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 GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__psRCH2:GFF1660 Length = 464 Score = 297 bits (761), Expect = 4e-85 Identities = 159/399 (39%), Positives = 240/399 (60%), Gaps = 24/399 (6%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 QRGL+NRHIQLIA+ G IGTGLFLG+ ++ GPS+I Y + G F +R +GEM+ Sbjct: 12 QRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMIV 71 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 +P SF +F KY G G+ + W+YW++ V V ++ELTA+G Y+QFW P+VP W Sbjct: 72 EEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWATA 131 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 L+ +N N + FGETEFWFA++KVAAI+GMI+ + L ++SGK Sbjct: 132 AAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFL---------LVSGKG-G 181 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 + AS+SN++ FP+G + AL ++MF+F +E +G+TAAE PK +PKAINQ+ Sbjct: 182 EQASISNLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQV 241 Query: 251 PVRILLFYVGALLAIMAIFNWHYI---------PADKSPFVMVFQLIGIKWAAALINFVV 301 RIL+FY+GAL ++A++ W + P SPFV +F LIG AA L+NFVV Sbjct: 242 VYRILIFYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVV 301 Query: 302 LTSAASALNSSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMATALSLLAPVL 361 LT+A S NS ++ +R +Y LA+Q D R K++ G+P+ A+ ++ ++LL + Sbjct: 302 LTAALSVYNSGVYCNSRMLYGLAEQGDAPR--SLMKINSRGVPVLAVGVSALVTLLCVAV 359 Query: 362 T-LIPQIKNAFDFAASCTTNLFLVVYFITLYTYWQYRKS 399 L PQ A + S ++ + + + ++R++ Sbjct: 360 NYLFPQ--GALELLMSLAVAALVINWAMISLAHLKFRRA 396 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: 604 Number of extensions: 33 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: 459 Length of database: 464 Length adjustment: 33 Effective length of query: 426 Effective length of database: 431 Effective search space: 183606 Effective search space used: 183606 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