Alignments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 207105 DVU1647 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>MicrobesOnline__882:207105
          Length = 412

 Score =  423 bits (1088), Expect = e-123
 Identities = 218/413 (52%), Positives = 289/413 (69%), Gaps = 3/413 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M  F Y+E G L+AE V + DLA+ YGTPLYVYS  TLERH+ AFD + G   HL C++V
Sbjct: 1   MHLFQYRE-GSLFAEDVSIIDLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KA SN+ +L  L  LG+G DIVS GEL R L AG    ++V+SGVGK   E++ AL+  I
Sbjct: 60  KACSNIHILKLLGSLGAGVDIVSGGELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
             FNVES  EL+ + +VA  +G  A +SLRINPDVD  THPYISTGL+ NKFGI   +A 
Sbjct: 120 LMFNVESLQELRTIEEVAASMGTTARVSLRINPDVDPHTHPYISTGLQKNKFGIEMTQAL 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
           + Y LA  LP++D  GIDCHIGSQLT+L+PF++A D++L   + L   G+ I +LD+GGG
Sbjct: 180 EGYMLARDLPHIDPIGIDCHIGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LG+ Y +E PP P ++ +A+L+R  +  +L L+ EPGR IA NAG+LVT+V + K T  K
Sbjct: 240 LGITYGEETPPHPRDFGRAVLER-TKGLNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL-VLQ 359
            F I+DAAMNDL+RP+LY ++  I  + P     QT D+VGP+CE+ DFL +DR L  ++
Sbjct: 299 QFVIVDAAMNDLVRPSLYASYHRIAEVLPHGRTEQTVDVVGPICESGDFLARDRVLPAVE 358

Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALE 412
           +G+LLAV S+GAYGF+MSS YN+RPR AEV+V G+    +R+RE    L ALE
Sbjct: 359 QGELLAVFSAGAYGFSMSSQYNSRPRAAEVLVRGDTAKSIRRRETYDDLTALE 411


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: 475
Number of extensions: 23
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: 417
Length of database: 412
Length adjustment: 31
Effective length of query: 386
Effective length of database: 381
Effective search space:   147066
Effective search space used:   147066
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 207105 DVU1647 (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.22014.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   2.1e-164  532.9   0.0   2.6e-164  532.6   0.0    1.0  1  lcl|MicrobesOnline__882:207105  DVU1647 diaminopimelate decarbox


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207105  DVU1647 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.6   0.0  2.6e-164  2.6e-164       4     416 ..       6     411 ..       4     412 .] 0.98

  Alignments for each domain:
  == domain 1  score: 532.6 bits;  conditional E-value: 2.6e-164
                       TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                      ++g+l++e+v++ +la ++gtPlYvy++ tl+++++a+++af+++ +l ++ vKA+sn+++l+ll ++G+g+d+vsgG
  lcl|MicrobesOnline__882:207105   6 YREGSLFAEDVSIIDLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSVKACSNIHILKLLGSLGAGVDIVSGG 84 
                                     57899****************************************99******************************** PP

                       TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyis 161
                                     El ral Ag++  +iv+sg+gk+ +e++ ale++i ++nv+s++el+++ee+a+++g++arv+lR+npdvd++th+yis
  lcl|MicrobesOnline__882:207105  85 ELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADILMFNVESLQELRTIEEVAASMGTTARVSLRINPDVDPHTHPYIS 163
                                     ******************************************************************************* PP

                       TIGR01048 162 TGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgi 240
                                     TGl+++KFGie+++a+e y la +l++++++Gi++HIGSq++ l+pf ea++kv+++ e+l+  g++++ ldlGGGlgi
  lcl|MicrobesOnline__882:207105 164 TGLQKNKFGIEMTQALEGYMLARDLPHIDPIGIDCHIGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGGLGI 242
                                     ******************************************************************************* PP

                       TIGR01048 241 syeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpal 319
                                     +y ee+ +p+++++ +++le+ ++     l+l+l+lEpGR +++nag+l+t+V ++K+++s++fv+vDa+mndl+Rp+l
  lcl|MicrobesOnline__882:207105 243 TYGEET-PPHPRDFGRAVLERTKG-----LNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSKQFVIVDAAMNDLVRPSL 315
                                     ***999.**********9987777.....8************************************************* PP

                       TIGR01048 320 YeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveeg 398
                                     Y +yh+ia++   + ++++tvdvvGp+CEsgD+la+dr lp+ve+G+llav+saGAYg+smss+Ynsrpr+aevlv+++
  lcl|MicrobesOnline__882:207105 316 YASYHRIAEV-LPHGRTEQTVDVVGPICESGDFLARDRVLPAVEQGELLAVFSAGAYGFSMSSQYNSRPRAAEVLVRGD 393
                                     **********.5577789************************************************************* PP

                       TIGR01048 399 karlirrretledllale 416
                                      a+ irrret++dl ale
  lcl|MicrobesOnline__882:207105 394 TAKSIRRRETYDDLTALE 411
                                     **************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (412 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: 00:00:00.02
# Mc/sec: 6.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis