GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysA in Shewanella sp. ANA-3

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 7023156 Shewana3_0390 diaminopimelate decarboxylase (RefSeq)

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__ANA3:7023156
          Length = 414

 Score =  581 bits (1497), Expect = e-170
 Identities = 290/416 (69%), Positives = 333/416 (80%), Gaps = 2/416 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MD+F YQ D  L+AE   + DLA QYGTPLY+YSRATLERHWHAF+ +V D+PHL+CYAV
Sbjct: 1   MDHFLYQ-DNTLYAEGCRVNDLAQQYGTPLYIYSRATLERHWHAFNNAVADHPHLVCYAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL VLN LARLGSGFDIVS GEL RV+ AGGDP+KVVFSGVGKT AEM++AL L I
Sbjct: 60  KANSNLAVLNVLARLGSGFDIVSGGELARVIEAGGDPAKVVFSGVGKTVAEMEQALNLGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVES  EL++LN VAG LG  AP+SLR+NPDVDA THPYISTGL++NKFGI  D A 
Sbjct: 120 YCFNVESSAELEQLNDVAGRLGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAMDEAE 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            V+  AH+LP+L V G+DCHIGSQLT + PF+DA DR+LALID L  +GI I H DVGGG
Sbjct: 180 VVFARAHALPHLQVKGVDCHIGSQLTEIQPFLDAMDRMLALIDRLADQGIVIEHFDVGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV Y DE PP P  YA ALL RL   R L+LIFEPGRAIAANAG+ VT+V +LK    K
Sbjct: 240 LGVTYDDETPPHPDVYAAALLARL-GDRKLKLIFEPGRAIAANAGIFVTQVLYLKENSDK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360
            FAI+D AMNDLIRPALY AWQ+IIP+ PR  +AQ +D+VGPVCET DFLGKDR L +  
Sbjct: 299 RFAIVDGAMNDLIRPALYSAWQNIIPVNPRDEQAQVFDIVGPVCETGDFLGKDRALAIAA 358

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
           GDLL VRSSGAYGF M+SNYNTRPR AEVMVDG+K YLVR+RE+L+ LW  E +LP
Sbjct: 359 GDLLVVRSSGAYGFAMASNYNTRPRAAEVMVDGDKAYLVREREKLAQLWQGEQLLP 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: 522
Number of extensions: 15
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: 414
Length adjustment: 31
Effective length of query: 386
Effective length of database: 383
Effective search space:   147838
Effective search space used:   147838
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 7023156 Shewana3_0390 (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.2472370.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     2e-165  536.3   0.0   2.4e-165  536.0   0.0    1.0  1  lcl|FitnessBrowser__ANA3:7023156  Shewana3_0390 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023156  Shewana3_0390 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  536.0   0.0  2.4e-165  2.4e-165       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 536.0 bits;  conditional E-value: 2.4e-165
                         TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsg 81 
                                       +d +l++eg+++++la+++gtPlY+y+++tl+++++a+++a++++ +lv+YAvKAnsnlavl++la++G+g+d+vsg
  lcl|FitnessBrowser__ANA3:7023156   7 QDNTLYAEGCRVNDLAQQYGTPLYIYSRATLERHWHAFNNAVADHPHLVCYAVKANSNLAVLNVLARLGSGFDIVSG 83 
                                       677899*********************************************************************** PP

                         TIGR01048  82 GEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakthe 158
                                       GEl+r+ +Ag ++ k+vfsg+gk+ +e+e+al+l+i ++nv+s +ele+l+++a++lgk a+v+lRvnpdvda th+
  lcl|FitnessBrowser__ANA3:7023156  84 GELARVIEAGGDPAKVVFSGVGKTVAEMEQALNLGIYCFNVESSAELEQLNDVAGRLGKVAPVSLRVNPDVDAGTHP 160
                                       ***************************************************************************** PP

                         TIGR01048 159 yisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlG 235
                                       yisTGlke+KFGi+++eae ++ +a++l++l++ G+++HIGSq+++++pf +a+++++ l+++l+++gi +e++d+G
  lcl|FitnessBrowser__ANA3:7023156 161 YISTGLKENKFGIAMDEAEVVFARAHALPHLQVKGVDCHIGSQLTEIQPFLDAMDRMLALIDRLADQGIVIEHFDVG 237
                                       ***************************************************************************** PP

                         TIGR01048 236 GGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmn 312
                                       GGlg++y++e+ +p+++ ya++ll++l +     +klkli+EpGR+++anag+++t+V ++Ke++ ++f++vD++mn
  lcl|FitnessBrowser__ANA3:7023156 238 GGLGVTYDDET-PPHPDVYAAALLARLGD-----RKLKLIFEPGRAIAANAGIFVTQVLYLKENSDKRFAIVDGAMN 308
                                       *********99.***************99.....69***************************************** PP

                         TIGR01048 313 dliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrpr 389
                                       dliRpalY+a+++i+++ + ++e+++++d+vGp+CE+gD+l+kdr+l  +  Gdll+v+s+GAYg++m+snYn+rpr
  lcl|FitnessBrowser__ANA3:7023156 309 DLIRPALYSAWQNIIPV-NPRDEQAQVFDIVGPVCETGDFLGKDRALAIAA-GDLLVVRSSGAYGFAMASNYNTRPR 383
                                       *****************.568888***********************9877.************************* PP

                         TIGR01048 390 paevlveegkarlirrretledllale 416
                                       +aev+v+++ka+l+r+re+l++l++ e
  lcl|FitnessBrowser__ANA3:7023156 384 AAEVMVDGDKAYLVREREKLAQLWQGE 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 14.87
//
[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:

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:

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