GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Pseudomonas stutzeri RCH2

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate GFF3695 Psest_3764 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__psRCH2:GFF3695 Psest_3764 diaminopimelate
           decarboxylase
          Length = 415

 Score =  315 bits (807), Expect = 2e-90
 Identities = 168/389 (43%), Positives = 247/389 (63%), Gaps = 2/389 (0%)

Query: 7   LFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADC 66
           L Q   TP Y+Y    I+  +  Y +A  G   L+C+A+KANSNL +L++LA L +G D 
Sbjct: 21  LAQRFGTPTYVYSRAHIEAQYRAYADALDGMPHLVCFAVKANSNLGVLNVLARLGAGFDI 80

Query: 67  VSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSL 126
           VS GE++R L AG +P RIVFSGVGK+  ++ +AL++ +   NVES  EL+ ++ +A  L
Sbjct: 81  VSRGELERVLAAGGQPDRIVFSGVGKTRDDMRRALEVGVHCFNVESTDELERLQQVAAEL 140

Query: 127 GIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHI 186
           G KA +S+R+NP++DA THPYISTGLKENKFG+    A  ++  A +   LE V V  HI
Sbjct: 141 GKKAPVSLRVNPDVDAGTHPYISTGLKENKFGIDIDNAEAVYARAAELPNLEVVGVDCHI 200

Query: 187 GSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGIL 246
           GSQL  L P ++A  ++  +   L A GI +R  D+GGG+GV Y +E+     DY Q + 
Sbjct: 201 GSQLTSLPPFLDALDRLLALTDRLAARGIQIRHLDLGGGLGVRYRDEQPPLAGDYIQAVR 260

Query: 247 NALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKH 306
             ++G  L ++ EPGRSIVA +G L+T+V Y K   +K F IVDA MND +RP+LY A  
Sbjct: 261 QRIEGRGLALVFEPGRSIVANAGVLLTRVEYLKHTAHKDFAIVDAAMNDLIRPALYQAWM 320

Query: 307 AIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQY 366
            +  + P +G +    D+VGP+CE+ D   KD  L  +E GD +A+   GAYG  M+S Y
Sbjct: 321 NVIAVQPHEG-DTRRYDIVGPICETGDFLAKDRELALVE-GDLLAVCSAGAYGFVMSSNY 378

Query: 367 NSRPKLLELALEDHKIRVIRKREALEDLW 395
           N+R +  E+ ++  +   +R+RE++++L+
Sbjct: 379 NTRGRAAEVLVDGDQAFEVRRRESVQELY 407


Lambda     K      H
   0.319    0.138    0.389 

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: 378
Number of extensions: 12
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: 405
Length of database: 415
Length adjustment: 31
Effective length of query: 374
Effective length of database: 384
Effective search space:   143616
Effective search space used:   143616
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.24055.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.25
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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:

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:

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, or view the source code, or see 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