GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Bacteroides thetaiotaomicron VPI-5482

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate 350423 BT0895 dihydrodipicolinate synthase (NCBI ptt file)

Query= SwissProt::Q9X1K9
         (294 letters)



>FitnessBrowser__Btheta:350423
          Length = 297

 Score =  251 bits (642), Expect = 1e-71
 Identities = 130/289 (44%), Positives = 185/289 (64%), Gaps = 4/289 (1%)

Query: 3   RGVGTAIVTPFKNGE-LDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSR 61
           +G+G A++TPFK  E +D ++  RLV Y L+N  + L VLGTT E+PT+ E+E++ +   
Sbjct: 7   KGMGVALITPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKM 66

Query: 62  TLEIVDGKIPVIVGAGTNSTEKTLKLVKQAEKLGANGVLVVTPYYNKPTQEGLYQHYKYI 121
            ++ V+G+IP+++G G N+T   ++ +K  +  G + +L V PYYNKP+QEG+YQHYK I
Sbjct: 67  VIDRVNGRIPILLGVGGNNTRAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAI 126

Query: 122 SERTDLGIVVYNVPGRTGVNVLPETAARIAADLKNVVGIKEANPDIDQIDRTVSLTKQAR 181
           SE T+L IV+YNVPGRTGVN+  ET  RIA +  NV+ IKEA+ +I Q+D    + K   
Sbjct: 127 SEATELPIVLYNVPGRTGVNMTAETTLRIARNFSNVIAIKEASGNITQMD---DIIKNKP 183

Query: 182 SDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKLRP 241
            +F V SG+D  TF L+  G  GVISV+ N  P++   +      G+   +  +H +   
Sbjct: 184 DNFNVISGDDGITFPLITLGAVGVISVIGNAFPREFSRMTRLALQGDFANALTIHHRFTE 243

Query: 242 LMKALFVETNPIPVKAALNLMGFIENELRLPLVPASEKTVELLRNVLKE 290
           L   LFV+ NP  VK+ LN MG IEN+LRLPLVP    T E +R VL E
Sbjct: 244 LFDLLFVDGNPAGVKSMLNAMGMIENKLRLPLVPTRITTFEAIRKVLNE 292


Lambda     K      H
   0.316    0.135    0.378 

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: 267
Number of extensions: 16
Number of successful extensions: 3
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: 294
Length of database: 297
Length adjustment: 26
Effective length of query: 268
Effective length of database: 271
Effective search space:    72628
Effective search space used:    72628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 48 (23.1 bits)

Align candidate 350423 BT0895 (dihydrodipicolinate synthase (NCBI ptt file))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

# 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/TIGR00674.hmm
# target sequence database:        /tmp/gapView.3009.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00674  [M=286]
Accession:   TIGR00674
Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.6e-102  328.2   0.1   1.8e-102  328.0   0.1    1.0  1  lcl|FitnessBrowser__Btheta:350423  BT0895 dihydrodipicolinate synth


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:350423  BT0895 dihydrodipicolinate synthase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.0   0.1  1.8e-102  1.8e-102       4     285 ..      11     292 ..       8     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 328.0 bits;  conditional E-value: 1.8e-102
                          TIGR00674   4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsnat 79 
                                        +AliTPfked+svd++al +l++++++++ d + v+GtT E++tL+ eEkk++ +++++ v++r+p++ G+g+n+t
  lcl|FitnessBrowser__Btheta:350423  11 VALITPFKEDESVDYDALMRLVDYLLQNNADFLCVLGTTAETPTLTEEEKKTIKKMVIDRVNGRIPILLGVGGNNT 86 
                                        8*************************************************************************** PP

                          TIGR00674  80 eeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve.i 154
                                        +  +e  k  + +gvd++l+v+PyYnkP+qeG+y+h+kai e++elPi+lYnvP+Rtgv+++ et++r+a++ + +
  lcl|FitnessBrowser__Btheta:350423  87 RAIVETLKNDDFTGVDAILSVVPYYNKPSQEGIYQHYKAISEATELPIVLYNVPGRTGVNMTAETTLRIARNFSnV 162
                                        ***********************************************************************9988* PP

                          TIGR00674 155 vaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareih 230
                                        +aiKeasg+++++  i++ ++++f+v sGdD +t ++++lGa GviSV++n  p+e++ m + al+gd+++a+ ih
  lcl|FitnessBrowser__Btheta:350423 163 IAIKEASGNITQMDDIIKNKPDNFNVISGDDGITFPLITLGAVGVISVIGNAFPREFSRMTRLALQGDFANALTIH 238
                                        **************************************************************************** PP

                          TIGR00674 231 qkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285
                                        +++++lf+ lf++ NP +vK +l+++g+ie+ +lRlPL+++   + e +++vl+e
  lcl|FitnessBrowser__Btheta:350423 239 HRFTELFDLLFVDGNPAGVKSMLNAMGMIEN-KLRLPLVPTRITTFEAIRKVLNE 292
                                        *******************************.*****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (297 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: 8.86
//
[ok]

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

Links

Downloads

Related tools

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:

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