Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_090276036.1 BLU11_RS18920 BCCT family transporter
Query= SwissProt::G3XCN6 (706 letters) >NCBI__GCF_900105005.1:WP_090276036.1 Length = 555 Score = 421 bits (1082), Expect = e-122 Identities = 225/493 (45%), Positives = 309/493 (62%), Gaps = 22/493 (4%) Query: 53 VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112 ++ VF+ S I LFV + + +AE++FS ++ + W +L + +F+ L L Sbjct: 52 IHSKVFLISAGAILLFVLLTLALQGQAEAVFSSLRGWVTGKMDWFFLGAANIFVVLCLAL 111 Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEA----- 167 S G++++G ++ P++ Y W +MLFAAGMGIGLM++ V EP+ HF + + Sbjct: 112 IVSPLGKVRIGGKEATPDYTYFGWFSMLFAAGMGIGLMFYGVAEPLGHFTAAYDGVVVGA 171 Query: 168 -------EPLTIAA------QREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTV 214 PL AA R M+ T FHWG+H WAIY++V LSLA F Y LPL+V Sbjct: 172 DGVRTDWAPLGGAAGNAEEAMRLGMAATIFHWGLHPWAIYAIVALSLAIFSYNKGLPLSV 231 Query: 215 RSGLYPLLKEGIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQ 274 RS YPLL E I G GHVVDI A+ MFGL TSLG G Q ++G+ +L IP + Sbjct: 232 RSIFYPLLGERIWGWPGHVVDILAVFAIMFGLVTSLGIGAQQASAGMEHLFNIPTTSLTM 291 Query: 275 LLLVTVVTAIATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGL 334 +LL+ +TA+A SVV GVEKGV+ LS+ NL LA+LL++FV+VVGPT + + N+G Sbjct: 292 VLLILAITAVALWSVVAGVEKGVQQLSKINLMLALLLLVFVIVVGPTLAIFKGLFSNLGA 351 Query: 335 YLDSLVLRTFNIYAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVL 394 Y+ S + N E ++ WT FYWAWWISWSPFVGMFIAR+SRGRTVREF+ +V+ Sbjct: 352 YV-SYLPALANPVGREDVNFVQGWTAFYWAWWISWSPFVGMFIARVSRGRTVREFLVSVM 410 Query: 395 FVPAMFTFLWMTVFGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAV 454 VP++ + LWMT FG AI + IA G +A L + LF LP A+TS + + Sbjct: 411 LVPSLVSVLWMTSFGGGAI--NQVIAEG-FTGVQEAALELQLFTMLSQLPLSAITSFIGI 467 Query: 455 LLVSIFFVTSSDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSA 514 +LV +FF+TSSDSGSLVIDT+ +GG+ P QR+FW + G++A LL GGL ALQ+ Sbjct: 468 VLVIMFFITSSDSGSLVIDTVTAGGKVNAPVGQRVFWAIIEGVLAIALLLGGGLVALQAM 527 Query: 515 TISTALPFSLVML 527 +ST LPF+LV+L Sbjct: 528 AVSTGLPFTLVLL 540 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: 1050 Number of extensions: 77 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: 555 Length adjustment: 38 Effective length of query: 668 Effective length of database: 517 Effective search space: 345356 Effective search space used: 345356 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