Alignments for a candidate for serB in Pseudomonas fluorescens FW300-N2C3

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Pseudomonas fluorescens FW300-N2C3

Align Phosphoserine phosphatase; PSP; PSPase; EC 3.1.3.3 (characterized)
to candidate AO356_20835 AO356_20835 phosphoserine phosphatase

Query= SwissProt::Q883R9
         (237 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_20835
          Length = 205

 Score =  379 bits (974), Expect = e-110
 Identities = 186/205 (90%), Positives = 198/205 (96%)

Query: 33  VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLADI 92
           VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKL+DI
Sbjct: 1   VEIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLSDI 60

Query: 93  QAVISTLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLITDETD 152
           Q VI+TL+PL+GA+EFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRL+TD++ 
Sbjct: 61  QEVIATLQPLDGAIEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLVTDDSG 120

Query: 153 RVVSYQLRQKDPKRQSVLAFKSLYYRIIAAGDSYNDTTMLGEADAGILFHAPDNVIREFP 212
           RV  YQLRQKDPKRQSVLAFKSLYYR+IAAGDSYNDTTMLGEADAGILFHAP+NVIREFP
Sbjct: 121 RVTGYQLRQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADAGILFHAPENVIREFP 180

Query: 213 QFPAVHTFDELKKEFIKASNRELVL 237
           QFPAVHTF ELK+EF+KASNR L L
Sbjct: 181 QFPAVHTFAELKQEFLKASNRHLSL 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: 251
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 AO356_20835 AO356_20835 (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.5811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
     6e-122  390.7   0.0   6.9e-122  390.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835  AO356_20835 phosphoserine phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835  AO356_20835 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.5   0.0  6.9e-122  6.9e-122       2     203 .]       2     203 ..       1     203 [. 0.99

  Alignments for each domain:
  == domain 1  score: 390.5 bits;  conditional E-value: 6.9e-122
                                       TIGR02137   2 evvtldlegvlvpeiwiavaektgiddlklttrdipdydvlmkqrlkileeenlklsdiqevi 64 
                                                     e+++ldlegvlvpeiwia+aektgi++l++ttrdipdydvlmkqrl+il+e++lklsdiqevi
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835   2 EIACLDLEGVLVPEIWIAFAEKTGIESLRATTRDIPDYDVLMKQRLRILDEHGLKLSDIQEVI 64 
                                                     79************************************************************* PP

                                       TIGR02137  65 atlkllegavefvdtlreeaqvvilsdtfqefaqplmkqlgfptllchklvvedsdrvkgyql 127
                                                     atl++l+ga efvd+lre++qvvilsdtf+ef+qplm+qlgfptllch+lv +ds rv gyql
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835  65 ATLQPLDGAIEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHRLVTDDSGRVTGYQL 127
                                                     *************************************************************** PP

                                       TIGR02137 128 rqkdqkrkvvkalkelyykviaagdsyndttmlkeadkgilfhapesvvaefpqleavktyee 190
                                                     rqkd+kr++v a+k+lyy+viaagdsyndttml ead+gilfhape+v++efpq++av+t++e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835 128 RQKDPKRQSVLAFKSLYYRVIAAGDSYNDTTMLGEADAGILFHAPENVIREFPQFPAVHTFAE 190
                                                     *************************************************************** PP

                                       TIGR02137 191 lkdkflkasdrsl 203
                                                     lk++flkas+r l
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20835 191 LKQEFLKASNRHL 203
                                                     *********9975 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: 5.00
//
[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