GapMind for catabolism of small carbon sources

 

Alignments for a candidate for betS in Rhodococcus qingshengii djl-6-2

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_050655916.1 C1M55_RS03105 BCCT family transporter

Query= SwissProt::G3XCN6
         (706 letters)



>NCBI__GCF_002893965.1:WP_050655916.1
          Length = 617

 Score =  447 bits (1151), Expect = e-130
 Identities = 232/513 (45%), Positives = 322/513 (62%), Gaps = 8/513 (1%)

Query: 56  PVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFS 115
           PVF+ +  VI   +   VI    A   F  +   I  G GW Y+LS   F+   L+   S
Sbjct: 14  PVFIPASIVIFALIAFAVIYAGTAADAFETLNNVISDGVGWWYILSATGFVIFALYCGIS 73

Query: 116 RYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPL---TI 172
           R G ++LG DD +PEF  LSW AMLF+AGMGIGL+++ V EP++H+ +PP A  +   T 
Sbjct: 74  RIGNIRLGRDDEQPEFGMLSWFAMLFSAGMGIGLVFYGVAEPLSHYVNPPVAGQIAGSTD 133

Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLL-KEGIHGPIG 231
           AA  +AM +T FHWG+HAWAIY VVGL LAY  YR   PL++R  L PLL +  I G IG
Sbjct: 134 AAANQAMELTLFHWGLHAWAIYVVVGLGLAYMTYRKGRPLSIRWLLEPLLGRARIEGKIG 193

Query: 232 HVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVT 291
           H +D+ AI GT+FG+ATSLGFG+ QI++GL+YL  +    ++ + ++ +VT +AT SVV+
Sbjct: 194 HAIDVVAIVGTLFGVATSLGFGVQQISAGLDYLGWVETDNWLVITIIVIVTGMATFSVVS 253

Query: 292 GVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEP 351
           GV KG++ LS  N+ LA  L LFVL++GPT  LM+ +VQN+G Y+ +L         +  
Sbjct: 254 GVTKGLKWLSNINMMLAAALALFVLILGPTLFLMQSWVQNLGGYVQALPELMLRTSPFAE 313

Query: 352 RPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNT 411
             W  +WT+FYW WW+SW+PFVGMFIARISRGRT+REFV  VL  P +   LW T+FGN+
Sbjct: 314 DGWQGAWTIFYWGWWMSWAPFVGMFIARISRGRTIREFVFGVLLAPTLVGSLWFTIFGNS 373

Query: 412 AIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLV 471
            I          L      D + +LF   + LP   ++S LA++++  FFVTS+DSGS+V
Sbjct: 374 GILRQRN-EGTMLDASGAVDTNTSLFTLLDGLPLGTISSVLAIVVIVFFFVTSADSGSIV 432

Query: 472 IDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGG---LTALQSATISTALPFSLVMLI 528
           ID +A+GG   T  + R++W  LSG  AAVLL  GG   LTALQ+  I+TA+PFS++M++
Sbjct: 433 IDILATGGSLETSKITRVYWTFLSGAAAAVLLIVGGSGSLTALQTVAIATAVPFSVIMVL 492

Query: 529 LVWSLFVGMRADLARTQSPGSLGPRAYPASGVP 561
              S+    R ++A       +   A  ++ VP
Sbjct: 493 ACLSMLKAFRYEVASAPRYLRVSTNASASTDVP 525


Lambda     K      H
   0.326    0.139    0.422 

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: 1148
Number of extensions: 71
Number of successful extensions: 6
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: 706
Length of database: 617
Length adjustment: 38
Effective length of query: 668
Effective length of database: 579
Effective search space:   386772
Effective search space used:   386772
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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