query: 403 LKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSH 462 PE TA+++ DGW +TGD+G M DGY+ + DRSKD+IISGG N+ EVE +L +H Sbjct: 367 WNRPEATAETIR-DGWLWTGDMGRMDADGYVTMVDRSKDMIISGGSNVYPREVEEVLLTH 425 Query: 463 PDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKE 522 P + E +VV RP WGE AFV G P + +C S++ R+ PK + Sbjct: 426 PQVAEVSVVGRPHAEWGEEVVAFVVPAPGAEMDPGVLD--AHCLSQIARFKRPKAYIALP 483 Query: 523 ELPKTSTGKVQKFILR 538 ELPK + GKV K LR Sbjct: 484 ELPKNNYGKVLKIELR 499 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: 4 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: 505 Length adjustment: 35 Effective length of query: 521 Effective length of database: 470 Effective search space: 244870 Effective search space used: 244870 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: 52 (24.6 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