Align Glycine betaine/proline/choline/ectoine transporter VP1456 (characterized)
to candidate GFF3313 PGA1_c33650 putative transporter, BCCT family
Query= SwissProt::Q87PP5 (562 letters) >FitnessBrowser__Phaeo:GFF3313 Length = 604 Score = 283 bits (725), Expect = 1e-80 Identities = 175/579 (30%), Positives = 291/579 (50%), Gaps = 91/579 (15%) Query: 63 FDIHNPVFGISAGLVVFCLISLLLVEPVTARDALNGIKNGIIEQFDAFFMWSTNFFLLFA 122 ++ H+ + + +++ L+ LV P A L+ + + ++ F+AF++ S F F Sbjct: 20 YEGHSLPIALISKIIMTTLVLWALVWPSKASGILSWVNSELLNGFNAFYIVSVGAFAFFL 79 Query: 123 VGLLFSPL-GKIRLGGKEATPDHSTVSWLSMLFAAGMGIGLLFWSVAEPTAYFTDWWGTP 181 L P G +LG +A P+ S SW SM+F AG+G+GL+ ++ AEP W P Sbjct: 80 FVLAILPATGSKKLGPADAAPEFSNFSWFSMMFGAGLGVGLMVFATAEPLGL---WGSNP 136 Query: 182 L----NAEAYSADAKSLAMGATMFHWGVHGWSIYALVALALAFFAFNKGLPLSLRAAFYP 237 + A S +A A T H+G H W+IY L L+LA++A+ + +PL++R+A P Sbjct: 137 VVLSGAVAANSEEAVQSAYRYTFLHYGFHAWAIYVLTGLSLAYYAYTRDMPLTIRSALTP 196 Query: 238 IFGDRAWGWLGHVIDILAVLSTLFGLATSLGLGAQQATSGINHVFG----LNGGIGTQ-- 291 + G A G++GH++D+L V++T+ G++ ++G G Q G+ V G +NG Sbjct: 197 LLGKAANGFVGHLVDVLGVVATILGVSVTIGFGVSQFVDGVYAVSGMEWLMNGDTEAPKP 256 Query: 292 -----MVVIAFVTFIAVLSVVRGIDGGVKLLSNVNMIVAFALLI-FITFITFDTAM---- 341 + + + +++LS V G+ G+K LSN+N++++ LL+ F+ F +F AM Sbjct: 257 STVGLLSALFVIMGLSILSAVSGVGRGIKYLSNLNLVLSVILLLTFVFFGSFFFAMTKFG 316 Query: 342 GSLVDTTMAYIQ----------------------NIIP---LSNPHGREDETW------- 369 LVD + + Q +P LS +G W Sbjct: 317 SGLVDYILHFTQMSFGAYGPQSAEAFAAALPDAAQALPAEDLSTVYGSATSPWGSLGGFT 376 Query: 370 -----------------------MHGW----TVFYWAWWVSWSPFVGMFIARVSKGRTVR 402 GW T FYWAWW+++SPFVG+F+AR+SKGRTVR Sbjct: 377 EGLPASAAALDANAVYAAGEPGRQFGWQAGWTTFYWAWWIAFSPFVGLFLARISKGRTVR 436 Query: 403 EFLFAVIVIPTLVTLVWMSVFGGIALDQVVNKVGE---LGANGLTDISLTLFHVYDVLPY 459 EF+ ++ P +V +WM++ GG A+D +N +GA + TL + + Sbjct: 437 EFILGCVIAPAIVCFLWMTILGGTAIDLELNGGAAGSIIGATNTAKLFATLEQMISG-GF 495 Query: 460 SSVISILSIVLILVFFITSSDSGSLVIDSITAGGKIDAPVPQRIFWACIEGSIAAVMLWV 519 S I+++ +VLI+ F +TS+DSG LV+++I +GG+ + + RI W I S+ ++ Sbjct: 496 LSAITVMCVVLIMTFLVTSADSGILVMNTIMSGGEQETGIKHRIIWGLILTSVIGALIIA 555 Query: 520 G----GKEALQALQSGVVATGLPFTFVLLLMCVSLVKGL 554 G ALQ+ ++ LPFT V++ M +SL K L Sbjct: 556 GNSGTASNPFGALQNAMIIGALPFTIVMVFMMISLAKAL 594 Lambda K H 0.327 0.141 0.445 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: 958 Number of extensions: 72 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 562 Length of database: 604 Length adjustment: 36 Effective length of query: 526 Effective length of database: 568 Effective search space: 298768 Effective search space used: 298768 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: 53 (25.0 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