Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 5207767 Shew_0288 ketol-acid reductoisomerase (RefSeq)
Query= BRENDA::A0KS29 (492 letters) >FitnessBrowser__PV4:5207767 Length = 493 Score = 895 bits (2312), Expect = 0.0 Identities = 439/490 (89%), Positives = 466/490 (95%) Query: 1 MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60 MANYFNSLNLRQQL QLGQCRFMDRSEFS GC+YIK WNIVILGCGAQGLNQGLNMRDSG Sbjct: 1 MANYFNSLNLRQQLEQLGQCRFMDRSEFSQGCDYIKGWNIVILGCGAQGLNQGLNMRDSG 60 Query: 61 LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120 LNI++ALR +AIA++R S+QKAT NGF+VGTFEELIP ADLVLNLTPDKQH++ V+AVMP Sbjct: 61 LNISFALREQAIAEQRPSYQKATGNGFRVGTFEELIPDADLVLNLTPDKQHTDAVNAVMP 120 Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180 LMKQGA LSYSHGFNIVEEGMQ+RPDITV+MVAPKCPGTEVREEYKRGFGVPTLIAVHPE Sbjct: 121 LMKQGAVLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180 Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240 NDP GDGLE+AKAYASATGGDRAGVL SSFIAEVKSDLMGEQTILCGMLQTGAILGY+KM Sbjct: 181 NDPKGDGLEVAKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKM 240 Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300 VADG+EPGYAAKLIQQGWET TEALKHGGIT+MMDRLSNPAKIKAFE+AE+LK ILQPLF Sbjct: 241 VADGIEPGYAAKLIQQGWETTTEALKHGGITHMMDRLSNPAKIKAFEMAEELKAILQPLF 300 Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360 EKHMDDIISGEFS+TMM+DWANDDANLL+WRAET ETGFENAP E IDEQTYFDKGIF Sbjct: 301 EKHMDDIISGEFSKTMMEDWANDDANLLKWRAETNETGFENAPACDEAIDEQTYFDKGIF 360 Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG Sbjct: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420 Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480 CYLFNHAAVP+LRDYVN MSPEYLG GLKDS N VDNL+LI +NDAIRHT+VEYIGAELR Sbjct: 421 CYLFNHAAVPLLRDYVNQMSPEYLGGGLKDSGNGVDNLRLIEVNDAIRHTAVEYIGAELR 480 Query: 481 GYMTDMKSIV 490 GYMT+MK IV Sbjct: 481 GYMTEMKRIV 490 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: 928 Number of extensions: 14 Number of successful extensions: 1 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: 492 Length of database: 493 Length adjustment: 34 Effective length of query: 458 Effective length of database: 459 Effective search space: 210222 Effective search space used: 210222 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)
Align candidate 5207767 Shew_0288 (ketol-acid reductoisomerase (RefSeq))
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.21839.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-131 421.7 0.3 8.6e-121 388.7 0.1 2.1 2 lcl|FitnessBrowser__PV4:5207767 Shew_0288 ketol-acid reductoisom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207767 Shew_0288 ketol-acid reductoisomerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.7 0.1 8.6e-121 8.6e-121 2 312 .. 36 367 .. 35 369 .. 0.97 2 ! 37.3 0.0 8.1e-14 8.1e-14 185 249 .. 361 425 .. 359 486 .. 0.88 Alignments for each domain: == domain 1 score: 388.7 bits; conditional E-value: 8.6e-121 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlpDevqke 74 kg +++i+G+G+qG +q+ln+rdsgln++ +lr++a s++kA+ +Gf+v t+ee+i++adl+++L+pD+ q++ lcl|FitnessBrowser__PV4:5207767 36 KGWNIVILGCGAQGLNQGLNMRDSGLNISFALREQAiaeqrPSYQKATGNGFRVGTFEELIPDADLVLNLTPDK-QHT 112 7789*******************************9999999********************************.888 PP TIGR00465 75 vyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqd..vtgeakei 150 + ++ ++pl+k+g++l++sHGfniv+++++++ d++v++vAPK+pG++vReeyk+g+Gvp+liAv+++ ++g++ e+ lcl|FitnessBrowser__PV4:5207767 113 DAVNAVMPLMKQGAVLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPEndPKGDGLEV 190 88888************************************************************98877******** PP TIGR00465 151 AlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelklivdllkek 228 A+ayA a+Gg ragvl ++F +Ev+sDL+GEq++LcG+l+ + ++++++v++G +p +A ++i++++++ +++lk++ lcl|FitnessBrowser__PV4:5207767 191 AKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKMVADGIEPGYAAKLIQQGWETTTEALKHG 268 ****************************************************************************** PP TIGR00465 229 GlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek........eagkpafeearkke 294 G+++m+d++sn+Ak++a+e++e lk+ l++ ++k++++i++Gef+k +wa+++ e++++ fe+a+ + lcl|FitnessBrowser__PV4:5207767 269 GITHMMDRLSNPAKIKAFEMAEELKAILQPLFEKHMDDIISGEFSKtmmeDWANDDanllkwraETNETGFENAPACD 346 **********************************************99999***99*******************999 PP TIGR00465 295 ...keqeiekvGkelralvka 312 eq ++++G l a++ka lcl|FitnessBrowser__PV4:5207767 347 eaiDEQTYFDKGIFLVAMIKA 367 8999**************987 PP == domain 2 score: 37.3 bits; conditional E-value: 8.1e-14 TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr 249 L+ +++a++++afdt+v aG +e Ay e +he li++ + +k l +m +s+tA++g + + lcl|FitnessBrowser__PV4:5207767 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYGCYLFN 425 889*********************************************************87655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (493 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 3.70 // [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