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 WP_012103848.1 CKL_RS17165 amino acid permease
Query= TCDB::F2HQ25 (459 letters) >NCBI__GCF_000016505.1:WP_012103848.1 Length = 453 Score = 350 bits (899), Expect = e-101 Identities = 182/454 (40%), Positives = 280/454 (61%), Gaps = 19/454 (4%) Query: 4 LQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLR 63 + E RGL+NRH+QL+AI G IGTGLFLG+G++I + GPS++FAY + G+ F +R Sbjct: 1 MSENENLSRGLKNRHVQLLAIGGAIGTGLFLGSGRSIHLAGPSILFAYTITGVVCFLIMR 60 Query: 64 TIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQ 123 +GE+L ++ + HSF++FV +Y G + T W+YW + + +++LTA G YIQ+WLP Sbjct: 61 ALGELLLSNLNYHSFVDFVQEYMGNGAAFITGWTYWFCWISLAMADLTASGLYIQYWLPN 120 Query: 124 VPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTV 183 + W+ +V+L +L +N + FGE EFWFA+IK+ AI+ +I+ ++ F Sbjct: 121 IAQWVPSLVVLIILLIMNLTTVKLFGEMEFWFALIKIVAILALIIIGTFMIIKGF----- 175 Query: 184 LSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSL 243 T ++S +N+++ FP+G F+ + QMV+FAFT +E +G+TA ET NP+ + Sbjct: 176 ---STNVGASSFTNLWNHGGWFPNGTSGFILSFQMVVFAFTGIELVGLTAGETENPEYVI 232 Query: 244 PKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLT 303 PKAIN IP+RI++FY+GAL IM+I+ W+ I ADKSPFV VF +GI AA+++NFVVLT Sbjct: 233 PKAINNIPIRIIIFYIGALTVIMSIYPWNSINADKSPFVQVFAAVGIAAAASIVNFVVLT 292 Query: 304 SAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVLTL 363 SAASA NS +FS +R +YSLA++++ +L+ +P NAL + A+ L++ +L+ Sbjct: 293 SAASACNSGIFSTSRMVYSLAKENNAP--NSMKRLTSNKVPSNALMFSAAVILISVILSY 350 Query: 364 IPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPK-----GFLTPKPQITVPF 418 I + F S +T F+ ++ I + + +YRK+ NPK F P IT Sbjct: 351 I-MPEGVFVLITSISTFCFIFIWGIMVVCHLKYRKT---NPKLASKSKFKMPLYPITNYI 406 Query: 419 IVAIFAIVFASLFFNADTFYPALGAIVWTIFFGL 452 ++A V A L N +T VW I G+ Sbjct: 407 VLAFIVFVLAVLALNKETRVALFVTPVWFIMLGI 440 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: 596 Number of extensions: 39 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: 453 Length adjustment: 33 Effective length of query: 426 Effective length of database: 420 Effective search space: 178920 Effective search space used: 178920 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 24 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