Alignments for a candidate for ilvI in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Pseudomonas benzenivorans DSM 8628

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_090448334.1 BLS63_RS24040 acetolactate synthase 3 large subunit

Query= BRENDA::P00893
         (574 letters)



>NCBI__GCF_900100495.1:WP_090448334.1
          Length = 574

 Score =  765 bits (1975), Expect = 0.0
 Identities = 370/576 (64%), Positives = 455/576 (78%), Gaps = 4/576 (0%)

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

Query: 61  LARATGEVGVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVG 120
            ARATG+ GVVLVTSGPGATNAITGIATAYMDSIP+VVLSGQV ++++G DAFQE DM+G
Sbjct: 61  YARATGKAGVVLVTSGPGATNAITGIATAYMDSIPMVVLSGQVPSNMVGTDAFQETDMIG 120

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

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

Query: 241 LMGLGAFPATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATV 300
           LMGLG +P T RQ LGMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N   K+CPNA +
Sbjct: 241 LMGLGGYPGTDRQFLGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGANKFCPNAKI 300

Query: 301 LHIDIDPTSISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWR-A 359
           +HIDIDP SISKT+ ADIPIVG    VL +M+ ++ +   +   + +  WW+QI++WR +
Sbjct: 301 IHIDIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIGENLSKEALSSWWKQIDEWRGS 360

Query: 360 RQCLKYDT-HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSG 418
           R    YD      IKPQ VIETL  +T+GDA+VTSDVGQHQMFAA YY F+KP RWINSG
Sbjct: 361 RGMFPYDKGDGSIIKPQTVIETLCEVTRGDAFVTSDVGQHQMFAAQYYRFNKPNRWINSG 420

Query: 419 GLGTMGFGLPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYL 478
           GLGTMGFGLPAA+GVK+  P++ V CVTG+GSIQMNIQELST LQY+LPV +VNLNN  L
Sbjct: 421 GLGTMGFGLPAAMGVKLNFPDDDVACVTGEGSIQMNIQELSTCLQYDLPVKIVNLNNGAL 480

Query: 479 GMVKQWQDMIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNN 538
           GMV+QWQDM+YS RHS SYM+SLPDF++LAEAYGHVG++I+   +L+ K+ EA      +
Sbjct: 481 GMVRQWQDMMYSSRHSHSYMESLPDFIKLAEAYGHVGMRITELKDLKPKMEEAF--ALKD 538

Query: 539 RLVFVDVTVDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           RLVF+D+ VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 RLVFLDIQVDTSEHVYPMQIKDGAMRDMWLSKTERT 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: 1032
Number of extensions: 37
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 WP_090448334.1 BLS63_RS24040 (acetolactate synthase 3 large 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.14631.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-261  855.0   0.3   1.4e-261  854.8   0.3    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090448334.1  BLS63_RS24040 acetolactate synth


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090448334.1  BLS63_RS24040 acetolactate synthase 3 large subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  854.8   0.3  1.4e-261  1.4e-261       1     556 [.       4     569 ..       4     570 .. 0.97

  Alignments for each domain:
  == domain 1  score: 854.8 bits;  conditional E-value: 1.4e-261
                                 TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydaly.dselehilvrheqaaahaadGyarasGkvGvvl 68 
                                               l+gae++v+ l++egv+ ++GyPGGa+l+iydal+ + e++hilvrheqaa+h+adGyara+Gk+Gvvl
  lcl|NCBI__GCF_900100495.1:WP_090448334.1   4 LSGAEMVVRFLRDEGVKNIYGYPGGALLHIYDALFkEPEVNHILVRHEQAATHMADGYARATGKAGVVL 72 
                                               68*********************************889******************************* PP

                                 TIGR00118  69 atsGPGatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpei 137
                                               +tsGPGatn++tgiatay+ds+P+vvl+Gqv+++++G+dafqe d++Gi++p++khsf++k+a+++pe+
  lcl|NCBI__GCF_900100495.1:WP_090448334.1  73 VTSGPGATNAITGIATAYMDSIPMVVLSGQVPSNMVGTDAFQETDMIGISRPIVKHSFMIKHASEIPEV 141
                                               ********************************************************************* PP

                                 TIGR00118 138 lkeafeiastGrPGPvlvdlPkdvteaeieleve..ekvelpgykptvkghklqikkaleliekakkPv 204
                                               +k+af++a++GrPGPv+vd+Pkd+t+++ ++e+   +k +l++y p ++gh  qi+ka+el+ +ak+P+
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 142 MKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYVypKKAKLRSYSPALRGHSGQIRKAAELLLSAKRPI 210
                                               *************************99888777666********************************* PP

                                 TIGR00118 205 llvGgGviiaeaseelkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliav 273
                                               l+ GgGvi+++a + l+ela++l++pvt tl+GlG++p +++++lgmlGmhG+++anla+++ad+++av
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 211 LYSGGGVIMGGAAAPLTELAQMLNLPVTNTLMGLGGYPGTDRQFLGMLGMHGSYTANLAMHHADVILAV 279
                                               ********************************************************************* PP

                                 TIGR00118 274 GarfddrvtgnlakfapeakiihididPaeigknvkvdipivGdakkvleellkklkee....ekkeke 338
                                               Garfddrv +  +kf+p+akiihididPa+i+k++k+dipivG + +vl+e+++ +ke     +k+   
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 280 GARFDDRVINGANKFCPNAKIIHIDIDPASISKTIKADIPIVGPVDSVLTEMVAIVKEIgenlSKEALS 348
                                               *****************************************************9999887766455545 PP

                                 TIGR00118 339 .Wlekieewkkeyilk.ldeeees.ikPqkvikelskllkdeaivttdvGqhqmwaaqfyktkkprkfi 404
                                                W+++i+ew+ +  +  +d+ ++s ikPq+vi++l+++++++a+vt+dvGqhqm+aaq+y+++kp+++i
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 349 sWWKQIDEWRGSRGMFpYDKGDGSiIKPQTVIETLCEVTRGDAFVTSDVGQHQMFAAQYYRFNKPNRWI 417
                                               6*********8775554999888879******************************************* PP

                                 TIGR00118 405 tsgGlGtmGfGlPaalGakvakpeetvvavtGdgsfqmnlqelstiveydipvkivilnnellGmvkqW 473
                                               +sgGlGtmGfGlPaa+G+k+  p+++v +vtG+gs+qmn+qelst+ +yd+pvkiv+lnn  lGmv+qW
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 418 NSGGLGTMGFGLPAAMGVKLNFPDDDVACVTGEGSIQMNIQELSTCLQYDLPVKIVNLNNGALGMVRQW 486
                                               ********************************************************************* PP

                                 TIGR00118 474 qelfyeerysetklaselpdfvklaeayGvkgiriekpeeleeklkealesk.epvlldvevdkeeevl 541
                                               q+++y+ r+s+++++s lpdf+klaeayG++g+ri++ ++l+ k++ea++ k ++v+ld++vd++e+v+
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 487 QDMMYSSRHSHSYMES-LPDFIKLAEAYGHVGMRITELKDLKPKMEEAFALKdRLVFLDIQVDTSEHVY 554
                                               ***************5.*******************************9987699************** PP

                                 TIGR00118 542 PmvapGagldelvee 556
                                               Pm+++ +++ +++ +
  lcl|NCBI__GCF_900100495.1:WP_090448334.1 555 PMQIKDGAMRDMWLS 569
                                               ************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: 00:00:00.04
# Mc/sec: 7.38
//
[ok]

This GapMind analysis is from Apr 10 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