Align D-serine/D-alanine/glycine transporter (characterized)
to candidate RR42_RS28305 RR42_RS28305 proline-specific permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS28305 Length = 472 Score = 436 bits (1121), Expect = e-127 Identities = 212/466 (45%), Positives = 318/466 (68%), Gaps = 5/466 (1%) Query: 1 MVDQVKVVADDQAPAEQSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVY 60 M D K++ +++ E+ L R L +RHIQ+IAIGGAIG GLF+G+G+ I++AGP ++ Y Sbjct: 1 MTDVRKLLNEERVHEEKDLHRGLKDRHIQMIAIGGAIGVGLFLGAGRAIAIAGPGLMLSY 60 Query: 61 MIIGFMLFFVMRAMGELLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVV 120 I G +FF+MRA+GELLL SF+ +A + +GP+AG+ TGW+YWF WVVTGMA++ Sbjct: 61 AIGGVAIFFIMRALGELLLYRPVSGSFATYAEEFVGPFAGFATGWSYWFMWVVTGMAEIT 120 Query: 121 AITAYAQFWFPDLSDWVASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGL 180 A+ Y +WFPD+ W+ +LA + +L +N V +FGE+EFWFA+IK+V IV++IV+GL Sbjct: 121 AVAVYVHYWFPDVPQWIPALATLAVLYLVNCVAVAVFGELEFWFALIKVVTIVAMIVIGL 180 Query: 181 VMVAMHFQSPTGVEASFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKD 240 ++ +P G ASF++LW GG+ P G G QI +FA+ G+EL+G TA E ++ Sbjct: 181 AIIFFGV-TPLGPTASFSNLWTHGGFMPFGTLGVVLTLQIVMFAYQGVELIGVTAGEAQN 239 Query: 241 PEKSLPRAINSIPIRIIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVIN 300 PEK LP A N + RI++FYV ALI++M++ PW+ + P SPFV +F +G+P AA+++N Sbjct: 240 PEKVLPHATNGVVWRILIFYVGALIIMMALVPWNELKPGVSPFVYVFERIGVPGAAAIVN 299 Query: 301 FVVLTSAASSANSGVFSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVV 360 VV+T+AASS NSG+FST RML+ LAQ G AP+AF ++S + VP+ +TFS + GV+ Sbjct: 300 LVVITAAASSCNSGIFSTGRMLYTLAQFGQAPRAFGRVSSKHVPSIAITFSAALMGIGVL 359 Query: 361 MLYVNPSVIGAFTMITTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMC 419 + Y+ P + F +T++S + ++ W+II+ ++L YRK K++ ++MP Sbjct: 360 LNYIVPEQV--FVWVTSISLVGSLWTWSIIMIAHLGYRKAIAAGRVKAVAFRMPGAPYAN 417 Query: 420 WVCMAFFVFVVVLLTLEDDTRQALLVTPLWFIALGLGWLFIGKKRA 465 W+ +AF + V VLL+L+ TR AL V P+WF LG+G+ F K RA Sbjct: 418 WLVVAFMIAVAVLLSLDPGTRVALYVAPVWFALLGIGYRFT-KSRA 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: 698 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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