Align Proline-specific permease (ProY) (characterized)
to candidate BWI76_RS01140 BWI76_RS01140 amino acid permease
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Koxy:BWI76_RS01140 Length = 461 Score = 399 bits (1025), Expect = e-115 Identities = 201/446 (45%), Positives = 289/446 (64%), Gaps = 11/446 (2%) Query: 2 ESNNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRA 61 E +L+RGL RHI +ALG IG GLF G+A +K AGPSVLLAYII G+ + IMR+ Sbjct: 3 EKKAELQRGLEARHIELIALGGTIGVGLFMGAASTLKWAGPSVLLAYIIAGLFVFFIMRS 62 Query: 62 LGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAV 121 +GEM P SF+ YA + P GY+T W+Y F + V I+++TA G+Y+ WFP + Sbjct: 63 MGEMLFLEPVTGSFAVYAHRYMSPFFGYLTAWSYWFMWMAVGISEITAIGVYVQFWFPEM 122 Query: 122 PHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNGGQP 181 WI L V ++ NL +V+++GE+EFWF+ KV TII+MIV G+G+I +G GNGG Sbjct: 123 AQWIPALIAVGLVALANLAAVRLYGEIEFWFAMIKVTTIIVMIVVGLGVIFFGFGNGGHA 182 Query: 182 TGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPM 241 G NL +GGFF+ GW G + +L +V+ +Y G+E+IGITAGEAK+P+ ++ A+ V Sbjct: 183 IGFGNLTEHGGFFAGGWKGFLTALCIVVASYQGVELIGITAGEAKNPQVTLRSAVGKVLW 242 Query: 242 RILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSD 301 RIL+FYVG +FVI++I+PW+Q+G+NGSPFVLTF +GIT AA I+NFVVLTA+LS NS Sbjct: 243 RILIFYVGAIFVIVTIFPWDQIGSNGSPFVLTFAKIGITAAAGIINFVVLTAALSGCNSG 302 Query: 302 VFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIM--PENVFLV 359 ++ GRML+ +A P AK SR G+P V + + LL LNYI+ P+ VF+ Sbjct: 303 MYSCGRMLYALARNRQLPAAIAKVSRNGVPSAGVALSILILLVGSCLNYIIPNPQRVFVY 362 Query: 360 IASLATFATVWVWIMILLSQIAFR----RRLPPEEVKALKFKVPGGVVTTIAGLIFLVFI 415 + S + + W +IL+SQ+ FR + ++L F P T+A FLV + Sbjct: 363 VYSASVLPGMVPWFVILISQLRFRLVHKEAMASHPFRSLLF--PWANYLTMA---FLVCV 417 Query: 416 IALIGYHPDTRISLYVGFAWIVLLLI 441 + +G++ DTR+SL+VG ++ + + Sbjct: 418 LIGMGFNDDTRMSLFVGIIFLAAVTL 443 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: 616 Number of extensions: 41 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: 461 Length adjustment: 33 Effective length of query: 423 Effective length of database: 428 Effective search space: 181044 Effective search space used: 181044 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