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_134789831.1 BIBO1_RS17965 carbohydrate ABC transporter permease

Query= TCDB::Q72KX4
         (268 letters)



>NCBI__GCF_000182725.1:WP_134789831.1
          Length = 274

 Score =  131 bits (329), Expect = 2e-35
 Identities = 82/254 (32%), Positives = 135/254 (53%), Gaps = 6/254 (2%)

Query: 18  LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA--FRPKFQNSVVLAVSATL 75
           L P  ++ LTA+K PA+  L   W WP    W++F   W A  F     NS+ ++V A++
Sbjct: 23  LFPFAVMFLTAVK-PAQEVLSPNW-WPSTFRWQNFSEMWVATNFGNALLNSIYVSVIASV 80

Query: 76  LSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIGLYGSLFGLV 135
            + ++     Y ++++ F   G     +L    I    +++ LF+ + + GL  S+  + 
Sbjct: 81  GAIIISIPAAYAMSRFRFAAHGAFRQFLLVSQMISPIVLVLGLFRLLAAYGLIESVSAVG 140

Query: 136 LVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAIWQ 195
            V++ + I     + ++Y+  IP +L EA+ ++GAG       V LPL +PA  V AI+ 
Sbjct: 141 AVYMAFNIAFTVWMLQSYFDTIPRDLEEASWMEGAGRGKTLVKVFLPLCLPAIAVTAIFT 200

Query: 196 FTQIWNEFLFAVT-LTRPESQPITVALAQL-AGGEAVKWNLPMAGAILAALPTLLVYILL 253
           F   WNEF+ A+T L R ES  + + +  L AG   V+W+  MA   LA LP  +++I L
Sbjct: 201 FINAWNEFVVALTMLRRQESYTLPIQVFSLVAGRYTVEWHYVMAATFLATLPVAILFIWL 260

Query: 254 GRYFLRGLLAGSVK 267
            RY ++GL  G+VK
Sbjct: 261 QRYLIKGLALGAVK 274


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: 15
Number of successful extensions: 3
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: 274
Length adjustment: 25
Effective length of query: 243
Effective length of database: 249
Effective search space:    60507
Effective search space used:    60507
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.

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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