Alignments for a candidate for lysA in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Dechlorosoma suillum PS

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate Dsui_1182 Dsui_1182 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__PS:Dsui_1182
          Length = 418

 Score =  503 bits (1294), Expect = e-147
 Identities = 254/420 (60%), Positives = 323/420 (76%), Gaps = 6/420 (1%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPH----LI 56
           M +F+ +++G L AE V L+ +A Q+GTP YVYSRA LE  +  F  ++  +P     L+
Sbjct: 1   MTFFS-RKNGVLHAEAVALSSIAAQFGTPTYVYSRAALEAAYGEFRDALAAHPAGAGGLV 59

Query: 57  CYAVKANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRAL 116
           CYAVKANSNLG+L+  ARLG+GFDIVS GELERVLAAG +  KVVFSGVGKTEAEM RAL
Sbjct: 60  CYAVKANSNLGILSLFARLGAGFDIVSGGELERVLAAGAEAGKVVFSGVGKTEAEMARAL 119

Query: 117 QLKIKCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITF 176
           ++ I+CFNVES PEL RLN VA  LG KAP+SLR+NP+VDAKTHPYISTGL+ NKFG+ +
Sbjct: 120 EVGIRCFNVESVPELDRLNAVAVRLGKKAPLSLRVNPNVDAKTHPYISTGLKQNKFGVAY 179

Query: 177 DRAAQVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLD 236
           + A  +YR A SLP ++V GIDCHIGSQL   APF +A D++LAL+D L A GI + H+D
Sbjct: 180 EDALALYRRAASLPGIEVTGIDCHIGSQLLDAAPFAEALDKVLALVDQLAAAGIRLHHID 239

Query: 237 VGGGLGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKH 296
           +GGGLG+ Y DE PP+ ++Y   LL +LE  R L++I EPGR +  NAG+L+TK+E+LK 
Sbjct: 240 LGGGLGIRYLDEAPPRVADYLTPLLQKLE-GRGLQVILEPGRRLVGNAGLLLTKIEYLKP 298

Query: 297 TEHKNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL 356
            E KNFAI+DAAMNDL+RPALY A+ DI+ + P      +Y +VGP+CE+ DFLG  R+L
Sbjct: 299 GEEKNFAIVDAAMNDLMRPALYDAYHDIVEVAPGNAAKASYSIVGPICESGDFLGHGREL 358

Query: 357 VLQEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
            +  GDLLAV S+GAYGF+MSSNYNTRPR AEVMVDG++ +LVR+RE ++ L+ALES LP
Sbjct: 359 AVVPGDLLAVMSAGAYGFSMSSNYNTRPRAAEVMVDGDQVHLVRRRETVAELFALESPLP 418


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: 500
Number of extensions: 18
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: 418
Length adjustment: 32
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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 Dsui_1182 Dsui_1182 (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.26709.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
     1e-162  527.3   0.0   1.2e-162  527.1   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_1182  Dsui_1182 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_1182  Dsui_1182 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  527.1   0.0  1.2e-162  1.2e-162       4     416 ..       6     414 ..       3     415 .. 0.97

  Alignments for each domain:
  == domain 1  score: 527.1 bits;  conditional E-value: 1.2e-162
                         TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaees....lvlYAvKAnsnlavlrllaeeGlgl 76 
                                       +k+g l +e+v+l ++a++fgtP+Yvy++++l++++ +++ a +a+ +    lv+YAvKAnsnl +l+l+a++G+g+
  lcl|FitnessBrowser__PS:Dsui_1182   6 RKNGVLHAEAVALSSIAAQFGTPTYVYSRAALEAAYGEFRDALAAHPAgaggLVCYAVKANSNLGILSLFARLGAGF 82 
                                       68999*************************************9994444578************************* PP

                         TIGR01048  77 dvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvd 153
                                       d+vsgGEler+laAg++a k+vfsg+gk+e+e+++ale++i+++nv+sv el++l+++a +lgkka+++lRvnp+vd
  lcl|FitnessBrowser__PS:Dsui_1182  83 DIVSGGELERVLAAGAEAGKVVFSGVGKTEAEMARALEVGIRCFNVESVPELDRLNAVAVRLGKKAPLSLRVNPNVD 159
                                       ***************************************************************************** PP

                         TIGR01048 154 aktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegiele 230
                                       akth+yisTGlk++KFG+++e+a++ y++a++l+ +e++Gi++HIGSq+ld++pf ea++kv+ l+++l+++gi+l+
  lcl|FitnessBrowser__PS:Dsui_1182 160 AKTHPYISTGLKQNKFGVAYEDALALYRRAASLPGIEVTGIDCHIGSQLLDAAPFAEALDKVLALVDQLAAAGIRLH 236
                                       ***************************************************************************** PP

                         TIGR01048 231 eldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlv 307
                                       ++dlGGGlgi+y +e  +p++++y   ll+kle+     + l++ilEpGR lv+nag llt++e++K  e+++f++v
  lcl|FitnessBrowser__PS:Dsui_1182 237 HIDLGGGLGIRYLDEA-PPRVADYLTPLLQKLEG-----RGLQVILEPGRRLVGNAGLLLTKIEYLKPGEEKNFAIV 307
                                       **************99.****************9.....699*********************************** PP

                         TIGR01048 308 DagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnY 384
                                       Da+mndl+RpalY+ayh+i+++ +  +++++ +++vGp+CEsgD+l++ rel  v  Gdllav+saGAYg+smssnY
  lcl|FitnessBrowser__PS:Dsui_1182 308 DAAMNDLMRPALYDAYHDIVEV-APGNAAKASYSIVGPICESGDFLGHGRELAVVP-GDLLAVMSAGAYGFSMSSNY 382
                                       **********************.6688889**********************9886.******************** PP

                         TIGR01048 385 nsrprpaevlveegkarlirrretledllale 416
                                       n+rpr+aev+v++++++l+rrret+++l+ale
  lcl|FitnessBrowser__PS:Dsui_1182 383 NTRPRAAEVMVDGDQVHLVRRRETVAELFALE 414
                                       *****************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (418 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: 8.41
//
[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