Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_041099917.1 SUTH_RS13445 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000828635.1:WP_041099917.1 Length = 338 Score = 528 bits (1361), Expect = e-155 Identities = 257/338 (76%), Positives = 291/338 (86%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKV+YDKDADLSLIKG+ VTI+GYGSQGHAHA NLKDSGV VTVGLRK GASW+KA AG Sbjct: 1 MKVYYDKDADLSLIKGRKVTIVGYGSQGHAHAQNLKDSGVKVTVGLRKGGASWDKAKKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L+V+EVA+AVK ADVVM+LLPDE I VY EV N+K+GAALAFAHGFNVHY V+PR Sbjct: 61 LKVEEVAKAVKDADVVMMLLPDETIPSVYYGEVESNMKKGAALAFAHGFNVHYNQVVPRT 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 D+DVIM+APK PGHTVR+ Y +GGGVP LIA+HQ+KSG A+DIALSYA ANGG + G+IE Sbjct: 121 DVDVIMVAPKGPGHTVRSEYLRGGGVPSLIAIHQDKSGKAKDIALSYAAANGGTKGGVIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGG VELIKAG+ETL EAGYAPEMAYFECLHE+KLIVDLI+E Sbjct: 181 TNFREETETDLFGEQAVLCGGLVELIKAGYETLTEAGYAPEMAYFECLHEVKLIVDLIFE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGP+V+ E + AMK L IQ GEYAK F+LE + P Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPKVIGAEARAAMKDALKAIQEGEYAKKFILEGRTNYPE 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 + +RRRLTA H IE+VG +LRAMMPWI KNK+VDQ+KN Sbjct: 301 MTARRRLTAAHPIEQVGEQLRAMMPWIKKNKLVDQTKN 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: 517 Number of extensions: 18 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_041099917.1 SUTH_RS13445 (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.14820.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-135 436.3 2.9 3.1e-135 436.1 2.9 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041099917.1 SUTH_RS13445 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041099917.1 SUTH_RS13445 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 436.1 2.9 3.1e-135 3.1e-135 1 313 [. 14 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 436.1 bits; conditional E-value: 3.1e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 +kg+kv+i+GyGsqG+a+a nl+dsg++v+vglrk++asw+kA++ G+kv +v+ a+k+ad++m+LlpD lcl|NCBI__GCF_000828635.1:WP_041099917.1 14 IKGRKVTIVGYGSQGHAHAQNLKDSGVKVTVGLRKGGASWDKAKKAGLKVEEVAKAVKDADVVMMLLPD 82 6899***************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 e+ ++vy e++ ++k+g+al f+HGfn++++q+v++ dvdv++vAPKgpG++vR+ey +g GvpsliA lcl|NCBI__GCF_000828635.1:WP_041099917.1 83 ETIPSVYYGEVESNMKKGAALAFAHGFNVHYNQVVPRTDVDVIMVAPKGPGHTVRSEYLRGGGVPSLIA 151 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 ++qd +g+ak+iAl+yA+a Gg++ gv+et F+eE+e+DLfGEqavLcGgl +lika+++tL+eaGy+p lcl|NCBI__GCF_000828635.1:WP_041099917.1 152 IHQDKSGKAKDIALSYAAANGGTKGGVIETNFREETETDLFGEQAVLCGGLVELIKAGYETLTEAGYAP 220 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+klivdl+ e+G+++m ++sn A++g++ ++ +++ +e +++m++ lk iq+Ge+ak lcl|NCBI__GCF_000828635.1:WP_041099917.1 221 EMAYFECLHEVKLIVDLIFEGGIANMNYSISNNAEYGEYVTGpKVIGAEARAAMKDALKAIQEGEYAKK 289 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvkae 313 ++le ++++p++++ r+ + ie+vG++lra++++ lcl|NCBI__GCF_000828635.1:WP_041099917.1 290 FILEGRTNYPEMTARRRLTAAHPIEQVGEQLRAMMPWI 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.26 // [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