Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_085636394.1 MGEO_RS09025 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_002115805.1:WP_085636394.1 Length = 340 Score = 456 bits (1174), Expect = e-133 Identities = 225/340 (66%), Positives = 266/340 (78%), Gaps = 2/340 (0%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59 M+V+YD+D D++LIK V I+GYGSQGHAHALNL+DSG NV V LR+ AS KA Sbjct: 1 MRVYYDRDCDINLIKDMKVAILGYGSQGHAHALNLRDSGAKNVVVALREGSASAKKAEGE 60 Query: 60 GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119 GLQV +AEA D++M +PDE A+ YK VHDN+KEGAA+AFAHG NVH+G + P+ Sbjct: 61 GLQVMGIAEAAAWCDLIMFTMPDELQAETYKKYVHDNLKEGAAIAFAHGLNVHFGLIEPK 120 Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179 +DVIM+APK PGHTVR YT+GGGVP L+AVH + SG A +I LSY +A GGGR+GII Sbjct: 121 PGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVHNDASGRALEIGLSYCSAIGGGRSGII 180 Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239 ETNFREE ETDLFGEQAVLCGG VELI+ GFETLVEAGY PEMAYFECLHE+KLIVDLIY Sbjct: 181 ETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYEPEMAYFECLHEVKLIVDLIY 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVT-EETKKAMKQCLTDIQTGEYAKSFLLENKAGA 298 EGGIANMNYSISN AEYGEYV+GPR++ +ETK MK L+DIQTG++ + F+ EN G Sbjct: 241 EGGIANMNYSISNTAEYGEYVSGPRILPYDETKARMKAVLSDIQTGKFVRDFMQENAVGQ 300 Query: 299 PTLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 P RR+ EHQIE+VG LR MMPWI+ KMVD+SKN Sbjct: 301 PFFKGTRRINDEHQIEKVGETLRGMMPWISAGKMVDKSKN 340 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: 402 Number of extensions: 14 Number of successful extensions: 3 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: 340 Length adjustment: 28 Effective length of query: 310 Effective length of database: 312 Effective search space: 96720 Effective search space used: 96720 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_085636394.1 MGEO_RS09025 (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.857855.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-127 411.2 0.2 1.3e-127 411.0 0.2 1.0 1 NCBI__GCF_002115805.1:WP_085636394.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085636394.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 411.0 0.2 1.3e-127 1.3e-127 1 312 [. 14 328 .. 14 330 .. 0.98 Alignments for each domain: == domain 1 score: 411.0 bits; conditional E-value: 1.3e-127 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevq 72 +k+ kvai+GyGsqG+a+alnlrdsg nv+v+lr+++as kkAe +G++v+ ++ea++ dlim +pDe+q NCBI__GCF_002115805.1:WP_085636394.1 14 IKDMKVAILGYGSQGHAHALNLRDSGAkNVVVALREGSASAKKAEGEGLQVMGIAEAAAWCDLIMFTMPDELQ 86 6899**********************758******************************************** PP TIGR00465 73 kevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtg 145 e+y++ ++++lkeg+a+ f+HG n++f i+++ +vdv+++APKgpG++vR ey +g Gvp l+Av++d++g NCBI__GCF_002115805.1:WP_085636394.1 87 AETYKKYVHDNLKEGAAIAFAHGLNVHFGLIEPKPGVDVIMMAPKGPGHTVRGEYTKGGGVPCLVAVHNDASG 159 ************************************************************************* PP TIGR00465 146 eakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhel 218 a ei l+y aiGg+r g++et F+eE+e+DLfGEqavLcGgl +li+++f+tLveaGy+pe+Ayfe++he+ NCBI__GCF_002115805.1:WP_085636394.1 160 RALEIGLSYCSAIGGGRSGIIETNFREECETDLFGEQAVLCGGLVELIRMGFETLVEAGYEPEMAYFECLHEV 232 ************************************************************************* PP TIGR00465 219 klivdllkekGlelmrdavsntAklgalelr.eil.keelkkemqkilkeiqnGefakewalekeagkpafee 289 klivdl++e+G+++m ++sntA++g++ ++ +il +e+k++m+ +l +iq+G+f ++++ e+++g+p f+ NCBI__GCF_002115805.1:WP_085636394.1 233 KLIVDLIYEGGIANMNYSISNTAEYGEYVSGpRILpYDETKARMKAVLSDIQTGKFVRDFMQENAVGQPFFKG 305 *******************************88874589********************************** PP TIGR00465 290 arkkekeqeiekvGkelralvka 312 +r+ + e++iekvG++lr ++++ NCBI__GCF_002115805.1:WP_085636394.1 306 TRRINDEHQIEKVGETLRGMMPW 328 *********************97 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.87 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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