Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate PP_5374 PP_5374 Choline/carnitine/betaine transporter family protein
Query= SwissProt::G3XCN6 (706 letters) >FitnessBrowser__Putida:PP_5374 Length = 567 Score = 413 bits (1061), Expect = e-119 Identities = 208/513 (40%), Positives = 319/513 (62%), Gaps = 23/513 (4%) Query: 53 VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112 +N V + S+ + FV + + A ++F IL F W YL+SV L +++L Sbjct: 11 LNPTVTIWSLLAVVAFVLFCALFAEHAAAVFQRASDFILQNFKWFYLISVTGVLGLLIYL 70 Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEAEPLTI 172 S++G +KLG DD +PEF + SWIAMLF+ GMGIGL++++V EPM H+A P A LT Sbjct: 71 MCSKFGSMKLGRDDDKPEFSFGSWIAMLFSGGMGIGLIFWSVAEPMWHYAGNPFATGLTD 130 Query: 173 AAQREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTVRSGLYPLLKEGIHGPIGH 232 A AM +T FHWG+H WAI+++VGL LAYF YR LPL++RS LYPL+ E I+GPIGH Sbjct: 131 EAATTAMRITLFHWGLHPWAIFTIVGLGLAYFAYRKGLPLSMRSILYPLIGERIYGPIGH 190 Query: 233 VVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQLLLVTVVTAIATISVVTG 292 VVDI A+ T FG++ SLG G++Q+N+GL+ + +P S+ VQ+ L+ ++T + T+SV+ G Sbjct: 191 VVDILAVVITAFGVSQSLGLGVVQMNTGLSQVFDLPISLGVQITLIVLITLVTTVSVMAG 250 Query: 293 VEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGLYLDSLVLRTFNIYAYEPR 352 V +G++ LSE N+ L+V+L++ +L++GPT ++ +++ G Y +V +F + Sbjct: 251 VSRGMKRLSEWNMLLSVVLVVLILLLGPTRYIINLMLESTGDYASHVVGLSFWSDTQKDS 310 Query: 353 PWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVLFVPAMFTFLWMTVFGNTA 412 W + WT FYW WW++W PFVG+FIARIS+GR++RE + L VP + T +WM+VFG TA Sbjct: 311 GWQNWWTAFYWPWWMTWGPFVGLFIARISKGRSIRELIAGALLVPTLVTIIWMSVFGGTA 370 Query: 413 IYVD--------TTIANGELARD------------VKADLSVALFQFFEYL---PWPAVT 449 + + +A+GEL D K + + A+F + V Sbjct: 371 LKAEQLDRQQHAELVASGELQGDKAKYEGGTVLLATKQETTAAMFTLLHKIDAGTLGKVL 430 Query: 450 STLAVLLVSIFFVTSSDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLT 509 S L +L++ +F+TS+DSG+ V+ T+ S G P R+ WC L G +A LL GGL Sbjct: 431 SVLVCILLATYFITSADSGTQVLCTLNSMGSANPPQSIRLLWCILEGAIAMALLMAGGLK 490 Query: 510 ALQSATISTALPFSLVMLILVWSLFVGMRADLA 542 A+Q A+I+ LP + +L++ ++L +R ++A Sbjct: 491 AIQMASIAAGLPIAGFILLISYTLMRSLRQEMA 523 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: 1009 Number of extensions: 47 Number of successful extensions: 2 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: 567 Length adjustment: 38 Effective length of query: 668 Effective length of database: 529 Effective search space: 353372 Effective search space used: 353372 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