Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate Ac3H11_2529 3-methylmercaptopropionyl-CoA ligase (DmdB)
Query= BRENDA::A4YDR9 (549 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2529 Length = 547 Score = 245 bits (626), Expect = 3e-69 Identities = 159/506 (31%), Positives = 258/506 (50%), Gaps = 15/506 (2%) Query: 47 RYTYSTFYDNVMVQASALMRRGFSREDKLSFISRNRPEFLESFFGVPYAGGVLVPINFRL 106 RYTY A+AL D+++ ++ N +E +FGV +G VL +N RL Sbjct: 39 RYTYRDLAARARRLANALDDLQLQFSDRVATLAWNGYRHMEMYFGVSGSGRVLHTVNPRL 98 Query: 107 SPKEMAYIINHSDSKFVVVDEPYLNSLLEVKDQ---IKAEIILLEDPDNPSASETARKEV 163 P ++A+I+NH++ + + D +L + V + +K + L + P+ S Sbjct: 99 HPDQIAWIVNHAEDQVLCFDLTFLPLVQAVHAKCPTVKKWVALCDADKLPADSGVPGLS- 157 Query: 164 RMTYRELVKGGSRDPLPIPAKEEYSMITLYYTSGTTGLPKGVMHHHRGAFLNAMAEVLEH 223 +Y + + S D P +E S ++ YTSGTTG PK ++ HR L+A A L Sbjct: 158 --SYEDWIGAHSAD-YAWPEFDENSASSMCYTSGTTGNPKAALYSHRSTTLHAYAAALPD 214 Query: 224 QMDLNS--VYLWTLPMFHAASWGFSWATVAVGATNVCLDK-VDYPLIYRLVEKERVTHMC 280 M L++ L +PMFH +WG ++ G V +D IY L+E E+V++ Sbjct: 215 VMCLSARDSVLPVVPMFHVNAWGIPYSAALTGCKLVFPGPAMDGKSIYELIESEKVSYAA 274 Query: 281 AAPTVYVNLADYMKRNNLKFSNRVHMLVAGAAPAPATLKAMQE-IGGYMCHVYGLTETYG 339 PTV+ + +MK LKFS ++ G+A PA + A +E G + H +G+TE Sbjct: 275 GVPTVWQMMLGHMKPAGLKFSTLKRTVIGGSACPPAMIHAFKEDYGVEVLHAWGMTEMSP 334 Query: 340 PHSICEWRREWDSLPLEEQAKLKARQGIPYVSFEMDVFDANGKPVPWDGKTIGEVVMRGH 399 ++C + + SLP +EQ K+ +QG +M + +G+ +PWDGKT G+++++G Sbjct: 335 LGTLCTLKNKHLSLPKDEQMKVLLKQGRAIYGVDMKIVGGDGEELPWDGKTYGDLLVKGP 394 Query: 400 NVALGYYKNP---EKTAESFRDGWFHSGDAAVVHPDGYIEIVDRFKDLINTGGEKVSSIL 456 + Y+K + GWF +GD A + DG+++I DR KD+I +GGE +SSI Sbjct: 395 WIVDSYFKGEGGHPLVKDKQGRGWFPTGDVATIDADGFMQITDRSKDVIKSGGEWISSID 454 Query: 457 VEKTLMEIPGVKAVAVYGTPDEKWGEVVTARIELQEGVKLTEEEVIKFCKERLAHFECPK 516 +E M P + A G P KW E + + G ++T +E++ F + + A ++ P Sbjct: 455 IENIAMAHPAIAMAACVGMPHPKWDERPIVAVVKRPGTEVTRDELLAFYEGKTAKWQIPD 514 Query: 517 IVEF-GPIPMTATGKMQKYVLRNEAK 541 V F IP+ ATGKM K LR + K Sbjct: 515 DVVFVDAIPLGATGKMLKTKLREQLK 540 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: 732 Number of extensions: 34 Number of successful extensions: 7 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 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