Align D-serine/D-alanine/glycine transporter (characterized)
to candidate RR42_RS33495 RR42_RS33495 aromatic amino acid transporter
Query= SwissProt::A0A0H2VDI7 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS33495 Length = 465 Score = 363 bits (931), Expect = e-105 Identities = 184/452 (40%), Positives = 282/452 (62%), Gaps = 5/452 (1%) Query: 16 EQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMG 75 + +L+R L NRHIQLIA+GGAIGTGLF+G +TI +AGPS++ Y + G + FF+MR +G Sbjct: 10 DATLKRGLKNRHIQLIALGGAIGTGLFLGIAQTIKMAGPSVLLGYAVAGIIAFFIMRQLG 69 Query: 76 ELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPGLSD 135 E+++ SFS FA+ G +AG+ +GW YW +++ MA++ A+ Y Q+W+P + Sbjct: 70 EMVVDEPVAGSFSHFANKYCGSFAGFMSGWNYWVLYILVSMAELSAVGIYVQYWWPHIPT 129 Query: 136 WVASLSVIILLLVLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEA 195 W ++L +L+ +NL +VK FGEMEFWF+++K++AIV +IV G ++A G +A Sbjct: 130 WASALGFFLLINAINLTSVKSFGEMEFWFSIVKVLAIVGMIVFGGYLLA---SGTAGPQA 186 Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255 S ++LW GG+FP G+SG + +F+F G+ELVG TAAE +PEK++P+A N + R Sbjct: 187 SVSNLWQHGGFFPNGISGLVMAMAVIMFSFGGLELVGITAAEADEPEKTIPKATNQVIYR 246 Query: 256 IIMFYVFSLIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315 I++FYV +L V++S+ PW VV SPFV +F + A+V+N VVLT+A S NSGV Sbjct: 247 ILIFYVGALGVLLSLYPWEKVVTGGSPFVLIFHAMNSDIVATVLNAVVLTAALSVYNSGV 306 Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375 + SRMLFGLA++G APKA K++KR +P L S + VV+ Y P M Sbjct: 307 YCNSRMLFGLAKQGNAPKALLKVNKRGIPLAALGVSALATAACVVINYFMPGEAFELLMG 366 Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFVLVLLTL 435 VSA++ W +I +L +R+ + +++ +K L +VC+AF +L ++ L Sbjct: 367 LVVSALIIN--WAMISIIHLKFRRDKRAAGQETRFKSLGYPLTNYVCLAFLAGILYVMYL 424 Query: 436 EDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 R ++ + P W LGL + K++ AE Sbjct: 425 TPGLRISVYLIPAWLAVLGLSYRLRQKQKRAE 456 Lambda K H 0.329 0.141 0.441 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: 31 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: 470 Length of database: 465 Length adjustment: 33 Effective length of query: 437 Effective length of database: 432 Effective search space: 188784 Effective search space used: 188784 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