Align Ketol-acid reductoisomerase (NADP(+)); KARI; Acetohydroxy-acid isomeroreductase; AHIR; Alpha-keto-beta-hydroxylacyl reductoisomerase; Ketol-acid reductoisomerase type 1; Ketol-acid reductoisomerase type I; EC 1.1.1.86 (characterized)
to candidate WP_085219223.1 B9N75_RS13285 ketol-acid reductoisomerase
Query= SwissProt::Q9HVA2 (338 letters) >NCBI__GCF_900177405.1:WP_085219223.1 Length = 327 Score = 328 bits (841), Expect = 1e-94 Identities = 166/322 (51%), Positives = 223/322 (69%), Gaps = 1/322 (0%) Query: 1 MRVFYDKDCDLSIIQGKKVAIIGYGSQGHAHACNLKDSGV-DVTVGLRSGSATVAKAEAH 59 MR +D D DL++I+ +KVAI GYG+QG A NL DSGV ++ V LR GSA+ A+AEA Sbjct: 1 MRALFDADADLALIRDRKVAIFGYGNQGRPQALNLSDSGVGELVVALREGSASRARAEAD 60 Query: 60 GLKVADVKTAVAAADVVMILTPDEFQGRLYKEEIEPNLKKGATLAFAHGFSIHYNQVVPR 119 L V ++ A A ADV ++L PDE Q +Y+ + P+LK+GA L FAHG +I + +VPR Sbjct: 61 RLGVTNLADAAAWADVAVMLFPDEDQAEVYERHLAPHLKQGAALVFAHGLAIRFGLIVPR 120 Query: 120 ADLDVIMIAPKAPGHTVRSEFVKGGGIPDLIAIYQDASGNAKNVALSYACGVGGGRTGII 179 ADLDV+++APK PG +RSE+ G G+ L A+ QDASG A+ +ALSYA +GGGR G+I Sbjct: 121 ADLDVMLVAPKGPGTALRSEYAAGRGLVTLFAVAQDASGGAEALALSYAAALGGGRAGMI 180 Query: 180 ETTFKDETETDLFGEQAVLCGGCVELVKAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 239 ET+F +E E DLF E AV+ G EL++AGF+TLVEAG++PE+AYFECL E+KLI DL+ Sbjct: 181 ETSFAEECEADLFNEAAVIWGAIPELIQAGFDTLVEAGFSPEVAYFECLTEVKLIADLIT 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPEVINAESRAAMRNALKRIQDGEYAKMFITEGAANYP 299 E GIA M +ISN AE+G G ++ AE+R MR L+ +++G A+ I + A YP Sbjct: 241 ERGIAGMREAISNTAEFGALEGGRRIVTAETRTEMRRILRDVREGHLAQRLIADAKAGYP 300 Query: 300 SMTAYRRNNAAHPIEQIGEKLR 321 + A R AAHPIE G +LR Sbjct: 301 RLKASRAEAAAHPIEAAGARLR 322 Lambda K H 0.317 0.134 0.389 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: 289 Number of extensions: 11 Number of successful extensions: 2 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: 327 Length adjustment: 28 Effective length of query: 310 Effective length of database: 299 Effective search space: 92690 Effective search space used: 92690 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_085219223.1 B9N75_RS13285 (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.3728286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-109 349.3 0.0 9.6e-109 349.1 0.0 1.0 1 NCBI__GCF_900177405.1:WP_085219223.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177405.1:WP_085219223.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.1 0.0 9.6e-109 9.6e-109 2 310 .. 15 325 .. 14 327 .] 0.99 Alignments for each domain: == domain 1 score: 349.1 bits; conditional E-value: 9.6e-109 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 +++kvai GyG qG+ qalnl dsg+ +++v+lr+++as ++Ae d + v+++++a++ ad+ ++L pDe q NCBI__GCF_900177405.1:WP_085219223.1 15 RDRKVAIFGYGNQGRPQALNLSDSGVgELVVALREGSASRARAEADRLGVTNLADAAAWADVAVMLFPDEDQA 87 689***********************7799******************************************* PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 evye++++p lk+g+al+f+HG i f iv+++d+dv+lvAPKgpG+++R+ey grG+ +l+Av qd++g NCBI__GCF_900177405.1:WP_085219223.1 88 EVYERHLAPHLKQGAALVFAHGLAIRFGLIVPRADLDVMLVAPKGPGTALRSEYAAGRGLVTLFAVAQDASGG 160 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a + Al+yA+a+Gg+rag++et+F eE+e+DLf E av+ G + +li+a+fdtLveaG +pe+Ayfe++ e+k NCBI__GCF_900177405.1:WP_085219223.1 161 AEALALSYAAALGGGRAGMIETSFAEECEADLFNEAAVIWGAIPELIQAGFDTLVEAGFSPEVAYFECLTEVK 233 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 li+dl++e+G+++mr+a+sntA++gale + +i+++e+++em+ il ++++G+ a+ + + +ag+p++++ r NCBI__GCF_900177405.1:WP_085219223.1 234 LIADLITERGIAGMREAISNTAEFGALEGGrRIVTAETRTEMRRILRDVREGHLAQRLIADAKAGYPRLKASR 306 ****************************9999***************************************** PP TIGR00465 292 kkekeqeiekvGkelralv 310 + ie G +lr+l NCBI__GCF_900177405.1:WP_085219223.1 307 AEAAAHPIEAAGARLRNLA 325 ****************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (327 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: 25.79 // [ok]
This GapMind analysis is from Jul 26 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