Align Ketol-acid reductoisomerase (NAD(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.382 (characterized)
to candidate WP_017751808.1 PN53_RS01890 ketol-acid reductoisomerase
Query= SwissProt::K4LVZ1 (332 letters) >NCBI__GCF_000816635.1:WP_017751808.1 Length = 337 Score = 431 bits (1108), Expect = e-125 Identities = 202/329 (61%), Positives = 258/329 (78%) Query: 1 MKIYYDQDADLQYLDGKTVAVIGYGSQGHAQSQNLRDSGVKVVVADIPSSENWKKAEEAQ 60 +K+YYD+DA+L L GK +AV+G+GSQGHAQ+ NL+DSG+ V++ S++WKKAE+ Sbjct: 4 LKVYYDEDANLDLLKGKKIAVLGFGSQGHAQALNLKDSGLDVIIGLYKGSKSWKKAEDYG 63 Query: 61 FQPLTADEAAREADIIQILVPDEKQAALYRESIAPNLRPGKALVFSHGFNIHFKQIVPPP 120 F+ EA ++A ++ +L+PDEKQ +Y ES+ NL G AL+FSHGFNIHF QIVP Sbjct: 64 FKVYEVAEAVKQAQLVAMLLPDEKQKQIYEESVRDNLEDGDALLFSHGFNIHFNQIVPAK 123 Query: 121 DVDVFMVAPKGPGHLVRRMYEEGAGVPSLVAVEQDYSGQALNLALAYAKGIGATRAGVIQ 180 ++DV M+APKGPGH+VR+ Y EG GVP L AV QDY+G+ + ALAY KG+G TR GV+ Sbjct: 124 NIDVLMIAPKGPGHIVRKQYTEGGGVPCLYAVYQDYTGKGKDYALAYGKGVGGTRGGVMN 183 Query: 181 TTFKEETETDLFGEQAVLCGGITELIRAGFDTLVDAGYQPEIAYFECLHEMKLIVDLIYE 240 TTFK ETETDLFGEQAVLCGGI LI+AGFDTLV+AGY PE A+FEC HEMK+IVDL+YE Sbjct: 184 TTFKIETETDLFGEQAVLCGGICSLIQAGFDTLVEAGYAPENAFFECFHEMKMIVDLMYE 243 Query: 241 GGISTMRYSISDTAEYGDLTRGKRIITEATREEMKKILKEIQDGVFAREWLLENQVGRPV 300 GG+S MR+SISDTAEYGD G R+I ++ R+EMKK+LKEIQDG FA++WLLEN++GRP Sbjct: 244 GGMSKMRHSISDTAEYGDYKIGNRLINDSVRKEMKKVLKEIQDGTFAKDWLLENKIGRPT 303 Query: 301 YNALRRKEQNHLIETVGARLRGMMPWLKK 329 A RR E + +E VG RLRGMM W+++ Sbjct: 304 LEARRRIEADTQLEKVGKRLRGMMSWIEE 332 Lambda K H 0.318 0.136 0.393 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: 370 Number of extensions: 8 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: 332 Length of database: 337 Length adjustment: 28 Effective length of query: 304 Effective length of database: 309 Effective search space: 93936 Effective search space used: 93936 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_017751808.1 PN53_RS01890 (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.885979.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-142 458.4 0.8 5.8e-142 458.2 0.8 1.0 1 NCBI__GCF_000816635.1:WP_017751808.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000816635.1:WP_017751808.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.2 0.8 5.8e-142 5.8e-142 1 312 [. 17 329 .. 17 331 .. 0.99 Alignments for each domain: == domain 1 score: 458.2 bits; conditional E-value: 5.8e-142 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 lkgkk+a++G+GsqG+aqalnl+dsgl+vi+gl+k+++swkkAe+ Gfkv +v+ea+k+a+l+++LlpDe qk NCBI__GCF_000816635.1:WP_017751808.1 17 LKGKKIAVLGFGSQGHAQALNLKDSGLDVIIGLYKGSKSWKKAEDYGFKVYEVAEAVKQAQLVAMLLPDEKQK 89 79*********************************************************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + ye++++++l++g+allfsHGfni+f+qiv+ k++dv+++APKgpG+ vR++y eg Gvp l+Av+qd+tg+ NCBI__GCF_000816635.1:WP_017751808.1 90 QIYEESVRDNLEDGDALLFSHGFNIHFNQIVPAKNIDVLMIAPKGPGHIVRKQYTEGGGVPCLYAVYQDYTGK 162 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 +k++Alay k++Gg+r gv++ttFk E+e+DLfGEqavLcGg+ li+a+fdtLveaGy+pe A+fe+ he+k NCBI__GCF_000816635.1:WP_017751808.1 163 GKDYALAYGKGVGGTRGGVMNTTFKIETETDLFGEQAVLCGGICSLIQAGFDTLVEAGYAPENAFFECFHEMK 235 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 +ivdl++e+G+++mr+++s+tA++g+++ + + ++++++kem+k+lkeiq+G+fak+w+le++ g+p++e+ r NCBI__GCF_000816635.1:WP_017751808.1 236 MIVDLMYEGGMSKMRHSISDTAEYGDYKIGnRLINDSVRKEMKKVLKEIQDGTFAKDWLLENKIGRPTLEARR 308 ******************************9****************************************** PP TIGR00465 292 kkekeqeiekvGkelralvka 312 + e ++++ekvGk+lr ++++ NCBI__GCF_000816635.1:WP_017751808.1 309 RIEADTQLEKVGKRLRGMMSW 329 ******************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (337 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: 17.48 // [ok]
This GapMind analysis is from Jul 25 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