GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Paraburkholderia bryophila 376MFSha3.1

Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate H281DRAFT_02632 H281DRAFT_02632 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__Burk376:H281DRAFT_02632
          Length = 283

 Score =  166 bits (420), Expect = 5e-46
 Identities = 90/268 (33%), Positives = 159/268 (59%), Gaps = 5/268 (1%)

Query: 6   LYGFLLLMAGF-FLLPVYLVVLTALKEPARITLETVWQWP-HPPYWESFRTAWEA--FRP 61
           LY   L +A F +LLP+  V++T+++    ++    W WP H    +++  A        
Sbjct: 16  LYKASLPVALFVWLLPMLAVLITSIRSSDELSQGDYWAWPKHFALIDNYGAALTQTPMLH 75

Query: 62  KFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQF 121
            F NS+++ V + L + L+ S+ G+ LA + FRG+ ++    + G F+P Q ++IP+   
Sbjct: 76  YFANSMLITVPSVLGAILLASMAGFALATYRFRGNIVVLFTFVAGNFVPVQILMIPVRDM 135

Query: 122 MKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVIL 181
              +GL+ +++ L++ HV +     TL  RN+  ++P EL+EAAR++GA  + I+  ++L
Sbjct: 136 ALKVGLFNTVWALIIFHVAFQTGFCTLFLRNFIKQLPFELIEAARVEGASEWTIYARIVL 195

Query: 182 PLSVPAFVVVAIWQFTQIWNEFLFAVTLTR-PESQPITVALAQLAGGEAVKWNLPMAGAI 240
           PL  PA   + I  FT +WN++ +A+ LT+  ++ PITV +A L G     WNL  AG++
Sbjct: 196 PLIRPALAALGILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTAWNLVAAGSV 255

Query: 241 LAALPTLLVYILLGRYFLRGLLAGSVKG 268
           LAALP++L++  + ++F+ GL  G+ KG
Sbjct: 256 LAALPSVLMFFAMQKHFVAGLTFGASKG 283


Lambda     K      H
   0.330    0.146    0.461 

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: 266
Number of extensions: 15
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: 268
Length of database: 283
Length adjustment: 25
Effective length of query: 243
Effective length of database: 258
Effective search space:    62694
Effective search space used:    62694
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 47 (22.7 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