Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_057687532.1 ABB28_RS16900 BCCT family transporter
Query= SwissProt::G3XCN6 (706 letters) >NCBI__GCF_001431535.1:WP_057687532.1 Length = 517 Score = 431 bits (1109), Expect = e-125 Identities = 218/498 (43%), Positives = 309/498 (62%), Gaps = 9/498 (1%) Query: 52 KVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLF 111 ++N VF S I + + V+ P+ +E Q + + FGW Y+L + L +L+ Sbjct: 13 RLNGFVFFSSALSIGVLGLLTVLNPQASEHWLQVAQAQVSAAFGWWYMLLIVACLGFVLW 72 Query: 112 LAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLT 171 LAFSRYG ++LG ++ P F Y+ W++MLF+AG+GI L+Y+ EP+ HF +PP + T Sbjct: 73 LAFSRYGSIRLGHNEESPAFAYVPWVSMLFSAGIGIALLYYGAYEPLDHFLTPPGQQGGT 132 Query: 172 IAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIG 231 +AA REAM +TF HWG+H WA+Y++VG++L YF YR +LPL +RS LYP+ E IHG IG Sbjct: 133 VAASREAMVLTFLHWGLHGWALYALVGVALGYFAYRRSLPLALRSALYPIFGERIHGRIG 192 Query: 232 HVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVT 291 +VD F I T+ + T+LG G L + SGL YL +P + +++V V+ +ATI VV Sbjct: 193 DMVDGFGILATLVSMVTNLGIGALVVQSGLTYLFKMPDTPQTLVVIVLVMMVVATIGVVA 252 Query: 292 GVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEP 351 GVEKG+ LS N+ L LL+LFVLV GPT L+ VQN G YL S V ++F+IY +P Sbjct: 253 GVEKGIAWLSNLNVRLLCLLLLFVLVTGPTLHLLDGLVQNTGDYLASFVRKSFDIYLNQP 312 Query: 352 --RPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFG 409 R W+ SWTLFYWAWWI+W+PFVG+F+ARISRGRT+RE + VL +P FT W+++FG Sbjct: 313 DGRDWLGSWTLFYWAWWIAWAPFVGLFVARISRGRTIREVILGVLLIPLGFTLAWLSIFG 372 Query: 410 NTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGS 469 NTAI + L KAD ++ LF+ EYLPW + AVL+ + F+T DSG+ Sbjct: 373 NTAIDLVLNHGQAVLGEVAKADAAMTLFKLLEYLPWAPYVAGAAVLIGFVLFLTPVDSGT 432 Query: 470 LVIDTIAS----GGET---ATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPF 522 L+I + + GG P R+FW + +V+ LL G A+Q+A + LPF Sbjct: 433 LMIANLCTRRVDGGVEDGHDAPIWLRVFWAVVITVVSIGLLLAGNFGAMQTAVVLCGLPF 492 Query: 523 SLVMLILVWSLFVGMRAD 540 S + + L +R D Sbjct: 493 SFTLAFYMVGLLRALRTD 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: 1032 Number of extensions: 49 Number of successful extensions: 4 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: 517 Length adjustment: 37 Effective length of query: 669 Effective length of database: 480 Effective search space: 321120 Effective search space used: 321120 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 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