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 PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= TCDB::F2HQ24 (457 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 300 bits (767), Expect = 9e-86 Identities = 172/453 (37%), Positives = 259/453 (57%), Gaps = 24/453 (5%) Query: 13 QRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRAIGEMLY 72 +RGLKNRHIQLIA+ G IGTGLFLG+ + GPS+I Y I G + ++++R +GEM+ Sbjct: 12 KRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMIV 71 Query: 73 QDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDLPIWMTE 132 ++P SF +F +Y G G+ W+Y ++ V V MAEL A+G Y+ FW P++P W++ Sbjct: 72 EEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPSWVSA 131 Query: 133 VFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHTGTDTVSVTNI 192 VL+ L+N +N K FGE EFWF +IK+VAIIG+I ++FS TG SV+N+ Sbjct: 132 AVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLFS--GTGGPQASVSNL 189 Query: 193 TKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQIPIRIVLFY 252 FFPNG S + +MF+F +E +G+TAAE P + KAINQ+ R+++FY Sbjct: 190 WDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAINQVVYRVLIFY 249 Query: 253 VGALLAIMSIYQWRDI---------PADKSPFVTIFQLIGIKWAAALVNFVVLTSAASAL 303 VGAL ++S+Y W + SPFV IF LIG AA ++NFVVLT+A S Sbjct: 250 VGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNFVVLTAALSVY 309 Query: 304 NSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFIS-MIPAIS 362 NS ++ +R LY L++ + K K +K GVP+ AL ++L+ L + ++ + P + Sbjct: 310 NSGVYCNSRMLYGLAEQGDAP--KALMKLNKQGVPLLALGVSALITLLSVLVNYLAPHEA 367 Query: 363 NSFVFITSVATNLFLVVYLMTLITYLKYRKSSDFDPKGFVLPAAHIFIP----LAIAGFV 418 +F VA+ ++ + M +T+LK+RK +G V + P L +A V Sbjct: 368 LELLFALVVAS--LMINWAMISLTHLKFRKI--MSQQGIVPGFKSFWFPFSNYLCLAFMV 423 Query: 419 LIFISLFCFKDTIVPAIGSVIWVLIFGLFTFFK 451 +I + +WVLI +F F++ Sbjct: 424 MIVCVMLMIPGIRASVFAIPVWVLI--IFGFYR 454 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: 544 Number of extensions: 41 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: 467 Length adjustment: 33 Effective length of query: 424 Effective length of database: 434 Effective search space: 184016 Effective search space used: 184016 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