Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF1065 PS417_05405 D-alanine/D-serine/glycine permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__WCS417:GFF1065 Length = 472 Score = 378 bits (971), Expect = e-109 Identities = 187/436 (42%), Positives = 280/436 (64%), Gaps = 4/436 (0%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L+R L RHI+L+A+G IG GLF+GS K I +AGP+I+ Y+I G + +MRA+GE+ Sbjct: 18 LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77 Query: 79 LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138 + N SFS +A D LGP AG+ TGW YWF W+VT +A++ A+ Y WFPD W+ Sbjct: 78 VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137 Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198 +LA ++ + ++NL VK FGE EFWFA+IKIV I+++++ G+ ++A F + GV + Sbjct: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGN-DGVALGIS 196 Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258 +LW GG+ P G+ G Q+ +FA++G+E++G TA E K+P+K++P AI S+ RI++ Sbjct: 197 NLWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILL 256 Query: 259 FYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFST 318 FYV AL VI+S+ PW+ + + SPFV F +G+ AA +INFVV+T+A SS N G+FST Sbjct: 257 FYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIFST 316 Query: 319 SRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITTV 378 RML+ LAQ G AP FAK S VP K L S LL GV++ Y+ P + F +T++ Sbjct: 317 GRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKV--FVWVTSI 374 Query: 379 SAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLTLED 437 + ++ W +IL + L +RK + + Y+M L + ++ +AF + VV L+ Sbjct: 375 ATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFP 434 Query: 438 DTRQALLVTPLWFIAL 453 DTR AL V P++ + L Sbjct: 435 DTRIALYVGPVFLVLL 450 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: 650 Number of extensions: 38 Number of successful extensions: 4 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: 472 Length adjustment: 33 Effective length of query: 437 Effective length of database: 439 Effective search space: 191843 Effective search space used: 191843 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