Alignments for a candidate for lysA in Shewanella loihica PV-4

GapMind for Amino acid biosynthesis

Alignments for a candidate for lysA in Shewanella loihica PV-4

Align diaminopimelate decarboxylase (EC 4.1.1.20) (characterized)
to candidate 5207805 Shew_0322 diaminopimelate decarboxylase (RefSeq)

Query= BRENDA::Q9KVL7
         (417 letters)



>FitnessBrowser__PV4:5207805
          Length = 414

 Score =  569 bits (1466), Expect = e-167
 Identities = 286/416 (68%), Positives = 333/416 (80%), Gaps = 2/416 (0%)

Query: 1   MDYFNYQEDGQLWAEQVPLADLANQYGTPLYVYSRATLERHWHAFDKSVGDYPHLICYAV 60
           MD+F YQ+D +L+AEQ  +A LA  YGTPLYVYSRATLERHWHAFD +V D+PH+ICYAV
Sbjct: 1   MDHFLYQQD-ELYAEQCTVASLAETYGTPLYVYSRATLERHWHAFDNAVADHPHMICYAV 59

Query: 61  KANSNLGVLNTLARLGSGFDIVSVGELERVLAAGGDPSKVVFSGVGKTEAEMKRALQLKI 120
           KANSNL VLN LARLGSGFDIVS GEL RVL AGG+ SKVVFSGVGKT AEM+ AL+  I
Sbjct: 60  KANSNLAVLNVLARLGSGFDIVSGGELARVLEAGGEASKVVFSGVGKTVAEMEMALEAGI 119

Query: 121 KCFNVESEPELQRLNKVAGELGVKAPISLRINPDVDAKTHPYISTGLRDNKFGITFDRAA 180
            CFNVES  EL++LN VA  LG  AP+SLR+NPDVDA THPYISTGL++NKFGI  + A 
Sbjct: 120 YCFNVESAAELEQLNLVALRLGKVAPVSLRVNPDVDAGTHPYISTGLKENKFGIAMEEAE 179

Query: 181 QVYRLAHSLPNLDVHGIDCHIGSQLTALAPFIDATDRLLALIDSLKAEGIHIRHLDVGGG 240
            ++  A+ LP L V G DCHIGSQLT L PF+DA DR+LALID L  +G+ I HLDVGGG
Sbjct: 180 AIFLRANELPGLAVKGADCHIGSQLTELQPFLDAMDRMLALIDRLAEQGVKIAHLDVGGG 239

Query: 241 LGVVYRDELPPQPSEYAKALLDRLERHRDLELIFEPGRAIAANAGVLVTKVEFLKHTEHK 300
           LGV Y  E PP+PS YA ALL +L   RDL+LIFEPGRAIAANAG+ VT+V +LK    K
Sbjct: 240 LGVTYDGEQPPEPSAYASALLGKL-AGRDLKLIFEPGRAIAANAGIFVTQVLYLKENAEK 298

Query: 301 NFAIIDAAMNDLIRPALYQAWQDIIPLRPRQGEAQTYDLVGPVCETSDFLGKDRDLVLQE 360
           NFA++D AMNDLIRP+LY AWQ IIP+ PR GE + YD+VGPVCET DFLGKDR L ++ 
Sbjct: 299 NFALVDGAMNDLIRPSLYSAWQKIIPVVPRPGETRQYDVVGPVCETGDFLGKDRALNIRA 358

Query: 361 GDLLAVRSSGAYGFTMSSNYNTRPRVAEVMVDGNKTYLVRQREELSSLWALESVLP 416
            DLLAVRSSGAYGFTM+SNYN+RPR AEVMVDG + YLVR+RE+++ LW  E +LP
Sbjct: 359 NDLLAVRSSGAYGFTMASNYNSRPRAAEVMVDGERHYLVREREKVAQLWQGEQLLP 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: 505
Number of extensions: 14
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 5207805 Shew_0322 (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.17983.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   3.9e-161  522.1   0.0   4.6e-161  521.9   0.0    1.0  1  lcl|FitnessBrowser__PV4:5207805  Shew_0322 diaminopimelate decarb


