GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Methanosarcina mazei Go1

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_011033056.1 MM_RS05765 phosphoserine phosphatase SerB

Query= SwissProt::Q58989
         (211 letters)



>NCBI__GCF_000007065.1:WP_011033056.1
          Length = 235

 Score =  191 bits (486), Expect = 7e-54
 Identities = 96/208 (46%), Positives = 143/208 (68%)

Query: 4   KKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKDL 63
           + KLI+FD DSTL++ ETIDE+AR AGV  +V++IT  AM G L+FEQ+L +RV LL+ L
Sbjct: 10  ENKLIVFDMDSTLIDAETIDELARAAGVVSKVEEITNRAMHGDLDFEQALAERVRLLEGL 69

Query: 64  PIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRL 123
           P+E    A+ +I    GA E +  +K+RGY  A++SGGF IA  +I + LG+D+  +N L
Sbjct: 70  PVETALDAVNQINLMPGAAELVLYVKSRGYKTAMISGGFTIAAERIGKTLGIDFVVSNEL 129

Query: 124 IVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIA 183
           +V+DG L G+V G V + ++K ++ E++A++  +  E  V VGDGAND  +F+ AG  IA
Sbjct: 130 LVEDGYLLGEVVGPVTQSDSKAKVFEELAQLYNVRPEQCVVVGDGANDACIFEIAGFAIA 189

Query: 184 FCAKPILKEKADICIEKRDLREILKYIK 211
           F  KPIL+E AD+ I  +DLR ++  ++
Sbjct: 190 FNPKPILREYADVVITVKDLRAVIPVLE 217


Lambda     K      H
   0.314    0.136    0.358 

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: 135
Number of extensions: 3
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: 211
Length of database: 235
Length adjustment: 22
Effective length of query: 189
Effective length of database: 213
Effective search space:    40257
Effective search space used:    40257
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate WP_011033056.1 MM_RS05765 (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.3809737.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-80  255.4   0.2    2.7e-80  255.1   0.2    1.0  1  NCBI__GCF_000007065.1:WP_011033056.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000007065.1:WP_011033056.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.1   0.2   2.7e-80   2.7e-80      12     219 .]       9     216 ..       4     216 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.1 bits;  conditional E-value: 2.7e-80
                             TIGR00338  12 kkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkkveekl 84 
                                           +++kl+vfD+Dstli++E+Ide+a++aGv  +V+eiT+rAm+g+ldF+++l eRv+ll glpve++  + +++
  NCBI__GCF_000007065.1:WP_011033056.1   9 TENKLIVFDMDSTLIDAETIDELARAAGVVSKVEEITNRAMHGDLDFEQALAERVRLLEGLPVETALDAVNQI 81 
                                           6789********************************************************************* PP

                             TIGR00338  85 elteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesakaktl 157
                                           +l++G+ elv   k +gyk+a+iSGgF+++ae++ + Lg+d+v++N+L vedg l G+v g+++++++kak+ 
  NCBI__GCF_000007065.1:WP_011033056.1  82 NLMPGAAELVLYVKSRGYKTAMISGGFTIAAERIGKTLGIDFVVSNELLVEDGYLLGEVVGPVTQSDSKAKVF 154
                                           ************************************************************************* PP

                             TIGR00338 158 lkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilell 219
                                           ++l++ +++ +e++v+vGDGanD  +++ Ag+ iafn kp+l+e ad+vi  kdl++++++l
  NCBI__GCF_000007065.1:WP_011033056.1 155 EELAQLYNVRPEQCVVVGDGANDACIFEIAGFAIAFNPKPILREYADVVITVKDLRAVIPVL 216
                                           *********************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (219 nodes)
Target sequences:                          1  (235 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: 11.00
//
[ok]

This GapMind analysis is from Jul 25 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