Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_012385380.1 BIND_RS12225 ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >NCBI__GCF_000019845.1:WP_012385380.1 Length = 339 Score = 465 bits (1196), Expect = e-136 Identities = 224/339 (66%), Positives = 275/339 (81%), Gaps = 1/339 (0%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGV-DVTVGLRSGSATVAKAEAH 59 MRV+YD+D D+++++GKKVAIIGYGSQGHAHA NL+DSGV ++ + LR GS+T KAEA Sbjct: 1 MRVYYDRDADINLVKGKKVAIIGYGSQGHAHALNLRDSGVKEIAIALREGSSTAKKAEAE 60 Query: 60 GLKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPR 119 GL V V A ADVVM+LTPDE Q +Y + + NLK+GA L FAHG S+H+N + PR Sbjct: 61 GLTVKTVVDAAQWADVVMVLTPDELQADIYHQLLAKNLKQGAALLFAHGLSVHFNLIEPR 120 Query: 120 ADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGII 179 ADLDV+M+APK PGHTVRSE+ +GGG+P LIA+ Q+ASGNA ++ALSYA +GGGR GII Sbjct: 121 ADLDVLMVAPKGPGHTVRSEYKRGGGVPCLIAVAQNASGNAHDIALSYASAIGGGRAGII 180 Query: 180 ETTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 239 ETTFK+E ETDLFGEQAVLCGG VEL++AGFETLVEAGYAPEMAYFECLHE+KLIVDL+Y Sbjct: 181 ETTFKEECETDLFGEQAVLCGGLVELIRAGFETLVEAGYAPEMAYFECLHEVKLIVDLIY 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYP 299 EGGIANMNYSISN AEYGEYVTGP +I E++A M+ L+ IQ G++ + ++ E + Sbjct: 241 EGGIANMNYSISNTAEYGEYVTGPRIITPETKAEMKRVLEDIQGGKFTRDWMLENKVHQT 300 Query: 300 SMTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338 S A R AAHPIE++G +LRAMMPWI A+K+VDKSKN Sbjct: 301 SFKATRAKVAAHPIEKVGAELRAMMPWIGASKLVDKSKN 339 Lambda K H 0.317 0.134 0.389 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: 402 Number of extensions: 9 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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: 49 (23.5 bits)
Align candidate WP_012385380.1 BIND_RS12225 (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.28961.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-136 437.8 0.6 1.1e-135 437.5 0.6 1.0 1 lcl|NCBI__GCF_000019845.1:WP_012385380.1 BIND_RS12225 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019845.1:WP_012385380.1 BIND_RS12225 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.5 0.6 1.1e-135 1.1e-135 1 312 [. 14 327 .. 14 329 .. 0.99 Alignments for each domain: == domain 1 score: 437.5 bits; conditional E-value: 1.1e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsgln.vivglrkeaaswkkAeedGfkvltveeaikkadlimiLlp 68 +kgkkvaiiGyGsqG+a+alnlrdsg++ + ++lr+++++ kkAe +G+ v+tv +a++ ad++m+L+p lcl|NCBI__GCF_000019845.1:WP_012385380.1 14 VKGKKVAIIGYGSQGHAHALNLRDSGVKeIAIALREGSSTAKKAEAEGLTVKTVVDAAQWADVVMVLTP 82 589************************5499************************************** PP TIGR00465 69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137 De+q + y++ ++ +lk+g+allf+HG +++f+ i++++d+dv++vAPKgpG++vR+eyk+g Gvp li lcl|NCBI__GCF_000019845.1:WP_012385380.1 83 DELQADIYHQLLAKNLKQGAALLFAHGLSVHFNLIEPRADLDVLMVAPKGPGHTVRSEYKRGGGVPCLI 151 ********************************************************************* PP TIGR00465 138 AveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206 Av q+++g+a++iAl+yA aiGg+rag++ettFkeE+e+DLfGEqavLcGgl +li+a+f+tLveaGy+ lcl|NCBI__GCF_000019845.1:WP_012385380.1 152 AVAQNASGNAHDIALSYASAIGGGRAGIIETTFKEECETDLFGEQAVLCGGLVELIRAGFETLVEAGYA 220 ********************************************************************* PP TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274 pe+Ayfe++he+klivdl++e+G+++m ++sntA++g++ ++ +i++ e+k+em+ +l++iq G+f++ lcl|NCBI__GCF_000019845.1:WP_012385380.1 221 PEMAYFECLHEVKLIVDLIYEGGIANMNYSISNTAEYGEYVTGpRIITPETKAEMKRVLEDIQGGKFTR 289 *******************************************9************************* PP TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312 +w+le+++ +++f+++r k + iekvG elra++++ lcl|NCBI__GCF_000019845.1:WP_012385380.1 290 DWMLENKVHQTSFKATRAKVAAHPIEKVGAELRAMMPW 327 ************************************97 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.61 // [ok]
This GapMind analysis is from Apr 10 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