Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate BPHYT_RS06555 BPHYT_RS06555 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS06555 Length = 338 Score = 617 bits (1590), Expect = 0.0 Identities = 308/338 (91%), Positives = 322/338 (95%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKVFYDKDADLSLIKGK VTIIGYGSQGHAHALNLK+SGVN+TVGLRK GASW+KA NAG Sbjct: 1 MKVFYDKDADLSLIKGKQVTIIGYGSQGHAHALNLKESGVNITVGLRKGGASWSKAENAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 LQVKEVAEAVKGADVVM+LLPDEQIA+VY EVH NIK+GAALAFAHGFNVHYG VIPRA Sbjct: 61 LQVKEVAEAVKGADVVMMLLPDEQIAEVYAKEVHANIKQGAALAFAHGFNVHYGQVIPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDVIMIAPKAPGHTVR TY+QGGGVPHLIAV Q+KSGAARDIALSYA ANGGGRAGIIE Sbjct: 121 DLDVIMIAPKAPGHTVRGTYSQGGGVPHLIAVAQDKSGAARDIALSYAAANGGGRAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGGTV+LIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE Sbjct: 181 TNFREETETDLFGEQAVLCGGTVDLIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGPR+VT ETKKAMK LTDIQTGEYAKSF++ENKAGAPT Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTAETKKAMKAVLTDIQTGEYAKSFIIENKAGAPT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 L SRRRLTAEHQIE VGAKLR+MMPWIA NK+VDQSKN Sbjct: 301 LQSRRRLTAEHQIETVGAKLRSMMPWIAANKLVDQSKN 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: 547 Number of extensions: 16 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 BPHYT_RS06555 BPHYT_RS06555 (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.8013.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-136 439.0 3.8 4.7e-136 438.8 3.8 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS06555 BPHYT_RS06555 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS06555 BPHYT_RS06555 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 438.8 3.8 4.7e-136 4.7e-136 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 438.8 bits; conditional E-value: 4.7e-136 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +kgk+v+iiGyGsqG+a+alnl++sg+n++vglrk++asw+kAe+ G++v++v+ea+k ad++m+LlpDe lcl|FitnessBrowser__BFirm:BPHYT_RS06555 14 IKGKQVTIIGYGSQGHAHALNLKESGVNITVGLRKGGASWSKAENAGLQVKEVAEAVKGADVVMMLLPDE 83 689******************************************************************* PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAve 140 + evy +e++ ++k+g+al f+HGfn+++ q+ +++d+dv+++APK+pG++vR +y +g Gvp+liAv lcl|FitnessBrowser__BFirm:BPHYT_RS06555 84 QIAEVYAKEVHANIKQGAALAFAHGFNVHYGQVIPRADLDVIMIAPKAPGHTVRGTYSQGGGVPHLIAVA 153 ********************************************************************** PP TIGR00465 141 qdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelA 210 qd +g a++iAl+yA+a Gg+rag++et F+eE+e+DLfGEqavLcGg +lika+f+tLveaGy+pe+A lcl|FitnessBrowser__BFirm:BPHYT_RS06555 154 QDKSGAARDIALSYAAANGGGRAGIIETNFREETETDLFGEQAVLCGGTVDLIKAGFETLVEAGYAPEMA 223 ********************************************************************** PP TIGR00465 211 yfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewale 279 yfe++helklivdl++e+G+++m ++sn A++g++ ++ +i+++e+kk+m+ +l +iq+Ge+ak +++e lcl|FitnessBrowser__BFirm:BPHYT_RS06555 224 YFECLHELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpRIVTAETKKAMKAVLTDIQTGEYAKSFIIE 293 ***************************************9****************************** PP TIGR00465 280 keagkpafeearkkekeqeiekvGkelralvka 312 ++ag+p++++ r+ e++ie vG +lr ++++ lcl|FitnessBrowser__BFirm:BPHYT_RS06555 294 NKAGAPTLQSRRRLTAEHQIETVGAKLRSMMPW 326 *******************************97 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: 00:00:00.01 # Mc/sec: 7.47 // [ok]
This GapMind analysis is from Apr 09 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