Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_035704422.1 BA79_RS18230 AMP-binding protein
Query= metacyc::MONOMER-20125 (556 letters) >NCBI__GCF_000691145.1:WP_035704422.1 Length = 545 Score = 214 bits (544), Expect = 9e-60 Identities = 162/541 (29%), Positives = 259/541 (47%), Gaps = 57/541 (10%) Query: 32 SVVYD--AVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGA 89 +VVY ++ Y++ ++ + +LG++ G ++++APN+P+ L FA GA Sbjct: 25 AVVYPERSLRYSYEAFYQEVKATGKGLMALGVQKGDHIAIMAPNIPEWLILQFACASIGA 84 Query: 90 ILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVPRLVFMADESE 149 +L VN ++ ++ LL HS+SK++F+ + F + + V L + E + Sbjct: 85 VLVTVNTNFQSQELAYLLKHSDSKMLFI-----------VDGFKETSYVNMLEELIPELQ 133 Query: 150 SGNSSELGKEFFCSYKDLIDRGD-------------------PDFKWVMPKSEWDP---M 187 + + E+ F K I G D +W +E P + Sbjct: 134 TAHQEEITSTQFPYLKRCIYIGQHVPNGMLSWDRLQVAAKRTEDHEWEKRMNELTPDDVI 193 Query: 188 ILNYTSGTTSSPKGVVHCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMA 247 + YTSGTT PKGV+ H I + +Q +P FH G S +A Sbjct: 194 NMQYTSGTTGYPKGVMLSHTNIVCNASQIADCMKLTEQDRMCIPVPFFHCFG-SVLGVLA 252 Query: 248 AV--GGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPG--SEPLKTTVQIMT 303 + GGT I L F E + +++ T + G P + + P S L T + Sbjct: 253 CLTKGGTIIPLESFHPERVLQTVEKEKCTVLHGVPTMFIAELDHPNFHSYDLSTLRTGIM 312 Query: 304 AGAPPPSAVLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQG 361 AG+ PS V+ E +G ++ YG TE++ ++ T+ + + Q Sbjct: 313 AGSLCPSHVMKAVIEKMGLRELTIAYGQTESSPVITQTR----------TDDSFERRVQT 362 Query: 362 VGTVM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFY 420 VG + Q ++ + P T V R GE+ RG VM GY K+ E T + + DGW + Sbjct: 363 VGRALPQIEVKIALPGTSEEVPRGQQ--GELCTRGYHVMKGYYKNEEATNEVIDEDGWLH 420 Query: 421 TGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGE 480 TGD+ M DGY++I R KD+II GGEN+ E+E +LY+HP IL+A VV PDE +GE Sbjct: 421 TGDLAEMDHDGYVKITGRLKDMIIRGGENVYPKEIEDVLYTHPAILDAQVVGIPDETYGE 480 Query: 481 TPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDM 540 AF+ LK+G K + + + YC+S++ RY +PK +E P T++GK+QKF L+ Sbjct: 481 EAAAFIRLKQG--KSVSIETLTSYCQSQMARYKIPKYFFITDEYPMTASGKIQKFRLKKQ 538 Query: 541 A 541 A Sbjct: 539 A 539 Lambda K H 0.319 0.135 0.412 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: 733 Number of extensions: 45 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: 556 Length of database: 545 Length adjustment: 36 Effective length of query: 520 Effective length of database: 509 Effective search space: 264680 Effective search space used: 264680 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