Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate Ac3H11_527 Ketol-acid reductoisomerase (EC 1.1.1.86)
Query= metacyc::MONOMER-18814 (338 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_527 Length = 338 Score = 540 bits (1390), Expect = e-158 Identities = 263/338 (77%), Positives = 293/338 (86%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKVFYDKD DLSLIKGK V IIGYGSQGHAHA NL DSGV V VGLRK GASW+K AG Sbjct: 1 MKVFYDKDTDLSLIKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWDKVGKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L V EV +AVK ADVVMILLPDE IA VYKN V NIK+GA+LAFAHGFNVHY V+PRA Sbjct: 61 LNVLEVNDAVKAADVVMILLPDEDIAAVYKNNVEPNIKQGASLAFAHGFNVHYNQVVPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDV M+APKAPGHTVR TYTQGGGVPHL+AVHQ+KSG ARD+ALSYA ANGGG+AGIIE Sbjct: 121 DLDVWMVAPKAPGHTVRNTYTQGGGVPHLVAVHQDKSGKARDLALSYAAANGGGKAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNF+EETETDLFGEQAVLCGG VELIK G+ETLVEAGYAPEMAYFECLHELKLIVDLIYE Sbjct: 181 TNFKEETETDLFGEQAVLCGGAVELIKMGYETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGP V+ E+++ AM+ L IQ G+YAK F+ E + P+ Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPEVINEQSRAAMRNALKRIQNGDYAKMFIQEGRLNYPS 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 + +RRR TA+H IE+VG++LRAMMPWIAKNK+VDQ++N Sbjct: 301 MTARRRNTADHSIEKVGSQLRAMMPWIAKNKLVDQTRN 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: 484 Number of extensions: 13 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 Ac3H11_527 (Ketol-acid reductoisomerase (EC 1.1.1.86))
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.3594.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-135 435.7 1.8 4.8e-135 435.5 1.8 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 Ketol-acid reductoisomerase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 Ketol-acid reductoisomerase (EC 1.1.1.86) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.5 1.8 4.8e-135 4.8e-135 1 312 [. 14 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 435.5 bits; conditional E-value: 4.8e-135 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadli 63 +kgk+vaiiGyGsqG+a+a nl dsg++v+vglrk++asw+k + G++vl+v++a+k+ad++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 14 IKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWDKVGKAGLNVLEVNDAVKAADVV 76 689************************************************************ PP TIGR00465 64 miLlpDevqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvRee 126 miLlpDe +vy+++++p++k+g++l f+HGfn++++q+v+++d+dv +vAPK+pG++vR++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 77 MILLPDEDIAAVYKNNVEPNIKQGASLAFAHGFNVHYNQVVPRADLDVWMVAPKAPGHTVRNT 139 *************************************************************** PP TIGR00465 127 ykegrGvpsliAveqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGgl 189 y +g Gvp+l+Av+qd +g+a++ Al+yA+a Gg++ag++et FkeE+e+DLfGEqavLcGg lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 140 YTQGGGVPHLVAVHQDKSGKARDLALSYAAANGGGKAGIIETNFKEETETDLFGEQAVLCGGA 202 *************************************************************** PP TIGR00465 190 ealikaafdtLveaGyqpelAyfeivhelklivdllkekGlelmrdavsntAklgalelr.ei 251 +lik++++tLveaGy+pe+Ayfe++helklivdl++e+G+++m ++sn A++g++ ++ e+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 203 VELIKMGYETLVEAGYAPEMAYFECLHELKLIVDLIYEGGIANMNYSISNNAEYGEYVTGpEV 265 ************************************************************9** PP TIGR00465 252 lkeelkkemqkilkeiqnGefakewalekeagkpafeearkkekeqeiekvGkelralvka 312 ++e+ +++m++ lk iqnG++ak ++ e + ++p++++ r+ +++iekvG++lra++++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_527 266 INEQSRAAMRNALKRIQNGDYAKMFIQEGRLNYPSMTARRRNTADHSIEKVGSQLRAMMPW 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.24 // [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