Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate AO356_01575 AO356_01575 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01575 Length = 565 Score = 168 bits (426), Expect = 4e-46 Identities = 149/539 (27%), Positives = 244/539 (45%), Gaps = 41/539 (7%) Query: 26 LFLERAGKYFKDKTAVVYRDS-RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPE 84 +F + +Y + + VV S RYT+ + V + A AL+ G D+L + N + Sbjct: 29 VFDQTVARYPEGEALVVRHQSLRYTWQQLAEAVDLHARALLALGLKTGDRLGVWAPNCAQ 88 Query: 85 FLESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQIKAEI 144 + S F G +LV IN E+ Y++ S +++V + S Q A Sbjct: 89 WCISQFASAKLGVILVNINPAYRVSELEYVLKQSGCQWLVCAGAFKTSDYHAMLQTLAPE 148 Query: 145 ILLEDPDNPSASETARKEVR-------------MTYRELVKGGSRDPLPIPAKEEYSM-- 189 L E P SE E+R + + +L G+ A+ + S+ Sbjct: 149 -LAEQPIGQMQSERL-PELRGVISLDSQPPAGFLPWSQLAALGAAVTPGQLAERQSSLRF 206 Query: 190 ---ITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAASWGF- 245 + + YTSGTTG PKG H N + + +P++H Sbjct: 207 DQPVNIQYTSGTTGFPKGATLSHHNILNNGYMVGESLGLTAGDRLVIPVPLYHCFGMVMG 266 Query: 246 SWATVAVGATNVCLDKVDYPLI-YRLVEKERVTHMCAAPTVYVNLADYMKRNNLKFSNRV 304 + + G+T + + PL+ + V +E+ T + PT+++ L D +R + S+ Sbjct: 267 NLGCMTHGSTMIYPNDAFDPLLTLKAVAEEKATALYGVPTMFIALLDQPQRGDFDLSSLR 326 Query: 305 HMLVAGAA-PAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLEEQAK 360 ++AGA P + + E+ +M V YG+TET P S+ + P +E Sbjct: 327 TGIMAGATCPIEVMRRVINEM--HMAEVQIAYGMTET-SPVSL-------QTGPSDELEL 376 Query: 361 LKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESFR-DG 419 G E + D G V +GE+ RG++V LGY+ NP+ T+++ +G Sbjct: 377 RVTTVGRTQPQLESKIIDEAGNLV--SRGAVGELCTRGYSVMLGYWNNPKGTSDAIDPEG 434 Query: 420 WFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGTPDEK 479 W H+GD A + GY+ IV R KD+I GGE + +E+ P V V V G P + Sbjct: 435 WMHTGDLATMDEQGYVCIVGRNKDMIIRGGENIYPRELEEFFFTHPAVADVQVIGIPCSR 494 Query: 480 WGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKYVLR 537 +GE + A I+ G +E+E+ +CKER+AHF+ P+ +F PMT TGK+QK+ +R Sbjct: 495 YGEEIVAWIKFHPGHSASEQELQAWCKERIAHFKTPRHFKFVEEFPMTVTGKIQKFRMR 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: 677 Number of extensions: 32 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: 565 Length adjustment: 36 Effective length of query: 513 Effective length of database: 529 Effective search space: 271377 Effective search space used: 271377 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 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