Alignments for a candidate for serB in Thiohalomonas denitrificans HLD2

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Thiohalomonas denitrificans HLD2

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_092991383.1 BLP65_RS00080 phosphoserine phosphatase SerB

Query= SwissProt::Q9S281
         (410 letters)



>NCBI__GCF_900102855.1:WP_092991383.1
          Length = 407

 Score =  272 bits (696), Expect = 1e-77
 Identities = 168/396 (42%), Positives = 232/396 (58%), Gaps = 22/396 (5%)

Query: 12  LLVKIFGKDRPGITAGLFDTLAAYSVDVVDIEQVVTRGRIVLCALVTEPPRGLEG----- 66
           +LV + G DRPGITA L   LA Y+V ++D+ Q V    + L  L+ E PR   G     
Sbjct: 5   VLVTVVGPDRPGITAALTGCLANYNVTILDVGQSVIHDTVSLGMLI-ELPRDAGGCLVFK 63

Query: 67  DLRATVHSWAESLKLQAEIISGIGDNR---PRGFGRSLVTVLGHPLTAEATAAIAARITE 123
           DL    H     L ++   +S     +    +G  R +VT+LG  +++   A +A  +  
Sbjct: 64  DLLLKAHEL--DLNVRFTPVSEEDYEQWVAAQGQSRHIVTLLGRQISSRHLARVAEVVAH 121

Query: 124 SGSNIDRIFRLA---------KYPVTAVEFAVSG--VETEPLRTALATEAAALGVDIAVV 172
            G NID I RL          +  + +VE ++ G   +   L       A AL +DIA+ 
Sbjct: 122 HGLNIDNITRLTGRISLRRPEEKRIASVELSIRGDVPDLTMLHAHFLETARALEIDIAIQ 181

Query: 173 AAGLHRRAQRLVVMDVDSTLIQDEVIELFAAHAGCEDEVAEVTAAAMRGELDFEQSLHAR 232
              ++RR +RLV  D+DSTLIQ EVI+  A  AG E+EVA +T +AM GELDF  S   R
Sbjct: 182 EDNIYRRNRRLVCFDMDSTLIQAEVIDELAREAGVEEEVAAITRSAMAGELDFADSFRKR 241

Query: 233 VALLAGLDASVVDKVRAEVRLTPGARTLIRTLKRLGYQVGVVSGGFTQVTDALQEQLGLD 292
           +ALL GLD SV+  +   + +T GA  LIR LKR GY+V ++SGGFT   + L+ +LG+D
Sbjct: 242 MALLEGLDESVLRDIAERLPITEGAERLIRNLKRFGYKVAILSGGFTFFAEHLRRKLGID 301

Query: 293 FAQANTLEIVDGRLTGRVTGEIVDRAGKARLLRRFAAAAGVPLSQTVAIGDGANDLDMLN 352
           +  AN L+I  G+LTG+V GEI+D   KA LL + AA  G+ L Q +A+GDGANDL ML+
Sbjct: 302 YVFANPLDIRQGKLTGKVKGEIIDGRRKAYLLHQLAAQEGISLEQVIAVGDGANDLPMLS 361

Query: 353 AAGLGVAFNAKPVVREAAHTAVNVPFLDTVLYLLGI 388
            AGLG+AF+AKPVV+E A  A+    LD +LYLLG+
Sbjct: 362 IAGLGIAFHAKPVVKEQAQHAITTLGLDAILYLLGM 397


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: 394
Number of extensions: 18
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: 407
Length adjustment: 31
Effective length of query: 379
Effective length of database: 376
Effective search space:   142504
Effective search space used:   142504
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_092991383.1 BLP65_RS00080 (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.7348.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.7e-89  283.5   0.1    7.3e-89  283.1   0.1    1.1  1  lcl|NCBI__GCF_900102855.1:WP_092991383.1  BLP65_RS00080 phosphoserine phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900102855.1:WP_092991383.1  BLP65_RS00080 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.1   0.1   7.3e-89   7.3e-89       1     219 []     177     395 ..     177     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 283.1 bits;  conditional E-value: 7.3e-89
                                 TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 
                                               dia +e++ ++++++lv+fD+Dstli++EvIde+a++aGveeeV++iT++Am geldF +s+r+R++ll
  lcl|NCBI__GCF_900102855.1:WP_092991383.1 177 DIAIQEDNIYRRNRRLVCFDMDSTLIQAEVIDELAREAGVEEEVAAITRSAMAGELDFADSFRKRMALL 245
                                               689999*************************************************************** PP

                                 TIGR00338  70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138
                                                gl++++l+ ++e+l++teG+e l+++Lk+ gykva++SGgF+++ae+l+ kLg+d+vfaN L++++gk
  lcl|NCBI__GCF_900102855.1:WP_092991383.1 246 EGLDESVLRDIAERLPITEGAERLIRNLKRFGYKVAILSGGFTFFAEHLRRKLGIDYVFANPLDIRQGK 314
                                               ********************************************************************* PP

                                 TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207
                                               ltGkv+gei+d + ka  l +l+ +egisle+++avGDGanDl+m++ Aglgiaf+akpv+ke+a+++i
  lcl|NCBI__GCF_900102855.1:WP_092991383.1 315 LTGKVKGEIIDGRRKAYLLHQLAAQEGISLEQVIAVGDGANDLPMLSIAGLGIAFHAKPVVKEQAQHAI 383
                                               ********************************************************************* PP

                                 TIGR00338 208 ekkdltdilell 219
                                                +  l +il+ll
  lcl|NCBI__GCF_900102855.1:WP_092991383.1 384 TTLGLDAILYLL 395
                                               *******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (407 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 9.05
//
[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