GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TM1750 in Bacteroides thetaiotaomicron VPI-5482

Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate 353365 BT3839 ABC transporter ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9X272
         (328 letters)



>FitnessBrowser__Btheta:353365
          Length = 256

 Score =  125 bits (314), Expect = 1e-33
 Identities = 75/213 (35%), Positives = 120/213 (56%), Gaps = 3/213 (1%)

Query: 33  VDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLNDKEMKPY 92
           +  I+   + G+T  ++G+SG GK+ L + I+ LL P+ G++ ++G+++  +  KE K  
Sbjct: 17  LSNINASFENGKTNLIIGQSGSGKTVLMKCIVGLLTPEKGEVLYDGRNLVLMGKKEKKML 76

Query: 93  RKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTKKERRKRVEELLDMVGIGREFINS 152
           RK+M +IFQ    +L   M+V   +  PL +    T ++R KR    L+ V +  E  + 
Sbjct: 77  RKEMGMIFQS--AALFDSMSVLDNVMFPLNMFSNDTLRDRTKRAMFCLERVNL-TEAKDK 133

Query: 153 FPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQKMGISYLF 212
           FP E SGG Q+R+ IARA+ALNP+++ CDEP S LD      I DL+ +I Q+  ++ + 
Sbjct: 134 FPGEISGGMQKRVAIARAIALNPQYLFCDEPNSGLDPKTSLVIDDLIHDITQEYNMTTII 193

Query: 213 IAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIF 245
             H++  V  I  KV  +Y G     G  D IF
Sbjct: 194 NTHDMNSVLGIGEKVIYIYEGHKEWEGTKDDIF 226


Lambda     K      H
   0.321    0.142    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: 221
Number of extensions: 13
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: 328
Length of database: 256
Length adjustment: 26
Effective length of query: 302
Effective length of database: 230
Effective search space:    69460
Effective search space used:    69460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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