Alignments for a candidate for lysA in Persephonella marina EX-H1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Persephonella marina EX-H1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_012676382.1 PERMA_RS06885 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_000021565.1:WP_012676382.1
          Length = 426

 Score =  376 bits (965), Expect = e-109
 Identities = 193/412 (46%), Positives = 277/412 (67%), Gaps = 5/412 (1%)

Query: 3   YFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAVKA 62
           YF Y+E+ QL+ E +P+ ++A++ GTP Y+YS+  +      + K+  +Y  LICYA KA
Sbjct: 8   YFYYREN-QLFCENIPIKEIASKVGTPFYLYSKQAILDRIDQYKKAFEEYNTLICYAAKA 66

Query: 63  NSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKIKC 122
           NSNL +L        G DIVS GEL +   AG   +K+V++GVGKT+ E++ A++  I  
Sbjct: 67  NSNLSILKIFEENDLGLDIVSGGELYKAKKAGFPSNKIVYAGVGKTDFELEYAIRENILS 126

Query: 123 FNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAAQV 182
           FNVESE E+  L+++A +L     IS+R+NPDVD KTHPYISTGLR +KFGI  D A  V
Sbjct: 127 FNVESEMEIDVLDELAEKLNKTVRISIRVNPDVDPKTHPYISTGLRKSKFGIDIDEALNV 186

Query: 183 YRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGGLG 242
           YR A    N+DV GI CHIGSQ+  ++P+++A ++   L+  LK EGI ++H D+GGG+G
Sbjct: 187 YRKAVKKKNIDVIGIHCHIGSQIMEISPYVEAVEKTAELVFRLKKEGIELQHFDIGGGIG 246

Query: 243 VVYR-DELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHKN 301
           + YR ++ PP P + AKA++  + R   L LI EPGR++   AG L+T+V FLK+   K+
Sbjct: 247 IRYRPEDNPPTPEDLAKAVIP-IVRTTGLRLIIEPGRSLIGEAGALITQVVFLKNKGDKH 305

Query: 302 FAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDL-VLQE 360
           F I+D+ MNDL+RPA+Y A+  I+ +  ++ +    D+VGP+CET DF   DR++  +Q 
Sbjct: 306 FIIVDSGMNDLLRPAMYNAYHHILSVEKKERKV-VADIVGPICETGDFFALDREIDDVQR 364

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALE 412
            D LAV S+GAYG +MSSNYN RPR AEV+V  N  YL+++RE+ S +  LE
Sbjct: 365 KDYLAVMSAGAYGSSMSSNYNVRPRAAEVLVSDNSFYLIKEREDYSYITKLE 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: 437
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: 426
Length adjustment: 32
Effective length of query: 385
Effective length of database: 394
Effective search space:   151690
Effective search space used:   151690
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_012676382.1 PERMA_RS06885 (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.31962.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-166  540.5   0.0   1.3e-166  540.2   0.0    1.0  1  lcl|NCBI__GCF_000021565.1:WP_012676382.1  PERMA_RS06885 diaminopimelate de


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000021565.1:WP_012676382.1  PERMA_RS06885 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.2   0.0  1.3e-166  1.3e-166       5     416 ..      12     416 ..       9     417 .. 0.98

  Alignments for each domain:
  == domain 1  score: 540.2 bits;  conditional E-value: 1.3e-166
                                 TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeG 73 
                                               ++ +l++e++++ke+a + gtP+Y+y+++++  r+ ++k+af+++++l++YA+KAnsnl++l++++e++
  lcl|NCBI__GCF_000021565.1:WP_012676382.1  12 RENQLFCENIPIKEIASKVGTPFYLYSKQAILDRIDQYKKAFEEYNTLICYAAKANSNLSILKIFEEND 80 
                                               5679***************************************************************** PP

                                 TIGR01048  74 lgldvvsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkka 142
                                               lgld+vsgGEl+ a++Ag++++kiv++g+gk++ ele a++ +i  +nv+s++e++ l+e+a++l+k++
  lcl|NCBI__GCF_000021565.1:WP_012676382.1  81 LGLDIVSGGELYKAKKAGFPSNKIVYAGVGKTDFELEYAIRENILSFNVESEMEIDVLDELAEKLNKTV 149
                                               ********************************************************************* PP

                                 TIGR01048 143 rvllRvnpdvdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfvea 211
                                               r+++Rvnpdvd+kth+yisTGl++sKFGi+++ea+++y+ a+k+++++++Gih+HIGSqi++++p+vea
  lcl|NCBI__GCF_000021565.1:WP_012676382.1 150 RISIRVNPDVDPKTHPYISTGLRKSKFGIDIDEALNVYRKAVKKKNIDVIGIHCHIGSQIMEISPYVEA 218
                                               ********************************************************************* PP

                                 TIGR01048 212 aekvvklleelkeegieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGR 280
                                               +ek ++l+ +lk+egiel+++d+GGG+gi+y++e+++p++e++a++++  ++      + l+li+EpGR
  lcl|NCBI__GCF_000021565.1:WP_012676382.1 219 VEKTAELVFRLKKEGIELQHFDIGGGIGIRYRPEDNPPTPEDLAKAVIPIVRT-----TGLRLIIEPGR 282
                                               *************************************************9999.....599******** PP

                                 TIGR01048 281 slvanagvlltrVesvKevesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEs 349
                                               sl+++ag l+t+V ++K+++ ++f++vD+gmndl+Rpa+Y+ayh+i  +++  +e+++++d+vGp+CE+
  lcl|NCBI__GCF_000021565.1:WP_012676382.1 283 SLIGEAGALITQVVFLKNKGDKHFIIVDSGMNDLLRPAMYNAYHHILSVEK--KERKVVADIVGPICET 349
                                               *************************************************66..6668************ PP

                                 TIGR01048 350 gDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                               gD++a dre+++v++ d+lav+saGAYg smssnYn rpr+aevlv++++ +li++re ++ + +le
  lcl|NCBI__GCF_000021565.1:WP_012676382.1 350 GDFFALDREIDDVQRKDYLAVMSAGAYGSSMSSNYNVRPRAAEVLVSDNSFYLIKEREDYSYITKLE 416
                                               *************************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (426 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: 9.06
//
[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