GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpS in Bacteroides thetaiotaomicron VPI-5482

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>lcl|FitnessBrowser__Btheta:351279 BT1751 Glycine betaine transport
           ATP-binding protein (NCBI ptt file)
          Length = 408

 Score =  124 bits (311), Expect = 4e-33
 Identities = 74/230 (32%), Positives = 130/230 (56%), Gaps = 8/230 (3%)

Query: 8   ISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVT 67
           I K  G    + D +L++  G + V++G + +GK++L+R +  L  PT+G V ++G D+ 
Sbjct: 33  ILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTDIA 92

Query: 68  G------MPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHID 121
                  + +R + +AMV+Q F   P   V  NIA  L+L+G K  +   + + S   + 
Sbjct: 93  KVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQGVKKGEREQKAMESMQLVG 152

Query: 122 M--FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAA 179
           +  + ++  +ELSGG QQRV LARALA    ++L+DE    LD  +R ++++EL  L + 
Sbjct: 153 LKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTLQSK 212

Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVAR 229
            + T+V+ T +  EA+ LG   A++ +G+++Q G + E+   P +  V R
Sbjct: 213 MKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVER 262


Lambda     K      H
   0.318    0.133    0.375 

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: 214
Number of extensions: 11
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 1
Length of query: 363
Length of database: 408
Length adjustment: 30
Effective length of query: 333
Effective length of database: 378
Effective search space:   125874
Effective search space used:   125874
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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