Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate Pf6N2E2_1879 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1879 Length = 511 Score = 169 bits (429), Expect = 2e-46 Identities = 146/528 (27%), Positives = 247/528 (46%), Gaps = 41/528 (7%) Query: 22 RAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELH 81 R+A +G+ +++++ +++ + LA+S+ S+G++ VVS+ +PN P+ + Sbjct: 11 RSAARFGNKPAIIFEGKYWSFLDIDVQSSRLAASLESMGVKREDVVSIYSPNSPEWIITY 70 Query: 82 FAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRL 141 +A+ GAI+N +N L AR + + + + +F + D +L AL P + Sbjct: 71 YAILKIGAIVNPLNTMLTAREAAFAIKNCGAVAVFS---TSDKLL---ALQEHIGPTEVI 124 Query: 142 VFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPM-ILNYTSGTTSSPK 200 ++ + + G F L+D ++ + + D + + YTSGTT PK Sbjct: 125 SLISFDG----ITVAGMRHF---NLLVDANVAVREYPVTGIQKDDISTIGYTSGTTGQPK 177 Query: 201 GVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAAVGGTNICLRKFD 260 G V HR I + + + LP+ H G A G T + + FD Sbjct: 178 GAVLSHRCILTNVSMTATMHLRTASDIAVSALPLSHVYGNVVMNSAIAYGMTLVLHKTFD 237 Query: 261 SEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKTTVQIMTAGAPPPSAVLFRTE- 317 +E I I+ +G T + G P + L N P G+ + + + G P + E Sbjct: 238 AEAILSSIQIYGATLLEGVPTMYIYLLNCPNLGAYDVSSLTRCTVGGQMMPYTAMENVER 297 Query: 318 SLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTKIDVVDPVT 377 +LG + +G+TE GL + H ER RL S ++ +I Sbjct: 298 ALGCRLLELWGMTELGGLGTT--------HSLYGER-RLGSIGVALPHLEARI------- 341 Query: 378 GAAVKRDGSTL-----GEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGY 432 A ++ DG L GE+ +RG VM YL P+ TA++ T +GW TGD+ M +G+ Sbjct: 342 -AQLELDGDALPLGEIGELQIRGPVVMKHYLGRPDATAETKTDEGWLRTGDLARMDSEGF 400 Query: 433 LEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGL 492 + I DR KD+ I+ G N+ E+E ++ HP + AV + DE GE A++ K G Sbjct: 401 IYIVDRLKDMFITAGFNIYPAELERVIAEHPSVAMVAVGSVLDEIKGELAKAYIVPKTGY 460 Query: 493 TKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDM 540 + ++I +CR +L Y VP+ E+LPKTS+GKV + +LR + Sbjct: 461 --EIDIQQIERHCRDRLAAYKVPRLFQIVEDLPKTSSGKVMRRMLRQI 506 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: 625 Number of extensions: 35 Number of successful extensions: 5 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: 511 Length adjustment: 35 Effective length of query: 521 Effective length of database: 476 Effective search space: 247996 Effective search space used: 247996 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 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