Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PfGW456L13_4400 Aromatic amino acid transport protein AroP
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4400 Length = 473 Score = 345 bits (886), Expect = 1e-99 Identities = 175/467 (37%), Positives = 283/467 (60%), Gaps = 19/467 (4%) Query: 12 QAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVM 71 Q P L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I GF+ F +M Sbjct: 4 QNPQSGELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAICGFIAFMIM 63 Query: 72 RAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFP 131 R +GE+++ + SFS FA G +AG+ +GW W +++ GM+++ A+ Y +W P Sbjct: 64 RQLGEMIVEDPVAGSFSHFAHKYWGGFAGFLSGWNCWILYILVGMSELTAVGKYIHYWAP 123 Query: 132 DLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPT 191 D+ W ++ A VL+ +NLA VK+FGE EFWFA+IK+VAIV +I +G ++ Sbjct: 124 DIPTWASAAAFFVLINAINLANVKVFGEAEFWFAIIKVVAIVGMIALGSYLLV---SGNG 180 Query: 192 GVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINS 251 G +A+ ++LW+ GG+FP G++G +F+F G+E++G TAAE P+ +P+AIN Sbjct: 181 GPQAAVSNLWSHGGFFPNGVTGLVMAMAFIMFSFGGLEMLGFTAAEADKPKTVIPKAINQ 240 Query: 252 IPIRIIMFYVFALIVIMSVTPWSSVVP---------EKSPFVELFVLVGLPAAASVINFV 302 + RI++FY+ AL++++S+TPW S++ SPFV++F ++G AA ++NFV Sbjct: 241 VIYRILIFYIGALVILLSLTPWDSLLTTLNASGDSYSGSPFVQVFSMLGSNTAAHILNFV 300 Query: 303 VLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVML 362 VLT+A S NSG + SRML G+A++G APKA AK+ KR VP + + S L V++ Sbjct: 301 VLTAALSVYNSGTYCNSRMLLGMAEQGDAPKALAKIDKRGVPVRSILASAAVTLIAVLLN 360 Query: 363 YVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVC 422 Y+ P A ++ ++ + W +I S+ +R+ + ++K ++C Sbjct: 361 YLIPH--SALELLMSLVVATLVINWAMISYSHFKFRQHMNKTKQTPLFKALWYPYGNYIC 418 Query: 423 MAFFVFVVVLLTLEDDTRQALLVTPLWFIALGLGWLFIG--KKRAAE 467 +AF +F++ ++ L + ++ P+W + + W+ G KR+A+ Sbjct: 419 LAFVLFILGVMLLIPGIQTSVYAIPVWLVFM---WVCYGIKNKRSAQ 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: 607 Number of extensions: 34 Number of successful extensions: 6 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: 473 Length adjustment: 33 Effective length of query: 437 Effective length of database: 440 Effective search space: 192280 Effective search space used: 192280 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