GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Escherichia coli BW25113

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate 14312 b0166 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI)

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__Keio:14312
          Length = 274

 Score =  542 bits (1397), Expect = e-159
 Identities = 274/274 (100%), Positives = 274/274 (100%)

Query: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK 60
           MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK
Sbjct: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK 60

Query: 61  KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120
           KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN
Sbjct: 61  KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
           TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED
Sbjct: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS
Sbjct: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240

Query: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
           KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID
Sbjct: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274


Lambda     K      H
   0.318    0.136    0.391 

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: 390
Number of extensions: 6
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 14312 b0166 (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI))
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.5258.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   3.1e-169  547.4   2.5   3.5e-169  547.2   2.5    1.0  1  lcl|FitnessBrowser__Keio:14312  b0166 2,3,4,5-tetrahydropyridine


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14312  b0166 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  547.2   2.5  3.5e-169  3.5e-169       1     271 []       3     273 ..       3     273 .. 1.00

  Alignments for each domain:
  == domain 1  score: 547.2 bits;  conditional E-value: 3.5e-169
                       TIGR00965   1 slqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnqvlndavnk 79 
                                     +lq+iietaferraei+pa+++++++eavn++ia ldsgalrvaek+dgqw++++w+kkavllsfri+dnqv+++a+++
  lcl|FitnessBrowser__Keio:14312   3 QLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVIEGAESR 81 
                                     69***************************************************************************** PP

                       TIGR00965  80 yfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatvgscaqigknvhlsg 158
                                     yfdkv++kfadyde++f+++g+r+vp+a+vr+gafia+n+vlmpsyvnigayvdegtmvdtwatvgscaqigknvhlsg
  lcl|FitnessBrowser__Keio:14312  82 YFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSG 160
                                     ******************************************************************************* PP

                       TIGR00965 159 gvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdretgeiiygrvpagsvvvsgslp 237
                                     gvgiggvleplqa+p+iiedncfigarse+vegviveegsvismgv+igqst+i+dretgei+ygrvpagsvvvsg+lp
  lcl|FitnessBrowser__Keio:14312 161 GVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239
                                     ******************************************************************************* PP

                       TIGR00965 238 skdgkkslycavivkkvdaktrgkvsinellrti 271
                                     skdgk+slycavivkkvdaktrgkv+inellrti
  lcl|FitnessBrowser__Keio:14312 240 SKDGKYSLYCAVIVKKVDAKTRGKVGINELLRTI 273
                                     ********************************97 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 2.69
//
[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:

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:

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:

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:

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