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 WP_160173842.1 JG50_RS0109790 amino acid permease
Query= TCDB::F2HQ24 (457 letters) >NCBI__GCF_000763315.1:WP_160173842.1 Length = 453 Score = 207 bits (528), Expect = 4e-58 Identities = 117/383 (30%), Positives = 204/383 (53%), Gaps = 12/383 (3%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 QR L R + +I + IGTGLF+G+ +IH GP ++F YL+ ++ ++ + + Sbjct: 16 QRSLSERQMIMIGLGSAIGTGLFMGSSLTIHYAGPGVLFSYLLSSLIVLAMVFCLSRLSV 75 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 P SF YLG G+ ++++Y V E AIG Y+ +W P LP W+ Sbjct: 76 IHPTAGSFGLHAETYLGSWFGFAVRFTYWAANAIVIGGEATAIGLYMKYWFPGLPSWIWI 135 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDTVSVTNI 192 + +L+ +N ++ + FG E+WF +K+VA+IG IL I LIF G T S + Sbjct: 136 IAFSLLIIGINAISVQSFGWFEYWFSTLKVVAVIGFILLGIALIF-----GNSTQSTHYL 190 Query: 193 TKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLFY 252 F P+G + M MF+F+ E I +TA E P+ L +A+ + R+V+FY Sbjct: 191 LAYGGFLPHGWKGVWMGSAMAMFSFMGTEIIAITAGEAKKPKQALTRAMKWMVARLVIFY 250 Query: 253 VGALLAIMSIYQWRDIPAD---KSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFS 309 + + L ++ I W I + +SPFV + Q + I +AA ++NF++LT+A S +N+ L++ Sbjct: 251 LLSTLVMVCIVPWNQIGGEQIQESPFVKVLQSLHIPYAAGVMNFIILTAALSTMNANLYA 310 Query: 310 ITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAISNSFVFIT 369 TR ++SLSK + F K ++ G+P+ AL+ +S + ++M + + +F Sbjct: 311 CTRMMFSLSKSGYAPAV--FGKVNRRGIPLMALIVSSFGLGVAVLLNMFDPQAYNTLFGI 368 Query: 370 SVATNLFLVVYLMTLITYLKYRK 392 S+ +F ++ ++Y + R+ Sbjct: 369 SIFGGIF--TWITIFLSYARLRR 389 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: 522 Number of extensions: 25 Number of successful extensions: 3 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 24 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