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_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1562
          Length = 384

 Score =  187 bits (474), Expect = 6e-52
 Identities = 104/240 (43%), Positives = 140/240 (58%), Gaps = 10/240 (4%)

Query: 29  LSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID 88
           LS  Q+  + G    + D SL I EGE   ++G SGSGKS+++R+L  L +P RG VL D
Sbjct: 3   LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62

Query: 89  GVDIAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERRE----K 144
           G D+  +        +R+ I +VFQ +AL PHMTV DN AFG+ +   A +  R     +
Sbjct: 63  GTDLLALP------AQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAAR 116

Query: 145 ALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQ 204
             D LR+V LE     YP +LSGG RQRV LARALA+ P +LL+DE F ALD  +R  ++
Sbjct: 117 VEDLLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLR 176

Query: 205 DELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
             L  LQ     T V ++HD DEA+ + DR+ +M  G + QVG P EI   PA  +V  F
Sbjct: 177 VWLRDLQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGF 236


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: 363
Number of extensions: 20
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: 400
Length of database: 384
Length adjustment: 31
Effective length of query: 369
Effective length of database: 353
Effective search space:   130257
Effective search space used:   130257
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: 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 (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