Align D-serine/D-alanine/glycine transporter (characterized)
to candidate GFF4632 PS417_23700 aromatic amino acid transporter
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__WCS417:GFF4632 Length = 467 Score = 352 bits (902), Expect = e-101 Identities = 181/440 (41%), Positives = 266/440 (60%), Gaps = 14/440 (3%) Query: 19 LRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGELL 78 L+R L NRHIQLIA+GGAIGTGLF+GS + AGPS+I Y I GF+ F +MR +GE++ Sbjct: 11 LKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEMI 70 Query: 79 LSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDWVA 138 + SFS FA G +AG+ GW YW +V+ GMA++ A+ Y QFW+PD+ WV+ Sbjct: 71 VEEPVAGSFSHFAHKYWGGYAGFLAGWNYWVLYVLVGMAELTAVGKYIQFWWPDIPTWVS 130 Query: 139 SLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQSPTGVEASFA 198 +L V + +N VK FGE EFWFA+IK+VAIV +IV+G ++ F G +AS + Sbjct: 131 ALVFFVAVNLINTLNVKFFGETEFWFAIIKVVAIVGMIVLGCYLL---FSGTGGPQASVS 187 Query: 199 HLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIRIIM 258 +LW+ GG+FP G G +F+F G+ELVG TAAE +P K +P+AIN + RI++ Sbjct: 188 NLWSHGGFFPNGGMGLLMSMAFIMFSFGGLELVGITAAEASEPRKVIPKAINQVVYRILI 247 Query: 259 FYVFALIVIMSVTPWSSVVP---------EKSPFVELFVLVGLPAAASVINFVVLTSAAS 309 FYV AL V++S+ PW ++ SPFV++F L+G AA ++NFVVLT+A S Sbjct: 248 FYVGALTVLLSLYPWDQLLQTLGASGDAYSGSPFVQIFSLIGNDTAAHILNFVVLTAALS 307 Query: 310 SANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVI 369 NSGV+ SRMLFGLA++G APK+ KL+K+ VP + L S + + VV+ YV P Sbjct: 308 VYNSGVYCNSRMLFGLAEQGDAPKSLMKLNKQGVPIRALAISALVTMLCVVVNYVAPQ-- 365 Query: 370 GAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSIYKMPLGKLMCWVCMAFFVFV 429 A ++ + M W +I +++ +RK +K ++C+AF V + Sbjct: 366 SALELLFALVVASLMINWALISITHIKFRKAMGEQGVTPSFKTFWFPFSNYLCLAFMVMI 425 Query: 430 VVLLTLEDDTRQALLVTPLW 449 + ++ +++ P+W Sbjct: 426 ISVMLAIPGISESVYAMPVW 445 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: 637 Number of extensions: 44 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