Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate 5207515 Shew_0049 choline/carnitine/betaine transporter (RefSeq)
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__PV4:5207515 Length = 523 Score = 433 bits (1113), Expect = e-125 Identities = 222/499 (44%), Positives = 329/499 (65%), Gaps = 13/499 (2%) Query: 51 FKVNLPVFVGSVAVIALFVGIGVIAP-KRAESIFSGMQTAILSGFGWLYLLSVAVFLFSM 109 F V+ PVF S +IA F+ ++ + A+S+ G++ I+ F WL++ S +F+ Sbjct: 27 FDVHNPVFGVSAGLIAAFLLATLLTDAETAKSVLDGIKWKIIGAFDWLFIWSGNIFVIFC 86 Query: 110 LFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFA----SPP 165 L L S YG+++LG +++ ++ +LSW++MLFAAGMGIGLM+++V EP+ +F +P Sbjct: 87 LGLILSPYGKIRLGGNEATADYSFLSWLSMLFAAGMGIGLMFWSVAEPVAYFTGWYETPL 146 Query: 166 EAEPLTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEG 225 EP T A + A+ T FHWG+H WAIY VV LSLA+F Y +PL++RS YPLL + Sbjct: 147 GVEPNTPEAAKLALGATMFHWGLHPWAIYGVVALSLAFFTYNKGMPLSIRSIFYPLLGDR 206 Query: 226 IHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIA 285 G GH+VDI A+ T+FGLATSLG G Q SG++++ GI S+ +Q++++ VT +A Sbjct: 207 AWGWAGHIVDILAVLATLFGLATSLGLGAQQAASGIHHVFGIEASLGLQMIVIVAVTLLA 266 Query: 286 TISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFN 345 +SVV G++ GV+++S N+ +A LL++ V ++G +L + Y+++++ + N Sbjct: 267 VVSVVRGIDGGVKVISNINMIVAFLLLILVAMIGYAVSL-GSIPTTLMAYVENIIPLS-N 324 Query: 346 IYAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWM 405 + W WT+FYWAWWISWSPFVGMFIAR+S+GRTVREF+TAVL VP T +WM Sbjct: 325 PHGRTDEAWFQGWTVFYWAWWISWSPFVGMFIARVSKGRTVREFITAVLLVPTAVTLIWM 384 Query: 406 TVFGNTAIYVDTTIAN-GELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTS 464 +VFG AI D + GEL D+ +A+F+ F+ LP+ + S +AV+LV +FF+TS Sbjct: 385 SVFGGMAI--DQVVNKVGELGAKGLTDVPLAMFEMFDVLPFGTLLSIIAVVLVLVFFITS 442 Query: 465 SDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGG---LTALQSATISTALP 521 SDSGSLVID+I +GG+ P QR+FW L G +A LL GG + ALQ+ ISTALP Sbjct: 443 SDSGSLVIDSITAGGKIDAPVPQRVFWALLEGAIAMALLWIGGTEAIQALQAGAISTALP 502 Query: 522 FSLVMLILVWSLFVGMRAD 540 F++++L++ SL GMR + Sbjct: 503 FTVILLLMCVSLLKGMRTE 521 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: 1024 Number of extensions: 73 Number of successful extensions: 6 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: 523 Length adjustment: 37 Effective length of query: 669 Effective length of database: 486 Effective search space: 325134 Effective search space used: 325134 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