Alignments for a candidate for serB in Sedimenticola selenatireducens DSM 17993

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Sedimenticola selenatireducens DSM 17993

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_029133694.1 A3GO_RS0112575 phosphoserine phosphatase SerB

Query= SwissProt::Q9S281
         (410 letters)



>NCBI__GCF_000428045.1:WP_029133694.1
          Length = 403

 Score =  282 bits (721), Expect = 1e-80
 Identities = 174/400 (43%), Positives = 239/400 (59%), Gaps = 18/400 (4%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEGDLRAT 71
           +L+ + GKD PG+TA L   LA + ++++D+ Q V    + L  L+  PP    G +   
Sbjct: 5   ILLNVTGKDHPGLTASLTGVLADHRINILDLGQAVIHDHLSLGMLLEIPPEAQSGPVIKD 64

Query: 72  VHSWAESLKLQAEIISGIGDNR------PRGFGRSLVTVLGHPLTAEATAAIAARITESG 125
           +   A  L LQ    + I +         +G  R +VT+LG  L+A   A +A  ++  G
Sbjct: 65  LLFQAHQLGLQINF-TPIDEEAYETWVSHQGKLRYIVTLLGRKLSASTIAHVAQVVSGHG 123

Query: 126 SNIDRIFRLA---------KYPVTAVEFAVSGVETE--PLRTALATEAAALGVDIAVVAA 174
            NID I RL+          +    VEF V G   +   LR  L   ++   VD+A  A 
Sbjct: 124 MNIDGITRLSGRFSLRSANPHRRACVEFTVRGEPADLGALRQDLLEISSRDAVDVAFQAD 183

Query: 175 GLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHARVA 234
            L+RR +RL+V D+DSTLIQ EVI+  A  AG  D VA +T +AM+GE+DF +S   R+A
Sbjct: 184 DLYRRNRRLIVFDMDSTLIQVEVIDELAKAAGVGDAVAAITESAMQGEIDFNESFRRRMA 243

Query: 235 LLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLDFA 294
           LL GLD SV+  +   + +T GA  LI  LKRLGYQVG++SGGF+     LQE+LG+DF 
Sbjct: 244 LLKGLDESVLAGIAERLPITEGAERLISNLKRLGYQVGILSGGFSYFARHLQEKLGVDFF 303

Query: 295 QANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLNAA 354
            AN L+I +GRLTG V GEIV+ A KA L+++ A   G+ L Q +A+GDGANDL ML+ A
Sbjct: 304 SANELDIRNGRLTGEVKGEIVNGARKAELMQQMARDRGISLEQVIAVGDGANDLPMLSLA 363

Query: 355 GLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGITREEVE 394
           GLGVAF+AKPVVRE A  A++   LD +LYLLG+   EV+
Sbjct: 364 GLGVAFHAKPVVRENARHAISTLGLDGILYLLGVRDREVK 403


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: 398
Number of extensions: 14
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: 403
Length adjustment: 31
Effective length of query: 379
Effective length of database: 372
Effective search space:   140988
Effective search space used:   140988
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 WP_029133694.1 A3GO_RS0112575 (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.3861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.4e-85  272.4   0.1    1.8e-85  272.0   0.1    1.1  1  lcl|NCBI__GCF_000428045.1:WP_029133694.1  A3GO_RS0112575 phosphoserine pho


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029133694.1  A3GO_RS0112575 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  272.0   0.1   1.8e-85   1.8e-85       2     219 .]     178     395 ..     177     395 .. 0.98

  Alignments for each domain:
  == domain 1  score: 272.0 bits;  conditional E-value: 1.8e-85
                                 TIGR00338   2 iakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllk 70 
                                               +a + +  ++++++l+vfD+Dstli+ EvIde+ak+aGv+++V++iTe+Am+ge+dF+es+r R++llk
  lcl|NCBI__GCF_000428045.1:WP_029133694.1 178 VAFQADDLYRRNRRLIVFDMDSTLIQVEVIDELAKAAGVGDAVAAITESAMQGEIDFNESFRRRMALLK 246
                                               67777888999********************************************************** PP

                                 TIGR00338  71 glpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkl 139
                                               gl++++l  ++e+l++teG+e l+++Lk+ gy+v ++SGgF+++a +l+ekLg+d+  aN+L++++g+l
  lcl|NCBI__GCF_000428045.1:WP_029133694.1 247 GLDESVLAGIAERLPITEGAERLISNLKRLGYQVGILSGGFSYFARHLQEKLGVDFFSANELDIRNGRL 315
                                               ********************************************************************* PP

                                 TIGR00338 140 tGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivie 208
                                               tG+v+geiv+   ka+ +++++++ gisle+++avGDGanDl+m++ Aglg+af+akpv++e+a ++i+
  lcl|NCBI__GCF_000428045.1:WP_029133694.1 316 TGEVKGEIVNGARKAELMQQMARDRGISLEQVIAVGDGANDLPMLSLAGLGVAFHAKPVVRENARHAIS 384
                                               ********************************************************************* PP

                                 TIGR00338 209 kkdltdilell 219
                                               +  l +il+ll
  lcl|NCBI__GCF_000428045.1:WP_029133694.1 385 TLGLDGILYLL 395
                                               ******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (403 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.73
//
[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