Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_012567154.1 RC1_RS09480 acetolactate synthase 3 large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000016185.1:WP_012567154.1 Length = 596 Score = 652 bits (1683), Expect = 0.0 Identities = 326/571 (57%), Positives = 413/571 (72%), Gaps = 6/571 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 ++ GAEI++ AL ++GV+ ++GYPGGAVL IYD L KQ + HILVRHEQAAVHAA+GYA Sbjct: 14 KLTGAEIVIKALRDQGVDVIFGYPGGAVLPIYDALFKQNEIRHILVRHEQAAVHAAEGYA 73 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R+TGKVGV LVTSGPG TNAVTG+ A +DSIP+V +TG VPTH IG DAFQECDT GIT Sbjct: 74 RSTGKVGVVLVTSGPGATNAVTGLVDALMDSIPVVCLTGQVPTHLIGNDAFQECDTTGIT 133 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 RP KHN+LVK V +LA TI + F++A GRPGPVV+DIPKDV Y P +S Sbjct: 134 RPASKHNYLVKHVDNLARTIHEGFYVARNGRPGPVVIDIPKDVQFAEGPYRTPGECAPKS 193 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLAN--ASDELRQLAALTGHPVTNTLM 255 Y P + ++ +AV L+ A RP Y GGGV+ + AS L QL +TG+P T TLM Sbjct: 194 YRPQIRPDLNRVEEAVELIANARRPIFYVGGGVINSGPIASQLLTQLVRMTGYPCTTTLM 253 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315 GLGAFP + QF+GMLGMHGTYEAN+AM CDV+I IGARFDDRV G + F ++K I Sbjct: 254 GLGAFPASDPQFLGMLGMHGTYEANLAMHGCDVMINIGARFDDRVTGKLSEFAPGSKK-I 312 Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375 H+DIDPSSI+K V VD+ IVG+ VL+++I KA +P REALA WW+QIE WR+ D Sbjct: 313 HVDIDPSSINKNVPVDVAIVGDAAHVLEDMIRLWKARAKQPDREALAAWWKQIEGWRARD 372 Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG--DAFICSDVGQHQMWAAQFYKFDEPRRWINSGG 433 CL+Y+++ ++IKPQY +E++ ELT+G D FI ++VGQHQMWAAQF F++P RW+ SGG Sbjct: 373 CLRYEKTDKVIKPQYALERLRELTRGRDDVFITTEVGQHQMWAAQFLPFEKPNRWLTSGG 432 Query: 434 LGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLG 493 LGTMG GLP A+G++ A P+ VV + GE SI M IQE+ST LQY PVK+ LNN ++G Sbjct: 433 LGTMGYGLPAAIGVQIAHPKALVVDVAGEASILMNIQEMSTALQYRLPVKVFILNNQWMG 492 Query: 494 MVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTV 553 MVRQWQ++ + RYS SY ALPDFVKLAEA+G VG+R K S+V+ +R + V Sbjct: 493 MVRQWQQLLHGERYSESYSQALPDFVKLAEAFGAVGLRATKVSEVDDVIRTMIE-TPKAV 551 Query: 554 FLDFQTDPTENVWPMVQAGKGISEMLLGAED 584 +D D EN +PM+ GK +EMLLG E+ Sbjct: 552 IVDMCVDQKENCFPMIPGGKAHNEMLLGPEE 582 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: 954 Number of extensions: 35 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: 596 Length adjustment: 37 Effective length of query: 548 Effective length of database: 559 Effective search space: 306332 Effective search space used: 306332 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_012567154.1 RC1_RS09480 (acetolactate synthase 3 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.12347.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-245 802.3 0.0 1.3e-245 802.0 0.0 1.0 1 lcl|NCBI__GCF_000016185.1:WP_012567154.1 RC1_RS09480 acetolactate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016185.1:WP_012567154.1 RC1_RS09480 acetolactate synthase 3 large subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 802.0 0.0 1.3e-245 1.3e-245 1 554 [. 