Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate PfGW456L13_439 High-affinity choline uptake protein BetT
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_439 Length = 664 Score = 530 bits (1366), Expect = e-155 Identities = 272/654 (41%), Positives = 409/654 (62%), Gaps = 20/654 (3%) Query: 52 KVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLF 111 ++N PVF S + I LF + + P++A + Q + GW YLL++ ++L ++ Sbjct: 13 RMNPPVFWFSASFILLFGVVVIAMPEQAGAWLLAAQNWAANTVGWYYLLAMTLYLVFVVV 72 Query: 112 LAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLT 171 A S YG++KLG D EPEF YLSW MLFAAG+ I L +F V EP+TH PP+ E T Sbjct: 73 TALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMLQPPQGEAGT 132 Query: 172 IAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIG 231 A R+AM + F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GPIG Sbjct: 133 ADAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGPIG 192 Query: 232 HVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVT 291 + VD F I T+FGL +GFG+L +NSGL+YL GI + +VQ+ L+T++ A I V+ Sbjct: 193 YAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWVQVGLITLMMGAAIIVAVS 252 Query: 292 GVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYE- 350 GV+KGVR++S+ N+ LA L+LFVL GPT L+ +QN+G YL +L +++F++YAY+ Sbjct: 253 GVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNLGDYLGALPMKSFDLYAYDK 312 Query: 351 PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGN 410 P W+ WT+FYWAWWI+WSPFVG+FIARISRGRT+REFV VL +P FT WM++FGN Sbjct: 313 PSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIFGN 372 Query: 411 TAIYVDTTIANGELARDVKA--DLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSG 468 +AI D + +G A + A + S+ L+ E PW + V + +FFVTS+DSG Sbjct: 373 SAI--DQVLNHGMSALGMSAIDNPSMTLYLLLETYPWSKTVIAVTVFISFVFFVTSADSG 430 Query: 469 SLVIDTIASGG---ETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLV 525 ++V+ T+++ G + P R+FW +++ +V + LL +G + AL+SA + T+LPFSL+ Sbjct: 431 TVVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTSALLFSGSIDALKSAVVLTSLPFSLI 490 Query: 526 MLILVWSL----FVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKF 581 +L+++W L ++ + +A+ SL P + G W++RL+ + P R V +F Sbjct: 491 LLLMMWGLHKAFYLESQKQIAQMH---SLAPVSGSRRG-GWRQRLSQAVHFPSRDEVYRF 546 Query: 582 LQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAF 641 L +V PA+E V+ T + + D +++L + FVY VQM + P+F Sbjct: 547 LDTTVRPAIEEVSAVFTEKGLHVATHPDPANDSVSLEIGHGDQHPFVYQVQMRGYFTPSF 606 Query: 642 TAYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 + Y A S+GS+ YD++G + QIIND+L Q+ER+ F+ Sbjct: 607 ARGGMGSKQLNNRRYYRAEVHLSEGSQDYDLVGYSKEQIINDILDQYERHMQFL 660 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: 1245 Number of extensions: 71 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: 664 Length adjustment: 39 Effective length of query: 667 Effective length of database: 625 Effective search space: 416875 Effective search space used: 416875 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