Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate N515DRAFT_3653 N515DRAFT_3653 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_3653 Length = 453 Score = 271 bits (693), Expect = 3e-77 Identities = 161/440 (36%), Positives = 246/440 (55%), Gaps = 17/440 (3%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 QR L RHI +A+ IG GLFLG+ +I+L GPS++F YL GA+++I++RA+GEM Sbjct: 6 QRRLTPRHITFMALGMAIGAGLFLGSANAINLAGPSVLFAYLFGGAMIFIIMRALGEMAV 65 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 DP SF + RYLG GY W+Y +++V V MAE A+G Y+ W P+LP W+ Sbjct: 66 HDPVAGSFSTYAHRYLGPFAGYLTGWNYWILMVGVGMAESTAVGIYMRQWFPELPQWIWV 125 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDTVSVTNI 192 + ++ LN + K +GE EFWF +IK+V ++ +IL +I+ + G V + N+ Sbjct: 126 FGSVAMIGGLNLMAVKVYGEMEFWFTLIKVVTVVLMILGGAGMIWLGWGNGGQPVGLANL 185 Query: 193 TKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLFY 252 +FP+G + + +V+FAF +E IGM A E P T+ +A+N + RI++FY Sbjct: 186 WSHGGWFPHGFTGMVLALPVVVFAFGGIETIGMAAGEAAQPERTIPRAVNSVLWRILIFY 245 Query: 253 VGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSITR 312 VGAL IM+IY W + SPFVT F +GI AA L+NFVV+T+A S NS FS +R Sbjct: 246 VGALFVIMAIYPWDQLGTQGSPFVTTFGKLGIPQAAGLINFVVITAALSGFNSTTFSGSR 305 Query: 313 NLYSLSKLNNDKILKP--FTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAISNSFVFIT 369 LYSLS K P + S+ GVPV A+L T ++F ++ ++P F + Sbjct: 306 MLYSLS----TKAQAPAFLGQVSEHGVPVRAVLVTLACLVFGVVLNYLLP--ERIFAMMM 359 Query: 370 SVATNLFLVVYLMTLITYLKYRK---SSDFDPKGFVLPAAHIFIPLAIAGFVLIFISLFC 426 S+ + ++M LI + +R+ ++ F + + L + + LA F+L + + Sbjct: 360 SILAFNTVWTWMMVLIAHYSFRRRHGATAFPLRAWPLTSVVCLLFLAFVLFMLGYSA--- 416 Query: 427 FKDTIVPAIGSVIWVLIFGL 446 DT V WV++ L Sbjct: 417 --DTRVALYVGAGWVVLLSL 434 Lambda K H 0.330 0.144 0.431 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: 552 Number of extensions: 26 Number of successful extensions: 1 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: 457 Length of database: 453 Length adjustment: 33 Effective length of query: 424 Effective length of database: 420 Effective search space: 178080 Effective search space used: 178080 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