Align D-serine/D-alanine/glycine transporter (characterized)
to candidate AO353_05965 AO353_05965 aromatic amino acid transporter
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__pseudo3_N2E3:AO353_05965 Length = 466 Score = 355 bits (912), Expect = e-102 Identities = 183/455 (40%), Positives = 278/455 (61%), Gaps = 15/455 (3%) Query: 8 VADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFML 67 +AD+Q + L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I GF+ Sbjct: 1 MADEQLQ-QGVLKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIA 59 Query: 68 FFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQ 127 F +MR +GE+++ SFS FA + G +AG+ +GW YW +V+ GMA++ A+ Y Q Sbjct: 60 FLIMRQLGEMIVEEPVAGSFSHFAHNYWGSFAGFLSGWNYWVLYVLVGMAELTAVGKYVQ 119 Query: 128 FWFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHF 187 FW+P++ WV++ VL+ +N VK+FGEMEFWFA+IK+VAI+ +I +G M+ Sbjct: 120 FWWPEVPTWVSAAVFFVLVNLINTMNVKVFGEMEFWFAIIKVVAIIGMIALGCYMLV--- 176 Query: 188 QSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPR 247 G +AS ++LW+ GG+FP G +G +F+F G+ELVG TAAE +P K +P+ Sbjct: 177 SGTGGPQASVSNLWSHGGFFPNGTNGLLMAMAFIMFSFGGLELVGITAAEASEPRKVIPK 236 Query: 248 AINSIPIRIIMFYVFALIVIMSVTPWSSVVP---------EKSPFVELFVLVGLPAAASV 298 AIN + R+++FYV AL V++S+ PW ++ SPFV++F L+G AA + Sbjct: 237 AINQVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFALIGSNTAAQI 296 Query: 299 INFVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGG 358 +NFVVLT+A S NSGV+ SRML+GLA++G APK+ KL+K+ VP + L S + + Sbjct: 297 LNFVVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKSLMKLNKQGVPLRALGISALITMLC 356 Query: 359 VVMLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLM 418 VV+ YV P+ A ++ + M W +I ++L +RK +K Sbjct: 357 VVVNYVAPN--EALELLFALVVASLMINWAMISLTHLKFRKAMGQRGIVPGFKAFWSPYT 414 Query: 419 CWVCMAFFVFVVVLLTLEDDTRQALLVTPLWFIAL 453 ++C+AF ++ ++ L R ++ P+W + L Sbjct: 415 NYLCLAFMAMIIYVMLLIPGVRASVYAIPVWVLIL 449 Lambda K H 0.329 0.141 0.440 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: 613 Number of extensions: 37 Number of successful extensions: 4 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: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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