Align D-serine/D-alanine/glycine transporter (characterized)
to candidate AO353_12275 AO353_12275 proline-specific permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12275 Length = 468 Score = 372 bits (956), Expect = e-107 Identities = 187/457 (40%), Positives = 283/457 (61%), Gaps = 4/457 (0%) Query: 12 QAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVM 71 Q PA L+R L+ RHI+ +A+G AIGTGLF GS I +AGP+++ Y+I G +F VM Sbjct: 2 QKPAN-GLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVM 60 Query: 72 RAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFP 131 RA+GE+ + N SF +AS LGP AG+ GWTY F V+ GMADV A Y FWFP Sbjct: 61 RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120 Query: 132 DLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPT 191 ++S W+ L V+ ++ LNL VK+FGEMEFW +++K+ AIV++I+ G ++ + Sbjct: 121 EVSRWIWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180 Query: 192 GVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINS 251 G ++LW GG+ P G+ G A F + +FAF GIE++G TA E KDP+ LPRAIN+ Sbjct: 181 GQVTDISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINA 240 Query: 252 IPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSA 311 +P+RI++FYV ++V+MS+ PW + + SPFV++F +G+ +AA+++N VV+T+A S+ Sbjct: 241 VPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAI 300 Query: 312 NSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGA 371 NS +F RM+FGLAQ+G APK FA LS+ VP + + LL GV++ Y+ P Sbjct: 301 NSDIFGAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPE--NV 358 Query: 372 FTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVV 430 F +I +++ ++VW +IL + + R+ + + +P +AF +FV Sbjct: 359 FLLIASIATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVF 418 Query: 431 VLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 +L DT+ AL+V +W + L L +L K A + Sbjct: 419 GVLGYFPDTQAALIVGVVWIVLLVLAYLMWVKPAAGQ 455 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: 645 Number of extensions: 31 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: 470 Length of database: 468 Length adjustment: 33 Effective length of query: 437 Effective length of database: 435 Effective search space: 190095 Effective search space used: 190095 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