Aligments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

GapMind for Amino acid biosynthesis

Aligments for a candidate for lysA in Desulfovibrio vulgaris Hildenborough

Align Diaminopimelate decarboxylase; DAP decarboxylase; DAPDC; EC 4.1.1.20 (characterized)
to candidate 207105 DVU1647 diaminopimelate decarboxylase

Query= SwissProt::B4XMC6
         (405 letters)



>MicrobesOnline__882:207105
          Length = 412

 Score =  352 bits (904), Expect = e-102
 Identities = 181/393 (46%), Positives = 254/393 (64%), Gaps = 1/393 (0%)

Query: 6   ELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGAD 65
           +L  T+ TP Y+Y    +++ +  +  AF     L C+++KA SN+ IL LL  L +G D
Sbjct: 20  DLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSVKACSNIHILKLLGSLGAGVD 79

Query: 66  CVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQS 125
            VS GE+ RAL AGI   RIV+SGVGK   EI  AL+ +IL  NVES  EL+TIE +A S
Sbjct: 80  IVSGGELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADILMFNVESLQELRTIEEVAAS 139

Query: 126 LGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFH 185
           +G  AR+S+RINP++D  THPYISTGL++NKFG+   +ALE ++ A+    ++P+ +  H
Sbjct: 140 MGTTARVSLRINPDVDPHTHPYISTGLQKNKFGIEMTQALEGYMLARDLPHIDPIGIDCH 199

Query: 186 IGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGI 245
           IGSQL  L P +EA  KV +  + L  LG+D+ + D+GGG+G++Y  E      D+ + +
Sbjct: 200 IGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGGLGITYGEETPPHPRDFGRAV 259

Query: 246 LNALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAK 305
           L   +GL+LT++ EPGR I   +G L+T+VLY K   +K+FVIVDA MND +RPSLY + 
Sbjct: 260 LERTKGLNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSKQFVIVDAAMNDLVRPSLYASY 319

Query: 306 HAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQ 365
           H I  + P  GR     DVVGP+CES D   +D  LP +E G+ +A+   GAYG SM+SQ
Sbjct: 320 HRIAEVLP-HGRTEQTVDVVGPICESGDFLARDRVLPAVEQGELLAVFSAGAYGFSMSSQ 378

Query: 366 YNSRPKLLELALEDHKIRVIRKREALEDLWRLE 398
           YNSRP+  E+ +     + IR+RE  +DL  LE
Sbjct: 379 YNSRPRAAEVLVRGDTAKSIRRRETYDDLTALE 411


Lambda     K      H
   0.319    0.138    0.389 

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: 385
Number of extensions: 10
Number of successful extensions: 2
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: 405
Length of database: 412
Length adjustment: 31
Effective length of query: 374
Effective length of database: 381
Effective search space:   142494
Effective search space used:   142494
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 207105 DVU1647 (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.934.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-164  532.9   0.0   2.6e-164  532.6   0.0    1.0  1  lcl|MicrobesOnline__882:207105  DVU1647 diaminopimelate decarbox


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207105  DVU1647 diaminopimelate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  532.6   0.0  2.6e-164  2.6e-164       4     416 ..       6     411 ..       4     412 .] 0.98

  Alignments for each domain:
  == domain 1  score: 532.6 bits;  conditional E-value: 2.6e-164
                       TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                      ++g+l++e+v++ +la ++gtPlYvy++ tl+++++a+++af+++ +l ++ vKA+sn+++l+ll ++G+g+d+vsgG
  lcl|MicrobesOnline__882:207105   6 YREGSLFAEDVSIIDLASTYGTPLYVYSAGTLERHYRAFDSAFGKAAHLTCFSVKACSNIHILKLLGSLGAGVDIVSGG 84 
                                     57899****************************************99******************************** PP

                       TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyis 161
                                     El ral Ag++  +iv+sg+gk+ +e++ ale++i ++nv+s++el+++ee+a+++g++arv+lR+npdvd++th+yis
  lcl|MicrobesOnline__882:207105  85 ELHRALLAGIPGRRIVYSGVGKRPDEIRSALEADILMFNVESLQELRTIEEVAASMGTTARVSLRINPDVDPHTHPYIS 163
                                     ******************************************************************************* PP

                       TIGR01048 162 TGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgi 240
                                     TGl+++KFGie+++a+e y la +l++++++Gi++HIGSq++ l+pf ea++kv+++ e+l+  g++++ ldlGGGlgi
  lcl|MicrobesOnline__882:207105 164 TGLQKNKFGIEMTQALEGYMLARDLPHIDPIGIDCHIGSQLTSLSPFLEALDKVLEFREHLSILGLDISYLDLGGGLGI 242
                                     ******************************************************************************* PP

                       TIGR01048 241 syeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpal 319
                                     +y ee+ +p+++++ +++le+ ++     l+l+l+lEpGR +++nag+l+t+V ++K+++s++fv+vDa+mndl+Rp+l
  lcl|MicrobesOnline__882:207105 243 TYGEET-PPHPRDFGRAVLERTKG-----LNLTLVLEPGRVIAGNAGILVTEVLYTKTTPSKQFVIVDAAMNDLVRPSL 315
                                     ***999.**********9987777.....8************************************************* PP

                       TIGR01048 320 YeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveeg 398
                                     Y +yh+ia++   + ++++tvdvvGp+CEsgD+la+dr lp+ve+G+llav+saGAYg+smss+Ynsrpr+aevlv+++
  lcl|MicrobesOnline__882:207105 316 YASYHRIAEV-LPHGRTEQTVDVVGPICESGDFLARDRVLPAVEQGELLAVFSAGAYGFSMSSQYNSRPRAAEVLVRGD 393
                                     **********.5577789************************************************************* PP

                       TIGR01048 399 karlirrretledllale 416
                                      a+ irrret++dl ale
  lcl|MicrobesOnline__882:207105 394 TAKSIRRRETYDDLTALE 411
                                     **************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (412 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: 8.97
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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