Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_038215898.1 Q392_RS26720 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000745855.1:WP_038215898.1 Length = 338 Score = 581 bits (1498), Expect = e-171 Identities = 290/338 (85%), Positives = 306/338 (90%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKVFYDKD DLSLIKGK V IIGYGSQGHAHA NL DSGV V VGLRK GASW K AG Sbjct: 1 MKVFYDKDCDLSLIKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L+V EVAEAVK ADVVMILLPDEQIA VYKN+V NIKEGA+L FAHGFNVHYG V PRA Sbjct: 61 LKVAEVAEAVKQADVVMILLPDEQIASVYKNDVAPNIKEGASLVFAHGFNVHYGFVQPRA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 DLDV M+APKAPGHTVR+TYTQGGGVPHL+AVHQ+KSG ARD+ALSYA ANGGG+AGIIE Sbjct: 121 DLDVWMVAPKAPGHTVRSTYTQGGGVPHLVAVHQDKSGKARDLALSYAMANGGGKAGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE Sbjct: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GGIANMNYSISNNAEYGEYVTGPR+VT+ETK MK+ L DIQTGEYAKSF+LEN AGAPT Sbjct: 241 GGIANMNYSISNNAEYGEYVTGPRIVTDETKATMKKVLRDIQTGEYAKSFVLENAAGAPT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 LISRRRL AEHQIE VG KLRAMMPWI KNK+VDQ++N Sbjct: 301 LISRRRLNAEHQIEVVGEKLRAMMPWIKKNKLVDQTRN 338 Lambda K H 0.316 0.133 0.379 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: 495 Number of extensions: 11 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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_038215898.1 Q392_RS26720 (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.3780684.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-138 446.5 1.5 2.6e-138 446.2 1.5 1.0 1 NCBI__GCF_000745855.1:WP_038215898.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000745855.1:WP_038215898.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.2 1.5 2.6e-138 2.6e-138 1 313 [. 14 327 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 446.2 bits; conditional E-value: 2.6e-138 TIGR00465 1 lkgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 +kgk+vaiiGyGsqG+a+a nl dsg++v+vglrk++asw k e+ G+kv +v+ea+k+ad++miLlpDe+ NCBI__GCF_000745855.1:WP_038215898.1 14 IKGKTVAIIGYGSQGHAHAQNLNDSGVKVVVGLRKGGASWPKVEKAGLKVAEVAEAVKQADVVMILLPDEQIA 86 689********************************************************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 +vy+++++p++keg++l+f+HGfn+++ +++++d+dv +vAPK+pG++vR++y +g Gvp+l+Av+qd +g+ NCBI__GCF_000745855.1:WP_038215898.1 87 SVYKNDVAPNIKEGASLVFAHGFNVHYGFVQPRADLDVWMVAPKAPGHTVRSTYTQGGGVPHLVAVHQDKSGK 159 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a++ Al+yA a Gg++ag++et F+eE+e+DLfGEqavLcGg +lika+f+tLveaGy+pe+Ayfe++helk NCBI__GCF_000745855.1:WP_038215898.1 160 ARDLALSYAMANGGGKAGIIETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELK 232 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl++e+G+++m ++sn A++g++ ++ +i+++e+k++m+k+l +iq+Ge+ak ++le++ag+p++ + r NCBI__GCF_000745855.1:WP_038215898.1 233 LIVDLIYEGGIANMNYSISNNAEYGEYVTGpRIVTDETKATMKKVLRDIQTGEYAKSFVLENAAGAPTLISRR 305 ******************************9****************************************** PP TIGR00465 292 kkekeqeiekvGkelralvkae 313 + + e++ie vG++lra++++ NCBI__GCF_000745855.1:WP_038215898.1 306 RLNAEHQIEVVGEKLRAMMPWI 327 *******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (338 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 13.16 // [ok]
This GapMind analysis is from Jul 25 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