Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N1B4

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N1B4

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf1N1B4_2878 Acetolactate synthase large subunit (EC 2.2.1.6)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878
          Length = 566

 Score =  749 bits (1933), Expect = 0.0
 Identities = 359/568 (63%), Positives = 444/568 (78%), 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  Y++P+   +RSY+P 
Sbjct: 121 SFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYIFPKKAKLRSYSPA 180

Query: 189 TTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMGLGAFP 248
             GH GQI++A + L+AAK+PV+Y GGG I  G    L E  + LNLPV  +LMGLGA+P
Sbjct: 181 VRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAYP 240

Query: 249 ATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPT 308
            T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N  AK+CPNA ++HIDIDP 
Sbjct: 241 GTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPA 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
                IKPQ VIETL  +TKGDA+VTSDVGQHQMFAA YY F+KP RWINSGGLGTMGFG
Sbjct: 361 GDGSVIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYTFNKPNRWINSGGLGTMGFG 420

Query: 427 LPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGMVKQWQD 486
           LPAA+G+K++ P++ V CVTG+GSIQMNIQELST LQY LPV +V LNN  LGMV+QWQD
Sbjct: 421 LPAAMGIKLSFPDDDVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQD 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: 1015
Number of extensions: 32
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 Pf1N1B4_2878 (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.974620.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.2e-258  845.0   0.9   1.4e-258  844.8   0.9    1.0  1  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  844.8   0.9  1.4e-258  1.4e-258       6     556 ..       1     561 [.       1     562 [. 0.97

  Alignments for each domain:
  == domain 1  score: 844.8 bits;  conditional E-value: 1.4e-258
                                  TIGR00118   6 ilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsG 72 
                                                +lv+ l++egv++++GyPGGa+l++ydal+ + e++hilvrheqaa+h+adGyara+Gk+Gvvl+tsG
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878   1 MLVRFLRDEGVKYIYGYPGGALLHVYDALFkEPEVTHILVRHEQAATHMADGYARATGKAGVVLVTSG 68 
                                                7899**************************889*********************************** PP

                                  TIGR00118  73 PGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilke 140
                                                PGatn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d++Gi++p++khsf++k+a+++pe++k+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878  69 PGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKHASEIPEVMKK 136
                                                ******************************************************************** PP

                                  TIGR00118 141 afeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvll 206
                                                af++a++GrPGPv+vd+Pkd+t+++ ++e+   +k +l++y p v+gh  qi+ka+e++ +ak+Pvl+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 137 AFYLAQSGRPGPVVVDIPKDMTNPAEKFEYIfpKKAKLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLY 204
                                                ***********************9988888777*********************************** PP

                                  TIGR00118 207 vGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavG 274
                                                 GgGvi +++s+ l+ela++l++pvt tl+GlGa+p ++++++gmlGmhG+++anla+++ad+++avG
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 205 SGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAYPGTDRQFIGMLGMHGSYTANLAMHHADVILAVG 272
                                                ******************************************************************** PP

                                  TIGR00118 275 arfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                                arfddrv +  akf+p+akiihididPa+i+k++k+d+pivG +++vl+e+++ lke     +k++  
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 273 ARFDDRVINGPAKFCPNAKIIHIDIDPASISKTIKADVPIVGPVESVLTEMVAILKEIgetpNKESVA 340
                                                ***************************************************99988877776444444 PP

                                  TIGR00118 339 .Wlekieewkkeyilk.ldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkf 403
                                                 W+++++ew+ +  l  +d+ ++s ikPq+vi++l++++k++a+vt+dvGqhqm+aaq+y+++kp+++
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 341 sWWKQVDEWRGDRGLFpYDKGDGSvIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYTFNKPNRW 408
                                                6*********999877688888777******************************************* PP

                                  TIGR00118 404 itsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvk 471
                                                i+sgGlGtmGfGlPaa+G+k++ p+++v +vtG+gs+qmn+qelst+ +y++pvkivilnn +lGmv+
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 409 INSGGLGTMGFGLPAAMGIKLSFPDDDVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVR 476
                                                ******************************************************************** PP

                                  TIGR00118 472 qWqelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkee 538
                                                qWq++ y  r+s+++++s lpdfvklaeayG++g+ri++ ++l++k++ea+++k ++v++d++vd++e
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 477 QWQDMSYGSRHSHSYMES-LPDFVKLAEAYGHVGVRITESKDLKSKMEEAFAMKdRLVVIDISVDTSE 543
                                                *****************5.*******************************9988799*********** PP

                                  TIGR00118 539 evlPmvapGagldelvee 556
                                                +v+Pm+++ +++ +++ +
  FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878 544 HVYPMQIKDGSMRDMWLS 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 17.29
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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