GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Ruegeria conchae TW15

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 WP_010440698.1 G7G_RS0109130 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>NCBI__GCF_000192475.1:WP_010440698.1
          Length = 275

 Score =  342 bits (876), Expect = 7e-99
 Identities = 177/272 (65%), Positives = 212/272 (77%), Gaps = 5/272 (1%)

Query: 3   QLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEK-IDGQWVTHQWLKK 61
           QL+  IE+A++ R  ITPA      REA+   +  LDSG+LRVAEK  DG W  +QW KK
Sbjct: 5   QLEAAIEAAWDMRDTITPATTGE-QREAIEDTLNALDSGSLRVAEKQADGNWHVNQWAKK 63

Query: 62  AVLLSFRINDNKVMDGAETR--YYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119
           AVLL FRI D ++ +G      ++DKV  KFA +DE +++  GFR VP   VR+ A+IA 
Sbjct: 64  AVLLGFRIKDMEIQNGGPQAGGWWDKVDSKFAGWDENQWRAAGFRAVPNCVVRKSAYIAP 123

Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179
             VLMPS+VN+GAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTIIE
Sbjct: 124 GAVLMPSFVNLGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIE 183

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

Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           SK+ + SLYCAVIVK+VD KTR K GIN+LLR
Sbjct: 244 SKN-NVSLYCAVIVKRVDEKTRSKTGINDLLR 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: 284
Number of extensions: 11
Number of successful extensions: 5
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 WP_010440698.1 G7G_RS0109130 (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.2097017.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.6e-133  429.6   0.8     3e-133  429.4   0.8    1.0  1  NCBI__GCF_000192475.1:WP_010440698.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010440698.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.4   0.8    3e-133    3e-133       2     269 ..       6     274 ..       5     275 .] 0.97

  Alignments for each domain:
  == domain 1  score: 429.4 bits;  conditional E-value: 3e-133
                             TIGR00965   2 lqkiietaferraeilpasklikvkeavnesiasldsgalrvaekl.dgqwkvnewvkkavllsfritdnqvl 73 
                                           l   ie a+++r+ i+pa++  + +ea++++++ ldsg lrvaek+ dg+w+vn+w+kkavll fri+d ++ 
  NCBI__GCF_000192475.1:WP_010440698.1   6 LEAAIEAAWDMRDTITPATT-GEQREAIEDTLNALDSGSLRVAEKQaDGNWHVNQWAKKAVLLGFRIKDMEIQ 77 
                                           6788*************975.678*********************999************************* PP

                             TIGR00965  74 nda..vnkyfdkvatkfadydedefkeaglrkvpgavvrrgafiaknvvlmpsyvnigayvdegtmvdtwatv 144
                                           n++     ++dkv +kfa +de++++ ag+r+vp+ vvr+ a+ia   vlmps+vn+gayvdegtmvdtwatv
  NCBI__GCF_000192475.1:WP_010440698.1  78 NGGpqAGGWWDKVDSKFAGWDENQWRAAGFRAVPNCVVRKSAYIAPGAVLMPSFVNLGAYVDEGTMVDTWATV 150
                                           *9722457***************************************************************** PP

                             TIGR00965 145 gscaqigknvhlsggvgiggvleplqakpviiedncfigarseivegviveegsvismgvfigqstkivdret 217
                                           gscaqigknvhlsggvgiggvlep+qa p+iiedncfigarse+veg iv egsv+ mgvfig+stkivdret
  NCBI__GCF_000192475.1:WP_010440698.1 151 GSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRET 223
                                           ************************************************************************* PP

                             TIGR00965 218 geiiygrvpagsvvvsgslpskdgkkslycavivkkvdaktrgkvsinellr 269
                                           ge++yg vp +svvv+gs+psk+ + slycavivk+vd+ktr+k++in+llr
  NCBI__GCF_000192475.1:WP_010440698.1 224 GEVMYGEVPPYSVVVAGSMPSKN-NVSLYCAVIVKRVDEKTRSKTGINDLLR 274
                                           *********************97.68*************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.34
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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