Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF1053 Psest_1086 Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__psRCH2:GFF1053 Length = 560 Score = 142 bits (359), Expect = 3e-38 Identities = 139/532 (26%), Positives = 237/532 (44%), Gaps = 43/532 (8%) Query: 33 VVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMAGAILN 92 V + + YTW++ A + +LG++ G V + +PN Q FA G +L Sbjct: 39 VRHQQLRYTWAELAEAVDRCARGLLALGLQAGERVGIWSPNNAQWCITQFATAKIGVVLV 98 Query: 93 AVNLRLDARTISILLHHSESK-LIFVDHLS--------RDLI--LEAIALFPKQAPV-PR 140 +N + L S + LI D +L+ LE+ A+ Q+ + P Sbjct: 99 NINPAYRLSELEYALKQSGCRWLICADAFKTSDYHAMLHELLPELESAAVGALQSHMLPE 158 Query: 141 LVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWD-PMILNYTSGTTSSP 199 L + + L + + + G + + ++D P+ + YTSGTT P Sbjct: 159 LRGVISLCDKPVDGMLQWQALMEMAEQV--GPEQLRQCGERLQFDDPINIQYTSGTTGFP 216 Query: 200 KGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAAVGGTNICL 256 KG H I M +SL + + + +P++H G GT + Sbjct: 217 KGATLSHYNILNNGYMVGESL---RLTEHDRLVIPVPLYHCFGMVMGNLGCVTHGTTMIY 273 Query: 257 RK--FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAPGSEPLKTT---VQIMTAGAPPPSA 311 F+ T M G P + + + P + L + IM AG+ P Sbjct: 274 PSAAFEPLAALQAAAEEKATGMYGVPTMFIAMLDHPERQSLDLSSLRTGIM-AGSTCPIE 332 Query: 312 VLFRT-ESLGFA-VSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGTVMQTK 369 V+ R + + A + YG+TET+ + + + R+ S +++K Sbjct: 333 VMKRVIDDMHLAEMQIAYGMTETSPVSTQTSADDDLER-------RVTSVGRTQPHLESK 385 Query: 370 IDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHP 429 I VD GA V R +GE+ RG SVMLGY +P+ T ++ W +TGD+ VM Sbjct: 386 I--VDE-HGAVVPR--GQIGELCTRGYSVMLGYWNNPDATRDAIDGARWMHTGDLAVMDD 440 Query: 430 DGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWGETPCAFVSLK 489 +GY++I R+KD+II GGEN+ E+E L++HP + + V+ PD +GE A+V L Sbjct: 441 EGYIKIVGRNKDMIIRGGENVYPREIEEFLFTHPAVADVQVIGVPDSKFGEEIVAWVKLH 500 Query: 490 KGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRDMA 541 G + + + E+C+ ++ + P+ + F ++ P T +GKVQKF +R+++ Sbjct: 501 PG--HEVEGEALREFCKGRIAHFKTPRHIKFVDDFPMTISGKVQKFRMREIS 550 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: 730 Number of extensions: 38 Number of successful extensions: 4 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: 556 Length of database: 560 Length adjustment: 36 Effective length of query: 520 Effective length of database: 524 Effective search space: 272480 Effective search space used: 272480 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