Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate N515DRAFT_0567 N515DRAFT_0567 acetolactate synthase, large subunit
Query= SwissProt::P0DP90 (548 letters) >FitnessBrowser__Dyella79:N515DRAFT_0567 Length = 625 Score = 424 bits (1091), Expect = e-123 Identities = 240/580 (41%), Positives = 336/580 (57%), Gaps = 37/580 (6%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHL-----------LCRHEQG 49 M+GA+ VV L +GV+ +FGY GGAI+PVYDA++ H+ + +EQG Sbjct: 26 MSGAEVVVQVLADEGVDVLFGYSGGAILPVYDAVFRYNATHIGPSGGEPMPLIVPANEQG 85 Query: 50 AAMAAIGYARATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAF 109 A A GYARA+GK GV I TSGPGATN++T + D++ DS+P+V + GQV IG+DAF Sbjct: 86 AGFMAAGYARASGKVGVAIVTSGPGATNMVTPVRDSMSDSVPMVVLCGQVPTTAIGSDAF 145 Query: 110 QEVDVLGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQ------- 162 QE + + AC KH FLV E+L + AF++A SGRPGPV+VDIPKD+Q Sbjct: 146 QEAPIANIMSACAKHVFLVTDAEKLEATLRTAFEIARSGRPGPVVVDIPKDVQNTLLPFH 205 Query: 163 ----LASGDLEPWFTTVENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALRE 218 L +E T A+ + LA++++P++Y GGG + A LR Sbjct: 206 GEGLLPMPGYRARLQRLEQS-TLDDAQCVAFFEALAQSKRPLIYAGGGTIASGASHELRA 264 Query: 219 FLAATKMPATCTLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVT 278 F+A +P T TL GLGA + P L MLGMHGT AN+AV++CD L +GARFDDRV Sbjct: 265 FVADYGLPVTTTLMGLGAYDTTEPLALHMLGMHGTAYANYAVEDCDFLFTLGARFDDRVA 324 Query: 279 GKLNTFAPHASVI-HMDIDPAEMNKLRQAHVALQGDLNALLPAL-----------QQPLN 326 G + FAP A I +DIDPAE+ K++ GDL L L Q Sbjct: 325 GVPDKFAPQAKFIAQIDIDPAEIGKVKSVDWHHTGDLTRTLAQLRAWGERHGWREQLSAR 384 Query: 327 QYDWQQHCAQLRDEHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHI 386 W +H A+L+ H+ YD I ++++++ V++T VGQHQMWAAQ+ Sbjct: 385 YAPWHRHVAELKQVHALDYDRASPLIQPYAVIEEINRHTQGHAVISTGVGQHQMWAAQYF 444 Query: 387 AHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQL 446 P ++++S +GTMGFGLPAA+GAQ ARP V+ I GD S MN+ EL TV L Sbjct: 445 DFREPRHWLSSGSMGTMGFGLPAAIGAQFARPGAVVIDIDGDASIRMNLGELETVTTYGL 504 Query: 447 PLKIVLLDNQRLGMVRQWQQLFFQERYSETTLT-DNPDFLMLASAFGIH-GQHITRKDQV 504 P+K+V+L+N GMVRQWQ+LFF+ R++ + + DF+ A A G + + R++++ Sbjct: 505 PVKVVVLNNIGDGMVRQWQKLFFRGRFASSDKSLHRKDFIKAAQADGFEWARRLERREEL 564 Query: 505 EAALDTMLNSDGPYLLHVSIDELENVWPLVPPGASNSEML 544 A + L GP L V ID V+P+V PGA+ ++M+ Sbjct: 565 AATIADFLAHPGPAFLEVMIDPDAGVYPMVGPGATYAQMI 604 Lambda K H 0.320 0.135 0.410 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: 949 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: 548 Length of database: 625 Length adjustment: 37 Effective length of query: 511 Effective length of database: 588 Effective search space: 300468 Effective search space used: 300468 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 N515DRAFT_0567 N515DRAFT_0567 (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.22624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-199 649.1 0.0 3.3e-199 648.8 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 N515DRAFT_0567 acetolactate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 N515DRAFT_0567 acetolactate synthase, large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 648.8 0.0 3.3e-199 3.3e-199 1 555 [. 26 605 .. 26 607 .. 