GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Pseudomonas fluorescens GW456-L13

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate PfGW456L13_845 Diaminopimelate decarboxylase (EC 4.1.1.20)

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845
           Diaminopimelate decarboxylase (EC 4.1.1.20)
          Length = 415

 Score =  318 bits (814), Expect = 2e-91
 Identities = 169/383 (44%), Positives = 245/383 (63%), Gaps = 2/383 (0%)

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

Query: 73  QRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARI 132
           +R L AG    +IVFSGVGK+  ++ +AL++ +   NVES  EL+ ++ +A  LG++A I
Sbjct: 87  ERVLAAGGSADKIVFSGVGKTRDDMRRALEVGVHCFNVESTDELERLQVVAAELGVRAPI 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 I+A  ++  +   L   GI LR  D+GGG+GV Y++EE     DY + +   L G 
Sbjct: 207 LPPFIDALDRLLGLVDRLGDCGIYLRHIDLGGGLGVRYKDEEPPLAADYIKAVRERLDGR 266

Query: 253 DLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIRVIT 312
           DL ++ EPGR IVA +G L+TQV Y K  ++K F IVDA MND +RP+LY A   +  ++
Sbjct: 267 DLALVFEPGRFIVANAGVLLTQVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAVS 326

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

Query: 373 LELALEDHKIRVIRKREALEDLW 395
            E+ ++  +   +R+RE + +L+
Sbjct: 385 AEVLVDGDQAFEVRRRETVAELY 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: 381
Number of extensions: 11
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 PfGW456L13_845 (Diaminopimelate decarboxylase (EC 4.1.1.20))
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.13147.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
     1e-162  527.3   0.0   1.3e-162  527.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845  Diaminopimelate decarboxylase (E


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845  Diaminopimelate decarboxylase (EC 4.1.1.20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.0   0.0  1.3e-162  1.3e-162       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 527.0 bits;  conditional E-value: 1.3e-162
                                              TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAn 60 
                                                            +dgel++egv+l ++ae+fgtP+Yvy+++++++++ a++ a  ++ +lv+YAvKAn
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845   7 RDGELFAEGVALSAIAERFGTPTYVYSRAHIEAQYLAYADALVGTPHLVCYAVKAN 62 
                                                            799******************************************9********** PP

                                              TIGR01048  61 snlavlrllaeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaalele 116
                                                            snl vl++la++G+g+d+vs GEler+laAg +a+kivfsg+gk+++++++ale++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845  63 SNLGVLNVLARLGAGFDIVSRGELERVLAAGGSADKIVFSGVGKTRDDMRRALEVG 118
                                                            ******************************************************** PP

                                              TIGR01048 117 iklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyisTGlkesKFGie 172
                                                            ++++nv+s++ele+l+ +a+elg +a+++lRvnpdvda th+yisTGlke+KFGi+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 119 VHCFNVESTDELERLQVVAAELGVRAPISLRVNPDVDAGTHPYISTGLKENKFGIA 174
                                                            ******************************************************** PP

                                              TIGR01048 173 veeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegie 228
                                                            +++ae++y +a++l++le+vG+++HIGSq++ l pf++a+++++ l+++l + gi 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 175 IADAEDVYVRAAQLPNLEVVGVDCHIGSQLTTLPPFIDALDRLLGLVDRLGDCGIY 230
                                                            ******************************************************** PP

                                              TIGR01048 229 leeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslva 284
                                                            l+++dlGGGlg++y++ee +p +++y +++ e+l +     ++l l++EpGR++va
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 231 LRHIDLGGGLGVRYKDEE-PPLAADYIKAVRERLDG-----RDLALVFEPGRFIVA 280
                                                            *****************9.999*********99999.....6************** PP

                                              TIGR01048 285 nagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetv 340
                                                            nagvllt+Ve++K++e++ f++vDa+mndliRpalY+a+++++a++  +  ++  +
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 281 NAGVLLTQVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVTAVS-PRTSAARAY 335
                                                            *********************************************5.5777799** PP

                                              TIGR01048 341 dvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlve 396
                                                            d+vGp+CE+gD+lakdr+l   e Gdllav+saGAYg+ mssnYn+r+r+aevlv+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 336 DIVGPICETGDFLAKDRQLALEE-GDLLAVHSAGAYGFVMSSNYNTRGRAAEVLVD 390
                                                            *******************8776.******************************** PP

                                              TIGR01048 397 egkarlirrretledllale 416
                                                            +++a  +rrret+++l a e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_845 391 GDQAFEVRRRETVAELYAGE 410
                                                            ***************99866 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: 00:00:00.02
# Mc/sec: 7.04
//
[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