Alignments for a candidate for lysA in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Dechloromonas agitata is5

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_027456776.1 K420_RS0103165 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000519045.1:WP_027456776.1
          Length = 420

 Score =  490 bits (1261), Expect = e-143
 Identities = 245/415 (59%), Positives = 314/415 (75%), Gaps = 6/415 (1%)

Query: 8   EDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPH----LICYAVKAN 63
           ++G L  E V L+ +A ++GTP YVYSRA L      F   +  +P     L+CYAVKAN
Sbjct: 7   KNGVLHVESVALSAIAERFGTPAYVYSRAALTASLREFQDVLTAHPAGQDALVCYAVKAN 66

Query: 64  SNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKCF 123
           SNL +LN  ARLG+GFDIVS GEL+RVLAAG DP KVVFSGVGKT AEMK AL   I CF
Sbjct: 67  SNLAILNLFARLGAGFDIVSGGELQRVLAAGADPKKVVFSGVGKTAAEMKLALDAGIFCF 126

Query: 124 NVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQVY 183
           N+ES PEL+RLN+VAG+ G +APISLR+NP+VD KTHPYISTGL++ KFG+ ++ A  +Y
Sbjct: 127 NIESIPELERLNEVAGQCGKQAPISLRVNPNVDPKTHPYISTGLKEAKFGVAYEHALDLY 186

Query: 184 RLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLGV 243
           R A +LP++ V GIDCHIGSQL   +PF++A +R+LALID L  EGI + H+D+GGGLG+
Sbjct: 187 RRAAALPHIAVAGIDCHIGSQLLDPSPFVEALERILALIDQLADEGITLHHIDLGGGLGI 246

Query: 244 VYR-DELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHKNF 302
            Y+ +++ P  + Y   LLD+L+  R L+++ EPGR +  NAG+L+T++EFLK  E KNF
Sbjct: 247 KYKAEQVQPTVASYLNPLLDKLQ-GRGLQVVLEPGRRLVGNAGLLLTRIEFLKEGEGKNF 305

Query: 303 AIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQEGD 362
           AIIDAAMNDL+RPALY+AW DI P+ PR G  + YD+VGPVCET DFLG+ R L +Q GD
Sbjct: 306 AIIDAAMNDLMRPALYEAWHDIEPVEPRDGATRDYDVVGPVCETGDFLGQARPLCVQPGD 365

Query: 363 LLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLPE 417
           LLAV S+GAYG  M+SNYNTRPR  EVMVDG+  +++RQRE +  L+A ES+LP+
Sbjct: 366 LLAVMSAGAYGMAMASNYNTRPRAVEVMVDGDAVHVIRQRETVEQLYAGESILPQ 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: 504
Number of extensions: 14
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: 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 WP_027456776.1 K420_RS0103165 (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.11717.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.2e-160  518.4   0.0   6.3e-160  518.1   0.0    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027456776.1  K420_RS0103165 diaminopimelate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027456776.1  K420_RS0103165 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.1   0.0  6.3e-160  6.3e-160       5     416 ..       7     415 ..       4     416 .. 0.97

  Alignments for each domain:
  == domain 1  score: 518.1 bits;  conditional E-value: 6.3e-160
                                 TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafka....eeslvlYAvKAnsnlavlrll 69 
                                               k+g l +e v+l ++ae+fgtP Yvy++++l++ l++++ + +a    +++lv+YAvKAnsnla+l+l+
  lcl|NCBI__GCF_000519045.1:WP_027456776.1   7 KNGVLHVESVALSAIAERFGTPAYVYSRAALTASLREFQDVLTAhpagQDALVCYAVKANSNLAILNLF 75 
                                               7899***********************************999885543445****************** PP

                                 TIGR01048  70 aeeGlgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakel 138
                                               a++G+g+d+vsgGEl+r+laAg++++k+vfsg+gk+ +e++ al+++i ++n++s+ ele+l+e+a++ 
  lcl|NCBI__GCF_000519045.1:WP_027456776.1  76 ARLGAGFDIVSGGELQRVLAAGADPKKVVFSGVGKTAAEMKLALDAGIFCFNIESIPELERLNEVAGQC 144
                                               ********************************************************************* PP

                                 TIGR01048 139 gkkarvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlep 207
                                               gk+a+++lRvnp+vd+kth+yisTGlke KFG+++e+a++ y++a++l+++ + Gi++HIGSq+ld +p
  lcl|NCBI__GCF_000519045.1:WP_027456776.1 145 GKQAPISLRVNPNVDPKTHPYISTGLKEAKFGVAYEHALDLYRRAAALPHIAVAGIDCHIGSQLLDPSP 213
                                               ********************************************************************* PP

                                 TIGR01048 208 fveaaekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklil 276
                                               fvea+e+++ l+++l++egi+l+++dlGGGlgi+y+ e+ +p++++y + ll+kl++     + l+++l
  lcl|NCBI__GCF_000519045.1:WP_027456776.1 214 FVEALERILALIDQLADEGITLHHIDLGGGLGIKYKAEQVQPTVASYLNPLLDKLQG-----RGLQVVL 277
                                               *******************************************************99.....699**** PP

                                 TIGR01048 277 EpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGp 345
                                               EpGR lv+nag lltr+e++Ke e ++f+++Da+mndl+RpalYea+h+i ++ + ++ +t  +dvvGp
  lcl|NCBI__GCF_000519045.1:WP_027456776.1 278 EPGRRLVGNAGLLLTRIEFLKEGEGKNFAIIDAAMNDLMRPALYEAWHDIEPV-EPRDGATRDYDVVGP 345
                                               *****************************************************.779999********* PP

                                 TIGR01048 346 lCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledlla 414
                                               +CE+gD+l++ r l +v++Gdllav+saGAYg++m+snYn+rpr+ ev+v+++ +++ir+ret+e+l a
  lcl|NCBI__GCF_000519045.1:WP_027456776.1 346 VCETGDFLGQARPL-CVQPGDLLAVMSAGAYGMAMASNYNTRPRAVEVMVDGDAVHVIRQRETVEQLYA 413
                                               *************9.6899***********************************************998 PP

                                 TIGR01048 415 le 416
                                                e
  lcl|NCBI__GCF_000519045.1:WP_027456776.1 414 GE 415
                                               66 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: 12.34
//
[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