GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate Echvi_3354 Echvi_3354 threonine dehydratase

Query= SwissProt::P25306
         (595 letters)



>FitnessBrowser__Cola:Echvi_3354
          Length = 416

 Score =  247 bits (631), Expect = 6e-70
 Identities = 144/405 (35%), Positives = 231/405 (57%), Gaps = 8/405 (1%)

Query: 95  FQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNL 154
           FQ +++  +  + +V   +PL+  E+LS+  G   Y+KRED Q V S+K+RGAY+ +S+L
Sbjct: 6   FQGIIEA-SEALQEVLHPTPLQFNEQLSEEYGCRVYLKREDLQAVRSYKIRGAYHKISSL 64

Query: 155 SREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVL 211
           S EE  +GV+ ASAGNHAQGVA A ++L     I +P+TT   KI+ ++  G +   +VL
Sbjct: 65  SEEEKSRGVVCASAGNHAQGVAFACKKLGIKGTIFIPSTTSAQKINRMKLFGKEMVEIVL 124

Query: 212 YGKTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-DIHAVFIPVGG 270
            G T+D+A   A E  E+ G  ++ PFDDP VI+GQGTI  EI    +  +  +F+P+GG
Sbjct: 125 SGDTYDDAYQTAAEYCEERGAVFVHPFDDPKVIEGQGTIAKEILDDAEFPVDYLFLPIGG 184

Query: 271 GGLIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGE 330
           GG+ AGV+T+F+Q +P TK+IG EP GA SM  S+       L  +D F DG AV  VG 
Sbjct: 185 GGMAAGVSTYFEQSSPETKLIGTEPKGAPSMLTSIQNLKNTVLDEIDGFVDGAAVKKVGN 244

Query: 331 YTFAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNEN 390
            TF  C++ +D M+LV    I   I ++Y+    ++E +GA+ +A  + Y +  K+K +N
Sbjct: 245 ITFEICRKSLDEMLLVPEGRICTTILNLYNNEGIVVEPAGAMTLAALSLY-DKEKLKGKN 303

Query: 391 IVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTY 450
           +V + SG N D  +  ++ E + L  G +        ++ G+ K FV  +   +     +
Sbjct: 304 VVCVVSGGNNDIMRTAEIKERSLLYEGLKHYFMVQFPQRPGALKDFVSKILGPDDDIAYF 363

Query: 451 RFT--SERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHN 493
           +FT  + R+N   +  + +    +L  + + +K +      L+ N
Sbjct: 364 QFTKKNNRENGPAVVGIELKDPQNLPGIFDRLKENRFKYNYLNEN 408


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: 560
Number of extensions: 28
Number of successful extensions: 4
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.

Links

Downloads

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:

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