Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF344 PS417_01755 proline-specific permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__WCS417:GFF344 Length = 469 Score = 366 bits (940), Expect = e-106 Identities = 184/457 (40%), Positives = 286/457 (62%), Gaps = 4/457 (0%) Query: 16 EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75 E+ L+R L+ RHI+ +A+G AIGTGLF GS I +AGP+++ Y+I G +F VMRA+G Sbjct: 5 EKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALG 64 Query: 76 ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSD 135 E+ + N SF +AS LGP AG+ GWTY F ++ +ADV A Y FWFPD++ Sbjct: 65 EMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMIIVCLADVTAFGIYMGFWFPDVAR 124 Query: 136 WVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195 WV L +++L+ LNL VK+FGEMEFW +++K+ AIV++I+ G ++ S +A Sbjct: 125 WVWVLGIVLLIGGLNLCNVKVFGEMEFWLSLLKVGAIVAMILGGFGIMLFGIHSAGETQA 184 Query: 196 S-FAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPI 254 S ++LW GG+ P G+ G A F + +FAF GIE++G TA E KDP++ +P+AIN++P+ Sbjct: 185 SGLSNLWAHGGFMPNGIGGLIASFAVVMFAFGGIEIIGITAGEAKDPQRVIPKAINAVPL 244 Query: 255 RIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSG 314 RI++FYV L V+M++ PW + + SPFV++F +G+ +AA+++N VV+++A S+ NS Sbjct: 245 RILLFYVLTLFVLMAIYPWPQIGSQGSPFVQIFSNLGIGSAATILNIVVISAAVSAINSD 304 Query: 315 VFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTM 374 +F RM++GLAQ+G APK FA+LSK+ VP + LLGGVV+ Y+ P F + Sbjct: 305 IFGAGRMMYGLAQQGQAPKGFAQLSKQGVPWMTVVVMGAALLGGVVLNYLIPE--NVFLV 362 Query: 375 ITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLL 433 I +++ ++VW +IL + + R+ + + +P + F +FV +L Sbjct: 363 IASIATFATVWVWLMILFTQVAMRRSMTKEQVAELKFPVPFWPYAPAAAIVFMLFVFGVL 422 Query: 434 TLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAELRK 470 DT+ ALLV +W + L + +L K A + K Sbjct: 423 GYFPDTQAALLVGAVWIVLLVVAYLLWVKPSAGQAAK 459 Lambda K H 0.329 0.141 0.440 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: 668 Number of extensions: 34 Number of successful extensions: 3 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: 470 Length of database: 469 Length adjustment: 33 Effective length of query: 437 Effective length of database: 436 Effective search space: 190532 Effective search space used: 190532 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 (21.8 bits) S2: 51 (24.3 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