GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Phyllobacterium brassicacearum STM 196

Align Phosphoserine phosphatase; PSP; PSPase; O-phosphoserine phosphohydrolase; EC 3.1.3.3 (characterized)
to candidate WP_106710192.1 CU102_RS06440 phosphoserine phosphatase SerB

Query= SwissProt::Q12A06
         (236 letters)



>NCBI__GCF_003010955.1:WP_106710192.1
          Length = 295

 Score =  165 bits (418), Expect = 8e-46
 Identities = 99/208 (47%), Positives = 129/208 (62%), Gaps = 5/208 (2%)

Query: 25  KLIAFDMDSTLINIECVDEIADAAGRKAEVAAITEAAMRGEISDYKESLRQRVALLKGVS 84
           K++  DMDST+I  EC+DE+A+ AG + +VAAIT  AM GEI+ ++ +LR+RVALLKG+ 
Sbjct: 81  KILIADMDSTMIQQECIDELAEEAGLRDKVAAITARAMNGEIA-FEPALRERVALLKGLP 139

Query: 85  VASMDEVYRTRLRLNPGAARLVQACKDAGLKVLLVSGGFTFFTDRIRDELGIDYTRSNVL 144
            + +D+V  +R+ L PG   LV+  K  G    LVSGGFT FT RI D +G     +NVL
Sbjct: 140 YSVIDKVIASRITLMPGGPELVRTMKKHGAYTALVSGGFTVFTQRIADMIGFHENSANVL 199

Query: 145 ETTDGLLTGRMVDQPWGDICDGEEKRKMLLETCGQLGISPRQAIAMGDGANDLPMMGEAG 204
                 LTG  V +P   I   E K   L   C +  +SP++AIA+GDGANDL M+  AG
Sbjct: 200 IDNGIALTGE-VKKP---ILGREAKVAALTSICERFSLSPQEAIAVGDGANDLGMLQLAG 255

Query: 205 LSVAYHAKPRVREQAMVAINEGGLDRLL 232
             VA HAKP V  QA V I+ G L  LL
Sbjct: 256 TGVALHAKPSVAAQAKVRIDHGDLTALL 283


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: 192
Number of extensions: 10
Number of successful extensions: 4
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 WP_106710192.1 CU102_RS06440 (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.3072990.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-66  209.6   0.3    2.8e-66  209.3   0.3    1.1  1  NCBI__GCF_003010955.1:WP_106710192.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106710192.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.3   0.3   2.8e-66   2.8e-66       7     218 ..      73     285 ..      68     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.3 bits;  conditional E-value: 2.8e-66
                             TIGR00338   7 lskllkkkklvvfDlDstlieeEvIdeiaklaGveeeVseiTerAmrgeldFkeslreRvkllkglpvellkk 79 
                                           +++  + kk+++ D+Dst+i++E+Ide+a +aG  ++V++iT rAm+ge+ F+ +lreRv+llkglp ++++k
  NCBI__GCF_003010955.1:WP_106710192.1  73 QNQDSRRKKILIADMDSTMIQQECIDELAEEAGLRDKVAAITARAMNGEIAFEPALRERVALLKGLPYSVIDK 145
                                           45667899*************************************************************7766 PP

                             TIGR00338  80 .veeklelteGveelvkkLkekgykvaviSGgFdlvaeklkekLgldavfaNrLevedgkltGkvegeivdes 151
                                            ++++++l++G  elv+++k++g  +a++SGgF+++++++++ +g     aN L+ +  +ltG+v+ +i+  +
  NCBI__GCF_003010955.1:WP_106710192.1 146 vIASRITLMPGGPELVRTMKKHGAYTALVSGGFTVFTQRIADMIGFHENSANVLIDNGIALTGEVKKPILGRE 218
                                           15789*************************************************877779************* PP

                             TIGR00338 152 akaktllkllekegislektvavGDGanDlsmikaAglgiafnakpvlkekadiviekkdltdilel 218
                                           ak   l++++e+  +s+++ +avGDGanDl m++ Ag g+a +akp +  +a++ i++ dlt++l++
  NCBI__GCF_003010955.1:WP_106710192.1 219 AKVAALTSICERFSLSPQEAIAVGDGANDLGMLQLAGTGVALHAKPSVAAQAKVRIDHGDLTALLYI 285
                                           ***************************************************************9986 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: 15.54
//
[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