GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Shewanella oneidensis MR-1

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate 201554 SO2410 phosphoserine aminotransferase (NCBI ptt file)

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__MR1:201554
          Length = 367

 Score =  410 bits (1053), Expect = e-119
 Identities = 212/364 (58%), Positives = 270/364 (74%), Gaps = 5/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           ++ I+NF +GPAMLPA V+K+AQQEL DWNGLG SVMEVSHRGKEFI + ++AE D R+L
Sbjct: 3   VSAIYNFCAGPAMLPAAVMKKAQQELLDWNGLGVSVMEVSHRGKEFIALTKQAEADLREL 62

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           +++P NY VLF HGGGRGQF+AV  N LG++  A Y+ +G W+++A+ EA+K       D
Sbjct: 63  MHIPQNYHVLFMHGGGRGQFSAVVNNFLGNQGRALYLVSGQWSSAALAEAQKLAGDAQID 122

Query: 121 AKVTVDG---LRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177
           +   V+    L AV      ++  +  Y+HYCPNET+DGI I +  D    +V  AD SS
Sbjct: 123 SLNIVEKHNCLNAVVLPDLHKIDADYRYVHYCPNETVDGIEIFDELDSPWPIV--ADLSS 180

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
           TI+SR IDVSRYG+IYAGAQKNIGP+GL+IVIVR+D+L   ++   SI+DY +  ++ SM
Sbjct: 181 TIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDMLTLPSLPQSSIMDYRLAVEHDSM 240

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           FNTPPTFAWYL+  VF WLK+ GGVA + KINQQKA++LY  ID + FY+N V  ANRS+
Sbjct: 241 FNTPPTFAWYLAAEVFAWLKSIGGVASIAKINQQKAQMLYACIDANPFYKNGVVAANRSQ 300

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV FQLAD +LD  FL+E+ A GL ALKGHR+VGGMRAS+YNAMPLEGV AL  FM EF
Sbjct: 301 MNVTFQLADESLDGAFLKEAEAVGLVALKGHRIVGGMRASLYNAMPLEGVAALVTFMNEF 360

Query: 358 ERRH 361
             +H
Sbjct: 361 AAKH 364


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: 386
Number of extensions: 7
Number of successful extensions: 3
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: 367
Length adjustment: 29
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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 201554 SO2410 (phosphoserine aminotransferase (NCBI ptt file))
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.17072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.8e-148  478.7   0.0   5.5e-148  478.5   0.0    1.0  1  lcl|FitnessBrowser__MR1:201554  SO2410 phosphoserine aminotransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201554  SO2410 phosphoserine aminotransferase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  478.5   0.0  5.5e-148  5.5e-148       1     358 []       6     364 ..       6     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 478.5 bits;  conditional E-value: 5.5e-148
                       TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGattqfaa 79 
                                     i+nF+aGPa+lp +v++kaq+elld+nglg+svme+sHR kef +++++ae dlreL++ip+ny+vlf+ GG+++qf+a
  lcl|FitnessBrowser__MR1:201554   6 IYNFCAGPAMLPAAVMKKAQQELLDWNGLGVSVMEVSHRGKEFIALTKQAEADLRELMHIPQNYHVLFMHGGGRGQFSA 84 
                                     69***************************************************************************** PP

                       TIGR01364  80 vplnllkekkvadyivtGawskkalkeakkltk..evkvvase.eekkyskipdeeelelkedaayvylcanetieGve 155
                                     v  n+l ++  a y+v+G+ws+ al+ea+kl    ++++++   +++  +++   +  +++ d+ yv++c net++G+e
  lcl|FitnessBrowser__MR1:201554  85 VVNNFLGNQGRALYLVSGQWSSAALAEAQKLAGdaQIDSLNIVeKHNCLNAVVLPDLHKIDADYRYVHYCPNETVDGIE 163
                                     *******************************9867555444442445556666678889999***************** PP

                       TIGR01364 156 fkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsvldYkilaendsly 234
                                     + ++   +  p+vaDlss i+sr+idvs+ygliyaGaqKniGp+G+++vivr+d+l   +   +s++dY+ ++e+ds++
  lcl|FitnessBrowser__MR1:201554 164 IFDEL-DSPWPIVADLSSTIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDMLTLPSLPQSSIMDYRLAVEHDSMF 241
                                     **998.7889********************************************************************* PP

                       TIGR01364 235 ntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslmnvvFtlkkeelekeFlke 313
                                     ntpptfa+y+++ v+ wlk+ GGv++++k nq+Ka++lY +id++  fykn v +++Rs+mnv+F+l++e l+  Flke
  lcl|FitnessBrowser__MR1:201554 242 NTPPTFAWYLAAEVFAWLKSIGGVASIAKINQQKAQMLYACIDANP-FYKNGVVAANRSQMNVTFQLADESLDGAFLKE 319
                                     *******************************************886.******************************** PP

                       TIGR01364 314 aeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                     ae+ glv+lkGhr+vGG+Ras+Yna+ple+v aLv+fm+eF++kh
  lcl|FitnessBrowser__MR1:201554 320 AEAVGLVALKGHRIVGGMRASLYNAMPLEGVAALVTFMNEFAAKH 364
                                     ******************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (367 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.27
//
[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