Align isovalerate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate WP_051008846.1 UYS_RS0215615 AMP-binding protein
Query= metacyc::MONOMER-20124 (573 letters) >NCBI__GCF_000265245.1:WP_051008846.1 Length = 574 Score = 172 bits (435), Expect = 4e-47 Identities = 162/540 (30%), Positives = 234/540 (43%), Gaps = 50/540 (9%) Query: 56 RDNTSLVYGSVRYTWAQTHHRCLKLASALTTHLGISPGDVVATFSYNLPEIYELHFAVPM 115 RD + +RY W + + A AL LG++ GD V +S N E FA Sbjct: 49 RDALISRHQGLRYRWRELQTEVDRAARALMA-LGVAKGDRVGIWSPNTAEWAITQFATAK 107 Query: 116 AGGILCTLNARNDSAMVSTLLAHSEAKLIFVEPQLLETARAA--------LDLLAQKDIK 167 G IL +N + + L S + ++ Q T A LD + D+K Sbjct: 108 IGAILVNINPSYRTHELEYALRQSGTSTLILQGQFKTTDYVAMLAELVPELDDVTPADLK 167 Query: 168 PPTL-----VLLTDSESFTSSSYDHYNHLL-ANGSDDFEI--RRPKNEWD-PISINYTSG 218 L V+ D S + L A+ D ++ R+ E+D PI+I YTSG Sbjct: 168 SGALPDLRRVICLDGARALSGMHSWETMLTHADRVSDAQLAERQAGLEFDEPINIQYTSG 227 Query: 219 TTARPKAVVYSHRGAYLNSIATVLLHGMGTTSVYLWSVPMFHCNGWCFP-WGAAAQGATN 277 TT PK SH N + + VP++HC G G GA Sbjct: 228 TTGAPKGATLSHHNILNNGFFVARTLDLSEADRMVIPVPLYHCFGMVMGNLGCMTHGAAM 287 Query: 278 ICIRK-VSPKAIFDNIHLHKVTHFGAAPTVLNMIVNSPEGNLHTPLPHKVEVMTGGSPPP 336 I P+A + + T PT+ + PE + VM G P Sbjct: 288 IYPGDGFDPQATLAAVAEERATALYGVPTMFIAELEHPEFEHFDLSSLRTGVMAGSICPI 347 Query: 337 P---KVIARMEEMGFQVNHIYGLTETCGPAANCVCKPEWDALQPEERYALKARQGLNHLA 393 KVI RM G + YG+TET P + + DA P E+ HL Sbjct: 348 EVMRKVIERMHMQGVTI--CYGMTET-SPVS---LQTRTDA--PLEKRVTTVGSIHPHL- 398 Query: 394 MEEMDVRDPVTMESVRADGATI-----GEVMFRGNTVMSGYFKDLKATEEAFE-GGWFRS 447 E+ + DP T GA + GE+ RG +VM GY+ + +AT +A + GW + Sbjct: 399 --EVKLVDPGT-------GAVVPRGEPGELCTRGYSVMLGYWHNEEATAKAIDDAGWMHT 449 Query: 448 GDLGVKHEDGYIQLKDRKKDVVISGGENISTVEVETVLYSHEAVLEAAVVARPDKLWGET 507 GDL +DGY+ + R KD++I GGENI E+E LY+H A+ + V+ PD +GE Sbjct: 450 GDLATMDDDGYVAIVGRIKDMIIRGGENIYPREIEDFLYTHPAISDVQVIGVPDDKYGEE 509 Query: 508 PCAFVTLKEGFDNDVSADQIIKFCRDRLPHYMAPKTVVF-EELPKTSTGKIQKYILKEKA 566 A+V L E D + D + FC+ R+ HY P+ V F ++ P T TGKIQK+ ++E+A Sbjct: 510 VMAWVKLAE--DETLDEDGLKAFCQGRIAHYKIPRYVKFVDDFPMTVTGKIQKFKMREEA 567 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: 730 Number of extensions: 44 Number of successful extensions: 6 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: 573 Length of database: 574 Length adjustment: 36 Effective length of query: 537 Effective length of database: 538 Effective search space: 288906 Effective search space used: 288906 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: 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