Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate YP_004142432.1 Mesci_3259 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000185905.1:YP_004142432.1 Length = 339 Score = 462 bits (1188), Expect = e-135 Identities = 227/339 (66%), Positives = 273/339 (80%), Gaps = 1/339 (0%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVN-VTVGLRKSGASWNKAANA 59 M+V+YD+DADL+LIKGK V IIGYGSQG AHALNLKDSG + +GL+ A+ K Sbjct: 1 MRVYYDRDADLNLIKGKKVAIIGYGSQGRAHALNLKDSGAKEIAIGLKAGSATAKKVEAD 60 Query: 60 GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119 GL+V VA+A K AD++M+ PDE AD+YKNE+ NI++GAA+AFAHG NVH+G + P+ Sbjct: 61 GLKVMSVADAAKWADLMMMATPDELQADIYKNEIAPNIRDGAAIAFAHGLNVHFGLIEPK 120 Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179 + +DV+MIAPK PGHTVR Y +GGGVP L+AV+Q+ SG A D+ALSYA GGGR+GII Sbjct: 121 STVDVVMIAPKGPGHTVRGEYQKGGGVPCLVAVNQDASGNALDLALSYACGVGGGRSGII 180 Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239 ETNFREE ETDLFGEQ VLCGG VELI+AGFETLVEAGYAPEMAYFECLHE+KLIVDLIY Sbjct: 181 ETNFREECETDLFGEQVVLCGGLVELIRAGFETLVEAGYAPEMAYFECLHEVKLIVDLIY 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299 EGGIANMNYSISN AE+GEYV+GPR++T ETK MK+ L DIQTG++ ++ E +AG Sbjct: 241 EGGIANMNYSISNTAEWGEYVSGPRIITAETKAEMKRVLKDIQTGKFTSEWMQEYRAGMS 300 Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 RR HQIEEVGAKLRAMMPWI+KNK+VD++KN Sbjct: 301 RFKGIRRNNDSHQIEEVGAKLRAMMPWISKNKLVDKAKN 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: 425 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: 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_004142432.1 Mesci_3259 (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.19713.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-130 420.9 0.8 1.6e-130 420.6 0.8 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004142432.1 Mesci_3259 ketol-acid reductoiso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004142432.1 Mesci_3259 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.6 0.8 1.6e-130 1.6e-130 1 312 [. 14 327 .. 14 329 .. 0.99 Alignments for each domain: == domain 1 score: 420.6 bits; conditional E-value: 1.6e-130 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlp 68 +kgkkvaiiGyGsqG+a+alnl+dsg ++ +gl+ ++a+ kk e dG+kv++v++a+k adl+m+ +p lcl|NCBI__GCF_000185905.1:YP_004142432.1 14 IKGKKVAIIGYGSQGRAHALNLKDSGAkEIAIGLKAGSATAKKVEADGLKVMSVADAAKWADLMMMATP 82 689***********************83699************************************** PP TIGR00465 69 DevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsli 137 De+q + y++ei+p++++g+a+ f+HG n++f i+++ vdvv++APKgpG++vR ey++g Gvp l+ lcl|NCBI__GCF_000185905.1:YP_004142432.1 83 DELQADIYKNEIAPNIRDGAAIAFAHGLNVHFGLIEPKSTVDVVMIAPKGPGHTVRGEYQKGGGVPCLV 151 ********************************************************************* PP TIGR00465 138 AveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyq 206 Av+qd++g+a + Al+yA ++Gg+r g++et F+eE+e+DLfGEq+vLcGgl +li+a+f+tLveaGy+ lcl|NCBI__GCF_000185905.1:YP_004142432.1 152 AVNQDASGNALDLALSYACGVGGGRSGIIETNFREECETDLFGEQVVLCGGLVELIRAGFETLVEAGYA 220 ********************************************************************* PP TIGR00465 207 pelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefak 274 pe+Ayfe++he+klivdl++e+G+++m ++sntA++g++ ++ +i+++e+k+em+ +lk+iq+G+f++ lcl|NCBI__GCF_000185905.1:YP_004142432.1 221 PEMAYFECLHEVKLIVDLIYEGGIANMNYSISNTAEWGEYVSGpRIITAETKAEMKRVLKDIQTGKFTS 289 ********************************************************************* PP TIGR00465 275 ewalekeagkpafeearkkekeqeiekvGkelralvka 312 ew+ e +ag ++f+ +r+ + ++ie+vG +lra++++ lcl|NCBI__GCF_000185905.1:YP_004142432.1 290 EWMQEYRAGMSRFKGIRRNNDSHQIEEVGAKLRAMMPW 327 ************************************98 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.85 // [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