GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Pseudomonas stutzeri RCH2

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate GFF937 Psest_0966 dihydrodipicolinate reductase

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__psRCH2:GFF937
          Length = 268

 Score =  318 bits (816), Expect = 6e-92
 Identities = 167/265 (63%), Positives = 198/265 (74%), Gaps = 1/265 (0%)

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

Query: 66  LDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVF 125
           L    D+FDV IDFT P  TL +L  CR+ GK MVIGTTGF    K+ +  AA +I IVF
Sbjct: 63  LARAVDEFDVLIDFTHPSVTLKNLEVCRRAGKAMVIGTTGFSPEEKERLAAAAREIPIVF 122

Query: 126 AANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKD 185
           AANFSVGVN+ LKLL+ AA+V+GD  DIEIIEAHHRHKVDAPSGTAL MGE IA AL +D
Sbjct: 123 AANFSVGVNLCLKLLDTAARVLGDDVDIEIIEAHHRHKVDAPSGTALRMGEVIAEALGRD 182

Query: 186 LKDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFAN 245
           L+  AVY REG TG R   TIGFATVRAGD+VG+HT +FA  GER+EITHKASSRMTFA 
Sbjct: 183 LQKVAVYGREGQTGARQRETIGFATVRAGDVVGDHTVLFAADGERVEITHKASSRMTFAK 242

Query: 246 GAVRSALWLSGKESGLFDMRDVLDL 270
           GAVR+ALWL  K +GL+DM+DVL L
Sbjct: 243 GAVRAALWLDEKPAGLYDMQDVLGL 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: 262
Number of extensions: 11
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 GFF937 Psest_0966 (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.16470.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
     4e-107  343.7   2.3   4.5e-107  343.6   2.3    1.0  1  lcl|FitnessBrowser__psRCH2:GFF937  Psest_0966 dihydrodipicolinate r


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF937  Psest_0966 dihydrodipicolinate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  343.6   2.3  4.5e-107  4.5e-107       3     270 .]       3     266 ..       1     266 [. 0.97

  Alignments for each domain:
  == domain 1  score: 343.6 bits;  conditional E-value: 4.5e-107
                          TIGR00036   3 kvavaGaaGrmGrevikavkea.edlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvli 77 
                                        ++av+GaaGrmG+ +i+av+++     l+aa++r++s ++g D+Gela ig++gvp++ +l  +     +++dvli
  lcl|FitnessBrowser__psRCH2:GFF937   3 RIAVTGAAGRMGKTLIEAVQQTgGAAGLTAAIDRPDSTLVGADAGELAAIGRLGVPLTGELARA----VDEFDVLI 74 
                                        89*******************944567********************************99977....9******* PP

                          TIGR00036  78 DfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv. 152
                                        Dft+p+ +l+n++++ ++g+ +V+GTTGfs e++++l+++a +  +++v+a+Nf++Gvnl lkll +aa+vl+d  
  lcl|FitnessBrowser__psRCH2:GFF937  75 DFTHPSVTLKNLEVCRRAGKAMVIGTTGFSPEEKERLAAAARE--IPIVFAANFSVGVNLCLKLLDTAARVLGDDv 148
                                        *******************************************..***************************8644 PP

                          TIGR00036 153 DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasd 228
                                        DiEiiE+HHrhK+DaPSGTAl+++e+ia+a g+dl+++av++reg tG+r++e+iG+a+vR+gdvvg+htvlFa d
  lcl|FitnessBrowser__psRCH2:GFF937 149 DIEIIEAHHRHKVDAPSGTALRMGEVIAEALGRDLQKVAVYGREGQTGARQRETIGFATVRAGDVVGDHTVLFAAD 224
                                        **************************************************************************** PP

                          TIGR00036 229 GerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                        Ger+eitHkassR++fakG+vra+ wl +k +++yd++dvl+
  lcl|FitnessBrowser__psRCH2:GFF937 225 GERVEITHKASSRMTFAKGAVRAALWLDEKPAGLYDMQDVLG 266
                                        ****************************************96 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: 8.13
//
[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:

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