Aligments for a candidate for serB in Pseudomonas fluorescens GW456-L13

GapMind for Amino acid biosynthesis

Aligments for a candidate for serB in Pseudomonas fluorescens GW456-L13

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate PfGW456L13_172 Phosphoserine phosphatase (EC 3.1.3.3)

Query= SwissProt::Q9S281
         (410 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 Phosphoserine
           phosphatase (EC 3.1.3.3)
          Length = 404

 Score =  263 bits (673), Expect = 5e-75
 Identities = 166/395 (42%), Positives = 231/395 (58%), Gaps = 22/395 (5%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALV----TEPPRGLEGD 67
           +L+ I G DRPG+TA +   LA   V+++DI Q V    +    LV    TE  + +  D
Sbjct: 5   VLINITGVDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPDTEQGKSVLKD 64

Query: 68  LRATVHSWAESLKL----QAEIISGIGDNRPRGFGRSLVTVLGHPLTAEATAAIAARITE 123
           +    +   + ++     + +    +G+   +G  R +VT+L   +TA    A+++   +
Sbjct: 65  ILFKGYELDQQVRFTPVSEQDYQQWVGN---QGKKRHIVTLLTRKVTAGQLQAVSSITAK 121

Query: 124 SGSNIDRIFRLA-KYPVTA--------VEFAVSGVETEP--LRTALATEAAALGVDIAVV 172
            G NID I RL+ + P+          +EF+V G   +P  LR    + A  L VDIA  
Sbjct: 122 YGLNIDHIDRLSGRMPLDTPADKGKGCIEFSVRGEAADPQALRAEFLSVAQELNVDIAFQ 181

Query: 173 AAGLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHAR 232
              L RR +RL V D+DSTLI+ EVI+  A  AG  D+V+E+T  AM GELDF  S   R
Sbjct: 182 EDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSEITERAMAGELDFRASFKER 241

Query: 233 VALLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLD 292
           +ALL GLD +V+D + A +RLT GA TL   LKRLGY+  ++SGGFT     LQ +LG+D
Sbjct: 242 LALLKGLDVNVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGID 301

Query: 293 FAQANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLN 352
           +  AN LE+VDG++TG     IVD   KA LL+  A   G+ L QT+A+GDGANDL ML 
Sbjct: 302 YVFANELEVVDGKVTGVAVEPIVDAQRKADLLKELAHKEGLRLEQTIAVGDGANDLPMLA 361

Query: 353 AAGLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLG 387
            AGLGVAF AKP+V+++A  A++   LD VLYLLG
Sbjct: 362 IAGLGVAFRAKPLVKQSAKQAISTLGLDGVLYLLG 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: 387
Number of extensions: 20
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 PfGW456L13_172 (Phosphoserine phosphatase (EC 3.1.3.3))
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.2405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                              -----------
    2.9e-84  268.1   0.9    3.8e-84  267.7   0.9    1.2  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172  Phosphoserine phosphatase (EC 3.


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172  Phosphoserine phosphatase (EC 3.1.3.3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.7   0.9   3.8e-84   3.8e-84       1     219 []     177     395 ..     177     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 267.7 bits;  conditional E-value: 3.8e-84
                                              TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgel 56 
                                                            dia +e+s ++++++l+vfD+Dstlie+EvIde+ak+aGv+++VseiTerAm gel
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 177 DIAFQEDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGDKVSEITERAMAGEL 232
                                                            688999999*********************************************** PP

                                              TIGR00338  57 dFkeslreRvkllkglpvellkkveeklelteGveelvkkLkekgykvaviSGgFd 112
                                                            dF++s++eR++llkgl+v++l+ +  +l+lteG+e l  +Lk+ gyk+a++SGgF+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 233 DFRASFKERLALLKGLDVNVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFT 288
                                                            ******************************************************** PP

                                              TIGR00338 113 lvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkllekegisl 168
                                                            ++a++l++kLg+d+vfaN+Lev dgk tG    +ivd++ ka+ l++l++keg+ l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 289 YFAKQLQAKLGIDYVFANELEVVDGKVTGVAVEPIVDAQRKADLLKELAHKEGLRL 344
                                                            ******************************************************** PP

                                              TIGR00338 169 ektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                                            e+t+avGDGanDl+m++ Aglg+af akp +k+ a+++i++  l ++l+ll
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_172 345 EQTIAVGDGANDLPMLAIAGLGVAFRAKPLVKQSAKQAISTLGLDGVLYLL 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.49
//
[ok]

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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, or view the source code, or see 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