Align Proline-specific permease (ProY) (characterized)
to candidate RR42_RS14635 RR42_RS14635 proline-specific permease
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Cup4G11:RR42_RS14635 Length = 466 Score = 585 bits (1508), Expect = e-171 Identities = 277/444 (62%), Positives = 352/444 (79%), Gaps = 2/444 (0%) Query: 2 ESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRA 61 E + L+RGLS RHIRFMALGSAIGTGLFYGSA AI+ AGP+VLLAY+IGG A Y++MRA Sbjct: 3 EQSQGLQRGLSARHIRFMALGSAIGTGLFYGSASAIQTAGPAVLLAYVIGGAAVYMVMRA 62 Query: 62 LGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAV 121 LGEM+V NP A SF +YA LGPLAG++ GWTY FE+++V +ADVTAFGIYMG WFP V Sbjct: 63 LGEMAVRNPVAGSFGQYASTGLGPLAGFLLGWTYAFEMIVVCLADVTAFGIYMGFWFPDV 122 Query: 122 PHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIG--NGG 179 P WIWVL +V +I +NL+SVKVFGELEFW S KV I+ MI G+ I+++G G +GG Sbjct: 123 PRWIWVLGIVFLIGGLNLLSVKVFGELEFWLSLLKVGAIVAMIGGGVAIMLFGFGMADGG 182 Query: 180 QPTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSV 239 TGIHNLW++GGF NG G+I S +VMFA+GGIEIIGITAGEA+DP++ IPRAIN+V Sbjct: 183 VATGIHNLWTHGGFMPNGIAGVIASFAVVMFAFGGIEIIGITAGEARDPQRVIPRAINAV 242 Query: 240 PMRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAIN 299 P+RIL+FYV TL V+MS+YPW+++G+ GSPFV F +GI AA++LN VV++A++SAIN Sbjct: 243 PLRILLFYVLTLAVLMSLYPWHRIGSEGSPFVQIFSRLGIGSAAAVLNIVVISAAVSAIN 302 Query: 300 SDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLV 359 SD+FG GRML+GMA Q AP++FA SR+G+PW+TV+VM ALL V LNY+MPE+VF + Sbjct: 303 SDIFGAGRMLYGMAVQRQAPRIFASVSRKGVPWMTVVVMAFALLAGVVLNYVMPEDVFTL 362 Query: 360 IASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALI 419 IAS+ATFATVWVW+MILLSQ+A RRR+ EV ALKF VP V +A F++FI ++ Sbjct: 363 IASIATFATVWVWLMILLSQVALRRRMSRAEVAALKFPVPFWPVAPLAATAFMLFIFGVL 422 Query: 420 GYHPDTRISLYVGFAWIVLLLIGW 443 G+ P TR +L VG W++LL++ W Sbjct: 423 GWFPQTRAALLVGAVWLLLLVVAW 446 Lambda K H 0.329 0.143 0.449 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: 721 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: 456 Length of database: 466 Length adjustment: 33 Effective length of query: 423 Effective length of database: 433 Effective search space: 183159 Effective search space used: 183159 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