GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sphingomonas indica Dd16

Align phosphoserine phosphatase; EC 3.1.3.3 (characterized)
to candidate WP_085219702.1 B9N75_RS13275 phosphoserine phosphatase SerB

Query= CharProtDB::CH_024035
         (322 letters)



>NCBI__GCF_900177405.1:WP_085219702.1
          Length = 291

 Score =  178 bits (451), Expect = 2e-49
 Identities = 107/240 (44%), Positives = 136/240 (56%), Gaps = 7/240 (2%)

Query: 82  SLTARATRLAHE---AQLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGE 138
           S + RA   A E   A +D+A  G+    R   LLV DMDST I +ECIDE+A  AG   
Sbjct: 48  SASPRAAEAALEPLRAHVDIAVQGEAG--RRKRLLVADMDSTVITVECIDELADFAGVRA 105

Query: 139 MVAEVTERAMRGELDFTASLRSRVATLKGADANILQQV-RENLPLMPGLTQLVLKLETLG 197
            VAEVTERAMRGE DF  +L  RVA LKG     L +   E + L PG   L   +   G
Sbjct: 106 RVAEVTERAMRGEFDFEGALEERVALLKGLPERTLARCYEERVKLTPGAKALAHTMRAHG 165

Query: 198 WKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLA 257
            +  + SGGFT+FA+ +  +       AN LE+ DG  TG  +  ++ AQ K + L   A
Sbjct: 166 ARCLLVSGGFTYFADRVAQRAGFDRAAANRLEVADGALTGTALPPVLGAQAKKQALIDEA 225

Query: 258 QEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEKAEVTIRHADLMGVFCILSG 317
               I L++T+A+GDGAND+PMI+ AGLG+AYH K  VN  A+V I H DL G    L G
Sbjct: 226 IAMSIDLSETMAVGDGANDIPMIETAGLGVAYHGKAAVNAAAQVRIAHNDL-GALLYLQG 284


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: 200
Number of extensions: 6
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: 322
Length of database: 291
Length adjustment: 27
Effective length of query: 295
Effective length of database: 264
Effective search space:    77880
Effective search space used:    77880
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_085219702.1 B9N75_RS13275 (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.3547366.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    2.3e-69  219.4   0.1      3e-69  219.0   0.1    1.1  1  NCBI__GCF_900177405.1:WP_085219702.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900177405.1:WP_085219702.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.0   0.1     3e-69     3e-69      10     218 ..      73     282 ..      65     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.0 bits;  conditional E-value: 3e-69
                             TIGR00338  10 llkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpve.llkkve 81 
                                             + k+l+v D+Dst+i+ E+Ide+a  aGv   V+e+TerAmrge dF+ +l+eRv+llkglp+  l++  e
  NCBI__GCF_900177405.1:WP_085219702.1  73 AGRRKRLLVADMDSTVITVECIDELADFAGVRARVAEVTERAMRGEFDFEGALEERVALLKGLPERtLARCYE 145
                                           56789*************************************************************4455567 PP

                             TIGR00338  82 eklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdesaka 154
                                           e+++lt+G++ l ++++ +g +  ++SGgF+++a++++++ g d ++aNrLev dg+ltG+   +++ ++ak 
  NCBI__GCF_900177405.1:WP_085219702.1 146 ERVKLTPGAKALAHTMRAHGARCLLVSGGFTYFADRVAQRAGFDRAAANRLEVADGALTGTALPPVLGAQAKK 218
                                           89*********************************************************************** PP

                             TIGR00338 155 ktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218
                                           + l   +    i+l +t+avGDGanD++mi++Aglg+a+++k +++ +a++ i ++dl ++l+l
  NCBI__GCF_900177405.1:WP_085219702.1 219 QALIDEAIAMSIDLSETMAVGDGANDIPMIETAGLGVAYHGKAAVNAAAQVRIAHNDLGALLYL 282
                                           **********************************************************999875 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: 18.43
//
[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