Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_057509297.1 ABB28_RS14470 ketol-acid reductoisomerase
Query= BRENDA::A0A0K2AZ61 (332 letters) >NCBI__GCF_001431535.1:WP_057509297.1 Length = 324 Score = 395 bits (1015), Expect = e-115 Identities = 191/314 (60%), Positives = 237/314 (75%) Query: 19 KVAVIGYGSQGHAHALSLRDSGVDVRVGLHEGSKSKAKAEEQGLRVVSPSEAAAEADVIM 78 K+AV+GYGSQG AHAL+LR+SG DV VGL G ++ KA+ G V +P+EA +AD++ Sbjct: 10 KIAVVGYGSQGRAHALNLRESGFDVVVGLRPGGPTEVKAQADGFTVKAPAEAVKDADLVA 69 Query: 79 ILVPDPIQAQVYEEHIKDNLKDGDALFFGHGLNIRFGFIKPPAGVDVCMVAPKGPGHLVR 138 +L PD +Q ++Y+E + N+K G L F HGLN+ F I P +DV +VAPKGPG LVR Sbjct: 70 VLTPDMVQKKLYDEVLAPNMKQGAVLLFAHGLNVHFDMITPREDLDVVLVAPKGPGALVR 129 Query: 139 RQYEEGRGVPCIAAVEQDASGNAFALALSYAKGIGGTRAGVIKTTFTEETETDLFGEQAV 198 R+YE GRGVPCI AV QD SGNA AL+YA G+GG RA +I+TTF EETETDLFGEQAV Sbjct: 130 REYEIGRGVPCIWAVHQDKSGNAAKHALAYATGLGGARANLIQTTFKEETETDLFGEQAV 189 Query: 199 LCGGTAALVKAGFETLTEAGYQPEIAYFECLHELKLIVDLMYEGGLEKMRWSISETAEWG 258 LCGG +ALV+AGFETL EAGYQPEIAY+E LHELKLIVDL YEGG+ +M ISETA++G Sbjct: 190 LCGGASALVQAGFETLVEAGYQPEIAYYEVLHELKLIVDLFYEGGISRMLEFISETAQYG 249 Query: 259 DYVTGPRIITDATKAEMKKVLAEIQDGTFAKNWMDEYHGGLKKYNEYKQQDSEHLLETTG 318 DYV+GPR+I TK MK+VL +IQDGTF KNW+ EY GL YN++KQ D +H +E G Sbjct: 250 DYVSGPRVIDAGTKERMKEVLKDIQDGTFTKNWVAEYEAGLPNYNKFKQADLDHPIEKVG 309 Query: 319 KQLRKLMSWVDEEA 332 K+LR M W+ +A Sbjct: 310 KELRAKMVWLQGQA 323 Lambda K H 0.316 0.135 0.395 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: 376 Number of extensions: 7 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: 332 Length of database: 324 Length adjustment: 28 Effective length of query: 304 Effective length of database: 296 Effective search space: 89984 Effective search space used: 89984 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_057509297.1 ABB28_RS14470 (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.26197.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-129 417.8 0.0 1.4e-129 417.6 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057509297.1 ABB28_RS14470 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057509297.1 ABB28_RS14470 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.6 0.0 1.4e-129 1.4e-129 3 312 .. 8 318 .. 6 320 .. 0.99 Alignments for each domain: == domain 1 score: 417.6 bits; conditional E-value: 1.4e-129 TIGR00465 3 gkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDev 71 + k+a++GyGsqG+a+alnlr+sg +v+vglr+++ + kA+ dGf v+ +ea+k+adl+++L+pD+v lcl|NCBI__GCF_001431535.1:WP_057509297.1 8 QTKIAVVGYGSQGRAHALNLRESGFDVVVGLRPGGPTEVKAQADGFTVKAPAEAVKDADLVAVLTPDMV 76 679****************************************************************** PP TIGR00465 72 qkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAve 140 qk+ y + ++p++k+g++llf+HG n++f i++++d+dvvlvAPKgpGalvR+ey+ grGvp + Av+ lcl|NCBI__GCF_001431535.1:WP_057509297.1 77 QKKLYDEVLAPNMKQGAVLLFAHGLNVHFDMITPREDLDVVLVAPKGPGALVRREYEIGRGVPCIWAVH 145 ********************************************************************* PP TIGR00465 141 qdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpel 209 qd +g+a + AlayA ++Ggara +++ttFkeE+e+DLfGEqavLcGg +al++a+f+tLveaGyqpe+ lcl|NCBI__GCF_001431535.1:WP_057509297.1 146 QDKSGNAAKHALAYATGLGGARANLIQTTFKEETETDLFGEQAVLCGGASALVQAGFETLVEAGYQPEI 214 ********************************************************************* PP TIGR00465 210 AyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewa 277 Ay e++helklivdl +e+G++ m + +s+tA++g++ ++ +++++ +k++m+++lk+iq+G+f+k+w+ lcl|NCBI__GCF_001431535.1:WP_057509297.1 215 AYYEVLHELKLIVDLFYEGGISRMLEFISETAQYGDYVSGpRVIDAGTKERMKEVLKDIQDGTFTKNWV 283 ****************************************9**************************** PP TIGR00465 278 lekeagkpafeearkkekeqeiekvGkelralvka 312 e eag p++++ ++++ ++ iekvGkelra + + lcl|NCBI__GCF_001431535.1:WP_057509297.1 284 AEYEAGLPNYNKFKQADLDHPIEKVGKELRAKMVW 318 ******************************98866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (324 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: 00:00:00.01 # Mc/sec: 7.51 // [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