Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_013817655.1 METME_RS04795 ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >NCBI__GCF_000214665.1:WP_013817655.1 Length = 338 Score = 556 bits (1433), Expect = e-163 Identities = 276/338 (81%), Positives = 300/338 (88%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGVDVTVGLRSGSATVAKAEAHG 60 M+V+YDKD DLS+I+GKKVAIIGYGSQGHAHA NLKDSGVDV VGLR+ SA+VAKA+A G Sbjct: 1 MQVYYDKDADLSVIRGKKVAIIGYGSQGHAHANNLKDSGVDVVVGLRASSASVAKAQASG 60 Query: 61 LKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPRA 120 L V DV A+A ADVVMILTPDEFQ +LYKEEIEPN+K+GA LAFAHGF+I YNQ+VPRA Sbjct: 61 LTVKDVPDAIAGADVVMILTPDEFQSKLYKEEIEPNIKQGAALAFAHGFAILYNQIVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGIIE 180 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAI+QDASG AK + LSYA +GGGR+GIIE Sbjct: 121 DLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIHQDASGQAKAICLSYASAIGGGRSGIIE 180 Query: 181 TTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 TTF+DETETDLFGEQAVLCGG VELVKAGFETL EAGY PEMAYFECLHELKLIVDLMYE Sbjct: 181 TTFRDETETDLFGEQAVLCGGAVELVKAGFETLTEAGYPPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYPS 300 GGIANMNYSISNNAEYGEYVTGP+VIN ESR AM+ AL+ IQ G+YAK FI EG YP Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPKVINEESRWAMKQALEDIQQGKYAKQFILEGQTGYPE 300 Query: 301 MTAYRRNNAAHPIEQIGEKLRAMMPWIAANKIVDKSKN 338 MTA RR NA HPIEQ+G KLR MMPWI AN+IVDKSKN Sbjct: 301 MTARRRLNAEHPIEQVGAKLRGMMPWIKANQIVDKSKN 338 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: 447 Number of extensions: 6 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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: 49 (23.5 bits)
Align candidate WP_013817655.1 METME_RS04795 (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.22880.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-134 433.1 0.3 3e-134 432.9 0.3 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013817655.1 METME_RS04795 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013817655.1 METME_RS04795 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.9 0.3 3e-134 3e-134 2 313 .. 15 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 432.9 bits; conditional E-value: 3e-134 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +gkkvaiiGyGsqG+a+a nl+dsg++v+vglr ++as++kA+ G+ v++v +ai+ ad++miL+pDe lcl|NCBI__GCF_000214665.1:WP_013817655.1 15 RGKKVAIIGYGSQGHAHANNLKDSGVDVVVGLRASSASVAKAQASGLTVKDVPDAIAGADVVMILTPDE 83 79******************************************************************* PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 q++ y++ei+p++k+g+al f+HGf i ++qiv+++d+dv+++APK+pG++vR+e+ +g G+p liA+ lcl|NCBI__GCF_000214665.1:WP_013817655.1 84 FQSKLYKEEIEPNIKQGAALAFAHGFAILYNQIVPRADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAI 152 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 +qd++g+ak+i l+yA aiGg+r g++ettF++E+e+DLfGEqavLcGg +l+ka+f+tL+eaGy pe lcl|NCBI__GCF_000214665.1:WP_013817655.1 153 HQDASGQAKAICLSYASAIGGGRSGIIETTFRDETETDLFGEQAVLCGGAVELVKAGFETLTEAGYPPE 221 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 +Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ ++++ee + +m++ l++iq+G++ak++ lcl|NCBI__GCF_000214665.1:WP_013817655.1 222 MAYFECLHELKLIVDLMYEGGIANMNYSISNNAEYGEYVTGpKVINEESRWAMKQALEDIQQGKYAKQF 290 *****************************************9*************************** PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvkae 313 +le ++g+p++++ r+ + e+ ie+vG +lr ++++ lcl|NCBI__GCF_000214665.1:WP_013817655.1 291 ILEGQTGYPEMTARRRLNAEHPIEQVGAKLRGMMPWI 327 **********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (338 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: 10.78 // [ok]
This GapMind analysis is from Apr 10 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