Align Proline-specific permease (ProY) (characterized)
to candidate AO353_12275 AO353_12275 proline-specific permease
Query= TCDB::P37460 (456 letters) >FitnessBrowser__pseudo3_N2E3:AO353_12275 Length = 468 Score = 580 bits (1495), Expect = e-170 Identities = 276/441 (62%), Positives = 350/441 (79%), Gaps = 1/441 (0%) Query: 5 NKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYIIMRALGE 64 N LKRGLS RHIRFMALGSAIGTGLFYGSA AI+MAGP+VLLAY+IGG A +++MRALGE Sbjct: 6 NGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGPAVLLAYLIGGAAVFMVMRALGE 65 Query: 65 MSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPAVPHW 124 M+VHNP A SF +YA LGP+AG+I GWTY FE++IV +ADVTAFGIYMG WFP V W Sbjct: 66 MAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFPEVSRW 125 Query: 125 IWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNG-GQPTG 183 IWVL VV I+ +NL +VKVFGE+EFW S KVA I+ MI+ G GI+++GI GQ T Sbjct: 126 IWVLGVVSIVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAPGQVTD 185 Query: 184 IHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINSVPMRI 243 I NLW+ GGF NG G+I S +VMFA+GGIEIIG+TAGEAKDP+ +PRAIN+VP+RI Sbjct: 186 ISNLWTQGGFMPNGMGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQHVLPRAINAVPLRI 245 Query: 244 LVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAINSDVF 303 L+FYV T+ V+MSI+PW Q+G+ GSPFV F +GI+ AA+ILN VV+TA++SAINSD+F Sbjct: 246 LLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDKLGISSAATILNIVVITAAISAINSDIF 305 Query: 304 GVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFLVIASL 363 G GRM+ G+A+QG APK FA SR G+PW+TV+VM++ALL V LNY++PENVFL+IAS+ Sbjct: 306 GAGRMMFGLAQQGHAPKGFAHLSRNGVPWMTVVVMSVALLLGVLLNYLIPENVFLLIASI 365 Query: 364 ATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIALIGYHP 423 ATFATVWVW+MIL +Q+A RR + E+V LKF VP +A + F++F+ ++GY P Sbjct: 366 ATFATVWVWLMILFTQVAMRRSMTAEQVAQLKFPVPFWPYAPMAAIAFMLFVFGVLGYFP 425 Query: 424 DTRISLYVGFAWIVLLLIGWI 444 DT+ +L VG WIVLL++ ++ Sbjct: 426 DTQAALIVGVVWIVLLVLAYL 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: 719 Number of extensions: 41 Number of successful extensions: 2 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: 468 Length adjustment: 33 Effective length of query: 423 Effective length of database: 435 Effective search space: 184005 Effective search space used: 184005 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