Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_011813498.1 HHAL_RS03565 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000015585.1:WP_011813498.1 Length = 336 Score = 482 bits (1241), Expect = e-141 Identities = 232/335 (69%), Positives = 277/335 (82%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVNVTVGLRKSGASWNKAANAG 60 MKV+YD+DADLS I + V IIGYGSQGHAHA NLK+SGVNV VGLR +S KA AG Sbjct: 1 MKVYYDQDADLSRITSRRVAIIGYGSQGHAHANNLKESGVNVVVGLRPGSSSAAKAQEAG 60 Query: 61 LQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPRA 120 L+V V EA +GADVVM+L+PDE D+Y +V N+K+GAA+AFAHGFN+HYG + P A Sbjct: 61 LEVASVEEATQGADVVMMLVPDEAAPDIYNQQVAPNLKDGAAIAFAHGFNIHYGQIQPAA 120 Query: 121 DLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGIIE 180 D DVIMIAPK PGHTVR+TY G GVP LIA+ Q+ SG A++IAL+YA ANGGGR+GIIE Sbjct: 121 DHDVIMIAPKGPGHTVRSTYVAGAGVPSLIAIEQDASGQAKEIALAYAVANGGGRSGIIE 180 Query: 181 TNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIYE 240 T+FREETETDLFGEQ VLCGG LI+AGFETLVEAGYAPEMAYFECLHE KLIVDL+YE Sbjct: 181 TSFREETETDLFGEQTVLCGGIAALIEAGFETLVEAGYAPEMAYFECLHETKLIVDLLYE 240 Query: 241 GGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAPT 300 GG+ANM YS+SN AEYG++ GPRV+ EE+++AM++ L +IQ G++AK ++LENKAGAPT Sbjct: 241 GGLANMRYSVSNTAEYGDFTRGPRVINEESREAMREILEEIQNGDFAKEYVLENKAGAPT 300 Query: 301 LISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQ 335 L +RRRL AEH IEEVG +LR MMPWIA NK+VD+ Sbjct: 301 LHARRRLAAEHPIEEVGERLRGMMPWIAANKLVDR 335 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: 449 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: 338 Length of database: 336 Length adjustment: 28 Effective length of query: 310 Effective length of database: 308 Effective search space: 95480 Effective search space used: 95480 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_011813498.1 HHAL_RS03565 (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.15798.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-141 455.8 0.5 3.8e-141 455.6 0.5 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011813498.1 HHAL_RS03565 ketol-acid reductoi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011813498.1 HHAL_RS03565 ketol-acid reductoisomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.6 0.5 3.8e-141 3.8e-141 2 312 .. 15 326 .. 14 328 .. 0.99 Alignments for each domain: == domain 1 score: 455.6 bits; conditional E-value: 3.8e-141 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsglnvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDe 70 +++vaiiGyGsqG+a+a nl++sg+nv+vglr++++s +kA+e G++v +veea + ad++m+L+pDe lcl|NCBI__GCF_000015585.1:WP_011813498.1 15 TSRRVAIIGYGSQGHAHANNLKESGVNVVVGLRPGSSSAAKAQEAGLEVASVEEATQGADVVMMLVPDE 83 5789***************************************************************** PP TIGR00465 71 vqkevyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAv 139 + ++ y+++++p+lk+g+a+ f+HGfni++ qi++ +d dv+++APKgpG++vR++y g+GvpsliA+ lcl|NCBI__GCF_000015585.1:WP_011813498.1 84 AAPDIYNQQVAPNLKDGAAIAFAHGFNIHYGQIQPAADHDVIMIAPKGPGHTVRSTYVAGAGVPSLIAI 152 ********************************************************************* PP TIGR00465 140 eqdvtgeakeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpe 208 eqd++g+akeiAlayA+a Gg+r g++et+F+eE+e+DLfGEq+vLcGg++ali+a+f+tLveaGy+pe lcl|NCBI__GCF_000015585.1:WP_011813498.1 153 EQDASGQAKEIALAYAVANGGGRSGIIETSFREETETDLFGEQTVLCGGIAALIEAGFETLVEAGYAPE 221 ********************************************************************* PP TIGR00465 209 lAyfeivhelklivdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakew 276 +Ayfe++he klivdll+e+Gl++mr +vsntA++g+++++ ++++ee +++m++il+eiqnG+fake+ lcl|NCBI__GCF_000015585.1:WP_011813498.1 222 MAYFECLHETKLIVDLLYEGGLANMRYSVSNTAEYGDFTRGpRVINEESREAMREILEEIQNGDFAKEY 290 ********************************************************************* PP TIGR00465 277 alekeagkpafeearkkekeqeiekvGkelralvka 312 +le++ag+p++++ r+ e+ ie+vG++lr ++++ lcl|NCBI__GCF_000015585.1:WP_011813498.1 291 VLENKAGAPTLHARRRLAAEHPIEEVGERLRGMMPW 326 **********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (336 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: 00:00:00.01 # Mc/sec: 8.96 // [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