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

GapMind for Amino acid biosynthesis

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

Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate PfGW456L13_3832 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)

Query= SwissProt::Q57695
         (289 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832
          Length = 291

 Score =  172 bits (437), Expect = 6e-48
 Identities = 98/289 (33%), Positives = 156/289 (53%), Gaps = 8/289 (2%)

Query: 2   FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61
           F+G++  ++TPF N  +DF GL   ++ L+E GV G++  GTTGE   +   E   V++ 
Sbjct: 4   FQGIWVPLVTPFHNGAIDFVGLHRLVSHLLEKGVDGLIVCGTTGEPAAMGKHEQLAVLDA 63

Query: 62  VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSI---TPYYNKPTQEGLRKHF 118
           V++ V  +  V+  AG+N TE    L  F  ++    V  +    PYY +P+Q GL   F
Sbjct: 64  VLERVPAQQVVMGLAGNNLTE----LLQFQSEILKRPVAGLLVPAPYYIRPSQAGLEAFF 119

Query: 119 GKVAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK 178
             VA++ ++P++LY++P RT V  E  T+ L    +  I A+K+   N S    L++   
Sbjct: 120 RTVADASSVPLILYDIPYRTGVAFEQATL-LNIVAHERIVAIKDCGGNFSNTLALLNSGL 178

Query: 179 ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLM 238
           + VL G D      + LG KG I+  A++ P+ FV++     +    + R   ++L PL+
Sbjct: 179 VDVLCGEDNQIFNALCLGAKGAIAASAHVHPELFVQLHRQIRDNQLAEGRATFFRLLPLI 238

Query: 239 KAMFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDLG 287
            ++F+E NP PVKTAL + G    ELR P+   SE   + L+ VL  LG
Sbjct: 239 NSLFLEPNPAPVKTALALQGLIGDELRAPMQRSSEPMTERLKGVLSALG 287


Lambda     K      H
   0.315    0.135    0.374 

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: 224
Number of extensions: 14
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: 289
Length of database: 291
Length adjustment: 26
Effective length of query: 263
Effective length of database: 265
Effective search space:    69695
Effective search space used:    69695
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate PfGW456L13_3832 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
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.6263.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
    7.5e-75  237.4   0.0    8.4e-75  237.2   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832  4-hydroxy-tetrahydrodipicolinate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832  4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   0.0   8.4e-75   8.4e-75       4     285 ..       9     285 ..       6     286 .. 0.97

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 8.4e-75
                                               TIGR00674   4 tAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvie 58 
                                                             + l+TPf++   +df  l++l+++++ekgvd+++v+GtTGE a++ + E+ +v+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832   9 VPLVTPFHNGA-IDFVGLHRLVSHLLEKGVDGLIVCGTTGEPAAMGKHEQLAVLD 62 
                                                             679****9887.******************************************* PP

                                               TIGR00674  59 vavelvknrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGly 113
                                                              ++e v    +v+ G ++n+++e +++ +e+ k +v+g+lv +PyY +P+q Gl 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832  63 AVLERVPA-QQVVMGLAGNNLTELLQFQSEILKRPVAGLLVPAPYYIRPSQAGLE 116
                                                             ******98.9********************************************* PP

                                               TIGR00674 114 khfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervs 168
                                                             ++f ++a+++++P+ilY++P Rtgv +e+ t+++++++++ivaiK+++g+ ++  
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832 117 AFFRTVADASSVPLILYDIPYRTGVAFEQATLLNIVAHERIVAIKDCGGNFSNTL 171
                                                             ****************************************************999 PP

                                               TIGR00674 169 eikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdt 223
                                                              + +     + vl+G+D+   + l+lGakG i   ++v p+++ ++ +++ +++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832 172 ALLNSG--LVDVLCGEDNQIFNALCLGAKGAIAASAHVHPELFVQLHRQIRDNQL 224
                                                             998854..69********************************************* PP

                                               TIGR00674 224 eeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkek 278
                                                             +e r    +ll+l++ lf+e+NP pvKtalal+gli   elR P+   se  +e+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832 225 AEGRATFFRLLPLINSLFLEPNPAPVKTALALQGLIGD-ELRAPMQRSSEPMTER 278
                                                             ************************************98.**************** PP

                                               TIGR00674 279 lkevlke 285
                                                             lk vl+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3832 279 LKGVLSA 285
                                                             **99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (286 nodes)
Target sequences:                          1  (291 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.90
//
[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