Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_011842442.1 RSPH17029_RS17960 AMP-binding protein
Query= metacyc::MONOMER-20124 (573 letters) >NCBI__GCF_000015985.1:WP_011842442.1 Length = 520 Score = 211 bits (536), Expect = 8e-59 Identities = 157/522 (30%), Positives = 249/522 (47%), Gaps = 40/522 (7%) Query: 57 DNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYELHFAVPMA 116 D+ +L++ +WA+ ++ L G+ G VA N + L +A+ Sbjct: 25 DSAALIFRGRTRSWAEFAADMARIQQGLAAQ-GVRRGSRVAVLDRNSDDYVLLGYALAGM 83 Query: 117 GGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAALDLLAQKDIKPPTLVLLTD 176 G +L +N A +S +L + + L+ + L+ AR A+ LA PP LVL D Sbjct: 84 GAVLAPVNMWLRPAELSYILGNCQPLLLVTSAEFLDAAREAIAPLAD----PPALVLRGD 139 Query: 177 SESFTSSSYDHYNHLLANGSDDFEIRRPKNEWDPISINYTSGTTARPKAVVYSHRGAYLN 236 T + + +A G + RP++ DP + YTSGTT RPK + SHR L+ Sbjct: 140 EAPGTIAWAE-----IAAGEGRAPVSRPESWDDPHLVLYTSGTTGRPKGALISHRRTVLD 194 Query: 237 SIATVLLHGMGTTSVYLWSVPMFHCNGWCFPWGAAAQGATNICIRKVSPKAIFDNIHLHK 296 ++A + + G+G + +P+FH W + + + + A I H+ Sbjct: 195 ALAALPVFGIGQHERFFCYMPLFHTGAWDYLKLYFMRRGAAVIAERFEADAAVAEIEAHR 254 Query: 297 VTHFGAAPTVLNMIVNSPEGNLHTPLPHKVEVMTGGSPPPPKVIARMEEM-------GFQ 349 P VL +V S T + ++ + P +I R+ E G + Sbjct: 255 CNGMFGVPLVLRQMVESQAWG--TSDMSSMRLIAYANYDPSALILRIVEAFRERGAEGLR 312 Query: 350 VNHIYGLTETCGPAANCVCKPEWDALQPEERYALKARQGLN--HLAMEEMDVRDPVTMES 407 + + YGLTE G C+ +PE +P L Q + +A+ + D+R+ Sbjct: 313 IANAYGLTE--GGPYICINRPETAMSKP-----LSIGQPVPGVQVALLDEDLRE------ 359 Query: 408 VRADGATIGEVMFRGNTVMSGYFKDLKATEEAFEGGWFRSGDLGVKHEDGYIQLKDRKKD 467 +GE+ RG +MSGY +AT EAF GGW +GDLG E+G++ L DRKKD Sbjct: 360 --VPPGALGEICVRGPALMSGYLNRPEATAEAFAGGWLHTGDLGRVDEEGFVHLVDRKKD 417 Query: 468 VVISGGENISTVEVETVLYSHEAVLEAAVVARPDKLWGETPCAFVTLKEGFDNDVSADQI 527 ++ +GGEN+ EVE L +H A+ + AVV PD +GE A V + G D++ ++ Sbjct: 418 MIRTGGENVFAKEVEQTLVTHPAIRDCAVVGLPDDDYGERVVAVVVAEPG--TDLAEAEV 475 Query: 528 IKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYILKEKAMA 568 F RDRL + AP+ V+F ELPKT GKI+K+ ++ KA+A Sbjct: 476 RSFVRDRLAGFKAPRQVIFVPELPKTPAGKIKKHEVR-KAIA 516 Lambda K H 0.318 0.133 0.408 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: 714 Number of extensions: 35 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: 1 Length of query: 573 Length of database: 520 Length adjustment: 35 Effective length of query: 538 Effective length of database: 485 Effective search space: 260930 Effective search space used: 260930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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