Align D-serine/D-alanine/glycine transporter (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 358 bits (919), Expect = e-103 Identities = 186/456 (40%), Positives = 276/456 (60%), Gaps = 10/456 (2%) Query: 17 QSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGE 76 Q L+R LT RHI +A+G AIG GLF+GS I+LAGPS++F Y+ G M+F +MRA+GE Sbjct: 3 QHLQRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGE 62 Query: 77 LLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDW 136 + + + SFS +A LGP+AGY TGW YW V GMA+ A+ Y + WFP+L W Sbjct: 63 MAVHDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQW 122 Query: 137 VASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEAS 196 + + ++ LNL VK++GEMEFWF +IK+V +V +I+ G M+ + + + G Sbjct: 123 IWVFGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGN-GGQPVG 181 Query: 197 FAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRI 256 A+LW+ GGWFP G +G + VFAF GIE +G A E PE+++PRA+NS+ RI Sbjct: 182 LANLWSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRI 241 Query: 257 IMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGVF 316 ++FYV AL VIM++ PW + + SPFV F +G+P AA +INFVV+T+A S NS F Sbjct: 242 LIFYVGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTF 301 Query: 317 STSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMIT 376 S SRML+ L+ + AP ++S+ VP + + + CL+ GVV+ Y+ P I F M+ Sbjct: 302 SGSRMLYSLSTKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLPERI--FAMMM 359 Query: 377 TVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVVVLLTLE 436 ++ A ++ W ++L ++ +R++ H + + + L VC+ F FV+ +L Sbjct: 360 SILAFNTVWTWMMVLIAHYSFRRR----HGATAFPLRAWPLTSVVCLLFLAFVLFMLGYS 415 Query: 437 DDTRQALLVTPLWFIALGLGWLFIG---KKRAAELR 469 DTR AL V W + L L + +G + RA E R Sbjct: 416 ADTRVALYVGAGWVVLLSLAYRLLGIGARMRALEPR 451 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: 693 Number of extensions: 41 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: 453 Length adjustment: 33 Effective length of query: 437 Effective length of database: 420 Effective search space: 183540 Effective search space used: 183540 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