Alignments for a candidate for serB in Dechloromonas agitata is5

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Dechloromonas agitata is5

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_027458322.1 K420_RS0112285 phosphoserine phosphatase SerB

Query= SwissProt::Q12A06
         (236 letters)



>NCBI__GCF_000519045.1:WP_027458322.1
          Length = 280

 Score =  237 bits (605), Expect = 2e-67
 Identities = 127/220 (57%), Positives = 158/220 (71%), Gaps = 5/220 (2%)

Query: 15  ATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLR 74
           A P  KLSDF LI FDMDSTLI IEC+DE+AD AG+KAEV+ +TEAAMRGEI DY+ESLR
Sbjct: 63  AQPGKKLSDFGLICFDMDSTLITIECIDELADFAGKKAEVSEVTEAAMRGEI-DYRESLR 121

Query: 75  QRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDEL 134
           +R+ALL G+    +  VY  RL L+ GA  L++AC++AGL+  ++SGGFT+FT+R+R EL
Sbjct: 122 RRLALLAGLDARVLARVYGERLLLSHGARELLEACQNAGLRTAILSGGFTYFTERLRIEL 181

Query: 135 GIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGA 194
           G D+  SN LE + G LTG++V    GDI D   K   +     +LG+   Q IA GDGA
Sbjct: 182 GFDFATSNELEISGGKLTGKVV----GDIVDASAKAHHIARLTDELGLRKEQVIACGDGA 237

Query: 195 NDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234
           NDL MM +AGLSVA+HAKP  R +A VAIN GGLD LL L
Sbjct: 238 NDLMMMAQAGLSVAFHAKPATRAKADVAINFGGLDSLLNL 277


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: 212
Number of extensions: 8
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: 280
Length adjustment: 24
Effective length of query: 212
Effective length of database: 256
Effective search space:    54272
Effective search space used:    54272
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 WP_027458322.1 K420_RS0112285 (phosphoserine phosphatase SerB)
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.23210.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.7e-73  231.8   0.1    4.5e-73  231.5   0.1    1.0  1  lcl|NCBI__GCF_000519045.1:WP_027458322.1  K420_RS0112285 phosphoserine pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000519045.1:WP_027458322.1  K420_RS0112285 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.5   0.1   4.5e-73   4.5e-73      11     218 ..      69     277 ..      61     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 231.5 bits;  conditional E-value: 4.5e-73
                                 TIGR00338  11 lkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 
                                               l+  +l++fD+Dstli++E+Ide+a  aG + eVse+Te Amrge+d++eslr R++ll gl++ +l +
  lcl|NCBI__GCF_000519045.1:WP_027458322.1  69 LSDFGLICFDMDSTLITIECIDELADFAGKKAEVSEVTEAAMRGEIDYRESLRRRLALLAGLDARVLAR 137
                                               56678************************************************************9999 PP

                                 TIGR00338  80 ve.eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegei 147
                                               v+ e+l l +G++el ++ +++g+++a++SGgF++++e+l+ +Lg d++ +N+Le++ gkltGkv g+i
  lcl|NCBI__GCF_000519045.1:WP_027458322.1 138 VYgERLLLSHGARELLEACQNAGLRTAILSGGFTYFTERLRIELGFDFATSNELEISGGKLTGKVVGDI 206
                                               97588999************************************************************* PP

                                 TIGR00338 148 vdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdil 216
                                               vd+saka+ + +l+ + g+ +e+++a GDGanDl m+++Agl +af+akp+ + kad++i+   l ++l
  lcl|NCBI__GCF_000519045.1:WP_027458322.1 207 VDASAKAHHIARLTDELGLRKEQVIACGDGANDLMMMAQAGLSVAFHAKPATRAKADVAINFGGLDSLL 275
                                               *************************************************************99998887 PP

                                 TIGR00338 217 el 218
                                               +l
  lcl|NCBI__GCF_000519045.1:WP_027458322.1 276 NL 277
                                               65 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (280 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: 7.06
//
[ok]

This GapMind analysis is from Apr 10 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