Alignments for a candidate for dapD in Shewanella oneidensis MR-1

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapD in Shewanella oneidensis MR-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 200790 SO1625 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI ptt file)

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__MR1:200790
          Length = 274

 Score =  446 bits (1147), Expect = e-130
 Identities = 220/274 (80%), Positives = 241/274 (87%)

Query: 1   MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60
           M+ L+  IE+AFE R DITP+ VD   R  V  VI +LD G LRVAEKIDG W  HQWLK
Sbjct: 1   MEALRQRIEAAFEARTDITPSTVDERVRSDVQHVINMLDKGELRVAEKIDGLWHVHQWLK 60

Query: 61  KAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARN 120
           KAVLLSFRI DN V+DGAET+Y+DKVP+KFA+YDEARF+ E  RVVP ATVR+G+FI +N
Sbjct: 61  KAVLLSFRIFDNAVIDGAETKYFDKVPLKFAEYDEARFKAEAIRVVPSATVRKGSFIGKN 120

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
           TVLMPSYVN+GAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQA PTIIED
Sbjct: 121 TVLMPSYVNLGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQAGPTIIED 180

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSE+VEGV+VEEGSVISMGVY+GQSTRIYDRETGE+HYGRVPAGSVVVSGNLPS
Sbjct: 181 NCFIGARSEIVEGVVVEEGSVISMGVYIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPS 240

Query: 241 KDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
             G YSLY A+IVKKVDAKTR KVGINELLR +D
Sbjct: 241 ACGKYSLYAAIIVKKVDAKTRSKVGINELLRIVD 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: 319
Number of extensions: 5
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: 274
Length of database: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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 200790 SO1625 (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI ptt file))
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.24241.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.2e-151  489.7   2.3   1.4e-151  489.5   2.3    1.0  1  lcl|FitnessBrowser__MR1:200790  SO1625 2,3,4,5-tetrahydropyridin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200790  SO1625 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.5   2.3  1.4e-151  1.4e-151       2     270 ..       4     272 ..       3     273 .. 0.99

  Alignments for each domain:
  == domain 1  score: 489.5 bits;  conditional E-value: 1.4e-151
                       TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnqvlndavnky 80 
                                     l++ ie afe r +i+p++++ +v+  v+++i++ld+g lrvaek+dg w+v++w+kkavllsfri dn v+++a++ky
  lcl|FitnessBrowser__MR1:200790   4 LRQRIEAAFEARTDITPSTVDERVRSDVQHVINMLDKGELRVAEKIDGLWHVHQWLKKAVLLSFRIFDNAVIDGAETKY 82 
                                     6789*************************************************************************** PP

                       TIGR00965  81 fdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatvgscaqigknvhlsgg 159
                                     fdkv+ kfa+yde++fk +++r+vp+a vr+g+fi kn+vlmpsyvn+gayvdegtmvdtwatvgscaqigknvhlsgg
  lcl|FitnessBrowser__MR1:200790  83 FDKVPLKFAEYDEARFKAEAIRVVPSATVRKGSFIGKNTVLMPSYVNLGAYVDEGTMVDTWATVGSCAQIGKNVHLSGG 161
                                     ******************************************************************************* PP

                       TIGR00965 160 vgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdretgeiiygrvpagsvvvsgslps 238
                                     vgiggvleplqa p+iiedncfigarseivegv+veegsvismgv+igqst+i+dretge++ygrvpagsvvvsg+lps
  lcl|FitnessBrowser__MR1:200790 162 VGIGGVLEPLQAGPTIIEDNCFIGARSEIVEGVVVEEGSVISMGVYIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPS 240
                                     ******************************************************************************* PP

                       TIGR00965 239 kdgkkslycavivkkvdaktrgkvsinellrt 270
                                       gk+sly a+ivkkvdaktr+kv+inellr 
  lcl|FitnessBrowser__MR1:200790 241 ACGKYSLYAAIIVKKVDAKTRSKVGINELLRI 272
                                     ******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (271 nodes)
Target sequences:                          1  (274 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: 7.77
//
[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