Alignments for a candidate for lysA in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Shewanella oneidensis MR-1

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 203388 SO4309 diaminopimelate decarboxylase (NCBI ptt file)

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__MR1:203388
          Length = 414

 Score =  575 bits (1483), Expect = e-169
 Identities = 286/416 (68%), Positives = 329/416 (79%), Gaps = 2/416 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MD+F YQ D  L+AE   + DLA  YGTPLY+YSRATLERHWHAF+ +V  +PHL+CYAV
Sbjct: 1   MDHFLYQ-DNTLYAEGCRVNDLAQTYGTPLYIYSRATLERHWHAFNNAVAGHPHLVCYAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL VLN LARLGSGFDIVS GEL RV+ AGGDP+KVVFSGVGKT AEM++AL L I
Sbjct: 60  KANSNLAVLNVLARLGSGFDIVSGGELARVIEAGGDPAKVVFSGVGKTVAEMEQALNLGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVES  EL++LN VAG LG  AP+SLR+NPDVDA THPYISTGL++NKFGI  D A 
Sbjct: 120 YCFNVESSAELEQLNLVAGRLGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAMDEAE 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            V+  AH+LP+L V G+DCHIGSQLT + PF+DA DR+L+LID L  +GI I H DVGGG
Sbjct: 180 AVFARAHALPHLQVKGVDCHIGSQLTEIQPFLDAMDRMLSLIDRLAEQGIVIEHFDVGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV Y DE PP P  YA ALL RL  HR L+LIFEPGRAIAANAG+ VT+V +LK    K
Sbjct: 240 LGVTYDDETPPHPDVYAAALLKRL-GHRKLKLIFEPGRAIAANAGIFVTEVLYLKENSDK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360
            FAI+D AMNDLIRPALY AWQ IIP+ PR  +A  +D+VGPVCET DFLGKDR+  +  
Sbjct: 299 RFAIVDGAMNDLIRPALYSAWQKIIPVTPRDDQAHVFDIVGPVCETGDFLGKDREFAIAP 358

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
           GDLL VRSSGAYGF M+SNYNTRPR AEVMVDG+K YLVR+RE+L  LW  E +LP
Sbjct: 359 GDLLVVRSSGAYGFAMASNYNTRPRAAEVMVDGDKAYLVREREKLPQLWQGEQLLP 414


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: 517
Number of extensions: 17
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: 417
Length of database: 414
Length adjustment: 31
Effective length of query: 386
Effective length of database: 383
Effective search space:   147838
Effective search space used:   147838
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 203388 SO4309 (diaminopimelate decarboxylase (NCBI ptt file))
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.3851.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.6e-163  528.8   0.0   4.3e-163  528.6   0.0    1.0  1  lcl|FitnessBrowser__MR1:203388  SO4309 diaminopimelate decarboxy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:203388  SO4309 diaminopimelate decarboxylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  528.6   0.0  4.3e-163  4.3e-163       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 528.6 bits;  conditional E-value: 4.3e-163
                       TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgGE 83 
                                     +d +l++eg+++++la+++gtPlY+y+++tl+++++a+++a++++ +lv+YAvKAnsnlavl++la++G+g+d+vsgGE
  lcl|FitnessBrowser__MR1:203388   7 QDNTLYAEGCRVNDLAQTYGTPLYIYSRATLERHWHAFNNAVAGHPHLVCYAVKANSNLAVLNVLARLGSGFDIVSGGE 85 
                                     677899***************************************9********************************* PP

                       TIGR01048  84 leralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyisT 162
                                     l+r+ +Ag ++ k+vfsg+gk+ +e+e+al+l+i ++nv+s +ele+l+ +a++lgk a+v+lRvnpdvda th+yisT
  lcl|FitnessBrowser__MR1:203388  86 LARVIEAGGDPAKVVFSGVGKTVAEMEQALNLGIYCFNVESSAELEQLNLVAGRLGKVAPVSLRVNPDVDAGTHPYIST 164
                                     ******************************************************************************* PP

                       TIGR01048 163 GlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGlgis 241
                                     Glke+KFGi+++eae+++ +a++l++l++ G+++HIGSq+++++pf +a++++++l+++l+e+gi +e++d+GGGlg++
  lcl|FitnessBrowser__MR1:203388 165 GLKENKFGIAMDEAEAVFARAHALPHLQVKGVDCHIGSQLTEIQPFLDAMDRMLSLIDRLAEQGIVIEHFDVGGGLGVT 243
                                     ******************************************************************************* PP

                       TIGR01048 242 yeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliRpalY 320
                                     y++e+ +p+++ ya++ll++l +     +klkli+EpGR+++anag+++t+V ++Ke++ ++f++vD++mndliRpalY
  lcl|FitnessBrowser__MR1:203388 244 YDDET-PPHPDVYAAALLKRLGH-----RKLKLIFEPGRAIAANAGIFVTEVLYLKENSDKRFAIVDGAMNDLIRPALY 316
                                     ***99.************99988.....59************************************************* PP

                       TIGR01048 321 eayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevlveegk 399
                                     +a+++i+++ + ++ +++++d+vGp+CE+gD+l+kdre   + +Gdll+v+s+GAYg++m+snYn+rpr+aev+v+++k
  lcl|FitnessBrowser__MR1:203388 317 SAWQKIIPV-TPRDDQAHVFDIVGPVCETGDFLGKDREFAIA-PGDLLVVRSSGAYGFAMASNYNTRPRAAEVMVDGDK 393
                                     *********.5577779*********************9765.6*********************************** PP

                       TIGR01048 400 arlirrretledllale 416
                                     a+l+r+re+l +l++ e
  lcl|FitnessBrowser__MR1:203388 394 AYLVREREKLPQLWQGE 410
                                     **************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (414 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.12
//
[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