Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_089322508.1 CHB58_RS02405 acetolactate synthase, large subunit, biosynthetic type
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_900188395.1:WP_089322508.1 Length = 580 Score = 632 bits (1631), Expect = 0.0 Identities = 324/568 (57%), Positives = 401/568 (70%), Gaps = 7/568 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GAEIL+ AL EGVEY++GYPGGAVL IYD L T +HIL RHEQ A HAADGYA Sbjct: 2 KLSGAEILLEALKLEGVEYIFGYPGGAVLDIYDRL-TYTPLKHILTRHEQGAAHAADGYA 60 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R TGKVGV TSGPG TN VTGIATA +DS+P+V TGNVPT IG DAFQE DTVGIT Sbjct: 61 RTTGKVGVCFATSGPGATNLVTGIATAQIDSVPIVAFTGNVPTFMIGNDAFQEVDTVGIT 120 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKY---EYPKSID 194 RPI KHNFLVKDV +LA TIKKAF+IA TGRPG V+VD+PKDV R+ + EY + Sbjct: 121 RPITKHNFLVKDVNNLADTIKKAFYIAKTGRPGVVLVDLPKDVMRSIADFFEQEYRSPVQ 180 Query: 195 MRSYNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTL 254 +RSY PV KGH GQI++A + A+RP +Y GGG++ A+ASD + +LA L PVT TL Sbjct: 181 IRSYKPVKKGHPGQIKRAAKAIAQAKRPVLYVGGGIIKADASDLIVKLAELVTIPVTTTL 240 Query: 255 MGLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKI 314 MGLGA PGT F+GMLGMHGTY ANMA+ CD+LIA+GARFDDRV G A F A KI Sbjct: 241 MGLGAIPGTHPYFLGMLGMHGTYAANMAVTECDLLIAVGARFDDRVTGKVAEFAPNA-KI 299 Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAK--WWEQIEQWR 372 IHID+D + I K IPIVG+ K VL+EL+ +++ +K + +L + W + ++ W+ Sbjct: 300 IHIDVDSAEIGKVKDAHIPIVGDAKLVLEELLPEVEKQIMKNREVSLERDRWMDLVQHWK 359 Query: 373 SVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSG 432 L Y+ S +IKPQ+V+EKI+E+T GDA I +DVGQHQMW AQ+YKF P++ SG Sbjct: 360 VRYPLYYEPSDVVIKPQFVIEKIYEITDGDAIISTDVGQHQMWTAQYYKFKRPKQLATSG 419 Query: 433 GLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYL 492 GLGTMG G+P A+G + P+K V I+G+GS QM +QE+ T Y PVKI LNN YL Sbjct: 420 GLGTMGYGVPAAIGAQIGNPDKTVFCISGDGSFQMNMQEIVTAANYKIPVKIAILNNRYL 479 Query: 493 GMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRT 552 GMVRQWQ I YD YS + PDFVKL E+ G +G+R EK DVE L+EA + DR Sbjct: 480 GMVRQWQGIFYDRNYSEVDIAFQPDFVKLTESMGGIGLRAEKPEDVEKVLKEAMAINDRP 539 Query: 553 VFLDFQTDPTENVWPMVQAGKGISEMLL 580 V +DF + E+V+PMV G +SEM+L Sbjct: 540 VVIDFVVNREEDVFPMVPPGAAVSEMIL 567 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: 963 Number of extensions: 31 Number of successful extensions: 5 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: 580 Length adjustment: 36 Effective length of query: 549 Effective length of database: 544 Effective search space: 298656 Effective search space used: 298656 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_089322508.1 CHB58_RS02405 (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.21667.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-259 848.4 2.5 1.3e-259 848.2 2.5 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089322508.1 CHB58_RS02405 acetolactate synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089322508.1 CHB58_RS02405 acetolactate synthase, large subunit, biosynthetic type # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 848.2 2.5 1.3e-259 1.3e-259 1 555 [. 