Align D-serine/D-alanine/glycine transporter (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= SwissProt::P0AAE0 (470 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 362 bits (928), Expect = e-104 Identities = 182/453 (40%), Positives = 282/453 (62%), Gaps = 4/453 (0%) Query: 17 QSLRRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGE 76 Q L+R L+ RHI+ +A+G AIGTGLF GS I AGP+++ Y+I G ++ VMRA+GE Sbjct: 6 QGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRALGE 65 Query: 77 LLLSNLEYKSFSDFASDLLGPWAGYFTGWTYWFCWVVTGMADVVAITAYAQFWFPDLSDW 136 + + N SF +AS LGP AG+ GWTY F +V +ADV A Y FWFPD+ W Sbjct: 66 MAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDVPRW 125 Query: 137 VASLAVIVLLLTLNLATVKMFGEMEFWFAMIKIVAIVSLIVVGLVMVAMHF-QSPTGVEA 195 + L ++ L+ LNL +VK+FGE+EFW +++K+ AIV++I G+ ++ F + GV Sbjct: 126 IWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGGVAT 185 Query: 196 SFAHLWNDGGWFPKGLSGFFAGFQIAVFAFVGIELVGTTAAETKDPEKSLPRAINSIPIR 255 +LW GG+ P G++G A F + +FAF GIE++G TA E +DP++ +PRAIN++P+R Sbjct: 186 GIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAVPLR 245 Query: 256 IIMFYVFALIVIMSVTPWSSVVPEKSPFVELFVLVGLPAAASVINFVVLTSAASSANSGV 315 I++FYV L V+MS+ PW + E SPFV++F +G+ +AA+V+N VV+++A S+ NS + Sbjct: 246 ILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAINSDI 305 Query: 316 FSTSRMLFGLAQEGVAPKAFAKLSKRAVPAKGLTFSCICLLGGVVMLYVNPSVIGAFTMI 375 F RML+G+A + AP+ FA +S++ VP + LL GVV+ YV P + FT+I Sbjct: 306 FGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDV--FTLI 363 Query: 376 TTVSAILFMFVWTIILCSYLVYRKQRPHLHEKSI-YKMPLGKLMCWVCMAFFVFVVVLLT 434 +++ ++VW +IL S + R++ ++ + +P + AF +F+ +L Sbjct: 364 ASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVLG 423 Query: 435 LEDDTRQALLVTPLWFIALGLGWLFIGKKRAAE 467 TR ALLV +W + L + W G+ R E Sbjct: 424 WFPQTRAALLVGAVWLLLLVVAWWCWGRPRGQE 456 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: 669 Number of extensions: 48 Number of successful extensions: 4 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: 466 Length adjustment: 33 Effective length of query: 437 Effective length of database: 433 Effective search space: 189221 Effective search space used: 189221 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