GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Pontibacter ramchanderi LP43

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_101443593.1 BD749_RS02800 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_002846395.1:WP_101443593.1
          Length = 396

 Score =  141 bits (356), Expect = 3e-38
 Identities = 116/367 (31%), Positives = 177/367 (48%), Gaps = 39/367 (10%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRPTPL+ AKRL E   T   IY K E    TG+HKIN  I Q   AK  G   ++ ET
Sbjct: 55  VGRPTPLYFAKRLSEKYNT--NIYLKREDLNHTGAHKINNTIGQILLAKRLGKTRIIAET 112

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A A   ++ N++  ++M +V  E++    + M++ GA V  + +     G K 
Sbjct: 113 GAGQHGVATATVCALMNLECIVYMGEVDVERQAPNVARMKMLGATVVPATS-----GSKT 167

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL------DVVLLHQSVIGQETITQ 243
           L+           A +EAI   + N  +  Y++GSV+      D+V   Q+VI +E  +Q
Sbjct: 168 LKD----------ATNEAIRDWINNPEDTYYIIGSVVGPHPYPDMVARFQAVISEEMKSQ 217

Query: 244 L--DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFP 301
           L      E+ D ++ CVGGGSN  G  Y ++   + K  +A  +A +   S         
Sbjct: 218 LLEKTGSENPDYIVACVGGGSNAAGAFYHYLDTPEVK-LVAAEAAGLGIDSGESAATSVL 276

Query: 302 DSAGLL---PLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREIF 358
              G++     + M T       P   + GL Y GV P  + L + G   +    + E  
Sbjct: 277 GKEGIIHGSRTLLMQTEDGQVTEPYSISAGLDYPGVGPLHAHLHQSGRAIFESITDEEAL 336

Query: 359 EAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESMM 418
           +A       +GI+PA E+AHA+ A+    + A+ +   +V+V NLSG G  DL+ Y   +
Sbjct: 337 QAVLELTRLEGIIPALETAHALAAI--GRLGAKPD---EVVVINLSGRGDKDLATY---L 388

Query: 419 KRLNGNG 425
            R N +G
Sbjct: 389 DRFNFDG 395


Lambda     K      H
   0.318    0.138    0.403 

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: 377
Number of extensions: 22
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: 425
Length of database: 396
Length adjustment: 31
Effective length of query: 394
Effective length of database: 365
Effective search space:   143810
Effective search space used:   143810
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: 50 (23.9 bits)

Align candidate WP_101443593.1 BD749_RS02800 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))

# 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/TIGR00263.hmm
# target sequence database:        /tmp/gapView.3554437.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00263  [M=385]
Accession:   TIGR00263
Description: trpB: tryptophan synthase, beta subunit
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.1e-184  597.2   0.0   8.1e-184  597.0   0.0    1.0  1  NCBI__GCF_002846395.1:WP_101443593.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002846395.1:WP_101443593.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  597.0   0.0  8.1e-184  8.1e-184       1     381 [.       9     387 ..       9     391 .. 0.99

  Alignments for each domain:
  == domain 1  score: 597.0 bits;  conditional E-value: 8.1e-184
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g++g+fGG+yvpe+l +++eel+++y ++ ++++f++el+ llk+y+grptpl+fak+ls+k++ ++iylkre
  NCBI__GCF_002846395.1:WP_101443593.1   9 GFYGRFGGAYVPEMLYPNVEELRQNYLTIMAEPDFQEELQALLKDYVGRPTPLYFAKRLSEKYN-TNIYLKRE 80 
                                           68*************************************************************8.******** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl+htGahkinn++gq+llakrlGk+riiaetGaGqhGvatat++al++lec vymG+ dverq++nv rm++
  NCBI__GCF_002846395.1:WP_101443593.1  81 DLNHTGAHKINNTIGQILLAKRLGKTRIIAETGAGQHGVATATVCALMNLECIVYMGEVDVERQAPNVARMKM 153
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke.grl 218
                                           lga+vvp tsGsktlkda+nea+rdW+ + edt+y++Gs+vGphP+P++v +fq+vi+ee+k+q+lek   + 
  NCBI__GCF_002846395.1:WP_101443593.1 154 LGATVVPATSGSKTLKDATNEAIRDWINNPEDTYYIIGSVVGPHPYPDMVARFQAVISEEMKSQLLEKTgSEN 226
                                           *******************************************************************997899 PP

                             TIGR00263 219 PdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqiee 291
                                           Pd+++acvGGGsna G+f+++++++ev+l++ ea+G+Gid+ + aat   GkeG++hG++t l+q+edGq++e
  NCBI__GCF_002846395.1:WP_101443593.1 227 PDYIVACVGGGSNAAGAFYHYLDTPEVKLVAAEAAGLGIDSGESAATSVLGKEGIIHGSRTLLMQTEDGQVTE 299
                                           ************************************************************************* PP

                             TIGR00263 292 ahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkde 364
                                            +s+saGldypgvgP ha+l+++gra +e+itdeeal+a+  l++ eGiipale++halaa+ +l +  k de
  NCBI__GCF_002846395.1:WP_101443593.1 300 PYSISAGLDYPGVGPLHAHLHQSGRAIFESITDEEALQAVLELTRLEGIIPALETAHALAAIGRLGA--KPDE 370
                                           ****************************************************************998..789* PP

                             TIGR00263 365 ivvvnlsGrGdkdletv 381
                                           +vv+nlsGrGdkdl+t 
  NCBI__GCF_002846395.1:WP_101443593.1 371 VVVINLSGRGDKDLATY 387
                                           **************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (396 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.40
//
[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