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 Pf1N1B4_1580 Histidine transport protein (permease)
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 290 bits (742), Expect = 7e-83 Identities = 165/443 (37%), Positives = 254/443 (57%), Gaps = 10/443 (2%) Query: 10 KPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGE 69 K +RGL RHI+ +A+ IGTGLF G+ +I + GP+++ YLI GA +++++RA+GE Sbjct: 6 KGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65 Query: 70 MLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIW 129 M +P SF + S YLG G+ + W+Y +V V MA++ A G Y+ FW P++ W Sbjct: 66 MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRW 125 Query: 130 MTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLIL--TAIILIFSHYHTGTDTV 187 + + ++ ++ LN N K FGE EFW ++K+ AI+ +IL I+L G Sbjct: 126 IWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGAQAT 185 Query: 188 SVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIR 247 ++N+ F PNG+ SF +VMFAF +E IG+TA E +P+ L +AIN +P+R Sbjct: 186 DISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAVPLR 245 Query: 248 IVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALNSAL 307 I+LFYV +L +MSI+ W+ I + SPFV IF +GI AA ++N VV+++A SA+NS + Sbjct: 246 ILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAINSDI 305 Query: 308 FSITRNLYSLSKLNNDKILKPFTKFSKAGVP-VNALLFTSLLILFTPFISMIPAISNSFV 366 F R +Y L++ + K F + S+ GVP + ++ +S L+L +IP N F+ Sbjct: 306 FGAGRMMYGLAQQGHAP--KGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIP--ENVFL 361 Query: 367 FITSVATNLFLVVYLMTLITYLKYRKSSDFDPKG---FVLPAAHIFIPLAIAGFVLIFIS 423 I SVAT + V+LM L T + R+S + F +P AIA + IF Sbjct: 362 LIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFIFGV 421 Query: 424 LFCFKDTIVPAIGSVIWVLIFGL 446 L F DT I V+W+++ L Sbjct: 422 LGYFPDTQAALIVGVVWIVLLVL 444 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: 536 Number of extensions: 39 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: 469 Length adjustment: 33 Effective length of query: 424 Effective length of database: 436 Effective search space: 184864 Effective search space used: 184864 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