Alignments for a candidate for ilvI in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas stutzeri RCH2

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate GFF1003 Psest_1036 acetolactate synthase, large subunit, biosynthetic type

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__psRCH2:GFF1003
          Length = 574

 Score =  748 bits (1930), Expect = 0.0
 Identities = 359/576 (62%), Positives = 446/576 (77%), Gaps = 4/576 (0%)

Query: 1   MEMLSGAEMVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADG 60
           ME+LSGAEMVVRSL D+GVK ++GYPGGAVL IYDAL     I+H+LVRHEQAA HMADG
Sbjct: 1   MELLSGAEMVVRSLRDEGVKYIYGYPGGAVLHIYDALFKEKAIEHILVRHEQAATHMADG 60

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ GVVLVTSGPGATNAITGIATA+MDSIP+VV+SGQV ++++G DAFQE DM+G
Sbjct: 61  YARATGKAGVVLVTSGPGATNAITGIATAFMDSIPMVVISGQVPSTMVGTDAFQETDMIG 120

Query: 121 ISRPVVKHSFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESV 180
           ISRP+VKHSF++K   +IP+V+KKAF+LA SGRPGPVV+D+PKD+ NPA K  YV+P+  
Sbjct: 121 ISRPIVKHSFMIKHPSEIPEVMKKAFYLAESGRPGPVVIDIPKDMTNPAEKFEYVYPKKA 180

Query: 181 SMRSYNPTTTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCS 240
            +RSY+P   GH GQI++A + L+ AK+P++Y GGG I      QL E  + LNLPV  +
Sbjct: 181 KLRSYSPAVRGHSGQIRKAAELLLGAKRPIIYAGGGVILGKASAQLTELAKMLNLPVTNT 240

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLG +P   RQ +GMLGMHG+Y AN+ MH++DVI AVG RFDDR  N  +K+CPNA +
Sbjct: 241 LMGLGCYPGGDRQFVGMLGMHGSYTANLAMHHSDVILAVGARFDDRVINGASKFCPNAKI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRAR 360
           +HIDIDP SISKT+ ADIPIVG    VL +M+ ++ +       + +  WW+QI++WR  
Sbjct: 301 IHIDIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIGQAPNAETVASWWKQIDEWRGN 360

Query: 361 QCL--KYDTHSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
             L    +     IKPQA IE L  +TKG+AYV SDVGQHQMFA  YY FDKP RW+NSG
Sbjct: 361 GRLFPYNEGDGSIIKPQAAIEVLCEVTKGEAYVASDVGQHQMFACQYYKFDKPNRWLNSG 420

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFGLPAA+GVK+  PE  V  VTG+GSIQMNIQELST LQY+LPV ++NLNN  L
Sbjct: 421 GLGTMGFGLPAAMGVKLNFPEADVAVVTGEGSIQMNIQELSTCLQYDLPVKIINLNNGAL 480

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM+Y+ R+S SYM+SLPDFV+LAEAYGHVG++I+   +L+  + EA      +
Sbjct: 481 GMVRQWQDMVYNSRYSHSYMESLPDFVKLAEAYGHVGMRITDLKDLKPMMEEAF--AMKD 538

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLVF+D+ VD +EHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 RLVFLDIAVDTAEHVYPMQIKDGAMRDMWLSKTERT 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: 34
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 GFF1003 Psest_1036 (acetolactate synthase, large subunit, biosynthetic type)
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.18020.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.8e-259  846.1   1.6   6.7e-259  845.9   1.6    1.0  1  lcl|FitnessBrowser__psRCH2:GFF1003  Psest_1036 acetolactate synthase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF1003  Psest_1036 acetolactate synthase, large subunit, biosynthetic type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  845.9   1.6  6.7e-259  6.7e-259       1     556 [.       4     569 ..       4     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 845.9 bits;  conditional E-value: 6.7e-259
                           TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvlatsGPG 74 
                                         l+gae++v+sl++egv++++GyPGGavl+iydal+ ++ +ehilvrheqaa+h+adGyara+Gk+Gvvl+tsGPG
  lcl|FitnessBrowser__psRCH2:GFF1003   4 LSGAEMVVRSLRDEGVKYIYGYPGGAVLHIYDALFkEKAIEHILVRHEQAATHMADGYARATGKAGVVLVTSGPG 78 
                                         68*********************************8889************************************ PP

