GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Sinorhizobium meliloti 1021

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate SMa1466 SMa1466 ABC transporter ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__Smeli:SMa1466
          Length = 371

 Score =  190 bits (482), Expect = 7e-53
 Identities = 121/360 (33%), Positives = 201/360 (55%), Gaps = 22/360 (6%)

Query: 42  LGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELR 101
           + V + SL +  GEI V++G SG GK+T ++++NRLI+PT G+V I+G D + I   +LR
Sbjct: 19  IAVDNVSLDLPTGEICVLLGPSGCGKTTTMKMINRLIQPTSGKVFINGKDTSTIDPIKLR 78

Query: 102 EVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLEN--YAH 159
               + I  V Q   L P+ TV +N     +L G   ++ R +A + L  VGL+   +  
Sbjct: 79  ----RTIGYVIQQIGLFPNKTVEENICVVPDLLGWDRRKSRARAKELLELVGLQPDLFLK 134

Query: 160 AYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIV 219
            YP ELSGG +QRVG+ RALA +P ++LMDE F A+DP+ R  +Q+E +K+Q + ++TI+
Sbjct: 135 RYPKELSGGQQQRVGVLRALAADPPVMLMDEPFGAIDPINREAIQEEFLKMQREIRKTII 194

Query: 220 FISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF---RGVDISQVFSA 276
           F+SHDLDEA+++ D+IAI ++G + Q   PDE+L  PAN ++  F    R +   ++ S 
Sbjct: 195 FVSHDLDEAVKMADKIAIFRSGRLEQYAAPDELLARPANSFIEDFLGSDRALKRLRLVSV 254

Query: 277 KDIARRSPVGLIRKTPGFGPRSALKLLQDEDREYGYVIERGNKFVGVVS--IDSLKAAL- 333
           +D       G I          AL+ ++       +V+        ++S  +  L++   
Sbjct: 255 RDAME---TGFITVRSSDSVEHALERMRSSRSAAVFVLNADGAPQSLLSEQVAELRSGTV 311

Query: 334 -SQAQGIEAALIDDPLVVDAQTPLSELLSHVGQAPCAVPVVDEEHQYVGIISKRMLLQAL 392
              A+ +++A+   P   D +  +S + +H    P  +P VDE  +  G++S R ++  L
Sbjct: 312 GDHAEPVKSAV---PTTGDLRQAVSIMFAH--DMP-LLPCVDEGGRMAGVMSYRSIVHYL 365


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: 16
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: 371
Length adjustment: 30
Effective length of query: 370
Effective length of database: 341
Effective search space:   126170
Effective search space used:   126170
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