Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate Echvi_2058 Echvi_2058 ketol-acid reductoisomerase
Query= SwissProt::A8ZTR0 (352 letters) >FitnessBrowser__Cola:Echvi_2058 Length = 347 Score = 490 bits (1261), Expect = e-143 Identities = 239/344 (69%), Positives = 283/344 (82%) Query: 4 INFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQLEG 63 + FG VEE+VVT EEF L+KAREVLK+EVI VLGYGVQGP QALNLKDNGF VI+GQ + Sbjct: 3 LKFGTVEEDVVTREEFPLEKAREVLKDEVIAVLGYGVQGPGQALNLKDNGFNVIVGQRKN 62 Query: 64 DAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDALYFS 123 W+KA+ADG+VPG+TLF +EEA +KGTI++ LLSDAGQ+A+WP VKK L G ALYFS Sbjct: 63 SKTWDKAVADGWVPGETLFELEEACEKGTILQFLLSDAGQIALWPTVKKHLTPGKALYFS 122 Query: 124 HGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRAEER 183 HGFG+ YKDQTGIVPP++VDVILVAPKGSGT++RR F +G G+NSS+A++QDATG+A ER Sbjct: 123 HGFGVTYKDQTGIVPPEDVDVILVAPKGSGTSLRRMFVEGRGLNSSFAIYQDATGKARER 182 Query: 184 TIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSEAFN 243 IALGI +GSGYLF T F +EV SDLTGERG LMG + G AQY VLR++GHSPSEAFN Sbjct: 183 VIALGIGVGSGYLFETDFYREVTSDLTGERGTLMGAIQGIFAAQYEVLRENGHSPSEAFN 242 Query: 244 ETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVKNGA 303 ETVEELTQSL+ LVAENGMDWM+ANCSTTAQRGALDW FRDA PVF+ LY+ VK+G Sbjct: 243 ETVEELTQSLMPLVAENGMDWMYANCSTTAQRGALDWWKPFRDASKPVFEQLYKSVKDGK 302 Query: 304 ETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPEN 347 E + ++ NS +Y EKL EL ++ SEMW+AGA VR LRPEN Sbjct: 303 EAAKSIESNSKADYREKLEVELKELRESEMWKAGATVRKLRPEN 346 Lambda K H 0.316 0.134 0.391 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: 464 Number of extensions: 9 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: 352 Length of database: 347 Length adjustment: 29 Effective length of query: 323 Effective length of database: 318 Effective search space: 102714 Effective search space used: 102714 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate Echvi_2058 Echvi_2058 (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.25046.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-98 314.8 0.0 3e-98 314.6 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2058 Echvi_2058 ketol-acid reductoiso Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2058 Echvi_2058 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 314.6 0.0 3e-98 3e-98 1 313 [. 27 346 .. 27 347 .] 0.96 Alignments for each domain: == domain 1 score: 314.6 bits; conditional E-value: 3e-98 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpDe 70 lk++ +a++GyG qG +qalnl+d+g nvivg rk++++w+kA d G ++++eea +k+ ++ Ll+D+ lcl|FitnessBrowser__Cola:Echvi_2058 27 LKDEVIAVLGYGVQGPGQALNLKDNGFNVIVGQRKNSKTWDKAVADgwvpGETLFELEEACEKGTILQFLLSDA 100 68999*****************************************8888899********************* PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAveq 141 q + + +k l+ gkal+fsHGf + +k+ + +p+dvdv+lvAPKg+G+ +R+++ egrG++s++A++q lcl|FitnessBrowser__Cola:Echvi_2058 101 GQIALWPT-VKKHLTPGKALYFSHGFGVTYKDQTgivPPEDVDVILVAPKGSGTSLRRMFVEGRGLNSSFAIYQ 173 **999998.*********************9755555************************************* PP TIGR00465 142 dvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeiv 215 d+tg+a+e a+ ++G++ +++et F +Ev sDL GE++ L+G +++++ a++++L+e+G++p++A++e+v lcl|FitnessBrowser__Cola:Echvi_2058 174 DATGKARERVIALGIGVGSG--YLFETDFYREVTSDLTGERGTLMGAIQGIFAAQYEVLRENGHSPSEAFNETV 245 **********9999999999..**************************************************** PP TIGR00465 216 hel.klivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagkpafe 288 +el +++++l+ e+G++ m+ ++s+tA++gal++ + ++++ k+++++++k++++G++a+ ++e+ ++k++++ lcl|FitnessBrowser__Cola:Echvi_2058 246 EELtQSLMPLVAENGMDWMYANCSTTAQRGALDWWKPFRDASKPVFEQLYKSVKDGKEAA-KSIES-NSKADYR 317 ***9*******************************************************9.55565.7999999 PP TIGR00465 289 earkke....keqeiekvGkelralvkae 313 e+ + e +e e++k G ++r+l++++ lcl|FitnessBrowser__Cola:Echvi_2058 318 EKLEVElkelRESEMWKAGATVRKLRPEN 346 9999999899**************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (347 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: 00:00:00.01 # Mc/sec: 10.88 // [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