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 PP_4840 PP_4840 D-alanine, beta-alanine, D-serine, glycine permease
Query= TCDB::F2HQ25 (459 letters) >FitnessBrowser__Putida:PP_4840 Length = 468 Score = 355 bits (910), Expect = e-102 Identities = 184/441 (41%), Positives = 270/441 (61%), Gaps = 12/441 (2%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 QR L NRHIQLIAI G IGTGLF+G+GKTI + GPS+IF Y++IG +FF +R +GE+L Sbjct: 15 QRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELLL 74 Query: 71 NDPSQHSFLNFVTKYSGVRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPQVPLWLIE 130 ++ + SF++F G GYFT W+YW V I+++ AI Y QFW P +P W+ Sbjct: 75 SNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAYTQFWFPDLPQWIPA 134 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAIIGMIVTAIILVAGNFHYSTVLSGKTVH 190 + + LL LN + + FGE EFWFA++K+ AI+G++ T + +V F T SG+T Sbjct: 135 LTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVITGF---TSPSGRT-- 189 Query: 191 DSASLSNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 A L+N+++ +FPHG F Q+ +FAF +E +G TAAE NP+++LP+AIN I Sbjct: 190 --AQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTLPRAINSI 247 Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVMVFQLIGIKWAAALINFVVLTSAASALN 310 P+RI++FYV AL+AIMA+ W + KSPFV +F L G+ AA++INFVVLTSAAS+ N Sbjct: 248 PIRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLTSAASSAN 307 Query: 311 SSLFSATRNMYSLAQQHDKGRLTPFTKLSKAGIPINALYMA-TALSLLAPVLTLIPQIKN 369 S +FS +R +Y L+Q+ D + F KLS +P N LY + T L L A ++ L+P + Sbjct: 308 SGVFSTSRMLYGLSQEGDAPK--AFEKLSSRSVPANGLYFSCTCLLLGAVLIYLVPNVVE 365 Query: 370 AFDFAASCTTNLFLVVYFITLYTYWQYRKSED--YNPKGFLTPKPQITVPFIVAIFAIVF 427 AF + + LF+ V+ + L +Y +YRK + + P + ++ FA + Sbjct: 366 AFTLVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQASNYKMPGGRFMCYVCLSFFAFIL 425 Query: 428 ASLFFNADTFYPALGAIVWTI 448 L ADT + +W + Sbjct: 426 VLLSLEADTRSALVVTPIWFV 446 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: 624 Number of extensions: 36 Number of successful extensions: 5 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: 468 Length adjustment: 33 Effective length of query: 426 Effective length of database: 435 Effective search space: 185310 Effective search space used: 185310 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