Alignments for a candidate for lysA in Marinobacter adhaerens HP15

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Marinobacter adhaerens HP15

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate GFF248 HP15_247 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__Marino:GFF248
          Length = 416

 Score =  600 bits (1546), Expect = e-176
 Identities = 299/418 (71%), Positives = 353/418 (84%), Gaps = 3/418 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MD+FNY+ DG+L+AE +P++ +A+++GTP YVYSRATLERH+ A+D ++ D+PHL+CYAV
Sbjct: 1   MDHFNYR-DGELYAEDIPVSAIADRFGTPAYVYSRATLERHYRAYDDALRDHPHLVCYAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL VLN LARLG+GFDIVS GELERVL AGGDPS+VVFSGVGK E EMKRAL++ +
Sbjct: 60  KANSNLAVLNVLARLGAGFDIVSAGELERVLRAGGDPSRVVFSGVGKQEWEMKRALEVGV 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
           +CFNVES+ EL RLN VAGELGVKAPISLR+NPDVDA THPYISTGL++NKFGI    A+
Sbjct: 120 RCFNVESDTELDRLNAVAGELGVKAPISLRVNPDVDAGTHPYISTGLKENKFGIDIAEAS 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
           QVY  A  +PNLDV G+DCHIGSQLT+++PF+DA DR+LALIDSL  +GIHI HLD+GGG
Sbjct: 180 QVYARAAGMPNLDVKGVDCHIGSQLTSVSPFLDALDRVLALIDSLADQGIHIHHLDMGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV Y  E PPQPS+Y KAL +RL   R LELI EPGR+IAANAG+LVT+VEFLK TEH+
Sbjct: 240 LGVTYNQEQPPQPSDYVKALAERL-GDRKLELILEPGRSIAANAGILVTRVEFLKCTEHR 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQ-GEAQTYDLVGPVCETSDFLGKDRDLVLQ 359
           NFAIIDAAMNDLIRPALY AWQ IIP++P Q GE + +DLVGPVCET DFLGKDR L LQ
Sbjct: 299 NFAIIDAAMNDLIRPALYSAWQAIIPVKPHQDGEEKAWDLVGPVCETGDFLGKDRHLRLQ 358

Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417
            GDLLAVRS+GAYGF MSSNYNTR R  E+MVDG++ ++VR+RE L    A ES LPE
Sbjct: 359 AGDLLAVRSAGAYGFVMSSNYNTRNRPPELMVDGDQVHVVRRRETLEDQLAPESCLPE 416


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: 572
Number of extensions: 19
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: 416
Length adjustment: 31
Effective length of query: 386
Effective length of database: 385
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 GFF248 HP15_247 (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.12926.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     3e-167  542.3   0.0   3.7e-167  542.0   0.0    1.0  1  lcl|FitnessBrowser__Marino:GFF248  HP15_247 diaminopimelate decarbo


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF248  HP15_247 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.0   0.0  3.7e-167  3.7e-167       5     416 ..       7     411 ..       4     412 .. 0.99

  Alignments for each domain:
  == domain 1  score: 542.0 bits;  conditional E-value: 3.7e-167
                          TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvs 80 
                                        +dgel++e++++ ++a++fgtP Yvy+++tl+++++a++ a +++ +lv+YAvKAnsnlavl++la++G+g+d+vs
  lcl|FitnessBrowser__Marino:GFF248   7 RDGELYAEDIPVSAIADRFGTPAYVYSRATLERHYRAYDDALRDHPHLVCYAVKANSNLAVLNVLARLGAGFDIVS 82 
                                        789************************************************************************* PP

                          TIGR01048  81 gGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakt 156
                                         GEler+l Ag +++++vfsg+gk+e e+++ale++++++nv+s +el++l+++a+elg ka+++lRvnpdvda t
  lcl|FitnessBrowser__Marino:GFF248  83 AGELERVLRAGGDPSRVVFSGVGKQEWEMKRALEVGVRCFNVESDTELDRLNAVAGELGVKAPISLRVNPDVDAGT 158
                                        **************************************************************************** PP

                          TIGR01048 157 heyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleel 232
                                        h+yisTGlke+KFGi+++ea ++y +a+ +++l++ G+++HIGSq++ ++pf +a+++v+ l+++l+++gi++++l
  lcl|FitnessBrowser__Marino:GFF248 159 HPYISTGLKENKFGIDIAEASQVYARAAGMPNLDVKGVDCHIGSQLTSVSPFLDALDRVLALIDSLADQGIHIHHL 234
                                        **************************************************************************** PP

                          TIGR01048 233 dlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvD 308
                                        d+GGGlg++y++e+ +p++++y+++l+e+l +     +kl+lilEpGRs++anag+l+trVe++K +e+r+f+++D
  lcl|FitnessBrowser__Marino:GFF248 235 DMGGGLGVTYNQEQ-PPQPSDYVKALAERLGD-----RKLELILEPGRSIAANAGILVTRVEFLKCTEHRNFAIID 304
                                        *************9.**************999.....69************************************* PP

                          TIGR01048 309 agmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnY 384
                                        a+mndliRpalY+a++ i+++k  ++ e++ +d+vGp+CE+gD+l+kdr+l  + +Gdllav+saGAYg+ mssnY
  lcl|FitnessBrowser__Marino:GFF248 305 AAMNDLIRPALYSAWQAIIPVKPHQDGEEKAWDLVGPVCETGDFLGKDRHLRLQ-AGDLLAVRSAGAYGFVMSSNY 379
                                        ***************************************************865.5******************** PP

                          TIGR01048 385 nsrprpaevlveegkarlirrretledllale 416
                                        n+r+rp e++v++++++++rrretled+la e
  lcl|FitnessBrowser__Marino:GFF248 380 NTRNRPPELMVDGDQVHVVRRRETLEDQLAPE 411
                                        ****************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (416 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: 00:00:00.01
# Mc/sec: 11.23
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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