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

GapMind for Amino acid biosynthesis

Alignments for a candidate for serC 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.19633.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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.50
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis