GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdaB in Pedobacter sp. GW460-11-11-14-LB5

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15860 CA265_RS15860 threonine
           dehydratase
          Length = 416

 Score =  250 bits (639), Expect = 7e-71
 Identities = 141/397 (35%), Positives = 216/397 (54%), Gaps = 7/397 (1%)

Query: 109 VAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDKGVITASA 168
           V   +PLE    LS     N Y+KRED Q V S+KLRGAYN +S+L ++ L  GV+ ASA
Sbjct: 21  VVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQDALINGVVCASA 80

Query: 169 GNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVLYGKTFDEAQTHALE 225
           GNHAQGVA + ++L     I MP  TP+ K+      GGD   VVL G TFD+    AL 
Sbjct: 81  GNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGDTFDDCLKEALA 140

Query: 226 LSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIAGVATFFKQIA 285
            S +    +IPPFDD  VI+GQ T+G EI   L D+  + +PVGGGGL +GV+ + K + 
Sbjct: 141 YSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIVMPVGGGGLASGVSAYMKTVK 200

Query: 286 PNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQELIDGMVL 345
           P  K++GVEP GA SM  ++  G    L  +D F DG AV  +G  T+  C+EL+D M L
Sbjct: 201 PEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGHITYEYCKELLDQMHL 260

Query: 346 VANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMDFSKL 405
           +    I   I  +Y+E   ++E +GA+++A      +  +I  + +V I SG N D  ++
Sbjct: 261 IPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKD--QITGKTVVCIVSGGNNDIERM 318

Query: 406 HKVTELAGLGSGKEALLATFMVEQQGSFKTFVG--LVGSLNFTELTYRFTSERKNALILY 463
            ++ E + L  G +        ++ G+ K FV   L    + T   +   + ++N   L 
Sbjct: 319 QEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRFEFIKKTNKENGPALV 378

Query: 464 RVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHL 500
            + +  ++D   +++ MK      + L+ ++ + ++L
Sbjct: 379 GIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYL 415


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: 574
Number of extensions: 30
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: 595
Length of database: 416
Length adjustment: 34
Effective length of query: 561
Effective length of database: 382
Effective search space:   214302
Effective search space used:   214302
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: 52 (24.6 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