Alignments for a candidate for ilvI in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas simiae WCS417

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF4653 PS417_23810 acetolactate synthase 3 catalytic subunit

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__WCS417:GFF4653
          Length = 574

 Score =  753 bits (1945), Expect = 0.0
 Identities = 365/576 (63%), Positives = 445/576 (77%), Gaps = 4/576 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME+LSG EM+VR L D+GV  ++GYPGGA+L +YDAL     + H+LVRHEQAA HMADG
Sbjct: 1   MELLSGGEMLVRFLRDEGVDYIYGYPGGALLHVYDALFKEPAVTHILVRHEQAATHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ GVVLVTSGPGATNAITGIATAYMDSIP+V++SGQV ++++G DAFQE DM+G
Sbjct: 61  YARATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRP+VKHSF++K   +IP+V+KKAF+LA SGRPGPVVVD+PKD+ NPA K  Y++P+  
Sbjct: 121 ISRPIVKHSFMIKHPSEIPEVMKKAFYLAQSGRPGPVVVDVPKDMTNPAEKFEYIFPKKA 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            +RSY+P   GH GQI++A + L+AAK+PV+Y GGG I  G    L E  + LNLPV  +
Sbjct: 181 KLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKLLNLPVTNT 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N  +K+CPNA +
Sbjct: 241 LMGLGAFPGTDRQFVGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGASKFCPNAKI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRA- 359
           +HIDIDP SISKT+ AD+PIVG    VL +M+  L         + +  WW+QI++WR  
Sbjct: 301 IHIDIDPASISKTIKADVPIVGPVESVLTEMVAALKDIGETPNKESVASWWKQIDEWRGD 360

Query: 360 RQCLKYDT-HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
           R    YD      IKPQ VIETL  +TKGDA+VTSDVGQHQMFAA YY FDKP RWINSG
Sbjct: 361 RGLFPYDKGDGSIIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYKFDKPNRWINSG 420

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFG PAA+GVK++ P+  V CVTG+GSIQMNIQELST LQY LPV +V LNN  L
Sbjct: 421 GLGTMGFGFPAAMGVKLSFPDTDVACVTGEGSIQMNIQELSTCLQYGLPVKIVCLNNGVL 480

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM Y+ RHS SYM+SLPDFV+L EAYGHVGI+I+   +L+ K+ EA      +
Sbjct: 481 GMVRQWQDMSYNSRHSHSYMESLPDFVKLVEAYGHVGIRITDLKDLKPKMEEAF--AMKD 538

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLVF+D+ VD SEHVYPMQI+ G M +MWL+KTERT
Sbjct: 539 RLVFIDIQVDTSEHVYPMQIKDGSMRDMWLNKTERT 574


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: 1027
Number of extensions: 36
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: 574
Length adjustment: 36
Effective length of query: 538
Effective length of database: 538
Effective search space:   289444
Effective search space used:   289444
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 GFF4653 PS417_23810 (acetolactate synthase 3 catalytic 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.23718.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.5e-260  849.8   0.3   5.2e-260  849.6   0.3    1.0  1  lcl|FitnessBrowser__WCS417:GFF4653  PS417_23810 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4653  PS417_23810 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  849.6   0.3  5.2e-260  5.2e-260       1     555 [.       4     568 ..       4     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 849.6 bits;  conditional E-value: 5.2e-260
                           TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                         l+g+e+lv+ l++egv++++GyPGGa+l++ydal+ +  ++hilvrheqaa+h+adGyara+Gk+Gvvl+tsGPG
  lcl|FitnessBrowser__WCS417:GFF4653   4 LSGGEMLVRFLRDEGVDYIYGYPGGALLHVYDALFkEPAVTHILVRHEQAATHMADGYARATGKAGVVLVTSGPG 78 
                                         689********************************7889************************************ PP

                           TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149
                                         atn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d++Gi++p++khsf++k+++++pe++k+af++a++Gr
  lcl|FitnessBrowser__WCS417:GFF4653  79 ATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKHPSEIPEVMKKAFYLAQSGR 153
                                         *************************************************************************** PP

                           TIGR00118 150 PGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelke 222
                                         PGPv+vd+Pkd+t+++ ++e+   +k +l++y p v+gh  qi+ka+e++ +ak+Pvl+ GgGvi +++s+ l+e
  lcl|FitnessBrowser__WCS417:GFF4653 154 PGPVVVDVPKDMTNPAEKFEYIfpKKAKLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTE 228
                                         **************9988888777*************************************************** PP

                           TIGR00118 223 laerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihi 297
                                         la+ l++pvt tl+GlGafp ++++++gmlGmhG+++anla+++ad+++avGarfddrv +  +kf+p+akiihi
  lcl|FitnessBrowser__WCS417:GFF4653 229 LAKLLNLPVTNTLMGLGAFPGTDRQFVGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGASKFCPNAKIIHI 303
                                         *************************************************************************** PP

                           TIGR00118 298 didPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqk 365
                                         didPa+i+k++k+d+pivG +++vl+e++++lk+     +k++   W+++i+ew+ +  l  +d+ ++s ikPq+
  lcl|FitnessBrowser__WCS417:GFF4653 304 DIDPASISKTIKADVPIVGPVESVLTEMVAALKDIgetpNKESVAsWWKQIDEWRGDRGLFpYDKGDGSiIKPQT 378
                                         ******************************9998877764444446*********9998777999888879**** PP

                           TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440
                                         vi++l++++k++a+vt+dvGqhqm+aaq+yk++kp+++i+sgGlGtmGfG+Paa+G+k++ p+++v +vtG+gs+
  lcl|FitnessBrowser__WCS417:GFF4653 379 VIETLCEVTKGDAFVTSDVGQHQMFAAQYYKFDKPNRWINSGGLGTMGFGFPAAMGVKLSFPDTDVACVTGEGSI 453
                                         *************************************************************************** PP

                           TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515
                                         qmn+qelst+ +y++pvkiv+lnn +lGmv+qWq++ y+ r+s+++++s lpdfvkl eayG++giri++ ++l+
  lcl|FitnessBrowser__WCS417:GFF4653 454 QMNIQELSTCLQYGLPVKIVCLNNGVLGMVRQWQDMSYNSRHSHSYMES-LPDFVKLVEAYGHVGIRITDLKDLK 527
                                         ************************************************5.************************* PP

                           TIGR00118 516 eklkealesk.epvlldvevdkeeevlPmvapGagldelve 555
                                          k++ea+++k ++v++d++vd++e+v+Pm+++ +++ +++ 
  lcl|FitnessBrowser__WCS417:GFF4653 528 PKMEEAFAMKdRLVFIDIQVDTSEHVYPMQIKDGSMRDMWL 568
                                         ******9988799*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (574 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.78
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis