Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate PP_0229 PP_0229 choline/carnitine/betaine transporter
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Putida:PP_0229 Length = 667 Score = 518 bits (1335), Expect = e-151 Identities = 266/654 (40%), Positives = 398/654 (60%), Gaps = 14/654 (2%) Query: 50 RFKVNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSM 109 + ++N PVF + + I +F + + P+ A Q + GW Y+L++ ++L + Sbjct: 12 KIRMNPPVFYFAASFILIFGLVVISNPQAAGDWLLAAQNWAANTVGWYYMLAMTLYLVFV 71 Query: 110 LFLAFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEP 169 + A S YG++KLG D EPEF YLSW MLFAAG+ I L +F V EP+TH PP+ E Sbjct: 72 VVTALSGYGKIKLGADHDEPEFSYLSWAGMLFAAGISITLFFFCVSEPLTHMLQPPQGEA 131 Query: 170 LTIAAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGP 229 T+ A R+AM + F HWG+H W +++ VG++LAYF YR+NLPL +RS LYPL+ + I+GP Sbjct: 132 GTVEAGRQAMQILFLHWGLHGWGVFAFVGMALAYFAYRHNLPLALRSALYPLIGKRINGP 191 Query: 230 IGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISV 289 IG+ VD F I T+FGL +GFG+L +N+GL+YL GI S +VQ++L+T++ A Sbjct: 192 IGYAVDGFGIIATVFGLGADMGFGVLHLNAGLDYLFGISHSQWVQVILITLMMGAAVAVA 251 Query: 290 VTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAY 349 V GVEKGVR++S+ NLFLA L+LFVL GPT L +QN+G YL +L ++F++YAY Sbjct: 252 VAGVEKGVRVMSDINLFLACALLLFVLFAGPTQHLFNTLIQNLGDYLGALPRKSFDVYAY 311 Query: 350 -EPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVF 408 E R W+ WT+FYWAWWI+W+PFVG+FIARISRGRT+REFV VL +P FT WM++F Sbjct: 312 GENRGWLGGWTVFYWAWWIAWAPFVGLFIARISRGRTIREFVFGVLLIPLGFTLAWMSIF 371 Query: 409 GNTAIYVDTTIANG--ELARDVKADLSVALFQFFEYLPWPAVTSTLAVLLVSIFFVTSSD 466 GN+A+ D I +G L + + S++L+ E PW V + +FFVTS+D Sbjct: 372 GNSAL--DQVINHGMTALGQSALDNPSMSLYLLLETYPWSKAVIATTVFISFVFFVTSAD 429 Query: 467 SGSLVIDTIASGGETAT---PALQRIFWCSLSGIVAAVLLSTGGLTALQSATISTALPFS 523 SG++V+ T+++ G A P RIFW +++ ++ + LL G + +L+SA + T+LPFS Sbjct: 430 SGTVVLSTLSAKGGDADEDGPNWLRIFWGAMTALITSALLFAGSIDSLKSAVVLTSLPFS 489 Query: 524 LVMLILVWSLFVGMRADLAR-TQSPGSLGPRAYPASG-VPWQRRLAMTLSTPDRRAVEKF 581 L++L ++W L + R SL P A G W++RL+ + P R V +F Sbjct: 490 LILLCMMWGLHKAFYLESQRQIAQMHSLAPFAQSRRGRGGWRQRLSQAVHFPSRDEVYRF 549 Query: 582 LQASVLPALEAVARELTRRSRPASVGRDAETGALTLTVPAEGHRDFVYGVQMSEHKLPAF 641 + V PA+ V ++ D ++L + + F+Y VQM + P+F Sbjct: 550 MDDVVRPAIADVREVFEQKGLVLITQDDPSHDNVSLKIGHGEEQPFIYQVQMRGYFTPSF 609 Query: 642 TAYDATVADVR----YEARTFFSDGSRGYDIMGMADNQIINDVLFQFERYTGFV 691 +++ Y A S+GS+ YD++G + QIIND+L Q+ER+ ++ Sbjct: 610 ALGGLGTQELKNRRYYRAEVHLSEGSQNYDLVGYSKEQIINDILDQYERHMQYL 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: 1227 Number of extensions: 73 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