Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas fluorescens FW300-N2E3

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate AO353_14495 AO353_14495 acetolactate synthase 3 catalytic subunit

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_14495
          Length = 574

 Score =  753 bits (1944), Expect = 0.0
 Identities = 362/576 (62%), 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: 1   VELLSGGEMLVRFLRDEGVKYIYGYPGGALLHVYDALFKEPEVTHILVRHEQAATHMADG 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  YV+P+  
Sbjct: 121 ISRPIVKHSFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYVFPKKA 180

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

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLG +P T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N  AK+CPNA +
Sbjct: 241 LMGLGGYPGTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKI 300

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

Query: 360 RQCLKYDT-HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
           R    Y+      IKPQ VIETL  +TKGDA+VTSDVGQHQMFAA YY F+KP RWINSG
Sbjct: 361 RGLFPYEKGDGSVIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYTFNKPNRWINSG 420

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFG PAA+G+K++ P+  V CVTG+GSIQMNIQELST LQY LPV +V LNN  L
Sbjct: 421 GLGTMGFGFPAAMGIKLSFPDADVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVL 480

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM Y  RHS SYM+SLPDFV+LAEAYGHVG++I+   +L+SK+ EA      +
Sbjct: 481 GMVRQWQDMSYGSRHSHSYMESLPDFVKLAEAYGHVGVRITDSKDLKSKMEEAF--AMKD 538

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLV +D++VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 RLVVLDISVDTSEHVYPMQIKDGSMRDMWLSKTERT 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: 1031
Number of extensions: 31
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 AO353_14495 AO353_14495 (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.11091.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.7e-260  851.1   0.7     2e-260  850.9   0.7    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495  AO353_14495 acetolactate synthas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495  AO353_14495 acetolactate synthase 3 catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  850.9   0.7    2e-260    2e-260       1     556 [.       4     569 ..       4     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 850.9 bits;  conditional E-value: 2e-260
                                     TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkv 64 
                                                   l+g+e+lv+ l++egv++++GyPGGa+l++ydal+ + e++hilvrheqaa+h+adGyara+Gk+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495   4 LSGGEMLVRFLRDEGVKYIYGYPGGALLHVYDALFkEPEVTHILVRHEQAATHMADGYARATGKA 68 
                                                   689********************************889*************************** PP

                                     TIGR00118  65 GvvlatsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvk 129
                                                   Gvvl+tsGPGatn++tgiatay+ds+P+v+++Gqv+++++G+dafqe d++Gi++p++khsf++k
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495  69 GVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIK 133
                                                   ***************************************************************** PP

                                     TIGR00118 130 kaedlpeilkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikk 192
                                                   +a+++pe++k+af++a++GrPGPv+vd+Pkd+t+++ ++e+   +k +l++y p v+gh  qi+k
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 134 HASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYVfpKKAKLRSYSPAVRGHSGQIRK 198
                                                   **********************************9999999888********************* PP

                                     TIGR00118 193 aleliekakkPvllvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGt 257
                                                   a+e++ +ak+Pvl+ GgGvi +++s+ l+ela++l++pvt tl+GlG++p ++++++gmlGmhG+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 199 AAEMLLAAKRPVLYSGGGVILGGGSAPLTELAQMLNLPVTNTLMGLGGYPGTDRQFIGMLGMHGS 263
                                                   ***************************************************************** PP

                                     TIGR00118 258 keanlavseadlliavGarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvl 322
                                                   ++anla+++ad+++avGarfddrv +  akf+p+akiihididPa+i+k++k+d+pivG +++vl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 264 YTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPASISKTIKADVPIVGPVESVL 328
                                                   ***************************************************************** PP

                                     TIGR00118 323 eellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqkvikelskllkdeaiv 380
                                                   +e+++ lke     +k++   W+++++ew+ +  l  +++ ++s ikPq+vi++l++++k++a+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 329 TEMVAILKEIgetpNKESVAsWWKQVDEWRGDRGLFpYEKGDGSvIKPQTVIETLCEVTKGDAFV 393
                                                   ***999888777764444446*********999877677777666******************** PP

                                     TIGR00118 381 ttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlq 445
                                                   t+dvGqhqm+aaq+y+++kp+++i+sgGlGtmGfG+Paa+G+k++ p+++v +vtG+gs+qmn+q
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 394 TSDVGQHQMFAAQYYTFNKPNRWINSGGLGTMGFGFPAAMGIKLSFPDADVACVTGEGSIQMNIQ 458
                                                   ***************************************************************** PP

                                     TIGR00118 446 elstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriek 510
                                                   elst+ +y++pvkivilnn +lGmv+qWq++ y  r+s+++++s lpdfvklaeayG++g+ri++
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 459 ELSTCLQYGLPVKIVILNNGVLGMVRQWQDMSYGSRHSHSYMES-LPDFVKLAEAYGHVGVRITD 522
                                                   *******************************************5.******************** PP

                                     TIGR00118 511 peeleeklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556
                                                    ++l++k++ea+++k ++v+ld++vd++e+v+Pm+++ +++ +++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_14495 523 SKDLKSKMEEAFAMKdRLVVLDISVDTSEHVYPMQIKDGSMRDMWLS 569
                                                   ***********9988699**************************976 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.76
//
[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