Alignments for a candidate for serB in Klebsiella variicola At-22

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Klebsiella variicola At-22

Align phosphoserine phosphatase; EC 3.1.3.3 (characterized)
to candidate WP_012542919.1 KVAR_RS21965 phosphoserine phosphatase SerB

Query= CharProtDB::CH_024035
         (322 letters)



>NCBI__GCF_000025465.1:WP_012542919.1
          Length = 323

 Score =  566 bits (1458), Expect = e-166
 Identities = 286/323 (88%), Positives = 303/323 (93%), Gaps = 1/323 (0%)

Query: 1   MPN-ITWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKQRLTQYQSKL 59
           MPN +TWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGL+K+RLT +Q +L
Sbjct: 1   MPNSLTWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLNKRRLTDWQREL 60

Query: 60  GAAMVIVAAWCVEDYQVIRLAGSLTARATRLAHEAQLDVAPLGKIPHLRTPGLLVMDMDS 119
           GAA+VIVA+W VEDYQVIRLAGSLT RATRLAHEA LDVAPLGKIPHLRTPGLLVMDMDS
Sbjct: 61  GAALVIVASWVVEDYQVIRLAGSLTPRATRLAHEAGLDVAPLGKIPHLRTPGLLVMDMDS 120

Query: 120 TAIQIECIDEIAKLAGTGEMVAEVTERAMRGELDFTASLRSRVATLKGADANILQQVREN 179
           TAIQIECIDEIAKLAGTGE+V+EVTERAMRGELDFTASLR RVATLK ADA IL QVR+ 
Sbjct: 121 TAIQIECIDEIAKLAGTGELVSEVTERAMRGELDFTASLRQRVATLKDADATILLQVRDA 180

Query: 180 LPLMPGLTQLVLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNV 239
           LPLMPGL QLVLKLETLGWKVAIASGGFTFFAEYLRDKL L AV ANELEI DGK TGNV
Sbjct: 181 LPLMPGLAQLVLKLETLGWKVAIASGGFTFFAEYLRDKLHLDAVFANELEIRDGKLTGNV 240

Query: 240 IGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKA 299
           +GDIVDA+YKA TL +LA++YEIP AQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNE+A
Sbjct: 241 LGDIVDAKYKANTLRKLAEKYEIPTAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEQA 300

Query: 300 EVTIRHADLMGVFCILSGSLNQK 322
           EVTIRHADLMGVFCILSGS+NQK
Sbjct: 301 EVTIRHADLMGVFCILSGSMNQK 323


Lambda     K      H
   0.320    0.136    0.399 

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: 432
Number of extensions: 10
Number of successful extensions: 1
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: 322
Length of database: 323
Length adjustment: 28
Effective length of query: 294
Effective length of database: 295
Effective search space:    86730
Effective search space used:    86730
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: 48 (23.1 bits)

Align candidate WP_012542919.1 KVAR_RS21965 (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.23434.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    5.3e-97  309.7   0.0    6.5e-97  309.4   0.0    1.1  1  lcl|NCBI__GCF_000025465.1:WP_012542919.1  KVAR_RS21965 phosphoserine phosp


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000025465.1:WP_012542919.1  KVAR_RS21965 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.4   0.0   6.5e-97   6.5e-97       1     219 []      98     316 ..      98     316 .. 0.99

  Alignments for each domain:
  == domain 1  score: 309.4 bits;  conditional E-value: 6.5e-97
                                 TIGR00338   1 diakselskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkll 69 
                                               d+a + + ++l++ +l+v+D+Dst+i++E+IdeiaklaG++e Vse+TerAmrgeldF++slr+Rv++l
  lcl|NCBI__GCF_000025465.1:WP_012542919.1  98 DVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGELVSEVTERAMRGELDFTASLRQRVATL 166
                                               578888999************************************************************ PP

                                 TIGR00338  70 kglpvellkkveeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgk 138
                                               k++++ +l +v++ l+l++G+ +lv kL++ g+kva++SGgF+++ae+l++kL+ldavfaN+Le++dgk
  lcl|NCBI__GCF_000025465.1:WP_012542919.1 167 KDADATILLQVRDALPLMPGLAQLVLKLETLGWKVAIASGGFTFFAEYLRDKLHLDAVFANELEIRDGK 235
                                               ********************************************************************* PP

                                 TIGR00338 139 ltGkvegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadivi 207
                                               ltG+v g+ivd+++ka+tl kl+ek++i++++tva+GDGanDl+mikaAglgia++akp+++e+a+++i
  lcl|NCBI__GCF_000025465.1:WP_012542919.1 236 LTGNVLGDIVDAKYKANTLRKLAEKYEIPTAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEQAEVTI 304
                                               ********************************************************************* PP

                                 TIGR00338 208 ekkdltdilell 219
                                               +++dl++++++l
  lcl|NCBI__GCF_000025465.1:WP_012542919.1 305 RHADLMGVFCIL 316
                                               **********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (323 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.56
//
[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