GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysA in Shewanella loihica PV-4

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate 5207805 Shew_0322 diaminopimelate decarboxylase (RefSeq)

Query= SwissProt::B4XMC6
         (405 letters)



>lcl|FitnessBrowser__PV4:5207805 Shew_0322 diaminopimelate
           decarboxylase (RefSeq)
          Length = 414

 Score =  320 bits (819), Expect = 6e-92
 Identities = 172/393 (43%), Positives = 245/393 (62%), Gaps = 2/393 (0%)

Query: 7   LFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADC 66
           L +T+ TP Y+Y    +++ +  +  A      +ICYA+KANSNL++L++LA L SG D 
Sbjct: 21  LAETYGTPLYVYSRATLERHWHAFDNAVADHPHMICYAVKANSNLAVLNVLARLGSGFDI 80

Query: 67  VSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSL 126
           VS GE+ R L+AG +  ++VFSGVGK+  E+E AL+  I   NVES  EL+ +  +A  L
Sbjct: 81  VSGGELARVLEAGGEASKVVFSGVGKTVAEMEMALEAGIYCFNVESAAELEQLNLVALRL 140

Query: 127 GIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHI 186
           G  A +S+R+NP++DA THPYISTGLKENKFG+  +EA  +FL A +   L       HI
Sbjct: 141 GKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAMEEAEAIFLRANELPGLAVKGADCHI 200

Query: 187 GSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGIL 246
           GSQL +L+P ++A  ++  +   L   G+ +   DVGGG+GV+Y+ E+  +   YA  +L
Sbjct: 201 GSQLTELQPFLDAMDRMLALIDRLAEQGVKIAHLDVGGGLGVTYDGEQPPEPSAYASALL 260

Query: 247 NALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKH 306
             L G DL +I EPGR+I A +G  +TQVLY K+   K F +VD  MND +RPSLY A  
Sbjct: 261 GKLAGRDLKLIFEPGRAIAANAGIFVTQVLYLKENAEKNFALVDGAMNDLIRPSLYSAWQ 320

Query: 307 AIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQY 366
            I  + P  G E    DVVGPVCE+ D   KD  L  +   D +A+   GAYG +MAS Y
Sbjct: 321 KIIPVVPRPG-ETRQYDVVGPVCETGDFLGKDRAL-NIRANDLLAVRSSGAYGFTMASNY 378

Query: 367 NSRPKLLELALEDHKIRVIRKREALEDLWRLEE 399
           NSRP+  E+ ++  +  ++R+RE +  LW+ E+
Sbjct: 379 NSRPRAAEVMVDGERHYLVREREKVAQLWQGEQ 411


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: 411
Number of extensions: 15
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: 414
Length adjustment: 31
Effective length of query: 374
Effective length of database: 383
Effective search space:   143242
Effective search space used:   143242
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 5207805 Shew_0322 (diaminopimelate decarboxylase (RefSeq))
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.29985.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.9e-161  522.1   0.0   4.6e-161  521.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207805  Shew_0322 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207805  Shew_0322 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.9   0.0  4.6e-161  4.6e-161       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 521.9 bits;  conditional E-value: 4.6e-161
                        TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                      ++ el++e++ +++lae++gtPlYvy+++tl+++++a+++a++++ ++++YAvKAnsnlavl++la++G+g+d+vsgG
  lcl|FitnessBrowser__PV4:5207805   7 QQDELYAEQCTVASLAETYGTPLYVYSRATLERHWHAFDNAVADHPHMICYAVKANSNLAVLNVLARLGSGFDIVSGG 84 
                                      566899************************************************************************ PP

                        TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyi 160
                                      El+r+l+Ag +a+k+vfsg+gk+ +e+e+ale++i ++nv+s +ele+l+ +a +lgk a+v+lRvnpdvda th+yi
  lcl|FitnessBrowser__PV4:5207805  85 ELARVLEAGGEASKVVFSGVGKTVAEMEMALEAGIYCFNVESAAELEQLNLVALRLGKVAPVSLRVNPDVDAGTHPYI 162
                                      ****************************************************************************** PP

                        TIGR01048 161 sTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGl 238
                                      sTGlke+KFGi++eeae+++ +a +l+ l + G ++HIGSq+++l+pf +a+++++ l+++l+e+g+++++ld+GGGl
  lcl|FitnessBrowser__PV4:5207805 163 STGLKENKFGIAMEEAEAIFLRANELPGLAVKGADCHIGSQLTELQPFLDAMDRMLALIDRLAEQGVKIAHLDVGGGL 240
                                      ****************************************************************************** PP

                        TIGR01048 239 gisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliR 316
                                      g++y+ e+ +p+++ ya++ll kl++     ++lkli+EpGR+++anag+++t+V ++Ke+ +++f+lvD++mndliR
  lcl|FitnessBrowser__PV4:5207805 241 GVTYDGEQ-PPEPSAYASALLGKLAG-----RDLKLIFEPGRAIAANAGIFVTQVLYLKENAEKNFALVDGAMNDLIR 312
                                      *****999.**************999.....6********************************************** PP

                        TIGR01048 317 palYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevl 394
                                      p+lY+a+++i+++   +  et ++dvvGp+CE+gD+l+kdr+l+  ++ dllav+s+GAYg++m+snYnsrpr+aev+
  lcl|FitnessBrowser__PV4:5207805 313 PSLYSAWQKIIPV-VPRPGETRQYDVVGPVCETGDFLGKDRALNI-RANDLLAVRSSGAYGFTMASNYNSRPRAAEVM 388
                                      *************.668888***********************85.559***************************** PP

                        TIGR01048 395 veegkarlirrretledllale 416
                                      v++++ +l+r+re++++l++ e
  lcl|FitnessBrowser__PV4:5207805 389 VDGERHYLVREREKVAQLWQGE 410
                                      *******************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.58
//
[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