GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Escherichia coli BW25113

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 15031 b0907 phosphoserine aminotransferase (NCBI)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__Keio:15031
          Length = 362

 Score =  730 bits (1884), Expect = 0.0
 Identities = 362/362 (100%), Positives = 362/362 (100%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL
Sbjct: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD
Sbjct: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
           AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL
Sbjct: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT
Sbjct: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300
           PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV
Sbjct: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300

Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
           PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR
Sbjct: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360

Query: 361 HG 362
           HG
Sbjct: 361 HG 362


Lambda     K      H
   0.319    0.136    0.405 

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: 602
Number of extensions: 5
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: 362
Length of database: 362
Length adjustment: 29
Effective length of query: 333
Effective length of database: 333
Effective search space:   110889
Effective search space used:   110889
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: 49 (23.5 bits)

Align candidate 15031 b0907 (phosphoserine aminotransferase (NCBI))
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

# 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/TIGR01364.hmm
# target sequence database:        /tmp/gapView.23836.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01364  [M=358]
Accession:   TIGR01364
Description: serC_1: phosphoserine transaminase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.6e-158  511.7   0.0   5.1e-158  511.5   0.0    1.0  1  lcl|FitnessBrowser__Keio:15031  b0907 phosphoserine aminotransfe


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15031  b0907 phosphoserine aminotransferase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  511.5   0.0  5.1e-158  5.1e-158       1     358 []       4     361 ..       4     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 511.5 bits;  conditional E-value: 5.1e-158
                       TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaa 79 
                                     i+nFs+GPa+lp evl++aq+el d+nglg+svme+sHR kef +v+eeae+d+r+Lln+p+ny+vlf+ GG+++qfaa
  lcl|FitnessBrowser__Keio:15031   4 IFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVPSNYKVLFCHGGGRGQFAA 82 
                                     68***************************************************************************** PP

                       TIGR01364  80 vplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylcanetieGvefke 158
                                     vpln+l +k++ady+ +G+w++ a+keakk+++   + a+   +   ++    e++l+++aay+++c neti+G+ ++e
  lcl|FitnessBrowser__Keio:15031  83 VPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDE 161
                                     *********************************4444555588999********************************* PP

                       TIGR01364 159 lpevkk.aplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendslynt 236
                                     +p++   +++ aD+ss ilsr+idvs+yg+iyaGaqKniGpaG+t+vivr+dll++a+  +ps+ldY+il +n s++nt
  lcl|FitnessBrowser__Keio:15031 162 TPDFGAdVVVAADFSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
                                     ***998466668******************************************************************* PP

                       TIGR01364 237 pptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeae 315
                                     pptfa+y++glv+kwlk++GGv++++k nq+Ka+llY +id+s+ fy+n+v+k++Rs+mnv+F+l+++ l+k Fl+e+ 
  lcl|FitnessBrowser__Keio:15031 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSD-FYRNDVAKANRSRMNVPFQLADSALDKLFLEESF 318
                                     *****************************************996.********************************** PP

                       TIGR01364 316 ekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                     ++gl++lkGhr+vGG+RasiYna+ple+v+aL dfm eFe++h
  lcl|FitnessBrowser__Keio:15031 319 AAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRH 361
                                     ****************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (362 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.55
//
[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