GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_21725 in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for D-Glucosamine, putative ATPase component (characterized)
to candidate 353365 BT3839 ABC transporter ATP-binding protein (NCBI ptt file)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2050
         (263 letters)



>FitnessBrowser__Btheta:353365
          Length = 256

 Score =  136 bits (343), Expect = 4e-37
 Identities = 82/235 (34%), Positives = 130/235 (55%), Gaps = 10/235 (4%)

Query: 13  LLDIRGLRKQYGPLEVLKGVDLSMQRGNVVTLIGSSGSGKTTLLRCVNMLEEFQGGQIML 72
           ++DIRGL K +    VL  ++ S + G    +IG SGSGKT L++C+  L   + G+++ 
Sbjct: 1   MIDIRGLYKSFEDKTVLSNINASFENGKTNLIIGQSGSGKTVLMKCIVGLLTPEKGEVLY 60

Query: 73  DGESIGYDDIDGKRVRHPEKVIARHRAMTGMAFQQFNLFPHLTALQNVTLGLLKVKKLPK 132
           DG ++    + GK+    EK + R     GM FQ   LF  ++ L NV   L        
Sbjct: 61  DGRNLV---LMGKK----EKKMLRKEM--GMIFQSAALFDSMSVLDNVMFPLNMFSNDTL 111

Query: 133 DEAVALAEKWLERVGLLERRDHFPGQLSGGQQQRVAIARAIAMNPSLMLFDEVTSALDPE 192
            +    A   LERV L E +D FPG++SGG Q+RVAIARAIA+NP  +  DE  S LDP+
Sbjct: 112 RDRTKRAMFCLERVNLTEAKDKFPGEISGGMQKRVAIARAIALNPQYLFCDEPNSGLDPK 171

Query: 193 LVGEVLNVIKGLAED-GMTMLLVTHEMRFAFEVSDKIVFMNQGRIEEQGPPKELF 246
               + ++I  + ++  MT ++ TH+M     + +K++++ +G  E +G   ++F
Sbjct: 172 TSLVIDDLIHDITQEYNMTTIINTHDMNSVLGIGEKVIYIYEGHKEWEGTKDDIF 226


Lambda     K      H
   0.320    0.138    0.392 

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: 171
Number of extensions: 10
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: 263
Length of database: 256
Length adjustment: 24
Effective length of query: 239
Effective length of database: 232
Effective search space:    55448
Effective search space used:    55448
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: 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