GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens FW300-N2E3

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate AO353_10515 AO353_10515 3-phosphoserine/phosphohydroxythreonine aminotransferase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10515
          Length = 360

 Score =  362 bits (929), Expect = e-105
 Identities = 187/363 (51%), Positives = 247/363 (68%), Gaps = 4/363 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           MA+  NFS+GP  LP EVL QA +E  D+ G G SVME+SHR + F++VA + E+D RD+
Sbjct: 1   MARSHNFSAGPTALPMEVLTQAHEEFFDFAGTGMSVMEISHRCEVFMEVAYQTERDLRDI 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           L VPS YKVLF  GG   QFA VP+N+LG+K TADY+  G W+  AI+ A++YC   +  
Sbjct: 61  LQVPSEYKVLFLQGGASLQFAQVPMNLLGNKRTADYLHTGLWSGKAIEAARRYCDVRIV- 119

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
           A     G   +  + +W L+ NAAY+HY  NET+ G+   + PD  A +V   D  S++L
Sbjct: 120 ASGKESGFDRIPDVSDWNLNPNAAYLHYTENETVHGVQFVDAPDGLAPLV--CDACSSLL 177

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           S+PIDV+++G++YA AQKN+G AGLT+VI+   LL  A    P IL+Y+ + D  SM NT
Sbjct: 178 SKPIDVAKHGLVYAAAQKNMGVAGLTVVIIDPALLDGAQAFTPDILNYARITDAQSMLNT 237

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSD-FYRNDVAKANRSRMN 299
           P TF WYL+GL  KW+K  GG+  + ++NQ KAELLY  ID+SD FYRN V    RS  N
Sbjct: 238 PATFPWYLTGLTLKWIKRRGGLEALHRLNQTKAELLYRTIDDSDGFYRNSVRAPFRSINN 297

Query: 300 VPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFER 359
           VPF LAD+AL+K F++ +  AGL+ LKGH  VGG+RAS+YNA+ LE V+ALTDFM  F R
Sbjct: 298 VPFVLADAALEKTFVQLAEQAGLNGLKGHASVGGIRASLYNAVTLEAVEALTDFMKGFVR 357

Query: 360 RHG 362
            HG
Sbjct: 358 VHG 360


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: 380
Number of extensions: 18
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: 362
Length of database: 360
Length adjustment: 29
Effective length of query: 333
Effective length of database: 331
Effective search space:   110223
Effective search space used:   110223
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 AO353_10515 AO353_10515 (3-phosphoserine/phosphohydroxythreonine aminotransferase)
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.22665.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   7.2e-147  474.9   0.0   8.1e-147  474.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515  AO353_10515 3-phosphoserine/phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515  AO353_10515 3-phosphoserine/phosphohydroxythreonine aminotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  474.7   0.0  8.1e-147  8.1e-147       2     357 ..       5     358 ..       4     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 474.7 bits;  conditional E-value: 8.1e-147
                                     TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyev 66 
                                                   +nFsaGP+alp evl++a++e++df g+g+svmeisHR + f++v+ ++e+dlr++l++p++y+v
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515   5 HNFSAGPTALPMEVLTQAHEEFFDFAGTGMSVMEISHRCEVFMEVAYQTERDLRDILQVPSEYKV 69 
                                                   7**************************************************************** PP

                                     TIGR01364  67 lflqGGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipde 131
                                                   lflqGGa+ qfa+vp+nll +k++ady+ tG ws ka++ a+++++ v++vas +e+ +++ipd 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515  70 LFLQGGASLQFAQVPMNLLGNKRTADYLHTGLWSGKAIEAARRYCD-VRIVASGKESGFDRIPDV 133
                                                   *********************************************9.****************** PP

                                     TIGR01364 132 eelelkedaayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKni 196
                                                   ++++l+++aay+++++net++Gv+f ++p    aplv+D  s++ls++idv+k+gl+ya aqKn+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 134 SDWNLNPNAAYLHYTENETVHGVQFVDAP-DGLAPLVCDACSSLLSKPIDVAKHGLVYAAAQKNM 197
                                                   *****************************.6789******************************* PP

                                     TIGR01364 197 GpaGvtvvivrkdllerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkkl 261
                                                   G+aG+tvvi+   ll+ a++ +p++l+Y+ +++ +s++ntp+tf +y++gl+lkw+k++GG+++l
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 198 GVAGLTVVIIDPALLDGAQAFTPDILNYARITDAQSMLNTPATFPWYLTGLTLKWIKRRGGLEAL 262
                                                   ***************************************************************** PP

                                     TIGR01364 262 ekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhr 326
                                                   ++ nq+Ka+llY +id+s+gfy+n+v++  Rs+ nv+F l+++ lek+F++ ae++gl +lkGh 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 263 HRLNQTKAELLYRTIDDSDGFYRNSVRAPFRSINNVPFVLADAALEKTFVQLAEQAGLNGLKGHA 327
                                                   ***************************************************************** PP

                                     TIGR01364 327 svGGiRasiYnalpleevqaLvdfmkeFekk 357
                                                   svGGiRas+Yna++le+v+aL dfmk F + 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_10515 328 SVGGIRASLYNAVTLEAVEALTDFMKGFVRV 358
                                                   ***************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (360 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: 6.77
//
[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