Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_014450635.1 LFE_RS12760 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000284315.1:WP_014450635.1 Length = 583 Score = 627 bits (1616), Expect = 0.0 Identities = 312/571 (54%), Positives = 404/571 (70%), Gaps = 7/571 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GAE+L+ +L E V++++GYPGG VL I+D L K + +L RHEQ AVHAA+GYA Sbjct: 2 KMSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFKDPSLQVVLTRHEQGAVHAAEGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+T KVGV LVTSGPG TN VTG+A A +DSIP+VVITG VPT IG DAFQE D VGI+ Sbjct: 62 RSTNKVGVVLVTSGPGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGIS 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 R KHNFLV+ ++DL IK+AF+IA TGRPGPV+VD+PKDV + + YP S+ +RS Sbjct: 122 RSCTKHNFLVRKIQDLPRIIKEAFYIARTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRS 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 YNP +G+ QIRKA + A+RP +Y GGG++ ++A+ EL L LT P T TLMGL Sbjct: 182 YNPTMQGNRWQIRKAAQAISKAKRPVLYAGGGIISSDATKELLDLVTLTNIPTTLTLMGL 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 GA GT +F+GMLGMHGTY ANMA+ +CD+LIA+G RFDDRV G + F+ + K+IHI Sbjct: 242 GALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGVRFDDRVTGKISEFSPHS-KVIHI 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKP----KREALAKWWEQIEQWRS 373 DIDP+SI K VDIPIVG+ K +L++LI +IK + KP K + + W EQ+E+W Sbjct: 301 DIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELN-KPEPPSKEKLIDPWIEQVEEWEK 359 Query: 374 VDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433 L Y+ +E+IKPQYV+EK+++ T+GD + +DVGQHQMW AQF+KF +P W+ SGG Sbjct: 360 EHPLTYEHDTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLTSGG 419 Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493 LGTMG G P A+G +KA P+K V+ ITGEGS M IQEL+T D PVKI LNN YLG Sbjct: 420 LGTMGYGFPAAIGAQKAHPDKRVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLG 479 Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553 MVRQWQE Y RYS S++ PDFVKLAEA+G VG++ + +VE + + F + V Sbjct: 480 MVRQWQEFFYGGRYSSSFIGQSPDFVKLAEAFGIVGLKASRHDEVENIILDGFSRRG-PV 538 Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584 ++F DP ENV+PMV AG EM+ A + Sbjct: 539 LMEFHVDPEENVFPMVPAGGSNIEMIFEAPE 569 Lambda K H 0.319 0.135 0.407 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: 918 Number of extensions: 36 Number of successful extensions: 4 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: 585 Length of database: 583 Length adjustment: 36 Effective length of query: 549 Effective length of database: 547 Effective search space: 300303 Effective search space used: 300303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
Align candidate WP_014450635.1 LFE_RS12760 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))
# 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/TIGR00118.hmm # target sequence database: /tmp/gapView.1059616.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00118 [M=557] Accession: TIGR00118 Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-261 854.4 0.2 2.1e-261 854.2 0.2 1.0 1 NCBI__GCF_000284315.1:WP_014450635.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000284315.1:WP_014450635.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 854.2 0.2 2.1e-261 2.1e-261 1 554 [. 3 564 .. 3 567 .. 0.98 Alignments for each domain: == domain 1 score: 854.2 bits; conditional E-value: 2.1e-261 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++gae+l+eslk+e+v+++fGyPGG vlpi+dal+ d l+ +l+rheq+a+haa+Gyar++ kvGvvl+tsG NCBI__GCF_000284315.1:WP_014450635.1 3 MSGAEMLLESLKRENVQHIFGYPGGVVLPIFDALFkDPSLQVVLTRHEQGAVHAAEGYARSTNKVGVVLVTSG 75 79*********************************8889********************************** PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatn+vtg+a+a +ds+P+vv+tGqv+t++iG+dafqe+di+Gi++++tkh+flv+k +dlp+i+keaf+ia NCBI__GCF_000284315.1:WP_014450635.1 76 PGATNTVTGLADANMDSIPIVVITGQVPTKMIGNDAFQEADIVGISRSCTKHNFLVRKIQDLPRIIKEAFYIA 148 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218 tGrPGPvlvdlPkdv ++ ++++v++++y+pt++g++ qi+ka+++i+kak+Pvl++GgG+i ++a++ NCBI__GCF_000284315.1:WP_014450635.1 149 RTGRPGPVLVDLPKDVIVDRADFIYPDSVSIRSYNPTMQGNRWQIRKAAQAISKAKRPVLYAGGGIISSDATK 221 ************************************************************************* PP TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291 el +l+ ++ip t tl+GlGa+ +hp+++gmlGmhGt++an+a++++dlliavG+rfddrvtg++++f+p+ NCBI__GCF_000284315.1:WP_014450635.1 222 ELLDLVTLTNIPTTLTLMGLGALSGTHPRFMGMLGMHGTYAANMAIHHCDLLIAVGVRFDDRVTGKISEFSPH 294 ************************************************************************* PP TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkeke.Wlekieewkkeyilklde 356 +k+ihididP++i kn +vdipivGdak++l++l++++ke ++k ++ W+e++eew ke++l++++ NCBI__GCF_000284315.1:WP_014450635.1 295 SKVIHIDIDPTSIRKNFHVDIPIVGDAKHILKDLIEEIKELnkpeppsKEKLIDpWIEQVEEWEKEHPLTYEH 367 **************************************99888888643444458****************** PP TIGR00118 357 eeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429 + e ikPq+vi++++++++++ iv+tdvGqhqmw+aqf+k+ kp++++tsgGlGtmG+G+Paa+Ga+ a+p++ NCBI__GCF_000284315.1:WP_014450635.1 368 DTEVIKPQYVIEKVYQFTQGDCIVSTDVGQHQMWTAQFFKFIKPNTWLTSGGLGTMGYGFPAAIGAQKAHPDK 440 ************************************************************************* PP TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502 v+a+tG+gsf+mn+qel+t++ +dipvkivilnn++lGmv+qWqe+fy +rys++ +++ +pdfvklaea+G NCBI__GCF_000284315.1:WP_014450635.1 441 RVIAITGEGSFMMNIQELATVASLDIPVKIVILNNKYLGMVRQWQEFFYGGRYSSSFIGQ-SPDFVKLAEAFG 512 ***********************************************************6.************ PP TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554 ++g++ ++++e+e+ + + ++ ++pvl++++vd ee+v+Pmv+ G+++ e++ NCBI__GCF_000284315.1:WP_014450635.1 513 IVGLKASRHDEVENIILDGFSRRGPVLMEFHVDPEENVFPMVPAGGSNIEMI 564 ************************************************9998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (583 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: 20.99 // [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