Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_083760869.1 SARO_RS11385 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_000013325.1:WP_083760869.1 Length = 355 Score = 464 bits (1195), Expect = e-135 Identities = 229/339 (67%), Positives = 269/339 (79%), Gaps = 1/339 (0%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGV-NVTVGLRKSGASWNKAANA 59 MKV+YD D DL+LI K + I+GYGSQGHAHA NL+DSGV +V + LR AS KA A Sbjct: 17 MKVYYDADCDLNLITDKKIAILGYGSQGHAHAQNLRDSGVKDVAIALRPGSASAKKAEAA 76 Query: 60 GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119 G +V A+A AD++MIL PDE A +Y +++H N+K GAALAFAHG N+H+G + R Sbjct: 77 GFKVLANADAAAWADILMILAPDEHQAAIYADDLHANMKPGAALAFAHGLNIHFGLIEAR 136 Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179 AD+DVIMIAPK PGHTVR+ Y +GGGVP LIAVHQN +G A D+AL+YA+ GGGR+GII Sbjct: 137 ADIDVIMIAPKGPGHTVRSEYQRGGGVPCLIAVHQNVTGNAHDVALAYASGVGGGRSGII 196 Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239 ETNFREE ETDLFGEQ VLCGGT LI+AGFETLVEAGYAPEMAYFECLHELKLIVDL+Y Sbjct: 197 ETNFREECETDLFGEQVVLCGGTTALIQAGFETLVEAGYAPEMAYFECLHELKLIVDLLY 256 Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299 EGGIANM YSISN AEYG+ TGPR++TEETKK MK+ L DIQ G + K F+L+N+AG P Sbjct: 257 EGGIANMRYSISNTAEYGDIKTGPRIITEETKKEMKRVLADIQEGRFVKDFVLDNRAGQP 316 Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 L + R L HQIEE GAKLRAMMPWI NK+VDQ+KN Sbjct: 317 ELKAARGLAKRHQIEETGAKLRAMMPWIGANKLVDQTKN 355 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: 463 Number of extensions: 18 Number of successful extensions: 2 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: 355 Length adjustment: 29 Effective length of query: 309 Effective length of database: 326 Effective search space: 100734 Effective search space used: 100734 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_083760869.1 SARO_RS11385 (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.3517343.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-133 430.4 0.3 2e-133 430.1 0.3 1.0 1 NCBI__GCF_000013325.1:WP_083760869.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013325.1:WP_083760869.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 430.1 0.3 2e-133 2e-133 2 312 .. 31 343 .. 30 345 .. 0.99 Alignments for each domain: == domain 1 score: 430.1 bits; conditional E-value: 2e-133 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsgl.nvivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 +kk+ai+GyGsqG+a+a nlrdsg+ +v ++lr+++as kkAe Gfkvl ++a++ ad++miL pDe q NCBI__GCF_000013325.1:WP_083760869.1 31 TDKKIAILGYGSQGHAHAQNLRDSGVkDVAIALRPGSASAKKAEAAGFKVLANADAAAWADILMILAPDEHQA 103 79************************67********************************************* PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + y +++ ++k g+al f+HG ni+f i++++d+dv+++APKgpG++vR+ey++g Gvp liAv+q+vtg+ NCBI__GCF_000013325.1:WP_083760869.1 104 AIYADDLHANMKPGAALAFAHGLNIHFGLIEARADIDVIMIAPKGPGHTVRSEYQRGGGVPCLIAVHQNVTGN 176 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a+++AlayA ++Gg+r g++et F+eE+e+DLfGEq+vLcGg +ali+a+f+tLveaGy+pe+Ayfe++helk NCBI__GCF_000013325.1:WP_083760869.1 177 AHDVALAYASGVGGGRSGIIETNFREECETDLFGEQVVLCGGTTALIQAGFETLVEAGYAPEMAYFECLHELK 249 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdll+e+G+++mr ++sntA++g+++++ +i++ee+kkem+ +l +iq+G+f k+++l+++ag+p++++ar NCBI__GCF_000013325.1:WP_083760869.1 250 LIVDLLYEGGIANMRYSISNTAEYGDIKTGpRIITEETKKEMKRVLADIQEGRFVKDFVLDNRAGQPELKAAR 322 ************************************************************************* PP TIGR00465 292 kkekeqeiekvGkelralvka 312 k ++ie++G +lra++++ NCBI__GCF_000013325.1:WP_083760869.1 323 GLAKRHQIEETGAKLRAMMPW 343 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (355 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: 22.53 // [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