Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Pf1N1B4_3988 Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3988 Length = 568 Score = 174 bits (440), Expect = 1e-47 Identities = 148/528 (28%), Positives = 239/528 (45%), Gaps = 50/528 (9%) Query: 41 VVYRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLV 100 V ++ RYT+ + V + A A + G D+L + N ++ S F G +LV Sbjct: 45 VRHQQLRYTWQQLSETVDLHARAFLALGLQTGDRLGIWAPNCAQWCISQFASAKIGVILV 104 Query: 101 PINFRLSPKEMAYIINHSDSKFVVVDEPYLNS---------LLEVKDQIKAEI------- 144 IN E+ Y++ S +++V Y S + E+ +Q ++ Sbjct: 105 NINPAYRSSELEYVLKQSGCQWLVCAGAYKTSDYHGMLQGLIPELAEQSIGQLQSERLPE 164 Query: 145 ---ILLEDPDNPSA----SETARKEVRMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSG 197 ++ D PS S+ ++ +L + +D L + + YTSG Sbjct: 165 LRGVISLDAQPPSGFLPWSQLTDLAASVSIEQLRE--RQDSLHFD-----QAVNIQYTSG 217 Query: 198 TTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF-SWATVAVGATN 256 TTG PKG H N + N + +P++H + V G+T Sbjct: 218 TTGFPKGATLSHYNILNNGYMVGESLGLTANDRLVIPVPLYHCFGMVMGNLGCVTHGSTM 277 Query: 257 VCLDKVDYPLI-YRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRVHMLVAGAA-PA 314 + + PL+ V +E+ T + PT+++ + D KR S+ ++AGA P Sbjct: 278 IYPNDAFDPLLTLSTVAEEKATALYGVPTMFIAMLDQPKRAEFDLSSLRTGIMAGATCPI 337 Query: 315 PATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLEEQAKLKARQGIPYVS 371 + + E+ +M V YG+TET P S+ + P +E G Sbjct: 338 EVMRRVINEM--HMSEVQIAYGMTET-SPVSL-------QTGPSDELELRVTTVGRTQPQ 387 Query: 372 FEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFRD-GWFHSGDAAVVH 430 E + D G VP TIGE+ RG++V LGY+ NP+ TAE+ + GW H+GD A ++ Sbjct: 388 LESKIIDEAGNLVPRG--TIGELCTRGYSVMLGYWNNPQGTAEAIDEAGWMHTGDLASMN 445 Query: 431 PDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIEL 490 +GY+ I R KD+I GGE + +E+ P V V V G P ++GE + A I+ Sbjct: 446 DEGYVCIAGRNKDMIIRGGENIYPRELEEFFFTHPAVADVQVIGIPCSRYGEEIVAWIKF 505 Query: 491 QEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 G TE+E+ +CKER+AHF+ P+ +F PMT TGK+QK+ +R Sbjct: 506 HPGHSATEQELQAWCKERIAHFKTPRYFKFVEEFPMTVTGKIQKFRMR 553 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: 658 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 549 Length of database: 568 Length adjustment: 36 Effective length of query: 513 Effective length of database: 532 Effective search space: 272916 Effective search space used: 272916 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