GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztB in Pseudomonas stutzeri RCH2

Align glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= CharProtDB::CH_011913
         (426 letters)



>FitnessBrowser__psRCH2:GFF3103
          Length = 394

 Score =  294 bits (752), Expect = 4e-84
 Identities = 173/409 (42%), Positives = 244/409 (59%), Gaps = 33/409 (8%)

Query: 20  DTRFRSITIQIVVLLLFLAGLVWLLNNAYVNLEAKGKDFNFSFLWTRAGYDLAQTLIPYS 79
           D R R+   Q++ +L  +A   +L +N   NL  +G    F FL   AG+ ++Q LI YS
Sbjct: 17  DPRIRAWVFQVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQHLIDYS 76

Query: 80  NDDTHFRALIEGLLNTLLVSVLGCILATILGTIIGVLRLSQNWLVARIMTVYVETFRNIP 139
             DT+ R    GLLNTLLVSV+G  LAT++G I+GV RLS NWL+ ++ T+Y+E FRNIP
Sbjct: 77  ESDTYGRVFWVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIP 136

Query: 140 LLLWILLMGTILAETRPVPKDFRLTEAMKAAGEEPKASMWFFDSVAVTNRGTNLPAPAFD 199
            LL I  +    A   P+P               P+ S+  +D V V NRG  +PAP+  
Sbjct: 137 PLLLIFFV--YFAVISPLPG--------------PRNSLSLWDVVFVNNRGVQMPAPSAG 180

Query: 200 HSLGVVDLGWNLPVSLNALAILAVMSASFWGWRRFMARAKAVQEATGTRPTTWW--PSLL 257
                    W   ++L  +A++AV+  + W        A+A + ATG     +W  P L 
Sbjct: 181 DGF------WAFWLAL-LVALVAVVVLNRW--------ARARRHATGRMFPVFWTSPGLF 225

Query: 258 ILFAPISALLYGLGFHLDYPQITKFDFTGGFQMLHSFTALLIALTLYTAAFIAEIVRAGI 317
           +    +   + G  F  + P++ +F+  GG+ ++    ++++AL++YTAAFI E VR+GI
Sbjct: 226 LAIPWLMTFIAGAPFTWEVPELQRFNIRGGWVVIPELVSIVVALSVYTAAFIGETVRSGI 285

Query: 318 QAISRGQTEAAYALGLRPGRTMSLVILPQALRVIVPPLISQFLNLTKNSSLAIAVSYMDL 377
           Q++S GQTEAA +LGLRPG+ + LVI+PQALRVIVPPL SQ+LNL KNSSLA A+ Y D+
Sbjct: 286 QSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTSQYLNLAKNSSLAAAIGYPDM 345

Query: 378 RGTLGGITLNQTGRELECMLLMMLIYLTISLTISSLMNLYNKSIKLKER 426
                G  LNQTG+ +E M + M +YL IS++IS LMN YNK I L ER
Sbjct: 346 VSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWYNKRIALIER 394


Lambda     K      H
   0.326    0.139    0.419 

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: 406
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: 426
Length of database: 394
Length adjustment: 31
Effective length of query: 395
Effective length of database: 363
Effective search space:   143385
Effective search space used:   143385
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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 (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