Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate AO353_11690 AO353_11690 choline transporter
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11690 Length = 667 Score = 522 bits (1345), Expect = e-152 Identities = 264/656 (40%), Positives = 401/656 (61%), Gaps = 17/656 (2%) Query: 50 RFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSM 109 + ++N PVF + I LF + + P+ + + Q + GW Y+L++ ++L + Sbjct: 11 QIRMNPPVFYFAATFILLFGLVVIAFPQESGAWLLAAQNWAANTVGWYYMLAMTLYLVFV 70 Query: 110 LFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEP 169 + A S YG++KLG D EPEF YLSW MLFAAG+ I L +F V EP+TH PP+ E Sbjct: 71 VVTALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMLQPPQGEA 130 Query: 170 LTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGP 229 T A R+AM V F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GP Sbjct: 131 GTADAARQAMQVLFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGP 190 Query: 230 IGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISV 289 IG+ VD F I T+FGL +GFG+L +NSGL+YL GI + ++Q+ L+T++ A I Sbjct: 191 IGYAVDGFGIIATVFGLGADMGFGVLHLNSGLDYLFGIAHTQWIQVGLITLMMGAAIIVA 250 Query: 290 VTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAY 349 V GV+KGVR++S+ N+ LA L+LFVL GPT L+ +QN+G YL +L +++F++YAY Sbjct: 251 VAGVDKGVRVMSDINMLLACALLLFVLFAGPTQHLLNTLIQNLGDYLGALPMKSFDLYAY 310 Query: 350 E-PRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVF 408 + P W+ WT+FYWAWWI+WSPFVG+FIARISRGRT+REFV VL +P FT WM++F Sbjct: 311 DKPSDWLGGWTVFYWAWWIAWSPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIF 370 Query: 409 GNTAIYVDTTIANGELARDVKA--DLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSD 466 GN+AI D + +G A + A + S+ L+ E PW + V + +FFVTS+D Sbjct: 371 GNSAI--DQVLNHGMSALGLSAIENPSMTLYLLLETYPWSKTVIAVTVFISFVFFVTSAD 428 Query: 467 SGSLVIDTIASGGETAT---PALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFS 523 SG++V+ T+++ G A P R+FW +++ +V + LL G + +L+SA + T+LPFS Sbjct: 429 SGTVVLSTLSAKGGNADEDGPKWLRVFWGAMTALVTSALLFAGSIDSLKSAVVLTSLPFS 488 Query: 524 LVMLILVWSL----FVGMRADLARTQSPGSLGPRAYPASGVPWQRRLAMTLSTPDRRAVE 579 L++L+++W L ++ + +A+ S + + G W++RL+ + P R V Sbjct: 489 LILLLMMWGLHKAFYLESQKQIAQLHSLAPVSASSRRGKG-GWRQRLSQAVHFPSRDEVY 547 Query: 580 KFLQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLP 639 +FL +V PA+E V + D +++L + F+Y QM + P Sbjct: 548 RFLDTTVRPAIEEVTAVFAEKGLNVVTQPDPANDSVSLEIGHGEQHPFIYQAQMRGYFTP 607 Query: 640 AFTAYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 +F ++ Y A S+GS+ YD++G QIIND+L Q+ER+ F+ Sbjct: 608 SFARGGMGSKELNNRRYYRAEVHLSEGSQDYDLVGYTKEQIINDILDQYERHMQFL 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: 1230 Number of extensions: 72 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: 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