GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Streptacidiphilus oryzae TH49

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117) (characterized)
to candidate WP_051939867.1 BS73_RS12745 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= BRENDA::P9WP21
         (317 letters)



>NCBI__GCF_000744815.1:WP_051939867.1
          Length = 333

 Score =  412 bits (1060), Expect = e-120
 Identities = 219/321 (68%), Positives = 244/321 (76%), Gaps = 7/321 (2%)

Query: 4   VTGAAGIGLATLAADGSVLDTWFPAPELTESGT--SATSRLAVSDVPVEL----AALIGR 57
           ++GA   GLATLAADG+VLDTWFPAPELT S +  + T RL        L    A  IG 
Sbjct: 12  LSGAVAAGLATLAADGTVLDTWFPAPELTASPSEPAGTERLTAEQAVAALGEGAAEAIGP 71

Query: 58  DDDRRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWT 117
           D  R  E +AVRT I SL +  AD YD YLRLHLLSHRLV P+  +  G+F  L NV WT
Sbjct: 72  DPRRGVEVVAVRTTISSLSEEPADAYDVYLRLHLLSHRLVRPNVQSLEGIFAHLANVAWT 131

Query: 118 NHGPCAIDGFEAVRARLRRRG-PVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAP 176
           + GP  +D  E+ R  +R +G  +TVYGVDKFPRM+DYVVP GVRIADADRVRLGAHLA 
Sbjct: 132 SVGPVPVDRIESTRLAVRAQGGSLTVYGVDKFPRMLDYVVPAGVRIADADRVRLGAHLAA 191

Query: 177 GTTVMHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGK 236
           GTTVMHEGFVN+NAGTLG SMVEGRIS GVVVGD SD+GGGASIMGTLSGGG  V+SIG+
Sbjct: 192 GTTVMHEGFVNFNAGTLGTSMVEGRISQGVVVGDSSDIGGGASIMGTLSGGGKEVVSIGE 251

Query: 237 RCLLGANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVSG 296
           RCLLGAN+G+GISLGDDCVVEAGLYVTAGTRVT PD    KA ELSG SNLLFRRNS +G
Sbjct: 252 RCLLGANAGIGISLGDDCVVEAGLYVTAGTRVTTPDGQVAKAAELSGQSNLLFRRNSQTG 311

Query: 297 AVEVLARDGQGIALNEDLHAN 317
           AVEVLAR G    LNE LHA+
Sbjct: 312 AVEVLARKGSWGGLNEVLHAH 332


Lambda     K      H
   0.318    0.136    0.397 

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: 367
Number of extensions: 13
Number of successful extensions: 3
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: 317
Length of database: 333
Length adjustment: 28
Effective length of query: 289
Effective length of database: 305
Effective search space:    88145
Effective search space used:    88145
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: 48 (23.1 bits)

Align candidate WP_051939867.1 BS73_RS12745 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
to HMM TIGR03535 (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/TIGR03535.hmm
# target sequence database:        /tmp/gapView.2140041.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03535  [M=320]
Accession:   TIGR03535
Description: DapD_actino: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-156  505.8   7.3   2.5e-156  505.6   7.3    1.0  1  NCBI__GCF_000744815.1:WP_051939867.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_051939867.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  505.6   7.3  2.5e-156  2.5e-156       2     320 .]      14     332 ..      13     332 .. 0.96

  Alignments for each domain:
  == domain 1  score: 505.6 bits;  conditional E-value: 2.5e-156
                             TIGR03535   2 salglGlatvtadgtvldvWypelelgea..aeagterleae..leelaa....lagedeargvervvvttki 66 
                                           +a+++Glat++adgtvld+W+p++el++   ++agterl+ae  +++l +    ++g d +rgve+v+v+t+i
  NCBI__GCF_000744815.1:WP_051939867.1  14 GAVAAGLATLAADGTVLDTWFPAPELTASpsEPAGTERLTAEqaVAALGEgaaeAIGPDPRRGVEVVAVRTTI 86 
                                           699***********************998668999**99998663334334444899**************** PP

                             TIGR03535  67 adldeapadaadaylrlhllshrlvkPntvnldGifgllanvvWtnlGPvavedlektraklraeg.pvtvys 138
                                           ++l+e pada+d+ylrlhllshrlv+Pn ++l+Gif++lanv+Wt++GPv v+ +e+tr+++ra+g ++tvy+
  NCBI__GCF_000744815.1:WP_051939867.1  87 SSLSEEPADAYDVYLRLHLLSHRLVRPNVQSLEGIFAHLANVAWTSVGPVPVDRIESTRLAVRAQGgSLTVYG 159
                                           *****************************************************************65****** PP

                             TIGR03535 139 vdkfPrmvdyvvPtgvrigdadrvrlGaylaeGttvmheGfvnfnaGtlGasmveGrisaGvvvgdGsdiGGG 211
                                           vdkfPrm+dyvvP+gvri+dadrvrlGa+la+GttvmheGfvnfnaGtlG+smveGris+Gvvvgd sdiGGG
  NCBI__GCF_000744815.1:WP_051939867.1 160 VDKFPRMLDYVVPAGVRIADADRVRLGAHLAAGTTVMHEGFVNFNAGTLGTSMVEGRISQGVVVGDSSDIGGG 232
                                           ************************************************************************* PP

                             TIGR03535 212 asimGtlsGGGkevisiGercllGansGvGislGddcvveaGlyvtaGtkvtlvdkakeaageegevvkaael 284
                                           asimGtlsGGGkev+siGercllGan+G+GislGddcvveaGlyvtaGt+vt+         ++g+v kaael
  NCBI__GCF_000744815.1:WP_051939867.1 233 ASIMGTLSGGGKEVVSIGERCLLGANAGIGISLGDDCVVEAGLYVTAGTRVTT---------PDGQVAKAAEL 296
                                           *****************************************************.........99********* PP

                             TIGR03535 285 sGasnllfrrnsvsGaveavarkgkaielnealhan 320
                                           sG+snllfrrns++Gave++arkg++  lne lha+
  NCBI__GCF_000744815.1:WP_051939867.1 297 SGQSNLLFRRNSQTGAVEVLARKGSWGGLNEVLHAH 332
                                           **********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (320 nodes)
Target sequences:                          1  (333 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.28
//
[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