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 BWI76_RS04870 BWI76_RS04870 aromatic amino acid transporter AroP
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Koxy:BWI76_RS04870 Length = 455 Score = 290 bits (741), Expect = 9e-83 Identities = 160/453 (35%), Positives = 258/453 (56%), Gaps = 22/453 (4%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 +RGLKNRHIQLIA+ G IGTGLFLG+ I GP II Y I G + ++++R +GEM+ Sbjct: 11 KRGLKNRHIQLIALGGAIGTGLFLGSASVIQNAGPGIILGYAIAGFIAFLIMRQLGEMVV 70 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 ++P SF +F +Y G G+ W+Y ++ V VAMAEL A+G Y+ FW P++P W++ Sbjct: 71 EEPVAGSFSHFAYKYWGGFAGFASGWNYWVLYVLVAMAELTAVGKYVQFWWPEIPTWVSA 130 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDTVSVTNI 192 + + +N N K FGE EFWF +IK+VA++ +IL L+FS G +V N+ Sbjct: 131 AIFFIAINAINLTNVKVFGEMEFWFAIIKVVAVVAMILFGGWLLFS--GNGGPQATVRNL 188 Query: 193 TKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLFY 252 + F P+G + ++MF+F +E +G+TAAE DNP ++ KA NQ+ RI++FY Sbjct: 189 WEQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKATNQVIYRILIFY 248 Query: 253 VGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSALFSITR 312 VG+L ++S+ W + AD SPFV IF +G + A +N VVLT+A S NS ++ +R Sbjct: 249 VGSLAVLLSLLPWSRVTADTSPFVLIFHELGDTFVANALNIVVLTAALSVYNSCVYCNSR 308 Query: 313 NLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAISNSFVFITSVA 372 L+ L++ N K K GVPVN +L ++L+ I+ A ++F + ++ Sbjct: 309 MLFGLAQQGNAP--KALMSVDKRGVPVNTILVSALVTALCVLINYF-APESAFGLLMALV 365 Query: 373 TNLFLVVYLMTLITYLKYRKSSDFDPKGFVLPAAHIFIPLA-------IAGFVLIFISL- 424 + ++ + M + ++K+R++ +G V + PL+ +AG ++I + Sbjct: 366 VSALVINWAMISLAHIKFRRAK--QQQGVVTRFPALLYPLSNWICLLFMAGVLVIMLMTP 423 Query: 425 -FCFKDTIVPAIGSVIWVLIFGLFTFFKKIKTA 456 ++P +W+ + G+ FK+ KTA Sbjct: 424 GMAISVYLIP-----VWIAVLGVGYLFKQ-KTA 450 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: 526 Number of extensions: 26 Number of successful extensions: 2 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: 455 Length adjustment: 33 Effective length of query: 424 Effective length of database: 422 Effective search space: 178928 Effective search space used: 178928 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