Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF3780 PGA1_262p01840 ATP-dependent AMP binding enzyme
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__Phaeo:GFF3780 Length = 543 Score = 377 bits (968), Expect = e-109 Identities = 222/540 (41%), Positives = 304/540 (56%), Gaps = 10/540 (1%) Query: 8 NYEGVDPTGSWYSVLTPLLFLERAGKYFKDKTAVVYRDSRYTYSTFYDNVMVQASALMRR 67 NYE + Y L+P+ FL RA D+ AV+Y D R T+ + A+ L+ Sbjct: 4 NYEKFGKVAANYVPLSPVSFLNRAETLHSDRPAVIYGDLRRTWGEVATRIRGVAAGLVSL 63 Query: 68 GFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDE 127 G R D +S + N PE E F +P G V+ +N RL P+ +AYI++H+D+K V+VD Sbjct: 64 GIGRGDTVSVLCPNIPELFELQFALPLTGAVINTLNTRLEPETIAYILDHADTKAVIVDR 123 Query: 128 PYLNSLLEVKDQIKAEIILLE-DPDNPSASETARKEVRMTYRELVKGGSRD-PLPIPAKE 185 + L + + ++E D N +A T V Y EL+ G+ PL +P ++ Sbjct: 124 ELIPLLSMAFAAMGRSVSVIEIDDRNVAAPHTL---VGKPYEELLTDGAGGAPLDLP-QD 179 Query: 186 EYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF 245 E+ I L YTSGT+G PKGV++HHRGA+L A+ Q +YL +PMFH WG Sbjct: 180 EWDAIALNYTSGTSGRPKGVVYHHRGAYLMALGTAAAWQTPHYPIYLSVVPMFHCNGWGH 239 Query: 246 SWATVAVGATNVCLDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKR--NNLKFSNR 303 SW +G T V LI + VTH AAP V LA+ + F Sbjct: 240 SWVMAMLGGTMVFTRTPSPDLILDAIRSHGVTHFGAAPIVLQMLAEAEAETGSTTPFDPA 299 Query: 304 VHMLVAGAAPAPATLKAMQEIGGYMCHVYGLTETYGPHSICEWRREWDSLPLEEQAKLKA 363 + +L AGA P P+ L+ + +G + VYGLTETYG S C W+ W EQA+L+A Sbjct: 300 IKVLTAGAPPPPSVLQKTKAMGLDVMQVYGLTETYGHISKCLWQDSWADKIEAEQAQLQA 359 Query: 364 RQGIPYVSFE-MDVFDAN-GKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRDGWF 421 +QGI E + V D + G PV DG+T GE+ +RG+ V GYYK+ + T ++F +GWF Sbjct: 360 QQGIAMPMVEAVSVIDTDTGIPVARDGQTQGEIAVRGNTVMKGYYKDADATDKAFENGWF 419 Query: 422 HSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWG 481 SGD AVVH DGY++I DR KD+I +GGE +SS+ VE L P V+A AV PD KWG Sbjct: 420 WSGDGAVVHADGYMQIRDRLKDVIISGGENISSVEVEAVLYRHPAVQAAAVVAKPDPKWG 479 Query: 482 EVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEFGPIPMTATGKMQKYVLRNEAK 541 EV A IEL+ G LT EE+I FC+ LA F+ PK V F +P T+TGK+QK+ LR+ AK Sbjct: 480 EVPCAFIELRTGSDLTSEEIIAFCRTHLAGFKAPKTVVFTSLPKTSTGKIQKFQLRDAAK 539 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: 754 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: 549 Length of database: 543 Length adjustment: 35 Effective length of query: 514 Effective length of database: 508 Effective search space: 261112 Effective search space used: 261112 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