Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate PfGW456L13_1538 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= BRENDA::P00893
(574 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538
Length = 566
Score = 743 bits (1919), Expect = 0.0
Identities = 356/568 (62%), Positives = 441/568 (77%), Gaps = 4/568 (0%)
Query: 9 MVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLARATGEV 68
M+VR L D+GVK ++GYPGGA+L +YDAL + H+LVRHEQAA HMADG ARATG+
Sbjct: 1 MLVRFLRDEGVKYIYGYPGGALLHVYDALFKEPEVTHILVRHEQAATHMADGYARATGKA 60
Query: 69 GVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISRPVVKH 128
GVVLVTSGPGATNAITGIATAYMDSIP+V++SGQV ++++G DAFQE DM+GISRP+VKH
Sbjct: 61 GVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKH 120
Query: 129 SFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSMRSYNPT 188
SF++K +IP+V+KKAF+LA SGRPGPVVVD+PKD+ NPA K YV+P+ +RSY+P
Sbjct: 121 SFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYVFPKKAKLRSYSPA 180
Query: 189 TTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMGLGAFP 248
GH GQI++A + L+AAK+PV+Y GGG I G L E + LNLPV +LMGLG +P
Sbjct: 181 VRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGGYP 240
Query: 249 ATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPT 308
T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR N +K+CPNA ++HIDIDP
Sbjct: 241 GTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGASKFCPNAKIIHIDIDPA 300
Query: 309 SISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRA-RQCLKYDT 367
SISKT+ AD+PIVG VL +M+ +L + + + WW+Q+++WR R YD
Sbjct: 301 SISKTIKADVPIVGPVESVLTEMVAILKEIGETPNKESVASWWKQVDEWRGDRGLFPYDK 360
Query: 368 -HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFG 426
KIKPQ VIETL +T GDA+VTSDVGQHQMFAA YY F+KP RWINSGGLGTMGFG
Sbjct: 361 GDGSKIKPQTVIETLCEVTNGDAFVTSDVGQHQMFAAQYYKFNKPNRWINSGGLGTMGFG 420
Query: 427 LPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGMVKQWQD 486
PAA+G++++ P+ V CVTG+GSIQMNIQELST LQY LPV +V LNN LGMV+QWQD
Sbjct: 421 FPAAMGIQLSYPDADVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQD 480
Query: 487 MIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRLVFVDVT 546
M Y RHS SYM+SLPDFV+LAEAYGHVG++I+ +L+SK+ EA +RLV +D++
Sbjct: 481 MSYGSRHSHSYMESLPDFVKLAEAYGHVGVRITESKDLKSKMEEAF--AMKDRLVVIDIS 538
Query: 547 VDGSEHVYPMQIRGGGMDEMWLSKTERT 574
VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 VDTSEHVYPMQIKDGSMRDMWLSKTERT 566
Lambda K H
0.319 0.135 0.403
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: 1023
Number of extensions: 34
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: 574
Length of database: 566
Length adjustment: 36
Effective length of query: 538
Effective length of database: 530
Effective search space: 285140
Effective search space used: 285140
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 PfGW456L13_1538 (Acetolactate synthase large subunit (EC 2.2.1.6))
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.1092.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
5.8e-259 846.1 1.1 6.6e-259 845.9 1.1 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 Acetolactate synthase large subu
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 Acetolactate synthase large subunit (EC 2.2.1.6)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 845.9 1.1 6.6e-259 6.6e-259 6 556 .. 1 561 [. 1 562 [. 0.97
Alignments for each domain:
== domain 1 score: 845.9 bits; conditional E-value: 6.6e-259
TIGR00118 6 ilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyar 59
+lv+ l++egv++++GyPGGa+l++ydal+ + e++hilvrheqaa+h+adGyar
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 1 MLVRFLRDEGVKYIYGYPGGALLHVYDALFkEPEVTHILVRHEQAATHMADGYAR 55
7899**************************889********************** PP
TIGR00118 60 asGkvGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidi 114
a+Gk+Gvvl+tsGPGatn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 56 ATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDM 110
******************************************************* PP
TIGR00118 115 lGitlpvtkhsflvkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeiele 169
+Gi++p++khsf++k+a+++pe++k+af++a++GrPGPv+vd+Pkd+t+++ ++e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 111 IGISRPIVKHSFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFE 165
*************************************************999999 PP
TIGR00118 170 ve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelke 222
+ +k +l++y p v+gh qi+ka+e++ +ak+Pvl+ GgGvi +++s+ l+e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 166 YVfpKKAKLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTE 220
9888*************************************************** PP
TIGR00118 223 laerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarf 277
la++l++pvt tl+GlG++p ++++++gmlGmhG+++anla+++ad+++avGarf
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 221 LAKMLNLPVTNTLMGLGGYPGTDRQFIGMLGMHGSYTANLAMHHADVILAVGARF 275
******************************************************* PP
TIGR00118 278 ddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee 332
ddrv + +kf+p+akiihididPa+i+k++k+d+pivG +++vl+e+++ lke
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 276 DDRVINGASKFCPNAKIIHIDIDPASISKTIKADVPIVGPVESVLTEMVAILKEI 330
************************************************9998887 PP
TIGR00118 333 ....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqkvikelskllkdeaiv 380
+k++ W+++++ew+ + l +d+ ++s ikPq+vi++l+++++++a+v
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 331 getpNKESVAsWWKQVDEWRGDRGLFpYDKGDGSkIKPQTVIETLCEVTNGDAFV 385
77764444446*********999877688877656******************** PP
TIGR00118 381 ttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavt 435
t+dvGqhqm+aaq+yk++kp+++i+sgGlGtmGfG+Paa+G++++ p+++v +vt
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 386 TSDVGQHQMFAAQYYKFNKPNRWINSGGLGTMGFGFPAAMGIQLSYPDADVACVT 440
******************************************************* PP
TIGR00118 436 GdgsfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklase 490
G+gs+qmn+qelst+ +y++pvkivilnn +lGmv+qWq++ y r+s+++++s
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 441 GEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQDMSYGSRHSHSYMES- 494
*****************************************************5. PP
TIGR00118 491 lpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmv 544
lpdfvklaeayG++g+ri++ ++l++k++ea+++k ++v++d++vd++e+v+Pm+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 495 LPDFVKLAEAYGHVGVRITESKDLKSKMEEAFAMKdRLVVIDISVDTSEHVYPMQ 549
*******************************9988799***************** PP
TIGR00118 545 apGagldelvee 556
++ +++ +++ +
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1538 550 IKDGSMRDMWLS 561
*********976 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (557 nodes)
Target sequences: 1 (566 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: 8.60
//
[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