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 14258 b0112 aromatic amino acid transporter (NCBI)
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Keio:14258 Length = 457 Score = 296 bits (757), Expect = 1e-84 Identities = 158/463 (34%), Positives = 261/463 (56%), Gaps = 21/463 (4%) Query: 1 MENLQEKHEAQRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFF 60 ME Q + +RGL+NRHIQLIA+ G IGTGLFLG+ IQ GP +I Y + G F Sbjct: 2 MEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAFL 61 Query: 61 FLRTIGEMLYNDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFW 120 +R +GEM+ +P SF +F KY G G+ + W+YW++ V V ++ELTA+G YIQFW Sbjct: 62 IMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQFW 121 Query: 121 LPQVPLWLIEIVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIV-TAIILVAGNFH 179 P++P W+ V ++ +N N + FGE EFWFA+IKV A++ MI+ +L +GN Sbjct: 122 YPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLLFSGN-- 179 Query: 180 YSTVLSGKTVHDSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNP 239 A++SN++D PHG V + ++MF+F +E +G+TAAE NP Sbjct: 180 ---------GGPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNP 230 Query: 240 KKSLPKAINQIPVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINF 299 ++S+PKA NQ+ RIL+FY+G+L ++++ W + AD SPFV++F +G + A +N Sbjct: 231 EQSIPKATNQVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNI 290 Query: 300 VVLTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAP 359 VVLT+A S NS ++ +R ++ LAQQ + + + K G+P+N + ++ ++ L Sbjct: 291 VVLTAALSVYNSCVYCNSRMLFGLAQQGNAPK--ALASVDKRGVPVNTILVSALVTALCV 348 Query: 360 VLTLIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKSEDYNPKGFLTPKPQITVP-- 417 ++ + ++AF + + ++ + + + ++R+++ +G +T P + P Sbjct: 349 LINYLAP-ESAFGLLMALVVSALVINWAMISLAHMKFRRAK--QEQGVVTRFPALLYPLG 405 Query: 418 -FIVAIF-AIVFASLFFNADTFYPALGAIVWTIFFGLYSHYKK 458 +I +F A V + VW I G+ +K+ Sbjct: 406 NWICLLFMAAVLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKE 448 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: 597 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: 457 Length adjustment: 33 Effective length of query: 426 Effective length of database: 424 Effective search space: 180624 Effective search space used: 180624 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