Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_015798946.1 AFER_RS08010 ketol-acid reductoisomerase
Query= BRENDA::D3PT81 (339 letters) >NCBI__GCF_000023265.1:WP_015798946.1 Length = 340 Score = 400 bits (1028), Expect = e-116 Identities = 203/336 (60%), Positives = 254/336 (75%), Gaps = 1/336 (0%) Query: 2 KIYYDQDADIGFIKDKTVAILGFGSQGHAHALNLRDSGIKVVVGLRPGSRNEEKARKAGL 61 ++YYD+DA+ I D+ VAI+G+GSQGHAHALNL DSG+ V VGLR GS + +KAR +GL Sbjct: 3 QMYYDKDANPALITDRRVAIIGYGSQGHAHALNLLDSGVPVRVGLREGSASADKARASGL 62 Query: 62 EVLPVGEAVRRADVVMILLPDETQGAVYKAEVEPNLKEGAALAFAHGFNIHFGQIKPRRD 121 EV V +AVR AD+VM+L+PD T +++ +V PNL+ G+A+AFAHGFNI FG I+P Sbjct: 63 EVSSVADAVRWADLVMLLVPDTTAPTLWREQVAPNLQPGSAVAFAHGFNIRFGLIEPDPS 122 Query: 122 LDVWMVAPKGPGHLVRSEYEKGSGVPSLVAVYQDASGSAFPTALAYAKANGGTRAGTIAT 181 +DV M+APKGPGHL+R YE+G G+PSL+AV DASG A TALAYA A G TRAG + T Sbjct: 123 VDVIMIAPKGPGHLLRRTYEEGGGIPSLIAVANDASGRAHDTALAYAWAIGSTRAGVLDT 182 Query: 182 TFKDETETDLFGEQTVLCGGLTQLIAAGFETLVEAGYPPEMAYFECLHEVKLIVDLIYES 241 TF +ETETDLFGEQ VLCGGL+QL+ AGF+TLVEAGY PE AYFECLHE+KLIVDL+YE Sbjct: 183 TFAEETETDLFGEQVVLCGGLSQLVRAGFDTLVEAGYQPESAYFECLHELKLIVDLLYEH 242 Query: 242 GFAGMRYSISNTAEYGDYTRGPMVINREETKARMREVLRQIQQGEFAREWMLENVVGQPT 301 G +GM +S+S TAEYG TRGP ++N +ET+A MR VL +I+ G FA E + E G+P Sbjct: 243 GLSGMWFSVSETAEYGGLTRGPRIVN-DETRAEMRRVLDEIRSGAFASELVDEIAAGRPR 301 Query: 302 LNANRNYWKDHPIEQVGPKLRAMMPFLKSRFTKEEV 337 A R ++ IEQVG LRAMMPFL S ++V Sbjct: 302 FEALRREAREAQIEQVGRDLRAMMPFLASATKLDQV 337 Lambda K H 0.318 0.136 0.398 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: 390 Number of extensions: 16 Number of successful extensions: 2 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: 339 Length of database: 340 Length adjustment: 28 Effective length of query: 311 Effective length of database: 312 Effective search space: 97032 Effective search space used: 97032 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_015798946.1 AFER_RS08010 (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.18724.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-133 428.1 0.0 9.7e-133 427.9 0.0 1.0 1 lcl|NCBI__GCF_000023265.1:WP_015798946.1 AFER_RS08010 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023265.1:WP_015798946.1 AFER_RS08010 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.9 0.0 9.7e-133 9.7e-133 2 312 .. 16 327 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 427.9 bits; conditional E-value: 9.7e-133 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +++vaiiGyGsqG+a+alnl dsg+ v+vglr+++as +kA+ G++v +v++a++ adl+m L+pD+ lcl|NCBI__GCF_000023265.1:WP_015798946.1 16 TDRRVAIIGYGSQGHAHALNLLDSGVPVRVGLREGSASADKARASGLEVSSVADAVRWADLVMLLVPDT 84 6899***************************************************************** PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 + ++ ++++++p+l+ g+a+ f+HGfni f i++ vdv+++APKgpG+l+R++y+eg G+psliAv lcl|NCBI__GCF_000023265.1:WP_015798946.1 85 TAPTLWREQVAPNLQPGSAVAFAHGFNIRFGLIEPDPSVDVIMIAPKGPGHLLRRTYEEGGGIPSLIAV 153 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 +d++g a+++AlayA aiG++ragvl+ttF eE+e+DLfGEq+vLcGgl++l++a+fdtLveaGyqpe lcl|NCBI__GCF_000023265.1:WP_015798946.1 154 ANDASGRAHDTALAYAWAIGSTRAGVLDTTFAEETETDLFGEQVVLCGGLSQLVRAGFDTLVEAGYQPE 222 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 Ayfe++helklivdll+e+Gl++m+ +vs+tA++g+l+++ +i+++e+++em+ +l+ei++G fa+e lcl|NCBI__GCF_000023265.1:WP_015798946.1 223 SAYFECLHELKLIVDLLYEHGLSGMWFSVSETAEYGGLTRGpRIVNDETRAEMRRVLDEIRSGAFASEL 291 ********************************************************************* PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvka 312 + e +ag+p+fe+ r+ +e +ie+vG++lra++++ lcl|NCBI__GCF_000023265.1:WP_015798946.1 292 VDEIAAGRPRFEALRREAREAQIEQVGRDLRAMMPF 327 *********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (340 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: 00:00:00.00 # Mc/sec: 10.84 // [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