15 577 .. 15 580 .. 0.97 Alignments for each domain: == domain 1 score: 802.0 bits; conditional E-value: 1.3e-245 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 l+gaei++++l+++gv+++fGyPGGavlpiydal+ ++e++hilvrheqaa+haa+Gyar++GkvGvvl lcl|NCBI__GCF_000016185.1:WP_012567154.1 15 LTGAEIVIKALRDQGVDVIFGYPGGAVLPIYDALFkQNEIRHILVRHEQAAVHAAEGYARSTGKVGVVL 83 68*********************************999******************************* PP TIGR00118 69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137 +tsGPGatn+vtg+++a +ds+P+v ltGqv+t+liG+dafqe+d +Git+p kh++lvk++++l+++ lcl|NCBI__GCF_000016185.1:WP_012567154.1 84 VTSGPGATNAVTGLVDALMDSIPVVCLTGQVPTHLIGNDAFQECDTTGITRPASKHNYLVKHVDNLART 152 ********************************************************************* PP TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvll 206 ++e f++a GrPGPv++d+Pkdv+ ae ++++ + ++y+p+++++ +++++a+eli++a++P+ + lcl|NCBI__GCF_000016185.1:WP_012567154.1 153 IHEGFYVARNGRPGPVVIDIPKDVQFAEGPYRTPGECAPKSYRPQIRPDLNRVEEAVELIANARRPIFY 221 ********************************************************************* PP TIGR00118 207 vGgGviiae..aseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273 vGgGvi ++ as+ l++l+ ++ p tttl+GlGafp+ +p++lgmlGmhGt+eanla++ +d++i + lcl|NCBI__GCF_000016185.1:WP_012567154.1 222 VGGGVINSGpiASQLLTQLVRMTGYPCTTTLMGLGAFPASDPQFLGMLGMHGTYEANLAMHGCDVMINI 290 ******99766899******************************************************* PP TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338 Garfddrvtg+l++fap +k ih+didP++i+knv vd++ivGda +vle++++ k++ +++ lcl|NCBI__GCF_000016185.1:WP_012567154.1 291 GARFDDRVTGKLSEFAPGSKKIHVDIDPSSINKNVPVDVAIVGDAAHVLEDMIRLWKARakqpDREALA 359 ****************************************************98777665454444444 PP TIGR00118 339 .WlekieewkkeyilkldeeeesikPqkvikelskllkd..eaivttdvGqhqmwaaqfyktkkprkfi 404 W+++ie w+++ +l+++++++ ikPq+ +++l +l+++ ++++tt+vGqhqmwaaqf++++kp++++ lcl|NCBI__GCF_000016185.1:WP_012567154.1 360 aWWKQIEGWRARDCLRYEKTDKVIKPQYALERLRELTRGrdDVFITTEVGQHQMWAAQFLPFEKPNRWL 428 7***********************************987669*************************** PP TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473 tsgGlGtmG+GlPaa+G+++a+p++ vv+v+G++s+ mn+qe+st+ +y +pvk+ ilnn+++Gmv+qW lcl|NCBI__GCF_000016185.1:WP_012567154.1 429 TSGGLGTMGYGLPAAIGVQIAHPKALVVDVAGEASILMNIQEMSTALQYRLPVKVFILNNQWMGMVRQW 497 ********************************************************************* PP TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealeskepvlldvevdkeeevlP 542 q+l++ eryse++ ++ lpdfvklaea+G++g+r +k +e+++ ++ ++e+ + v++d+ vd++e+++P lcl|NCBI__GCF_000016185.1:WP_012567154.1 498 QQLLHGERYSESYSQA-LPDFVKLAEAFGAVGLRATKVSEVDDVIRTMIETPKAVIVDMCVDQKENCFP 565 *************995.**************************************************** PP TIGR00118 543 mvapGagldelv 554 m++ G++ +e++ lcl|NCBI__GCF_000016185.1:WP_012567154.1 566 MIPGGKAHNEML 577 **********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (596 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: 12.97 // [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