GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Flavobacterium glycines Gm-149

Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate WP_066328927.1 BLR17_RS13320 tryptophan synthase subunit beta

Query= BRENDA::Q97TX6
         (429 letters)



>NCBI__GCF_900100165.1:WP_066328927.1
          Length = 393

 Score =  135 bits (341), Expect = 2e-36
 Identities = 124/405 (30%), Positives = 182/405 (44%), Gaps = 61/405 (15%)

Query: 43  LKEVLPSKVLELEFAKERYVKIP---------DEVLERYLQVGRPTPIIRAKRLEEYLGN 93
           + E+L   V EL   +++Y+KI          D++L+ Y  VGRP+P+  AKRL E    
Sbjct: 19  IPEMLYPNVEEL---RQQYLKIMAEPDFKAEFDQLLKDY--VGRPSPLYFAKRLSEKY-- 71

Query: 94  NIKIYLKMESYTYTGSHKINSALAHVYYAKLDNAKFVTTETGAGQWGSSVALASALFRMK 153
           N KIYLK E   +TG+HKIN+ +  +  AK    K +  ETGAGQ G + A   AL  ++
Sbjct: 72  NTKIYLKREDLNHTGAHKINNTIGQILVAKKLGKKRIIAETGAGQHGVATATVCALMGLE 131

Query: 154 AHIFMVRTSYYAKPYRKYMMQMYGAEVHPSPSDLTEFGRQLLAKDSNHPGSLGIAISDAV 213
             ++M       +      M+M GA V P+ S     G + L   +N       AI D +
Sbjct: 132 CIVYMGEIDIARQAPNVARMKMLGATVRPALS-----GSRTLKDATNE------AIRDWI 180

Query: 214 EYAHKNGGKYVVGSVVNSD------IMFKTIAGMEAKKQM-ELIG-EDPDYIIGVVGGGS 265
              +     Y++GS +           F+++   E K Q+ E  G E+PDY++  +GGGS
Sbjct: 181 N--NPVDTHYIIGSAIGPHPYPDMVTRFQSVISEEIKWQLKEKEGRENPDYVVACIGGGS 238

Query: 266 NYAALAYPFLGDELRSGKVRRKYIASGSSEVPKMTKGVYKYDYPDTAKL--------LPM 317
           N A   Y FL +              G   V    KG++      T+KL           
Sbjct: 239 NAAGTFYHFLHEP-----------EVGIIAVEAAGKGIHSGHSAATSKLGKVGIIHGCKT 287

Query: 318 LKMYTIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGIVQARDYSQEESFKWAKLFSELEG 377
           L M T       P   + GL Y GV P  + L   G  +    + +++ +      +LEG
Sbjct: 288 LLMQTPDGQITEPYSISAGLDYPGVGPMHAHLAETGRAEFFSVTDDDAMQAGLELCKLEG 347

Query: 378 YIPAPETSHALPILAEIAEEAKKSGERKTVLVSFSGHGLLDLGNY 422
            IPA E+SHAL +L +     KK      V++  SG G  DL NY
Sbjct: 348 IIPAIESSHALAVLND-----KKFKPEDVVVICLSGRGDKDLNNY 387


Lambda     K      H
   0.316    0.135    0.392 

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: 415
Number of extensions: 28
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: 429
Length of database: 393
Length adjustment: 31
Effective length of query: 398
Effective length of database: 362
Effective search space:   144076
Effective search space used:   144076
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_066328927.1 BLR17_RS13320 (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.818201.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-181  588.2   0.0   4.5e-181  588.0   0.0    1.0  1  NCBI__GCF_900100165.1:WP_066328927.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900100165.1:WP_066328927.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  588.0   0.0  4.5e-181  4.5e-181       1     383 [.       9     389 ..       9     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 588.0 bits;  conditional E-value: 4.5e-181
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g++g+fGG+y+pe+l +++eel+++y k+ ++++fk+e+++llk+y+grp+pl+fak+ls+k++ +kiylkre
  NCBI__GCF_900100165.1:WP_066328927.1   9 GYYGQFGGAYIPEMLYPNVEELRQQYLKIMAEPDFKAEFDQLLKDYVGRPSPLYFAKRLSEKYN-TKIYLKRE 80 
                                           79*************************************************************8.******** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl+htGahkinn++gq+l+ak+lGkkriiaetGaGqhGvatat++al+glec vymG+ d++rq++nv rm++
  NCBI__GCF_900100165.1:WP_066328927.1  81 DLNHTGAHKINNTIGQILVAKKLGKKRIIAETGAGQHGVATATVCALMGLECIVYMGEIDIARQAPNVARMKM 153
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke.grl 218
                                           lga+v p  sGs+tlkda+nea+rdW+ +  dthy++Gsa+GphP+P++v +fqsvi+ee+k+q++eke  + 
  NCBI__GCF_900100165.1:WP_066328927.1 154 LGATVRPALSGSRTLKDATNEAIRDWINNPVDTHYIIGSAIGPHPYPDMVTRFQSVISEEIKWQLKEKEgREN 226
                                           *********************************************************************5568 PP

                             TIGR00263 219 PdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqiee 291
                                           Pd+v+ac+GGGsna G+f++f++++ev +i+vea+GkGi++ + aat + Gk+G++hG kt l+q+ dGqi+e
  NCBI__GCF_900100165.1:WP_066328927.1 227 PDYVVACIGGGSNAAGTFYHFLHEPEVGIIAVEAAGKGIHSGHSAATSKLGKVGIIHGCKTLLMQTPDGQITE 299
                                           ************************************************************************* PP

                             TIGR00263 292 ahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkde 364
                                            +s+saGldypgvgP ha+laetgrae+ ++td++a++a   l+k eGiipa+esshala+l+    k k ++
  NCBI__GCF_900100165.1:WP_066328927.1 300 PYSISAGLDYPGVGPMHAHLAETGRAEFFSVTDDDAMQAGLELCKLEGIIPAIESSHALAVLNDK--KFKPED 370
                                           *************************************************************9865..458899 PP

                             TIGR00263 365 ivvvnlsGrGdkdletvak 383
                                           +vv+ lsGrGdkdl++ ++
  NCBI__GCF_900100165.1:WP_066328927.1 371 VVVICLSGRGDKDLNNYIE 389
                                           **************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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: 26.33
//
[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