GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Pseudomonas simiae WCS417

Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate GFF4123 PS417_21120 phosphoserine phosphatase

Query= SwissProt::Q883R9
         (237 letters)



>FitnessBrowser__WCS417:GFF4123
          Length = 205

 Score =  385 bits (990), Expect = e-112
 Identities = 190/205 (92%), Positives = 201/205 (98%)

Query: 33  VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 92
           +EIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI
Sbjct: 1   MEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 60

Query: 93  QAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETD 152
           QAVI+TLKPL+GA+EFV+WLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITD+TD
Sbjct: 61  QAVIATLKPLDGAIEFVNWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDDTD 120

Query: 153 RVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEADAGILFHAPDNVIREFP 212
           RVVSYQLRQKDPKRQSVLAFKSLYYR+IAAGDSYNDTTMLGEAD GILFHAP+NVIREFP
Sbjct: 121 RVVSYQLRQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADCGILFHAPENVIREFP 180

Query: 213 QFPAVHTFDELKKEFIKASNRELVL 237
           QFPAVHTF++LK+ FIKASNR L L
Sbjct: 181 QFPAVHTFEDLKQAFIKASNRPLSL 205


Lambda     K      H
   0.324    0.139    0.410 

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: 266
Number of extensions: 3
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: 237
Length of database: 205
Length adjustment: 22
Effective length of query: 215
Effective length of database: 183
Effective search space:    39345
Effective search space used:    39345
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)

Align candidate GFF4123 PS417_21120 (phosphoserine phosphatase)
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.11899.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-119  382.9   0.0   1.7e-119  382.7   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF4123  PS417_21120 phosphoserine phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF4123  PS417_21120 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.7   0.0  1.7e-119  1.7e-119       1     202 [.       1     202 [.       1     203 [. 0.99

  Alignments for each domain:
  == domain 1  score: 382.7 bits;  conditional E-value: 1.7e-119
                           TIGR02137   1 qevvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqeviatlkllegave 75 
                                         +e+++ldlegvlvpeiwia+aektgi++l++ttrdipdydvlmkqrl+il+e++lkl+diq viatlk+l+ga e
  lcl|FitnessBrowser__WCS417:GFF4123   1 MEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADIQAVIATLKPLDGAIE 75 
                                         79************************************************************************* PP

                           TIGR02137  76 fvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyqlrqkdqkrkvvkalkelyykviaa 150
                                         fv++lre++qvvilsdtf+ef+qplm+qlgfptllch+l  +d+drv+ yqlrqkd+kr++v a+k+lyy+viaa
  lcl|FitnessBrowser__WCS417:GFF4123  76 FVNWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDDTDRVVSYQLRQKDPKRQSVLAFKSLYYRVIAA 150
                                         *************************************************************************** PP

                           TIGR02137 151 gdsyndttmlkeadkgilfhapesvvaefpqleavktyeelkdkflkasdrs 202
                                         gdsyndttml ead gilfhape+v++efpq++av+t+e+lk+ f kas+r 
  lcl|FitnessBrowser__WCS417:GFF4123 151 GDSYNDTTMLGEADCGILFHAPENVIREFPQFPAVHTFEDLKQAFIKASNRP 202
                                         *************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (203 nodes)
Target sequences:                          1  (205 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 4.99
//
[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:

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