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 Pf1N1B4_1580 Histidine transport protein (permease)
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Length = 469 Score = 283 bits (723), Expect = 1e-80 Identities = 163/450 (36%), Positives = 256/450 (56%), Gaps = 22/450 (4%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 +RGL RHI+ +A+ IGTGLF G+ IQM GP+V+ AY++ G A+F +R +GEM Sbjct: 9 KRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGEMAV 68 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 ++P SF + + Y G G+ W+Y +V V ++++TA G Y+ FW P+V W+ Sbjct: 69 HNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVDRWIWV 128 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 + +++++ GLN N + FGE EFW +++KVAAI+ MI+ ++ F ST + Sbjct: 129 LGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIML--FGISTAPGAQ--- 183 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 + +SN++ P+G + + +VMFAF +E IG+TA E +P++ LP+AIN + Sbjct: 184 -ATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAINAV 242 Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310 P+RILLFYV +L +M+IF W I + SPFV +F +GI AA ++N VV+++A SA+N Sbjct: 243 PLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSAIN 302 Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIP-INALYMATALSLLAPVLTLIPQIKN 369 S +F A R MY LAQQ + F +LS+ G+P + + M++AL L + LIP+ N Sbjct: 303 SDIFGAGRMMYGLAQQGHAPK--GFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPE--N 358 Query: 370 AFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYN-------PKGFLTPKPQITVPFIVAI 422 F AS T + V+ + L+T R+S P F P + F++ I Sbjct: 359 VFLLIASVATFATVWVWLMILFTQVAMRRSMSAEQVAQLKFPVPFWPYAPMAAIAFMLFI 418 Query: 423 FAIVFASLFFNADTFYPALGAIVWTIFFGL 452 F + L + DT + +VW + L Sbjct: 419 FGV----LGYFPDTQAALIVGVVWIVLLVL 444 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: 579 Number of extensions: 25 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: 469 Length adjustment: 33 Effective length of query: 426 Effective length of database: 436 Effective search space: 185736 Effective search space used: 185736 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