Alignments for a candidate for lysA in Cupriavidus basilensis 4G11

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Cupriavidus basilensis 4G11

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate RR42_RS19050 RR42_RS19050 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__Cup4G11:RR42_RS19050
          Length = 422

 Score =  483 bits (1242), Expect = e-141
 Identities = 247/420 (58%), Positives = 313/420 (74%), Gaps = 5/420 (1%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M  F ++ DG L  E VPLA +A +YGTP YVYSRA L   + A+  +       + YA+
Sbjct: 1   MTAFFHRHDGALSVEHVPLARIAAEYGTPTYVYSRAALTAAYQAYAAACQGRRARVQYAM 60

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL +L   ARLG+GFDIVS GEL+RVLA GGDP KVVFSGVGKT AEM+ ALQ  +
Sbjct: 61  KANSNLAILQVFARLGAGFDIVSGGELQRVLAVGGDPRKVVFSGVGKTAAEMELALQHDV 120

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
             FNVES PEL RLN VAG LG +A +SLRINPDVDAKTHPYISTGL+ NKFG+ F+   
Sbjct: 121 LSFNVESIPELDRLNAVAGRLGKRARVSLRINPDVDAKTHPYISTGLKGNKFGVAFEDVL 180

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
             YR A +LP+L+V GIDCHIGSQ+T +AP+++A D++L ++++L+ EGI++ H+DVGGG
Sbjct: 181 PTYRAAAALPHLEVAGIDCHIGSQITEVAPYLEALDKVLDVVEALEREGINLEHIDVGGG 240

Query: 241 LGVVYRDELPPQPSEYAKALLDRLER--HRDLELIFEPGRAIAANAGVLVTKVEFLKHTE 298
           LG+ Y DE PP  + +A+ LLDR+    H   E++FEPGR++  NAGVL+T+VEFLK   
Sbjct: 241 LGITYDDETPPDITGFARTLLDRVAERGHGHREVLFEPGRSLVGNAGVLLTQVEFLKPGA 300

Query: 299 HKNFAIIDAAMNDLIRPALYQAWQDIIPLRPR---QGEAQTYDLVGPVCETSDFLGKDRD 355
            KNF I+DAAMNDL RPA+Y+A+  I P++ R   Q  A TYD+VGPVCE+ D+LG+DR 
Sbjct: 301 AKNFCIVDAAMNDLARPAMYEAYHRIEPVQLREAAQATALTYDVVGPVCESGDWLGRDRA 360

Query: 356 LVLQEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVL 415
           L +Q GDLLAV S+GAYGF MSSNYNTRPR AEVMVDG+  +LVR RE ++ L+  E +L
Sbjct: 361 LAVQPGDLLAVMSAGAYGFVMSSNYNTRPRAAEVMVDGDDVHLVRGREHVADLFRDERLL 420


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: 498
Number of extensions: 15
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: 422
Length adjustment: 32
Effective length of query: 385
Effective length of database: 390
Effective search space:   150150
Effective search space used:   150150
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 RR42_RS19050 RR42_RS19050 (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.6495.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.3e-163  528.3   0.0   6.1e-163  528.1   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS19050  RR42_RS19050 diaminopimelate dec


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS19050  RR42_RS19050 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.1   0.0  6.1e-163  6.1e-163       4     416 ..       7     417 ..       4     418 .. 0.97

  Alignments for each domain:
  == domain 1  score: 528.1 bits;  conditional E-value: 6.1e-163
                                 TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaee 72 
                                               ++dg l++e+v+l+++a+e+gtP+Yvy++++l+++++a+++a ++++++v YA+KAnsnla+l+++a++
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050   7 RHDGALSVEHVPLARIAAEYGTPTYVYSRAALTAAYQAYAAACQGRRARVQYAMKANSNLAILQVFARL 75 
                                               6799*****************************************999********************* PP

                                 TIGR01048  73 GlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkk 141
                                               G+g+d+vsgGEl+r+la g ++ k+vfsg+gk+ +e+e al++++  +nv+s+ el++l+++a++lgk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050  76 GAGFDIVSGGELQRVLAVGGDPRKVVFSGVGKTAAEMELALQHDVLSFNVESIPELDRLNAVAGRLGKR 144
                                               ********************************************************************* PP

                                 TIGR01048 142 arvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfve 210
                                               arv+lR+npdvdakth+yisTGlk +KFG+++e+ +++y++a++l++le+ Gi++HIGSqi++++p+ e
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050 145 ARVSLRINPDVDAKTHPYISTGLKGNKFGVAFEDVLPTYRAAAALPHLEVAGIDCHIGSQITEVAPYLE 213
                                               ********************************************************************* PP

                                 TIGR01048 211 aaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelgl.klklilEp 278
                                               a++kv++++e l++egi+le++d+GGGlgi+y++e+ +pd++ +a++ll++++++   g+ + ++++Ep
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050 214 ALDKVLDVVEALEREGINLEHIDVGGGLGITYDDET-PPDITGFARTLLDRVAER---GHgHREVLFEP 278
                                               **********************************99.************999995...66699****** PP

                                 TIGR01048 279 GRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkr..leeeetetvdvvGp 345
                                               GRslv+nagvllt+Ve++K    ++f++vDa+mndl Rpa+Yeayh+i +++     ++++ t+dvvGp
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050 279 GRSLVGNAGVLLTQVEFLKPGAAKNFCIVDAAMNDLARPAMYEAYHRIEPVQLreAAQATALTYDVVGP 347
                                               ************************************************998642266777889****** PP

                                 TIGR01048 346 lCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414
                                               +CEsgD l++dr+l  v++Gdllav+saGAYg+ mssnYn+rpr+aev+v++++++l+r re ++dl++
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050 348 VCESGDWLGRDRALA-VQPGDLLAVMSAGAYGFVMSSNYNTRPRAAEVMVDGDDVHLVRGREHVADLFR 415
                                               **************6.789************************************************99 PP

                                 TIGR01048 415 le 416
                                               +e
  lcl|FitnessBrowser__Cup4G11:RR42_RS19050 416 DE 417
                                               87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (422 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: 8.78
//
[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