Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_010961502.1 MCA_RS11125 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000008325.1:WP_010961502.1 Length = 338 Score = 498 bits (1282), Expect = e-146 Identities = 245/338 (72%), Positives = 283/338 (83%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 M+++YDKDADLS+I+GK V IIGYGSQGHAHA NLKDSGV V VGLR AS KA NAG Sbjct: 1 MQIYYDKDADLSIIQGKKVAIIGYGSQGHAHANNLKDSGVQVVVGLRPGSASAKKAENAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L V V +AVK ADV+MIL PDE A +Y ++ NIK+GAALAFAHGFN+H+ + PRA Sbjct: 61 LAVASVEDAVKQADVIMILAPDEHQARLYNEQIAPNIKQGAALAFAHGFNIHFEQITPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDVIMIAPK PGH VR+TYTQGGGVP LIAV+QN SG A+++ALSYA+ANGGGRAGIIE Sbjct: 121 DLDVIMIAPKGPGHLVRSTYTQGGGVPSLIAVYQNASGRAKELALSYASANGGGRAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 T FREETETDLFGEQAVLCGG L++AGFETLVEAGYAPEMAYFECLHELKLIVDL+YE Sbjct: 181 TTFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELKLIVDLMYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANM YSISN AEYG+ GPR+VTE+TK+ MK+ L +IQTGE+A+ F+LEN+AGA T Sbjct: 241 GGIANMRYSISNTAEYGDLTRGPRIVTEQTKQEMKKILREIQTGEFAREFILENQAGAAT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 L ++RRL EH IE VGA+LR MMPWI N++VD SKN Sbjct: 301 LKAKRRLGREHLIESVGARLRDMMPWIKANRIVDTSKN 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: 449 Number of extensions: 10 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_010961502.1 MCA_RS11125 (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.3691261.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-144 465.2 1.2 5e-144 465.0 1.2 1.0 1 NCBI__GCF_000008325.1:WP_010961502.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000008325.1:WP_010961502.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 465.0 1.2 5e-144 5e-144 1 313 [. 14 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 465.0 bits; conditional E-value: 5e-144 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 ++gkkvaiiGyGsqG+a+a nl+dsg++v+vglr+++as kkAe+ G+ v +ve+a+k+ad+imiL pDe q NCBI__GCF_000008325.1:WP_010961502.1 14 IQGKKVAIIGYGSQGHAHANNLKDSGVQVVVGLRPGSASAKKAENAGLAVASVEDAVKQADVIMILAPDEHQA 86 689********************************************************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + y+++i+p++k+g+al f+HGfni+f+qi++++d+dv+++APKgpG+lvR++y +g GvpsliAv+q+++g NCBI__GCF_000008325.1:WP_010961502.1 87 RLYNEQIAPNIKQGAALAFAHGFNIHFEQITPRADLDVIMIAPKGPGHLVRSTYTQGGGVPSLIAVYQNASGR 159 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 ake Al+yA a Gg+rag++ettF+eE+e+DLfGEqavLcGg +al++a+f+tLveaGy+pe+Ayfe++helk NCBI__GCF_000008325.1:WP_010961502.1 160 AKELALSYASANGGGRAGIIETTFREETETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELK 232 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl++e+G+++mr ++sntA++g+l+++ +i++e++k+em+kil eiq+Gefa+e++le++ag+++++++r NCBI__GCF_000008325.1:WP_010961502.1 233 LIVDLMYEGGIANMRYSISNTAEYGDLTRGpRIVTEQTKQEMKKILREIQTGEFAREFILENQAGAATLKAKR 305 ************************************************************************* PP TIGR00465 292 kkekeqeiekvGkelralvkae 313 + +e+ ie+vG +lr+++++ NCBI__GCF_000008325.1:WP_010961502.1 306 RLGREHLIESVGARLRDMMPWI 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 12.81 // [ok]
This GapMind analysis is from Jul 25 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