GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0327 in Paraburkholderia bryophila 376MFSha3.1

Align Glucose transport system permease protein aka TT_C0327, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate H281DRAFT_02631 H281DRAFT_02631 carbohydrate ABC transporter membrane protein 1, CUT1 family

Query= TCDB::Q72KX3
         (369 letters)



>FitnessBrowser__Burk376:H281DRAFT_02631
          Length = 300

 Score =  105 bits (262), Expect = 2e-27
 Identities = 104/362 (28%), Positives = 149/362 (41%), Gaps = 91/362 (25%)

Query: 7   AFLVLLPSVLAVGVFVYGFIGQNLWVSLTDW-GKDPAQALALRPELRFVGLENYRELFTG 65
           AF  LLP      + V   I  ++ +S  +W G  P           F+GL NY ELF  
Sbjct: 27  AFFFLLPGCALFALCVIYPIFSSIALSFYNWDGMTPRT---------FIGLANYVELF-- 75

Query: 66  FVDVRFRQSVVNLIFFTLFFMAGSLGLGLLLALAVDKAPRGEGFFRTVFLFPMALSFVVT 125
             D  +     NLI+   F +A  LGL  L AL +++  +G    +++F  P  LS VV 
Sbjct: 76  HADTFYLALKNNLIWLVFFLLAPPLGL--LFALYLNQQIKGMRVVKSLFFAPFVLSGVVV 133

Query: 126 GTIWRWLLQPQGGVNVLPTLFGLPPLSFPWLATREQVLVFDWNRLPFYTALVVGLVLLYV 185
           G                                    LVF W   P +     GL+ L V
Sbjct: 134 G------------------------------------LVFSWFYDPAF-----GLLKLIV 152

Query: 186 AYTAYREGERRRALWGLASAGVLLLWAFAFGQGLRLLPYPEVHGFSLALVGVILAAVWQM 245
                                         G G+ +L  P    F     G++ AA+W  
Sbjct: 153 ------------------------------GHGIPVLGDPRTVTF-----GIVFAALWPQ 177

Query: 246 SGYTMALYLAGLRGIPVEVLEAARVDGASEWQLFRRVIFPMLAPITLSAMIVLGHIALKI 305
           + Y M LYL GL  I  EV+EAAR++GA  W L   VI P L P T  A+++    AL+ 
Sbjct: 178 TPYCMVLYLTGLTSINPEVVEAARMEGAKGWSLLWHVILPQLRPATFMAVVLTVIGALRS 237

Query: 306 FDLVFAMA-GLDYAPTDVPAIYMYLLAFRGNQFAKGAAIGILLLLLVAVVVVPYLATQLR 364
           FDL+  M+ G  +  + V A YMY  A +  +    A+I ++L  ++ V +V +L   LR
Sbjct: 238 FDLISVMSGGGPFDSSTVLAYYMYDQAIKYYREGYSASIAVVLFAIMLVYIVFHLRRMLR 297

Query: 365 KE 366
           +E
Sbjct: 298 EE 299


Lambda     K      H
   0.331    0.146    0.458 

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: 296
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 369
Length of database: 300
Length adjustment: 28
Effective length of query: 341
Effective length of database: 272
Effective search space:    92752
Effective search space used:    92752
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 49 (23.5 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