Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate HSERO_RS08650 HSERO_RS08650 acetolactate synthase
Query= metacyc::MONOMER-18810 (585 letters) >FitnessBrowser__HerbieS:HSERO_RS08650 Length = 572 Score = 874 bits (2258), Expect = 0.0 Identities = 420/571 (73%), Positives = 491/571 (85%) Query: 15 AAPEMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAAD 74 +A ++ GA+ILV LAEEGVE+V+GYPGGAVLYIYD + KQ KF+HILVRHEQAAVHAAD Sbjct: 2 SAEQLTGADILVRCLAEEGVEHVFGYPGGAVLYIYDAIFKQDKFQHILVRHEQAAVHAAD 61 Query: 75 GYARATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTV 134 Y+R++ KVGVA+VTSGPGVTNAVTG+ATAY+DSIPMVVI+G VP+ AIGQDAFQECDTV Sbjct: 62 AYSRSSQKVGVAIVTSGPGVTNAVTGLATAYMDSIPMVVISGQVPSTAIGQDAFQECDTV 121 Query: 135 GITRPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSID 194 GITRP VKHNFLVKDV+DLA T+KKAF+IA TGRPGPV+VDIPKD++ + C Y YPK+++ Sbjct: 122 GITRPCVKHNFLVKDVKDLAETVKKAFYIATTGRPGPVLVDIPKDITMHTCAYAYPKAVE 181 Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254 MRSY PV+KGHSGQIRKA+ LL AERP IYTGGG++LANA+ EL +L G+P TNTL Sbjct: 182 MRSYKPVDKGHSGQIRKALQLLLSAERPMIYTGGGIILANAAPELNKLVDRLGYPCTNTL 241 Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314 MGLGA+ +S +FVGM GMHGTYEANMAMQ+CDVLIAIGARFDDRVIGNP HF S ARKI Sbjct: 242 MGLGAYRSSSDKFVGMPGMHGTYEANMAMQHCDVLIAIGARFDDRVIGNPKHFASHARKI 301 Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSV 374 IHIDIDPSSISKRVKVDIPIVGNVKDVLQEL++Q+ A++ + AL WW+QI +WR Sbjct: 302 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELLSQLDAAETRQNGAALDAWWKQINEWRKR 361 Query: 375 DCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434 DCLK+ S E IKPQ VV+K+WE+TKGDAFI SDVGQHQMWAAQ+Y FD+PRRWINSGGL Sbjct: 362 DCLKFATSEEFIKPQSVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPRRWINSGGL 421 Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494 GTMGVGLPYAMG++ A P+ V ITGE SIQMCIQEL+TC QY KI LNN +LGM Sbjct: 422 GTMGVGLPYAMGVQMANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGM 481 Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554 VRQWQ+I+Y +RYS SYMD+LPDF KLAE+YGHVGM++EK DV+ ALREAF +KDR VF Sbjct: 482 VRQWQQIDYGSRYSESYMDSLPDFNKLAESYGHVGMKIEKPGDVDGALREAFAMKDRLVF 541 Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAEDL 585 ++F TD TENVWPMV+AGKG++EMLLG+EDL Sbjct: 542 MNFITDQTENVWPMVKAGKGLTEMLLGSEDL 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: 31 Number of successful extensions: 1 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: 572 Length adjustment: 36 Effective length of query: 549 Effective length of database: 536 Effective search space: 294264 Effective search space used: 294264 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 HSERO_RS08650 HSERO_RS08650 (acetolactate synthase)
