Alignments for a candidate for serB in Herbaspirillum autotrophicum IAM 14942

GapMind for Amino acid biosynthesis

Alignments for a candidate for serB in Herbaspirillum autotrophicum IAM 14942

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_050464489.1 AKL27_RS19290 phosphoserine phosphatase SerB

Query= SwissProt::Q12A06
         (236 letters)



>NCBI__GCF_001189915.1:WP_050464489.1
          Length = 291

 Score =  185 bits (470), Expect = 7e-52
 Identities = 101/212 (47%), Positives = 131/212 (61%), Gaps = 4/212 (1%)

Query: 21  LSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALL 80
           L+ + L+ FDMDSTLINIEC+DE+AD  GRKAEVAAITE AMRGE  DY +S+  RV LL
Sbjct: 72  LASYGLLVFDMDSTLINIECIDELADCVGRKAEVAAITERAMRGEEMDYDQSMIARVQLL 131

Query: 81  KGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTR 140
           +G++   +  VY  RL + PGA +LVQ  + AGLK  ++SGGF +F DR+R EL ID   
Sbjct: 132 RGLAARDLKRVYDERLTITPGARQLVQQARRAGLKTAIISGGFDYFADRLRAELEIDVAI 191

Query: 141 SNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMM 200
           SN L    G +TG M + P     + + K   +   C + G++    I  GDGANDL MM
Sbjct: 192 SNRLSMEHGYVTGGMDNPP----VNAQVKASTVKSLCAEWGVALSDTIVAGDGANDLQMM 247

Query: 201 GEAGLSVAYHAKPRVREQAMVAINEGGLDRLL 232
             AG+SV Y  K  V E+  + I    LD +L
Sbjct: 248 AIAGVSVGYRPKQIVAEKVDIQIAHLALDSVL 279


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: 180
Number of extensions: 7
Number of successful extensions: 2
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: 291
Length adjustment: 25
Effective length of query: 211
Effective length of database: 266
Effective search space:    56126
Effective search space used:    56126
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_050464489.1 AKL27_RS19290 (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.18743.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.8e-67  213.1   0.1    2.3e-67  212.8   0.1    1.0  1  lcl|NCBI__GCF_001189915.1:WP_050464489.1  AKL27_RS19290 phosphoserine phos


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001189915.1:WP_050464489.1  AKL27_RS19290 phosphoserine phosphatase SerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.8   0.1   2.3e-67   2.3e-67       7     217 ..      68     280 ..      65     282 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 2.3e-67
                                 TIGR00338   7 lskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrg.eldFkeslreRvkllkglpv 74 
                                               ++++l + +l+vfD+Dstli++E+Ide+a  +G + eV++iTerAmrg e+d+++s+  Rv+ll+gl++
  lcl|NCBI__GCF_001189915.1:WP_050464489.1  68 KRRVLASYGLLVFDMDSTLINIECIDELADCVGRKAEVAAITERAMRGeEMDYDQSMIARVQLLRGLAA 136
                                               567788999**************************************9459****************** PP

                                 TIGR00338  75 ellkkve.eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGk 142
                                                +lk+v+ e+l++t+G+++lv++ +++g+k+a+iSGgFd++a++l+++L++d++++NrL++e g  tG 
  lcl|NCBI__GCF_001189915.1:WP_050464489.1 137 RDLKRVYdERLTITPGARQLVQQARRAGLKTAIISGGFDYFADRLRAELEIDVAISNRLSMEHGYVTGG 205
                                               *****97368*********************************************************** PP

                                 TIGR00338 143 vegeivdesakaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkd 211
                                               +  ++v++++ka t+++l+ + g+ l +t++ GDGanDl+m++ Ag+ +++  k+++ ek di i +  
  lcl|NCBI__GCF_001189915.1:WP_050464489.1 206 MDNPPVNAQVKASTVKSLCAEWGVALSDTIVAGDGANDLQMMAIAGVSVGYRPKQIVAEKVDIQIAHLA 274
                                               ******************************************************************999 PP

                                 TIGR00338 212 ltdile 217
                                               l ++l 
  lcl|NCBI__GCF_001189915.1:WP_050464489.1 275 LDSVLG 280
                                               988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (291 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: 8.55
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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