Align Proline-specific permease (ProY) (characterized)
to candidate BWI76_RS08745 BWI76_RS08745 proline-specific permease
Query= TCDB::P37460 (456 letters) >FitnessBrowser__Koxy:BWI76_RS08745 Length = 459 Score = 565 bits (1456), Expect = e-165 Identities = 275/456 (60%), Positives = 352/456 (77%), Gaps = 2/456 (0%) Query: 1 MESNNK--LKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPSVLLAYIIGGVAAYII 58 M+ NK L RGL+ RHIRF+ALGSAIGTGLFYGSA AIK AGP+VLLAY+IGG A +I+ Sbjct: 1 MQQQNKPHLLRGLNARHIRFIALGSAIGTGLFYGSASAIKAAGPAVLLAYLIGGAAVFIV 60 Query: 59 MRALGEMSVHNPAASSFSRYAQENLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWF 118 MRALGEM+V NP + SFS YA++ LGPLAG+ITGWTY FE++IVA+ADVTAFGIYMG+W+ Sbjct: 61 MRALGEMAVRNPVSGSFSSYARQYLGPLAGFITGWTYTFEMVIVALADVTAFGIYMGLWY 120 Query: 119 PAVPHWIWVLSVVLIICAINLMSVKVFGELEFWFSFFKVATIIIMIVAGIGIIVWGIGNG 178 P VP WIWVLS++ I A+NL SV+VFGE+EFW S KV II MIVAG II +G GN Sbjct: 121 PDVPRWIWVLSIIFFIGAMNLCSVRVFGEMEFWLSLIKVVAIIAMIVAGGSIIFFGFGNA 180 Query: 179 GQPTGIHNLWSNGGFFSNGWLGMIMSLQMVMFAYGGIEIIGITAGEAKDPEKSIPRAINS 238 TG+ NLWS+GGF NGW G+I SL +VMFA+GG+EIIG+TA EAK+P+K IP+AIN+ Sbjct: 181 FPATGLENLWSHGGFAPNGWEGIIASLGIVMFAFGGVEIIGVTAAEAKNPQKVIPQAINT 240 Query: 239 VPMRILVFYVGTLFVIMSIYPWNQVGTNGSPFVLTFQHMGITFAASILNFVVLTASLSAI 298 +P+RI++FYV TL ++M+I+PWN G GSPFVL F +GI AA+ILN +V++AS+SAI Sbjct: 241 IPLRIVLFYVCTLAILMAIFPWNSFGERGSPFVLIFDGLGIPAAATILNIIVISASISAI 300 Query: 299 NSDVFGVGRMLHGMAEQGSAPKVFAKTSRRGIPWVTVLVMTIALLFAVYLNYIMPENVFL 358 NSD+FG GRM++GMA++G APK F + + G+PW+TV+VM +ALL AV LNY+MPE VF+ Sbjct: 301 NSDIFGAGRMMYGMAKEGLAPKSFQRIASNGVPWMTVVVMGVALLAAVVLNYLMPEQVFV 360 Query: 359 VIASLATFATVWVWIMILLSQIAFRRRLPPEEVKALKFKVPGGVVTTIAGLIFLVFIIAL 418 +IASLA FATVWVW+MILL+ A RR L EE + F VP V + L+F+ +IA+ Sbjct: 361 LIASLAAFATVWVWVMILLAHFAMRRGLSAEERGNIAFPVPLWPVAPLLTLLFMGLVIAV 420 Query: 419 IGYHPDTRISLYVGFAWIVLLLIGWIFKRRRDRQLA 454 +G +TRI+L G W+ LL W + R++ LA Sbjct: 421 LGMVEETRIALIAGLVWLGLLTAVWFARVRKNAVLA 456 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: 701 Number of extensions: 30 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: 459 Length adjustment: 33 Effective length of query: 423 Effective length of database: 426 Effective search space: 180198 Effective search space used: 180198 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