Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf1N1B4_5982 Medium-chain-fatty-acid--CoA ligase (EC 6.2.1.-)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5982 Length = 547 Score = 234 bits (598), Expect = 5e-66 Identities = 169/538 (31%), Positives = 271/538 (50%), Gaps = 30/538 (5%) Query: 19 YSVLTPLLFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSF 77 Y +L L L +G ++ +VY D RY+Y T + A+AL G D ++ Sbjct: 16 YPLLIKQLLL--SGVRYEPGREIVYADKLRYSYQTLNRRIRRLANALTAAGVKAGDTVAL 73 Query: 78 ISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVK 137 + + +LE FF VP G VL +N RLSP ++ + +NH++ V+V + +L + ++ Sbjct: 74 LDWDSHRYLECFFAVPMIGAVLHTVNIRLSPDQVLFTMNHAEDDLVLVHDDFLPLVEQIH 133 Query: 138 DQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSG 197 +++ L+ D+ A++T+ V Y L+ G S D P +E S+ TL+YT+G Sbjct: 134 GRLETVKGYLQLTDD-IATDTSLP-VLGEYENLLSG-SADQYDFPDFDENSVATLFYTTG 190 Query: 198 TTGLPKGVMHHHRGAFL---NAMAEVLEHQ----MDLNSVYLWTLPMFHAASWGFSWATV 250 TTG PKGV HR L NA+ + +Q + + VY+ PMFH +WG + Sbjct: 191 TTGDPKGVYFTHRQLVLHTLNAVGTLGVYQGLPLLRSDDVYMPITPMFHVHAWGVPYVAT 250 Query: 251 AVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAG 310 +G V + + + RL +E+VT PT+ + + +F ML+ G Sbjct: 251 LMGLKQVYPGRYEPNSLVRLYREEKVTFSHCVPTILQMILSCEEAAQTRFDGW-KMLLGG 309 Query: 311 AA-----PAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQ 365 +A + A+ K +Q GY G++ET + R E + + Q + + Sbjct: 310 SALTLGIASEASAKGIQVHSGY-----GMSETCPLLCLTYLRDEDLAQSTQTQLATRIKT 364 Query: 366 GIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425 G P ++ + DANG V DG+++GE+V+R + GY K PEK AE + +GW H+GD Sbjct: 365 GTPVPMVDLKIIDANGNDVAHDGESLGEIVVRAPWLTQGYLKEPEKGAELWHNGWMHTGD 424 Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485 A + G +EI DR KD+I TGGE +SS+ +E + E V +VAV G DE+WGE Sbjct: 425 LASIDALGGVEIKDRIKDVIKTGGEWISSLELESLISEHAAVMSVAVVGIADEQWGERPM 484 Query: 486 ARIELQEGV----KLTEEEVIKFCKE-RLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 A + + G K+ E + F + R+ + PK +F IP T+ GK+ K ++R Sbjct: 485 ALVVCEPGQYLDRKILEAHLQGFVERGRINKWAIPKQFKFVAEIPKTSVGKINKKLIR 542 Lambda K H 0.319 0.136 0.411 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: 694 Number of extensions: 31 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: 549 Length of database: 547 Length adjustment: 36 Effective length of query: 513 Effective length of database: 511 Effective search space: 262143 Effective search space used: 262143 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