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 PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 291 bits (744), Expect = 4e-83 Identities = 171/452 (37%), Positives = 261/452 (57%), Gaps = 9/452 (1%) Query: 5 QNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILL 64 Q E P +R L RHI+L+A+ IG GLFLG+ K+I + GP+I+ Y+I G + +++ Sbjct: 11 QATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIM 70 Query: 65 RAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLP 124 RA+GEM +P SF + YLG G+ W+Y + + +AE+ A+ Y+ W P Sbjct: 71 RALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGIWFP 130 Query: 125 DLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGT 184 D+P W+ + L + +N + K FGE EFWF +IKIV II ++L I +I + Sbjct: 131 DVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFGNDG 190 Query: 185 DTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQI 244 V ++N+ F PNG++ S QMVMFA++ +E IG+TA E NP+ T+ +AI + Sbjct: 191 VAVGISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQAIGSV 250 Query: 245 PIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALN 304 RI+LFYVGAL I+SIY W +I + SPFV F+ +GIK AA ++NFVV+T+A S+ N Sbjct: 251 FWRILLFYVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAALSSCN 310 Query: 305 SALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFT-SLLILFTPFISMIPAISN 363 +FS R LYSL++ N + F + SK GVP NALL + L+L ++P Sbjct: 311 GGIFSTGRMLYSLAQ--NGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVP--EK 366 Query: 364 SFVFITSVATNLFLVVYLMTLITYLKYR---KSSDFDPKGFVLPAAHIFIPLAIAGFVLI 420 FV++TS+AT + ++M L+ LK+R +++ + + + LA+A VL+ Sbjct: 367 VFVWVTSIATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLVLV 426 Query: 421 FISLFCFKDTIVPA-IGSVIWVLIFGLFTFFK 451 + F+DT V IG VL+ L+ F+ Sbjct: 427 VGLMAYFEDTRVALYIGPAFLVLLTVLYYTFR 458 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: 550 Number of extensions: 31 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: 457 Length of database: 472 Length adjustment: 33 Effective length of query: 424 Effective length of database: 439 Effective search space: 186136 Effective search space used: 186136 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