Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate WP_066325987.1 BLR17_RS13770 ketol-acid reductoisomerase
Query= BRENDA::A0KS29 (492 letters) >NCBI__GCF_900100165.1:WP_066325987.1 Length = 490 Score = 732 bits (1890), Expect = 0.0 Identities = 361/490 (73%), Positives = 411/490 (83%) Query: 1 MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60 MANYFNSL LR QL QLG C FMD+SEF++G +K +VI+GCGAQGLNQGLNMRDSG Sbjct: 1 MANYFNSLPLRLQLEQLGVCEFMDQSEFANGIEALKGKKVVIVGCGAQGLNQGLNMRDSG 60 Query: 61 LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120 L+I+YALR EAIAQKRAS+ A DNGF VGT+EELIPTADLV NLTPDKQH+ VV+A+MP Sbjct: 61 LDISYALRAEAIAQKRASFMNAADNGFNVGTYEELIPTADLVCNLTPDKQHTAVVTAIMP 120 Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180 LMKQGATL+YSHGFNIVEEGMQIR D+TV+M APKCPG+EVREEYKRGFGVPTLIAVHPE Sbjct: 121 LMKQGATLAYSHGFNIVEEGMQIRKDLTVIMCAPKCPGSEVREEYKRGFGVPTLIAVHPE 180 Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240 NDPNG GL+ AKAYA ATGG RAGVL+SSF+AEVKSDLMGEQTILCG+LQTG+IL +DKM Sbjct: 181 NDPNGFGLDQAKAYAVATGGHRAGVLRSSFVAEVKSDLMGEQTILCGLLQTGSILCFDKM 240 Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300 VA+GVEPGYA+KLIQ GWET+TE LKHGGITNMMDRLSNPAKI AF AE+LK+I++PLF Sbjct: 241 VAEGVEPGYASKLIQYGWETITEGLKHGGITNMMDRLSNPAKIAAFNAAEELKDIMRPLF 300 Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360 +KHMDDIISG FS+TMM+DWANDD NLL WRA TAET FE P I EQ Y+D G Sbjct: 301 QKHMDDIISGHFSKTMMEDWANDDKNLLTWRAATAETNFEKTPAGDMEISEQEYYDNGTL 360 Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420 +VAM+KAGVELAF+ M +GI+EESAYYESLHETPLIANTIARK+L+EMN VISDTAEYG Sbjct: 361 MVAMVKAGVELAFEAMTDSGIIEESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYG 420 Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480 CYLF+HA P++ DYV +G + SN VDN +LI +N IR+ VE +GA LR Sbjct: 421 CYLFDHACKPLIADYVKNAPSNLVGRPFSNGSNGVDNKELIDVNSIIRNHPVEEVGAWLR 480 Query: 481 GYMTDMKSIV 490 MT MK IV Sbjct: 481 ESMTAMKKIV 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: 801 Number of extensions: 19 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: 490 Length adjustment: 34 Effective length of query: 458 Effective length of database: 456 Effective search space: 208848 Effective search space used: 208848 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 WP_066325987.1 BLR17_RS13770 (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.289019.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-135 436.5 0.1 7.2e-126 405.3 0.1 2.0 2 NCBI__GCF_900100165.1:WP_066325987.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900100165.1:WP_066325987.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.3 0.1 7.2e-126 7.2e-126 1 312 [. 35 367 .. 35 369 .. 0.97 2 ! 35.7 0.0 2.5e-13 2.5e-13 185 312 .. 361 485 .. 359 487 .. 0.86 Alignments for each domain: == domain 1 score: 405.3 bits; conditional E-value: 7.2e-126 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea.....aswkkAeedGfkvltveeaikkadlimiLlp 68 lkgkkv+i+G+G+qG +q+ln+rdsgl+++++lr ea as+ +A ++Gf+v t+ee+i++adl+ +L+p NCBI__GCF_900100165.1:WP_066325987.1 35 LKGKKVVIVGCGAQGLNQGLNMRDSGLDISYALRAEAiaqkrASFMNAADNGFNVGTYEELIPTADLVCNLTP 107 79**********************************999999******************************* PP TIGR00465 69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveq 141 D+ q++ ++ i+pl+k+g++l +sHGfniv+++++i+kd++v++ APK+pG++vReeyk+g+Gvp+liAv++ NCBI__GCF_900100165.1:WP_066325987.1 108 DK-QHTAVVTAIMPLMKQGATLAYSHGFNIVEEGMQIRKDLTVIMCAPKCPGSEVREEYKRGFGVPTLIAVHP 179 **.77777777************************************************************98 PP TIGR00465 142 d..vtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyf 212 + ++g + ++A+ayA+a+Gg+ragvl ++F++Ev+sDL+GEq++LcG l+ ++ ++fd++v++G +p +A + NCBI__GCF_900100165.1:WP_066325987.1 180 EndPNGFGLDQAKAYAVATGGHRAGVLRSSFVAEVKSDLMGEQTILCGLLQTGSILCFDKMVAEGVEPGYASK 252 87799******************************************************************** PP TIGR00465 213 eivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefak....ewalek. 280 +i++++++i++ lk++G+++m+d++sn+Ak+ a++++e lk+ +++ +qk++++i++G+f+k +wa+++ NCBI__GCF_900100165.1:WP_066325987.1 253 LIQYGWETITEGLKHGGITNMMDRLSNPAKIAAFNAAEELKDIMRPLFQKHMDDIISGHFSKtmmeDWANDDk 325 **************************************************************99999***999 PP TIGR00465 281 .......eagkpafeearkke...keqeiekvGkelralvka 312 ++++++fe+++ + +eqe++++G + a+vka NCBI__GCF_900100165.1:WP_066325987.1 326 nlltwraATAETNFEKTPAGDmeiSEQEYYDNGTLMVAMVKA 367 *****999999*****99988889****************97 PP == domain 2 score: 35.7 bits; conditional E-value: 2.5e-13 TIGR00465 185 LcGglealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelk 257 ++ +++a++++af+ +++ G +e Ay e +he li++ + +k l +m + +s+tA++g + ++++ k NCBI__GCF_900100165.1:WP_066325987.1 361 MVAMVKAGVELAFEAMTDSGIIEESAYYESLHETPLIANTIARKKLFEMNRVISDTAEYGCY----LFDHACK 429 6789********************************************************98....5677778 PP TIGR00465 258 kemqkilkeiqnGefakewalek.eagkpafeearkkekeqeiekvGkelralvka 312 + + + +k+ + + +++++ +++ ++ + + +++ +e+vG lr+ + a NCBI__GCF_900100165.1:WP_066325987.1 430 PLIADYVKNAPSNLVGRPFSNGSnGVDNKELIDVNSIIRNHPVEEVGAWLRESMTA 485 88888888888888888887775245667788888888999999999999998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (490 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 6.07 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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