Alignments for a candidate for dapB in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapB in Pseudomonas fluorescens GW456-L13

Align dihydrodipicolinate reductase; EC 1.3.1.26 (characterized)
to candidate PfGW456L13_5101 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)

Query= CharProtDB::CH_002128
         (273 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101
          Length = 267

 Score =  342 bits (876), Expect = 7e-99
 Identities = 174/264 (65%), Positives = 204/264 (77%)

Query: 7   RVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELAGAGKTGVTVQSSL 66
           R+A+ GA GRMG+ LI+A     G  L AA++R  S+L+G+DAGELA  G+ GV +   L
Sbjct: 3   RIAVMGAAGRMGKTLIEAVQQTPGAGLTAAVDRPDSTLVGADAGELAALGRIGVPLSGDL 62

Query: 67  DAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGTTGFDEAGKQAIRDAAADIAIVFA 126
           D V D+FDV IDFT P  TL +LAFCR+HGK M+IGTTGF    KQ + +A  DI IVFA
Sbjct: 63  DRVVDEFDVLIDFTHPTVTLKNLAFCRKHGKAMIIGTTGFSVEEKQLLAEAGKDIPIVFA 122

Query: 127 ANFSVGVNVMLKLLEKAAKVMGDYTDIEIIEAHHRHKVDAPSGTALAMGEAIAHALDKDL 186
           ANFSVGVN+ LKLL+ AA+V+GD  DIEI EAHHRHKVDAPSGTA+ MGE IA AL +DL
Sbjct: 123 ANFSVGVNLCLKLLDTAARVLGDDVDIEITEAHHRHKVDAPSGTAVRMGEVIADALGRDL 182

Query: 187 KDCAVYSREGHTGERVPGTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANG 246
           K  AVY REG TG R   TIGFATVRAGDIVG+HT +FA  GER+EITHKASSRMTFA G
Sbjct: 183 KKVAVYGREGQTGARDRETIGFATVRAGDIVGDHTVLFAADGERVEITHKASSRMTFAKG 242

Query: 247 AVRSALWLSGKESGLFDMRDVLDL 270
           AVR+ALWL G+E GL+DM+DVLDL
Sbjct: 243 AVRAALWLDGREPGLYDMQDVLDL 266


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: 276
Number of extensions: 7
Number of successful extensions: 1
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: 267
Length adjustment: 25
Effective length of query: 248
Effective length of database: 242
Effective search space:    60016
Effective search space used:    60016
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 PfGW456L13_5101 (4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
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.20219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   1.8e-105  338.3   2.1     2e-105  338.1   2.1    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101  4-hydroxy-tetrahydrodipicolinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101  4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.1   2.1    2e-105    2e-105       3     270 .]       3     265 ..       1     265 [. 0.99

  Alignments for each domain:
  == domain 1  score: 338.1 bits;  conditional E-value: 2e-105
                                               TIGR00036   3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvp 57 
                                                             ++av GaaGrmG+ +i+av+++++  l+aa++r++s ++g D+Gela +g++gvp
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101   3 RIAVMGAAGRMGKTLIEAVQQTPGAGLTAAVDRPDSTLVGADAGELAALGRIGVP 57 
                                                             89***************************************************** PP

                                               TIGR00036  58 veddleavkvlaekkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlk 112
                                                             ++ dl+ v     +++dvliDft+p  +l+n++++ ++g+ +++GTTGfs e+++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101  58 LSGDLDRV----VDEFDVLIDFTHPTVTLKNLAFCRKHGKAMIIGTTGFSVEEKQ 108
                                                             ******99....9****************************************** PP

                                               TIGR00036 113 elkdlaekkgvalviapNfaiGvnlllkllekaakvledv.DiEiiElHHrhKkD 166
                                                              l+++ ++  +++v+a+Nf++Gvnl lkll +aa+vl+d  DiEi E+HHrhK+D
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101 109 LLAEAGKD--IPIVFAANFSVGVNLCLKLLDTAARVLGDDvDIEITEAHHRHKVD 161
                                                             *****999..***************************8644************** PP

                                               TIGR00036 167 aPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgeh 221
                                                             aPSGTA++++e+ia+a g+dlk++av++reg tG+r +e+iG+a+vR+gd+vg+h
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101 162 APSGTAVRMGEVIADALGRDLKKVAVYGREGQTGARDRETIGFATVRAGDIVGDH 216
                                                             ******************************************************* PP

                                               TIGR00036 222 tvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270
                                                             tvlFa dGer+eitHkassR++fakG+vra+ wl   e ++yd++dvld
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5101 217 TVLFAADGERVEITHKASSRMTFAKGAVRAALWLDGREPGLYDMQDVLD 265
                                                             ***********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (270 nodes)
Target sequences:                          1  (267 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: 9.91
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
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

GapMind for Amino acid biosynthesis