GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Paraburkholderia bryophila 376MFSha3.1

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate H281DRAFT_03485 H281DRAFT_03485 osmoprotectant transport system ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__Burk376:H281DRAFT_03485
          Length = 372

 Score =  186 bits (471), Expect = 1e-51
 Identities = 129/372 (34%), Positives = 200/372 (53%), Gaps = 38/372 (10%)

Query: 39  GLSLGVKDA-SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISD 97
           G S  V D   + +  GEI V++G SG GK+T ++++NRLI+P+ G++ IDG D  +   
Sbjct: 13  GASAPVVDGIDMEVGAGEICVLLGPSGCGKTTTLKMINRLIQPSSGKIFIDGRDTDEFEV 72

Query: 98  AELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLE-- 155
            ELR    ++I  V Q   L P+MTV +N +    L G      + +A + +  V L+  
Sbjct: 73  VELR----RQIGYVIQQIGLFPNMTVEENISVVPRLLGWDKARAKRRAAELMEIVALDPS 128

Query: 156 NYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQ 215
            Y   YP +LSGG +QRVG+ARALA +P ++LMDE F A+DP+ R  +QDE +++Q + +
Sbjct: 129 TYLSRYPKDLSGGQQQRVGVARALATDPPVMLMDEPFGAIDPINRELIQDEFLRIQQQVK 188

Query: 216 RTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF---------FR 266
           +TI+F+SHD+DEA+++ DRIAI + G + Q  TPD IL  PA+ ++  F          R
Sbjct: 189 KTIMFVSHDIDEAVKMADRIAIFRGGRLEQFDTPDTILARPASPFIAGFVGADRALKRLR 248

Query: 267 GVDISQVFSAKDIARRSPVGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGVVSI 326
            V  S   SA D A R          G     A  LL+    E   +++   K  G +S 
Sbjct: 249 LVRASDALSACDCAAR---------VGDSSERARALLERHGVEQIVLLDAAGKPQGYLS- 298

Query: 327 DSLKAALSQAQGIEAALIDDPL------VVDAQTPLSELLSHVGQAPCAVPVVDEEHQYV 380
               A LS  +G   A    P+        D ++ +S + S +GQ+  A   VD+E ++V
Sbjct: 299 ---AAELSAIEGTLMAAHAKPVQGVARHSDDLRSVISSMFS-LGQSWLA--TVDDEGRFV 352

Query: 381 GIISKRMLLQAL 392
           G +++  ++  L
Sbjct: 353 GYVNQAHIVDML 364


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: 364
Number of extensions: 14
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: 372
Length adjustment: 30
Effective length of query: 370
Effective length of database: 342
Effective search space:   126540
Effective search space used:   126540
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