Align Proline-specific permease (ProY) (characterized)
to candidate WP_013076931.1 BTUS_RS15100 amino acid permease
Query= TCDB::P37460 (456 letters) >NCBI__GCF_000092905.1:WP_013076931.1 Length = 462 Score = 479 bits (1232), Expect = e-139 Identities = 220/449 (48%), Positives = 315/449 (70%) Query: 1 MESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMR 60 M ++L RGL RH++ +ALG AIG GLF GSA AI +AGP++ ++Y++GG+ ++IMR Sbjct: 1 MPEESELVRGLKERHLQLIALGGAIGVGLFLGSARAIHLAGPALTISYLVGGLVIFLIMR 60 Query: 61 ALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPA 120 ALGE++++ P A SFS YA+E +GP AG+ITGWTY F + A+A++TA G+Y+ WFPA Sbjct: 61 ALGELALYKPVAGSFSTYAEEFVGPWAGFITGWTYWFMWITTAMAEITAVGVYVRYWFPA 120 Query: 121 VPHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQ 180 VP W+ L ++++ +NL++V +GE EFWF+ KV TI+ MIV G+ II++G+ N G Sbjct: 121 VPQWLPALIALVVMFLVNLIAVGAYGEFEFWFALIKVVTIVAMIVVGLLIILFGVWNQGV 180 Query: 181 PTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVP 240 P G NLWS+GGFF G G +++LQMVMFAY G+E+IG+TAGEA+DP K+IP A N + Sbjct: 181 PVGFSNLWSHGGFFPTGIGGALLALQMVMFAYVGVELIGVTAGEARDPSKTIPSATNKII 240 Query: 241 MRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINS 300 RIL+FYVG L +IMS+YPWN++ SPFVLTFQ +G AA ++NFVVLTA+LS+ NS Sbjct: 241 WRILIFYVGALVIIMSLYPWNELDAQNSPFVLTFQRIGFPAAADVINFVVLTAALSSCNS 300 Query: 301 DVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVI 360 VF GRML+ +A+ G AP+ S R +P + +L V LNY++P+ VF + Sbjct: 301 GVFSTGRMLYSLAQYGQAPRFLRGLSSRRVPAAAIAASAAVMLVGVILNYVVPQQVFTYV 360 Query: 361 ASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIG 420 SL A +W W MIL++ +A+RRR+ +V+A+K+++PG VT GL FL ++ L+ Sbjct: 361 TSLGAEAAIWTWGMILVAHMAYRRRVAAGQVQAVKYRMPGSPVTNWIGLAFLALVVVLLL 420 Query: 421 YHPDTRISLYVGFAWIVLLLIGWIFKRRR 449 + PDTR++ YV W +L+I + F RRR Sbjct: 421 FDPDTRVAFYVALVWFAILVIAYQFVRRR 449 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: 668 Number of extensions: 33 Number of successful extensions: 1 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: 462 Length adjustment: 33 Effective length of query: 423 Effective length of database: 429 Effective search space: 181467 Effective search space used: 181467 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 24 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