Align acetohydroxyacid isomeroreductase (EC 1.1.1.86) (characterized)
to candidate WP_059150279.1 V474_RS04405 ketol-acid reductoisomerase
Query= metacyc::MONOMER-18814 (338 letters) >NCBI__GCF_001046635.1:WP_059150279.1 Length = 339 Score = 456 bits (1172), Expect = e-133 Identities = 218/339 (64%), Positives = 268/339 (79%), Gaps = 1/339 (0%) Query: 1 MKVFYDKDADLSLIKGKNVTIIGYGSQGHAHALNLKDSGVN-VTVGLRKSGASWNKAANA 59 MKV+YD D+D++LI K + ++GYGSQGHAHA NL+DSGV V + LR+ A+ KA A Sbjct: 1 MKVYYDADSDINLITDKKIVVLGYGSQGHAHAQNLRDSGVKEVAIALREGSATAKKAEGA 60 Query: 60 GLQVKEVAEAVKGADVVMILLPDEQIADVYKNEVHDNIKEGAALAFAHGFNVHYGAVIPR 119 G +V +A AD++MIL PDE A +Y ++H N+K GAALAFAHG NVH+G + PR Sbjct: 61 GFKVMSNKDAAAWADIIMILAPDEHQAAIYAEDLHANMKPGAALAFAHGLNVHFGLIEPR 120 Query: 120 ADLDVIMIAPKAPGHTVRATYTQGGGVPHLIAVHQNKSGAARDIALSYATANGGGRAGII 179 D+DVIMIAPK PGHTVR+ Y +GGGVP L+A+HQ+ +G A D+AL+YA+ GGGR+GII Sbjct: 121 TDIDVIMIAPKGPGHTVRSEYQRGGGVPCLVAIHQDVTGNAHDVALAYASGVGGGRSGII 180 Query: 180 ETNFREETETDLFGEQAVLCGGTVELIKAGFETLVEAGYAPEMAYFECLHELKLIVDLIY 239 ETNFREE ETDLFGEQAVLCGG L++AGFETLVEAGYAPEMAYFECLHELKLIVDL+Y Sbjct: 181 ETNFREECETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELKLIVDLMY 240 Query: 240 EGGIANMNYSISNNAEYGEYVTGPRVVTEETKKAMKQCLTDIQTGEYAKSFLLENKAGAP 299 EGGIANM YSISN AEYG+ TGPR++TEETKK MK+ L DIQ+G + K F+++N+AG P Sbjct: 241 EGGIANMRYSISNTAEYGDIKTGPRIITEETKKEMKRVLEDIQSGRFVKDFVMDNRAGQP 300 Query: 300 TLISRRRLTAEHQIEEVGAKLRAMMPWIAKNKMVDQSKN 338 L + R+ H IEE GAKLRAMMPWIA N +VD++KN Sbjct: 301 ELKASRKAALRHPIEETGAKLRAMMPWIAANALVDKAKN 339 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: 20 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: 339 Length adjustment: 28 Effective length of query: 310 Effective length of database: 311 Effective search space: 96410 Effective search space used: 96410 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_059150279.1 V474_RS04405 (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.883955.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-134 433.1 0.6 3.1e-134 432.8 0.6 1.0 1 NCBI__GCF_001046635.1:WP_059150279.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001046635.1:WP_059150279.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.8 0.6 3.1e-134 3.1e-134 2 312 .. 15 327 .. 14 329 .. 0.99 Alignments for each domain: == domain 1 score: 432.8 bits; conditional E-value: 3.1e-134 TIGR00465 2 kgkkvaiiGyGsqGeaqalnlrdsgln.vivglrkeaaswkkAeedGfkvltveeaikkadlimiLlpDevqk 73 +kk++++GyGsqG+a+a nlrdsg++ v ++lr+++a+ kkAe Gfkv++ ++a++ ad+imiL pDe q NCBI__GCF_001046635.1:WP_059150279.1 15 TDKKIVVLGYGSQGHAHAQNLRDSGVKeVAIALREGSATAKKAEGAGFKVMSNKDAAAWADIIMILAPDEHQA 87 79************************559******************************************** PP TIGR00465 74 evyeaeikpllkegkallfsHGfnivfkqivipkdvdvvlvAPKgpGalvReeykegrGvpsliAveqdvtge 146 + y ++++ ++k g+al f+HG n++f i+++ d+dv+++APKgpG++vR+ey++g Gvp l+A++qdvtg+ NCBI__GCF_001046635.1:WP_059150279.1 88 AIYAEDLHANMKPGAALAFAHGLNVHFGLIEPRTDIDVIMIAPKGPGHTVRSEYQRGGGVPCLVAIHQDVTGN 160 ************************************************************************* PP TIGR00465 147 akeiAlayAkaiGgaragvlettFkeEvesDLfGEqavLcGglealikaafdtLveaGyqpelAyfeivhelk 219 a+++AlayA ++Gg+r g++et F+eE+e+DLfGEqavLcGg +al++a+f+tLveaGy+pe+Ayfe++helk NCBI__GCF_001046635.1:WP_059150279.1 161 AHDVALAYASGVGGGRSGIIETNFREECETDLFGEQAVLCGGATALVQAGFETLVEAGYAPEMAYFECLHELK 233 ************************************************************************* PP TIGR00465 220 livdllkekGlelmrdavsntAklgalelr.eilkeelkkemqkilkeiqnGefakewalekeagkpafeear 291 livdl++e+G+++mr ++sntA++g+++++ +i++ee+kkem+ +l++iq+G+f k+++++++ag+p++++ r NCBI__GCF_001046635.1:WP_059150279.1 234 LIVDLMYEGGIANMRYSISNTAEYGDIKTGpRIITEETKKEMKRVLEDIQSGRFVKDFVMDNRAGQPELKASR 306 ************************************************************************* PP TIGR00465 292 kkekeqeiekvGkelralvka 312 k+ + ie++G +lra++++ NCBI__GCF_001046635.1:WP_059150279.1 307 KAALRHPIEETGAKLRAMMPW 327 *******************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (314 nodes) Target sequences: 1 (339 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: 18.11 // [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