Alignments for a candidate for serB in Dechlorosoma suillum PS

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Dechlorosoma suillum PS

Align Phosphoserine phosphatase ThrH; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate Dsui_0761 Dsui_0761 phosphoserine phosphatase/homoserine phosphotransferase

Query= SwissProt::Q9I2Y2
         (205 letters)



>FitnessBrowser__PS:Dsui_0761
          Length = 202

 Score =  276 bits (705), Expect = 2e-79
 Identities = 139/201 (69%), Positives = 159/201 (79%)

Query: 1   MEIACLDLEGVLVPEIWIAFAEKTGIDALKATTRDIPDYDVLMKQRLRILDEHGLKLGDI 60
           M+I CLDLEGVLVPEIWI FAE+TGI  L+ TTR+ P+YDVLM+ RL IL +HGL L DI
Sbjct: 1   MQIVCLDLEGVLVPEIWIEFAERTGIPELRRTTREEPNYDVLMQYRLGILKQHGLGLPDI 60

Query: 61  QEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSD 120
           Q+VIA + PL GA EFV+WLR RFQVVILSDTFYEF+ PLM+QLGFPTL CHKLE D   
Sbjct: 61  QKVIAEMGPLPGAKEFVEWLRPRFQVVILSDTFYEFAMPLMQQLGFPTLFCHKLEADAQG 120

Query: 121 RVVGYQLRQKDPKRQSVIAFKSLYYRVIAAGDSYNDTTMLSEAHAGILFHAPENVIREFP 180
            +V Y LR  + K+++V  FK L ++VIA+GDSYNDTTML EAHAGILF  PENVIREFP
Sbjct: 121 FLVNYHLRMPNQKQEAVKRFKELNFKVIASGDSYNDTTMLGEAHAGILFCPPENVIREFP 180

Query: 181 QFPAVHTYEDLKREFLKASSR 201
           QFP V  YE LK E LKAS R
Sbjct: 181 QFPVVKDYEALKGEILKASER 201


Lambda     K      H
   0.323    0.140    0.408 

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: 179
Number of extensions: 4
Number of successful extensions: 1
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: 205
Length of database: 202
Length adjustment: 21
Effective length of query: 184
Effective length of database: 181
Effective search space:    33304
Effective search space used:    33304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)

Align candidate Dsui_0761 Dsui_0761 (phosphoserine phosphatase/homoserine phosphotransferase)
to HMM TIGR02137 (thrH: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein (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/TIGR02137.hmm
# target sequence database:        /tmp/gapView.25966.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02137  [M=203]
Accession:   TIGR02137
Description: HSK-PSP: phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    7.9e-99  315.2   0.0    8.8e-99  315.1   0.0    1.0  1  lcl|FitnessBrowser__PS:Dsui_0761  Dsui_0761 phosphoserine phosphat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PS:Dsui_0761  Dsui_0761 phosphoserine phosphatase/homoserine phosphotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.1   0.0   8.8e-99   8.8e-99       1     201 [.       1     201 [.       1     202 [] 0.99

  Alignments for each domain:
  == domain 1  score: 315.1 bits;  conditional E-value: 8.8e-99
                         TIGR02137   1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkllegavefv 77 
                                       +++v+ldlegvlvpeiwi +ae+tgi +l+ ttr+ p+ydvlm+ rl il++++l l diq+via++++l ga+efv
  lcl|FitnessBrowser__PS:Dsui_0761   1 MQIVCLDLEGVLVPEIWIEFAERTGIPELRRTTREEPNYDVLMQYRLGILKQHGLGLPDIQKVIAEMGPLPGAKEFV 77 
                                       689************************************************************************** PP

                         TIGR02137  78 dtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvkalkelyykviaagdsy 154
                                       ++lr ++qvvilsdtf+efa plm+qlgfptl+chkl+ +    ++ y+lr+ +qk+++vk +kel++kvia+gdsy
  lcl|FitnessBrowser__PS:Dsui_0761  78 EWLRPRFQVVILSDTFYEFAMPLMQQLGFPTLFCHKLEADAQGFLVNYHLRMPNQKQEAVKRFKELNFKVIASGDSY 154
                                       ***************************************************************************** PP

                         TIGR02137 155 ndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflkasdr 201
                                       ndttml ea++gilf+ pe+v++efpq++ vk ye lk ++lkas+r
  lcl|FitnessBrowser__PS:Dsui_0761 155 NDTTMLGEAHAGILFCPPENVIREFPQFPVVKDYEALKGEILKASER 201
                                       ********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (203 nodes)
Target sequences:                          1  (202 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: 5.43
//
[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