Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_019895674.1 A377_RS0107645 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000384235.1:WP_019895674.1 Length = 573 Score = 766 bits (1979), Expect = 0.0 Identities = 369/566 (65%), Positives = 450/566 (79%), Gaps = 4/566 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTK-FEHILVRHEQAAVHAADGY 76 E+ GA+ILVH L +EGVE VWGYPGGA L IYD L K +H LVRHEQAAVHAADGY Sbjct: 8 ELTGAQILVHFLEDEGVELVWGYPGGAALPIYDALDTDAKKLKHTLVRHEQAAVHAADGY 67 Query: 77 ARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGI 136 ARATG+ GV++VTSGPG TN VTGIATAY+DSIP+VVITG V ++ IG DAFQE DTVGI Sbjct: 68 ARATGRPGVSMVTSGPGATNTVTGIATAYMDSIPLVVITGQVASNMIGLDAFQEIDTVGI 127 Query: 137 TRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMR 196 TRPIVKHNFLVKDV+DL T+KKAF+IA TGRPGPVVVDIPKD+ Y+YP+S+ +R Sbjct: 128 TRPIVKHNFLVKDVKDLTMTLKKAFYIATTGRPGPVVVDIPKDIQNAKADYQYPESVSLR 187 Query: 197 SYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMG 256 SY P+ KGH+GQI+KA+ ++ A+RP IYTGGGVVL AS+ L +LA L G+PVTNTLMG Sbjct: 188 SYEPITKGHTGQIKKAIDMMVSAKRPIIYTGGGVVLGGASEALTELARLLGYPVTNTLMG 247 Query: 257 LGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIH 316 LG +P KQFVGMLGMHGTYEAN++M N D++IAIGARFDDRV GN F A +++H Sbjct: 248 LGGYPAEDKQFVGMLGMHGTYEANLSMHNSDLIIAIGARFDDRVTGNLEKFCPDA-QVVH 306 Query: 317 IDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDC 376 +DIDP+SISK V VDIPIVG VK VL+++++ +K + P +ALA WW+QIE WRS +C Sbjct: 307 VDIDPASISKNVVVDIPIVGPVKQVLEKMLSLLKKHKMTPDADALADWWKQIEDWRSTNC 366 Query: 377 LKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGT 436 L+Y++ IKPQ +E +W +T+GDA++ SDVGQHQM+AAQ+YKF++PRRWINSGGLGT Sbjct: 367 LRYEQIGHKIKPQTAMEAVWRITEGDAYVTSDVGQHQMFAAQYYKFNKPRRWINSGGLGT 426 Query: 437 MGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVR 496 MG GLP AMG++ AFP+ VV +TGEGSIQM IQELSTCLQY P+K+ LNNG+LGMVR Sbjct: 427 MGFGLPAAMGVQAAFPDATVVCVTGEGSIQMNIQELSTCLQYGLPIKVLCLNNGFLGMVR 486 Query: 497 QWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAF--RLKDRTVF 554 QWQE YD RYS SYMD+LPDF KL EAYGHVG+R++ ++ L EAF + KDR VF Sbjct: 487 QWQEFFYDRRYSMSYMDSLPDFTKLVEAYGHVGIRIDDPETMQAQLEEAFSDKYKDRFVF 546 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLL 580 +D TD ENV+PM+ AG G+ EM+L Sbjct: 547 IDVITDQQENVYPMIPAGAGMDEMIL 572 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: 1036 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: 573 Length adjustment: 36 Effective length of query: 549 Effective length of database: 537 Effective search space: 294813 Effective search space used: 294813 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_019895674.1 A377_RS0107645 (acetolactate synthase 3 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.9923.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-266 868.9 1.8 8.3e-266 868.7 1.8 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019895674.1 A377_RS0107645 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019895674.1 A377_RS0107645 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 868.7 1.8 8.3e-266 8.3e-266 1 555 [. 