Align Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized)
to candidate 1937132 b3795 predicted transporter (NCBI)
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Keio:1937132 Length = 461 Score = 293 bits (751), Expect = 6e-84 Identities = 174/467 (37%), Positives = 263/467 (56%), Gaps = 32/467 (6%) Query: 7 KHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIG 66 K E QRGL+ RHI+LIA+ GTIG GLF+GA T++ GPSV+ AYI+ G+ +FF +R++G Sbjct: 5 KPELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRSMG 64 Query: 67 EMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPL 126 EML+ +P SF + +Y GY T WSYW + + V ISE+TAIG Y+QFW P++ Sbjct: 65 EMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEMAQ 124 Query: 127 WLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSG 186 W+ ++ +AL+ N R +GE EFWFAMIKV II MIV + ++ F Sbjct: 125 WIPALIAVALVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVIGLGVIFFGFGNG----- 179 Query: 187 KTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKA 246 S SN+ + F G F+ AL +V+ ++ +E IG+TA E NP+ +L A Sbjct: 180 ---GQSIGFSNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSA 236 Query: 247 INQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAA 306 + ++ RIL+FYVGA+ I+ IF W+ I ++ SPFV+ F IGI AA +INFVVLT+A Sbjct: 237 VGKVLWRILIFYVGAIFVIVTIFPWNEIGSNGSPFVLTFAKIGITAAAGIINFVVLTAAL 296 Query: 307 SALNSSLFSATRNMYSLAQQHDKGRLTP--FTKLSKAGIPINALYMATALSLLAPVLT-L 363 S NS ++S R +Y+LA K R P K+S+ G+P+ + ++ A+ L+ L + Sbjct: 297 SGCNSGMYSCGRMLYALA----KNRQLPAAMAKVSRHGVPVAGVAVSIAILLIGSCLNYI 352 Query: 364 IPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPKPQITVPF----- 418 IP + F + S + +V +F+ L + ++R++ K + P ++ F Sbjct: 353 IPNPQRVFVYVYSASVLPGMVPWFVILISQLRFRRAH----KAAIASHPFRSILFPWANY 408 Query: 419 -IVAIFAIVFASLFFNADTFYPALGAIVWTI-------FFGLYSHYK 457 +A V ++FN DT I++ + FGL H K Sbjct: 409 VTMAFLICVLIGMYFNEDTRMSLFVGIIFMLAVTAIYKVFGLNRHGK 455 Lambda K H 0.329 0.141 0.434 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: 661 Number of extensions: 33 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: 459 Length of database: 461 Length adjustment: 33 Effective length of query: 426 Effective length of database: 428 Effective search space: 182328 Effective search space used: 182328 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