Alignments for a candidate for dapB in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Pseudomonas simiae WCS417

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate GFF4701 PS417_24050 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__WCS417:GFF4701
          Length = 268

 Score =  337 bits (864), Expect = 2e-97
 Identities = 172/266 (64%), Positives = 204/266 (76%), Gaps = 1/266 (0%)

Query: 7   RVAIAGAGGRMGRQLIQAALALEGVQ-LGAALEREGSSLLGSDAGELAGAGKTGVTVQSS 65
           R+A+ GA GRMG+ L++A         L AA+ R GS+L+G+DAGELA  G+ GV++  S
Sbjct: 3   RIAVMGAAGRMGKTLVEAVQQRSPASGLTAAIVRPGSTLIGADAGELASLGRIGVSLSGS 62

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           L+ V D+FDV IDFT P+  L +LAFCR+ GK MVIGTTG     KQ + +A  DI IVF
Sbjct: 63  LEQVADEFDVLIDFTLPDVMLKNLAFCRKAGKAMVIGTTGLTAQQKQLLEEAGKDIPIVF 122

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           AANFSVGVN+ LKLL+ AA+V+GD  DIEIIE HHRHK+DAPSGTAL MGEAIA AL +D
Sbjct: 123 AANFSVGVNLSLKLLDLAARVLGDEADIEIIETHHRHKIDAPSGTALRMGEAIADALGRD 182

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L   AVY REGHTG R   TIGFATVR GD+VG+HT +FA  GERLEITHKASSRMTFA 
Sbjct: 183 LSKVAVYGREGHTGARARDTIGFATVRGGDVVGDHTVLFATEGERLEITHKASSRMTFAK 242

Query: 246 GAVRSALWLSGKESGLFDMRDVLDLN 271
           GAVR+ALWL G+E GL+DMRDVLDL+
Sbjct: 243 GAVRAALWLEGREPGLYDMRDVLDLH 268


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: 274
Number of extensions: 8
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: 273
Length of database: 268
Length adjustment: 25
Effective length of query: 248
Effective length of database: 243
Effective search space:    60264
Effective search space used:    60264
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 GFF4701 PS417_24050 (dihydrodipicolinate reductase)
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.5077.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     6e-104  333.3   1.1   6.6e-104  333.2   1.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF4701  PS417_24050 dihydrodipicolinate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4701  PS417_24050 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  333.2   1.1  6.6e-104  6.6e-104       3     270 .]       3     266 ..       1     266 [. 0.98

  Alignments for each domain:
  == domain 1  score: 333.2 bits;  conditional E-value: 6.6e-104
                           TIGR00036   3 kvavaGaaGrmGrevikavkea.edlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvl 76 
                                         ++av GaaGrmG+ +++av++  +   l+aa+ r+gs + g D+Gela++g++gv+++ +le v     +++dvl
  lcl|FitnessBrowser__WCS417:GFF4701   3 RIAVMGAAGRMGKTLVEAVQQRsPASGLTAAIVRPGSTLIGADAGELASLGRIGVSLSGSLEQV----ADEFDVL 73 
                                         89******************9878999***********************************88....9****** PP

                           TIGR00036  77 iDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvled 151
                                         iDft+p+ +l+n++++ ++g+ +V+GTTG++ ++++ l+++ ++  +++v+a+Nf++Gvnl lkll  aa+vl+d
  lcl|FitnessBrowser__WCS417:GFF4701  74 IDFTLPDVMLKNLAFCRKAGKAMVIGTTGLTAQQKQLLEEAGKD--IPIVFAANFSVGVNLSLKLLDLAARVLGD 146
                                         *****************************************999..***************************99 PP

                           TIGR00036 152 v.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlF 225
                                           DiEiiE+HHrhK DaPSGTAl+++e+ia+a g+dl+++av++reg+tG+r +++iG+a+vRggdvvg+htvlF
  lcl|FitnessBrowser__WCS417:GFF4701 147 EaDIEIIETHHRHKIDAPSGTALRMGEAIADALGRDLSKVAVYGREGHTGARARDTIGFATVRGGDVVGDHTVLF 221
                                         88************************************************************************* PP

                           TIGR00036 226 asdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                         a++GerleitHkassR++fakG+vra+ wle  e ++yd++dvld
  lcl|FitnessBrowser__WCS417:GFF4701 222 ATEGERLEITHKASSRMTFAKGAVRAALWLEGREPGLYDMRDVLD 266
                                         *******************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (268 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: 00:00:00.00
# Mc/sec: 7.80
//
[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