Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_086511888.1 BZY95_RS21275 BCCT family transporter
Query= SwissProt::G3XCN6 (706 letters) >NCBI__GCF_002151265.1:WP_086511888.1 Length = 559 Score = 445 bits (1144), Expect = e-129 Identities = 236/502 (47%), Positives = 326/502 (64%), Gaps = 23/502 (4%) Query: 57 VFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSR 116 VF S V FV I + E +F+ M+ + W +LL+ +F+ L L S Sbjct: 60 VFTISALVTVFFVVITLALQAEVEPLFNAMRDWLTGNLAWFFLLAGNIFVLLCLVLIVSP 119 Query: 117 YGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPP---EAE----- 168 G++++G ++P+F Y W AMLFAAGMGIGLM++ V EPM+HF + +AE Sbjct: 120 LGKVRIGGMHAKPDFSYTGWFAMLFAAGMGIGLMFYGVSEPMSHFGAALGGIDAENGART 179 Query: 169 ---PLTIAAQ------REAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLY 219 PL AA R M+ T +HWG+H WAIY+VV L+LA F + LPLT+RS Y Sbjct: 180 DWAPLGAAADDPAAAARLGMAATIYHWGLHPWAIYAVVALALAIFSFNKGLPLTMRSIFY 239 Query: 220 PLLKEGIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVT 279 P+L E + G GH+VDI A+ T+FGLATSLG G Q ++GL+YL G+P++ +LL+ Sbjct: 240 PILGERVWGWPGHIVDILAVFATLFGLATSLGLGASQASAGLSYLFGVPEADATMVLLIM 299 Query: 280 VVTAIATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSL 339 +TA+A +S++ GV+KGVR LSE N+ LAVLL+LFV++VGPT ++ F QN+G Y+ +L Sbjct: 300 GITAVAIVSILAGVDKGVRRLSEINMILAVLLLLFVILVGPTLLILTGFFQNLGAYVVNL 359 Query: 340 VLRTFNIYAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAM 399 + N + E + WT FYWAWWISWSPFVGMFIAR+SRGRTVREF+TAVL VP++ Sbjct: 360 PALS-NPFGREDANFTQGWTAFYWAWWISWSPFVGMFIARVSRGRTVREFLTAVLLVPSL 418 Query: 400 FTFLWMTVFGNTAIYVDTTIANG-ELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVS 458 + LWMT FG TAI D + G E +D A L + LF LP A+TS + ++LV Sbjct: 419 VSVLWMTAFGGTAI--DQLVGAGFEGVQD--AALELQLFVMLGELPLTAITSFVGIVLVV 474 Query: 459 IFFVTSSDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATIST 518 +FF+TSSDSGSLVIDTI +GG+ P QR+FW + G++A LL GGL ALQ+ +ST Sbjct: 475 VFFITSSDSGSLVIDTITAGGKVDAPKPQRVFWAIIEGVIAIALLLGGGLIALQAMAVST 534 Query: 519 ALPFSLVMLILVWSLFVGMRAD 540 LPF+LV+L+ +++ G+ ++ Sbjct: 535 GLPFTLVLLVGCYAIVKGLMSE 556 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: 1105 Number of extensions: 69 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: 559 Length adjustment: 38 Effective length of query: 668 Effective length of database: 521 Effective search space: 348028 Effective search space used: 348028 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