Align Serine permease SerP1 (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= SwissProt::A2RI87 (459 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 289 bits (740), Expect = 1e-82 Identities = 149/388 (38%), Positives = 237/388 (61%), Gaps = 13/388 (3%) Query: 11 QRGLQNRHIQLIAIAGTIGTGLFLGAGKTIQMTGPSVIFAYILIGIAMFFFLRTIGEMLY 70 +RGL+NRHIQLIA+ G IGTGLFLG +TI+M GPSV+ Y + GI FF +R +GEM+ Sbjct: 14 KRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLGEMVV 73 Query: 71 NDPSQHSFLNFVTKYSGIRTGYFTQWSYWLVIVFVCISELTAIGTYIQFWLPHLPLWLIE 130 ++P SF +F KY G G+ + W+YW++ + V ++EL+A+G Y+Q+W PH+P W Sbjct: 74 DEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPTWASA 133 Query: 131 IVMLALLFGLNTLNSRFFGETEFWFAMIKVAAILGMIVTAIILVASNFHYTTVLSGKTVN 190 + L+ +N + + FGE EFWF+++KV AI+GMIV L+AS T Sbjct: 134 LGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLASG----------TAG 183 Query: 191 DTASLNNIFDGFQLFPHGAWNFVGALQMVMFAFTSMEFIGMTAAETVNPKKSLPKAINQI 250 AS++N++ FP+G V A+ ++MF+F +E +G+TAAE P+K++PKA NQ+ Sbjct: 184 PQASVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQV 243 Query: 251 PVRILLFYVGALLAIMAIFNWHYIPADKSPFVIVFQLIGIKWAAALINFVVLTSAASALN 310 RIL+FYVGAL +++++ W + SPFV++F + A ++N VVLT+A S N Sbjct: 244 IYRILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYN 303 Query: 311 SSLFSATRNMYSLAKQHDKGRLTAFTKLSKAGIPINALYMATALSLLAPVLTLIPQIKNA 370 S ++ +R ++ LAKQ + + A K++K GIP+ AL + +AL+ A V+ A Sbjct: 304 SGVYCNSRMLFGLAKQGNAPK--ALLKVNKRGIPLAALGV-SALATAACVVINYFMPGEA 360 Query: 371 FNFAASCTTNLFLVVYFITLYTYWQYRK 398 F + ++ + + + ++R+ Sbjct: 361 FELLMGLVVSALIINWAMISIIHLKFRR 388 Lambda K H 0.329 0.141 0.435 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: 545 Number of extensions: 26 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: 465 Length adjustment: 33 Effective length of query: 426 Effective length of database: 432 Effective search space: 184032 Effective search space used: 184032 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