GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdaB in Dyella japonica UNC79MFTsu3.2

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0565 N515DRAFT_0565
           threonine dehydratase
          Length = 523

 Score =  400 bits (1029), Expect = e-116
 Identities = 223/499 (44%), Positives = 305/499 (61%), Gaps = 6/499 (1%)

Query: 102 LASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDK 161
           LA+ VY+VA E+ LE A  LS RLG    +KRED+Q VFSFKLRGAYN M  L   +  +
Sbjct: 23  LAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLDAAQRAR 82

Query: 162 GVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYGKTFDE 218
           GVI ASAGNHAQGVALA  +L   A IVMP T PQ+KIDAVR LGG   +VVL G ++ +
Sbjct: 83  GVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGAWVEVVLAGDSYSD 142

Query: 219 AQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGGLIAGV 277
           AQ  A  L ++ G  ++ PFDDP VI GQ T+G EI RQ    +HAVF+PVGGGGL+AGV
Sbjct: 143 AQAEAARLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGGGLLAGV 202

Query: 278 ATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQ 337
           A + K + P  K+IGV+   + +M  SL +G RV L  V  FADG AV  VG  TFA CQ
Sbjct: 203 AAYIKALRPEVKVIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAETFALCQ 262

Query: 338 ELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASG 397
             +D M+ V  D I AAI+DV+ E R++ E SGA+A+AG   Y   +++ +  +VAI SG
Sbjct: 263 RHVDAMLRVDTDAICAAIRDVFQETRSVPEPSGALALAGLKQYAATHQLDDATLVAIVSG 322

Query: 398 ANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTSERK 457
           AN++F +L  V E A +G  +EA+ A  + E++GSF+ F   +G  + TE  YR   +  
Sbjct: 323 ANLNFDRLRFVAERAEVGEQREAVFAVTIPEERGSFRRFCATLGQRSITEFNYRI-GDAA 381

Query: 458 NALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS-DEIFG 516
           +A I   + + +  + E +     +     L+L+ +EL   HL+H++GG + ++ DE+  
Sbjct: 382 SAHIFVGIQIRQRDEREALTAAFAAEGFGVLDLTDDELAKLHLRHMIGGRSPLAHDELLY 441

Query: 517 EFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQADKL 576
            F  PE+   L  FL    P WNI+L  YRN G     +L+G QVP  E   F+    +L
Sbjct: 442 RFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYGRILVGIQVPAGERAMFEQFLAQL 501

Query: 577 GYPYELDNYNEAFNLVVSE 595
           GYP   ++ N A+ L++ E
Sbjct: 502 GYPCRDESGNPAYRLLLRE 520


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: 32
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: 523
Length adjustment: 36
Effective length of query: 559
Effective length of database: 487
Effective search space:   272233
Effective search space used:   272233
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 paper from 2022 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