Alignments for a candidate for lysA in Thioalkalivibrio halophilus HL17

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Thioalkalivibrio halophilus HL17

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate WP_077244043.1 B1A74_RS05725 diaminopimelate decarboxylase

Query= BRENDA::Q9KVL7
         (417 letters)



>NCBI__GCF_001995255.1:WP_077244043.1
          Length = 429

 Score =  513 bits (1320), Expect = e-150
 Identities = 257/417 (61%), Positives = 323/417 (77%), Gaps = 3/417 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MDYF+Y+  G L  E V L  LA + GTP YVYSRATLERH+ AF +++   PH +C+AV
Sbjct: 1   MDYFDYR-GGTLHCESVDLHALARRVGTPAYVYSRATLERHYRAFAEALIGMPHQVCFAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANS+L VLN LAR+GSGFDIVS GELERVL AGGDP++VVFSGVGKT AEM+RAL + I
Sbjct: 60  KANSSLAVLNVLARMGSGFDIVSGGELERVLRAGGDPARVVFSGVGKTAAEMQRALDVGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVESE EL+RL  VA E G  AP+SLR+NPDVDA+THPYI+TGLRDNKFG+  + A 
Sbjct: 120 HCFNVESEAELERLEAVAAERGEVAPVSLRVNPDVDAETHPYIATGLRDNKFGVAIEDAP 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            +YR   +  +LD  G+D HIGSQLT+  PF+DA +R+L L+D L  +GI + H+DVGGG
Sbjct: 180 ALYRRIQASAHLDAIGVDFHIGSQLTSTEPFVDALERVLGLVDRLAEDGIELSHIDVGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV YRDE PP+P  +A AL + L + R L+++ EPGRAIAANAGV +T+VE+LKH+EH+
Sbjct: 240 LGVRYRDETPPEPDVWAAALRETLGQ-RPLKVLLEPGRAIAANAGVFLTRVEYLKHSEHR 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQG-EAQTYDLVGPVCETSDFLGKDRDLVLQ 359
           +FAI+D AMNDL+RPALY AWQ I P+ PR   E ++YD+VGPVCET DFLG++RDL L 
Sbjct: 299 DFAIVDGAMNDLLRPALYGAWQAIDPIVPRDDTETRSYDVVGPVCETGDFLGRERDLALA 358

Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
             D+LAVRS+GAYG+ M+ NYN+RPR  EVMVDG+   +V +RE++  L   ES+LP
Sbjct: 359 PDDVLAVRSAGAYGYVMAGNYNSRPRPPEVMVDGDHYQIVNRREQVDHLMMRESMLP 415


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: 510
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: 429
Length adjustment: 32
Effective length of query: 385
Effective length of database: 397
Effective search space:   152845
Effective search space used:   152845
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_077244043.1 B1A74_RS05725 (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.2254033.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-156  504.6   0.0     1e-155  504.3   0.0    1.0  1  NCBI__GCF_001995255.1:WP_077244043.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001995255.1:WP_077244043.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.3   0.0    1e-155    1e-155       6     416 ..       8     411 ..       4     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 504.3 bits;  conditional E-value: 1e-155
                             TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldv 78 
                                            g+l +e vdl++la++ gtP Yvy+++tl+++++a++ea  +  ++v++AvKAns+lavl++la+ G+g+d+
  NCBI__GCF_001995255.1:WP_077244043.1   8 GGTLHCESVDLHALARRVGTPAYVYSRATLERHYRAFAEALIGMPHQVCFAVKANSSLAVLNVLARMGSGFDI 80 
                                           58999***************************************9**************************** PP

                             TIGR01048  79 vsgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpd 151
                                           vsgGEler+l Ag ++ ++vfsg+gk+ +e+++al+++i+++nv+s++ele+le++a+e g+ a+v+lRvnpd
  NCBI__GCF_001995255.1:WP_077244043.1  81 VSGGELERVLRAGGDPARVVFSGVGKTAAEMQRALDVGIHCFNVESEAELERLEAVAAERGEVAPVSLRVNPD 153
                                           ************************************************************************* PP

                             TIGR01048 152 vdaktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelke 224
                                           vda+th+yi+TGl+++KFG+++e+a + y+++ ++++l+ +G+++HIGSq++ +epfv+a+e+v+ l+++l+e
  NCBI__GCF_001995255.1:WP_077244043.1 154 VDAETHPYIATGLRDNKFGVAIEDAPALYRRIQASAHLDAIGVDFHIGSQLTSTEPFVDALERVLGLVDRLAE 226
                                           ************************************************************************* PP

                             TIGR01048 225 egieleeldlGGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvK 297
                                           +giel+++d+GGGlg++y++e+ +p+++ +a++l e+l +     + lk++lEpGR+++anagv+ltrVe++K
  NCBI__GCF_001995255.1:WP_077244043.1 227 DGIELSHIDVGGGLGVRYRDET-PPEPDVWAAALRETLGQ-----RPLKVLLEPGRAIAANAGVFLTRVEYLK 293
                                           *********************9.************99999.....6*************************** PP

                             TIGR01048 298 evesrkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllav 370
                                           ++e+r f++vD++mndl+RpalY+a++ i ++   +++et  +dvvGp+CE+gD+l+++r+l  +  +d+lav
  NCBI__GCF_001995255.1:WP_077244043.1 294 HSEHRDFAIVDGAMNDLLRPALYGAWQAIDPIVPRDDTETRSYDVVGPVCETGDFLGRERDLALAP-DDVLAV 365
                                           **************************************************************8765.****** PP

                             TIGR01048 371 asaGAYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                           +saGAYg+ m+ nYnsrprp ev+v++++++++ rre+++ l+  e
  NCBI__GCF_001995255.1:WP_077244043.1 366 RSAGAYGYVMAGNYNSRPRPPEVMVDGDHYQIVNRREQVDHLMMRE 411
                                           *****************************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (429 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 14.86
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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 2024 update 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 original 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