Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_004300548.1 C665_RS03825 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000310185.1:WP_004300548.1 Length = 570 Score = 838 bits (2164), Expect = 0.0 Identities = 402/566 (71%), Positives = 475/566 (83%), Gaps = 1/566 (0%) Query: 21 GAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYARAT 80 GAEI++ L EE VEYV+GYPGGAVL++YD L +Q H+LVRHEQAAVHAADG+AR+T Sbjct: 5 GAEIVIRCLQEEKVEYVFGYPGGAVLFLYDALFQQETVRHVLVRHEQAAVHAADGFARST 64 Query: 81 GKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGITRPI 140 KVGVALVTSGPG TNAVTGIATAY DSIPMV+I+G VP AIGQDAFQE DTVGITRP Sbjct: 65 EKVGVALVTSGPGATNAVTGIATAYCDSIPMVIISGQVPVAAIGQDAFQEVDTVGITRPC 124 Query: 141 VKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRSYNP 200 VKHNFLV+DVRD+AAT+KKAF +A TGRPGPV+VDIPKDVS C+YEYPK I MRSYNP Sbjct: 125 VKHNFLVRDVRDIAATMKKAFHLARTGRPGPVLVDIPKDVSMQRCEYEYPKEISMRSYNP 184 Query: 201 VNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGLGAF 260 V KGHSGQI+KAV LL A+RP IYTGGGVVL+NA+++L +L L G+P+TNTLMGLG + Sbjct: 185 VTKGHSGQIKKAVQLLLEAKRPMIYTGGGVVLSNAAEQLVKLTRLLGYPITNTLMGLGGY 244 Query: 261 PGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHIDID 320 P + +QF+GM GMHGT+EANMAM DVL+A+GARFDDRVIGNPAHF + RKIIH+DID Sbjct: 245 PSSDRQFLGMPGMHGTFEANMAMHYSDVLLAVGARFDDRVIGNPAHFAEEPRKIIHVDID 304 Query: 321 PSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCLKYD 380 PSSISKRV+VD PIVG+VK+VL E+I QI++ + +P EALA WW+QIEQWR C+ Y Sbjct: 305 PSSISKRVRVDTPIVGDVKEVLDEMIRQIESGEARPNPEALASWWKQIEQWRERKCMVYK 364 Query: 381 RSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTMGVG 440 S EIIKPQ+V++K+WE+T GDA + SDVGQHQMWAAQ+Y FD+PRRW+NSGGLGTMGVG Sbjct: 365 NSDEIIKPQFVIQKLWEVTGGDAIVTSDVGQHQMWAAQYYGFDKPRRWLNSGGLGTMGVG 424 Query: 441 LPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQWQE 500 +PYAMG K A P+ +V +TGE SIQM IQELSTC Q+ P+KIC+LNN YLGMVRQWQE Sbjct: 425 MPYAMGAKLANPDMQVACVTGEASIQMNIQELSTCKQFRLPIKICNLNNRYLGMVRQWQE 484 Query: 501 IEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRL-KDRTVFLDFQT 559 + + RYS SYMD+LPDF KLAE+YGHVG+RV++ +DVE ALREAF KD VFLDFQ Sbjct: 485 LFHGGRYSESYMDSLPDFAKLAESYGHVGIRVDRPADVEGALREAFTTHKDELVFLDFQI 544 Query: 560 DPTENVWPMVQAGKGISEMLLGAEDL 585 D TENV+PMVQ GKG++EM+L AEDL Sbjct: 545 DQTENVYPMVQGGKGLTEMILSAEDL 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: 1071 Number of extensions: 33 Number of successful extensions: 2 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: 570 Length adjustment: 36 Effective length of query: 549 Effective length of database: 534 Effective search space: 293166 Effective search space used: 293166 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_004300548.1 C665_RS03825 (acetolactate synthase, large subunit, biosynthetic type)
