Alignments for a candidate for lysA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Echinicola vietnamensis KMM 6221, DSM 17526

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate Echvi_1295 Echvi_1295 diaminopimelate decarboxylase

Query= reanno::Cola:Echvi_1295
         (410 letters)



>FitnessBrowser__Cola:Echvi_1295
          Length = 410

 Score =  816 bits (2109), Expect = 0.0
 Identities = 410/410 (100%), Positives = 410/410 (100%)

Query: 1   MTIDNQQYQVQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVNLKIKYATKALS 60
           MTIDNQQYQVQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVNLKIKYATKALS
Sbjct: 1   MTIDNQQYQVQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVNLKIKYATKALS 60

Query: 61  NINILKLMKKAGTGVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINI 120
           NINILKLMKKAGTGVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINI
Sbjct: 61  NINILKLMKKAGTGVDAVSIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVMINI 120

Query: 121 DNIPMLEHFGTYYGNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEV 180
           DNIPMLEHFGTYYGNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEV
Sbjct: 121 DNIPMLEHFGTYYGNSVPLCIRLNPHILAGGNAKISVGHIDSKFGISILQLKHVLKIVEV 180

Query: 181 HNLKVAGLHVHTGSDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTD 240
           HNLKVAGLHVHTGSDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTD
Sbjct: 181 HNLKVAGLHVHTGSDILDAEVFLKGAEILFDAAKEFKDLQFLDFGGGFKVGYKEGDITTD 240

Query: 241 MVEVGRKVSAAFKEFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDS 300
           MVEVGRKVSAAFKEFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDS
Sbjct: 241 MVEVGRKVSAAFKEFCKNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTPASTFIGVDS 300

Query: 301 GLNHLIRPMMYDAYHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIK 360
           GLNHLIRPMMYDAYHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIK
Sbjct: 301 GLNHLIRPMMYDAYHGVENISRVTGPDRVYTIVGYICETDTIAADRKLKEVKEGDVLAIK 360

Query: 361 NAGAYGFSMASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDIGL 410
           NAGAYGFSMASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDIGL
Sbjct: 361 NAGAYGFSMASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQIDIGL 410


Lambda     K      H
   0.320    0.139    0.403 

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: 780
Number of extensions: 13
Number of successful extensions: 1
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: 410
Length of database: 410
Length adjustment: 31
Effective length of query: 379
Effective length of database: 379
Effective search space:   143641
Effective search space used:   143641
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate Echvi_1295 Echvi_1295 (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.9220.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.4e-120  388.5   0.2   1.6e-120  388.4   0.2    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1295  Echvi_1295 diaminopimelate decar


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1295  Echvi_1295 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.4   0.2  1.6e-120  1.6e-120       6     416 ..       5     405 ..       1     406 [. 0.96

  Alignments for each domain:
  == domain 1  score: 388.4 bits;  conditional E-value: 1.6e-120
                            TIGR01048   6 dgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvv 79 
                                          + + +++gv+l ++a e+gtP+Yvyd +++  ++++l++af++ + ++ YA+KA sn+++l+l++++G+g+d+v
  lcl|FitnessBrowser__Cola:Echvi_1295   5 NQQYQVQGVPLLDIASEYGTPVYVYDGQKILDQVATLQNAFSSVNLKIKYATKALSNINILKLMKKAGTGVDAV 78 
                                          678899************************************9888**************************** PP

                            TIGR01048  80 sgGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvd 153
                                          s  E++  l+ g+++++i+f+ n++  ee+++a++l++  in+d++ +le++ +     g+++++++R+np++ 
  lcl|FitnessBrowser__Cola:Echvi_1295  79 SIEEVKLCLHVGYEPSEIMFTPNCVAFEEIQEAVDLGVM-INIDNIPMLEHFGTYY---GNSVPLCIRLNPHIL 148
                                          **************************************6.**********996665...555************ PP

                            TIGR01048 154 aktheyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegi 227
                                          a    +is G+ +sKFGi++  +++ +  +++ ++l++ G+hvH GS ild+e f + ae ++++++e      
  lcl|FitnessBrowser__Cola:Echvi_1295 149 AGGNAKISVGHIDSKFGISIL-QLKHVLKIVEVHNLKVAGLHVHTGSDILDAEVFLKGAEILFDAAKE----FK 217
                                          ********************9.78888889999*********************************99....58 PP

                            TIGR01048 228 eleeldlGGGlgisyeeeeeapdleeyaeklleklekea.elglklklilEpGRslvanagvlltrVesvKeve 300
                                          +l++ld+GGG+ + y+e + + d+ e+ +k+ +++++ + ++g++l++++EpG++lv++ g+ll++ ++vK+++
  lcl|FitnessBrowser__Cola:Echvi_1295 218 DLQFLDFGGGFKVGYKEGDITTDMVEVGRKVSAAFKEFCkNYGRELEIWFEPGKFLVSECGYLLVNANVVKSTP 291
                                          9**************************************9********************************** PP

                            TIGR01048 301 srkfvlvDagmndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaG 374
                                            +f+ vD+g+n liRp++Y+ayh + +++r++  ++ ++++vG +CE+ D++a dr+l+ev+eGd+la+++aG
  lcl|FitnessBrowser__Cola:Echvi_1295 292 ASTFIGVDSGLNHLIRPMMYDAYHGVENISRVT-GPDRVYTIVGYICET-DTIAADRKLKEVKEGDVLAIKNAG 363
                                          *****************************9965.6699**********7.9*********************** PP

                            TIGR01048 375 AYgasmssnYnsrprpaevlveegkarlirrretledllale 416
                                          AYg+sm+snYnsr rpaevlv +gka+lir re++ed+l+++
  lcl|FitnessBrowser__Cola:Echvi_1295 364 AYGFSMASNYNSRLRPAEVLVLDGKAHLIRARESFEDILRHQ 405
                                          ***************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (410 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: 10.41
//
[ok]

This GapMind analysis is from Apr 09 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