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.24056.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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 8.55
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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