Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_011606916.1 FRAAL_RS25480 ketol-acid reductoisomerase
Query= BRENDA::A0A0K2AZ61 (332 letters) >NCBI__GCF_000058485.1:WP_011606916.1 Length = 330 Score = 461 bits (1186), Expect = e-134 Identities = 219/328 (66%), Positives = 270/328 (82%) Query: 1 MAELFYDADADLSIIQGRKVAVIGYGSQGHAHALSLRDSGVDVRVGLHEGSKSKAKAEEQ 60 M E++YD DA L ++ GRKVAVIGYGSQGHAHAL+LRDSGVDVRVGL S+S+AKA E+ Sbjct: 1 MVEIYYDDDASLDVLAGRKVAVIGYGSQGHAHALNLRDSGVDVRVGLPADSRSRAKAAEE 60 Query: 61 GLRVVSPSEAAAEADVIMILVPDPIQAQVYEEHIKDNLKDGDALFFGHGLNIRFGFIKPP 120 GLRV++P+EA+AEAD+IM+L PD ++Y + I +L +G AL FGHG NIR+G I+PP Sbjct: 61 GLRVLTPAEASAEADIIMLLTPDTTHRKIYADSIAPHLSEGKALAFGHGFNIRYGLIEPP 120 Query: 121 AGVDVCMVAPKGPGHLVRRQYEEGRGVPCIAAVEQDASGNAFALALSYAKGIGGTRAGVI 180 AGVDV MVAPKGPGHLVRR +EEG+GVP + AVE DASGNA A+AL+YAKGIGGTRAG + Sbjct: 121 AGVDVFMVAPKGPGHLVRRVFEEGKGVPVLVAVENDASGNALAVALAYAKGIGGTRAGAL 180 Query: 181 KTTFTEETETDLFGEQAVLCGGTAALVKAGFETLTEAGYQPEIAYFECLHELKLIVDLMY 240 +TTFTEETETDLFGEQAVLCGG +ALV+AGFETL EAGY PE+AYFECLHELKLIVDLMY Sbjct: 181 RTTFTEETETDLFGEQAVLCGGASALVQAGFETLVEAGYTPEVAYFECLHELKLIVDLMY 240 Query: 241 EGGLEKMRWSISETAEWGDYVTGPRIITDATKAEMKKVLAEIQDGTFAKNWMDEYHGGLK 300 EGG+ +MR+SIS+TAE+GD GPR++T A KAEM+K+L EI+DGTFA+ W+ E G Sbjct: 241 EGGISQMRYSISDTAEYGDVTRGPRVVTPAVKAEMRKILDEIRDGTFAREWVAEDDNGRP 300 Query: 301 KYNEYKQQDSEHLLETTGKQLRKLMSWV 328 + + ++ +H +E G +LR LMSW+ Sbjct: 301 NFTKLVEEGKQHPIEQVGAKLRPLMSWI 328 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: 402 Number of extensions: 12 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: 332 Length of database: 330 Length adjustment: 28 Effective length of query: 304 Effective length of database: 302 Effective search space: 91808 Effective search space used: 91808 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_011606916.1 FRAAL_RS25480 (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.18733.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-136 438.1 0.0 8.8e-136 437.9 0.0 1.0 1 lcl|NCBI__GCF_000058485.1:WP_011606916.1 FRAAL_RS25480 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_011606916.1 FRAAL_RS25480 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 437.9 0.0 8.8e-136 8.8e-136 1 312 [. 15 327 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 437.9 bits; conditional E-value: 8.8e-136 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 l+g+kva+iGyGsqG+a+alnlrdsg++v+vgl ++ s +kA e+G++vlt +ea ++ad+im L+pD lcl|NCBI__GCF_000058485.1:WP_011606916.1 15 LAGRKVAVIGYGSQGHAHALNLRDSGVDVRVGLPADSRSRAKAAEEGLRVLTPAEASAEADIIMLLTPD 83 6899***************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +++++ y +i+p l egkal f HGfni + i++p++vdv++vAPKgpG+lvR+ ++eg+Gvp l+A lcl|NCBI__GCF_000058485.1:WP_011606916.1 84 TTHRKIYADSIAPHLSEGKALAFGHGFNIRYGLIEPPAGVDVFMVAPKGPGHLVRRVFEEGKGVPVLVA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 ve+d++g+a ++AlayAk+iGg+rag l ttF eE+e+DLfGEqavLcGg +al++a+f+tLveaGy p lcl|NCBI__GCF_000058485.1:WP_011606916.1 153 VENDASGNALAVALAYAKGIGGTRAGALRTTFTEETETDLFGEQAVLCGGASALVQAGFETLVEAGYTP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++helklivdl++e+G+++mr ++s+tA++g+++++ ++++ ++k+em+kil+ei++G+fa+e lcl|NCBI__GCF_000058485.1:WP_011606916.1 222 EVAYFECLHELKLIVDLMYEGGISQMRYSISDTAEYGDVTRGpRVVTPAVKAEMRKILDEIRDGTFARE 290 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 w+ e+ +g+p+f++ + k++ ie+vG +lr l+++ lcl|NCBI__GCF_000058485.1:WP_011606916.1 291 WVAEDDNGRPNFTKLVEEGKQHPIEQVGAKLRPLMSW 327 ********************************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (330 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: 11.51 // [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