GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Shewanella sp. ANA-3

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 7025668 Shewana3_2818 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (RefSeq)

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__ANA3:7025668
          Length = 274

 Score =  454 bits (1167), Expect = e-132
 Identities = 224/274 (81%), Positives = 244/274 (89%)

Query: 1   MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60
           M+ L+  IE+AFE RADITP+ VD   R  V  VI +LD G LRVAEKIDGQW  HQWLK
Sbjct: 1   MEALRQRIEAAFEARADITPSTVDASVRNDVQNVINMLDKGELRVAEKIDGQWHVHQWLK 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+GQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS
Sbjct: 181 NCFIGARSEIVEGVVVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240

Query: 241 KDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
             G YSLY A+IVKKVDAKTRGKVGINELLR +D
Sbjct: 241 ACGKYSLYAAIIVKKVDAKTRGKVGINELLRIVD 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: 329
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 7025668 Shewana3_2818 (2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (RefSeq))
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.22745.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   6.3e-154  497.2   3.1     7e-154  497.0   3.1    1.0  1  lcl|FitnessBrowser__ANA3:7025668  Shewana3_2818 2,3,4,5-tetrahydro


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025668  Shewana3_2818 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase (Ref
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.0   3.1    7e-154    7e-154       2     270 ..       4     272 ..       3     273 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.0 bits;  conditional E-value: 7e-154
                         TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekldgqwkvnewvkkavllsfritdnqvlndavn 78 
                                       l++ ie afe ra+i+p+++++ v++ v+++i++ld+g lrvaek+dgqw+v++w+kkavllsfri dn v+++a++
  lcl|FitnessBrowser__ANA3:7025668   4 LRQRIEAAFEARADITPSTVDASVRNDVQNVINMLDKGELRVAEKIDGQWHVHQWLKKAVLLSFRIFDNAVIDGAET 80 
                                       6789************************************************************************* PP

                         TIGR00965  79 kyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatvgscaqigknvh 155
                                       kyfdkv+ kfa+yde++fk +++r+vp+a vr+g+fi kn+vlmpsyvn+gayvdegtmvdtwatvgscaqigknvh
  lcl|FitnessBrowser__ANA3:7025668  81 KYFDKVPLKFAEYDEARFKAEAIRVVPSATVRKGSFIGKNTVLMPSYVNLGAYVDEGTMVDTWATVGSCAQIGKNVH 157
                                       ***************************************************************************** PP

                         TIGR00965 156 lsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdretgeiiygrvpagsvvv 232
                                       lsggvgiggvleplqa p+iiedncfigarseivegv+veegsvismgv+igqst+i+dretgei+ygrvpagsvvv
  lcl|FitnessBrowser__ANA3:7025668 158 LSGGVGIGGVLEPLQAGPTIIEDNCFIGARSEIVEGVVVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVV 234
                                       ***************************************************************************** PP

                         TIGR00965 233 sgslpskdgkkslycavivkkvdaktrgkvsinellrt 270
                                       sg+lps  gk+sly a+ivkkvdaktrgkv+inellr 
  lcl|FitnessBrowser__ANA3:7025668 235 SGNLPSACGKYSLYAAIIVKKVDAKTRGKVGINELLRI 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: 9.30
//
[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