Alignments for a candidate for dapC in Burkholderia phytofirmans PsJN

GapMind for Amino acid biosynthesis

Alignments for a candidate for dapC in Burkholderia phytofirmans PsJN

Align phosphoserine transaminase (EC 2.6.1.52) (characterized)
to candidate BPHYT_RS14915 BPHYT_RS14915 phosphoserine aminotransferase

Query= BRENDA::P23721
         (362 letters)



>FitnessBrowser__BFirm:BPHYT_RS14915
          Length = 360

 Score =  400 bits (1027), Expect = e-116
 Identities = 194/358 (54%), Positives = 261/358 (72%), Gaps = 1/358 (0%)

Query: 3   QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62
           ++FNFS+GPA +P EVL+QA  E+ DW G G SVME+SHRGKEF+ + EEA  D RDLL 
Sbjct: 2   RVFNFSAGPAAMPEEVLRQAADEMLDWQGSGMSVMEMSHRGKEFMSIHEEALVDLRDLLE 61

Query: 63  VPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAK 122
           VP+++++LF  GGG G+ A VP+N++G K  AD+V  G W+  + KEA+KY T ++  + 
Sbjct: 62  VPASHRILFLQGGGLGENAIVPMNLMGAKPRADFVVTGSWSQKSFKEAQKYGTVHLAASG 121

Query: 123 VTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSR 182
            T +G        EWQLSD+ AY+H C NETI G+   E PD G D+ + AD SS ILSR
Sbjct: 122 QTAEGFTRAPARSEWQLSDDPAYVHLCTNETIHGVETFEIPDLG-DIPLVADASSHILSR 180

Query: 183 PIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPP 242
           P+D+++YGV++ GAQKNIG AG+T+VIVRED+L +A   CPS  ++  + +N SM+NTPP
Sbjct: 181 PMDIAKYGVLFGGAQKNIGMAGVTVVIVREDMLDRAQSICPSAFEWKTVAENNSMYNTPP 240

Query: 243 TFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPF 302
           T+A Y++GLVFKWLK  GG+A M+  N +K++LLY  +D S FY N V + +RSRMNVPF
Sbjct: 241 TYAIYIAGLVFKWLKKQGGLAAMEARNVEKSKLLYDAVDTSSFYLNKVERGSRSRMNVPF 300

Query: 303 QLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERR 360
            LAD + ++ FL  + A G+  LKGH+ VGGMRASIYNA+PLEGVKAL ++M EFE+R
Sbjct: 301 FLADESRNEDFLAGAKARGMVQLKGHKSVGGMRASIYNAVPLEGVKALVEYMKEFEQR 358


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: 390
Number of extensions: 11
Number of successful extensions: 2
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 BPHYT_RS14915 BPHYT_RS14915 (phosphoserine 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.355625.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   2.7e-158  512.5   0.0     3e-158  512.3   0.0    1.0  1  FitnessBrowser__BFirm:BPHYT_RS14915  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__BFirm:BPHYT_RS14915  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.3   0.0    3e-158    3e-158       1     357 [.       3     358 ..       3     359 .. 0.99

  Alignments for each domain:
  == domain 1  score: 512.3 bits;  conditional E-value: 3e-158
                            TIGR01364   1 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflqGGat 74 
                                          ++nFsaGPaa+peevl++a++e+ld++g+g+svme+sHR kef++++eea  dlr+Ll++p ++++lflqGG+ 
  FitnessBrowser__BFirm:BPHYT_RS14915   3 VFNFSAGPAAMPEEVLRQAADEMLDWQGSGMSVMEMSHRGKEFMSIHEEALVDLRDLLEVPASHRILFLQGGGL 76 
                                          58************************************************************************ PP

                            TIGR01364  75 tqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvase.eekkyskipdeeelelkedaayvylca 147
                                          ++ a vp+nl+ +k  ad++vtG+ws+k++kea+k+++ v+ +as    + +++ p ++e++l++d ayv+lc+
  FitnessBrowser__BFirm:BPHYT_RS14915  77 GENAIVPMNLMGAKPRADFVVTGSWSQKSFKEAQKYGT-VHLAASGqTAEGFTRAPARSEWQLSDDPAYVHLCT 149
                                          ************************************99.888888867899*********************** PP

                            TIGR01364 148 netieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkdllerakkelpsv 221
                                          neti+Gve  e+p+  ++plvaD ss+ilsr++d++kyg++++GaqKniG+aGvtvvivr+d+l+ra++++ps 
  FitnessBrowser__BFirm:BPHYT_RS14915 150 NETIHGVETFEIPDLGDIPLVADASSHILSRPMDIAKYGVLFGGAQKNIGMAGVTVVIVREDMLDRAQSICPSA 223
                                          ************************************************************************** PP

                            TIGR01364 222 ldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaidesegfyknkvekkaRslm 295
                                          +++k++aen+s+yntppt+aiy++glv+kwlk++GG++++e++n eK+kllY+a+d+s+ fy nkve+ +Rs+m
  FitnessBrowser__BFirm:BPHYT_RS14915 224 FEWKTVAENNSMYNTPPTYAIYIAGLVFKWLKKQGGLAAMEARNVEKSKLLYDAVDTSS-FYLNKVERGSRSRM 296
                                          ********************************************************996.************** PP

                            TIGR01364 296 nvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvdfmkeFekk 357
                                          nv+F l++e  ++ Fl+ a+++g+v+lkGh+svGG+RasiYna+ple+v+aLv++mkeFe++
  FitnessBrowser__BFirm:BPHYT_RS14915 297 NVPFFLADESRNEDFLAGAKARGMVQLKGHKSVGGMRASIYNAVPLEGVKALVEYMKEFEQR 358
                                          ***********************************************************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.23
//
[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