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.30644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-254 831.2 0.7 2.2e-254 831.0 0.7 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS08650 HSERO_RS08650 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS08650 HSERO_RS08650 acetolactate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 831.0 0.7 2.2e-254 2.2e-254 1 554 [. 6 566 .. 6 569 .. 0.98 Alignments for each domain: == domain 1 score: 831.0 bits; conditional E-value: 2.2e-254 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvv 67 l+ga+ilv+ l +egve+vfGyPGGavl iyda++ +++++hilvrheqaa+haad y+r+s kvGv+ lcl|FitnessBrowser__HerbieS:HSERO_RS08650 6 LTGADILVRCLAEEGVEHVFGYPGGAVLYIYDAIFkQDKFQHILVRHEQAAVHAADAYSRSSQKVGVA 73 68*********************************999****************************** PP TIGR00118 68 latsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlp 135 ++tsGPG tn+vtg+atay+ds+P+vv++Gqv++++iG+dafqe+d +Git+p++kh+flvk+++dl+ lcl|FitnessBrowser__HerbieS:HSERO_RS08650 74 IVTSGPGVTNAVTGLATAYMDSIPMVVISGQVPSTAIGQDAFQECDTVGITRPCVKHNFLVKDVKDLA 141 ******************************************************************** PP TIGR00118 136 eilkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkP 203 e++k+af+ia+tGrPGPvlvd+Pkd+t +++ + +++ ve+++ykp kgh qi+kal+l+ +a++P lcl|FitnessBrowser__HerbieS:HSERO_RS08650 142 ETVKKAFYIATTGRPGPVLVDIPKDITMHTCAYAYPKAVEMRSYKPVDKGHSGQIRKALQLLLSAERP 209 ******************************************************************** PP TIGR00118 204 vllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlli 271 +++ GgG+i a+a el++l++rl p t tl+GlGa+ + +++gm GmhGt+ean+a++++d+li lcl|FitnessBrowser__HerbieS:HSERO_RS08650 210 MIYTGGGIILANAAPELNKLVDRLGYPCTNTLMGLGAYRSSSDKFVGMPGMHGTYEANMAMQHCDVLI 277 ******************************************************************** PP TIGR00118 272 avGarfddrvtgnlakfapeak.iihididPaeigknvkvdipivGdakkvleellkklkee....ek 334 a+Garfddrv gn ++fa++a+ iihididP++i+k vkvdipivG++k vl+ell++l + + lcl|FitnessBrowser__HerbieS:HSERO_RS08650 278 AIGARFDDRVIGNPKHFASHARkIIHIDIDPSSISKRVKVDIPIVGNVKDVLQELLSQLDAAetrqNG 345 ********************965***********************************9988443222 PP TIGR00118 335 keke.WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkpr 401 + W+++i+ew+k+ +lk+ ++ee ikPq+v++++++++k++a++t+dvGqhqmwaaq+y ++kpr lcl|FitnessBrowser__HerbieS:HSERO_RS08650 346 AALDaWWKQINEWRKRDCLKFATSEEFIKPQSVVQKVWEVTKGDAFITSDVGQHQMWAAQYYGFDKPR 413 23346*************************************************************** PP TIGR00118 402 kfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGm 469 ++i+sgGlGtmG GlP a+G+++a+p++tv ++tG++s+qm +qel+t+++y++ ki++lnn++lGm lcl|FitnessBrowser__HerbieS:HSERO_RS08650 414 RWINSGGLGTMGVGLPYAMGVQMANPDATVACITGEASIQMCIQELATCKQYHLTPKIILLNNRFLGM 481 ******************************************************************** PP TIGR00118 470 vkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdk 536 v+qWq++ y ryse+++ s lpdf+klae+yG++g++iekp +++ +l+ea+++k ++v++++ d+ lcl|FitnessBrowser__HerbieS:HSERO_RS08650 482 VRQWQQIDYGSRYSESYMDS-LPDFNKLAESYGHVGMKIEKPGDVDGALREAFAMKdRLVFMNFITDQ 548 *******************5.*******************************9988799********* PP TIGR00118 537 eeevlPmvapGagldelv 554 +e+v+Pmv G+gl+e++ lcl|FitnessBrowser__HerbieS:HSERO_RS08650 549 TENVWPMVKAGKGLTEML 566 ****************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (572 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 9.82 // [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