Alignments for a candidate for serB in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Phaeobacter inhibens BS107

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate GFF3562 PGA1_c36160 phosphoserine phosphatase SerB

Query= SwissProt::Q58989
         (211 letters)



>FitnessBrowser__Phaeo:GFF3562
          Length = 309

 Score =  165 bits (418), Expect = 7e-46
 Identities = 92/206 (44%), Positives = 130/206 (63%), Gaps = 1/206 (0%)

Query: 3   KKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKD 62
           ++KK++L D DST++  E IDE+A EAGV   VK+IT  AM G+LNF+ +LR+RV+LLK 
Sbjct: 92  RRKKMLLADMDSTMIQQECIDELAEEAGVGARVKEITARAMNGELNFDGALRERVALLKG 151

Query: 63  LPIEKVEKAI-KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFAN 121
           LP+E + + + +RIT   G    +  +K  G   A+VSGGF    +++ E+LG D   AN
Sbjct: 152 LPVEVIAQVLDRRITLMPGGAALLATMKADGAYAALVSGGFTAFTSRVAEQLGFDENRAN 211

Query: 122 RLIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK 181
            L+V DG LTG+V   +L   AK E LE+I    G++  D +AVGDGAND+ M  +AG  
Sbjct: 212 TLLVADGLLTGEVGMPILGRAAKVEALEQITARLGLSEADVMAVGDGANDLGMLGRAGAG 271

Query: 182 IAFCAKPILKEKADICIEKRDLREIL 207
           +A  AKP +  + DI I   DL  +L
Sbjct: 272 VALHAKPSVAAECDIRINHGDLTALL 297


Lambda     K      H
   0.314    0.136    0.358 

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: 148
Number of extensions: 5
Number of successful extensions: 2
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: 211
Length of database: 309
Length adjustment: 24
Effective length of query: 187
Effective length of database: 285
Effective search space:    53295
Effective search space used:    53295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate GFF3562 PGA1_c36160 (phosphoserine phosphatase SerB)
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.13362.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    2.4e-67  212.7   0.4    3.1e-67  212.4   0.4    1.1  1  lcl|FitnessBrowser__Phaeo:GFF3562  PGA1_c36160 phosphoserine phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3562  PGA1_c36160 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.4   3.1e-67   3.1e-67      11     218 ..      91     299 ..      84     300 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 3.1e-67
                          TIGR00338  11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkv.eekle 85 
                                         + kk+++ D+Dst+i++E+Ide+a +aGv+  V+eiT rAm+gel+F+ +lreRv+llkglpve++ +v   +++
  lcl|FitnessBrowser__Phaeo:GFF3562  91 GRRKKMLLADMDSTMIQQECIDELAEEAGVGARVKEITARAMNGELNFDGALRERVALLKGLPVEVIAQVlDRRIT 166
                                        578999***********************************************************666661568** PP

                          TIGR00338  86 lteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktllkll 161
                                        l++G   l  ++k  g   a++SGgF+ ++ +++e+Lg d   aN+L v dg ltG+v  +i+   ak + l++++
  lcl|FitnessBrowser__Phaeo:GFF3562 167 LMPGGAALLATMKADGAYAALVSGGFTAFTSRVAEQLGFDENRANTLLVADGLLTGEVGMPILGRAAKVEALEQIT 242
                                        **************************************************************************** PP

                          TIGR00338 162 ekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218
                                         + g+s ++++avGDGanDl m+ +Ag+g+a +akp +  + di i++ dlt++l+l
  lcl|FitnessBrowser__Phaeo:GFF3562 243 ARLGLSEADVMAVGDGANDLGMLGRAGAGVALHAKPSVAAECDIRINHGDLTALLYL 299
                                        *****************************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (309 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: 9.39
//
[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