Alignments for a candidate for ilvI in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas putida KT2440

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate PP_4680 PP_4680 acetohydroxybutanoate synthase / acetolactate synthase

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__Putida:PP_4680
          Length = 574

 Score =  770 bits (1989), Expect = 0.0
 Identities = 375/576 (65%), Positives = 453/576 (78%), Gaps = 4/576 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME+LSGAEMVVR L D+GVK ++GYPGGA+L +YDAL     ++H+LVRHEQAA HMADG
Sbjct: 1   MELLSGAEMVVRFLRDEGVKHIYGYPGGALLHVYDALFKEPEVEHILVRHEQAATHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ GVVLVTSGPGATNAITGIATAYMDSIP+V+LSGQV ++++G DAFQE DM+G
Sbjct: 61  YARATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVILSGQVPSTMVGTDAFQETDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRP+VKHSF++K   +IP+VLKKAF+LA SGRPGPVVVD+PKD+ NPA K  YV+P+ V
Sbjct: 121 ISRPIVKHSFMIKNPTEIPEVLKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYVYPKKV 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            +RSY+P   GH GQI++A + L+AAK+PVVY GGG I  G  + L E  ++LNLPV  +
Sbjct: 181 KLRSYSPAVRGHSGQIRKAAEMLLAAKRPVVYSGGGVILGGGSEALTEIAKSLNLPVTNT 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLG FP T RQ LGMLGMHG+Y ANM MH+ADVIFAVG RFDDR  N  AK+CPNA +
Sbjct: 241 LMGLGGFPGTDRQFLGMLGMHGSYTANMAMHHADVIFAVGARFDDRVVNGPAKFCPNAKI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           +HIDIDP SISK + AD+PIVG    VL +ML +L +         +  WW+QI++WR  
Sbjct: 301 IHIDIDPASISKMIKADVPIVGPVDSVLSEMLGILKEIGEQPDKAALDAWWKQIDEWRGN 360

Query: 361 -QCLKYDT-HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
            +   YD      IKPQ VIETL  +T GDA+VTSDVGQHQMFAA YY F+KP RWINSG
Sbjct: 361 GELFPYDKGDGNVIKPQKVIETLCEVTNGDAFVTSDVGQHQMFAAQYYRFNKPNRWINSG 420

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFG PAA+GVK+  P++ V CVTG+GSIQMNIQELST +QY LPV +VNLNN  L
Sbjct: 421 GLGTMGFGFPAAMGVKLNFPDQDVACVTGEGSIQMNIQELSTCMQYGLPVKIVNLNNGVL 480

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM Y+GRHS SY++SLPDF++LAEAYGHVGI+I+   +L+ KL EA      +
Sbjct: 481 GMVRQWQDMAYNGRHSHSYVESLPDFIKLAEAYGHVGIRITSLKDLKPKLEEAF--AMKD 538

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLVF+D+ VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 RLVFIDIAVDRSEHVYPMQIKDGSMRDMWLSKTERT 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: 1051
Number of extensions: 33
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 PP_4680 PP_4680 (acetohydroxybutanoate synthase / acetolactate synthase)
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.28324.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-261  854.7   0.5   1.7e-261  854.5   0.5    1.0  1  lcl|FitnessBrowser__Putida:PP_4680  PP_4680 acetohydroxybutanoate sy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4680  PP_4680 acetohydroxybutanoate synthase / acetolactate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.5   0.5  1.7e-261  1.7e-261       1     556 [.       4     569 ..       4     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 854.5 bits;  conditional E-value: 1.7e-261
                           TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                         l+gae++v+ l++egv++++GyPGGa+l++ydal+ + e+ehilvrheqaa+h+adGyara+Gk+Gvvl+tsGPG
  lcl|FitnessBrowser__Putida:PP_4680   4 LSGAEMVVRFLRDEGVKHIYGYPGGALLHVYDALFkEPEVEHILVRHEQAATHMADGYARATGKAGVVLVTSGPG 78 
                                         68*********************************889************************************* PP

                           TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149
                                         atn++tgiatay+ds+P+v+l+Gqv+++++G+dafqe d++Gi++p++khsf++k++ ++pe+lk+af++a++Gr
  lcl|FitnessBrowser__Putida:PP_4680  79 ATNAITGIATAYMDSIPMVILSGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKNPTEIPEVLKKAFYLAQSGR 153
                                         *************************************************************************** PP

                           TIGR00118 150 PGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelke 222
                                         PGPv+vd+Pkd+t+++ ++e+   +kv+l++y p v+gh  qi+ka+e++ +ak+Pv++ GgGvi +++se l+e
  lcl|FitnessBrowser__Putida:PP_4680 154 PGPVVVDIPKDMTNPAEKFEYVypKKVKLRSYSPAVRGHSGQIRKAAEMLLAAKRPVVYSGGGVILGGGSEALTE 228
                                         *************99887777666*************************************************** PP

                           TIGR00118 223 laerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihi 297
                                         +a+ l++pvt tl+GlG+fp +++++lgmlGmhG+++an+a+++ad+++avGarfddrv +  akf+p+akiihi
  lcl|FitnessBrowser__Putida:PP_4680 229 IAKSLNLPVTNTLMGLGGFPGTDRQFLGMLGMHGSYTANMAMHHADVIFAVGARFDDRVVNGPAKFCPNAKIIHI 303
                                         *************************************************************************** PP

                           TIGR00118 298 didPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqk 365
                                         didPa+i+k++k+d+pivG + +vl+e+l  lke     +k   + W+++i+ew+ +  l  +d+ +++ ikPqk
  lcl|FitnessBrowser__Putida:PP_4680 304 DIDPASISKMIKADVPIVGPVDSVLSEMLGILKEIgeqpDKAALDaWWKQIDEWRGNGELFpYDKGDGNvIKPQK 378
                                         ****************************998888775554444457*********988776688877656***** PP

                           TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440
                                         vi++l+++++++a+vt+dvGqhqm+aaq+y+++kp+++i+sgGlGtmGfG+Paa+G+k+  p+++v +vtG+gs+
  lcl|FitnessBrowser__Putida:PP_4680 379 VIETLCEVTNGDAFVTSDVGQHQMFAAQYYRFNKPNRWINSGGLGTMGFGFPAAMGVKLNFPDQDVACVTGEGSI 453
                                         *************************************************************************** PP

                           TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515
                                         qmn+qelst+++y++pvkiv+lnn +lGmv+qWq++ y++r+s+++++s lpdf+klaeayG++giri++ ++l+
  lcl|FitnessBrowser__Putida:PP_4680 454 QMNIQELSTCMQYGLPVKIVNLNNGVLGMVRQWQDMAYNGRHSHSYVES-LPDFIKLAEAYGHVGIRITSLKDLK 527
                                         ************************************************5.************************* PP

                           TIGR00118 516 eklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556
                                          kl+ea+++k ++v++d+ vd++e+v+Pm+++ +++ +++ +
  lcl|FitnessBrowser__Putida:PP_4680 528 PKLEEAFAMKdRLVFIDIAVDRSEHVYPMQIKDGSMRDMWLS 569
                                         ******9988799**************************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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 8.17
//
[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