GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpB in Desulforamulus ruminis DSM 2154

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013841408.1 DESRU_RS06950 tryptophan synthase subunit beta

Query= uniprot:P50383
         (425 letters)



>NCBI__GCF_000215085.1:WP_013841408.1
          Length = 396

 Score =  139 bits (349), Expect = 2e-37
 Identities = 112/363 (30%), Positives = 169/363 (46%), Gaps = 54/363 (14%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+P++ A+ L E +   ARI+ K E    TG+HKIN  + Q   A+  G + ++ ET
Sbjct: 53  VGRPSPVYLARGLSEKMGG-ARIWLKREDLNHTGAHKINNTLGQVLLARRMGKKRIIAET 111

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A A AA+M+ ++  ++M +    ++ +    M+L GA V    +         
Sbjct: 112 GAGQHGVATATAAAMFGLQCVVYMGEEDIRRQSLNVFRMKLLGAEVVEVSSG-------- 163

Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243
                   G+L  AM+EA+   + N     Y++GSV        +V   Q +IGQE   Q
Sbjct: 164 -------TGTLKDAMNEAMRDWVTNVRNTYYIIGSVAGPHPYPMMVRDFQKIIGQEAREQ 216

Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGK--------------RYIAVSSAEI 288
            L+  G     ++ CVGGGSN  G  Y F+ +++ +              R+ A  +A  
Sbjct: 217 MLEQSGGLPHCVVACVGGGSNAMGAFYAFLEDREVELVGVEAGGLGLDTDRHAAPLTAGR 276

Query: 289 PKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVE 348
           P    G Y Y   D  G +  V  ++ G D            Y GV P  S L   G V 
Sbjct: 277 PGVLHGSYSYLIQDGDGQVTPVHSVSAGLD------------YPGVGPEHSYLKDTGRVS 324

Query: 349 WREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGL 408
           +    +RE   A  +    +GI+PA ESAHA+   +  A  AR + ER ++V  LSG G 
Sbjct: 325 YTVATDREALNAFHLLCRTEGIIPALESAHALAEAIKRA--ARMSKERSILVC-LSGRGD 381

Query: 409 LDL 411
            D+
Sbjct: 382 KDV 384


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: 373
Number of extensions: 20
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: 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_013841408.1 DESRU_RS06950 (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.3529828.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.3e-197  640.0   0.3   8.2e-197  639.8   0.3    1.0  1  NCBI__GCF_000215085.1:WP_013841408.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000215085.1:WP_013841408.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  639.8   0.3  8.2e-197  8.2e-197       1     384 [.       7     390 ..       7     391 .. 1.00

  Alignments for each domain:
  == domain 1  score: 639.8 bits;  conditional E-value: 8.2e-197
                             TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkre 73 
                                           g+fg++GG +vpe+l++aleel+kay++a++d +f++e+e++lk+y+grp+p++ a+ ls+k+gga+i+lkre
  NCBI__GCF_000215085.1:WP_013841408.1   7 GYFGSYGGIFVPETLIPALEELTKAYQQAQQDGNFQREVEHYLKNYVGRPSPVYLARGLSEKMGGARIWLKRE 79 
                                           79*********************************************************************** PP

                             TIGR00263  74 dllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmel 146
                                           dl+htGahkinn+lgq+lla+r+GkkriiaetGaGqhGvatataaa++gl+c+vymG+ed+ rq+lnvfrm+l
  NCBI__GCF_000215085.1:WP_013841408.1  80 DLNHTGAHKINNTLGQVLLARRMGKKRIIAETGAGQHGVATATAAAMFGLQCVVYMGEEDIRRQSLNVFRMKL 152
                                           ************************************************************************* PP

                             TIGR00263 147 lgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlP 219
                                           lga+vv v+sG+ tlkda+nea+rdWvt+v++t+y++Gs++GphP+P +vr+fq++ig+e++eq+le+ g lP
  NCBI__GCF_000215085.1:WP_013841408.1 153 LGAEVVEVSSGTGTLKDAMNEAMRDWVTNVRNTYYIIGSVAGPHPYPMMVRDFQKIIGQEAREQMLEQSGGLP 225
                                           ************************************************************************* PP

                             TIGR00263 220 daviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhGaktkllqdedGqieea 292
                                             v+acvGGGsna+G+f+af+ed evel+gveagG+G+dt++haa l++G++GvlhG++++l+qd dGq++++
  NCBI__GCF_000215085.1:WP_013841408.1 226 HCVVACVGGGSNAMGAFYAFLEDREVELVGVEAGGLGLDTDRHAAPLTAGRPGVLHGSYSYLIQDGDGQVTPV 298
                                           ************************************************************************* PP

                             TIGR00263 293 hsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdei 365
                                           hsvsaGldypgvgPeh++l++tgr++y+ +td+eal+a++ll+++eGiipales+hala ++k a++++k++ 
  NCBI__GCF_000215085.1:WP_013841408.1 299 HSVSAGLDYPGVGPEHSYLKDTGRVSYTVATDREALNAFHLLCRTEGIIPALESAHALAEAIKRAARMSKERS 371
                                           ************************************************************************* PP

                             TIGR00263 366 vvvnlsGrGdkdletvaka 384
                                           ++v lsGrGdkd++tvak+
  NCBI__GCF_000215085.1:WP_013841408.1 372 ILVCLSGRGDKDVHTVAKE 390
                                           ****************986 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: 27.62
//
[ok]

This GapMind analysis is from Jul 25 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