Align Ketol-acid reductoisomerase (NAD(P)(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.383 (characterized)
to candidate WP_028951196.1 Q385_RS0108180 ketol-acid reductoisomerase
Query= SwissProt::B4U6I9 (333 letters) >NCBI__GCF_000619805.1:WP_028951196.1 Length = 332 Score = 517 bits (1331), Expect = e-151 Identities = 252/332 (75%), Positives = 288/332 (86%) Query: 1 MAKIYYDEDASLGILAMKTVAIVGYGSQGHAHALNLRDSGIRVIVALDDKSPHRKTAMED 60 MA IYYDEDASL L KTVAI+GYGSQGHAHALNLRDSGI+VI+ L S + A + Sbjct: 1 MANIYYDEDASLDYLKDKTVAIIGYGSQGHAHALNLRDSGIKVIIGLLAGSRSIEKAKAE 60 Query: 61 GFSVYTTSRATQEADVIMILTPDTVQPAVYKECIEPNLTPGKAIAFAHGFNIHFGQIVPP 120 GF VY+ A ++ADVIMILTPDTVQP ++ I PNL G A+AFAHGFNIHFGQIVPP Sbjct: 61 GFEVYSPDEAAKKADVIMILTPDTVQPQLFYSAILPNLDEGNALAFAHGFNIHFGQIVPP 120 Query: 121 KDIDVFMVAPKGPGHLVRWMYEEGKGVPALISIHQDATGSCRDIALAYAKGIGATRAGVI 180 +DVF+VAPKGPGHLVRWMYEEGKGVP L +++QD TG+ R+IA+AYA GIG TRAG+I Sbjct: 121 AYVDVFLVAPKGPGHLVRWMYEEGKGVPGLFAVYQDFTGNAREIAMAYAIGIGCTRAGLI 180 Query: 181 ETTFREETETDLFGEQAVLCGGATALIKAGFETLVEAGYQPEMAYFECLHELKLIVDLIY 240 ETTF+EETETDLFGEQAVLCGGATALIKAGFETL+EAGYQPE+AYFECLHELKLIVDLIY Sbjct: 181 ETTFKEETETDLFGEQAVLCGGATALIKAGFETLIEAGYQPEVAYFECLHELKLIVDLIY 240 Query: 241 QHGIAGMRYSISDTAKYGDVTRGDRVYEAVKPLMKQMLKEIQDGEFAREWILENQANRPV 300 Q+GI+GMRYSISDTA+YGDVTRG RVYEAVKP+ K++L+EIQ+GEFA+EWILEN ANRP Sbjct: 241 QYGISGMRYSISDTARYGDVTRGKRVYEAVKPIYKKILEEIQEGEFAKEWILENVANRPH 300 Query: 301 YNALLNKDKEHLVEKVGKELRQMMPWLSGKEL 332 +NAL+ KD+EH VEKVGKELR+MMPWL GK L Sbjct: 301 FNALVKKDEEHPVEKVGKELRKMMPWLGGKSL 332 Lambda K H 0.319 0.136 0.402 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: 475 Number of extensions: 11 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: 333 Length of database: 332 Length adjustment: 28 Effective length of query: 305 Effective length of database: 304 Effective search space: 92720 Effective search space used: 92720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_028951196.1 Q385_RS0108180 (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.24033.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-145 468.9 0.0 3.7e-145 468.7 0.0 1.0 1 lcl|NCBI__GCF_000619805.1:WP_028951196.1 Q385_RS0108180 ketol-acid reduct Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000619805.1:WP_028951196.1 Q385_RS0108180 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.7 0.0 3.7e-145 3.7e-145 1 312 [. 15 326 .. 15 328 .. 1.00 Alignments for each domain: == domain 1 score: 468.7 bits; conditional E-value: 3.7e-145 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k+vaiiGyGsqG+a+alnlrdsg++vi+gl ++ s++kA+ +Gf+v + +ea+kkad+imiL+pD lcl|NCBI__GCF_000619805.1:WP_028951196.1 15 LKDKTVAIIGYGSQGHAHALNLRDSGIKVIIGLLAGSRSIEKAKAEGFEVYSPDEAAKKADVIMILTPD 83 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq++ + i p+l eg+al f+HGfni+f qiv+p++vdv+lvAPKgpG+lvR +y+eg+Gvp+l+A lcl|NCBI__GCF_000619805.1:WP_028951196.1 84 TVQPQLFYSAILPNLDEGNALAFAHGFNIHFGQIVPPAYVDVFLVAPKGPGHLVRWMYEEGKGVPGLFA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd tg+a+eiA+ayA +iG +rag++ettFkeE+e+DLfGEqavLcGg +alika+f+tL+eaGyqp lcl|NCBI__GCF_000619805.1:WP_028951196.1 153 VYQDFTGNAREIAMAYAIGIGCTRAGLIETTFKEETETDLFGEQAVLCGGATALIKAGFETLIEAGYQP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelreilkeelkkemqkilkeiqnGefakew 276 e+Ayfe++helklivdl++++G+++mr ++s+tA++g++++++ + e++k+ ++kil+eiq+Gefakew lcl|NCBI__GCF_000619805.1:WP_028951196.1 222 EVAYFECLHELKLIVDLIYQYGISGMRYSISDTARYGDVTRGKRVYEAVKPIYKKILEEIQEGEFAKEW 290 ********************************************************************* PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvka 312 +le+ a++p+f++ kk++e+ +ekvGkelr+++++ lcl|NCBI__GCF_000619805.1:WP_028951196.1 291 ILENVANRPHFNALVKKDEEHPVEKVGKELRKMMPW 326 **********************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (332 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: 11.18 // [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