Alignments for a candidate for lysA in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Burkholderia phytofirmans PsJN

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate BPHYT_RS17930 BPHYT_RS17930 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__BFirm:BPHYT_RS17930
          Length = 420

 Score =  482 bits (1240), Expect = e-140
 Identities = 240/410 (58%), Positives = 304/410 (74%), Gaps = 2/410 (0%)

Query: 9   DGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKANSNLGV 68
           DG L AE V    LA Q+GTPLYVYSRA L   W+A+  +       +  AVKANSNL V
Sbjct: 10  DGVLHAEGVSAVSLAEQFGTPLYVYSRAALTEAWNAYAGACAGRRASVHVAVKANSNLAV 69

Query: 69  LNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCFNVESE 128
           LN  ARLG+GFDIVS GEL RVLAAGG     VFSGVGK   EM+ AL   +KCFNVES 
Sbjct: 70  LNVFARLGAGFDIVSGGELARVLAAGGRAENTVFSGVGKHADEMRDALAAGVKCFNVESI 129

Query: 129 PELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQVYRLAHS 188
           PEL RLN VA  +G KAP+SLR+NPDVDAKTHPYISTGL+ NKFG+ F+ A   Y+ A +
Sbjct: 130 PELDRLNAVAAAMGKKAPVSLRVNPDVDAKTHPYISTGLKSNKFGVAFEDARATYQAAAA 189

Query: 189 LPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGVVYRDE 248
           + NL+V GIDCHIGSQ+T +AP++DA D++L L++ ++ +G+ IRH+DVGGGLG+ Y DE
Sbjct: 190 MANLEVVGIDCHIGSQITEVAPYLDAVDKVLELVEQIEQDGVKIRHIDVGGGLGITYDDE 249

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

Query: 307 AAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQEGDLLAV 366
           AAM DL RPA+Y+A+  I P+  R   A  YD+VGPVCE+ D+LG++R L ++ GDLLA+
Sbjct: 310 AAMTDLARPAMYEAYHAIDPVVKRDVPAHVYDVVGPVCESGDWLGRERLLSVEPGDLLAI 369

Query: 367 RSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
           RS+GAYGF MSSNYNTRPR AEVMVDG + ++VR REE+  L+A E++LP
Sbjct: 370 RSAGAYGFVMSSNYNTRPRAAEVMVDGTQVHVVRAREEVKQLFAGETILP 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: 470
Number of extensions: 12
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 BPHYT_RS17930 BPHYT_RS17930 (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.20328.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.3e-160  520.4   0.0   1.5e-160  520.2   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS17930  BPHYT_RS17930 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS17930  BPHYT_RS17930 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  520.2   0.0  1.5e-160  1.5e-160       6     416 ..      10     415 ..       6     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 520.2 bits;  conditional E-value: 1.5e-160
                                TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlg 75 
                                              dg l +egv++ +lae+fgtPlYvy++++l+e+++a++ a +++++ v+ AvKAnsnlavl+++a++G+g
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930  10 DGVLHAEGVSAVSLAEQFGTPLYVYSRAALTEAWNAYAGACAGRRASVHVAVKANSNLAVLNVFARLGAG 79 
                                              78999**************************************999************************ PP

                                TIGR01048  76 ldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvl 145
                                              +d+vsgGEl+r+laAg +ae+ vfsg+gk  +e+++al++++k++nv+s+ el++l+++a+ +gkka+v+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930  80 FDIVSGGELARVLAAGGRAENTVFSGVGKHADEMRDALAAGVKCFNVESIPELDRLNAVAAAMGKKAPVS 149
                                              ********************************************************************** PP

                                TIGR01048 146 lRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekv 215
                                              lRvnpdvdakth+yisTGlk++KFG+++e+a+++y++a+++++le+vGi++HIGSqi++++p+ +a++kv
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930 150 LRVNPDVDAKTHPYISTGLKSNKFGVAFEDARATYQAAAAMANLEVVGIDCHIGSQITEVAPYLDAVDKV 219
                                              ********************************************************************** PP

                                TIGR01048 216 vklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelgl.klklilEpGRslva 284
                                              ++l+e+++++g++++++d+GGGlgi+y++e+ +p++ e+++++l+++e +   g+ + ++ +EpGRslv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930 220 LELVEQIEQDGVKIRHIDVGGGLGITYDDET-PPEIGEFVRTVLDRIEAR---GHgHREVYFEPGRSLVG 285
                                              *****************************99.************999994...66699************ PP

                                TIGR01048 285 nagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvla 354
                                              nag+lltrVe++K   +++f++vDa+m+dl Rpa+Yeayh i ++   ++ +++++dvvGp+CEsgD l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930 286 NAGMLLTRVEFLKPGAEKNFAIVDAAMTDLARPAMYEAYHAIDPV-VKRDVPAHVYDVVGPVCESGDWLG 354
                                              *********************************************.56999******************* PP

                                TIGR01048 355 kdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                              ++r l +ve+Gdlla++saGAYg+ mssnYn+rpr+aev+v++ +++++r re++++l+a e
  lcl|FitnessBrowser__BFirm:BPHYT_RS17930 355 RERLL-SVEPGDLLAIRSAGAYGFVMSSNYNTRPRAAEVMVDGTQVHVVRAREEVKQLFAGE 415
                                              *9966.6999************************************************9876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.70
//
[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:

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