GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRET1 in Pedobacter sp. GW460-11-11-14-LB5

Align Facilitated trehalose transporter Tret1; BmTRET1 (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter

Query= SwissProt::A9ZSY3
         (505 letters)



>FitnessBrowser__Pedo557:CA265_RS23325
          Length = 443

 Score =  186 bits (471), Expect = 2e-51
 Identities = 135/409 (33%), Positives = 200/409 (48%), Gaps = 36/409 (8%)

Query: 92  WVG---GLMPLAALVGGIVGGPLIEYLGRKKTIMGTAVPFTIGWMLIANAINVVMVFAGR 148
           W G   G + L A+VG ++ G + +  GRK  +M  A  F    + +A A N       R
Sbjct: 49  WEGFATGSLALGAMVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSR 108

Query: 149 VICGVCVGIVSLAFPVYIGETIQPEVRGALGLLPTAFGNTGILLAFLVGSYL-----DWS 203
              G+ VG+ S+  P+YI E   P+ RG L  +       GIL+  L+   L     D  
Sbjct: 109 FFSGIGVGMASMLSPMYIAELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNTGEDAW 168

Query: 204 NLAFFGAAIPVPFFLLMI-LTPETPRWYVSKARVQEARKSLRWLRGKNVNIEKEMRDLTI 262
              F   AIP   FL+ I + PE+PRW V K + ++A K L     K  N E     L  
Sbjct: 169 RWMFGLGAIPSGIFLIGISILPESPRWLVQKGKNEKALKVLN----KIGNHEFAADALKN 224

Query: 263 SQTESDRTGGNAFKQLFSKRYLPAVMISLGLMLFQQLTGINAVIFYAASIFQMSGSSVDE 322
            +    R      + +F+K Y PAVMI +GL +FQQ  GIN V  YA  +F+  G+S D+
Sbjct: 225 IEQTLQRKSNVEHESIFNKMYFPAVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDD 284

Query: 323 N-LASIIIGVVNFISTFIATMLIDRLGRKVLLYISS------VAMITTLLALGAYFYLKQ 375
             L ++ IG VN I T  A  L+D++GRK L+ I +        +I+ LLA G+      
Sbjct: 285 QLLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAVLYVLISQLLASGS------ 338

Query: 376 NHIDVTAYGWLPLACLVIYVLGFSIGFGPIPWLMLGEILPSKIRGTAASLATGFNWTCTF 435
                T   W  L+ + +Y    ++   P+ W+++ EI P+K+R  A + A    W   F
Sbjct: 339 -----TMVSWFLLSAIGVY----AVSLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYF 389

Query: 436 IVTKTFQNIIDAIYMHGTLWLFAVICIGGLLFVIFFVPETKGKSLEEIE 484
           ++  TF  + D +      +++A IC  G + +  FV ETKGK+LEEIE
Sbjct: 390 VLVFTFPILFDWL-KESIFYIYAAICTLGCIGIWKFVKETKGKTLEEIE 437


Lambda     K      H
   0.325    0.140    0.420 

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: 572
Number of extensions: 28
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 443
Length adjustment: 33
Effective length of query: 472
Effective length of database: 410
Effective search space:   193520
Effective search space used:   193520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 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:

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