Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate GFF140 Psest_0140 choline/carnitine/betaine transport
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__psRCH2:GFF140 Length = 685 Score = 590 bits (1521), Expect = e-173 Identities = 308/652 (47%), Positives = 431/652 (66%), Gaps = 13/652 (1%) Query: 56 PVFVGSVAVIALFVGIGVIA-PKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFLAF 114 PVF+ +V V L V IG I+ P+ A +FS I + FGW Y+LSVA FL ++ +A Sbjct: 15 PVFIPAVIVTLLLV-IGTISNPELAGEVFSSTLAFITTNFGWFYMLSVAFFLVFIVGIAM 73 Query: 115 SRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTIAA 174 + +G +KLGPD +EP++ + +W AMLF+AG GI L++F V EP+ H+ASPP T+ A Sbjct: 74 TPWGSIKLGPDHAEPQYSFPAWFAMLFSAGYGIALLFFGVAEPVLHYASPPAGAGETVDA 133 Query: 175 QREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGHVV 234 ++AM + FFHWG H WAIY + GL LAYF +R+ LPL++RS LYP++ E IHGPIGHVV Sbjct: 134 AKQAMQIAFFHWGFHIWAIYGLTGLVLAYFSFRHGLPLSMRSALYPIIGERIHGPIGHVV 193 Query: 235 DIFAICGTMFGLATSLGFGILQINSGLNYLL-GIPQSIYVQLLLVTVVTAIATISVVTGV 293 DIFAI GT+FG+AT+LG + QIN+G+NYL IP SI VQ++ + ++T +A SVV G+ Sbjct: 194 DIFAILGTLFGIATTLGLSVTQINAGINYLWPSIPISINVQIIAIAIITGLAICSVVAGL 253 Query: 294 EKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPRP 353 +KGV+ LS N+ LA+ LMLFV +VGP+ ++ F+QN G YL++++ RTFN+ AY Sbjct: 254 DKGVKNLSLLNMVLAIGLMLFVFLVGPSIFILETFLQNTGSYLNNIIERTFNLQAYSRSD 313 Query: 354 WIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTAI 413 WI +WTLF + W I+WSPFVG+FIA+ISRGRT+R+FV V+FVP +FTFLW +VFG+TA+ Sbjct: 314 WIGNWTLFIFGWTIAWSPFVGLFIAKISRGRTIRQFVFGVMFVPTIFTFLWFSVFGDTAL 373 Query: 414 YVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGSLVID 473 ++ L DV+AD ++ALF+ FE LP ++ S LAV+L+ FFVTSSDSGSLVID Sbjct: 374 HMIMVEGYTSLISDVQADNAIALFKLFELLPLTSIASFLAVVLIITFFVTSSDSGSLVID 433 Query: 474 TIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVMLIL---V 530 ++A+GG TP QR+FW S+ GIVA+ LL GGL+ALQ+ TI++ALPF+++M+I + Sbjct: 434 SLAAGGALHTPVWQRVFWASIEGIVASTLLLAGGLSALQTMTIASALPFAIIMMIAALGM 493 Query: 531 WSLFV--GMRADLARTQSPGS-LGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFLQASVL 587 W V G ++ GS L A P W++RLA +S P R V+ F+ +VL Sbjct: 494 WRALVIEGHHETSLQSHMQGSRLASNAGPGL---WKKRLAGMVSFPSREEVDGFMNTTVL 550 Query: 588 PALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFTAYDAT 647 A+ V REL+ + A V D L L V + DF+Y ++ + +PAF + Sbjct: 551 KAMRRVQRELSGQEWAAEVHTDEAHSRLYLEVIKDDQVDFIYEIRAVGYAMPAFALTEDP 610 Query: 648 VADVR-YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFVRSPESSL 698 D + Y A F G + YD+ G II+D+L QFE+Y F+ SL Sbjct: 611 ETDEQYYRAEVFLRRGGQHYDVYGYDQADIISDILDQFEKYLHFLHISPGSL 662 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: 1281 Number of extensions: 62 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: 685 Length adjustment: 39 Effective length of query: 667 Effective length of database: 646 Effective search space: 430882 Effective search space used: 430882 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 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