Align 4-hydroxybutyrate-CoA ligase (AMP-forming) (EC 6.2.1.40) (characterized)
to candidate GFF2651 HP15_2595 acyl-CoA synthetase
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Marino:GFF2651 Length = 547 Score = 270 bits (689), Expect = 1e-76 Identities = 173/536 (32%), Positives = 273/536 (50%), Gaps = 21/536 (3%) Query: 19 YSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFI 78 Y +L L L +Y D+ V S+YTY+ + + A+AL G D ++ + Sbjct: 16 YPLLIKRLLLS-GPRYNPDQEIVYSNRSKYTYTDLVERIHRLANALTDAGVKPGDTVAVM 74 Query: 79 SRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKD 138 + P +LE FF +P G +L +N RLSP ++ Y +NH++ V+V + +L + VKD Sbjct: 75 DWDTPRYLECFFAIPMIGAILHTVNIRLSPDQIVYTMNHAEDDVVLVHDDFLPIIEAVKD 134 Query: 139 QIKA--EIILLEDPDNPSASETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTS 196 +IK I L D DN ++ A E Y +L+ + D P +E S+ T +YT+ Sbjct: 135 EIKTVKTWIQLTDSDN---AQQAPVEAVGEYEDLL-ARANDKFDFPDFDENSVATTFYTT 190 Query: 197 GTTGLPKGVMHHHRGAFLNAMAEVLE----HQMDL---NSVYLWTLPMFHAASWGFSWAT 249 GTTG PKGV HR L+ +A +M L +SVY+ PMFH +WG +A Sbjct: 191 GTTGNPKGVYFSHRQLVLHTLAMTGTVASFDEMPLMRSSSVYMPVTPMFHVHAWGVPYAA 250 Query: 250 VAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVA 309 +G V + + L+ L+++ +VT PT+ + SN H+L+ Sbjct: 251 TMMGIKQVYPGRYEPELLVDLLKEHKVTFSHCVPTIMQMMMATESIKTADLSNW-HVLIG 309 Query: 310 GAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPY 369 G+A A ++G + YG++ET + E LPLE+Q ++ + GI Sbjct: 310 GSALTKGLCDAGAKLGIKLYTAYGMSETCPLLCASHLKPEDLELPLEQQTAIRVKTGIAT 369 Query: 370 VSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWFHSGDAAVV 429 E+++ D G PVP DG+ GE+V R + GY+K PEK + + GW H+GD A + Sbjct: 370 PMVELEIVDPEGNPVPHDGEAKGEIVARAPWLTQGYFKEPEKGEQLWEGGWLHTGDVASM 429 Query: 430 HPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIE 489 PD I I DR KD+I TGGE +SS+ +E + + V AV G PDEKWGE A + Sbjct: 430 EPDNTITIKDRIKDVIKTGGEWLSSLDLENLISQHSAVAGAAVVGVPDEKWGERPHALVT 489 Query: 490 LQEGVKLTEEEVIKFCKE-----RLAHFECPKIVEF-GPIPMTATGKMQKYVLRNE 539 L+ G + + E++ K+ + + P+ ++F IP T+ GK+ K ++R++ Sbjct: 490 LKPGEQASAEDIQNHLKQFVESGEINKWAIPEHIDFVEDIPKTSVGKINKKLIRDQ 545 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: 745 Number of extensions: 37 Number of successful extensions: 6 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 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