Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate WP_101445085.1 BD749_RS13340 ketol-acid reductoisomerase
Query= SwissProt::A8ZTR0 (352 letters) >NCBI__GCF_002846395.1:WP_101445085.1 Length = 348 Score = 466 bits (1199), Expect = e-136 Identities = 226/348 (64%), Positives = 276/348 (79%) Query: 1 MPTINFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQ 60 M TINFGGV+E VVT EEF L KAREVL++E+I V+GYGVQGP QALNL+DNGF VI+GQ Sbjct: 1 MATINFGGVDETVVTREEFPLAKAREVLQHELIAVIGYGVQGPGQALNLRDNGFNVIVGQ 60 Query: 61 LEGDAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDAL 120 + A W+KA+ADG+V G+TLF IEEAA++GTII LLSDAGQ+AVWP +++ L G L Sbjct: 61 RKDSASWQKALADGWVEGETLFSIEEAAERGTIIANLLSDAGQIAVWPTLRERLTAGKTL 120 Query: 121 YFSHGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRA 180 YFSHGFGI + + T IVPP +VDVIL APKGSGT++RR + G G+NSS+AV+QDATG+A Sbjct: 121 YFSHGFGITFHEHTNIVPPADVDVILAAPKGSGTSLRRLYLQGGGLNSSFAVYQDATGKA 180 Query: 181 EERTIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSE 240 E+ +A+GI IGSGYLF T F KEV+SDLTGERGVLMG LAG +EAQY VLR+ GHSPSE Sbjct: 181 YEKAVAMGIGIGSGYLFETDFRKEVYSDLTGERGVLMGALAGIIEAQYQVLRQRGHSPSE 240 Query: 241 AFNETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVK 300 AFNETVEELTQSL+ LV ENGMDWMF+NCS TAQRGALDW +F++A PV LY V Sbjct: 241 AFNETVEELTQSLVPLVGENGMDWMFSNCSVTAQRGALDWKGRFKEATLPVLHELYDSVA 300 Query: 301 NGAETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPENR 348 +G E +R ++ SAP Y +L EL ++ SE+WQ GA VR LR +++ Sbjct: 301 SGTEAQRTIQRGSAPGYRTELEAELQELRESELWQTGARVRELRSQSK 348 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: 422 Number of extensions: 10 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: 348 Length adjustment: 29 Effective length of query: 323 Effective length of database: 319 Effective search space: 103037 Effective search space used: 103037 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 WP_101445085.1 BD749_RS13340 (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.239335.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-99 319.0 0.0 1.6e-99 318.8 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101445085.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101445085.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.8 0.0 1.6e-99 1.6e-99 1 313 [. 28 347 .. 28 348 .] 0.95 Alignments for each domain: == domain 1 score: 318.8 bits; conditional E-value: 1.6e-99 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpD 69 l+ + +a+iGyG qG +qalnlrd+g nvivg rk++asw+kA d G ++++eea++++ +i++Ll+D NCBI__GCF_002846395.1:WP_101445085.1 28 LQHELIAVIGYGVQGPGQALNLRDNGFNVIVGQRKDSASWQKALADgwveGETLFSIEEAAERGTIIANLLSD 100 57788****************************************98888899******************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 + q +v+ +++ l++gk+l+fsHGf i f++ + +p+dvdv+l+APKg+G+ +R+ y +g G++s++Av NCBI__GCF_002846395.1:WP_101445085.1 101 AGQIAVWPT-LRERLTAGKTLYFSHGFGITFHEHTnivPPADVDVILAAPKGSGTSLRRLYLQGGGLNSSFAV 172 *******99.*******************998644444*********************************** PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyf 212 +qd+tg+a e+A a+ +iG++ +++et F++Ev sDL GE++vL+G l+++i+a++++L++ G++p++A++ NCBI__GCF_002846395.1:WP_101445085.1 173 YQDATGKAYEKAVAMGIGIGSG--YLFETDFRKEVYSDLTGERGVLMGALAGIIEAQYQVLRQRGHSPSEAFN 243 *********************9..************************************************* PP TIGR00465 213 eivhel.klivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagk 284 e+v+el +++v+l+ e+G++ m++++s tA++gal+++ +ke++ ++++++++++ +G++a+ +++++ ++ NCBI__GCF_002846395.1:WP_101445085.1 244 ETVEELtQSLVPLVGENGMDWMFSNCSVTAQRGALDWKGRFKEATLPVLHELYDSVASGTEAQ-RTIQR-GSA 314 ******9********************************************************.44444.577 PP TIGR00465 285 pafeearkke....keqeiekvGkelralvkae 313 p ++++ ++e +e e++++G ++r+l++++ NCBI__GCF_002846395.1:WP_101445085.1 315 PGYRTELEAElqelRESELWQTGARVRELRSQS 347 88888877777777**************98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (348 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: 27.07 // [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