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

GapMind for Amino acid biosynthesis

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

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate 5210399 Shew_2840 dihydrodipicolinate reductase (RefSeq)

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__PV4:5210399
          Length = 271

 Score =  332 bits (852), Expect = 4e-96
 Identities = 169/267 (63%), Positives = 201/267 (75%)

Query: 6   IRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           +RVAI G  GRMGR LI++A     + LGAA+ER GS+L+G DAGELAG G   V +  S
Sbjct: 5   VRVAITGGSGRMGRTLIESAKLSSNIYLGAAVERAGSTLIGVDAGELAGVGAMNVAITDS 64

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           LD   DDFD+ IDFT PE ++ H  +C ++GK +VIGTTGF+ A K+ I   A +  IV 
Sbjct: 65  LDNAVDDFDILIDFTSPEASVVHTDWCSRNGKAIVIGTTGFNHAQKEQIAAYAENTPIVM 124

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A N SVGVN+M +LLE AA+VMGDYTDIEIIE HHRHK DAPSGTAL MGE IA  L +D
Sbjct: 125 APNMSVGVNLMWRLLELAAEVMGDYTDIEIIEGHHRHKKDAPSGTALKMGEVIAEVLGRD 184

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L+ CAVY REG T ER   TIGF+T+RAGD+VGEHTAMFADIGERLEITHKASSRMTFAN
Sbjct: 185 LEKCAVYGREGITEERSRETIGFSTIRAGDLVGEHTAMFADIGERLEITHKASSRMTFAN 244

Query: 246 GAVRSALWLSGKESGLFDMRDVLDLNN 272
           GA+R+A WL  +  GL+DM+ VL L +
Sbjct: 245 GAMRAAFWLGDQGPGLYDMQQVLGLKD 271


Lambda     K      H
   0.319    0.135    0.383 

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: 293
Number of extensions: 10
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: 273
Length of database: 271
Length adjustment: 25
Effective length of query: 248
Effective length of database: 246
Effective search space:    61008
Effective search space used:    61008
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: 47 (22.7 bits)

Align candidate 5210399 Shew_2840 (dihydrodipicolinate reductase (RefSeq))
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

# 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/TIGR00036.hmm
# target sequence database:        /tmp/gapView.17536.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00036  [M=270]
Accession:   TIGR00036
Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   6.1e-105  336.6   1.3   6.9e-105  336.4   1.3    1.0  1  lcl|FitnessBrowser__PV4:5210399  Shew_2840 dihydrodipicolinate re


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210399  Shew_2840 dihydrodipicolinate reductase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  336.4   1.3  6.9e-105  6.9e-105       2     270 .]       5     268 ..       4     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 336.4 bits;  conditional E-value: 6.9e-105
                        TIGR00036   2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDf 79 
                                      ++va++G +GrmGr +i+++k + ++ l+aa+er gs + g D+Gelag+g ++v+++d+l+ +     +++d+liDf
  lcl|FitnessBrowser__PV4:5210399   5 VRVAITGGSGRMGRTLIESAKLSSNIYLGAAVERAGSTLIGVDAGELAGVGAMNVAITDSLDNA----VDDFDILIDF 78 
                                      79************************************************************87....9********* PP

                        TIGR00036  80 ttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv.DiEi 156
                                      t pea + ++  + ++g+ +V+GTTGf+ ++++++++ ae+  +++v+apN+++Gvnl+++lle aa+v++d+ DiEi
  lcl|FitnessBrowser__PV4:5210399  79 TSPEASVVHTDWCSRNGKAIVIGTTGFNHAQKEQIAAYAEN--TPIVMAPNMSVGVNLMWRLLELAAEVMGDYtDIEI 154
                                      ****************************************9..*********************************** PP

                        TIGR00036 157 iElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerlei 234
                                      iE HHrhKkDaPSGTAlk++e+ia++ g+dl+++av++reg+t er++e+iG++++R+gd+vgeht +Fa++Gerlei
  lcl|FitnessBrowser__PV4:5210399 155 IEGHHRHKKDAPSGTALKMGEVIAEVLGRDLEKCAVYGREGITEERSRETIGFSTIRAGDLVGEHTAMFADIGERLEI 232
                                      ****************************************************************************** PP

                        TIGR00036 235 tHkassRaafakGvvrairwledkeekvydledvld 270
                                      tHkassR++fa+G++ra+ wl d+  ++yd+++vl+
  lcl|FitnessBrowser__PV4:5210399 233 THKASSRMTFANGAMRAAFWLGDQGPGLYDMQQVLG 268
                                      **********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (271 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: 00:00:00.00
# Mc/sec: 10.80
//
[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