GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Novosphingobium barchaimii LL02

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_059150771.1 V474_RS04385 phosphoserine phosphatase SerB

Query= SwissProt::Q12A06
         (236 letters)



>NCBI__GCF_001046635.1:WP_059150771.1
          Length = 293

 Score =  156 bits (395), Expect = 4e-43
 Identities = 89/211 (42%), Positives = 126/211 (59%), Gaps = 6/211 (2%)

Query: 25  KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84
           +L   DMDST+I  EC+DE+ D AG K  +AAITE AM+GE+ D++++L +RV LL+G+S
Sbjct: 80  RLFISDMDSTMIGQECIDELGDFAGLKERIAAITERAMQGEL-DFEQALYERVGLLEGLS 138

Query: 85  VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144
            +++DE    R+R   GA  LV+  K  G + +LV+GGF  F D +   LG ++   N L
Sbjct: 139 TSAIDECLAARIRPMAGAKTLVETLKKLGCRTVLVTGGFHHFADPVAARLGFEHVVGNRL 198

Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204
           E  +G LTG +     G I D   K+  LL    ++G      +A GDGAND+PM+  A 
Sbjct: 199 EVANGKLTGGLE----GGIVDSAVKKATLLAEMAKMG-EGATCLATGDGANDIPMLEAAT 253

Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLLELV 235
             +AYHAKP+ R  A   IN G L  +L L+
Sbjct: 254 YGIAYHAKPKARIAANGWINRGDLTSVLRLL 284


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: 203
Number of extensions: 13
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: 293
Length adjustment: 25
Effective length of query: 211
Effective length of database: 268
Effective search space:    56548
Effective search space used:    56548
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_059150771.1 V474_RS04385 (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.1814663.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.2e-65  206.3   0.0      3e-65  205.9   0.0    1.1  1  NCBI__GCF_001046635.1:WP_059150771.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001046635.1:WP_059150771.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.9   0.0     3e-65     3e-65      14     219 .]      79     284 ..      71     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 205.9 bits;  conditional E-value: 3e-65
                             TIGR00338  14 kklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkveekle 85 
                                            +l++ D+Dst+i +E+Ide++  aG +e +++iTerAm+geldF+++l eRv ll gl+ + + +  + +++
  NCBI__GCF_001046635.1:WP_059150771.1  79 PRLFISDMDSTMIGQECIDELGDFAGLKERIAAITERAMQGELDFEQALYERVGLLEGLSTSaIDECLAARIR 151
                                           6899**********************************************************44555789*** PP

                             TIGR00338  86 lteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktll 158
                                            + G++ lv++Lk+ g++++++ GgF+ +a+ ++++Lg + v++NrLev +gkltG  eg ivd+ +k  tll
  NCBI__GCF_001046635.1:WP_059150771.1 152 PMAGAKTLVETLKKLGCRTVLVTGGFHHFADPVAARLGFEHVVGNRLEVANGKLTGGLEGGIVDSAVKKATLL 224
                                           *******************************************************************999999 PP

                             TIGR00338 159 kllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                             + k g + + ++a GDGanD++m++aA  gia++akp+ + +a+  i++ dlt++l ll
  NCBI__GCF_001046635.1:WP_059150771.1 225 AEMAKMG-EGATCLATGDGANDIPMLEAATYGIAYHAKPKARIAANGWINRGDLTSVLRLL 284
                                           8888887.67889********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (293 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: 13.29
//
[ok]

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

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:

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:

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:

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