3 567 .. 3 569 .. 0.97 Alignments for each domain: == domain 1 score: 848.2 bits; conditional E-value: 1.3e-259 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvla 69 l+gaeil+e+lk egve++fGyPGGavl+iyd+l l+hil+rheq+aahaadGyar++GkvGv++a lcl|NCBI__GCF_900188395.1:WP_089322508.1 3 LSGAEILLEALKLEGVEYIFGYPGGAVLDIYDRLTYTPLKHILTRHEQGAAHAADGYARTTGKVGVCFA 71 68******************************************************************* PP TIGR00118 70 tsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeil 138 tsGPGatnlvtgiata +dsvP+v++tG v+t +iG+dafqe+d +Git+p+tkh+flvk++++l+ ++ lcl|NCBI__GCF_900188395.1:WP_089322508.1 72 TSGPGATNLVTGIATAQIDSVPIVAFTGNVPTFMIGNDAFQEVDTVGITRPITKHNFLVKDVNNLADTI 140 ********************************************************************* PP TIGR00118 139 keafeiastGrPGPvlvdlPkdvteaeiel...eveekvelpgykptvkghklqikkaleliekakkPv 204 k+af+ia+tGrPG vlvdlPkdv+++ ++ e+++ v++++ykp +kgh+ qik+a+++i++ak+Pv lcl|NCBI__GCF_900188395.1:WP_089322508.1 141 KKAFYIAKTGRPGVVLVDLPKDVMRSIADFfeqEYRSPVQIRSYKPVKKGHPGQIKRAAKAIAQAKRPV 209 ***********************998766511156699******************************* PP TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 l+vGgG+i+a+as+ +++lae + ipvtttl+GlGa+p +hp +lgmlGmhGt++an+av+e+dlliav lcl|NCBI__GCF_900188395.1:WP_089322508.1 210 LYVGGGIIKADASDLIVKLAELVTIPVTTTLMGLGAIPGTHPYFLGMLGMHGTYAANMAVTECDLLIAV 278 ********************************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee.......ekk 335 Garfddrvtg++a+fap+akiihid+d aeigk+ ++ipivGdak vleell +++++ + + lcl|NCBI__GCF_900188395.1:WP_089322508.1 279 GARFDDRVTGKVAEFAPNAKIIHIDVDSAEIGKVKDAHIPIVGDAKLVLEELLPEVEKQimknrevSLE 347 *****************************************************9999988877654444 PP TIGR00118 336 ekeWlekieewkkeyilkldeeeesikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404 +W++ +++wk +y+l ++ ++ ikPq vi++++++++++ai++tdvGqhqmw+aq+yk+k+p++ lcl|NCBI__GCF_900188395.1:WP_089322508.1 348 RDRWMDLVQHWKVRYPLYYEPSDVVIKPQFVIEKIYEITDGDAIISTDVGQHQMWTAQYYKFKRPKQLA 416 446****************************************************************** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 tsgGlGtmG+G+Paa+Ga++++p++tv +++Gdgsfqmn+qe+ t+++y+ipvki ilnn++lGmv+qW lcl|NCBI__GCF_900188395.1:WP_089322508.1 417 TSGGLGTMGYGVPAAIGAQIGNPDKTVFCISGDGSFQMNMQEIVTAANYKIPVKIAILNNRYLGMVRQW 485 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541 q +fy++ yse+ +a +pdfvkl+e++G g+r ekpe++e+ lkea++ + +pv++d++v++ee+v+ lcl|NCBI__GCF_900188395.1:WP_089322508.1 486 QGIFYDRNYSEVDIAF-QPDFVKLTESMGGIGLRAEKPEDVEKVLKEAMAINdRPVVIDFVVNREEDVF 553 ***************6.********************************99879*************** PP TIGR00118 542 PmvapGagldelve 555 Pmv+pGa+++e++ lcl|NCBI__GCF_900188395.1:WP_089322508.1 554 PMVPPGAAVSEMIL 567 ************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (580 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: 10.98 // [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