Alignments for a candidate for trpB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate Echvi_2510 Echvi_2510 tryptophan synthase, beta subunit

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__Cola:Echvi_2510
          Length = 392

 Score =  141 bits (356), Expect = 3e-38
 Identities = 120/377 (31%), Positives = 178/377 (47%), Gaps = 43/377 (11%)

Query: 58  YIKIPE--EVRDRYLS-----IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKIN 110
           Y KI E  E +D + +     +GRPTPL+ AKRL +  +  A+IY K E    TG+HK+N
Sbjct: 33  YEKITESDEFKDEFHALLKDYVGRPTPLYYAKRLSQ--EYGAKIYLKREDLCHTGAHKVN 90

Query: 111 TAIPQAYFAKEEGIEHVVTETGAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIM 170
             I Q   AK+ G + ++ ETGAGQ G A A   ++  M  T++M  +  E++      M
Sbjct: 91  NTIGQIILAKKLGKKRIIAETGAGQHGVATATVCALMGMDCTVYMGAIDMERQKPNVERM 150

Query: 171 QLYGANVYASPTNLTEYGRKILETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVL-- 226
           ++ GA V  + +     G + L+           A +EA+   + N  +  Y++GSV+  
Sbjct: 151 RILGAKVVPATS-----GSQTLKD----------ATNEALRQWINNPVDTHYIIGSVVGP 195

Query: 227 ----DVVLLHQSVIGQETITQLDLL--GEDADILIGCVGGGSNFGGFTYPFIGNKKGKRY 280
               ++V   QSVI +E   QL      ED D++I CVGGGSN  G  Y +  N    R 
Sbjct: 196 HPYPEMVARFQSVISEEIKYQLKEKEGKEDPDMVIACVGGGSNAAGAFYHYY-NTPSVRL 254

Query: 281 IAVSSAEIPKFSKGEYKYDFPDSAGLL---PLVKMITLGKDYVPPPIYAGGLRYHGVAPT 337
           +AV +A +   S          + G+L     + M T     V P   + GL Y G+ P 
Sbjct: 255 VAVEAAGLGVASGKSAATTALGTPGVLHGSKTLLMQTEDGQVVEPHSISAGLDYPGIGPV 314

Query: 338 LSLLTKEGIVEWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERK 397
            + L      E+    + +  +A       +GI+PA ESAHA+       ++  K     
Sbjct: 315 HAHLFDSKRGEFYAVEDEDAMKAGVELSRLEGIIPAIESAHAL-----SVLKQLKFKPSD 369

Query: 398 VIVFNLSGHGLLDLSNY 414
           VIV NLSG G  DL  Y
Sbjct: 370 VIVINLSGRGDKDLDTY 386


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: 406
Number of extensions: 18
Number of successful extensions: 4
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: 392
Length adjustment: 31
Effective length of query: 394
Effective length of database: 361
Effective search space:   142234
Effective search space used:   142234
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 Echvi_2510 Echvi_2510 (tryptophan synthase, beta subunit)
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.6572.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   6.2e-182  590.8   0.1   7.5e-182  590.5   0.1    1.0  1  lcl|FitnessBrowser__Cola:Echvi_2510  Echvi_2510 tryptophan synthase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2510  Echvi_2510 tryptophan synthase, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  590.5   0.1  7.5e-182  7.5e-182       1     382 [.       8     387 ..       8     389 .. 0.98

  Alignments for each domain:
  == domain 1  score: 590.5 bits;  conditional E-value: 7.5e-182
                            TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkred 74 
                                          g++g+fGG+y+pe+l +++eel+++yek+++ +efk+e++ llk+y+grptpl++ak+ls+++g akiylkred
  lcl|FitnessBrowser__Cola:Echvi_2510   8 GFYGKFGGAYIPEMLYPNVEELRTNYEKITESDEFKDEFHALLKDYVGRPTPLYYAKRLSQEYG-AKIYLKRED 80 
                                          68*************************************************************8.********* PP

                            TIGR00263  75 llhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellg 148
                                          l htGahk+nn++gq++lak+lGkkriiaetGaGqhGvatat++al+g++c+vymGa d+erqk+nv rm++lg
  lcl|FitnessBrowser__Cola:Echvi_2510  81 LCHTGAHKVNNTIGQIILAKKLGKKRIIAETGAGQHGVATATVCALMGMDCTVYMGAIDMERQKPNVERMRILG 154
                                          ************************************************************************** PP

                            TIGR00263 149 akvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqileke.grlPda 221
                                          akvvp tsGs+tlkda+nealr+W+ +  dthy++Gs+vGphP+Pe+v +fqsvi+ee+k q++eke ++ Pd+
  lcl|FitnessBrowser__Cola:Echvi_2510 155 AKVVPATSGSQTLKDATNEALRQWINNPVDTHYIIGSVVGPHPYPEMVARFQSVISEEIKYQLKEKEgKEDPDM 228
                                          *******************************************************************7789*** PP

                            TIGR00263 222 viacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieeahsv 295
                                          viacvGGGsna G+f+++ ++++v+l++vea+G+G+++ k aat + G++GvlhG+kt l+q+edGq+ e hs+
  lcl|FitnessBrowser__Cola:Echvi_2510 229 VIACVGGGSNAAGAFYHYYNTPSVRLVAVEAAGLGVASGKSAATTALGTPGVLHGSKTLLMQTEDGQVVEPHSI 302
                                          ************************************************************************** PP

                            TIGR00263 296 saGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvn 369
                                          saGldypg+gP ha+l +++r e+ a++de+a++a   ls+ eGiipa+es+hal++l++l+   k  +++v+n
  lcl|FitnessBrowser__Cola:Echvi_2510 303 SAGLDYPGIGPVHAHLFDSKRGEFYAVEDEDAMKAGVELSRLEGIIPAIESAHALSVLKQLKF--KPSDVIVIN 374
                                          ***********************************************************9987..6789***** PP

                            TIGR00263 370 lsGrGdkdletva 382
                                          lsGrGdkdl+t +
  lcl|FitnessBrowser__Cola:Echvi_2510 375 LSGRGDKDLDTYI 387
                                          *********9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 00:00:00.01
# Mc/sec: 11.88
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis