GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sinorhizobium meliloti 1021

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate SMc01494 SMc01494 phosphoserine phosphatase

Query= SwissProt::Q12A06
         (236 letters)



>FitnessBrowser__Smeli:SMc01494
          Length = 295

 Score =  165 bits (418), Expect = 8e-46
 Identities = 101/226 (44%), Positives = 136/226 (60%), Gaps = 5/226 (2%)

Query: 9   GLVVNVATPDLKLSDFKLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISD 68
           G  ++VA  D +    + +  DMDST+I  EC+DE+A   G K +VAAIT  AM GEI+ 
Sbjct: 65  GAAIDVAVQDAESRRKRFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIA- 123

Query: 69  YKESLRQRVALLKGVSVASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTD 128
           ++ +L +RVALL+G+ V  + EV  TR+ L PG   L+   K  G    LVSGGFT FT 
Sbjct: 124 FEPALVERVALLQGLPVTVVAEVIATRITLTPGGRELIATMKAKGHYSALVSGGFTVFTG 183

Query: 129 RIRDELGIDYTRSNVLETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAI 188
            I ++LG D  R+N+L   +G LTG  V +P   I   + K   L++   +LGI+P   I
Sbjct: 184 PIAEKLGFDENRANILVEENGKLTGD-VARP---ILGKQAKVDALIDISERLGITPADVI 239

Query: 189 AMGDGANDLPMMGEAGLSVAYHAKPRVREQAMVAINEGGLDRLLEL 234
           A+GDGANDL M+  AG  VA HAKP V +QA + I+ G L  LL L
Sbjct: 240 AVGDGANDLGMLQLAGTGVALHAKPVVADQAKIRIDHGDLTALLYL 285


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: 189
Number of extensions: 9
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: 295
Length adjustment: 25
Effective length of query: 211
Effective length of database: 270
Effective search space:    56970
Effective search space used:    56970
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 SMc01494 SMc01494 (phosphoserine phosphatase)
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.26083.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    6.3e-69  217.9   0.8    7.5e-69  217.7   0.8    1.1  1  lcl|FitnessBrowser__Smeli:SMc01494  SMc01494 phosphoserine phosphata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc01494  SMc01494 phosphoserine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7   0.8   7.5e-69   7.5e-69       9     218 ..      75     285 ..      67     286 .. 0.96

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 7.5e-69
                           TIGR00338   9 kllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkvee 82 
                                            + k+ ++ D+Dst+i +E+Ide+a+++G +e+V++iT rAm+ge+ F+ +l eRv+ll+glpv  +++ ++ 
  lcl|FitnessBrowser__Smeli:SMc01494  75 AESRRKRFLIADMDSTMIGQECIDELAAEVGLKEKVAAITARAMNGEIAFEPALVERVALLQGLPVTvVAEVIAT 149
                                         456789999**********************************************************66777889 PP

                           TIGR00338  83 klelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktl 157
                                         +++lt+G +el+ ++k kg   a++SGgF+++++ ++ekLg d   aN L  e+gkltG+v  +i+ ++ak + l
  lcl|FitnessBrowser__Smeli:SMc01494 150 RITLTPGGRELIATMKAKGHYSALVSGGFTVFTGPIAEKLGFDENRANILVEENGKLTGDVARPILGKQAKVDAL 224
                                         *************************************************************************** PP

                           TIGR00338 158 lkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218
                                           + e+ gi +++++avGDGanDl m++ Ag g+a +akpv+ ++a+i i++ dlt++l+l
  lcl|FitnessBrowser__Smeli:SMc01494 225 IDISERLGITPADVIAVGDGANDLGMLQLAGTGVALHAKPVVADQAKIRIDHGDLTALLYL 285
                                         *********************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (295 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: 11.04
//
[ok]

This GapMind analysis is from Apr 09 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:

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