Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_044138357.1 GQW_RS0101510 biosynthetic-type acetolactate synthase large subunit
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000220155.1:WP_044138357.1 Length = 569 Score = 486 bits (1251), Expect = e-141 Identities = 269/577 (46%), Positives = 351/577 (60%), Gaps = 15/577 (2%) Query: 29 RPKHVALQQLTGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFD-SKKLRHVLVRHEQG 87 + K +++G++AVI+SL G +IFG PGGA++P+YD L D K+L HVL RHEQG Sbjct: 2 KEKTTKTTRMSGSEAVIQSLLREGTSIIFGYPGGAIMPIYDALHDHQKELHHVLTRHEQG 61 Query: 88 AGHAASGYAHVTGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAF 147 A HAA GYA VTG+VGVC ATSGPGATN VT LA+A MDS PVV ITGQV L+GTDAF Sbjct: 62 ALHAAEGYAKVTGKVGVCFATSGPGATNTVTGLANAMMDSTPVVLITGQVVSSLLGTDAF 121 Query: 148 QEADISGITMPITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFS 207 QE D+ G+T P+TK N+ VR +DIP +A AF+IA SGRPG V++DI KD Q F Sbjct: 122 QETDVVGVTQPVTKWNYQVRRAEDIPAAIARAFYIARSGRPGPVVIDITKDAQINQLDFY 181 Query: 208 WPPRMELPGYKPNTKPHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGI 267 + P + Y P Q+ EAA+LI ++KP+ VG GVI G A ++L + E +GI Sbjct: 182 YEPVKSIRSYTPEYPADLAQIEEAARLINLSKKPLALVGQGVIIGNAEKELLDFLEKSGI 241 Query: 268 PVVTTLMARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDSFA 327 P TL+ A P H N+GM GMHG +DL++A+G RFDDRVTG L +A Sbjct: 242 PAAWTLLGLSAVPSDHPLNVGMLGMHGNYGPNIKTNEADLIVAIGMRFDDRVTGDLSRYA 301 Query: 328 PEAKVIHADIDPAEIGKNRHADVPIVGDVK---AVITELIAMLRHHHIPGTIEMADWWAY 384 AK+IH +IDPAEI KN HADVPI+G+VK ++TE I H E Y Sbjct: 302 TNAKIIHMEIDPAEINKNVHADVPILGNVKKTLPLLTEKIVKNDHSDWLKEFEACQRVEY 361 Query: 385 LNGVRKTYPLSYGPQSDGSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRYEKPR 444 + K P G E V+ K+ + DA+ V VGQHQM A++ ++++ R Sbjct: 362 NRIIEK----QLNPIEKGITMGE-VVAKVSQAFDNDAIMVTDVGQHQMMGARYFKFKQSR 416 Query: 445 SWLNSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVAL 504 S + SGGLGTMGF +PAAMGAK+ P +V GDG QMT QEL T IPVK+ L Sbjct: 417 SVVTSGGLGTMGFGLPAAMGAKLGAPDRQVCVFVGDGGLQMTIQELGTIYQTQIPVKIVL 476 Query: 505 INNGNLGMVRQWQSLFYAERYSQTDLATHSHRIPDFVKLAEALGCVGLRCEREEDVVDVI 564 +NN LGMVRQWQ LF+ +RY+ T+L PDF +A+ L+ +D+ + I Sbjct: 477 LNNNFLGMVRQWQELFFDKRYASTELIN-----PDFQTIAKGYHIPSLKVSERQDLDEAI 531 Query: 565 NQARAINDCPVVIDFIVGADAQVWPMVAAGTSNDEIQ 601 Q D P +++ IV + V+PMV AG S +I+ Sbjct: 532 -QKMVEADGPFLLEVIVEKEGNVFPMVPAGASVSDIR 567 Lambda K H 0.319 0.136 0.414 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: 916 Number of extensions: 39 Number of successful extensions: 3 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: 618 Length of database: 569 Length adjustment: 37 Effective length of query: 581 Effective length of database: 532 Effective search space: 309092 Effective search space used: 309092 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_044138357.1 GQW_RS0101510 (biosynthetic-type 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.3397911.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-222 725.5 1.8 2.2e-222 725.4 1.8 1.0 1 NCBI__GCF_000220155.1:WP_044138357.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000220155.1:WP_044138357.