GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TT_C0326 in Azospirillum brasilense Sp245

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 AZOBR_RS25590 AZOBR_RS25590 sugar ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>FitnessBrowser__azobra:AZOBR_RS25590
          Length = 277

 Score =  141 bits (355), Expect = 2e-38
 Identities = 88/270 (32%), Positives = 139/270 (51%), Gaps = 8/270 (2%)

Query: 5   LLYGFLLL-MAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAW--EAFRP 61
           + +G L+L +  + + P    ++T+LK  A   L TV  WP  P   ++   +  + F  
Sbjct: 10  IAFGLLVLGIVAWAVFPFAWAIVTSLK--AGSALFTVEAWPSQPSLANYAAIFKEQPFGR 67

Query: 62  KFQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQF 121
              NS++ A +   LS  +  L  Y L +  FRG GLL  ++L     P  ++L  LF+ 
Sbjct: 68  NILNSLLAASAVVALSLGLAVLAAYALGRVRFRGRGLLLFVVLGVSMFPQVAVLSGLFEL 127

Query: 122 MKSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVIL 181
           ++ +GLY  +  LVL ++I+ +P    +   +  E+P EL EAA +DGAG F I   V L
Sbjct: 128 VRWLGLYNRIGSLVLSYLIFTLPFTVWVLTTFMRELPKELEEAAMVDGAGPFVIVTRVFL 187

Query: 182 PLSVPAFVVVAIWQFTQIWNEFLFAVTLTRPE---SQPITVALAQLAGGEAVKWNLPMAG 238
           PL  PA     +  F   WNEFLFA+T T  +   + P+ +AL   A    + W   MA 
Sbjct: 188 PLMGPALAATGLLAFIAAWNEFLFALTFTLTDDARTVPVAIALMSGASQYELPWGQIMAA 247

Query: 239 AILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           +++  +P + + +L  R  + GL AG+VKG
Sbjct: 248 SVVVTVPLIGLVLLFQRRIVSGLTAGAVKG 277


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: 231
Number of extensions: 13
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: 277
Length adjustment: 25
Effective length of query: 243
Effective length of database: 252
Effective search space:    61236
Effective search space used:    61236
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