Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF1153 HP15_1130 transporter, BCCT family protein
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Marino:GFF1153 Length = 530 Score = 447 bits (1149), Expect = e-130 Identities = 225/492 (45%), Positives = 319/492 (64%), Gaps = 9/492 (1%) Query: 53 VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112 ++ PVF + ++ FV ++ P A+ + G + I++ F W +L+S +F+ L L Sbjct: 27 LHAPVFPITAILVFAFVIGTLMFPGEAKELLDGTKWDIIATFDWFFLISANIFVVVCLAL 86 Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFA----SPPEAE 168 F G++++G D +PEF +SW MLFAAGMGIGLM++AV EP+ ++ +P E Sbjct: 87 IFLPMGKIRIGGQDCKPEFSTISWFCMLFAAGMGIGLMFWAVAEPVAYYTGWYETPLNVE 146 Query: 169 PLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHG 228 T A+ AM T +HWG+H W IY++V LSLA+F + N+PLT+RS +PLL++ + G Sbjct: 147 AGTNEARNLAMGATMYHWGLHPWGIYAIVALSLAFFAFNKNMPLTIRSAFFPLLRDKVWG 206 Query: 229 PIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATIS 288 GH++D+ A+ T+FGLATSLGFG Q SGLNYL GI I VQ+ ++ VTA+A IS Sbjct: 207 WPGHIIDVLAVVATIFGLATSLGFGAQQAASGLNYLFGIGAGINVQMAIIVGVTALALIS 266 Query: 289 VVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYA 348 V+ G++ GV++LS N+ +A +L+LFV+ GPT T++ Y+ + V + N + Sbjct: 267 VLRGLDGGVKVLSNINMGVAAVLLLFVIFAGPTMTILETLWVTSSNYVGNAV-QLSNPFG 325 Query: 349 YEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVF 408 E W WT+FYWAWWISWSPFVGMFIAR+S+GRTVREFVTAVL VP + T +WM+ F Sbjct: 326 REDEAWFQGWTVFYWAWWISWSPFVGMFIARVSKGRTVREFVTAVLIVPTVITVVWMSAF 385 Query: 409 GNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSG 468 G AI GELA + ++S+A FQ F LP + S + ++LV +FFVTSSDSG Sbjct: 386 GGAAI-EQIQQGVGELAENGLTEVSLATFQMFANLPLTGILSFVGIILVLVFFVTSSDSG 444 Query: 469 SLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGG---LTALQSATISTALPFSLV 525 SLVID+I +GG+T P QR+FW G +AA L+ GG L A+Q+ IS LPF++V Sbjct: 445 SLVIDSITAGGKTDAPTAQRVFWVVAEGAIAAALIFGGGEDALGAIQATAISAGLPFTVV 504 Query: 526 MLILVWSLFVGM 537 +LI+ W L G+ Sbjct: 505 LLIMTWGLLKGL 516 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: 1028 Number of extensions: 57 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: 530 Length adjustment: 37 Effective length of query: 669 Effective length of database: 493 Effective search space: 329817 Effective search space used: 329817 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