0.94 Alignments for each domain: == domain 1 score: 648.8 bits; conditional E-value: 3.3e-199 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly...........dselehilvrheqaaahaad 55 ++gae++v+ l +egv+++fGy GGa+lp+yda++ + + i++ eq+a +a lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 26 MSGAEVVVQVLADEGVDVLFGYSGGAILPVYDAVFrynathigpsgGEPMPLIVPANEQGAGFMAA 91 79********************************9444322222111224457899********** PP TIGR00118 56 GyarasGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpv 121 GyarasGkvGv+++tsGPGatn+vt++ +++ dsvP+vvl Gqv+t++iGsdafqe+ i i+ ++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 92 GYARASGKVGVAIVTSGPGATNMVTPVRDSMSDSVPMVVLCGQVPTTAIGSDAFQEAPIANIMSAC 157 ****************************************************************** PP TIGR00118 122 tkhsflvkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkg.. 185 kh flv++ae l ++l+ afeia +GrPGPv+vd+Pkdv+++ + ++ e + +pgy+ +++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 158 AKHVFLVTDAEKLEATLRTAFEIARSGRPGPVVVDIPKDVQNTLLPFHGEGLLPMPGYRARLQRle 223 **********************************************************98765411 PP TIGR00118 186 ....hklqikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhpl 247 + +q + e+++++k+P++++GgG i+++as+el+ ++ +pvtttl+GlGa++ ++pl lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 224 qstlDDAQCVAFFEALAQSKRPLIYAGGGTIASGASHELRAFVADYGLPVTTTLMGLGAYDTTEPL 289 1112456788999***************************************************** PP TIGR00118 248 algmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeak.iihididPaeigknvkvdi 312 al mlGmhGt++an+av+++d l+++Garfddrv+g +kfap+ak i ididPaeigk+ +vd lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 290 ALHMLGMHGTAYANYAVEDCDFLFTLGARFDDRVAGVPDKFAPQAKfIAQIDIDPAEIGKVKSVDW 355 **********************************************6679**************** PP TIGR00118 313 pivGdakkvleellkklkee......ekkeke.WlekieewkkeyilkldeeeesikPqkvikels 371 Gd ++ l++l + +++ + + W ++++e+k+ + l +d+ + i+P +vi+e+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 356 HHTGDLTRTLAQLRAWGERHgwreqlSARY-ApWHRHVAELKQVHALDYDRASPLIQPYAVIEEIN 420 *************98877766664333344.26********************************* PP TIGR00118 372 kllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGd 437 + ++++a+++t+vGqhqmwaaq++++++pr++++sg +GtmGfGlPaa+Ga+ a p + v++++Gd lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 421 RHTQGHAVISTGVGQHQMWAAQYFDFREPRHWLSSGSMGTMGFGLPAAIGAQFARPGAVVIDIDGD 486 ****************************************************************** PP TIGR00118 438 gsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGv 503 +s+ mnl el+t++ y++pvk+v+lnn Gmv+qWq+lf+++r++++ + + df+k a+a G lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 487 ASIRMNLGELETVTTYGLPVKVVVLNNIGDGMVRQWQKLFFRGRFASSDKSLHRKDFIKAAQADGF 552 ************************************************99999************9 PP TIGR00118 504 k.giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldelve 555 + + r+e++eel++ ++++l++ +p++l+v +d ++ v+Pmv pGa+ +++++ lcl|FitnessBrowser__Dyella79:N515DRAFT_0567 553 EwARRLERREELAATIADFLAHPGPAFLEVMIDPDAGVYPMVGPGATYAQMIT 605 75889*********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (625 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.62 // [ok]
This GapMind analysis is from Apr 09 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