GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpF in Bacteroides thetaiotaomicron VPI-5482

Align Hg2+-inhibitable aquaporin, AqpM (transports both water and glycerol as well as CO2) (Kozono et al., 2003; Araya-Secchi et al., 2011). Its 3-d structure has been determined to 1.7 Å. In AqpM, isoleucine replaces a key histidine residue found in the lumen of water channels, which becomes a glycine residue in aquaglyceroporins. As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies (characterized)
to candidate 354244 BT4718 putative aquaporin (NCBI ptt file)

Query= TCDB::Q9C4Z5
         (246 letters)



>FitnessBrowser__Btheta:354244
          Length = 222

 Score =  131 bits (329), Expect = 1e-35
 Identities = 76/230 (33%), Positives = 121/230 (52%), Gaps = 17/230 (7%)

Query: 13  IGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGLAFGFAIAASIYA 72
           IGT +LV  G GSA         G+       G+G +G       + LAFG ++ A  YA
Sbjct: 2   IGTMVLVLMGCGSAVFA------GSMAGTVGAGVGTVG-------VALAFGLSVVAMAYA 48

Query: 73  LGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLGAAFGSFIFLQCAGIGAATVGGL 132
           +G ISGCHINPA+T+G++   +  G++   Y++ Q++GA  GS I       G       
Sbjct: 49  IGGISGCHINPAITLGVFLSGRMNGKDAGMYMLFQVIGAIIGSAILYALVTTGGHDGPTA 108

Query: 133 GATAPFPGISYWQAMLAEVVGTFLLMITIMGIAVDERAPKGFAGIIIGLTVAGIITTLGN 192
             +  F      QA +AEVV TF+ ++ ++G    ++    FAG+ IGL++  +      
Sbjct: 109 TGSNGFGDGEMLQAFIAEVVFTFIFVLVVLGSTDPKKGAGAFAGLAIGLSLVLVHIVCIP 168

Query: 193 ISGSSLNPARTFGPYLNDMIFAGTDLWNYYSIYVIGPIVGAVLAALTYQY 242
           I+G+S+NPAR+ GP L    F G +  +   ++++ P VGA ++AL + Y
Sbjct: 169 ITGTSVNPARSIGPAL----FQGGEALSQLWLFIVAPFVGAAVSALVWNY 214


Lambda     K      H
   0.326    0.144    0.441 

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: 232
Number of extensions: 19
Number of successful extensions: 6
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: 246
Length of database: 222
Length adjustment: 23
Effective length of query: 223
Effective length of database: 199
Effective search space:    44377
Effective search space used:    44377
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 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