GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PA5503 in Bacteroides thetaiotaomicron VPI-5482

Align Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Query= TCDB::Q9HT70
         (335 letters)



>FitnessBrowser__Btheta:351279
          Length = 408

 Score =  161 bits (407), Expect = 3e-44
 Identities = 90/229 (39%), Positives = 137/229 (59%), Gaps = 2/229 (0%)

Query: 20  ALQPTRLNIQAGQIFGLIGHSGAGKSTLLRLINRLEEPSGGRILVEGEDVTAL-DAEGLR 78
           A++   L+I  G+IF ++G SG+GKSTLLR INRL  P+ G +++ G D+  + D E L+
Sbjct: 42  AVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIAKVSDKELLQ 101

Query: 79  RFRQRVGMIFQHFNLLSSKTVADNIAMPLRLAGGFSRAEVDARVSELLARVGLSDHARKY 138
             R+ + M+FQ+F LL  ++V  NIA  L L G   + E + +  E +  VGL  +  + 
Sbjct: 102 IRRKELAMVFQNFGLLPHRSVLHNIAFGLELQG-VKKGEREQKAMESMQLVGLKGYENQM 160

Query: 139 PAQLSGGQKQRVGIARALACRPSILLCDEATSALDPQTTASVLQLLAEINRELKLTIVLI 198
            ++LSGG +QRVG+ARALA  P +LL DEA SALDP     +   L  +  ++K TIV I
Sbjct: 161 VSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSKMKKTIVFI 220

Query: 199 THEMDVIRRVCDQVAVMDGGAIVEQGDVADVFLHPQHPTTRRFVFEAER 247
           TH++    ++ D++A+M  G IV+ G   ++   P +    RFV   +R
Sbjct: 221 THDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFVENVDR 269


Lambda     K      H
   0.322    0.138    0.393 

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: 252
Number of extensions: 11
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: 335
Length of database: 408
Length adjustment: 30
Effective length of query: 305
Effective length of database: 378
Effective search space:   115290
Effective search space used:   115290
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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