GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Caulobacter crescentus NA1000

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate CCNA_02182 CCNA_02182 phosphoserine phosphatase

Query= SwissProt::Q12A06
         (236 letters)



>FitnessBrowser__Caulo:CCNA_02182
          Length = 292

 Score =  179 bits (453), Expect = 7e-50
 Identities = 100/207 (48%), Positives = 132/207 (63%), Gaps = 5/207 (2%)

Query: 26  LIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVSV 85
           L+  DMDST+IN+EC+DE+AD AG KA+V+ ITE AMRGE++ ++ +LR+RV +LKG+ V
Sbjct: 79  LLIADMDSTIINVECLDELADFAGVKAQVSEITERAMRGELA-FEGALRERVGMLKGLGV 137

Query: 86  ASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVLE 145
           +++   Y  R+RLNPGA  LV+     G +  LVSGGFTFFT R+ +  G    R+N L 
Sbjct: 138 SALQACYDERVRLNPGAETLVRTMAKHGARCALVSGGFTFFTSRVAEAAGFHLNRANTLI 197

Query: 146 TTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAGL 205
             DG LTG + D     I   E K   L E    LG++P  A+A+GDGANDL M+  AGL
Sbjct: 198 ELDGALTGAVGD----PILGKEAKLAALREETAALGLTPADALAVGDGANDLAMIEAAGL 253

Query: 206 SVAYHAKPRVREQAMVAINEGGLDRLL 232
            VAY AKP V  QA   ++   L  LL
Sbjct: 254 GVAYRAKPIVAAQADAKVDHTDLTTLL 280


Lambda     K      H
   0.319    0.136    0.385 

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: 197
Number of extensions: 9
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: 236
Length of database: 292
Length adjustment: 25
Effective length of query: 211
Effective length of database: 267
Effective search space:    56337
Effective search space used:    56337
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate CCNA_02182 CCNA_02182 (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.28415.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    4.3e-66  208.7   0.1    5.7e-66  208.2   0.1    1.1  1  lcl|FitnessBrowser__Caulo:CCNA_02182  CCNA_02182 phosphoserine phospha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02182  CCNA_02182 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.2   0.1   5.7e-66   5.7e-66      10     217 ..      73     281 ..      66     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.2 bits;  conditional E-value: 5.7e-66
                             TIGR00338  10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkve. 81 
                                            ++ k+l++ D+Dst+i+ E++de+a  aGv+ +VseiTerAmrgel F+ +lreRv +lkgl v+ l+  + 
  lcl|FitnessBrowser__Caulo:CCNA_02182  73 ANRRKGLLIADMDSTIINVECLDELADFAGVKAQVSEITERAMRGELAFEGALRERVGMLKGLGVSALQACYd 145
                                           568899************************************************************8887752 PP

                             TIGR00338  82 eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesaka 154
                                           e+++l +G+e lv+++ ++g + a++SGgF++++ +++e  g     aN+L+  dg+ltG v  +i+ ++ak 
  lcl|FitnessBrowser__Caulo:CCNA_02182 146 ERVRLNPGAETLVRTMAKHGARCALVSGGFTFFTSRVAEAAGFHLNRANTLIELDGALTGAVGDPILGKEAKL 218
                                           789********************************************************************** PP

                             TIGR00338 155 ktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdile 217
                                             l + +   g+ +++ +avGDGanDl+mi+aAglg+a+ akp++  +ad++++++dlt +l+
  lcl|FitnessBrowser__Caulo:CCNA_02182 219 AALREETAALGLTPADALAVGDGANDLAMIEAAGLGVAYRAKPIVAAQADAKVDHTDLTTLLY 281
                                           ***********************************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (292 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: 8.53
//
[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