Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF2787 HP15_2731 choline/carnitine/betaine transporter
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Marino:GFF2787 Length = 494 Score = 241 bits (616), Expect = 5e-68 Identities = 160/501 (31%), Positives = 253/501 (50%), Gaps = 24/501 (4%) Query: 61 SVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSRYGEL 120 ++ I LFVG ++ + + G + + + + F + A SR G Sbjct: 3 TIGFILLFVGASIVDSGYVADLIGAGFAWTATYLGSFFQVLLLLTFFIAMGTALSRAGTA 62 Query: 121 KLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEA---EPLTIAAQRE 177 ++G D PE W++M+ + G ++FA GEP+ HF P A E + +A Sbjct: 63 RIGGLD-RPEIGRFRWLSMIMCTLLAGGGVFFAAGEPVYHFVVTPPAFDTEAGSASAVAP 121 Query: 178 AMSVTFFHWGVHAWAIY-SVVGLSLAYFGYRYNLPLTVRSGLYPLLKEG-IHGPIGHVVD 235 AM+ +F HWG AWA+ S+ L L Y PL R+ LYP+ E I G +G V+D Sbjct: 122 AMAQSFTHWGFLAWAVLGSLTALVLTRAHYGQGKPLQPRTLLYPVFGEKVIQGRLGGVID 181 Query: 236 IFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEK 295 F + + G +GF Q++ GL+ L G+P QL ++ V+ + S +TG+ K Sbjct: 182 AFCVIAVVAGTVGPIGFLATQMSFGLHELFGVPDGYGTQLTVLVVLAGVYMTSAMTGLHK 241 Query: 296 GVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRPWI 355 G+++LS N+ LA+++ + V GPT L + Q++G Y+ S P W+ Sbjct: 242 GIQLLSRFNVILALVIAGVIFVFGPTLFLANTYTQSMGEYVTSFFAMATMTAETAPAWWM 301 Query: 356 DSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAIY- 414 WT+F++AW+I ++P + +F+ARISRGRTVRE V AV + + T +W T+ G + IY Sbjct: 302 KWWTVFFFAWFIGYTPLMAVFVARISRGRTVREMVLAVAVLAPIATTIWFTLLGGSGIYH 361 Query: 415 -----VDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGS 469 D T A DV A L+VA + LP + +LL +IF T+ DS S Sbjct: 362 QLAGTFDLTEALNNFRFDV-ATLTVA-----QALPGGTWMAAAILLLTTIFVATTGDSMS 415 Query: 470 LVIDTIASGGETATPALQRIFWCSLSGIVAAVLL--STGGLTALQSATISTALPFSLVML 527 I + +G + P + R+FW ++AA+LL G + LQ + TA+P SL++L Sbjct: 416 YSIAMVGAGHDEPNPWI-RVFWGGAMALMAAILLYMGAGQIGVLQQFIVLTAIPVSLIIL 474 Query: 528 ILVWSLFVGMRADLARTQSPG 548 +W+ G +A LA + G Sbjct: 475 PSLWT---GPKAALAMAREQG 492 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: 948 Number of extensions: 60 Number of successful extensions: 5 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: 494 Length adjustment: 37 Effective length of query: 669 Effective length of database: 457 Effective search space: 305733 Effective search space used: 305733 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 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