GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvI in Pseudomonas fluorescens GW456-L13

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.3027637.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: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.86
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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