Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; EC 1.1.1.382 (characterized)
to candidate WP_010526302.1 GQW_RS0101520 ketol-acid reductoisomerase
Query= SwissProt::A8ZTR0 (352 letters) >NCBI__GCF_000220155.1:WP_010526302.1 Length = 349 Score = 505 bits (1301), Expect = e-148 Identities = 248/349 (71%), Positives = 284/349 (81%) Query: 1 MPTINFGGVEENVVTSEEFTLKKAREVLKNEVITVLGYGVQGPAQALNLKDNGFEVIIGQ 60 M INFGG EENVVT EEF L KA+EVLK+E I V+GYGVQGP Q+LNLKDNGF VI+GQ Sbjct: 1 MAKINFGGTEENVVTREEFPLSKAQEVLKDETIAVIGYGVQGPGQSLNLKDNGFNVIVGQ 60 Query: 61 LEGDAYWEKAIADGFVPGKTLFPIEEAAKKGTIIKMLLSDAGQVAVWPKVKKCLKKGDAL 120 + W+KAI DG+ PGKTLFPIEEA ++GTII+ LLSDAGQ+AVWP VKK LK G+AL Sbjct: 61 RKDSKSWDKAIKDGWEPGKTLFPIEEALERGTIIQYLLSDAGQIAVWPTVKKHLKPGNAL 120 Query: 121 YFSHGFGIVYKDQTGIVPPKNVDVILVAPKGSGTNVRRNFKDGSGINSSYAVFQDATGRA 180 YFSHGFGI YK++T I+PPK+VDVILVAPKGSGT++RR F +G G+NSSYA+FQDATGRA Sbjct: 121 YFSHGFGITYKERTNIIPPKDVDVILVAPKGSGTSLRRMFLEGRGLNSSYAIFQDATGRA 180 Query: 181 EERTIALGIAIGSGYLFPTTFEKEVFSDLTGERGVLMGCLAGTMEAQYNVLRKHGHSPSE 240 ER IALGI +GSGYLF TTF+KEV+SDLTGERG LMG + G AQY VLR +GHSPSE Sbjct: 181 FERVIALGIGVGSGYLFETTFQKEVYSDLTGERGTLMGAIQGLFAAQYEVLRANGHSPSE 240 Query: 241 AFNETVEELTQSLIRLVAENGMDWMFANCSTTAQRGALDWAPKFRDAVAPVFDSLYRRVK 300 AFNETVEELTQSL+ LVAENGMDWM+ANCSTTAQRGALDW KFRDA PVF LY V Sbjct: 241 AFNETVEELTQSLMPLVAENGMDWMYANCSTTAQRGALDWWKKFRDATLPVFKELYSEVA 300 Query: 301 NGAETRRVLKVNSAPNYLEKLRKELDTIKNSEMWQAGAAVRALRPENRK 349 G E +R + NS +Y EKL +EL ++ SEMW AGA VR LRPEN+K Sbjct: 301 KGNEAQRAIDANSQKDYREKLEEELKELRESEMWAAGAVVRTLRPENQK 349 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: 465 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: 349 Length adjustment: 29 Effective length of query: 323 Effective length of database: 320 Effective search space: 103360 Effective search space used: 103360 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_010526302.1 GQW_RS0101520 (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.1270686.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-99 316.9 0.0 7.2e-99 316.7 0.0 1.0 1 NCBI__GCF_000220155.1:WP_010526302.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_010526302.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 316.7 0.0 7.2e-99 7.2e-99 1 313 [. 28 347 .. 28 348 .. 0.96 Alignments for each domain: == domain 1 score: 316.7 bits; conditional E-value: 7.2e-99 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeed....GfkvltveeaikkadlimiLlpD 69 lk++++a+iGyG qG +q+lnl+d+g nvivg rk+++sw+kA++d G+ ++ +eea +++ +i Ll+D NCBI__GCF_000220155.1:WP_010526302.1 28 LKDETIAVIGYGVQGPGQSLNLKDNGFNVIVGQRKDSKSWDKAIKDgwepGKTLFPIEEALERGTIIQYLLSD 100 799*******************************************8888899******************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqiv...ipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 + q +v+ +k lk g+al+fsHGf i +k+ + +pkdvdv+lvAPKg+G+ +R+++ egrG++s++A+ NCBI__GCF_000220155.1:WP_010526302.1 101 AGQIAVWPT-VKKHLKPGNALYFSHGFGITYKERTniiPPKDVDVILVAPKGSGTSLRRMFLEGRGLNSSYAI 172 *******99.*********************9866666*********************************** PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyf 212 qd+tg a e a+ ++G++ +++ettF++Ev sDL GE++ L+G +++l+ a++++L+++G++p++A++ NCBI__GCF_000220155.1:WP_010526302.1 173 FQDATGRAFERVIALGIGVGSG--YLFETTFQKEVYSDLTGERGTLMGAIQGLFAAQYEVLRANGHSPSEAFN 243 ***********99999999999..************************************************* PP TIGR00465 213 eivhel.klivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakewalekeagk 284 e+v+el +++++l+ e+G++ m+ ++s+tA++gal++ + +++++ +++++++ e+ +G++a+ +a++ +++ NCBI__GCF_000220155.1:WP_010526302.1 244 ETVEELtQSLMPLVAENGMDWMYANCSTTAQRGALDWWKKFRDATLPVFKELYSEVAKGNEAQ-RAIDA-NSQ 314 ******9*******************************************************9.66666.677 PP TIGR00465 285 pafeearkke....keqeiekvGkelralvkae 313 +++e+ + e +e e++ G +r l++++ NCBI__GCF_000220155.1:WP_010526302.1 315 KDYREKLEEElkelRESEMWAAGAVVRTLRPEN 347 78888777777777**************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (349 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: 24.79 // [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