GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Pseudomonas simiae WCS417

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate GFF473 PS417_02415 phosphoserine phosphatase

Query= SwissProt::Q9S281
         (410 letters)



>FitnessBrowser__WCS417:GFF473
          Length = 404

 Score =  268 bits (685), Expect = 2e-76
 Identities = 167/392 (42%), Positives = 225/392 (57%), Gaps = 16/392 (4%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71
           +L+ I G+DRPG+TA +   LA   V+++DI Q V    +    LV  P       +   
Sbjct: 5   VLINITGEDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPSTEQASSVLKD 64

Query: 72  VHSWAESLKLQAEIISGIGDNRP-----RGFGRSLVTVLGHPLTAEATAAIAARITESGS 126
           +   A  L  Q        ++       +G  R +VT+L   +TAE    +++   + G 
Sbjct: 65  ILFTAYKLDQQVRFTPVSEEDYQHWVAGQGKKRHIVTLLTRKVTAEQLQRVSSITAQYGL 124

Query: 127 NIDRIFRLA-KYPVTA--------VEFAVSGVETEP--LRTALATEAAALGVDIAVVAAG 175
           NID I RL+ + P+          +EF+V G   +P  LR    + A  L VDIA     
Sbjct: 125 NIDHIDRLSGRMPLDTPADQGKGCIEFSVRGEPADPQALRAEFLSVAQELNVDIAFQEDS 184

Query: 176 LHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVAL 235
           L RR +RL V D+DSTLI+ EVI+  A  AG  ++VAE+T  AM GELDF  S   R+AL
Sbjct: 185 LFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVAEITERAMAGELDFRASFKERLAL 244

Query: 236 LAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQ 295
           L GLD SV+D + A +RLT GA TL   LKRLGY+  ++SGGFT     LQ +LG+D+  
Sbjct: 245 LKGLDVSVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGIDYVF 304

Query: 296 ANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAG 355
           AN LE+VDG++TG     IVD   KA LL+  A   G+ L QT+A+GDGANDL ML  AG
Sbjct: 305 ANELEVVDGKVTGMAVEPIVDAQRKADLLKELAHKEGLRLEQTIAVGDGANDLPMLAIAG 364

Query: 356 LGVAFNAKPVVREAAHTAVNVPFLDTVLYLLG 387
           LGVAF AKP+V+++A  A++   LD VLYLLG
Sbjct: 365 LGVAFRAKPLVKQSAKQAISTLGLDGVLYLLG 396


Lambda     K      H
   0.319    0.135    0.374 

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: 383
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: 410
Length of database: 404
Length adjustment: 31
Effective length of query: 379
Effective length of database: 373
Effective search space:   141367
Effective search space used:   141367
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate GFF473 PS417_02415 (phosphoserine phosphatase)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (EC 3.1.3.3))

# 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/TIGR00338.hmm
# target sequence database:        /tmp/gapView.8777.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00338  [M=219]
Accession:   TIGR00338
Description: serB: phosphoserine phosphatase SerB
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    4.4e-84  267.5   0.9    5.6e-84  267.1   0.9    1.1  1  lcl|FitnessBrowser__WCS417:GFF473  PS417_02415 phosphoserine phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF473  PS417_02415 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.1   0.9   5.6e-84   5.6e-84       1     219 []     177     395 ..     177     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 267.1 bits;  conditional E-value: 5.6e-84
                          TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvel 76 
                                        dia +e+s ++++++l+vfD+Dstlie+EvIde+ak+aGv+e+V+eiTerAm geldF++s++eR++llkgl+v++
  lcl|FitnessBrowser__WCS417:GFF473 177 DIAFQEDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVAEITERAMAGELDFRASFKERLALLKGLDVSV 252
                                        688999999******************************************************************* PP

                          TIGR00338  77 lkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesa 152
                                        l+ +  +l+lteG+e l  +Lk+ gyk+a++SGgF+++a++l++kLg+d+vfaN+Lev dgk tG    +ivd++ 
  lcl|FitnessBrowser__WCS417:GFF473 253 LDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGIDYVFANELEVVDGKVTGMAVEPIVDAQR 328
                                        **************************************************************************** PP

                          TIGR00338 153 kaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                        ka+ l++l++keg+ le+t+avGDGanDl+m++ Aglg+af akp +k+ a+++i++  l ++l+ll
  lcl|FitnessBrowser__WCS417:GFF473 329 KADLLKELAHKEGLRLEQTIAVGDGANDLPMLAIAGLGVAFRAKPLVKQSAKQAISTLGLDGVLYLL 395
                                        **********************************************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (404 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: 00:00:00.00
# Mc/sec: 9.00
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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