Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_041439965.1 TCUR_RS17505 ketol-acid reductoisomerase
Query= BRENDA::Q59818 (333 letters) >NCBI__GCF_000024385.1:WP_041439965.1 Length = 327 Score = 473 bits (1216), Expect = e-138 Identities = 231/327 (70%), Positives = 269/327 (82%) Query: 4 LFYDADADLSIIQGRKVAVIGYGSQGHAHALSLRDSGVDVRVGLHEGSKSKAKAEEQGLR 63 +FYD DADLS+IQGR VAVIGYGSQGHAHALSLRDSGVDVRVGL EGSKS+ KAE GLR Sbjct: 1 MFYDNDADLSVIQGRHVAVIGYGSQGHAHALSLRDSGVDVRVGLQEGSKSREKAEADGLR 60 Query: 64 VVTPSEAAAEADVIMILVPDPIQAQVYEESIKDNLKDGDALFFGHGLNIRFGFIKPPAGV 123 VVTP+EAA EAD+IMIL PD +Q +Y IK L +GDALFFGHGLNIR+G I+PP GV Sbjct: 61 VVTPAEAAEEADLIMILAPDHVQRDLYNTQIKPALVEGDALFFGHGLNIRYGLIEPPEGV 120 Query: 124 DVCMVAPKGPGHLVRRQYEEGRGVPCIAAVEQDATGNGFALALSYAKGIGGTRAGVIKTT 183 DV MVAPKGPGHLVRRQ+ GRGVP + AVE+DA+GN + LALSYAK IGG RAG IKTT Sbjct: 121 DVAMVAPKGPGHLVRRQFTAGRGVPVLVAVEKDASGNAWPLALSYAKAIGGLRAGGIKTT 180 Query: 184 FTEETETDLFGEQAVLCGGTAALVKAGFETLTEAGYQPEIAYFECLHELKLIVDLMYEGG 243 F EETETDLFGEQAVLCGG + L+KAGFETL EAGYQPE+AYFECLHE+KLIVDLMYEGG Sbjct: 181 FAEETETDLFGEQAVLCGGVSELIKAGFETLIEAGYQPEVAYFECLHEMKLIVDLMYEGG 240 Query: 244 LEKMRWSISETAEWGDYVTGPRIITDATKAEMKKVLAEIQDGTFAQAWMDEYHGGLKKYN 303 ++KM WS+S+TAE+G Y GPRIIT TK MK++LAEI+ G FA+ + E+ GG + Sbjct: 241 IQKMYWSVSDTAEYGGYTRGPRIITPQTKEAMKQILAEIKSGEFAKELVAEFDGGQVNHL 300 Query: 304 EYKTQDENHLLETTGKELRKLMSWVND 330 +Y+ + NH +E TG +LR +MSW+ND Sbjct: 301 KYREELGNHPIEKTGAKLRPMMSWLND 327 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: 430 Number of extensions: 10 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: 327 Length adjustment: 28 Effective length of query: 305 Effective length of database: 299 Effective search space: 91195 Effective search space used: 91195 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_041439965.1 TCUR_RS17505 (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.10014.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-129 418.0 0.0 1.2e-129 417.8 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_041439965.1 TCUR_RS17505 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_041439965.1 TCUR_RS17505 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.8 0.0 1.2e-129 1.2e-129 1 312 [. 12 324 .. 12 326 .. 0.99 Alignments for each domain: == domain 1 score: 417.8 bits; conditional E-value: 1.2e-129 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 ++g++va+iGyGsqG+a+al lrdsg++v+vgl+++++s +kAe dG++v+t +ea+++adlimiL pD lcl|NCBI__GCF_000024385.1:WP_041439965.1 12 IQGRHVAVIGYGSQGHAHALSLRDSGVDVRVGLQEGSKSREKAEADGLRVVTPAEAAEEADLIMILAPD 80 6899***************************************************************** PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq++ y+ +ikp l eg+al f HG ni + i++p++vdv++vAPKgpG+lvR+++ grGvp l+A lcl|NCBI__GCF_000024385.1:WP_041439965.1 81 HVQRDLYNTQIKPALVEGDALFFGHGLNIRYGLIEPPEGVDVAMVAPKGPGHLVRRQFTAGRGVPVLVA 149 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 ve+d++g+a Al+yAkaiGg rag ++ttF eE+e+DLfGEqavLcGg+++lika+f+tL+eaGyqp lcl|NCBI__GCF_000024385.1:WP_041439965.1 150 VEKDASGNAWPLALSYAKAIGGLRAGGIKTTFAEETETDLFGEQAVLCGGVSELIKAGFETLIEAGYQP 218 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++he+klivdl++e+G+++m+ +vs+tA++g+++++ +i++ ++k++m++il ei++Gefake lcl|NCBI__GCF_000024385.1:WP_041439965.1 219 EVAYFECLHEMKLIVDLMYEGGIQKMYWSVSDTAEYGGYTRGpRIITPQTKEAMKQILAEIKSGEFAKE 287 ********************************************************************* PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralvka 312 + e+ g+ ++ + r+ ++ iek+G +lr ++++ lcl|NCBI__GCF_000024385.1:WP_041439965.1 288 LVAEFDGGQVNHLKYREELGNHPIEKTGAKLRPMMSW 324 ***********************************98 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.43 // [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