Alignments for a candidate for dapD in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Phaeobacter inhibens BS107

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate GFF3576 PGA1_c36310 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase DapD

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__Phaeo:GFF3576
          Length = 275

 Score =  334 bits (856), Expect = 1e-96
 Identities = 174/272 (63%), Positives = 209/272 (76%), Gaps = 5/272 (1%)

Query: 3   QLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID-GQWVTHQWLKK 61
           QL+  IE+A+E R  IT A      R+A+ + +  LDSG LRVAE+ D G W  +QW KK
Sbjct: 5   QLETAIEAAWEARDTITSATTGE-QRDAIEETLNALDSGKLRVAERQDSGNWHVNQWAKK 63

Query: 62  AVLLSFRINDNKVMDGAE--TRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119
           AVLL FRI D +   G    + ++DKV  KF  + EA +++ GFR VP   VR+ A+IA 
Sbjct: 64  AVLLGFRIKDMEEQSGGPQGSGWWDKVDSKFKGWGEAEWKEAGFRAVPNCVVRKSAYIAP 123

Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179
             VLMPS+VN+GA+VDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTIIE
Sbjct: 124 GVVLMPSFVNLGAHVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIE 183

Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239
           DNCFIGARSEVVEG IV EGSV+ MGV++GQST+I DRETGE+ YG VP  SVVV+G++P
Sbjct: 184 DNCFIGARSEVVEGCIVREGSVLGMGVFIGQSTKIVDRETGEVMYGEVPPYSVVVAGSMP 243

Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           SK+G  +LYCAVIVK+VD +TR K GINELLR
Sbjct: 244 SKNG-INLYCAVIVKRVDERTRSKTGINELLR 274


Lambda     K      H
   0.318    0.136    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: 260
Number of extensions: 8
Number of successful extensions: 4
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: 274
Length of database: 275
Length adjustment: 25
Effective length of query: 249
Effective length of database: 250
Effective search space:    62250
Effective search space used:    62250
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: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate GFF3576 PGA1_c36310 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase DapD)
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

# 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/TIGR00965.hmm
# target sequence database:        /tmp/gapView.11020.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00965  [M=271]
Accession:   TIGR00965
Description: dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   1.5e-130  420.5   0.9   1.7e-130  420.3   0.9    1.0  1  lcl|FitnessBrowser__Phaeo:GFF3576  PGA1_c36310 2,3,4,5-tetrahydropy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3576  PGA1_c36310 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase Dap
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.3   0.9  1.7e-130  1.7e-130       2     269 ..       6     274 ..       5     275 .] 0.96

  Alignments for each domain:
  == domain 1  score: 420.3 bits;  conditional E-value: 1.7e-130
                          TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritdnqvlnda 76 
                                        l   ie a+e r+ i+ a+ + + ++a++e+++ ldsg+lrvae++ +g+w+vn+w+kkavll fri+d +   ++
  lcl|FitnessBrowser__Phaeo:GFF3576   6 LETAIEAAWEARDTITSAT-TGEQRDAIEETLNALDSGKLRVAERQdSGNWHVNQWAKKAVLLGFRIKDMEEQSGG 80 
                                        6789***********9876.5788**********************789*******************98877765 PP

                          TIGR00965  77 ..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatvgscaqi 150
                                           + ++dkv +kf  + e+e+keag+r+vp+ vvr+ a+ia  vvlmps+vn+ga+vdegtmvdtwatvgscaqi
  lcl|FitnessBrowser__Phaeo:GFF3576  81 pqGSGWWDKVDSKFKGWGEAEWKEAGFRAVPNCVVRKSAYIAPGVVLMPSFVNLGAHVDEGTMVDTWATVGSCAQI 156
                                        22678*********************************************************************** PP

                          TIGR00965 151 gknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdretgeiiygrvp 226
                                        gknvhlsggvgiggvlep+qa p+iiedncfigarse+veg iv egsv+ mgvfigqstkivdretge++yg vp
  lcl|FitnessBrowser__Phaeo:GFF3576 157 GKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGQSTKIVDRETGEVMYGEVP 232
                                        **************************************************************************** PP

                          TIGR00965 227 agsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269
                                         +svvv+gs+psk+g  +lycavivk+vd++tr+k++inellr
  lcl|FitnessBrowser__Phaeo:GFF3576 233 PYSVVVAGSMPSKNGI-NLYCAVIVKRVDERTRSKTGINELLR 274
                                        **************95.7************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (275 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: 00:00:00.00
# Mc/sec: 8.46
//
[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