GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdaB in Burkholderia phytofirmans PsJN

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate BPHYT_RS03145 BPHYT_RS03145 threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS03145 BPHYT_RS03145 threonine
           dehydratase
          Length = 507

 Score =  419 bits (1076), Expect = e-121
 Identities = 225/503 (44%), Positives = 325/503 (64%), Gaps = 6/503 (1%)

Query: 97  YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156
           YL   L + VYDVA E+ LE A  LS RL    Y+KRED Q VFSFK+RGAYN M+++S 
Sbjct: 6   YLKKTLTARVYDVARETELERAPNLSARLRNPVYLKREDNQPVFSFKVRGAYNKMAHISA 65

Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYG 213
           E L++GVITASAGNHAQGVAL+  R+   A IV+P TTPQ+K+DAVRA GG   +VV +G
Sbjct: 66  EALERGVITASAGNHAQGVALSAARMGVKAIIVVPVTTPQVKVDAVRAHGGPTVEVVQFG 125

Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGG 272
           +++ +A  HA++L ++  L ++ PFDDP VI GQGT+  EI  Q +  IHA+F+P+GGGG
Sbjct: 126 ESYSDAYEHAVKLQKERDLTFVHPFDDPYVIAGQGTVAMEILSQHQGPIHAIFVPIGGGG 185

Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332
           L AGVA + K + P  K+IGV+   + +M  SL  G RV L+ V  F+DG AV LVGE T
Sbjct: 186 LAAGVAAYVKSVRPEIKVIGVQTDDSCAMAASLKAGERVTLNEVGLFSDGTAVKLVGEET 245

Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392
           F  C E +D ++LV  D + AAIKDV+ + R++LE +G++A+AGA  Y E   I+N+ ++
Sbjct: 246 FRLCSEYLDDVLLVNTDALCAAIKDVFQDTRSVLEPAGSLAVAGAKQYAEREGIENQTLI 305

Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452
           AI SGANM+F ++  V E A +G  +EA+ A  + E++GSF+ F  LVG+ + TE  YR 
Sbjct: 306 AITSGANMNFDRMRFVAERAEVGEAREAVFAVTIPEERGSFRRFCELVGTRSVTEFNYRI 365

Query: 453 TSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS- 511
            ++  +A I   V +   S+  ++    ++    T++L+ +EL   H++++VGG + ++ 
Sbjct: 366 -ADANSAHIFVGVQIRNRSESAQIAGAFEAHGFATVDLTFDELSKQHIRYMVGGRSPLAH 424

Query: 512 DEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKN 571
           DE    F  PE+   L  FL + +P WNI+L  YRNQG   +S+L+G QVP +E + F  
Sbjct: 425 DERLFRFEFPERPGALMKFLSSMAPNWNISLFHYRNQGADYSSILVGIQVPDSENEAFNK 484

Query: 572 QADKLGYPYELDNYNEAFNLVVS 594
               LGYP   +  N  + L ++
Sbjct: 485 FLATLGYPNWEETQNPVYRLFLA 507


Lambda     K      H
   0.317    0.135    0.382 

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: 655
Number of extensions: 30
Number of successful extensions: 5
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: 595
Length of database: 507
Length adjustment: 36
Effective length of query: 559
Effective length of database: 471
Effective search space:   263289
Effective search space used:   263289
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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