Alignments for a candidate for lysA in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Paraburkholderia bryophila 376MFSha3.1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate H281DRAFT_05606 H281DRAFT_05606 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__Burk376:H281DRAFT_05606
          Length = 420

 Score =  476 bits (1225), Expect = e-139
 Identities = 242/417 (58%), Positives = 303/417 (72%), Gaps = 6/417 (1%)

Query: 2   DYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVK 61
           DY N    G L  E V    LA Q+GTPLYVYSRA L   W+A+  +       +  AVK
Sbjct: 7   DYVN----GVLHVEGVSAVSLAEQFGTPLYVYSRAALTDAWNAYAGACAGRRASVHVAVK 62

Query: 62  ANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIK 121
           ANSNL VLN  ARLG+GFDIVS GEL RVLAAGG     VFSGVGK  +EM+ AL   +K
Sbjct: 63  ANSNLAVLNVFARLGAGFDIVSGGELARVLAAGGKAENTVFSGVGKHASEMREALAAGVK 122

Query: 122 CFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQ 181
           CFNVES PEL RLN VA E+G  AP+SLR+NPDVDAKTHPYISTGL+ NKFG+ F+ A  
Sbjct: 123 CFNVESIPELDRLNTVAAEMGKIAPVSLRVNPDVDAKTHPYISTGLKSNKFGVAFEDARA 182

Query: 182 VYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGL 241
            Y+ A ++ NL+V GIDCHIGSQ+T +AP++DA D+LL L++ ++ +GI IRH+DVGGGL
Sbjct: 183 TYQAAAAMANLEVVGIDCHIGSQITEIAPYLDAVDKLLELVELIEKDGIAIRHIDVGGGL 242

Query: 242 GVVYRDELPPQPSEYAKALLDRLER--HRDLELIFEPGRAIAANAGVLVTKVEFLKHTEH 299
           G+ Y DE PP   E+ + +LDR+E   H   E+ FEPGR++  NAGVL+T+VEFLK    
Sbjct: 243 GITYDDETPPDIGEFVRTVLDRIEARGHGHREVYFEPGRSLVGNAGVLLTRVEFLKPGAE 302

Query: 300 KNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQ 359
           KNFAI+DAAM +L RPA+Y+A+  I  +  R   A  YD+VGPVCE+ D+LG++R L ++
Sbjct: 303 KNFAIVDAAMTELARPAMYEAYHAIDAVVERDVPAHVYDIVGPVCESGDWLGRERLLSVE 362

Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
            GDLL +RS+GAYGF MSSNYNTRPR AEVMVDG + ++VR REE+  L+A E+VLP
Sbjct: 363 PGDLLVIRSAGAYGFVMSSNYNTRPRAAEVMVDGTQAHVVRAREEIQQLFAGETVLP 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: 475
Number of extensions: 10
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 H281DRAFT_05606 H281DRAFT_05606 (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.14975.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.6e-159  516.9   0.1   1.9e-159  516.6   0.1    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05606  H281DRAFT_05606 diaminopimelate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05606  H281DRAFT_05606 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  516.6   0.1  1.9e-159  1.9e-159       6     416 ..      10     415 ..       6     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 516.6 bits;  conditional E-value: 1.9e-159
                                    TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllae 71 
                                                  +g l +egv++ +lae+fgtPlYvy++++l+ +++a++ a +++++ v+ AvKAnsnlavl+++a+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606  10 NGVLHVEGVSAVSLAEQFGTPLYVYSRAALTDAWNAYAGACAGRRASVHVAVKANSNLAVLNVFAR 75 
                                                  7899***************************************999******************** PP

                                    TIGR01048  72 eGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiake 137
                                                  +G+g+d+vsgGEl+r+laAg kae+ vfsg+gk  +e+++al++++k++nv+s+ el++l+++a+e
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606  76 LGAGFDIVSGGELARVLAAGGKAENTVFSGVGKHASEMREALAAGVKCFNVESIPELDRLNTVAAE 141
                                                  ****************************************************************** PP

                                    TIGR01048 138 lgkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqil 203
                                                  +gk a+v+lRvnpdvdakth+yisTGlk++KFG+++e+a+++y++a+++++le+vGi++HIGSqi+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606 142 MGKIAPVSLRVNPDVDAKTHPYISTGLKSNKFGVAFEDARATYQAAAAMANLEVVGIDCHIGSQIT 207
                                                  ****************************************************************** PP

                                    TIGR01048 204 dlepfveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelg 269
                                                  +++p+ +a++k+++l+e ++++gi ++++d+GGGlgi+y++e+ +pd+ e+++++l+++e +   g
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606 208 EIAPYLDAVDKLLELVELIEKDGIAIRHIDVGGGLGITYDDET-PPDIGEFVRTVLDRIEAR---G 269
                                                  *****************************************99.************999994...6 PP

                                    TIGR01048 270 l.klklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrlee 334
                                                  + + ++ +EpGRslv+nagvlltrVe++K   +++f++vDa+m++l Rpa+Yeayh i a+   ++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606 270 HgHREVYFEPGRSLVGNAGVLLTRVEFLKPGAEKNFAIVDAAMTELARPAMYEAYHAIDAVV-ERD 334
                                                  6699*******************************************************995.599 PP

                                    TIGR01048 335 eetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegka 400
                                                   +++++d+vGp+CEsgD l+++r l +ve+Gdll+++saGAYg+ mssnYn+rpr+aev+v++ +a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606 335 VPAHVYDIVGPVCESGDWLGRERLL-SVEPGDLLVIRSAGAYGFVMSSNYNTRPRAAEVMVDGTQA 399
                                                  99*******************9966.6999************************************ PP

                                    TIGR01048 401 rlirrretledllale 416
                                                  +++r re++++l+a e
  lcl|FitnessBrowser__Burk376:H281DRAFT_05606 400 HVVRAREEIQQLFAGE 415
                                                  ************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: 10.84
//
[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