Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_014027132.1 PYRFU_RS07845 ketol-acid reductoisomerase
Query= BRENDA::Q4J8K9 (332 letters) >NCBI__GCF_000223395.1:WP_014027132.1 Length = 333 Score = 404 bits (1038), Expect = e-117 Identities = 198/327 (60%), Positives = 256/327 (78%) Query: 1 MAKIYTDKDVSLDVIKEKRVAVLGYGSQGRAWALNLRDSGIKVSVGLEREGNSWKQAEND 60 MAKI+TDKD SLDV+K+K +AV+GYGSQGRA ALNLRDSG+ V +G+ G SW A+ + Sbjct: 1 MAKIFTDKDASLDVLKDKTIAVIGYGSQGRAQALNLRDSGLNVIIGVRPGGRSWNLAKQE 60 Query: 61 GFKPLRTEEAVRNSDIIIFLLPDMIQRTVYLERVKPYLKEGMDLVFAHGFNIHYRLIEPP 120 GF+ +EAV+ +D+I+ L+PDM+Q V+ ++++P+L+EGM + FAHGFNIH+ LI+PP Sbjct: 61 GFEVYPIDEAVKRADVILMLIPDMVQPEVWKKQIEPHLREGMVVDFAHGFNIHFGLIKPP 120 Query: 121 SNVDVYMIAPKAPGPIVREYFAKGGGVPALVATYQDHSGKALQKALAVAKAIGATRAGVI 180 VDV M+APK+PG +VRE F KG GVPALVA +QD+SG+AL ALA+AK IG TRAGVI Sbjct: 121 EYVDVVMVAPKSPGYMVREMFMKGYGVPALVAVHQDYSGRALDYALAIAKGIGCTRAGVI 180 Query: 181 ETTFKEETETDLFGEQVDLVGGVMQLMRYAFQTLVEAGYQPEVAYFETINEMKLIVDLVY 240 TTFKEETETDL GEQ LVGG+M+L++ F+ LVE GYQPEVAYFE +NE KLI+DL++ Sbjct: 181 LTTFKEETETDLIGEQTVLVGGLMELIKKGFEVLVELGYQPEVAYFEVLNEAKLIMDLIW 240 Query: 241 EKGFSGMLTAVSDTAKYGGMTVGKMVIDESVKERMKKALDNIRSGKFAEKWVEEYGKGAN 300 G GML VS+TA+YGG+TVG VIDE VKE MK+A + SG+FA++WVEEY +G Sbjct: 241 RYGIRGMLENVSETARYGGLTVGPKVIDEHVKENMKRAAQRVISGEFAKEWVEEYRRGMP 300 Query: 301 TIKEGMKEVDNSTEEKVGRSLRDIILR 327 T+K+ ++EV N E+VGR LR II R Sbjct: 301 TLKQLLEEVSNHPIERVGRELRKIIFR 327 Lambda K H 0.316 0.135 0.381 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: 400 Number of extensions: 15 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: 333 Length adjustment: 28 Effective length of query: 304 Effective length of database: 305 Effective search space: 92720 Effective search space used: 92720 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_014027132.1 PYRFU_RS07845 (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.24526.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-134 432.6 0.0 4.5e-134 432.3 0.0 1.0 1 lcl|NCBI__GCF_000223395.1:WP_014027132.1 PYRFU_RS07845 ketol-acid reducto Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000223395.1:WP_014027132.1 PYRFU_RS07845 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.3 0.0 4.5e-134 4.5e-134 1 310 [. 15 325 .. 15 329 .. 0.99 Alignments for each domain: == domain 1 score: 432.3 bits; conditional E-value: 4.5e-134 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpD 69 lk+k++a+iGyGsqG+aqalnlrdsglnvi+g+r+++ sw+ A+++Gf+v ++ea+k+ad+i++L+pD lcl|NCBI__GCF_000223395.1:WP_014027132.1 15 LKDKTIAVIGYGSQGRAQALNLRDSGLNVIIGVRPGGRSWNLAKQEGFEVYPIDEAVKRADVILMLIPD 83 79******************************************************************* PP TIGR00465 70 evqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliA 138 +vq+ev++++i+p l+eg ++ f+HGfni+f i++p++vdvv+vAPK+pG +vRe++ +g Gvp+l+A lcl|NCBI__GCF_000223395.1:WP_014027132.1 84 MVQPEVWKKQIEPHLREGMVVDFAHGFNIHFGLIKPPEYVDVVMVAPKSPGYMVREMFMKGYGVPALVA 152 ********************************************************************* PP TIGR00465 139 veqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqp 207 v+qd++g a ++Ala+Ak+iG +ragv+ ttFkeE+e+DL+GEq+vL+Ggl +lik +f++Lve Gyqp lcl|NCBI__GCF_000223395.1:WP_014027132.1 153 VHQDYSGRALDYALAIAKGIGCTRAGVILTTFKEETETDLIGEQTVLVGGLMELIKKGFEVLVELGYQP 221 ********************************************************************* PP TIGR00465 208 elAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefake 275 e+Ayfe++ e+kli+dl+ ++G+++m ++vs+tA++g+l+++ ++++e++k++m+ + +++Gefake lcl|NCBI__GCF_000223395.1:WP_014027132.1 222 EVAYFEVLNEAKLIMDLIWRYGIRGMLENVSETARYGGLTVGpKVIDEHVKENMKRAAQRVISGEFAKE 290 ******************************************9************************** PP TIGR00465 276 walekeagkpafeearkkekeqeiekvGkelralv 310 w+ e + g p++++ + +++ ie+vG+elr+++ lcl|NCBI__GCF_000223395.1:WP_014027132.1 291 WVEEYRRGMPTLKQLLEEVSNHPIERVGRELRKII 325 ********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (333 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: 7.67 // [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