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.
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:
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