Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF3740 PGA1_262p01440 BCCT transporter
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Phaeo:GFF3740 Length = 514 Score = 257 bits (656), Expect = 1e-72 Identities = 163/506 (32%), Positives = 270/506 (53%), Gaps = 17/506 (3%) Query: 49 QRFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLY-LLSVAVFLF 107 Q ++N P+F+ S IALF ++ ++ + FG + +L +A FL Sbjct: 11 QESRINKPLFLLSGGFIALFCVAALVNLDGLSALVDWGFNIAATYFGLYWQILLLATFLI 70 Query: 108 SMLFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFA-SPP- 165 ++ L G +G + PEF W +M+ + G +++A GEP+ HF SPP Sbjct: 71 GLV-LCILPGGRAIMG-GLATPEFTTFQWGSMIMCTLLAGGGVFWAAGEPIAHFLYSPPL 128 Query: 166 -EAEPLTIAAQREAMSVTFFHWGVHAWAIY-SVVGLSLAYFGYRYNLPLTVRSGLYPLLK 223 AE + AA A++ +F HWG AWAI S+ + L ++ Y LPL R+ LYP+ Sbjct: 129 YGAEGGSEAAVTPAIAQSFMHWGFLAWAILGSLSTVMLMHYHYEKGLPLAPRTLLYPVFG 188 Query: 224 E-GIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVT 282 + I+GPIG + D +I + G +GF LQ++ GL+ L GIP Q +++ + Sbjct: 189 DKAINGPIGVIADASSIIAVVAGTVGPIGFLGLQVSYGLSDLFGIPDVFATQFVVIGALV 248 Query: 283 AIATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDS---L 339 A+ TIS +TG+ +G+++LS+ N+ LA +L+++VL+ GPTG + F YL + + Sbjct: 249 ALYTISAMTGLSRGIQLLSKINVILAAVLLIYVLLAGPTGFIFGSFFSGFATYLGNFFQM 308 Query: 340 VLRTFNIYAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAM 399 L + + W+ WT+F+W W++ + P + MFIAR+SRGR++R + + + + Sbjct: 309 ALYRGDAAVFGAPGWLGWWTVFFWGWFMGYGPLMAMFIARVSRGRSIRSIIIMLSIIAPI 368 Query: 400 FTFLWMTVFGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSI 459 T W T+ G T I ++ A +L AL LP + S L ++L +I Sbjct: 369 VTNFWFTIIGGTGIAMELAEPGTVSAAFEGFNLPAALLAITNNLPMGFLVSILFLILTTI 428 Query: 460 FFVTSSDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLS--TGGLTALQSATIS 517 F T+ DS S VI + G+T + A+ R+FW G++A +L+S +GG++ LQS + Sbjct: 429 FVATTGDSMSYVISATMTKGDTPSTAV-RVFWGIAMGVMAVILISVGSGGVSKLQSFIVV 487 Query: 518 TALPFSLVMLILVWSLFVGMRADLAR 543 TA+P SL++L +W +R LA+ Sbjct: 488 TAVPVSLILLPSLWD---ALRITLAK 510 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: 987 Number of extensions: 58 Number of successful extensions: 8 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: 514 Length adjustment: 37 Effective length of query: 669 Effective length of database: 477 Effective search space: 319113 Effective search space used: 319113 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