Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011445904.1 SARO_RS11375 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000013325.1:WP_011445904.1 Length = 582 Score = 570 bits (1468), Expect = e-167 Identities = 299/571 (52%), Positives = 391/571 (68%), Gaps = 7/571 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 E GAEILV +L +GVE+V+GYPGGAVL IYD L + HILVRHE A HAA+GYA Sbjct: 4 ERSGAEILVESLVAKGVEFVFGYPGGAVLPIYDALFGDERLRHILVRHEAGAAHAAEGYA 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGK GV LVTSGPG TNAVTGIA A++DSIPMVVITG VPT IG DAFQE DT+GIT Sbjct: 64 RATGKPGVVLVTSGPGATNAVTGIADAFMDSIPMVVITGQVPTALIGSDAFQEADTIGIT 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 R KHN+LVKD LAATI +AF IA GRPGPVV+DIPKDV + Sbjct: 124 RHCTKHNYLVKDPSQLAATIDEAFRIATEGRPGPVVIDIPKDVQIATAAWSSAAPQQRNR 183 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255 Y P +G + +I +A+ L+ A+ P YTGGGV+ A A+ LR+L +LTG PVT+TLM Sbjct: 184 YAPQTEGGAKEIAEAIELIAKAKAPVFYTGGGVINAGPEAARLLRELQSLTGAPVTSTLM 243 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGAFP ++GMLGMHGTYEANM M D+++ IGARFDDRV G F+ ++K I Sbjct: 244 GLGAFPADHPAWLGMLGMHGTYEANMTMNRADLVVCIGARFDDRVTGRLDAFSPNSKK-I 302 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 HIDID +SI+K V+VD+P++G+ VL +LI +++ L +W +I+ WR+ Sbjct: 303 HIDIDRASINKTVQVDLPVIGDCGKVLAQLIEAWLERGY--QKQDLTEWNARIDGWRARQ 360 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTK-GDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 L + R + I PQ +E+++ELT+ + I ++VGQHQMWAAQ + F +P +W+ SGGL Sbjct: 361 SLAFPRRGKEIMPQLAIERLYELTRHKEPIISTEVGQHQMWAAQHFHFMKPNKWLTSGGL 420 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMG GLP A+G + FP+ V+ I G+ SIQM IQEL T QY PVK+ LNN ++GM Sbjct: 421 GTMGYGLPAAIGAQAGFPDALVIDIAGDASIQMNIQELGTATQYRLPVKVFVLNNEWMGM 480 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQE+ Y++RYS+SY D+LPDFVKLAEAYG G+R+ S+++ + +A D VF Sbjct: 481 VRQWQELTYESRYSNSYSDSLPDFVKLAEAYGWKGIRITDESELDAGI-QAMIDHDGPVF 539 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585 +D N +PM+ +G ++M+L +++ Sbjct: 540 VDCLVAKEANCFPMIPSGAAHTDMILYGDEV 570 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: 905 Number of extensions: 38 Number of successful extensions: 6 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: 582 Length adjustment: 36 Effective length of query: 549 Effective length of database: 546 Effective search space: 299754 Effective search space used: 299754 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_011445904.1 SARO_RS11375 (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.3506026.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-243 793.4 0.0 6.1e-243 793.2 0.0 1.0 1 NCBI__GCF_000013325.1:WP_011445904.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013325.1:WP_011445904.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 793.2 0.0 6.1e-243 6.1e-243 2 555 .. 6 565 .. 5 567 .. 0.98 Alignments for each domain: == domain 1 score: 793.2 bits; conditional E-value: 6.1e-243 TIGR00118 2 kgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 +gaeilvesl ++gve vfGyPGGavlpiydal+ d+ l+hilvrhe +aahaa+Gyara+Gk+Gvvl+tsGP NCBI__GCF_000013325.1:WP_011445904.1 6 SGAEILVESLVAKGVEFVFGYPGGAVLPIYDALFgDERLRHILVRHEAGAAHAAEGYARATGKPGVVLVTSGP 78 79********************************9999*********************************** PP TIGR00118 74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146 Gatn+vtgia+a++ds+P+vv+tGqv+t+liGsdafqe+d +Git+ +tkh++lvk++++l++++ eaf ia+ NCBI__GCF_000013325.1:WP_011445904.1 79 GATNAVTGIADAFMDSIPMVVITGQVPTALIGSDAFQEADTIGITRHCTKHNYLVKDPSQLAATIDEAFRIAT 151 ************************************************************************* PP TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviia..eas 217 GrPGPv++d+Pkdv+ a+ + + + y+p+++g + i++a+eli+kak Pv + GgGvi a ea NCBI__GCF_000013325.1:WP_011445904.1 152 EGRPGPVVIDIPKDVQIATAAWSSAAPQQRNRYAPQTEGGAKEIAEAIELIAKAKAPVFYTGGGVINAgpEAA 224 *************************9999*************************************8844689 PP TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290 + l+el + +pvt+tl+GlGafp+dhp lgmlGmhGt+ean++++ adl++++Garfddrvtg l+ f+p NCBI__GCF_000013325.1:WP_011445904.1 225 RLLRELQSLTGAPVTSTLMGLGAFPADHPAWLGMLGMHGTYEANMTMNRADLVVCIGARFDDRVTGRLDAFSP 297 99*********************************************************************** PP TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkee..ekkeke.Wlekieewkkeyilkldeeees 360 ++k ihidid a+i+k+v+vd+p++Gd+ kvl++l+++ e+ +k++ W ++i+ w++++ l++ ++ ++ NCBI__GCF_000013325.1:WP_011445904.1 298 NSKKIHIDIDRASINKTVQVDLPVIGDCGKVLAQLIEAWLERgyQKQDLTeWNARIDGWRARQSLAFPRRGKE 370 *************************************99888776666556********************** PP TIGR00118 361 ikPqkvikelskllkd.eaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvv 432 i Pq i++l++l+++ e i++t+vGqhqmwaaq++++ kp+k++tsgGlGtmG+GlPaa+Ga+ + p++ v+ NCBI__GCF_000013325.1:WP_011445904.1 371 IMPQLAIERLYELTRHkEPIISTEVGQHQMWAAQHFHFMKPNKWLTSGGLGTMGYGLPAAIGAQAGFPDALVI 443 *************987689****************************************************** PP TIGR00118 433 avtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkg 505 +++Gd+s+qmn+qel t+++y +pvk+ +lnne++Gmv+qWqel ye rys+++ s lpdfvklaeayG kg NCBI__GCF_000013325.1:WP_011445904.1 444 DIAGDASIQMNIQELGTATQYRLPVKVFVLNNEWMGMVRQWQELTYESRYSNSYSDS-LPDFVKLAEAYGWKG 515 *******************************************************95.*************** PP TIGR00118 506 iriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 iri++++el++ ++ ++ +++pv++d v+ke++++Pm+++Ga+ ++++ NCBI__GCF_000013325.1:WP_011445904.1 516 IRITDESELDAGIQAMIDHDGPVFVDCLVAKEANCFPMIPSGAAHTDMIL 565 ***********************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (582 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 37.66 // [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