Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate GFF3324 PS417_17010 AMP-binding protein
Query= metacyc::MONOMER-20125 (556 letters) >FitnessBrowser__WCS417:GFF3324 Length = 544 Score = 148 bits (374), Expect = 5e-40 Identities = 146/542 (26%), Positives = 232/542 (42%), Gaps = 69/542 (12%) Query: 28 GDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYELHFAVPMA 87 G+ V + YTW Q A + +LG++ G + + APN + A Sbjct: 36 GEALVVRHQQRRYTWRQLAETVDLHARAFLALGMQTGDRLGIWAPNCAEWCISQIASAKL 95 Query: 88 GAILNAVNLRLDARTISILLHHSESKLI-------------FVDHLSRDLILEAIALFPK 134 G IL +N + + +L S + + + L+ DL I+L P Sbjct: 96 GVILVNINPAYRSSELEYVLKQSGCQWLVCAGSFKTSDYHAMLQALNPDL-RGMISLDP- 153 Query: 135 QAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKSEWDPMI-LNYTS 193 +P P + A + G L + L R +D + + YTS Sbjct: 154 -SPPPGFLPWAQLAALGTGIPL--------EQLHSR--------QTSLHFDQAVNIQYTS 196 Query: 194 GTTSSPKGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLPMFHANGWSYPWGMAAVG 250 GTT PKG H I M +SL G+ Q + +P++H G Sbjct: 197 GTTGFPKGATLSHHNILNNGYMVGESL---GLTAQDRLVIPVPLYHCFGMVMGNLGCITH 253 Query: 251 GTNICLRK--FDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKTTVQIMTAGA 306 GT + FD + + T + G P + + + P G L + + AGA Sbjct: 254 GTTMIYPNDGFDPLLTLTAVAEEHATGLYGVPTMFIAMLDHPQLGGFDLSSLRTGIMAGA 313 Query: 307 PPPSAVLFR--TESLGFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARLKSRQGVGT 364 P V+ R +E V YG+TET+ + + + L+ R V T Sbjct: 314 TCPIEVMRRVISEMHMSEVQIAYGMTETSPVSLQTGADDD-----------LERR--VTT 360 Query: 365 VMQTKIDVVDPVTGAAVKRDGST-----LGEVVLRGGSVMLGYLKDPEGTAKSMTADGWF 419 V +T+ + + + A DG+T +GE+ RG SVMLGY +P+ T +++ GW Sbjct: 361 VGRTQPQLENKIIDA----DGNTVARGEIGELCTRGYSVMLGYWNNPDATREAIDDAGWM 416 Query: 420 YTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDEFWG 479 +TGD+ M GY+ I R+KD+II GGEN+ E+E ++HP + + V+ PDE +G Sbjct: 417 HTGDLASMDAHGYVCIAGRNKDMIIRGGENVYPRELEEFFFTHPAVADVQVIGIPDERYG 476 Query: 480 ETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFILRD 539 E A+V G E E+ +C+ ++ + PK F EE P T TGK+QKF +R+ Sbjct: 477 EAIVAWVKFHPG--HVANELELQTWCKGRIAHFKTPKHFKFVEEFPMTVTGKIQKFRMRE 534 Query: 540 MA 541 ++ Sbjct: 535 IS 536 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: 755 Number of extensions: 40 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: 544 Length adjustment: 36 Effective length of query: 520 Effective length of database: 508 Effective search space: 264160 Effective search space used: 264160 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