Alignments for a candidate for dapC in Thiomicrospira microaerophila ASL8-2

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Thiomicrospira microaerophila ASL8-2

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate WP_044406153.1 NA59_RS00265 3-phosphoserine/phosphohydroxythreonine transaminase

Query= BRENDA::P23721
         (362 letters)



>NCBI__GCF_000934765.1:WP_044406153.1
          Length = 356

 Score =  412 bits (1060), Expect = e-120
 Identities = 205/362 (56%), Positives = 257/362 (70%), Gaps = 6/362 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           M++ FNFS+GPAMLP  V++QA+QEL +WN  G SVMEVSHR  E++ +A+ AE+  RD+
Sbjct: 1   MSRAFNFSAGPAMLPESVIRQAEQELLNWNNSGMSVMEVSHRSVEYMAMAKHAEQTLRDI 60

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           + +P NYKVLF HGG   QF+A+PLN+     +ADY D G W+A AIKEA+KYC     D
Sbjct: 61  MAIPDNYKVLFLHGGASLQFSAIPLNLTRPGESADYFDTGVWSAKAIKEAQKYC-----D 115

Query: 121 AKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTIL 180
             V     + +    EWQLS NA Y+HY PNETI G+     PD G DV + AD SSTIL
Sbjct: 116 VNVVCQNHQRIPDASEWQLSKNAKYVHYTPNETIGGLEFLSVPDVG-DVPLIADMSSTIL 174

Query: 181 SRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNT 240
           SRP+DVS++G+IYAGAQKNIGPAGL I IVREDL+G      P++L++ +  +N SMFNT
Sbjct: 175 SRPVDVSKFGMIYAGAQKNIGPAGLAIAIVREDLIGHQRDITPNLLNWQLCAENDSMFNT 234

Query: 241 PPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNV 300
           PPTF WYL+GLVF W+KA GG+  M   N+ KA  LY  ID+ +FY N V  + RS MNV
Sbjct: 235 PPTFGWYLAGLVFDWIKAQGGLNAMAHHNESKANKLYQAIDSIEFYANPVDASQRSWMNV 294

Query: 301 PFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
           PF L D +LD LFL ++  AGL+ LKGH++VGGMRASIYNAMP EGV AL DFM +F + 
Sbjct: 295 PFTLKDPSLDSLFLTQAKEAGLYNLKGHKLVGGMRASIYNAMPAEGVDALIDFMRDFAQA 354

Query: 361 HG 362
           HG
Sbjct: 355 HG 356


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: 413
Number of extensions: 16
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: 356
Length adjustment: 29
Effective length of query: 333
Effective length of database: 327
Effective search space:   108891
Effective search space used:   108891
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 WP_044406153.1 NA59_RS00265 (3-phosphoserine/phosphohydroxythreonine transaminase)
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.4172686.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.6e-158  513.2   0.0   1.8e-158  513.1   0.0    1.0  1  NCBI__GCF_000934765.1:WP_044406153.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000934765.1:WP_044406153.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  513.1   0.0  1.8e-158  1.8e-158       2     358 .]       5     355 ..       4     355 .. 0.99

  Alignments for each domain:
  == domain 1  score: 513.1 bits;  conditional E-value: 1.8e-158
                             TIGR01364   2 vnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGat 74 
                                           +nFsaGPa+lpe+v+++a++ell++n++g+svme+sHRs e+++++++ae+ lr+++ ipdny+vlfl GGa+
  NCBI__GCF_000934765.1:WP_044406153.1   5 FNFSAGPAMLPESVIRQAEQELLNWNNSGMSVMEVSHRSVEYMAMAKHAEQTLRDIMAIPDNYKVLFLHGGAS 77 
                                           8************************************************************************ PP

                             TIGR01364  75 tqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvaseeekkyskipdeeelelkedaayvylca 147
                                            qf+a+plnl++ ++ ady  tG+ws+ka+kea+k+++ v+vv ++    +++ipd +e++l+++a+yv+++ 
  NCBI__GCF_000934765.1:WP_044406153.1  78 LQFSAIPLNLTRPGESADYFDTGVWSAKAIKEAQKYCD-VNVVCQN----HQRIPDASEWQLSKNAKYVHYTP 145
                                           *************************************9.9999887....578******************** PP

                             TIGR01364 148 netieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelps 220
                                           neti G+ef ++p+v ++pl+aD+ss ilsr++dvsk+g+iyaGaqKniGpaG+++ ivr+dl++++++++p+
  NCBI__GCF_000934765.1:WP_044406153.1 146 NETIGGLEFLSVPDVGDVPLIADMSSTILSRPVDVSKFGMIYAGAQKNIGPAGLAIAIVREDLIGHQRDITPN 218
                                           ************************************************************************* PP

                             TIGR01364 221 vldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRs 293
                                           +l+++  aends++ntpptf++y++glv++w+k++GG+++++++n++Ka+ lY+aid+  +fy n+v++++Rs
  NCBI__GCF_000934765.1:WP_044406153.1 219 LLNWQLCAENDSMFNTPPTFGWYLAGLVFDWIKAQGGLNAMAHHNESKANKLYQAIDSI-EFYANPVDASQRS 290
                                           *********************************************************77.5************ PP

                             TIGR01364 294 lmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekkh 358
                                           +mnv+Ftlk+  l++ Fl++a+e+gl +lkGh+ vGG+RasiYna+p e+v aL+dfm++F+++h
  NCBI__GCF_000934765.1:WP_044406153.1 291 WMNVPFTLKDPSLDSLFLTQAKEAGLYNLKGHKLVGGMRASIYNAMPAEGVDALIDFMRDFAQAH 355
                                           *************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (358 nodes)
Target sequences:                          1  (356 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: 27.39
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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