Alignments for a candidate for trpB in Pseudomonas stutzeri RCH2

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpB in Pseudomonas stutzeri RCH2

Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate GFF2586 Psest_2636 tryptophan synthase, beta subunit

Query= uniprot:P50383
         (425 letters)



>FitnessBrowser__psRCH2:GFF2586
          Length = 402

 Score =  124 bits (310), Expect = 7e-33
 Identities = 113/360 (31%), Positives = 161/360 (44%), Gaps = 55/360 (15%)

Query: 72  IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131
           +GRP+P+F A+RL E L   A+IY K E    TG+HKIN  + +A  AK  G + V+ ET
Sbjct: 61  VGRPSPIFHARRLSEQLGG-AQIYLKREDLNHTGAHKINHCLGEALLAKFMGKKKVIAET 119

Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191
           GAGQ G A+A A ++  +   I M +V  E++    + M++ G  + A            
Sbjct: 120 GAGQHGVALATACALVGIPCEIHMGQVDIEKEHPNVTKMKILGCKLIAV----------- 168

Query: 192 LETNPQHPGSLGIAMSEAIEYALKNEFRYL--VGSVL------DVVLLHQSVIGQETITQ 243
                +   +L  A+  A E  LK+   Y+  +GSV+       +V   QS+IG E   Q
Sbjct: 169 ----TRGAATLKEAVDSAFEEYLKDPHNYIYAIGSVVGPHPFPKMVRDFQSIIGTEAREQ 224

Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFIGN---------------KKGKRYIAVSSAE 287
            L   G   D ++ CVGGGSN  G    F+ +                K  R+ A  S  
Sbjct: 225 FLAKHGRLPDHVVACVGGGSNAMGMFTAFLEDAAVELVGIEPAGESLDKPGRHSATLSKG 284

Query: 288 IPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIV 347
            P    G   Y   D+ G    V  I            A GL Y GV P  S L   G V
Sbjct: 285 KPSELHGMACYVLEDADGNPSAVHSI------------ASGLDYPGVGPQHSYLKDIGRV 332

Query: 348 EWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHG 407
            ++   ++E  EA       +GI+PA ESAHA+   +  A    +++    I+ NLSG G
Sbjct: 333 NYQTATDQECLEAFMTLSRVEGIIPALESAHAVAWAIRTAPTLSEDSH---ILVNLSGRG 389


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: 379
Number of extensions: 19
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: 425
Length of database: 402
Length adjustment: 31
Effective length of query: 394
Effective length of database: 371
Effective search space:   146174
Effective search space used:   146174
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 GFF2586 Psest_2636 (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.13124.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     9e-167  540.9   0.0     1e-166  540.7   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF2586  Psest_2636 tryptophan synthase, 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF2586  Psest_2636 tryptophan synthase, beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  540.7   0.0    1e-166    1e-166       1     383 [.      15     398 ..      15     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 540.7 bits;  conditional E-value: 1e-166
                           TIGR00263   1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiylkredl 75 
                                         g+fg +GGq vp  l +a+++++ aye++++ e+f++el  l+ +y+grp+p+++a++ls++lgga+iylkredl
  lcl|FitnessBrowser__psRCH2:GFF2586  15 GYFGPYGGQLVPPHLKQAMDDINLAYEEIRQREDFQQELAALFADYVGRPSPIFHARRLSEQLGGAQIYLKREDL 89 
                                         79************************************************************************* PP

                           TIGR00263  76 lhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqklnvfrmellgak 150
                                         +htGahkin  lg allak +Gkk++iaetGaGqhGva ata+al+g+ ce++mG+ d+e+ ++nv +m++lg k
  lcl|FitnessBrowser__psRCH2:GFF2586  90 NHTGAHKINHCLGEALLAKFMGKKKVIAETGAGQHGVALATACALVGIPCEIHMGQVDIEKEHPNVTKMKILGCK 164
                                         *************************************************************************** PP

                           TIGR00263 151 vvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeevkeqilekegrlPdaviac 225
                                         +++vt G +tlk+av++a+ ++  + ++  y +Gs+vGphPfP++vr+fqs+ig+e++eq l+k+grlPd+v+ac
  lcl|FitnessBrowser__psRCH2:GFF2586 165 LIAVTRGAATLKEAVDSAFEEYLKDPHNYIYAIGSVVGPHPFPKMVRDFQSIIGTEAREQFLAKHGRLPDHVVAC 239
                                         *************************************************************************** PP

                           TIGR00263 226 vGGGsnaiGifaafiedeeveligveagGkGidt.ekhaatlskGkeGvlhGaktkllqdedGqieeahsvsaGl 299
                                         vGGGsna+G+f+af+ed  vel+g+e++G+ +d+  +h+atlskGk+  lhG+  ++l d dG+ + +hs+++Gl
  lcl|FitnessBrowser__psRCH2:GFF2586 240 VGGGSNAMGMFTAFLEDAAVELVGIEPAGESLDKpGRHSATLSKGKPSELHGMACYVLEDADGNPSAVHSIASGL 314
                                         *********************************9789************************************** PP

                           TIGR00263 300 dypgvgPehaalaetgraeyeaitdeealealkllskeeGiipalesshalaaleklapklkkdeivvvnlsGrG 374
                                         dypgvgP+h++l+++gr++y+++td+e+lea+++ls+ eGiipales+ha+a ++++ap+l++d+ ++vnlsGrG
  lcl|FitnessBrowser__psRCH2:GFF2586 315 DYPGVGPQHSYLKDIGRVNYQTATDQECLEAFMTLSRVEGIIPALESAHAVAWAIRTAPTLSEDSHILVNLSGRG 389
                                         *************************************************************************** PP

                           TIGR00263 375 dkdletvak 383
                                         dkd + va+
  lcl|FitnessBrowser__psRCH2:GFF2586 390 DKDADYVAN 398
                                         ***999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (402 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.85
//
[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