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.12686.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  lcl|FitnessBrowser__BFirm:BPHYT_RS14915  BPHYT_RS14915 phosphoserine amin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS14915  BPHYT_RS14915 phosphoserine aminotransferase
   #    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 ivnFsaGPaalpeevlekaqkelldfnglglsvmeisHRskefekvveeaesdlreLlnipdnyevlflq 70 
                                              ++nFsaGPaa+peevl++a++e+ld++g+g+svme+sHR kef++++eea  dlr+Ll++p ++++lflq
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915   3 VFNFSAGPAAMPEEVLRQAADEMLDWQGSGMSVMEMSHRGKEFMSIHEEALVDLRDLLEVPASHRILFLQ 72 
                                              58******************************************************************** PP

                                TIGR01364  71 GGattqfaavplnllkekkvadyivtGawskkalkeakkltkevkvvase.eekkyskipdeeelelked 139
                                              GG+ ++ a vp+nl+ +k  ad++vtG+ws+k++kea+k+++ v+ +as    + +++ p ++e++l++d
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915  73 GGGLGENAIVPMNLMGAKPRADFVVTGSWSQKSFKEAQKYGT-VHLAASGqTAEGFTRAPARSEWQLSDD 141
                                              ****************************************99.888888867899*************** PP

                                TIGR01364 140 aayvylcanetieGvefkelpevkkaplvaDlssdilsrkidvskygliyaGaqKniGpaGvtvvivrkd 209
                                               ayv+lc+neti+Gve  e+p+  ++plvaD ss+ilsr++d++kyg++++GaqKniG+aGvtvvivr+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915 142 PAYVHLCTNETIHGVETFEIPDLGDIPLVADASSHILSRPMDIAKYGVLFGGAQKNIGMAGVTVVIVRED 211
                                              ********************************************************************** PP

                                TIGR01364 210 llerakkelpsvldYkilaendslyntpptfaiyvlglvlkwlkekGGvkklekknqeKakllYeaides 279
                                              +l+ra++++ps +++k++aen+s+yntppt+aiy++glv+kwlk++GG++++e++n eK+kllY+a+d+s
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915 212 MLDRAQSICPSAFEWKTVAENNSMYNTPPTYAIYIAGLVFKWLKKQGGLAAMEARNVEKSKLLYDAVDTS 281
                                              ********************************************************************99 PP

                                TIGR01364 280 egfyknkvekkaRslmnvvFtlkkeelekeFlkeaeekglvslkGhrsvGGiRasiYnalpleevqaLvd 349
                                              + fy nkve+ +Rs+mnv+F l++e  ++ Fl+ a+++g+v+lkGh+svGG+RasiYna+ple+v+aLv+
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915 282 S-FYLNKVERGSRSRMNVPFFLADESRNEDFLAGAKARGMVQLKGHKSVGGMRASIYNAVPLEGVKALVE 350
                                              6.******************************************************************** PP

                                TIGR01364 350 fmkeFekk 357
                                              +mkeFe++
  lcl|FitnessBrowser__BFirm:BPHYT_RS14915 351 YMKEFEQR 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.92
//
[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