GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Escherichia coli BW25113

Align phosphoserine phosphatase; EC 3.1.3.3 (characterized)
to candidate 18409 b4388 3-phosphoserine phosphatase (NCBI)

Query= CharProtDB::CH_024035
         (322 letters)



>FitnessBrowser__Keio:18409
          Length = 322

 Score =  636 bits (1640), Expect = 0.0
 Identities = 322/322 (100%), Positives = 322/322 (100%)

Query: 1   MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLG 60
           MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLG
Sbjct: 1   MPNITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKLG 60

Query: 61  AAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDST 120
           AAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDST
Sbjct: 61  AAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDST 120

Query: 121 AIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENL 180
           AIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENL
Sbjct: 121 AIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVRENL 180

Query: 181 PLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVI 240
           PLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVI
Sbjct: 181 PLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVI 240

Query: 241 GDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAE 300
           GDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAE
Sbjct: 241 GDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAE 300

Query: 301 VTIRHADLMGVFCILSGSLNQK 322
           VTIRHADLMGVFCILSGSLNQK
Sbjct: 301 VTIRHADLMGVFCILSGSLNQK 322


Lambda     K      H
   0.320    0.136    0.399 

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: 508
Number of extensions: 15
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: 322
Length of database: 322
Length adjustment: 28
Effective length of query: 294
Effective length of database: 294
Effective search space:    86436
Effective search space used:    86436
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: 48 (23.1 bits)

Align candidate 18409 b4388 (3-phosphoserine phosphatase (NCBI))
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.4461.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
    7.9e-99  315.7   0.1      1e-98  315.3   0.1    1.2  1  lcl|FitnessBrowser__Keio:18409  b4388 3-phosphoserine phosphatas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:18409  b4388 3-phosphoserine phosphatase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.3   0.1     1e-98     1e-98       1     219 []      97     315 ..      97     315 .. 0.99

  Alignments for each domain:
  == domain 1  score: 315.3 bits;  conditional E-value: 1e-98
                       TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 
                                     d+a + + ++l++ +l+v+D+Dst+i++E+IdeiaklaG++e+V+e+TerAmrgeldF++slr+Rv++lkg+++++l++
  lcl|FitnessBrowser__Keio:18409  97 DVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQ 175
                                     578888999********************************************************************** PP

                       TIGR00338  80 veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktll 158
                                     v+e+l+l++G+++lv kL++ g+kva++SGgF+++ae+l++kL+l+av+aN+Le++dgk+tG+v g+ivd+++kaktl+
  lcl|FitnessBrowser__Keio:18409 176 VRENLPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLT 254
                                     ******************************************************************************* PP

                       TIGR00338 159 kllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                     +l+++++i+l++tva+GDGanDl+mikaAglgia++akp+++eka+++i+++dl++++++l
  lcl|FitnessBrowser__Keio:18409 255 RLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCIL 315
                                     ***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (322 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: 12.32
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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:

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:

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:

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:

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