Align D-serine/D-alanine/glycine transporter (characterized)
to candidate N515DRAFT_2630 N515DRAFT_2630 amino acid/polyamine/organocation transporter, APC superfamily
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_2630 Length = 454 Score = 387 bits (993), Expect = e-112 Identities = 197/454 (43%), Positives = 286/454 (62%), Gaps = 12/454 (2%) Query: 18 SLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGEL 77 SL+R L RHI+L+A+G AIG GLF+GS I LAGP+I+ Y++ G +F +MRA+GE+ Sbjct: 6 SLQRGLQERHIRLMALGSAIGVGLFLGSANAIRLAGPAILLSYLLGGVAIFIIMRALGEM 65 Query: 78 LLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWV 137 + N SFS +A D LGP GY TGW YWF W++T +A++ A+ Y WFPD+ W+ Sbjct: 66 AVQNPVAGSFSRYAQDYLGPLPGYLTGWNYWFMWLMTCIAEITAVGVYMGVWFPDVPQWI 125 Query: 138 ASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASF 197 +LA +V + +NLA VK +GE EFWFAMIK+V IV +IV G M+ + GV Sbjct: 126 WALAALVTMGAVNLAAVKAYGEFEFWFAMIKVVTIVLMIVGGGAMIVFGLGN-QGVPTGI 184 Query: 198 AHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRII 257 ++LW GG+ P G G Q+ +FA++G+E++G TA E +P+KS+P AINS+ RI+ Sbjct: 185 SNLWTHGGFMPNGAKGMLMALQMVMFAYLGVEMIGLTAGEADNPKKSIPDAINSVFWRIL 244 Query: 258 MFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVFS 317 +FYV AL VIMS+ PW+ + SPFV F +G+ +AA +INFVVLT+A SS N G++S Sbjct: 245 IFYVGALFVIMSIYPWNELGTHGSPFVMTFERLGIKSAAGIINFVVLTAALSSCNGGIYS 304 Query: 318 TSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMITT 377 T RMLF LAQ+G AP+ FA S +P + + S + LL GV++ Y+ P+ + F +T+ Sbjct: 305 TGRMLFNLAQQGQAPRTFAVTSPSGIPNRAVLVSLVALLFGVLLNYLVPAKV--FVWVTS 362 Query: 378 VSAILFMFVWTIILCSYLVYRK-----QRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVL 432 + ++ W I+L + + YR+ QR L +++MP ++ +AF V VV L Sbjct: 363 AATFGAIWTWGIVLITQMKYRRGLSEAQRSQL----VFRMPFFPYASYLALAFLVLVVGL 418 Query: 433 LTLEDDTRQALLVTPLWFIALGLGWLFIGKKRAA 466 + DTR AL+V PLW + L + + G R A Sbjct: 419 MGYFPDTRVALIVGPLWLVLLTVLYYVFGLGRRA 452 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: 658 Number of extensions: 37 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: 454 Length adjustment: 33 Effective length of query: 437 Effective length of database: 421 Effective search space: 183977 Effective search space used: 183977 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