Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate CCNA_01889 CCNA_01889 long-chain-fatty-acid--CoA ligase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Caulo:CCNA_01889 Length = 544 Score = 233 bits (594), Expect = 1e-65 Identities = 169/533 (31%), Positives = 266/533 (49%), Gaps = 26/533 (4%) Query: 22 LTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQA----SALMRRGFSREDKLSF 77 LT L+ A + F + +V R+ T Y V V+A +AL RRG D+++ Sbjct: 10 LTLSSLLDHAAR-FHGEVEIVSREPGGVTRTNYARVAVRARKLAAALRRRGLREGDRVAS 68 Query: 78 ISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE---PYLNSLL 134 ++ N LE ++G AGG+L +N RL P+++A+I+ H++++ V D P L +L+ Sbjct: 69 LALNSARHLELYYGATGAGGILNTVNPRLFPEQIAFILRHAENRIVFFDPAFGPLLETLV 128 Query: 135 EVKDQIKAEIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYY 194 + Q++A + L D PS R + Y +L+ D P E + L Y Sbjct: 129 DQAPQVEAYVCLSSAGDMPSL----RLPNLIAYEDLL-APEADDAPWTVVSENAGAILCY 183 Query: 195 TSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLN---SVYLWTLPMFHAASWGFSWATVA 251 TSGTTG PKGV++ HR L+A M ++ S+ L T P+FH +WG ++ Sbjct: 184 TSGTTGDPKGVLYSHRSLALHAFVATGADGMAISRRDSILLVT-PLFHVNAWGIPFSAAM 242 Query: 252 VGATNVCLDK-VDYPLIYRLVEKERVTHMCAAPTVYVNLADYMK--RNNLKFSNRV--HM 306 GA V VD ++ L+ ER T PTV++ DY+ R L + + Sbjct: 243 CGAKLVLPGAAVDGENLFNLMRAERCTFSLGVPTVWLGFLDYVATHREELDLAGLALERI 302 Query: 307 LVAG-AAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQ 365 LV G AAP + +G Y+ H +G+TET +I E L + + ++A Q Sbjct: 303 LVGGSAAPRSMIERFDYMLGVYVIHAWGMTETSPLATIGTPLPEHAFLDRQARYDIQALQ 362 Query: 366 GIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGD 425 G E+ + DA+G P DG +G++ +RG V Y+K + DGWF +GD Sbjct: 363 GRAIYGVELRIVDADGVVAPHDGMAVGDLQVRGPWVVRRYFK--ADAPATTEDGWFPTGD 420 Query: 426 AAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVT 485 A +HP+GY+++ DR KD+I +GGE +SS+ +E + P ++ AV G P KW E Sbjct: 421 VAKIHPNGYLQLTDRSKDIIKSGGEWISSVDLENVAIAHPDIREAAVIGVPHPKWQERPL 480 Query: 486 ARIELQEGVKLTEEEVIKFCKERLAHFECP-KIVEFGPIPMTATGKMQKYVLR 537 I +++++KF R+A ++ P +V +P TATGK+ K LR Sbjct: 481 LIIVPAPETTPDKDDILKFLASRVARWQVPDDVVIVESLPHTATGKLLKAKLR 533 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: 679 Number of extensions: 32 Number of successful extensions: 7 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: 544 Length adjustment: 36 Effective length of query: 513 Effective length of database: 508 Effective search space: 260604 Effective search space used: 260604 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