GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcU in Streptacidiphilus oryzae TH49

Align GlcU, component of Glucose, mannose, galactose porter (characterized)
to candidate WP_084704737.1 BS73_RS17900 carbohydrate ABC transporter permease

Query= TCDB::Q97UY9
         (287 letters)



>NCBI__GCF_000744815.1:WP_084704737.1
          Length = 247

 Score =  106 bits (265), Expect = 4e-28
 Identities = 75/252 (29%), Positives = 123/252 (48%), Gaps = 13/252 (5%)

Query: 32  MLINGFKSNFEVLSTPVLVPPTKITFEAYVSVLLSLAKPLINSL---IIVIPTSFISAFL 88
           M+I   + + E+     L  P    +  +V V  +   PL ++L   +IV   + +   L
Sbjct: 1   MVITSLRPSNELRDNTFL--PHHFQWSTFVDVWKNQQVPLGDNLRVTLIVAACATVLVLL 58

Query: 89  GAMGAYFFYTLSYSFSRASSAISDVLFSLISLATFIPQEATLLP-LTRLIVSMGLLDSYI 147
            ++ A ++   +    R        LF L+ L T + Q A+L+  L R      LLD+  
Sbjct: 59  VSLPAAYYTARNRYRGRR-------LFLLLVLVTQMFQPASLVVGLYREFSQFNLLDTIW 111

Query: 148 GIIFALLIFYIPTGALLMSMFISVIPRSLIEAAKMDGTGDLKIFMKIVFPLSMPGFISTL 207
            +I     F +     +++ +I  IP  L EAA +DGTG L    ++  PL+MPG ++ +
Sbjct: 112 VLILVNAAFNLAFAIWILTAYIGSIPAELEEAAMIDGTGRLGAMFRVTLPLAMPGVVTAM 171

Query: 208 IFIIIQAWNNFFIPLVLVTTPGMKLTSIAVLSYSGAYGTLYNDTFAAGMVASIIPLAIFV 267
           IF  I AWN F + L L TTP  +  ++ + S+ GAYG  +N  FA  ++A I  + +F 
Sbjct: 172 IFTFISAWNEFIMGLTLTTTPSHQPLTVGIDSFIGAYGVAWNQMFAGSVIAIIPVIILFA 231

Query: 268 FLGRYFIRGLMA 279
           F+ R  + GL A
Sbjct: 232 FIERRVVSGLTA 243


Lambda     K      H
   0.330    0.144    0.417 

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: 216
Number of extensions: 14
Number of successful extensions: 1
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: 287
Length of database: 247
Length adjustment: 25
Effective length of query: 262
Effective length of database: 222
Effective search space:    58164
Effective search space used:    58164
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