Alignments for a candidate for serB in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Sphingomonas koreensis DSMZ 15582

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate Ga0059261_0070 Ga0059261_0070 phosphoserine phosphatase SerB

Query= SwissProt::Q21YU0
         (237 letters)



>FitnessBrowser__Korea:Ga0059261_0070
          Length = 313

 Score =  169 bits (428), Expect = 6e-47
 Identities = 98/208 (47%), Positives = 128/208 (61%), Gaps = 5/208 (2%)

Query: 25  KLIAFDMDSTLINIECVDEIADAVGRKREVAAITEAAMRGEITDYKESLRQRVALLQGVT 84
           +LI  DMDST+I +EC+DE+AD  G K ++A +TEAAMRGE+ D+ E+L  RVALL+G+ 
Sbjct: 99  RLIVADMDSTMITVECIDELADYAGIKAQIAEVTEAAMRGEL-DFAEALDARVALLKGLG 157

Query: 85  EVQMNQIYQERMQFNPGAAELVAACKAAGLKVLLVSGGFTHFTDRVAQRLGIDYTRSNVL 144
              +++   ER+Q  PGA  LV   KA G   +LVSGGFT F   V +++G D   +N L
Sbjct: 158 ADAIDRCLAERVQLMPGARTLVQTMKANGATAILVSGGFTRFAQPVGEQIGFDRVIANEL 217

Query: 145 QIENGVLTGRMVDQPWGDICDGAEKRKMLLETCALLGIAPKQAIAVGDGANDLPMMREAG 204
            IE G LTG  V +P   I D   K   LL   A LG+     +AVGDGANDL M+++AG
Sbjct: 218 LIEGGALTG-AVTKP---IVDSTTKETTLLGAMAELGLDESATLAVGDGANDLAMIKKAG 273

Query: 205 LSVAFHAKSAVRELANVSIESGGLDRLL 232
           L VA+HAK  V   A   I+   L  LL
Sbjct: 274 LGVAYHAKPIVAAAAGARIDHNDLTALL 301


Lambda     K      H
   0.321    0.137    0.390 

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: 217
Number of extensions: 9
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: 237
Length of database: 313
Length adjustment: 25
Effective length of query: 212
Effective length of database: 288
Effective search space:    61056
Effective search space used:    61056
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate Ga0059261_0070 Ga0059261_0070 (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.2400.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.5e-70  220.9   1.6    1.1e-69  220.5   1.6    1.1  1  lcl|FitnessBrowser__Korea:Ga0059261_0070  Ga0059261_0070 phosphoserine pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_0070  Ga0059261_0070 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.5   1.6   1.1e-69   1.1e-69      10     217 ..      94     302 ..      87     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 220.5 bits;  conditional E-value: 1.1e-69
                                 TIGR00338  10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellk 78 
                                                ++ k+l+v D+Dst+i+ E+Ide+a +aG++ +++e+Te AmrgeldF e+l  Rv+llkgl ++ ++
  lcl|FitnessBrowser__Korea:Ga0059261_0070  94 ANRRKRLIVADMDSTMITVECIDELADYAGIKAQIAEVTEAAMRGELDFAEALDARVALLKGLGADAID 162
                                               56889*************************************************************666 PP

                                 TIGR00338  79 k.veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvege 146
                                               +  +e+++l++G++ lv+++k +g   +++SGgF+ +a+ + e++g d v+aN+L +e g+ltG v+ +
  lcl|FitnessBrowser__Korea:Ga0059261_0070 163 RcLAERVQLMPGARTLVQTMKANGATAILVSGGFTRFAQPVGEQIGFDRVIANELLIEGGALTGAVTKP 231
                                               52789**************************************************************** PP

                                 TIGR00338 147 ivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdi 215
                                               ivd+ +k  tll  + + g++  +t+avGDGanDl+mik+Aglg+a++akp++  +a + i+++dlt++
  lcl|FitnessBrowser__Korea:Ga0059261_0070 232 IVDSTTKETTLLGAMAELGLDESATLAVGDGANDLAMIKKAGLGVAYHAKPIVAAAAGARIDHNDLTAL 300
                                               *******************************************************************99 PP

                                 TIGR00338 216 le 217
                                               l+
  lcl|FitnessBrowser__Korea:Ga0059261_0070 301 LY 302
                                               75 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (313 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: 7.30
//
[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