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.4 1.8 2.2e-222 2.2e-222 1 553 [. 11 566 .. 11 569 .] 0.97 Alignments for each domain: == domain 1 score: 725.4 bits; conditional E-value: 2.2e-222 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydaly..dselehilvrheqaaahaadGyarasGkvGvvlats 71 ++g+e++++sl +eg ++fGyPGGa++piydal+ ++el+h+l+rheq+a haa+Gya+++GkvGv++ats NCBI__GCF_000220155.1:WP_044138357.1 11 MSGSEAVIQSLLREGTSIIFGYPGGAIMPIYDALHdhQKELHHVLTRHEQGALHAAEGYAKVTGKVGVCFATS 83 79*********************************88899********************************* PP TIGR00118 72 GPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafei 144 GPGatn+vtg+a+a++ds+P+v++tGqv +sl+G+dafqe d++G+t+pvtk++++v++aed+p+ + +af+i NCBI__GCF_000220155.1:WP_044138357.1 84 GPGATNTVTGLANAMMDSTPVVLITGQVVSSLLGTDAFQETDVVGVTQPVTKWNYQVRRAEDIPAAIARAFYI 156 ************************************************************************* PP TIGR00118 145 astGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeas 217 a +GrPGPv++d+ kd + +++++ +e ++++y p+ ++ +qi++a+ li+ +kkP+ lvG Gvii++a+ NCBI__GCF_000220155.1:WP_044138357.1 157 ARSGRPGPVVIDITKDAQINQLDFYYEPVKSIRSYTPEYPADLAQIEEAARLINLSKKPLALVGQGVIIGNAE 229 ***************************999******************************************* PP TIGR00118 218 eelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfap 290 +el ++ e+ ip + tllGl a+p+dhpl +gmlGmhG + n+ +eadl++a+G+rfddrvtg+l+++a+ NCBI__GCF_000220155.1:WP_044138357.1 230 KELLDFLEKSGIPAAWTLLGLSAVPSDHPLNVGMLGMHGNYGPNIKTNEADLIVAIGMRFDDRVTGDLSRYAT 302 ************************************************************************* PP TIGR00118 291 eakiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilk.....ldeee 358 +akiih++idPaei+knv++d+pi G++kk l l +k+ ++++++ Wl++ e ++ + l+ e NCBI__GCF_000220155.1:WP_044138357.1 303 NAKIIHMEIDPAEINKNVHADVPILGNVKKTLPLLTEKIVKNDHSD--WLKEFEACQRVEYNRiiekqLNPIE 373 ****************************************999988..9999887654333221001255667 PP TIGR00118 359 esikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetv 431 + i +v+ ++s+ +++ai+ tdvGqhqm a+++k+k++r+ +tsgGlGtmGfGlPaa+Gak++ p+ +v NCBI__GCF_000220155.1:WP_044138357.1 374 KGITMGEVVAKVSQAFDNDAIMVTDVGQHQMMGARYFKFKQSRSVVTSGGLGTMGFGLPAAMGAKLGAPDRQV 446 889999******************************************************************* PP TIGR00118 432 vavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvk 504 +Gdg++qm++qel ti + +ipvkiv+lnn++lGmv+qWqelf+++ry++t+l + pdf+ +a++y + NCBI__GCF_000220155.1:WP_044138357.1 447 CVFVGDGGLQMTIQELGTIYQTQIPVKIVLLNNNFLGMVRQWQELFFDKRYASTELIN--PDFQTIAKGYHIP 517 *********************************************************7..************* PP TIGR00118 505 giriekpeeleeklkealeskepvlldvevdkeeevlPmvapGagldel 553 +++++++++l+e++++++e ++p ll+v v+ke +v+Pmv+ Ga+++++ NCBI__GCF_000220155.1:WP_044138357.1 518 SLKVSERQDLDEAIQKMVEADGPFLLEVIVEKEGNVFPMVPAGASVSDI 566 ********************************************99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (569 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 27.52 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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