Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate Pf6N2E2_3917 High-affinity choline uptake protein BetT
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3917 Length = 667 Score = 518 bits (1333), Expect = e-151 Identities = 264/655 (40%), Positives = 400/655 (61%), Gaps = 19/655 (2%) Query: 52 KVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLF 111 ++N PVF + I LF + + P +A + Q + GW Y+L++ ++L ++ Sbjct: 13 RMNPPVFYFAATFILLFGLVVIAMPAQAGAWLLAAQNWAANTVGWYYMLAMTLYLVFVVV 72 Query: 112 LAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPL- 170 A S YG++KLG D EPEF YLSW MLFAAG+ I L +F V EP+TH PP+ E Sbjct: 73 TALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMVQPPQGEAGG 132 Query: 171 TIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPI 230 T A R+AM + F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GPI Sbjct: 133 TAEAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGPI 192 Query: 231 GHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVV 290 G+ VD F I T+FGL +GFG+L +NSGL+YL GI + ++Q+ L+ ++ A I V Sbjct: 193 GYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLIVLMMGAAIIVAV 252 Query: 291 TGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYE 350 GV+KGVR++S+ N+ LA L+LFVL GPT L+ +QNIG YL +L +++F++YAY+ Sbjct: 253 AGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNIGDYLGALPMKSFDLYAYD 312 Query: 351 -PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFG 409 P W+ WT+FYWAWWI+WSPFVG+FIARISRGRT+REFV VL +P FT WM++FG Sbjct: 313 KPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIFG 372 Query: 410 NTAIYVDTTIANGELARDVKA--DLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDS 467 N+AI D + +G A + A + S++L+ E PW + V + +FFVTS+DS Sbjct: 373 NSAI--DQVLNHGMSALGMSALENPSMSLYLLLETYPWSKTVIAVTVFISFVFFVTSADS 430 Query: 468 GSLVIDTIASGG---ETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSL 524 G++V+ T+++ G + P R+FW +++ +V + LL +G + AL+SA + T+LPFSL Sbjct: 431 GTVVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTSALLFSGSIDALKSAVVLTSLPFSL 490 Query: 525 VMLILVWSL----FVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEK 580 ++L+++W L ++ + +A+ S + G W++RL+ + P R V + Sbjct: 491 ILLLMMWGLHKAFYLESQKQIAQLHSLAPVSGSRRGTGG--WRQRLSQAVHFPSRDEVYR 548 Query: 581 FLQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPA 640 FL +V PA+E V + D ++L + F+Y VQM + P+ Sbjct: 549 FLDTTVRPAIEEVTAVFVEKGLTVVTQPDPANDNVSLEIGHGEQHPFIYQVQMRGYFTPS 608 Query: 641 FTAYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 F ++ Y A S+GS+ YD++G Q+IND+L Q+ER+ F+ Sbjct: 609 FARGGMGSKELNNRRYYRAEVHLSEGSQDYDLVGYTKEQVINDILDQYERHLQFL 663 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: 1257 Number of extensions: 73 Number of successful extensions: 8 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: 667 Length adjustment: 39 Effective length of query: 667 Effective length of database: 628 Effective search space: 418876 Effective search space used: 418876 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