GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PfGW456L13_1896 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized)
to candidate H281DRAFT_03232 H281DRAFT_03232 carbohydrate ABC transporter membrane protein 2, CUT1 family

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1896
         (281 letters)



>FitnessBrowser__Burk376:H281DRAFT_03232
          Length = 283

 Score =  181 bits (459), Expect = 2e-50
 Identities = 98/266 (36%), Positives = 155/266 (58%), Gaps = 6/266 (2%)

Query: 20  TLLLAAAVYLIPLVVMLLTSFKSPEDIRTGNLLSWP---TVIDGIGWIKAWDVVGGYFWN 76
           TL +A  ++L+P++ +L+TS +S E++  GN   WP    + D          +  YFWN
Sbjct: 20  TLPIALLIWLLPMIAVLVTSIRSSEELSEGNYWGWPKHFALFDNYREALTTSPMLHYFWN 79

Query: 77  SVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKF 136
           SV ITVPAV+ S  + AM G+ L+++RFRG+   F   + G F+P Q +++P      + 
Sbjct: 80  SVLITVPAVIGSIALAAMAGFALAIYRFRGNSSLFATFVAGNFVPVQVLMIPVRDLSLQL 139

Query: 137 GLANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKILLPMSI 196
           G+ NT + L+L HV +   F  LF RN+   +P  LV+AAR++GA  +T+F +I+LP+  
Sbjct: 140 GVFNTVSALILFHVSFQTGFCALFLRNFIKQLPFELVEAARIEGANEWTVFFRIVLPLIR 199

Query: 197 PIVMVCLIWQFTQIWNDFLFGVVFASG-DAQPITVALNNLVNTSTGAKEYNVDMAAAMIA 255
           P +    I  FT +WND+ + +    G DA PITV +  L    T A  +N+  A +++A
Sbjct: 200 PALAALAILVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTA--WNLVSAGSILA 257

Query: 256 GLPTLLVYIFAGKYFLRGLTSGAVKG 281
            LP++ ++    K+F+ GLT GA KG
Sbjct: 258 ALPSVAMFFAMQKHFVAGLTFGATKG 283


Lambda     K      H
   0.329    0.143    0.447 

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: 229
Number of extensions: 16
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: 281
Length of database: 283
Length adjustment: 26
Effective length of query: 255
Effective length of database: 257
Effective search space:    65535
Effective search space used:    65535
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