Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_027179442.1 G496_RS0111660 ketol-acid reductoisomerase
Query= BRENDA::A6UW80 (329 letters) >NCBI__GCF_000429985.1:WP_027179442.1 Length = 331 Score = 259 bits (661), Expect = 8e-74 Identities = 146/327 (44%), Positives = 204/327 (62%), Gaps = 7/327 (2%) Query: 2 KVYYEEDANYDAVKDKTIAVIGYGSQGMAQSCNMKDSGLNVIVGL--RPNGASWEKAKAD 59 K+Y +ED + ++ KTIAVIGYGSQG AQS NM++SG+N+IVG R +SW+KA+AD Sbjct: 8 KIYRDEDVDLSILEGKTIAVIGYGSQGRAQSMNMRESGMNIIVGAGDRTLHSSWDKAEAD 67 Query: 60 GHTVMSVEEAAEKADIIHILIPDEVQKDVYNNQIKQHLTEGKTLSFSHGYNVHFKYIDPI 119 G TV S+EEA EKADI+HIL+ D Q VY I HL G+TLSF+HG+ V + I P Sbjct: 68 GFTVYSIEEAVEKADIVHILLQDPAQPSVYYESIHGHLKAGQTLSFAHGFAVLYGTIKPP 127 Query: 120 KGVNVIMVAPKSPGAMVRRTYTEGFGVPGLVCVERDETGDALDIALGMAKAEGLTKAGVI 179 K V+V++ P PG + R+ + +G G+ G V ++D +G A + AL ++KA G T+ GV+ Sbjct: 128 KDVDVVLFVPNGPGPVTRQKFKDGSGIWGCVSADQDVSGHARETALAISKAVGSTRVGVV 187 Query: 180 KTTFKEETETDLFGEQAVLCGGVTELIKAGFDTLVEAGYSPEMAYFETCNELKLIVDLIY 239 TF+ ETE D + EQ VL GG L++ ++ +V+ GY AY + ++ I+D I Sbjct: 188 DMTFQHETEGDNYEEQ-VLYGGTIHLMRTMYNIMVKNGYPRSFAYAKAIRSIRSIIDDID 246 Query: 240 QKGLAG-MWNDVSNTAEYGGFVTRERVINEESRKAMREILKEIQNGKFARDWALENVSGI 298 G+ + + S T E+ + RVINEE AM EI KE ++G FAR+W E G+ Sbjct: 247 AVGIESYLTSRASRTCEFAVRHSGPRVINEE---AMEEIFKETESGTFARNWLQEFSLGM 303 Query: 299 PHLNAMRRLEDESLLETTGKKLRKMCG 325 P LN MRR ES +E TGK R+ G Sbjct: 304 PTLNRMRRTWAESDMEKTGKIWREKFG 330 Lambda K H 0.316 0.134 0.386 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: 292 Number of extensions: 14 Number of successful extensions: 4 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: 329 Length of database: 331 Length adjustment: 28 Effective length of query: 301 Effective length of database: 303 Effective search space: 91203 Effective search space used: 91203 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_027179442.1 G496_RS0111660 (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.1754.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-92 294.9 0.0 3.4e-92 294.7 0.0 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027179442.1 G496_RS0111660 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027179442.1 G496_RS0111660 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 294.7 0.0 3.4e-92 3.4e-92 1 309 [. 20 328 .. 20 331 .] 0.96 Alignments for each domain: == domain 1 score: 294.7 bits; conditional E-value: 3.4e-92 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkea..aswkkAeedGfkvltveeaikkadlimiLl 67 l+gk++a+iGyGsqG+aq++n+r+sg+n+ivg + +sw+kAe dGf v ++eea++kad+++iLl lcl|NCBI__GCF_000429985.1:WP_027179442.1 20 LEGKTIAVIGYGSQGRAQSMNMRESGMNIIVGAGDRTlhSSWDKAEADGFTVYSIEEAVEKADIVHILL 88 689****************************997777779***************************** PP TIGR00465 68 pDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsl 136 D +q++vy ++i+ lk+g++l+f+HGf + + +i++pkdvdvvl P gpG + R+++k g G+ + lcl|NCBI__GCF_000429985.1:WP_027179442.1 89 QDPAQPSVYYESIHGHLKAGQTLSFAHGFAVLYGTIKPPKDVDVVLFVPNGPGPVTRQKFKDGSGIWGC 157 ********************************************************************* PP TIGR00465 137 iAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGy 205 + qdv+g+a+e+Ala+ ka+G++r+gv++ tF++E+e D + Eq vL Gg l+++ ++ +v++Gy lcl|NCBI__GCF_000429985.1:WP_027179442.1 158 VSADQDVSGHARETALAISKAVGSTRVGVVDMTFQHETEGDNYEEQ-VLYGGTIHLMRTMYNIMVKNGY 225 *******************************************998.57788888999*********** PP TIGR00465 206 qpelAyfeivhelklivdllkekGle.lmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGef 272 + Ay + + +++i+d + G+e ++ ++ s t ++ +++ ++++e ++m++i+ke+++G+f lcl|NCBI__GCF_000429985.1:WP_027179442.1 226 PRSFAYAKAIRSIRSIIDDIDAVGIEsYLTSRASRTCEFAVRHSGpRVINE---EAMEEIFKETESGTF 291 *************************846899********999999788876...579************ PP TIGR00465 273 akewalekeagkpafeearkkekeqeiekvGkelral 309 a++w+ e++ g p+++++r++ e ++ek+Gk r+ lcl|NCBI__GCF_000429985.1:WP_027179442.1 292 ARNWLQEFSLGMPTLNRMRRTWAESDMEKTGKIWREK 328 ********************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (331 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: 10.33 // [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