Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_100845694.1 C0J26_RS16980 AMP-binding protein
Query= BRENDA::A4YDR9 (549 letters) >NCBI__GCF_003031005.1:WP_100845694.1 Length = 565 Score = 168 bits (425), Expect = 6e-46 Identities = 148/543 (27%), Positives = 244/543 (44%), Gaps = 51/543 (9%) Query: 27 FLERAGKYFKDKTAVV-YRDSRYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEF 85 F + +Y + VV ++ RY++ D V + A AL+ G D+L + N ++ Sbjct: 30 FAQTVAQYPDGEALVVRHQQLRYSWRQLADAVDLNARALLALGLQTGDRLGIWAPNCAQW 89 Query: 86 LESFFGVPYAGGVLVPINFRLSPKEMAYIINHSDSKFVVVDEPYLNS---------LLEV 136 + F G +LV IN E+ Y++ + +++V + +S + E+ Sbjct: 90 CITQFATAKIGVILVNINPAYRSSELEYVLKQAGCQWLVCAGAFKSSNYHGMLQGLVPEL 149 Query: 137 KDQIKAEI----------ILLEDPDNPSA----SETARKEVRMTYRELVKGGSRDPLPIP 182 +Q E+ ++ D PS S+ A V ++ +L + P Sbjct: 150 AEQSIGELRSERLPDLRGVISLDAQPPSGFLPWSQLADLAVTVSPEQLRERSDSLHFDQP 209 Query: 183 AKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEHQMDLNSVYLWTLPMFHAAS 242 + + YTSGTTG PKG H N + + +P++H Sbjct: 210 -------VNIQYTSGTTGFPKGATLSHYNILNNGYMVGESIGLTPLDRLVIPVPLYHCFG 262 Query: 243 WGF-SWATVAVGATNVC-LDKVDYPLIYRLVEKERVTHMCAAPTVYVNLADYMKRNNLKF 300 + + G+T + D D L + V +E+ T + PT+++ + D +R Sbjct: 263 MVMGNLGCITHGSTMIYPNDAFDPLLTLQTVAEEKATGLYGVPTMFIAMLDQPQRTEFDL 322 Query: 301 SNRVHMLVAGA-APAPATLKAMQEIGGYMCHV---YGLTETYGPHSICEWRREWDSLPLE 356 S+ ++AGA P + + E+ +M V YG+TET P S+ + P + Sbjct: 323 SSLRTGIMAGATCPIEVMRRVISEM--HMSEVQIAYGMTET-SPVSL-------QTGPND 372 Query: 357 EQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGHNVALGYYKNPEKTAESF 416 E G E + D G VP IGE+ RG++V LGY+ NP+ TAE+ Sbjct: 373 ELELRVTTVGRTQPQLESKIIDEAGNLVP--RGIIGELCTRGYSVMLGYWNNPQATAEAI 430 Query: 417 RD-GWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSILVEKTLMEIPGVKAVAVYGT 475 + GW H+GD A ++ DGY+ I R KD+I GGE + +E+ P V V V G Sbjct: 431 DEAGWMHTGDLASMNDDGYVNIAGRNKDMIIRGGENIYPRELEEFFFTHPAVADVQVVGI 490 Query: 476 PDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPKIVEF-GPIPMTATGKMQKY 534 P ++GE + A I+ G +E E+ +CKER+AHF+ P+ +F PMT TGK+QK+ Sbjct: 491 PCSRYGEEIVAWIKFHPGHSASELELQTWCKERIAHFKTPRHFKFVDEFPMTVTGKIQKF 550 Query: 535 VLR 537 +R Sbjct: 551 RMR 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: 660 Number of extensions: 29 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: 1 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 Sep 24 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