GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsC in Brucella inopinata BO1

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 WP_008509834.1 BIBO1_RS16195 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_000182725.1:WP_008509834.1
          Length = 275

 Score =  132 bits (333), Expect = 6e-36
 Identities = 83/269 (30%), Positives = 136/269 (50%), Gaps = 10/269 (3%)

Query: 5   LLYGFLLLMAGFFLLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWE--AFRPK 62
           LL   ++L+A F   P Y  ++T+ K      L  V  WP     +++       +F   
Sbjct: 12  LLVALIILVAVF---PFYYAIITSFKSGT--ALFQVDYWPKSLSLDNYTGVLTQGSFVRS 66

Query: 63  FQNSVVLAVSATLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFM 122
             NS+++A     +S L+     Y LA+  FRG GLL   IL     P  ++L  LF+ +
Sbjct: 67  LGNSLLVATVVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFELI 126

Query: 123 KSIGLYGSLFGLVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILP 182
           + +G++ +   LV  ++I+ +P    +   +  ++P E+ EAA +DGA  + I   V +P
Sbjct: 127 RFLGIFNTPLALVFSYMIFSLPFTVWVLTTFMRDLPVEIEEAAIVDGASPWVIITRVFMP 186

Query: 183 LSVPAFVVVAIWQFTQIWNEFLFAVTLTRPESQ-PITVALAQLAGGE--AVKWNLPMAGA 239
           L  PA V   +  F   WNEFLFA+T T   SQ  + VA+A L+G     + W   MA +
Sbjct: 187 LMWPALVTTGLLAFISAWNEFLFALTFTSSGSQRTVPVAIALLSGSSQFEIPWGNIMAAS 246

Query: 240 ILAALPTLLVYILLGRYFLRGLLAGSVKG 268
           ++  +P +++ ++  R  + GL AG VKG
Sbjct: 247 VIVTVPLVILVLIFQRRIVSGLTAGGVKG 275


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: 219
Number of extensions: 12
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: 275
Length adjustment: 25
Effective length of query: 243
Effective length of database: 250
Effective search space:    60750
Effective search space used:    60750
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 24 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