Alignments for a candidate for lysA in Desulfovibrio vulgaris Miyazaki F

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Desulfovibrio vulgaris Miyazaki F

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 8499585 DvMF_0353 diaminopimelate decarboxylase (RefSeq)

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__Miya:8499585
          Length = 416

 Score =  451 bits (1161), Expect = e-131
 Identities = 233/413 (56%), Positives = 302/413 (73%), Gaps = 3/413 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           M +F Y+E GQL+AE VP+ +LA++YGTPLYVYS ATL RH+ AFD +     HL CY+V
Sbjct: 1   MHHFQYRE-GQLYAEGVPVHELASRYGTPLYVYSAATLRRHFQAFDSAFTGVGHLTCYSV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSN+ +L  LA +G+G DIVS GEL R LAAG    ++V+SGVGK + E++ AL+  I
Sbjct: 60  KANSNVHLLRLLADMGAGMDIVSGGELHRALAAGVPGQRIVYSGVGKQDDEIRAALEADI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
             FNVES  EL+R+N VAG++G  A I +RINPDVD KTHPYISTG+R+NKFG+  ++A 
Sbjct: 120 LLFNVESVQELERINAVAGQMGRTARIGVRINPDVDPKTHPYISTGMRNNKFGLDMEQAL 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
             Y LA  LPN+   GIDCHIGSQLT LAPF++A DR+L   + L+  G+ I HLD+GGG
Sbjct: 180 AAYLLARDLPNVQPVGIDCHIGSQLTTLAPFLEALDRVLDFHERLRDLGLAITHLDLGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LG+ Y +E PP P E+ +A+ +RL R R L LI EPGR IA NAG+LV +V + K T  K
Sbjct: 240 LGITYGEETPPHPREFGEAVSERL-RGRGLSLILEPGRVIAGNAGILVGRVIYTKSTPSK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLV-LQ 359
           NF I DAAMNDL+RP+LYQ++  I  ++P   +  T D+VGP+CE+ DFL +DR L  +Q
Sbjct: 299 NFIIADAAMNDLVRPSLYQSYHRIAEVQPAGRDEITADVVGPICESGDFLARDRILPDMQ 358

Query: 360 EGDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALE 412
           +G+LLAV S+GAYGF+MSSNYN+RPR AEV+VDG     +R+RE L+ L A E
Sbjct: 359 QGELLAVFSAGAYGFSMSSNYNSRPRAAEVLVDGATARCIRKRETLADLVAPE 411


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: 507
Number of extensions: 19
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: 416
Length adjustment: 31
Effective length of query: 386
Effective length of database: 385
Effective search space:   148610
Effective search space used:   148610
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 8499585 DvMF_0353 (diaminopimelate decarboxylase (RefSeq))
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.28085.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.1e-165  537.2   0.0   1.2e-165  537.0   0.0    1.0  1  lcl|FitnessBrowser__Miya:8499585  DvMF_0353 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8499585  DvMF_0353 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  537.0   0.0  1.2e-165  1.2e-165       4     416 ..       6     411 ..       3     412 .. 0.98

  Alignments for each domain:
  == domain 1  score: 537.0 bits;  conditional E-value: 1.2e-165
                         TIGR01048   4 kkdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvs 80 
                                        ++g+l++egv+++ela ++gtPlYvy+++tlr++++a+++af++  +l +Y vKAnsn+++lrlla+ G+g+d+vs
  lcl|FitnessBrowser__Miya:8499585   6 YREGQLYAEGVPVHELASRYGTPLYVYSAATLRRHFQAFDSAFTGVGHLTCYSVKANSNVHLLRLLADMGAGMDIVS 82 
                                       6789*****************************************99****************************** PP

                         TIGR01048  81 gGEleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdakth 157
                                       gGEl ralaAgv+ ++iv+sg+gk+++e++aale++i l+nv+sv+ele+++++a+++g +ar+ +R+npdvd+kth
  lcl|FitnessBrowser__Miya:8499585  83 GGELHRALAAGVPGQRIVYSGVGKQDDEIRAALEADILLFNVESVQELERINAVAGQMGRTARIGVRINPDVDPKTH 159
                                       ***************************************************************************** PP

                         TIGR01048 158 eyisTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldl 234
                                       +yisTG++++KFG+++e+a++ay la +l+++++vGi++HIGSq++ l+pf ea+++v+++ e+l++ g+ +++ldl
  lcl|FitnessBrowser__Miya:8499585 160 PYISTGMRNNKFGLDMEQALAAYLLARDLPNVQPVGIDCHIGSQLTTLAPFLEALDRVLDFHERLRDLGLAITHLDL 236
                                       ***************************************************************************** PP

                         TIGR01048 235 GGGlgisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagm 311
                                       GGGlgi+y ee+ +p+++e+ e++ e+l++     + l+lilEpGR +++nag+l+ rV ++K+++s++f++ Da+m
  lcl|FitnessBrowser__Miya:8499585 237 GGGLGITYGEET-PPHPREFGEAVSERLRG-----RGLSLILEPGRVIAGNAGILVGRVIYTKSTPSKNFIIADAAM 307
                                       *********999.************99999.....699*************************************** PP

                         TIGR01048 312 ndliRpalYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrp 388
                                       ndl+Rp+lY++yh+ia+++    + + t+dvvGp+CEsgD+la+dr lp++++G+llav+saGAYg+smssnYnsrp
  lcl|FitnessBrowser__Miya:8499585 308 NDLVRPSLYQSYHRIAEVQ-PAGRDEITADVVGPICESGDFLARDRILPDMQQGELLAVFSAGAYGFSMSSNYNSRP 383
                                       ******************5.5777799************************************************** PP

                         TIGR01048 389 rpaevlveegkarlirrretledllale 416
                                       r+aevlv++  ar ir+retl+dl+a e
  lcl|FitnessBrowser__Miya:8499585 384 RAAEVLVDGATARCIRKRETLADLVAPE 411
                                       ************************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (416 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.99
//
[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