Alignments for a candidate for lysA in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Pseudomonas stutzeri RCH2

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate GFF3695 Psest_3764 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__psRCH2:GFF3695
          Length = 415

 Score =  551 bits (1421), Expect = e-161
 Identities = 273/416 (65%), Positives = 335/416 (80%), Gaps = 2/416 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M+ F+Y+ DGQL+AE V L  LA ++GTP YVYSRA +E  + A+  ++   PHL+C+AV
Sbjct: 1   MEAFSYR-DGQLFAEGVALPALAQRFGTPTYVYSRAHIEAQYRAYADALDGMPHLVCFAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNLGVLN LARLG+GFDIVS GELERVLAAGG P ++VFSGVGKT  +M+RAL++ +
Sbjct: 60  KANSNLGVLNVLARLGAGFDIVSRGELERVLAAGGQPDRIVFSGVGKTRDDMRRALEVGV 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVES  EL+RL +VA ELG KAP+SLR+NPDVDA THPYISTGL++NKFGI  D A 
Sbjct: 120 HCFNVESTDELERLQQVAAELGKKAPVSLRVNPDVDAGTHPYISTGLKENKFGIDIDNAE 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            VY  A  LPNL+V G+DCHIGSQLT+L PF+DA DRLLAL D L A GI IRHLD+GGG
Sbjct: 180 AVYARAAELPNLEVVGVDCHIGSQLTSLPPFLDALDRLLALTDRLAARGIQIRHLDLGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV YRDE PP   +Y +A+  R+E  R L L+FEPGR+I ANAGVL+T+VE+LKHT HK
Sbjct: 240 LGVRYRDEQPPLAGDYIQAVRQRIE-GRGLALVFEPGRSIVANAGVLLTRVEYLKHTAHK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360
           +FAI+DAAMNDLIRPALYQAW ++I ++P +G+ + YD+VGP+CET DFL KDR+L L E
Sbjct: 299 DFAIVDAAMNDLIRPALYQAWMNVIAVQPHEGDTRRYDIVGPICETGDFLAKDRELALVE 358

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
           GDLLAV S+GAYGF MSSNYNTR R AEV+VDG++ + VR+RE +  L+A ES+LP
Sbjct: 359 GDLLAVCSAGAYGFVMSSNYNTRGRAAEVLVDGDQAFEVRRRESVQELYAGESLLP 414


Lambda     K      H
   0.319    0.137    0.405 

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: 533
Number of extensions: 16
Number of successful extensions: 2
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: 417
Length of database: 415
Length adjustment: 31
Effective length of query: 386
Effective length of database: 384
Effective search space:   148224
Effective search space used:   148224
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate GFF3695 Psest_3764 (diaminopimelate decarboxylase)
to HMM TIGR01048 (lysA: diaminopimelate decarboxylase (EC 4.1.1.20))

# 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/TIGR01048.hmm
# target sequence database:        /tmp/gapView.27837.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01048  [M=417]
Accession:   TIGR01048
Description: lysA: diaminopimelate decarboxylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.3e-166  538.8   0.0   3.8e-166  538.6   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3695  Psest_3764 diaminopimelate decar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3695  Psest_3764 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  538.6   0.0  3.8e-166  3.8e-166       4     416 ..       6     410 ..       3     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 538.6 bits;  conditional E-value: 3.8e-166
                           TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldv 78 
                                          +dg+l++egv+l +la++fgtP+Yvy++++++++++a++ a  +  +lv++AvKAnsnl vl++la++G+g+d+
  lcl|FitnessBrowser__psRCH2:GFF3695   6 YRDGQLFAEGVALPALAQRFGTPTYVYSRAHIEAQYRAYADALDGMPHLVCFAVKANSNLGVLNVLARLGAGFDI 80 
                                         579*******************************************9**************************** PP

                           TIGR01048  79 vsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvd 153
                                         vs GEler+laAg ++++ivfsg+gk+++++++ale++++++nv+s++ele+l+++a+elgkka+v+lRvnpdvd
  lcl|FitnessBrowser__psRCH2:GFF3695  81 VSRGELERVLAAGGQPDRIVFSGVGKTRDDMRRALEVGVHCFNVESTDELERLQQVAAELGKKAPVSLRVNPDVD 155
                                         *************************************************************************** PP

                           TIGR01048 154 aktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegie 228
                                         a th+yisTGlke+KFGi++++ae++y +a++l++le+vG+++HIGSq++ l pf +a+++++ l+++l+++gi+
  lcl|FitnessBrowser__psRCH2:GFF3695 156 AGTHPYISTGLKENKFGIDIDNAEAVYARAAELPNLEVVGVDCHIGSQLTSLPPFLDALDRLLALTDRLAARGIQ 230
                                         *************************************************************************** PP

                           TIGR01048 229 leeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrk 303
                                         +++ldlGGGlg++y++e+ +p + +y +++ +++e+     + l l++EpGRs+vanagvlltrVe++K++ ++ 
  lcl|FitnessBrowser__psRCH2:GFF3695 231 IRHLDLGGGLGVRYRDEQ-PPLAGDYIQAVRQRIEG-----RGLALVFEPGRSIVANAGVLLTRVEYLKHTAHKD 299
                                         ****************99.9***********99999.....699******************************* PP

                           TIGR01048 304 fvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYga 378
                                         f++vDa+mndliRpalY+a+++++a+ + +e  t ++d+vGp+CE+gD+lakdrel  ve Gdllav+saGAYg+
  lcl|FitnessBrowser__psRCH2:GFF3695 300 FAIVDAAMNDLIRPALYQAWMNVIAV-QPHEGDTRRYDIVGPICETGDFLAKDRELALVE-GDLLAVCSAGAYGF 372
                                         **************************.668888**************************9.************** PP

                           TIGR01048 379 smssnYnsrprpaevlveegkarlirrretledllale 416
                                          mssnYn+r+r+aevlv++++a  +rrre++++l a e
  lcl|FitnessBrowser__psRCH2:GFF3695 373 VMSSNYNTRGRAAEVLVDGDQAFEVRRRESVQELYAGE 410
                                         **********************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (415 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.67
//
[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