Align D-serine/D-alanine/glycine transporter (characterized)
to candidate PP_1059 PP_1059 Uncharacterized amino acid permease YtnA
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Putida:PP_1059 Length = 472 Score = 380 bits (975), Expect = e-110 Identities = 190/446 (42%), Positives = 286/446 (64%), Gaps = 4/446 (0%) Query: 9 ADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLF 68 A QA L+R L RHI+L+A+G IG GLF+GS K I +AGP+I+ Y+I G + Sbjct: 8 AHGQATEGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAIL 67 Query: 69 FVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQF 128 +MRA+GE+ + N SFS +A D LGP AG+ TGW YWF W+VT +A++ A+ Y Sbjct: 68 VIMRALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAIYMGI 127 Query: 129 WFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHFQ 188 WFPD+ W+ +LA + + +NL VK FGE EFWFA+IKIV I+++++ G+ ++A F Sbjct: 128 WFPDVPRWIWALAALGSMGAVNLVAVKAFGEFEFWFALIKIVTIIAMVLGGIGIIAFGFG 187 Query: 189 SPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRA 248 + GV ++LW++GG+ P G++G Q+ +FA++G+E++G TA E ++P+K++P+A Sbjct: 188 N-DGVAVGISNLWSNGGFMPNGVTGVLMSLQMVMFAYLGVEMIGLTAGEARNPQKTIPQA 246 Query: 249 INSIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAA 308 I S+ RI++FYV AL VI+S+ PW+ + + SPFV F +G+ AA +INFVV+T+A Sbjct: 247 IGSVFWRILLFYVGALFVILSIYPWNEIGSQGSPFVMTFERLGIKTAAGIINFVVITAAL 306 Query: 309 SSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSV 368 SS N G+FST RML+ LAQ G AP AFA+ SK VP L S LL GV+ Y+ P Sbjct: 307 SSCNGGIFSTGRMLYSLAQNGQAPAAFARTSKNGVPRNALLLSIGALLLGVLANYLVPEK 366 Query: 369 IGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFV 427 + F +T+++ ++ W +IL + L +R K++ Y+M L L ++ +AF V Sbjct: 367 V--FVWVTSIATFGAIWTWVMILLAQLKFRAGLTTAERKALKYRMWLWPLSSYLALAFLV 424 Query: 428 FVVVLLTLEDDTRQALLVTPLWFIAL 453 VV L+ +DTR AL + P + + L Sbjct: 425 LVVGLMAYFEDTRVALYIGPAFLVLL 450 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: 644 Number of extensions: 35 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: 472 Length adjustment: 33 Effective length of query: 437 Effective length of database: 439 Effective search space: 191843 Effective search space used: 191843 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