GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Pseudomonas fluorescens FW300-N2E3

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate AO353_09035 AO353_09035 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 AO353_09035
           diaminopimelate decarboxylase
          Length = 415

 Score =  317 bits (811), Expect = 5e-91
 Identities = 166/383 (43%), Positives = 246/383 (64%), Gaps = 2/383 (0%)

Query: 13  TPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEI 72
           TP Y+Y    I+  +L + +A  G   L+C+A+KANSNL +L++LA L +G D VS GE+
Sbjct: 27  TPTYVYSRAHIEAQYLAFADALAGTPHLVCFAVKANSNLGVLNVLARLGAGFDIVSGGEL 86

Query: 73  QRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARI 132
           +R L AG +P +IVFSGVGK+  ++ +AL++ +   NVES  EL+ ++ +A  LG++A I
Sbjct: 87  ERVLAAGGQPDKIVFSGVGKTREDMRRALEVGVHCFNVESTDELERLQVVAAELGVRAPI 146

Query: 133 SIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLD 192
           S+R+NP++DA THPYISTGLKENKFG+   +A ++++ A +   LE V V  HIGSQL  
Sbjct: 147 SLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYVRAAQLPNLEVVGVDCHIGSQLTT 206

Query: 193 LEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL 252
           L P ++A  ++  +   L   GI LR  D+GGG+GV Y +EE     DY + +   + G 
Sbjct: 207 LPPFLDALDRLLALIDRLGDCGIYLRHIDLGGGLGVRYRDEEPPLAADYIKAVRERIDGR 266

Query: 253 DLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIRVIT 312
           DLT++ EPGR IVA +G L+T+V Y K  ++K F IVDA MND +RP+LY A   +  + 
Sbjct: 267 DLTLVFEPGRFIVANAGVLLTEVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAVR 326

Query: 313 PSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKL 372
           P +       D+VGP+CE+ D   KD  L  LE GD +A+   GAYG  M+S YN+R + 
Sbjct: 327 P-RATPARAYDIVGPICETGDFLAKDRQL-ALEEGDLLAVHSAGAYGFVMSSNYNTRGRA 384

Query: 373 LELALEDHKIRVIRKREALEDLW 395
            E+ ++  +   +R+RE + +L+
Sbjct: 385 AEVLVDGDQAIEVRRRETVAELF 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: 383
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 AO353_09035 AO353_09035 (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.6388.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   4.1e-163  528.6   0.0   5.2e-163  528.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035  AO353_09035 diaminopimelate deca


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035  AO353_09035 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.3   0.0  5.2e-163  5.2e-163       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.3 bits;  conditional E-value: 5.2e-163
                                     TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrll 69 
                                                   +dgel++egv+l ++ae+fgtP+Yvy+++++++++ a++ a +++ +lv++AvKAnsnl vl++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035   7 RDGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYLAFADALAGTPHLVCFAVKANSNLGVLNVL 71 
                                                   799******************************************9******************* PP

                                     TIGR01048  70 aeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleei 134
                                                   a++G+g+d+vsgGEler+laAg +++kivfsg+gk++e++++ale++++++nv+s++ele+l+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035  72 ARLGAGFDIVSGGELERVLAAGGQPDKIVFSGVGKTREDMRRALEVGVHCFNVESTDELERLQVV 136
                                                   ***************************************************************** PP

                                     TIGR01048 135 akelgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIG 199
                                                   a+elg +a+++lRvnpdvda th+yisTGlke+KFGi++++ae++y +a++l++le+vG+++HIG
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 137 AAELGVRAPISLRVNPDVDAGTHPYISTGLKENKFGIAIADAEDVYVRAAQLPNLEVVGVDCHIG 201
                                                   ***************************************************************** PP

                                     TIGR01048 200 SqildlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklek 264
                                                   Sq++ l pf +a+++++ l+++l + gi l+++dlGGGlg++y++ee +p +++y +++ e++ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 202 SQLTTLPPFLDALDRLLALIDRLGDCGIYLRHIDLGGGLGVRYRDEE-PPLAADYIKAVRERIDG 265
                                                   **********************************************9.999*******9999888 PP

                                     TIGR01048 265 eaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaal 329
                                                        ++l+l++EpGR++vanagvllt+Ve++K++e++ f++vDa+mndliRpalY+a+++++a+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 266 -----RDLTLVFEPGRFIVANAGVLLTEVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAV 325
                                                   .....7*********************************************************** PP

                                     TIGR01048 330 krleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevl 394
                                                    r +++++  +d+vGp+CE+gD+lakdr+l   e Gdllav+saGAYg+ mssnYn+r+r+aevl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 326 -RPRATPARAYDIVGPICETGDFLAKDRQLALEE-GDLLAVHSAGAYGFVMSSNYNTRGRAAEVL 388
                                                   .89***************************8776.****************************** PP

                                     TIGR01048 395 veegkarlirrretledllale 416
                                                   v++++a  +rrret+++l+a e
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_09035 389 VDGDQAIEVRRRETVAELFAGE 410
                                                   ******************9876 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.50
//
[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