Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate H281DRAFT_05558 H281DRAFT_05558 fatty-acyl-CoA synthase
Query= metacyc::MONOMER-20124 (573 letters) >FitnessBrowser__Burk376:H281DRAFT_05558 Length = 550 Score = 501 bits (1291), Expect = e-146 Identities = 257/544 (47%), Positives = 348/544 (63%), Gaps = 11/544 (2%) Query: 23 TTSWKSMEGLVQCSANHVPLSPITFLERSSKAYRDNTSLVYGSVRYTWAQTHHRCLKLAS 82 T+ W GL +AN L+P+TFL+R+ K + D T++VYGS R TW + C + AS Sbjct: 3 TSRWND-PGLRPRAANFDALTPVTFLQRAEKVFPDRTAVVYGSHRETWREHAATCRRFAS 61 Query: 83 ALTTHLGISPGDVVATFSYNLPEIYELHFAVPMAGGILCTLNARNDSAMVSTLLAHSEAK 142 AL GI GDVVA N P + HFAVPMAG +L T+N R D+ VS +L HSEA+ Sbjct: 62 ALA-RAGIEYGDVVALLMTNTPPMLAAHFAVPMAGAVLNTINTRLDAENVSYILGHSEAR 120 Query: 143 LIFVEPQLLETARAALDLLAQKDIKPPTLVLLTDSESF--TSSSYDHYNHLLANGSDDFE 200 LI V+ + LE AR A+ L PP LV D ++ SS + Y LA+G ++ Sbjct: 121 LIIVDAEFLELARTAVARLQH----PPRLVCFADEQAAFAASSDVEDYVSFLASGDENAS 176 Query: 201 IRRPKNEWDPISINYTSGTTARPKAVVYSHRGAYLNSIATVLLHGMGTTSVYLWSVPMFH 260 + + EW PI++NYTSGTT RPK VVYSHRGAYL+++++++ G+ + YLW++P+FH Sbjct: 177 FCKVEEEWTPIAVNYTSGTTGRPKGVVYSHRGAYLSAVSSIISWGVPKAASYLWTLPLFH 236 Query: 261 CNGWCFPWGAAAQGATNICIRKVSPKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHT 320 CNGWC PW A QG ++C+R+V I I+ +VTH+ AP +++ ++ Sbjct: 237 CNGWCMPWVLALQGGKSVCLRRVDGDKIVQLINDERVTHYCGAP-IVHALIRDRAQQQDL 295 Query: 321 PLPHKVEVMTGGSPPPPKVIARMEEMGFQVNHIYGLTETCGPAANCVCKPEWDALQPEER 380 V + GG+PPP +IA M+ +G Q+ HIYGLTET GPAA C +P W L ER Sbjct: 296 VFNPAVSALIGGAPPPASLIAAMDAIGVQLTHIYGLTETYGPAAICEQQPAWAELGEAER 355 Query: 381 YALKARQGLNHLAMEEMDVRDPVTMESVRADGATIGEVMFRGNTVMSGYFKDLKATEEAF 440 KARQG+N+ M V + + + V ADGA +GE++FRGN M GY KD ++T+ AF Sbjct: 356 ADRKARQGVNYALQAGMTVMNCNSSDEVSADGAMMGEIVFRGNMTMMGYLKDSESTDRAF 415 Query: 441 EGGWFRSGDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARP 500 +GGWFRSGDL V DGY+++KDR KD++ISGGENIS+VEVE VLY HE V AAVVA P Sbjct: 416 DGGWFRSGDLAVLEPDGYVRIKDRSKDIIISGGENISSVEVEDVLYRHETVAAAAVVAMP 475 Query: 501 DKLWGETPCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVFEELPKTSTGKIQKY 560 D+ WGE P A V L+EG + S D +I CR++L H+ PK V+F +PKT+TGKIQK Sbjct: 476 DEKWGEVPVAIVELREG--SHASEDALIAHCREQLAHFKCPKRVIFHPIPKTATGKIQKN 533 Query: 561 ILKE 564 +L+E Sbjct: 534 VLRE 537 Lambda K H 0.318 0.133 0.408 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: 822 Number of extensions: 38 Number of successful extensions: 5 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: 573 Length of database: 550 Length adjustment: 36 Effective length of query: 537 Effective length of database: 514 Effective search space: 276018 Effective search space used: 276018 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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