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.6768.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-256 836.4 0.1 5.7e-256 836.2 0.1 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004300548.1 C665_RS03825 acetolactate syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004300548.1 C665_RS03825 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 836.2 0.1 5.7e-256 5.7e-256 1 555 [. 3 565 .. 3 567 .. 0.98 Alignments for each domain: == domain 1 score: 836.2 bits; conditional E-value: 5.7e-256 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+gaei+++ l++e+ve+vfGyPGGavl +ydal+ ++ ++h+lvrheqaa+haadG+ar++ kvGv+l lcl|NCBI__GCF_000310185.1:WP_004300548.1 3 LSGAEIVIRCLQEEKVEYVFGYPGGAVLFLYDALFqQETVRHVLVRHEQAAVHAADGFARSTEKVGVAL 71 68*********************************88899***************************** PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtgiatay ds+P+v+++Gqv+ ++iG+dafqe+d +Git+p++kh+flv++++d++++ lcl|NCBI__GCF_000310185.1:WP_004300548.1 72 VTSGPGATNAVTGIATAYCDSIPMVIISGQVPVAAIGQDAFQEVDTVGITRPCVKHNFLVRDVRDIAAT 140 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 +k+af++a tGrPGPvlvd+Pkdv+ + +e+e+++++++++y+p +kgh qikka++l+ +ak+P+++ lcl|NCBI__GCF_000310185.1:WP_004300548.1 141 MKKAFHLARTGRPGPVLVDIPKDVSMQRCEYEYPKEISMRSYNPVTKGHSGQIKKAVQLLLEAKRPMIY 209 ********************************************************************* PP TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGa 275 GgGv+ ++a e+l++l+ l p+t tl+GlG++p+ ++++lgm GmhGt ean+a++ +d+l+avGa lcl|NCBI__GCF_000310185.1:WP_004300548.1 210 TGGGVVLSNAAEQLVKLTRLLGYPITNTLMGLGGYPSSDRQFLGMPGMHGTFEANMAMHYSDVLLAVGA 278 ********************************************************************* PP TIGR00118 276 rfddrvtgnlakfapea.kiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke. 338 rfddrv gn a+fa+e kiih+didP++i+k v+vd pivGd+k+vl+e+++++++ + + lcl|NCBI__GCF_000310185.1:WP_004300548.1 279 RFDDRVIGNPAHFAEEPrKIIHVDIDPSSISKRVRVDTPIVGDVKEVLDEMIRQIESGearpNPEALAs 347 **************99626***********************************998756653334446 PP TIGR00118 339 WlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsg 407 W+++ie+w++++++ +++++e ikPq vi++l++++ ++aivt+dvGqhqmwaaq+y ++kpr++++sg lcl|NCBI__GCF_000310185.1:WP_004300548.1 348 WWKQIEQWRERKCMVYKNSDEIIKPQFVIQKLWEVTGGDAIVTSDVGQHQMWAAQYYGFDKPRRWLNSG 416 ********************************************************************* PP TIGR00118 408 GlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqel 476 GlGtmG G+P a+Gak+a+p+ +v +vtG++s+qmn+qelst++++ +p+ki++lnn++lGmv+qWqel lcl|NCBI__GCF_000310185.1:WP_004300548.1 417 GLGTMGVGMPYAMGAKLANPDMQVACVTGEASIQMNIQELSTCKQFRLPIKICNLNNRYLGMVRQWQEL 485 ********************************************************************* PP TIGR00118 477 fyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk..epvlldvevdkeeevlPm 543 f+ +ryse+++ s lpdf+klae+yG++gir+ +p+++e +l+ea++++ e+v+ld+++d++e+v+Pm lcl|NCBI__GCF_000310185.1:WP_004300548.1 486 FHGGRYSESYMDS-LPDFAKLAESYGHVGIRVDRPADVEGALREAFTTHkdELVFLDFQIDQTENVYPM 553 ************5.*******************************9876569***************** PP TIGR00118 544 vapGagldelve 555 v G+gl+e++ lcl|NCBI__GCF_000310185.1:WP_004300548.1 554 VQGGKGLTEMIL 565 **********96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (570 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: 00:00:00.02 # Mc/sec: 11.68 // [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