Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate Pf1N1B4_1689 High-affinity choline uptake protein BetT
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1689 Length = 651 Score = 518 bits (1334), Expect = e-151 Identities = 265/653 (40%), Positives = 402/653 (61%), Gaps = 20/653 (3%) Query: 53 VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112 +N PVF + I LF + + P++A + Q + GW Y+L++ ++L ++ Sbjct: 1 MNPPVFYFAATFILLFAVVVMAIPEQAGAWLLEAQNWAANTVGWYYMLAMTLYLVFVVVT 60 Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTI 172 A S YG++KLG D EPEF YLSW MLFAAG+ I L +F V EP+TH A PP+ E T Sbjct: 61 ALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHLAQPPQGEAGTA 120 Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGH 232 A R+AM + F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GPIG+ Sbjct: 121 DAARQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGPIGY 180 Query: 233 VVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTG 292 VD F I T+FGL +GFG+L +NSGL+YL GI + ++Q+ L+T++ A I V+G Sbjct: 181 AVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLITLMMGAAIIVAVSG 240 Query: 293 VEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYE-P 351 V+KGVR++S+ N+ LA L+LFVL GPT L+ +QN+G YL +L +++F++YAY+ P Sbjct: 241 VDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNLGDYLGALPMKSFDLYAYDKP 300 Query: 352 RPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNT 411 W+ WT+FYWAWWI+WSPFVG+FIARISRGRT+REFV VL +P FT WM++FGN+ Sbjct: 301 SDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIFGNS 360 Query: 412 AIYVDTTIANGELARDVKA--DLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSDSGS 469 AI D + +G A + A + S+ L+ E PW + V + +FFVTS+DSG+ Sbjct: 361 AI--DQVLNHGMSALGMSAIDNPSMTLYLLLETYPWSKTVIAVTVFISFVFFVTSADSGT 418 Query: 470 LVIDTIASGG---ETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFSLVM 526 +V+ T+++ G + P R+FW +++ +V + LL +G + AL+SA + T+LPFSL++ Sbjct: 419 VVLSTLSAKGGNPDEDGPKWLRVFWGAMTALVTSALLFSGSIDALKSAVVLTSLPFSLIL 478 Query: 527 LILVWSL----FVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVEKFL 582 L+++W L ++ + +A+ SL P + G W++RL+ + P R V +FL Sbjct: 479 LLMMWGLHKAFYLESQKQIAQLH---SLAPVSGSRRG-GWRQRLSQAVHFPSRDEVYRFL 534 Query: 583 QASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAFT 642 +V PA+E V + D ++L + F+Y VQM + P+F Sbjct: 535 DTTVRPAIEEVTAVFVEKGLHVVTQPDPANDNVSLEIGHGELHPFIYQVQMRGYFTPSFA 594 Query: 643 AYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 + + A +GS+ YD++G Q+IND+L Q+ER+ F+ Sbjct: 595 RGGMGSKQLNNRRYHRAEVHLREGSQDYDLVGYTKEQVINDILDQYERHMQFL 647 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: 1238 Number of extensions: 74 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: 651 Length adjustment: 39 Effective length of query: 667 Effective length of database: 612 Effective search space: 408204 Effective search space used: 408204 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