Alignments for a candidate for dapA in Dyella japonica UNC79MFTsu3.2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapA in Dyella japonica UNC79MFTsu3.2

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate N515DRAFT_1147 N515DRAFT_1147 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1147
          Length = 297

 Score =  248 bits (632), Expect = 2e-70
 Identities = 132/272 (48%), Positives = 174/272 (63%)

Query: 2   IAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIR 61
           I GS+ AL TPF + G LD D+  +L+D+ +  GT A+V  G+TGE+  L+ +E+  ++ 
Sbjct: 3   IGGSICALATPFTSDGALDLDAFGRLLDYQVAGGTQAVVVAGSTGEAHMLEHDEYETLLS 62

Query: 62  RVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRH 121
             V ++ GRIPV+AGTG   T   VALT  A+  GADA L+V P+Y +PTQEG+ +HF  
Sbjct: 63  FAVKRIAGRIPVLAGTGEAGTARTVALTRRARELGADAALVVAPFYVRPTQEGLRRHFLE 122

Query: 122 IAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDF 181
           +AE   +P +LYNVPGRT+CD+LPETV  L + P I+GIKEA G  +R + + E    DF
Sbjct: 123 VAEHGGLPVLLYNVPGRTACDLLPETVAALREHPAIVGIKEAVGSDERIRALAELARADF 182

Query: 182 LVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHK 241
           +  SGDD TA + ML G  G ISV AN+AP+A  +LC AA  GDAAA    +D L PL +
Sbjct: 183 VYLSGDDPTAGKAMLAGAAGTISVVANLAPKAFRELCDAATSGDAAATTRCDDVLAPLVQ 242

Query: 242 ALFIESNPIPVKWALHEMGLIPEGIRLPLTWL 273
           AL    NPI VK  L  +GL     RLPL  L
Sbjct: 243 ALNCAPNPIAVKAGLPALGLGSAAPRLPLVEL 274


Lambda     K      H
   0.319    0.134    0.393 

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: 253
Number of extensions: 11
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: 292
Length of database: 297
Length adjustment: 26
Effective length of query: 266
Effective length of database: 271
Effective search space:    72086
Effective search space used:    72086
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: 48 (23.1 bits)

Align candidate N515DRAFT_1147 N515DRAFT_1147 (4-hydroxy-tetrahydrodipicolinate synthase)
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.5738.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.3e-88  281.7   0.0    2.6e-88  281.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147  N515DRAFT_1147 4-hydroxy-tetrahy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1147  N515DRAFT_1147 4-hydroxy-tetrahydrodipicolinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.6   0.0   2.6e-88   2.6e-88       2     276 ..       6     279 ..       5     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 281.6 bits;  conditional E-value: 2.6e-88
                                    TIGR00674   2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknr 67 
                                                  ++ Al TPf +dg +d++a+ +l+++q++ g++a+vv+G+TGE+  L ++E+++++++av+  ++r
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147   6 SICALATPFTSDGALDLDAFGRLLDYQVAGGTQAVVVAGSTGEAHMLEHDEYETLLSFAVKRIAGR 71 
                                                  799*************************************************************** PP

                                    TIGR00674  68 vpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvP 133
                                                  +pv+aGtg   t+ ++ lt++a++lg+d++lvv+P+Y++PtqeGl +hf ++ae+  lP++lYnvP
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147  72 IPVLAGTGEAGTARTVALTRRARELGADAALVVAPFYVRPTQEGLRRHFLEVAEHGGLPVLLYNVP 137
                                                  ****************************************************************** PP

                                    TIGR00674 134 sRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGv 199
                                                  +Rt+++l petv++L e++ iv+iKea g+ er+  + + a +df+ lsGdD ++ + ++ Ga+G 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147 138 GRTACDLLPETVAALREHPAIVGIKEAVGSDERIRALAELARADFVYLSGDDPTAGKAMLAGAAGT 203
                                                  ****************************************************************** PP

                                    TIGR00674 200 iSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelR 265
                                                  iSV++n+apk ++e++ aa+ gd +     +  l +l++al++++NPi vK+ l +lgl    + R
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147 204 ISVVANLAPKAFRELCDAATSGDAAATTRCDDVLAPLVQALNCAPNPIAVKAGLPALGLGSA-APR 268
                                                  ************************************************************99.*** PP

                                    TIGR00674 266 lPLtelseekk 276
                                                  lPL+el++  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1147 269 LPLVELQDGPE 279
                                                  *****987643 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.03
# Mc/sec: 2.15
//
[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