GapMind for Amino acid biosynthesis

 

Aligments for a candidate for dapB in Desulfovibrio vulgaris Hildenborough

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate 207060 DVU1609 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>lcl|MicrobesOnline__882:207060 DVU1609 dihydrodipicolinate
           reductase
          Length = 259

 Score =  192 bits (489), Expect = 5e-54
 Identities = 108/263 (41%), Positives = 152/263 (57%), Gaps = 12/263 (4%)

Query: 8   VAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSLD 67
           + + GAGGRMG  + +       + L A LER   +         +G  + G    S  D
Sbjct: 5   IIVMGAGGRMGSTICRLVQEEPQLCLAAVLERPDRA---------SGVARDGCIAGSDPD 55

Query: 68  AVKDDFD--VFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
            V       V IDFT PE ++       +HG  +VIGTTGF+E  K  + + A  I + +
Sbjct: 56  VVFPQVPGGVIIDFTAPEASMATARAAARHGNAVVIGTTGFNEEQKAELAELARQIRLFW 115

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           A N SVGVNV+LK+L +  +++G+  D+E++E HH  K D+PSGTAL + E +A A D +
Sbjct: 116 APNMSVGVNVLLKVLPELVRLLGEKYDLEMVELHHNRKKDSPSGTALRLAECLAEARDWN 175

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L D A Y REG  GER    IG  T+R GD+VG HT      GER+E+TH+A SR TFA 
Sbjct: 176 LPDVACYHREGIIGERPQKEIGVQTIRGGDVVGVHTVYCLGPGERIEVTHQAHSRETFAQ 235

Query: 246 GAVRSALWLSGKESG-LFDMRDV 267
           GA+R+A WL+ ++ G L++M D+
Sbjct: 236 GALRAAAWLATQKPGKLYNMADI 258


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: 185
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: 259
Length adjustment: 25
Effective length of query: 248
Effective length of database: 234
Effective search space:    58032
Effective search space used:    58032
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 207060 DVU1609 (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.21663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
      2e-80  256.2   0.0    3.9e-80  255.2   0.0    1.4  1  lcl|MicrobesOnline__882:207060  DVU1609 dihydrodipicolinate redu


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:207060  DVU1609 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.2   0.0   3.9e-80   3.9e-80       3     269 ..       4     259 .]       2     259 .] 0.93

  Alignments for each domain:
  == domain 1  score: 255.2 bits;  conditional E-value: 3.9e-80
                       TIGR00036   3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDftt 81 
                                     ++ v Ga+GrmG+ + + v+e+++l l+a+ler++         + +g+++ g  +  + + + v  +   +v+iDft 
  lcl|MicrobesOnline__882:207060   4 PIIVMGAGGRMGSTICRLVQEEPQLCLAAVLERPD---------RASGVARDGC-IAGS-DPDVVFPQVPGGVIIDFTA 71 
                                     589*****************************733.........2356666666.3222.223356688899******* PP

                       TIGR00036  82 peavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv.DiEiiEl 159
                                     pea + ++++a+++g  +V+GTTGf+ee+++el++la +  ++l  apN+++Gvn+llk+l ++ + l++  D+E++El
  lcl|MicrobesOnline__882:207060  72 PEASMATARAAARHGNAVVIGTTGFNEEQKAELAELARQ--IRLFWAPNMSVGVNVLLKVLPELVRLLGEKyDLEMVEL 148
                                     ***************************************..***************************8755******* PP

                       TIGR00036 160 HHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHka 238
                                     HH+ KkD+PSGTAl+lae++a+ar+ +l ++a ++reg+ Ger ++eiG++++Rggdvvg htv+  + Ger+e+tH+a
  lcl|MicrobesOnline__882:207060 149 HHNRKKDSPSGTALRLAECLAEARDWNLPDVACYHREGIIGERPQKEIGVQTIRGGDVVGVHTVYCLGPGERIEVTHQA 227
                                     ******************************************************************************* PP

                       TIGR00036 239 ssRaafakGvvrairwledkee.kvydledvl 269
                                     +sR++fa+G++ra+ wl+ ++  k+y++ d++
  lcl|MicrobesOnline__882:207060 228 HSRETFAQGALRAAAWLATQKPgKLYNMADIF 259
                                     ******************999889*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (259 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 2.90
//
[ok]

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

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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