GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Dyella japonica UNC79MFTsu3.2

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate N515DRAFT_1821 N515DRAFT_1821 putative ABC transport system ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1821
          Length = 238

 Score =  134 bits (336), Expect = 4e-36
 Identities = 73/203 (35%), Positives = 124/203 (61%), Gaps = 2/203 (0%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           ++D ++ ++EGE   + G SGSGK+T + +   L   T G+  +DGV+++ ++D    ++
Sbjct: 21  LRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFTGGEYHLDGVEVSNLNDNARSKI 80

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163
           R +KI  +FQ+F L+P + V DN    +   G+ A ER+++ +DAL +VGL + A  YP 
Sbjct: 81  RNEKIGFIFQAFNLIPDLNVYDNVEVPLRYRGMKALERKQRIMDALERVGLASRAKHYPA 140

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           ELSGG +QRV +ARALA +P +LL DE    LD  +   + + L ++  +   TIV ++H
Sbjct: 141 ELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGVMELLEEIH-REGATIVMVTH 199

Query: 224 DLDEAMRIGDRIAIMQNGEVVQV 246
           D + A R    + ++ +G+VV +
Sbjct: 200 DPELATRAQRNVHVI-DGQVVDL 221


Lambda     K      H
   0.319    0.137    0.378 

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: 228
Number of extensions: 13
Number of successful extensions: 1
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: 400
Length of database: 238
Length adjustment: 27
Effective length of query: 373
Effective length of database: 211
Effective search space:    78703
Effective search space used:    78703
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