Alignments for a candidate for dapD in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_00599 H281DRAFT_00599 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__Burk376:H281DRAFT_00599
          Length = 275

 Score =  413 bits (1061), Expect = e-120
 Identities = 207/271 (76%), Positives = 231/271 (85%), Gaps = 1/271 (0%)

Query: 2   QQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKK 61
           QQLQ +I++A++ RAD++P       REAV   I  LD GALRVAEK DG+WV +QWLKK
Sbjct: 3   QQLQQIIDTAWDNRADLSPKAAPADVREAVAHAIEQLDKGALRVAEKKDGEWVVNQWLKK 62

Query: 62  AVLLSFRINDNKVMD-GAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARN 120
           AVLLSFR+ DN  M  G  +++YDKVP KFA+Y    F   GFRVVPPA  R+G+FIA+N
Sbjct: 63  AVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKN 122

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
            VLMPSY NIGAYVDEG+MVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANP IIED
Sbjct: 123 VVLMPSYTNIGAYVDEGSMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIED 182

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSEVVEGVIVEE SVISMGVYLGQST+IYDRETGE+ YGR+PAGSVVV+GNLPS
Sbjct: 183 NCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPS 242

Query: 241 KDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           KDGS+SLYCAVIVKKVDAKTR KVG+NELLR
Sbjct: 243 KDGSHSLYCAVIVKKVDAKTRAKVGLNELLR 273


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: 323
Number of extensions: 5
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: 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 H281DRAFT_00599 H281DRAFT_00599 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
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.10503.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.3e-150  484.3   0.3     6e-150  484.1   0.3    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_00599  H281DRAFT_00599 2,3,4,5-tetrahyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_00599  H281DRAFT_00599 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinylt
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  484.1   0.3    6e-150    6e-150       1     270 [.       4     274 ..       4     275 .] 0.98

  Alignments for each domain:
  == domain 1  score: 484.1 bits;  conditional E-value: 6e-150
                                    TIGR00965   1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfr 66 
                                                  +lq+ii+ta+++ra++ p ++ ++v+eav ++i +ld+galrvaek dg+w+vn+w+kkavllsfr
  lcl|FitnessBrowser__Burk376:H281DRAFT_00599   4 QLQQIIDTAWDNRADLSPKAAPADVREAVAHAIEQLDKGALRVAEKKDGEWVVNQWLKKAVLLSFR 69 
                                                  699*************************************************************** PP

                                    TIGR00965  67 itdnqvl.ndavnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigay 131
                                                  ++dn  +  +++++++dkv++kfa+y  + f   g+r+vp+a++rrg+fiaknvvlmpsy nigay
  lcl|FitnessBrowser__Burk376:H281DRAFT_00599  70 LEDNAPMpAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAY 135
                                                  ***98552789******************************************************* PP

                                    TIGR00965 132 vdegtmvdtwatvgscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveeg 197
                                                  vdeg+mvdtwatvgscaqigknvhlsggvgiggvleplqa+pviiedncfigarse+vegvivee 
  lcl|FitnessBrowser__Burk376:H281DRAFT_00599 136 VDEGSMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEEN 201
                                                  ****************************************************************** PP

                                    TIGR00965 198 svismgvfigqstkivdretgeiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvs 263
                                                  svismgv++gqstki+dretge+ ygr+pagsvvv+g+lpskdg++slycavivkkvdaktr+kv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00599 202 SVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPSKDGSHSLYCAVIVKKVDAKTRAKVG 267
                                                  ****************************************************************** PP

                                    TIGR00965 264 inellrt 270
                                                  +nellr+
  lcl|FitnessBrowser__Burk376:H281DRAFT_00599 268 LNELLRG 274
                                                  *****96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 9.51
//
[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