Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2E2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2E2

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf6N2E2_5175 Acetolactate synthase large subunit (EC 2.2.1.6)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175
          Length = 577

 Score =  759 bits (1961), Expect = 0.0
 Identities = 366/576 (63%), Positives = 448/576 (77%), Gaps = 4/576 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           +E+LSG EM+VR L D+GVK ++GYPGGA+L +YDAL     + H+LVRHEQAA HMADG
Sbjct: 4   VELLSGGEMLVRFLRDEGVKYIYGYPGGALLHVYDALFKEPEVTHILVRHEQAATHMADG 63

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ GVVLVTSGPGATNAITGIATAYMDSIP+V++SGQV ++++G DAFQE DM+G
Sbjct: 64  YARATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIG 123

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRP+VKHSF++K   +IP+V+KKAF+LA SGRPGPVVVD+PKD+ NPA K  Y++P+  
Sbjct: 124 ISRPIVKHSFMIKHASEIPEVMKKAFYLAESGRPGPVVVDVPKDMTNPAEKFEYIFPKKA 183

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            +RSY+P   GH GQI++A + L+AAK+PV+Y GGG I  G    L E  + LNLPV  +
Sbjct: 184 KLRSYSPAVRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNT 243

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLGAFP T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N  AK+CPNA +
Sbjct: 244 LMGLGAFPGTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKI 303

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRA- 359
           +HIDIDP SISKT+ AD+PIVG    VL +M+ +L +       + +  WW+Q+++WR  
Sbjct: 304 IHIDIDPASISKTIKADVPIVGPVESVLTEMVAILKEIGEVPNKESVASWWKQVDEWRGD 363

Query: 360 RQCLKYDT-HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
           R    YD      IKPQ VIETL  +TKGDA+VTSDVGQHQMFAA YY FDKP RWINSG
Sbjct: 364 RGLFPYDKGDGSVIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYKFDKPNRWINSG 423

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFG PAA+G+K++ PE  V CVTG+GSIQMNIQELST LQY LPV +V LNN  L
Sbjct: 424 GLGTMGFGFPAAMGIKLSFPEADVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVL 483

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM Y  RHS SYM+SLPDFV+LAEAYGHVG++I+   +L+SK+ EA      +
Sbjct: 484 GMVRQWQDMSYGSRHSHSYMESLPDFVKLAEAYGHVGVRITESKDLKSKMEEAF--AMKD 541

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLV +D+ VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 542 RLVVIDIAVDTSEHVYPMQIKDGSMRDMWLSKTERT 577


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: 1032
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: 577
Length adjustment: 36
Effective length of query: 538
Effective length of database: 541
Effective search space:   291058
Effective search space used:   291058
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 Pf6N2E2_5175 (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.29182.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
     9e-261  852.1   0.9     1e-260  851.9   0.9    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175  Acetolactate synthase large subu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175  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 !  851.9   0.9    1e-260    1e-260       1     556 [.       7     572 ..       7     573 .. 0.97

  Alignments for each domain:
  == domain 1  score: 851.9 bits;  conditional E-value: 1e-260
                                      TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGk 63 
                                                    l+g+e+lv+ l++egv++++GyPGGa+l++ydal+ + e++hilvrheqaa+h+adGyara+Gk
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175   7 LSGGEMLVRFLRDEGVKYIYGYPGGALLHVYDALFkEPEVTHILVRHEQAATHMADGYARATGK 70 
                                                    689********************************889************************** PP

                                      TIGR00118  64 vGvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsfl 127
                                                    +Gvvl+tsGPGatn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d++Gi++p++khsf+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175  71 AGVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKHSFM 134
                                                    **************************************************************** PP

                                      TIGR00118 128 vkkaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklq 189
                                                    +k+a+++pe++k+af++a++GrPGPv+vd+Pkd+t+++ ++e+   +k +l++y p v+gh  q
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 135 IKHASEIPEVMKKAFYLAESGRPGPVVVDVPKDMTNPAEKFEYIfpKKAKLRSYSPAVRGHSGQ 198
                                                    ************************************9988888777****************** PP

                                      TIGR00118 190 ikkaleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlG 253
                                                    i+ka+e++ +ak+Pvl+ GgGvi +++s+ l+ela++l++pvt tl+GlGafp ++++++gmlG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 199 IRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAFPGTDRQFIGMLG 262
                                                    **************************************************************** PP

                                      TIGR00118 254 mhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGd 317
                                                    mhG+++anla+++ad+++avGarfddrv +  akf+p+akiihididPa+i+k++k+d+pivG 
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 263 MHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPASISKTIKADVPIVGP 326
                                                    **************************************************************** PP

                                      TIGR00118 318 akkvleellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqkvikelskll 374
                                                    +++vl+e+++ lke     +k++   W+++++ew+ +  l  +d+ ++s ikPq+vi++l++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 327 VESVLTEMVAILKEIgevpNKESVAsWWKQVDEWRGDRGLFpYDKGDGSvIKPQTVIETLCEVT 390
                                                    ********999888777764444446*********999877688888777************** PP

                                      TIGR00118 375 kdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438
                                                    k++a+vt+dvGqhqm+aaq+yk++kp+++i+sgGlGtmGfG+Paa+G+k++ pe++v +vtG+g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 391 KGDAFVTSDVGQHQMFAAQYYKFDKPNRWINSGGLGTMGFGFPAAMGIKLSFPEADVACVTGEG 454
                                                    **************************************************************** PP

                                      TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayG 502
                                                    s+qmn+qelst+ +y++pvkivilnn +lGmv+qWq++ y  r+s+++++s lpdfvklaeayG
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 455 SIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQDMSYGSRHSHSYMES-LPDFVKLAEAYG 517
                                                    **************************************************5.************ PP

                                      TIGR00118 503 vkgiriekpeeleeklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556
                                                    ++g+ri++ ++l++k++ea+++k ++v++d+ vd++e+v+Pm+++ +++ +++ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5175 518 HVGVRITESKDLKSKMEEAFAMKdRLVVIDIAVDTSEHVYPMQIKDGSMRDMWLS 572
                                                    *******************9988799**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (577 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: 00:00:00.02
# Mc/sec: 11.34
//
[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