Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate YP_001327631.1 Smed_1962 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000017145.1:YP_001327631.1 Length = 339 Score = 462 bits (1190), Expect = e-135 Identities = 228/339 (67%), Positives = 271/339 (79%), Gaps = 1/339 (0%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59 M+V+YD+DADL+LIK K V IIGYGSQG AHALNLKDSG NV + L+ A+ KA Sbjct: 1 MRVYYDRDADLNLIKSKKVAIIGYGSQGRAHALNLKDSGAQNVAIALKSGSATAKKAEAD 60 Query: 60 GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119 G +V VAEA AD++M+ PDE AD+YK E+ NI++GAA+AFAHG NVH+G + P+ Sbjct: 61 GFKVMTVAEAAAWADLMMMATPDELQADIYKAEIAGNIRDGAAIAFAHGLNVHFGLIEPK 120 Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179 A +DV+MIAPK PGHTVR Y +GGGVP L+AVHQ+ SG A D+ALSYA GGGR+GII Sbjct: 121 ASVDVVMIAPKGPGHTVRGEYQKGGGVPCLVAVHQDASGNALDLALSYACGVGGGRSGII 180 Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239 ETNF+EE ETDLFGEQ VLCGG VELI+AGFETLVEAGYAPEMAYFECLHE+KLIVDLIY Sbjct: 181 ETNFKEECETDLFGEQVVLCGGLVELIRAGFETLVEAGYAPEMAYFECLHEVKLIVDLIY 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299 EGGIANMNYSISN AE+GEYVTGPR++TEETK MK+ L DIQTG++ ++ E ++GA Sbjct: 241 EGGIANMNYSISNTAEWGEYVTGPRIITEETKAEMKRVLKDIQTGKFTSEWMQEYRSGAA 300 Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 RR+ HQIEEVGAKLR MMPWI KNK+VD++KN Sbjct: 301 RFKGIRRVNDAHQIEEVGAKLRGMMPWIGKNKLVDKAKN 339 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: 431 Number of extensions: 15 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: 338 Length of database: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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 YP_001327631.1 Smed_1962 (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.18363.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-131 423.0 2.0 3.7e-131 422.7 2.0 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001327631.1 Smed_1962 ketol-acid reductoisom Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001327631.1 Smed_1962 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.7 2.0 3.7e-131 3.7e-131 1 312 [. 14 327 .. 14 329 .. 0.99 Alignments for each domain: == domain 1 score: 422.7 bits; conditional E-value: 3.7e-131 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlp 68 +k+kkvaiiGyGsqG+a+alnl+dsg nv ++l++++a+ kkAe dGfkv+tv+ea++ adl+m+ +p lcl|NCBI__GCF_000017145.1:YP_001327631.1 14 IKSKKVAIIGYGSQGRAHALNLKDSGAqNVAIALKSGSATAKKAEADGFKVMTVAEAAAWADLMMMATP 82 689**********************9658**************************************** PP TIGR00465 69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137 De+q + y+aei+ ++++g+a+ f+HG n++f i++++ vdvv++APKgpG++vR ey++g Gvp l+ lcl|NCBI__GCF_000017145.1:YP_001327631.1 83 DELQADIYKAEIAGNIRDGAAIAFAHGLNVHFGLIEPKASVDVVMIAPKGPGHTVRGEYQKGGGVPCLV 151 ********************************************************************* PP TIGR00465 138 AveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206 Av+qd++g+a + Al+yA ++Gg+r g++et FkeE+e+DLfGEq+vLcGgl +li+a+f+tLveaGy+ lcl|NCBI__GCF_000017145.1:YP_001327631.1 152 AVHQDASGNALDLALSYACGVGGGRSGIIETNFKEECETDLFGEQVVLCGGLVELIRAGFETLVEAGYA 220 ********************************************************************* PP TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274 pe+Ayfe++he+klivdl++e+G+++m ++sntA++g++ ++ +i++ee+k+em+ +lk+iq+G+f++ lcl|NCBI__GCF_000017145.1:YP_001327631.1 221 PEMAYFECLHEVKLIVDLIYEGGIANMNYSISNTAEWGEYVTGpRIITEETKAEMKRVLKDIQTGKFTS 289 *******************************************9************************* PP TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312 ew+ e + g+++f+ +r+ + ++ie+vG +lr ++++ lcl|NCBI__GCF_000017145.1:YP_001327631.1 290 EWMQEYRSGAARFKGIRRVNDAHQIEEVGAKLRGMMPW 327 ************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (339 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.20 // [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