Alignments for a candidate for serB in Pseudomonas fluorescens FW300-N2E3

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Pseudomonas fluorescens FW300-N2E3

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate AO353_13070 AO353_13070 phosphoserine phosphatase

Query= SwissProt::Q9S281
         (410 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_13070
          Length = 404

 Score =  264 bits (675), Expect = 3e-75
 Identities = 167/392 (42%), Positives = 224/392 (57%), Gaps = 16/392 (4%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71
           +L+ I G DRPG+TA +   LA   V+++DI Q V    +    LV  P       +   
Sbjct: 5   VLINITGVDRPGLTAAITGVLAQGGVNILDIGQAVIHDTLSFGILVEIPDTEQGSSVLKD 64

Query: 72  VHSWAESLKLQAEIISGIGDNRP-----RGFGRSLVTVLGHPLTAEATAAIAARITESGS 126
           +   A  L  Q        ++       +G  R +VT+L   +TAE    +++   + G 
Sbjct: 65  ILFKAYELGQQVRFTPVSEEDYQLWVGAQGKKRHIVTLLTRKVTAEQLQRVSSITAKYGL 124

Query: 127 NIDRIFRLA-KYPVTA--------VEFAVSGVETEP--LRTALATEAAALGVDIAVVAAG 175
           NID I RL+ + P+          +EF+V G   +P  LR    + A  L VDIA     
Sbjct: 125 NIDHIDRLSGRMPLDTPADKGKGCIEFSVRGEAADPQALRAEFLSVAQELNVDIAFQEDS 184

Query: 176 LHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVAL 235
           L RR +RL V D+DSTLI+ EVI+  A  AG  ++V+E+T  AM GELDF  S   R+AL
Sbjct: 185 LFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEKVSEITERAMAGELDFRASFKERLAL 244

Query: 236 LAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFAQ 295
           L GLD SV+D + A +RLT GA TL   LKRLGY+  ++SGGFT     LQ +LG+D+  
Sbjct: 245 LKGLDVSVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGIDYVF 304

Query: 296 ANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAAG 355
           AN LE+VDG++TG     IVD   KA LLR  A   G+ L QT+A+GDGANDL ML  AG
Sbjct: 305 ANELEVVDGKVTGVAVEPIVDAQRKADLLRELAHKEGLRLEQTIAVGDGANDLPMLAIAG 364

Query: 356 LGVAFNAKPVVREAAHTAVNVPFLDTVLYLLG 387
           LGVAF AKP+V+++A  A++   LD VLYLLG
Sbjct: 365 LGVAFRAKPLVKQSAKQAISTLGLDGVLYLLG 396


Lambda     K      H
   0.319    0.135    0.374 

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: 378
Number of extensions: 21
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: 410
Length of database: 404
Length adjustment: 31
Effective length of query: 379
Effective length of database: 373
Effective search space:   141367
Effective search space used:   141367
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: 50 (23.9 bits)

Align candidate AO353_13070 AO353_13070 (phosphoserine phosphatase)
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.14616.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    5.6e-84  267.1   0.6    7.1e-84  266.8   0.6    1.1  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070  AO353_13070 phosphoserine phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070  AO353_13070 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  266.8   0.6   7.1e-84   7.1e-84       1     219 []     177     395 ..     177     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 266.8 bits;  conditional E-value: 7.1e-84
                                     TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreR 65 
                                                   dia +e+s ++++++l+vfD+Dstlie+EvIde+ak+aGv+e+VseiTerAm geldF++s++eR
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070 177 DIAFQEDSLFRRNRRLAVFDMDSTLIEAEVIDELAKAAGVGEKVSEITERAMAGELDFRASFKER 241
                                                   688999999******************************************************** PP

                                     TIGR00338  66 vkllkglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaN 130
                                                   ++llkgl+v++l+ +  +l+lteG+e l  +Lk+ gyk+a++SGgF+++a++l++kLg+d+vfaN
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070 242 LALLKGLDVSVLDSIGASLRLTEGAETLFAELKRLGYKTAILSGGFTYFAKQLQAKLGIDYVFAN 306
                                                   ***************************************************************** PP

                                     TIGR00338 131 rLevedgkltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafna 195
                                                   +Lev dgk tG    +ivd++ ka+ l +l++keg+ le+t+avGDGanDl+m++ Aglg+af a
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070 307 ELEVVDGKVTGVAVEPIVDAQRKADLLRELAHKEGLRLEQTIAVGDGANDLPMLAIAGLGVAFRA 371
                                                   ***************************************************************** PP

                                     TIGR00338 196 kpvlkekadiviekkdltdilell 219
                                                   kp +k+ a+++i++  l ++l+ll
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_13070 372 KPLVKQSAKQAISTLGLDGVLYLL 395
                                                   ***************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (404 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: 11.69
//
[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