Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PfGW456L13_4291 Aromatic amino acid transport protein AroP
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4291 Length = 467 Score = 356 bits (914), Expect = e-103 Identities = 188/465 (40%), Positives = 280/465 (60%), Gaps = 15/465 (3%) Query: 11 DQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFV 70 D+ + L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I GF+ F + Sbjct: 3 DEILRQGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLI 62 Query: 71 MRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWF 130 MR +GE+++ SFS FA G +AG+ +GW YW +V+ GMA++ A+ Y QFW+ Sbjct: 63 MRQLGEMIVEEPVAGSFSHFAHKYWGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWW 122 Query: 131 PDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSP 190 P++ WV++ VL+ +N+ VK+FGEMEFWFA+IK+VAI+ +I +G M+ F Sbjct: 123 PEVPSWVSAAVFFVLVNLINMMNVKVFGEMEFWFAIIKVVAIIGMIALGCYML---FSGT 179 Query: 191 TGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAIN 250 G +AS ++LW+ GG+FP G SG +F+F G+ELVG TAAE +P K +P+AIN Sbjct: 180 GGPQASVSNLWDHGGFFPNGYSGLLMAMAFIMFSFGGLELVGITAAEASEPGKVIPKAIN 239 Query: 251 SIPIRIIMFYVFALIVIMSVTPWSSVVPE---------KSPFVELFVLVGLPAAASVINF 301 + R+++FYV AL V++S+ PW ++ SPFV++F L+G AA ++NF Sbjct: 240 QVVYRVLIFYVGALTVLLSLYPWDQLLQTLGASGDAYGGSPFVQIFSLIGSDTAAHILNF 299 Query: 302 VVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVM 361 VVLT+A S NSGV+ SRML+GLA++G APKA KL+K+ VP L S + L V++ Sbjct: 300 VVLTAALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPLLALGVSALITLLSVLV 359 Query: 362 LYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWV 421 Y+ P A ++ + M W +I ++L +RK +K ++ Sbjct: 360 NYLAPH--EALELLFALVVASLMINWAMISLTHLKFRKIMSQQGIVPGFKSFWFPFSNYL 417 Query: 422 CMAFFVFVVVLLTLEDDTRQALLVTPLW-FIALGLGWLFIGKKRA 465 C+AF V +V ++ + R ++ P+W I G + + K RA Sbjct: 418 CLAFMVMIVCVMLMIPGIRASVFAIPVWVLIIFGFYRMRMAKDRA 462 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: 621 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: 470 Length of database: 467 Length adjustment: 33 Effective length of query: 437 Effective length of database: 434 Effective search space: 189658 Effective search space used: 189658 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