Alignments for a candidate for lysA in Paraburkholderia phymatum STM815

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Paraburkholderia phymatum STM815

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_012402171.1 BPHY_RS14245 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000020045.1:WP_012402171.1
          Length = 420

 Score =  501 bits (1290), Expect = e-146
 Identities = 249/410 (60%), Positives = 309/410 (75%), Gaps = 2/410 (0%)

Query: 9   DGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKANSNLGV 68
           DG L AE V    LA Q+GTPLYVYSR  L + WHA+  +       +  AVKANSNL V
Sbjct: 10  DGVLHAEGVSAVSLAEQFGTPLYVYSRDALTKAWHAYADACAGRRATVHVAVKANSNLAV 69

Query: 69  LNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCFNVESE 128
           LN  AR+G+GFDIVS GEL RVLAAGG     VFSGVGK+ AEM+ AL   +KCFNVES 
Sbjct: 70  LNLFARMGAGFDIVSGGELARVLAAGGKAENTVFSGVGKSVAEMRDALAAGVKCFNVESI 129

Query: 129 PELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQVYRLAHS 188
           PEL RLN VAGE+G KAP+SLR+NPDVDAKTHPYISTGL+ NKFG+ FD A   YR A +
Sbjct: 130 PELDRLNAVAGEMGKKAPVSLRVNPDVDAKTHPYISTGLKSNKFGVAFDDARATYRAAAA 189

Query: 189 LPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGVVYRDE 248
           + +LDV GIDCHIGSQ+T +AP++DA D+LL L+  ++A+G+ I+H+DVGGGLG+ Y DE
Sbjct: 190 MKHLDVVGIDCHIGSQITEVAPYLDAVDKLLELVAQIEADGVTIKHVDVGGGLGITYDDE 249

Query: 249 LPPQPSEYAKALLDRLER--HRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHKNFAIID 306
            PP   ++ + LLDR+E   H   E+ FEPGR++  NAG+L+T+VEFLK    KNFAI+D
Sbjct: 250 TPPDIGDFVRTLLDRIEARGHGHREVYFEPGRSLVGNAGMLLTRVEFLKTGAEKNFAIVD 309

Query: 307 AAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQEGDLLAV 366
           AAMNDL RPA+Y+A+  I P+  R G    YD+VGPVCE+ D+LG++R L ++ GDLLA+
Sbjct: 310 AAMNDLARPAMYEAYHAIEPVVQRDGARHVYDIVGPVCESGDWLGRERRLAVEPGDLLAI 369

Query: 367 RSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
           RS+GAYGF MSSNYNTR R AEVMVDG+K Y+VR+REE+  L+A ESVLP
Sbjct: 370 RSAGAYGFAMSSNYNTRARAAEVMVDGDKAYVVRKREEVKDLFAGESVLP 419


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: 492
Number of extensions: 9
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: 420
Length adjustment: 32
Effective length of query: 385
Effective length of database: 388
Effective search space:   149380
Effective search space used:   149380
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 WP_012402171.1 BPHY_RS14245 (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.13618.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.6e-164  530.9   0.1     1e-163  530.6   0.1    1.0  1  lcl|NCBI__GCF_000020045.1:WP_012402171.1  BPHY_RS14245 diaminopimelate dec


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000020045.1:WP_012402171.1  BPHY_RS14245 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  530.6   0.1    1e-163    1e-163       6     416 ..      10     415 ..       6     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 530.6 bits;  conditional E-value: 1e-163
                                 TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGl 74 
                                               dg l +egv++ +lae+fgtPlYvy++++l+++++a++ a ++++++v+ AvKAnsnlavl+l+a+ G+
  lcl|NCBI__GCF_000020045.1:WP_012402171.1  10 DGVLHAEGVSAVSLAEQFGTPLYVYSRDALTKAWHAYADACAGRRATVHVAVKANSNLAVLNLFARMGA 78 
                                               78999**************************************999*********************** PP

                                 TIGR01048  75 gldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkar 143
                                               g+d+vsgGEl+r+laAg kae+ vfsg+gks +e+++al++++k++nv+s+ el++l+++a+e+gkka+
  lcl|NCBI__GCF_000020045.1:WP_012402171.1  79 GFDIVSGGELARVLAAGGKAENTVFSGVGKSVAEMRDALAAGVKCFNVESIPELDRLNAVAGEMGKKAP 147
                                               ********************************************************************* PP

                                 TIGR01048 144 vllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaa 212
                                               v+lRvnpdvdakth+yisTGlk++KFG+++++a+++y++a+++++l++vGi++HIGSqi++++p+ +a+
  lcl|NCBI__GCF_000020045.1:WP_012402171.1 148 VSLRVNPDVDAKTHPYISTGLKSNKFGVAFDDARATYRAAAAMKHLDVVGIDCHIGSQITEVAPYLDAV 216
                                               ********************************************************************* PP

                                 TIGR01048 213 ekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelgl.klklilEpGR 280
                                               +k+++l+++++++g++++++d+GGGlgi+y++e+ +pd+ +++++ll+++e +   g+ + ++ +EpGR
  lcl|NCBI__GCF_000020045.1:WP_012402171.1 217 DKLLELVAQIEADGVTIKHVDVGGGLGITYDDET-PPDIGDFVRTLLDRIEAR---GHgHREVYFEPGR 281
                                               ********************************99.************999994...66699******** PP

                                 TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEs 349
                                               slv+nag+lltrVe++K+  +++f++vDa+mndl Rpa+Yeayh i ++  +++ +++++d+vGp+CEs
  lcl|NCBI__GCF_000020045.1:WP_012402171.1 282 SLVGNAGMLLTRVEFLKTGAEKNFAIVDAAMNDLARPAMYEAYHAIEPV-VQRDGARHVYDIVGPVCES 349
                                               *************************************************.668889************* PP

                                 TIGR01048 350 gDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               gD l+++r+l  ve+Gdlla++saGAYg++mssnYn+r+r+aev+v+++ka+++r+re+++dl+a e
  lcl|NCBI__GCF_000020045.1:WP_012402171.1 350 GDWLGRERRLA-VEPGDLLAIRSAGAYGFAMSSNYNTRARAAEVMVDGDKAYVVRKREEVKDLFAGE 415
                                               **********6.899************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (420 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: 7.64
//
[ok]

This GapMind analysis is from Apr 10 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:

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