Align ketol-acid reductoisomerase (NADP+) (EC 1.1.1.86) (characterized)
to candidate WP_069663722.1 BCR25_RS11380 ketol-acid reductoisomerase
Query= BRENDA::Q2FWK4 (334 letters) >NCBI__GCF_001730305.1:WP_069663722.1 Length = 331 Score = 501 bits (1290), Expect = e-146 Identities = 241/327 (73%), Positives = 277/327 (84%) Query: 1 MTTVYYDQDVKTDALQGKKIAVVGYGSQGHAHAQNLKDNGYDVVIGIRPGRSFDKAKEDG 60 M VYYD V+ + L+GK IA++GYGSQGHAHAQNL+DNG V+IGIR G+S + A+ DG Sbjct: 1 MAKVYYDHSVENNQLEGKTIAIIGYGSQGHAHAQNLRDNGNQVIIGIREGKSAEAARNDG 60 Query: 61 FDVFPVAEAVKQADVIMVLLPDEIQGDVYKNEIEPNLEKHNALAFAHGFNIHFGVIQPPA 120 FDVFPVAEA KQADV+M+L PDEIQGD+Y EI PNLE NALAF HGFNIHF VI PP Sbjct: 61 FDVFPVAEASKQADVVMILAPDEIQGDLYDKEIAPNLEAGNALAFGHGFNIHFEVIAPPK 120 Query: 121 DVDVFLVAPKGPGHLVRRTFVEGSAVPSLFGIQQGASGQARNIALSYAKGIGATRAGVIE 180 DVDVFLVAPKGPGHLVRRTF EG AVP+LF + Q ASG A ++ALSYAKGIGATR GV+E Sbjct: 121 DVDVFLVAPKGPGHLVRRTFTEGFAVPALFAVYQDASGNASDVALSYAKGIGATRVGVLE 180 Query: 181 TTFKEETETDLFGEQAVLCGGVSKLIQSGFETLVEAGYQPELAYFEVLHEMKLIVDLMYE 240 TTFKEETETDLFGEQAVLCGG++ LI++GFETL EAGYQPELAYFEV HE+KLIVDL+YE Sbjct: 181 TTFKEETETDLFGEQAVLCGGLTSLIEAGFETLTEAGYQPELAYFEVCHELKLIVDLIYE 240 Query: 241 GGMENVRYSISNTAEFGDYVSGPRVITPDVKENMKAVLTDIQNGNFSNRFIEDNKNGFKE 300 GG E +R SISNTAE+GDYVSGPRV+T + K NMK VLTDIQNG F+ FI+DNKNGFKE Sbjct: 241 GGFEKMRNSISNTAEYGDYVSGPRVVTAEAKANMKEVLTDIQNGKFAKGFIDDNKNGFKE 300 Query: 301 FYKLREEQHGHQIEKVGRELREMMPFI 327 F ++R++ GH IEKVG ELR+MMPF+ Sbjct: 301 FNQMRKDNAGHPIEKVGAELRKMMPFV 327 Lambda K H 0.317 0.137 0.391 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: 492 Number of extensions: 16 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: 334 Length of database: 331 Length adjustment: 28 Effective length of query: 306 Effective length of database: 303 Effective search space: 92718 Effective search space used: 92718 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_069663722.1 BCR25_RS11380 (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.883589.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-138 446.4 0.3 2.6e-138 446.2 0.3 1.0 1 NCBI__GCF_001730305.1:WP_069663722.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069663722.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.2 0.3 2.6e-138 2.6e-138 1 312 [. 15 326 .. 15 328 .. 0.99 Alignments for each domain: == domain 1 score: 446.2 bits; conditional E-value: 2.6e-138 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 l+gk++aiiGyGsqG+a+a nlrd+g +vi+g+r++ +s ++A++dGf+v+ v+ea k+ad++miL pDe+q NCBI__GCF_001730305.1:WP_069663722.1 15 LEGKTIAIIGYGSQGHAHAQNLRDNGNQVIIGIREG-KSAEAARNDGFDVFPVAEASKQADVVMILAPDEIQG 86 689******************************987.9*********************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + y +ei+p+l++g+al f HGfni+f+ i +pkdvdv+lvAPKgpG+lvR+++ eg+ vp+l+Av+qd++g+ NCBI__GCF_001730305.1:WP_069663722.1 87 DLYDKEIAPNLEAGNALAFGHGFNIHFEVIAPPKDVDVFLVAPKGPGHLVRRTFTEGFAVPALFAVYQDASGN 159 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a ++Al+yAk+iG++r+gvlettFkeE+e+DLfGEqavLcGgl+ li+a+f+tL+eaGyqpelAyfe++helk NCBI__GCF_001730305.1:WP_069663722.1 160 ASDVALSYAKGIGATRVGVLETTFKEETETDLFGEQAVLCGGLTSLIEAGFETLTEAGYQPELAYFEVCHELK 232 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl++e+G+e+mr+++sntA++g++ ++ +++++e k++m+++l +iqnG+fak ++ ++++g +f+++r NCBI__GCF_001730305.1:WP_069663722.1 233 LIVDLIYEGGFEKMRNSISNTAEYGDYVSGpRVVTAEAKANMKEVLTDIQNGKFAKGFIDDNKNGFKEFNQMR 305 ******************************9****************************************** PP TIGR00465 292 kkekeqeiekvGkelralvka 312 k + + iekvG elr+++++ NCBI__GCF_001730305.1:WP_069663722.1 306 KDNAGHPIEKVGAELRKMMPF 326 ******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (331 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: 28.95 // [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