                           TIGR00118  75 atnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeiastGr 149
                                         atn++tgiata++ds+P+vv++Gqv+++++G+dafqe d++Gi++p++khsf++k+++++pe++k+af++a++Gr
  lcl|FitnessBrowser__psRCH2:GFF1003  79 ATNAITGIATAFMDSIPMVVISGQVPSTMVGTDAFQETDMIGISRPIVKHSFMIKHPSEIPEVMKKAFYLAESGR 153
                                         *************************************************************************** PP

                           TIGR00118 150 PGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeaseelke 222
                                         PGPv++d+Pkd+t+++ ++e+   +k +l++y p v+gh  qi+ka+el+  ak+P++++GgGvi ++as++l+e
  lcl|FitnessBrowser__psRCH2:GFF1003 154 PGPVVIDIPKDMTNPAEKFEYVypKKAKLRSYSPAVRGHSGQIRKAAELLLGAKRPIIYAGGGVILGKASAQLTE 228
                                         *************99888777666*************************************************** PP

                           TIGR00118 223 laerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapeakiihi 297
                                         la++l++pvt tl+GlG++p  +++++gmlGmhG+++anla++++d+++avGarfddrv +  +kf+p+akiihi
  lcl|FitnessBrowser__psRCH2:GFF1003 229 LAKMLNLPVTNTLMGLGCYPGGDRQFVGMLGMHGSYTANLAMHHSDVILAVGARFDDRVINGASKFCPNAKIIHI 303
                                         *************************************************************************** PP

                           TIGR00118 298 didPaeigknvkvdipivGdakkvleellkklkee....ekkeke.Wlekieewkkeyilk.ldeeees.ikPqk 365
                                         didPa+i+k++k+dipivG + +vl+e+++ +ke     + ++   W+++i+ew+ +  l  ++e ++s ikPq+
  lcl|FitnessBrowser__psRCH2:GFF1003 304 DIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIgqapNAETVAsWWKQIDEWRGNGRLFpYNEGDGSiIKPQA 378
                                         *****************************99998877764444446*********9987765777776669**** PP

                           TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdgsf 440
                                          i+ l++++k+ea+v++dvGqhqm+a q+yk++kp+++++sgGlGtmGfGlPaa+G+k+  pe++v  vtG+gs+
  lcl|FitnessBrowser__psRCH2:GFF1003 379 AIEVLCEVTKGEAYVASDVGQHQMFACQYYKFDKPNRWLNSGGLGTMGFGLPAAMGVKLNFPEADVAVVTGEGSI 453
                                         *************************************************************************** PP

                           TIGR00118 441 qmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekpeele 515
                                         qmn+qelst+ +yd+pvki++lnn  lGmv+qWq+++y+ rys+++++s lpdfvklaeayG++g+ri++ ++l+
  lcl|FitnessBrowser__psRCH2:GFF1003 454 QMNIQELSTCLQYDLPVKIINLNNGALGMVRQWQDMVYNSRYSHSYMES-LPDFVKLAEAYGHVGMRITDLKDLK 527
                                         ************************************************5.************************* PP

                           TIGR00118 516 eklkealesk.epvlldvevdkeeevlPmvapGagldelvee 556
                                           ++ea+++k ++v+ld+ vd+ e+v+Pm+++ +++ +++ +
  lcl|FitnessBrowser__psRCH2:GFF1003 528 PMMEEAFAMKdRLVFLDIAVDTAEHVYPMQIKDGAMRDMWLS 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.23
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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