9 572 .. 9 573 .] 0.98 Alignments for each domain: == domain 1 score: 868.7 bits; conditional E-value: 8.3e-266 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvv 67 l+ga+ilv+ l++egve v+GyPGGa lpiydal +++l+h lvrheqaa+haadGyara+G++Gv lcl|NCBI__GCF_000384235.1:WP_019895674.1 9 LTGAQILVHFLEDEGVELVWGYPGGAALPIYDALDtdAKKLKHTLVRHEQAAVHAADGYARATGRPGVS 77 68********************************987889***************************** PP TIGR00118 68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpe 136 ++tsGPGatn+vtgiatay+ds+Plvv+tGqva+++iG dafqeid +Git+p++kh+flvk+++dl+ lcl|NCBI__GCF_000384235.1:WP_019895674.1 78 MVTSGPGATNTVTGIATAYMDSIPLVVITGQVASNMIGLDAFQEIDTVGITRPIVKHNFLVKDVKDLTM 146 ********************************************************************* PP TIGR00118 137 ilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvl 205 +lk+af+ia+tGrPGPv+vd+Pkd+++a+ +++++e+v+l++y+p +kgh+ qikka++++ +ak+P++ lcl|NCBI__GCF_000384235.1:WP_019895674.1 147 TLKKAFYIATTGRPGPVVVDIPKDIQNAKADYQYPESVSLRSYEPITKGHTGQIKKAIDMMVSAKRPII 215 ********************************************************************* PP TIGR00118 206 lvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274 + GgGv+ ++ase l+ela l pvt tl+GlG++p+++++++gmlGmhGt+eanl+++++dl+ia+G lcl|NCBI__GCF_000384235.1:WP_019895674.1 216 YTGGGVVLGGASEALTELARLLGYPVTNTLMGLGGYPAEDKQFVGMLGMHGTYEANLSMHNSDLIIAIG 284 ********************************************************************* PP TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338 arfddrvtgnl+kf+p+a+++h+didPa+i+knv vdipivG +k+vle++l+ lk++ + + lcl|NCBI__GCF_000384235.1:WP_019895674.1 285 ARFDDRVTGNLEKFCPDAQVVHVDIDPASISKNVVVDIPIVGPVKQVLEKMLSLLKKHkmtpDADALAd 353 *****************************************************9999877753333335 PP TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407 W+++ie+w+++++l++++ ++ikPq+ +++++++++++a+vt+dvGqhqm+aaq+yk++kpr++i+sg lcl|NCBI__GCF_000384235.1:WP_019895674.1 354 WWKQIEDWRSTNCLRYEQIGHKIKPQTAMEAVWRITEGDAYVTSDVGQHQMFAAQYYKFNKPRRWINSG 422 ********************************************************************* PP TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476 GlGtmGfGlPaa+G++ a p++tvv+vtG+gs+qmn+qelst+ +y++p+k+++lnn +lGmv+qWqe+ lcl|NCBI__GCF_000384235.1:WP_019895674.1 423 GLGTMGFGLPAAMGVQAAFPDATVVCVTGEGSIQMNIQELSTCLQYGLPIKVLCLNNGFLGMVRQWQEF 491 ********************************************************************* PP TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk...epvlldvevdkeeevlP 542 fy++rys +++ s lpdf+kl eayG++giri +pe ++++l+ea++ k + v++dv d++e+v+P lcl|NCBI__GCF_000384235.1:WP_019895674.1 492 FYDRRYSMSYMDS-LPDFTKLVEAYGHVGIRIDDPETMQAQLEEAFSDKykdRFVFIDVITDQQENVYP 559 ************5.********************************98777789*************** PP TIGR00118 543 mvapGagldelve 555 m++ Gag+de++ lcl|NCBI__GCF_000384235.1:WP_019895674.1 560 MIPAGAGMDEMIL 572 ***********95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (573 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 10.54 // [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