Align ketol-acid reductoisomerase (NAD+) (EC 1.1.1.382); ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate N515DRAFT_0568 N515DRAFT_0568 ketol-acid reductoisomerase
Query= BRENDA::C8WR67 (344 letters) >FitnessBrowser__Dyella79:N515DRAFT_0568 Length = 339 Score = 395 bits (1015), Expect = e-115 Identities = 194/316 (61%), Positives = 241/316 (76%), Gaps = 1/316 (0%) Query: 15 LADKRIAVIGYGSQGHAHAQNLRDSGFDVVIGLRPGS-SWAKAEADGFRVMAVGEAVEES 73 LA+ RIAV+GYGSQG AHA NLRDSG DVV+GLR G SW +A A+GF V GEAV + Sbjct: 10 LANARIAVLGYGSQGRAHALNLRDSGLDVVVGLRKGGPSWERASAEGFTVAEPGEAVRGA 69 Query: 74 DVIMILLPDERQPAVYEREIRPYLTAGKALAFAHGFNIHFSQIQPPKDVDVFMVAPKGPG 133 D++ +L PD QPA+Y+ I P + AG AL FAHGFN+HF QI P +D+DV +VAPKGPG Sbjct: 70 DLVAVLTPDMVQPALYKESIEPNIKAGAALLFAHGFNVHFKQIAPREDIDVILVAPKGPG 129 Query: 134 HLVRRVYEAGGGVPALIAVHQDASGQAKDLALAYARGIGAGRAGILTTTFREETETDLFG 193 LVRR YE G GVP++ A+HQD +GQA+ A AYA GIG GRA ++ T F+EETETDLFG Sbjct: 130 ALVRREYEIGRGVPSIWAIHQDVTGQAEAKAKAYADGIGGGRALLIKTDFKEETETDLFG 189 Query: 194 EQAVLCGGLSALIKAGFETLVEAGYQPEIAYFECLHEMKLIVDLIYEGGLEYMRYSISDT 253 EQAVLCGG S+L++AGFETLVEAGYQPEIAY+E LHE+KLIVDL YEGG+ M +S+T Sbjct: 190 EQAVLCGGASSLVQAGFETLVEAGYQPEIAYYEVLHELKLIVDLFYEGGIARMLEFVSET 249 Query: 254 AQWGDFTSGPRIINEETKKEMRRILADIQSGAFAKSWILENQANRPMFNAINRRELEHPI 313 AQ+GD+ SGPR+I+ TK M+ +L DIQ G FA++WI E QA P + + +LEHPI Sbjct: 250 AQYGDYVSGPRVIDAGTKARMKDVLTDIQDGTFARNWIAEYQAGLPNYKRFKQADLEHPI 309 Query: 314 EVVGRKLRSMMPFIKA 329 E VG KLR+ M +++A Sbjct: 310 EQVGAKLRARMSWLQA 325 Lambda K H 0.320 0.138 0.404 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: 395 Number of extensions: 12 Number of successful extensions: 2 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: 344 Length of database: 339 Length adjustment: 29 Effective length of query: 315 Effective length of database: 310 Effective search space: 97650 Effective search space used: 97650 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate N515DRAFT_0568 N515DRAFT_0568 (ketol-acid reductoisomerase)
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00465.hmm # target sequence database: /tmp/gapView.11321.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00465 [M=314] Accession: TIGR00465 Description: ilvC: ketol-acid reductoisomerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-134 431.6 0.0 8.3e-134 431.4 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 N515DRAFT_0568 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 N515DRAFT_0568 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.4 0.0 8.3e-134 8.3e-134 1 313 [. 10 323 .. 10 324 .. 0.99 Alignments for each domain: == domain 1 score: 431.4 bits; conditional E-value: 8.3e-134 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiL 66 l++ ++a++GyGsqG+a+alnlrdsgl+v+vglrk++ sw++A+ +Gf v + ea++ adl+++L lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 10 LANARIAVLGYGSQGRAHALNLRDSGLDVVVGLRKGGPSWERASAEGFTVAEPGEAVRGADLVAVL 75 67899************************************************************* PP TIGR00465 67 lpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrG 132 +pD+vq++ y+++i+p++k+g+allf+HGfn++fkqi +++d+dv+lvAPKgpGalvR+ey+ grG lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 76 TPDMVQPALYKESIEPNIKAGAALLFAHGFNVHFKQIAPREDIDVILVAPKGPGALVRREYEIGRG 141 ****************************************************************** PP TIGR00465 133 vpsliAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafd 198 vps+ A++qdvtg+a ++A+ayA +iGg+ra +++t FkeE+e+DLfGEqavLcGg + l++a+f+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 142 VPSIWAIHQDVTGQAEAKAKAYADGIGGGRALLIKTDFKEETETDLFGEQAVLCGGASSLVQAGFE 207 ****************************************************************** PP TIGR00465 199 tLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqki 263 tLveaGyqpe+Ay e++helklivdl +e+G++ m + vs+tA++g++ ++ +++++ +k++m+++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 208 TLVEAGYQPEIAYYEVLHELKLIVDLFYEGGIARMLEFVSETAQYGDYVSGpRVIDAGTKARMKDV 273 ***************************************************9************** PP TIGR00465 264 lkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvkae 313 l +iq+G+fa++w+ e +ag p++++ ++++ e+ ie+vG +lra +++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0568 274 LTDIQDGTFARNWIAEYQAGLPNYKRFKQADLEHPIEQVGAKLRARMSWL 323 *********************************************99885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (339 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.99 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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