Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_022947186.1 H035_RS0101185 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000421465.1:WP_022947186.1 Length = 338 Score = 499 bits (1285), Expect = e-146 Identities = 243/338 (71%), Positives = 283/338 (83%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 M+V+YDKDADLS+I+ + VTIIGYGSQGHAHA NLKDSGV+VTVGLR +SW KA AG Sbjct: 1 MQVYYDKDADLSIIRSRQVTIIGYGSQGHAHANNLKDSGVDVTVGLRPGSSSWGKAEKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L VK VAEAV+GADVVM+L PDE +Y+NE+ NIK+GAALAFAHGFN+H+ + PRA Sbjct: 61 LSVKPVAEAVQGADVVMVLAPDEHQPALYQNEIEPNIKQGAALAFAHGFNIHFQQIEPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDVIMIAPK PGH VR+TYTQ GGVP LIA+ ++ SG A+ IALSYA+ANGGGRAGIIE Sbjct: 121 DLDVIMIAPKGPGHLVRSTYTQNGGVPSLIAIDRDASGQAKSIALSYASANGGGRAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 T FREETETDLFGEQAVLCGG L++AGFETLVEAGYAPEMAYFECLHELKLIVDL+YE Sbjct: 181 TTFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANM YSISN AEYG+ GPRVV E +K M++ L +IQ+GE+A+ F+LEN+A PT Sbjct: 241 GGIANMRYSISNTAEYGDLTRGPRVVDESSKTEMRKILKEIQSGEFAREFILENQANCPT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 L ++RRL+ EH IEEVG +LR MMPWI NK+VDQ KN Sbjct: 301 LKAKRRLSREHAIEEVGGRLREMMPWIKANKLVDQEKN 338 Lambda K H 0.316 0.133 0.379 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: 454 Number of extensions: 11 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_022947186.1 H035_RS0101185 (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.24457.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-142 459.8 0.0 2.2e-142 459.6 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022947186.1 H035_RS0101185 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022947186.1 H035_RS0101185 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.6 0.0 2.2e-142 2.2e-142 2 313 .. 15 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 459.6 bits; conditional E-value: 2.2e-142 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 ++++v+iiGyGsqG+a+a nl+dsg++v+vglr++++sw kAe+ G+ v+ v+ea++ ad++m+L pDe lcl|NCBI__GCF_000421465.1:WP_022947186.1 15 RSRQVTIIGYGSQGHAHANNLKDSGVDVTVGLRPGSSSWGKAEKAGLSVKPVAEAVQGADVVMVLAPDE 83 6789***************************************************************** PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 q++ y++ei+p++k+g+al f+HGfni+f+qi++++d+dv+++APKgpG+lvR++y ++ GvpsliA+ lcl|NCBI__GCF_000421465.1:WP_022947186.1 84 HQPALYQNEIEPNIKQGAALAFAHGFNIHFQQIEPRADLDVIMIAPKGPGHLVRSTYTQNGGVPSLIAI 152 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 +d++g+ak iAl+yA a Gg+rag++ettF+eE+e+DLfGEqavLcGg +al++a+f+tLveaGy+pe lcl|NCBI__GCF_000421465.1:WP_022947186.1 153 DRDASGQAKSIALSYASANGGGRAGIIETTFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAPE 221 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 +Ayfe++helklivdl++e+G+++mr ++sntA++g+l+++ ++++e+ k+em+kilkeiq+Gefa+e+ lcl|NCBI__GCF_000421465.1:WP_022947186.1 222 MAYFECLHELKLIVDLMYEGGIANMRYSISNTAEYGDLTRGpRVVDESSKTEMRKILKEIQSGEFAREF 290 ********************************************************************* PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvkae 313 +le++a+ p+++++r+ +e+ ie+vG +lr+++++ lcl|NCBI__GCF_000421465.1:WP_022947186.1 291 ILENQANCPTLKAKRRLSREHAIEEVGGRLREMMPWI 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.94 // [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