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5207805  Shew_0322 diaminopimelate decarboxylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  521.9   0.0  4.6e-161  4.6e-161       5     416 ..       7     410 ..       4     411 .. 0.98

  Alignments for each domain:
  == domain 1  score: 521.9 bits;  conditional E-value: 4.6e-161
                        TIGR01048   5 kdgeleiegvdlkelaeefgtPlYvydeetlrerlealkeafkaeeslvlYAvKAnsnlavlrllaeeGlgldvvsgG 82 
                                      ++ el++e++ +++lae++gtPlYvy+++tl+++++a+++a++++ ++++YAvKAnsnlavl++la++G+g+d+vsgG
  lcl|FitnessBrowser__PV4:5207805   7 QQDELYAEQCTVASLAETYGTPLYVYSRATLERHWHAFDNAVADHPHMICYAVKANSNLAVLNVLARLGSGFDIVSGG 84 
                                      566899************************************************************************ PP

                        TIGR01048  83 EleralaAgvkaekivfsgngkseeeleaaleleiklinvdsveelelleeiakelgkkarvllRvnpdvdaktheyi 160
                                      El+r+l+Ag +a+k+vfsg+gk+ +e+e+ale++i ++nv+s +ele+l+ +a +lgk a+v+lRvnpdvda th+yi
  lcl|FitnessBrowser__PV4:5207805  85 ELARVLEAGGEASKVVFSGVGKTVAEMEMALEAGIYCFNVESAAELEQLNLVALRLGKVAPVSLRVNPDVDAGTHPYI 162
                                      ****************************************************************************** PP

                        TIGR01048 161 sTGlkesKFGieveeaeeayelalkleslelvGihvHIGSqildlepfveaaekvvklleelkeegieleeldlGGGl 238
                                      sTGlke+KFGi++eeae+++ +a +l+ l + G ++HIGSq+++l+pf +a+++++ l+++l+e+g+++++ld+GGGl
  lcl|FitnessBrowser__PV4:5207805 163 STGLKENKFGIAMEEAEAIFLRANELPGLAVKGADCHIGSQLTELQPFLDAMDRMLALIDRLAEQGVKIAHLDVGGGL 240
                                      ****************************************************************************** PP

                        TIGR01048 239 gisyeeeeeapdleeyaeklleklekeaelglklklilEpGRslvanagvlltrVesvKevesrkfvlvDagmndliR 316
                                      g++y+ e+ +p+++ ya++ll kl++     ++lkli+EpGR+++anag+++t+V ++Ke+ +++f+lvD++mndliR
  lcl|FitnessBrowser__PV4:5207805 241 GVTYDGEQ-PPEPSAYASALLGKLAG-----RDLKLIFEPGRAIAANAGIFVTQVLYLKENAEKNFALVDGAMNDLIR 312
                                      *****999.**************999.....6********************************************** PP

                        TIGR01048 317 palYeayheiaalkrleeeetetvdvvGplCEsgDvlakdrelpeveeGdllavasaGAYgasmssnYnsrprpaevl 394
                                      p+lY+a+++i+++   +  et ++dvvGp+CE+gD+l+kdr+l+  ++ dllav+s+GAYg++m+snYnsrpr+aev+
  lcl|FitnessBrowser__PV4:5207805 313 PSLYSAWQKIIPV-VPRPGETRQYDVVGPVCETGDFLGKDRALNI-RANDLLAVRSSGAYGFTMASNYNSRPRAAEVM 388
                                      *************.668888***********************85.559***************************** PP

                        TIGR01048 395 veegkarlirrretledllale 416
                                      v++++ +l+r+re++++l++ e
  lcl|FitnessBrowser__PV4:5207805 389 VDGERHYLVREREKVAQLWQGE 410
                                      *******************976 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.25
//
[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