Alignments for a candidate for lysA in Halomonas desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Halomonas desiderata SP1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_086511731.1 BZY95_RS20455 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_002151265.1:WP_086511731.1
          Length = 430

 Score =  563 bits (1452), Expect = e-165
 Identities = 285/420 (67%), Positives = 340/420 (80%), Gaps = 5/420 (1%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MD+F Y+ DG L+ E+VPL  +A++ GTP YVYSRATL RH+ A+ +++G +PHLICYAV
Sbjct: 1   MDHFEYR-DGVLYGEEVPLTQVADEIGTPCYVYSRATLTRHYRAYTEALGSHPHLICYAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL VLN LARLG+GFDIVS+GELERVLAAGGDP+KVVFSGV K E EM RAL++ I
Sbjct: 60  KANSNLAVLNLLARLGAGFDIVSLGELERVLAAGGDPAKVVFSGVAKQEHEMARALEVGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
           KCFNVES PEL+RL+ VA  LG  AP+SLR+NPDVDA THPYISTGL+DNKFGI    A 
Sbjct: 120 KCFNVESRPELERLSAVAERLGKVAPVSLRVNPDVDAGTHPYISTGLKDNKFGIAVGEAL 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
           +VY LA  LP L V GIDCHIGSQLT LAPF+DA DRLL L++ L   GI + HLD+GGG
Sbjct: 180 EVYELAARLPGLKVVGIDCHIGSQLTELAPFLDALDRLLVLLERLHERGISVEHLDLGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHR---DLELIFEPGRAIAANAGVLVTKVEFLKHT 297
           LGV YR E PPQP +YA +LL+RL + +   +L L+FEPGR+IAANAGVL+T+VEFLK  
Sbjct: 240 LGVPYRGERPPQPFDYAASLLERLAQWKHGENLTLLFEPGRSIAANAGVLLTRVEFLKPG 299

Query: 298 EHKNFAIIDAAMNDLIRPALYQAWQDIIPLRPRQ-GEAQTYDLVGPVCETSDFLGKDRDL 356
           E KNFAI+DA MNDLIRP+LYQAWQ IIP+  R   E+  YD+VGPVCET DFLGK+R+L
Sbjct: 300 ETKNFAIVDAGMNDLIRPSLYQAWQAIIPVDTRHVRESAVYDVVGPVCETGDFLGKEREL 359

Query: 357 VLQEGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
            +  GDLLAVRS+GAYGF M+SNYN+RPR AEVMVDG+  ++VRQRE + SLWA ES+LP
Sbjct: 360 AIGAGDLLAVRSAGAYGFVMASNYNSRPRPAEVMVDGDAYHVVRQRESVESLWAGESLLP 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: 572
Number of extensions: 26
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: 430
Length adjustment: 32
Effective length of query: 385
Effective length of database: 398
Effective search space:   153230
Effective search space used:   153230
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: 51 (24.3 bits)

Align candidate WP_086511731.1 BZY95_RS20455 (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.8378.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.1e-165  536.2   0.0   2.6e-165  535.9   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086511731.1  BZY95_RS20455 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086511731.1  BZY95_RS20455 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.9   0.0  2.6e-165  2.6e-165       5     416 ..       7     415 ..       4     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 535.9 bits;  conditional E-value: 2.6e-165
                                 TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 
                                               +dg l+ e+v+l+++a+e gtP Yvy+++tl+++++a++ea +++ +l++YAvKAnsnlavl+lla++G
  lcl|NCBI__GCF_002151265.1:WP_086511731.1   7 RDGVLYGEEVPLTQVADEIGTPCYVYSRATLTRHYRAYTEALGSHPHLICYAVKANSNLAVLNLLARLG 75 
                                               6889999************************************************************** PP

                                 TIGR01048  74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142
                                               +g+d+vs GEler+laAg ++ k+vfsg++k+e+e+++ale++ik++nv+s  ele+l+++a++lgk a
  lcl|NCBI__GCF_002151265.1:WP_086511731.1  76 AGFDIVSLGELERVLAAGGDPAKVVFSGVAKQEHEMARALEVGIKCFNVESRPELERLSAVAERLGKVA 144
                                               ********************************************************************* PP

                                 TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211
                                               +v+lRvnpdvda th+yisTGlk++KFGi+v ea+e+yela++l+ l++vGi++HIGSq+++l+pf +a
  lcl|NCBI__GCF_002151265.1:WP_086511731.1 145 PVSLRVNPDVDAGTHPYISTGLKDNKFGIAVGEALEVYELAARLPGLKVVGIDCHIGSQLTELAPFLDA 213
                                               ********************************************************************* PP

                                 TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGR 280
                                               +++++ lle+l+e+gi++e+ldlGGGlg++y+ e  +p++ +ya+ lle+l++  ++g++l+l++EpGR
  lcl|NCBI__GCF_002151265.1:WP_086511731.1 214 LDRLLVLLERLHERGISVEHLDLGGGLGVPYRGER-PPQPFDYAASLLERLAQ-WKHGENLTLLFEPGR 280
                                               *********************************99.****************9.59999********** PP

                                 TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEs 349
                                               s++anagvlltrVe++K  e+++f++vDagmndliRp+lY+a++ i+++++ + +e++++dvvGp+CE+
  lcl|NCBI__GCF_002151265.1:WP_086511731.1 281 SIAANAGVLLTRVEFLKPGETKNFAIVDAGMNDLIRPSLYQAWQAIIPVDTRHVRESAVYDVVGPVCET 349
                                               ***************************************************999*************** PP

                                 TIGR01048 350 gDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               gD+l+k+rel     Gdllav+saGAYg+ m+snYnsrprpaev+v+++ ++++r+re++e+l+a e
  lcl|NCBI__GCF_002151265.1:WP_086511731.1 350 GDFLGKERELAIGA-GDLLAVRSAGAYGFVMASNYNSRPRPAEVMVDGDAYHVVRQRESVESLWAGE 415
                                               **********8766.*************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (430 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: 7.50
//
[ok]

This GapMind analysis is from Apr 10 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