Alignments for a candidate for serB in Pseudomonas putida KT2440

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Pseudomonas putida KT2440

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate PP_4909 PP_4909 phosphoserine phosphatase

Query= SwissProt::Q9S281
         (410 letters)



>FitnessBrowser__Putida:PP_4909
          Length = 415

 Score =  272 bits (695), Expect = 2e-77
 Identities = 170/393 (43%), Positives = 229/393 (58%), Gaps = 16/393 (4%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71
           +L+ I G+DRPG+TA +   L    V ++DI   V  G +    LV  P   +   L  +
Sbjct: 16  VLINITGEDRPGLTAAITGVLLQGGVSILDIGLAVMHGTLSFGILVDIPDNEVATALLQS 75

Query: 72  VHSWAESLKLQAE---IISGIGDNRPRGFG--RSLVTVLGHPLTAEATAAIAARITESGS 126
           V + A  L LQA    I      +   G G  R +VT+L   +T E    ++A I++ G 
Sbjct: 76  VQAKAHELNLQARYTPISEADYQHWADGHGEARHIVTLLSRKITPEQLQRVSAVISQYGL 135

Query: 127 NIDRIFRLAKYPV---------TAVEFAVSGV--ETEPLRTALATEAAALGVDIAVVAAG 175
            I+RI RL+              AVE +V GV  + + LR      A  L VDIA     
Sbjct: 136 TIERIERLSARVALDAEIDKGKAAVEISVRGVPSDAQALRADFFALAEELSVDIAFQKDD 195

Query: 176 LHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVAL 235
           L RR +RL V D+DSTLI+ EVI+  A  AG  ++VA +T  AMRGELDF  S   R+AL
Sbjct: 196 LFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVAAITERAMRGELDFRASFKERMAL 255

Query: 236 LAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQ 295
           L GLD  V+D++ A +RLT GA  L   LKRLGY+  ++SGGFT     +Q +LG+D+  
Sbjct: 256 LKGLDVGVLDEIGASLRLTEGAENLFAELKRLGYKTAILSGGFTYFARQVQARLGIDYVF 315

Query: 296 ANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAG 355
           AN LE+VDG++TG     IVD   KA LL++ A+  G+ L QT+A+GDGANDL ML+ AG
Sbjct: 316 ANELEVVDGKVTGVAVEPIVDAQRKADLLKKLASDEGLQLEQTIAVGDGANDLPMLSLAG 375

Query: 356 LGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGI 388
           LGVAF AKP+VR++A  A++   LD VLYLLG+
Sbjct: 376 LGVAFRAKPLVRQSAKQAISTLGLDGVLYLLGL 408


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: 388
Number of extensions: 16
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: 415
Length adjustment: 31
Effective length of query: 379
Effective length of database: 384
Effective search space:   145536
Effective search space used:   145536
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 PP_4909 PP_4909 (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.26529.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    8.7e-83  263.2   0.6    1.1e-82  262.9   0.6    1.1  1  lcl|FitnessBrowser__Putida:PP_4909  PP_4909 phosphoserine phosphatas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_4909  PP_4909 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.9   0.6   1.1e-82   1.1e-82       1     219 []     188     406 ..     188     406 .. 0.98

  Alignments for each domain:
  == domain 1  score: 262.9 bits;  conditional E-value: 1.1e-82
                           TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve 75 
                                         dia +++  ++++++l+vfD+Dstlie+EvIde+ak+aGv+e+V++iTerAmrgeldF++s++eR++llkgl+v 
  lcl|FitnessBrowser__Putida:PP_4909 188 DIAFQKDDLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEQVAAITERAMRGELDFRASFKERMALLKGLDVG 262
                                         577888889999*************************************************************** PP

                           TIGR00338  76 llkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivde 150
                                         +l+++  +l+lteG+e+l  +Lk+ gyk+a++SGgF+++a +++++Lg+d+vfaN+Lev dgk tG    +ivd+
  lcl|FitnessBrowser__Putida:PP_4909 263 VLDEIGASLRLTEGAENLFAELKRLGYKTAILSGGFTYFARQVQARLGIDYVFANELEVVDGKVTGVAVEPIVDA 337
                                         *************************************************************************** PP

                           TIGR00338 151 sakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                         + ka+ l+kl+ +eg++le+t+avGDGanDl+m++ Aglg+af akp +++ a+++i++  l ++l+ll
  lcl|FitnessBrowser__Putida:PP_4909 338 QRKADLLKKLASDEGLQLEQTIAVGDGANDLPMLSLAGLGVAFRAKPLVRQSAKQAISTLGLDGVLYLL 406
                                         ************************************************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (415 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: 00:00:00.00
# Mc/sec: 9.51
//
[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