GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapB in Pseudomonas fluorescens FW300-N2E3

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate AO353_05640 AO353_05640 4-hydroxy-tetrahydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640 AO353_05640
           4-hydroxy-tetrahydrodipicolinate reductase
          Length = 268

 Score =  331 bits (849), Expect = 9e-96
 Identities = 173/265 (65%), Positives = 205/265 (77%), Gaps = 1/265 (0%)

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

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

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           AANFSVGVN+ LKLL+ AA+V+GD  DIEIIEAHHR+K+DAPSGTAL MGE IA ALD+D
Sbjct: 123 AANFSVGVNLSLKLLDMAARVLGDDADIEIIEAHHRNKIDAPSGTALRMGEVIASALDRD 182

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

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GAVR+ALWL G+E GL+DM+DVLDL
Sbjct: 243 GAVRAALWLDGREPGLYDMQDVLDL 267


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: 275
Number of extensions: 10
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 AO353_05640 AO353_05640 (4-hydroxy-tetrahydrodipicolinate 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.21011.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   2.1e-102  328.2   1.4   2.4e-102  328.1   1.4    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640  AO353_05640 4-hydroxy-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640  AO353_05640 4-hydroxy-tetrahydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.1   1.4  2.4e-102  2.4e-102       3     270 .]       3     266 ..       1     266 [. 0.98

  Alignments for each domain:
  == domain 1  score: 328.1 bits;  conditional E-value: 2.4e-102
                                     TIGR00036   3 kvavaGaaGrmGrevikavkea.edlelvaalerkgsskqgkDiGelagigkvgvpveddleavk 66 
                                                   ++av GaaGrmG+ +i+av++  +   l+aa+ r+gs + g D+Gela +g++gvp++ +le+v 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640   3 RIAVMGAAGRMGKILIEAVQQRaPLTGLTAAIVRPGSTLIGVDAGELAALGRIGVPLSGNLEMV- 66 
                                                   89******************9945567***********************************88. PP

                                     TIGR00036  67 vlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNf 131
                                                        ++dvliDft+pe +l+n++++ + g+ +V+GTTG++ ++++ l+++ ++  +++v+a+Nf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640  67 ---AAEFDVLIDFTLPEVMLKNLAFCRKVGKAMVIGTTGLDAAQKQLLAEAGKD--IPIVFAANF 126
                                                   ...899*********************************************999..********* PP

                                     TIGR00036 132 aiGvnlllkllekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveer 195
                                                   ++Gvnl lkll +aa+vl+d  DiEiiE+HHr+K DaPSGTAl+++e+ia a ++dl+++av++r
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640 127 SVGVNLSLKLLDMAARVLGDDaDIEIIEAHHRNKIDAPSGTALRMGEVIASALDRDLQKVAVYGR 191
                                                   ******************8766******************************************* PP

                                     TIGR00036 196 egltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkee 260
                                                   eg+tG r++e+iG+a+vRggdvvg+htvlFa +GerleitHkassR++fakG+vra+ wl   e 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640 192 EGHTGVRERETIGFATVRGGDVVGDHTVLFACEGERLEITHKASSRMTFAKGAVRAALWLDGREP 256
                                                   ***************************************************************** PP

                                     TIGR00036 261 kvydledvld 270
                                                   ++yd++dvld
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_05640 257 GLYDMQDVLD 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: 00:00:00.01
# Mc/sec: 7.19
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see 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