Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_011940524.1 GURA_RS18945 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000016745.1:WP_011940524.1 Length = 566 Score = 637 bits (1644), Expect = 0.0 Identities = 310/567 (54%), Positives = 414/567 (73%), Gaps = 4/567 (0%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA+IL+ L EGV+ V+GYPGG V+ +YDEL + HIL RHEQA VHAADGYA Sbjct: 2 KMNGAKILLECLKLEGVDTVFGYPGGTVINLYDELFSFKEIRHILPRHEQAGVHAADGYA 61 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RATGKVGVA+ TSGPG TN +TGIATAY+DSIPMV+ITG VPT IG DAFQE D +GIT Sbjct: 62 RATGKVGVAIATSGPGATNTITGIATAYMDSIPMVIITGQVPTALIGNDAFQEADIIGIT 121 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHNFLVKDV+DLA +KKAF+IA TGRPGPV++D+PKDV +++YP ++++R Sbjct: 122 RPCTKHNFLVKDVKDLALIVKKAFYIARTGRPGPVLIDLPKDVQIATAEFKYPDTVEIRG 181 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 Y P +GH Q+ KA++LL GA+RP IY GGGV+L NA++EL L+ PVT TLMGL Sbjct: 182 YKPTIEGHPKQVEKAMSLLLGAKRPVIYVGGGVILGNAAEELTALSKKLEAPVTTTLMGL 241 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 G+FP +G+LGMHGTY ANMA+ NCD+L+A+GARFDDRV G A F A KIIHI Sbjct: 242 GSFPEDDPLSLGLLGMHGTYYANMAVSNCDLLVAVGARFDDRVTGKIASFAPHA-KIIHI 300 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQEL--IAQIKASDIKPKREALAKWWEQIEQWRSVD 375 D+DP+SI K V+VD+PIVG+VKDVL ++ + + + + ++++ W E+IE W++ Sbjct: 301 DVDPTSIKKNVRVDLPIVGDVKDVLTQMLKVLEEQGDKLDDFKKSIVPWTEEIEGWKAKH 360 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLG 435 + Y +S+ +IKPQ+V++K+ EL+ DA + +DVGQHQMW AQF+KF+ PR ++SGGLG Sbjct: 361 PMSYKQSATVIKPQFVIQKLRELSDPDAIVATDVGQHQMWTAQFFKFNRPRTLLSSGGLG 420 Query: 436 TMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMV 495 TMG GLP AMG + AFP+++V+ I G+G QM +QEL+T +Q VKIC +NN +LGMV Sbjct: 421 TMGYGLPAAMGAQAAFPDRQVIVICGDGGFQMNLQELATVVQNRLAVKICIINNNFLGMV 480 Query: 496 RQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFL 555 RQWQE+ +D RYS + M+ DF+KLAEA+G G + K +VE +++ F V + Sbjct: 481 RQWQELFFDKRYSQTCMELPIDFIKLAEAFGAKGFQATKPDEVEAVIKKGFATPG-PVIM 539 Query: 556 DFQTDPTENVWPMVQAGKGISEMLLGA 582 +F+ E V PMV AG ++EM+L + Sbjct: 540 EFKVAREEKVLPMVPAGASLTEMVLAS 566 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: 898 Number of extensions: 28 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: 566 Length adjustment: 36 Effective length of query: 549 Effective length of database: 530 Effective search space: 290970 Effective search space used: 290970 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_011940524.1 GURA_RS18945 (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.940136.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-263 860.1 0.6 3.7e-263 859.9 0.6 1.0 1 NCBI__GCF_000016745.1:WP_011940524.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000016745.1:WP_011940524.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 859.9 0.6 3.7e-263 3.7e-263 1 555 [. 3 564 .. 3 566 .] 0.98 Alignments for each domain: == domain 1 score: 859.9 bits; conditional E-value: 3.7e-263 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 ++ga+il+e lk egv+tvfGyPGG+v+++yd+l+ +e++hil+rheqa +haadGyara+GkvGv++atsG NCBI__GCF_000016745.1:WP_011940524.1 3 MNGAKILLECLKLEGVDTVFGYPGGTVINLYDELFsFKEIRHILPRHEQAGVHAADGYARATGKVGVAIATSG 75 78*********************************889*********************************** PP TIGR00118 73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeia 145 PGatn++tgiatay+ds+P+v++tGqv+t+liG+dafqe+di+Git+p+tkh+flvk+++dl+ i+k+af+ia NCBI__GCF_000016745.1:WP_011940524.1 76 PGATNTITGIATAYMDSIPMVIITGQVPTALIGNDAFQEADIIGITRPCTKHNFLVKDVKDLALIVKKAFYIA 148 ************************************************************************* PP TIGR00118 146 stGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaease 218 tGrPGPvl+dlPkdv+ a+ e++++++ve++gykpt++gh++q++ka+ l+ ak+Pv++vGgGvi ++a e NCBI__GCF_000016745.1:WP_011940524.1 149 RTGRPGPVLIDLPKDVQIATAEFKYPDTVEIRGYKPTIEGHPKQVEKAMSLLLGAKRPVIYVGGGVILGNAAE 221 ************************************************************************* PP TIGR00118 219 elkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfape 291 el+ l+++l++pvtttl+GlG+fped+pl+lg+lGmhGt++an+avs++dll+avGarfddrvtg++a+fap+ NCBI__GCF_000016745.1:WP_011940524.1 222 ELTALSKKLEAPVTTTLMGLGSFPEDDPLSLGLLGMHGTYYANMAVSNCDLLVAVGARFDDRVTGKIASFAPH 294 ************************************************************************* PP TIGR00118 292 akiihididPaeigknvkvdipivGdakkvleellkklkee.......ekkeke.Wlekieewkkeyilklde 356 akiihid+dP++i knv+vd+pivGd+k vl+++lk l+e+ + k++ W+e+ie wk+++++++++ NCBI__GCF_000016745.1:WP_011940524.1 295 AKIIHIDVDPTSIKKNVRVDLPIVGDVKDVLTQMLKVLEEQgdklddfK-KSIVpWTEEIEGWKAKHPMSYKQ 366 **************************************99998887633.44446****************** PP TIGR00118 357 eeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpee 429 + + ikPq vi++l +l + +aiv+tdvGqhqmw+aqf+k+++pr+ ++sgGlGtmG+GlPaa+Ga+ a p+ NCBI__GCF_000016745.1:WP_011940524.1 367 SATVIKPQFVIQKLRELSDPDAIVATDVGQHQMWTAQFFKFNRPRTLLSSGGLGTMGYGLPAAMGAQAAFPDR 439 ************************************************************************* PP TIGR00118 430 tvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502 +v+ ++Gdg+fqmnlqel+t+v+ + vki+i+nn++lGmv+qWqelf+++rys+t+++ df+klaea+G NCBI__GCF_000016745.1:WP_011940524.1 440 QVIVICGDGGFQMNLQELATVVQNRLAVKICIINNNFLGMVRQWQELFFDKRYSQTCMEL-PIDFIKLAEAFG 511 ***********************************************************6.88********** PP TIGR00118 503 vkgiriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 +kg + +kp+e+e+ +k+ +++ +pv+++++v++ee+vlPmv+ Ga+l+e+v NCBI__GCF_000016745.1:WP_011940524.1 512 AKGFQATKPDEVEAVIKKGFATPGPVIMEFKVAREEKVLPMVPAGASLTEMVL 564 ***************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (566 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: 00:00:00.01 # Mc/sec: 29.37 // [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