Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate 3608727 Dshi_2119 choline/carnitine/betaine transporter (RefSeq)
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Dino:3608727 Length = 524 Score = 398 bits (1022), Expect = e-115 Identities = 208/489 (42%), Positives = 312/489 (63%), Gaps = 19/489 (3%) Query: 61 SVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAFSRYGEL 120 S +I LFV + + P R+ +T I FGW Y+L VFL ++ +AFS+YG + Sbjct: 19 SAGIILLFVLLVLAFPSRSADWIDAARTLITFYFGWWYVLLSGVFLVFLIAIAFSKYGAI 78 Query: 121 KLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFAS-PPEAEPL-TIAAQREA 178 +LG D P++ Y +W AML+AAG GIG++++++ EPM H++ P A+ T AA A Sbjct: 79 RLGDADERPKYSYFTWFAMLYAAGQGIGIIFWSIAEPMFHYSGGTPFADGSGTAAAADMA 138 Query: 179 MSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVVDIFA 238 M VTFFHWG++AWAIY +V L+L YR PL +R LYPL + + GP+G V+D+ A Sbjct: 139 MQVTFFHWGLNAWAIYCIVALALCLVSYRLKKPLGIRYTLYPLFGDRVEGPLGVVIDVVA 198 Query: 239 ICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTGVEKGVR 298 + T+FG+ATSLG G+ QIN+GLN+L G+P S VQL+L+ +TA+A SV++G+++G++ Sbjct: 199 VFATIFGIATSLGLGVTQINAGLNHLWGVPISETVQLVLIAAITAVALCSVLSGLDRGIK 258 Query: 299 ILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIY----AYEPRPW 354 LS+ N++L + L++F GPT L+ + Y SL +FN+Y E W Sbjct: 259 WLSQVNMWLTIALLVFFFTWGPTQYLLVSLGEVTLAYFVSLF--SFNVYIESVPAEATRW 316 Query: 355 IDS----WTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGN 410 D WT FYW WWISW+PFVG+F+AR+SRGRTVREF+ V+ V ++ +F+W+ +G Sbjct: 317 SDMWQGWWTTFYWGWWISWAPFVGVFVARVSRGRTVREFILGVVGVSSILSFVWIVAYGG 376 Query: 411 TAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPA---VTSTLAVLLVSIFFVTSSDS 467 TA++ + + G ++ V A++S+ALF F+ + A V +LV+ +FVTSSDS Sbjct: 377 TALWAE-VLGPGGVSDAVSANVSMALFATFDAMDVGAIGLVAGVFGTILVTTYFVTSSDS 435 Query: 468 GSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGG---LTALQSATISTALPFSL 524 G+LV+ TI S G R+ W + G+VAAVLL GG L+ LQ+A I ALPFS+ Sbjct: 436 GTLVVATILSEGNEHPMYRHRMIWGTFEGVVAAVLLVVGGSAALSTLQTAAIIAALPFSV 495 Query: 525 VMLILVWSL 533 +M+++ +++ Sbjct: 496 IMVLMCFAI 504 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: 1033 Number of extensions: 62 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 706 Length of database: 524 Length adjustment: 37 Effective length of query: 669 Effective length of database: 487 Effective search space: 325803 Effective search space used: 325803 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