BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0407.0004.p (357 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value VC1424 [E] COG0687 Spermidine/putrescine-binding periplasmic pro... 254 1e-67 STM1222 [E] COG0687 Spermidine/putrescine-binding periplasmic pr... 251 1e-66 ZpotD [E] COG0687 Spermidine/putrescine-binding periplasmic protein 248 2e-65 potD [E] COG0687 Spermidine/putrescine-binding periplasmic protein 248 2e-65 ZpotD [E] COG0687 Spermidine/putrescine-binding periplasmic protein 244 1e-64 >VC1424 [E] COG0687 Spermidine/putrescine-binding periplasmic protein Length = 345 Score = 254 bits (649), Expect = 1e-67, Method: Compositional matrix adjust. Identities = 130/340 (38%), Positives = 194/340 (57%), Gaps = 1/340 (0%) Query: 16 FGLMFLASRLNSAEGYSGGNTLTIYNWGDYIEPELLKQFEKETGITVIYQTFDSNEAMLT 75 F A+ L + + L YNW +YI E+L+ F KETGI VIY T++SNE+M Sbjct: 6 FASALCAAALFTTNAMAKDQELYFYNWSEYIPSEVLEDFTKETGIKVIYSTYESNESMYA 65 Query: 76 KVEQGGTTFDVVVPSDYAIAKMREENLLLPLDKSKIPNLANIDSRFMDLSFDPGNVYSVP 135 K++ G +D+VVPS Y ++KMR+E +L +D SK+ + ++D +++ FDPGN +S+P Sbjct: 66 KLKTQGAGYDLVVPSTYFVSKMRKEGMLQEIDHSKLSHFKDLDPNYLNKPFDPGNKFSIP 125 Query: 136 YFWGTVGIIFNPDMTKGMDFSSWDSLWDNRLKNNIFLVDGAREVMGMALNSLHYSVNDQN 195 Y WG GI N DM +W LWD + + L+D AREV +AL+ L YS N N Sbjct: 126 YIWGATGIGINTDMLDKKSLKNWGDLWDAKWAGQLMLMDDAREVFHIALSKLGYSPNTTN 185 Query: 196 EEHLQEALAKLNRLSPNVKAIVGDEIKMLLANEEAAVGIVWSGDASEIMDENDKLDYVVP 255 + ++ A +L +L PNV D E ++G++W+G A E + + P Sbjct: 186 PKEIKAAYRELKKLMPNVLVFNSDFPANPYLAGEVSLGMLWNGSAYMARQEGAPIQIIWP 245 Query: 256 KEGSNKWFDNMVVPRTAVNVEGAHKFIDFMLRPDVAAKNAEYVGYSTPNVPALKLLPEEI 315 ++G+ W D++ +P A N+E AHK IDF+LRP+ AAK A +GY TP A LLP+E Sbjct: 246 EKGTIFWMDSISIPAGAKNIEAAHKMIDFLLRPENAAKIALEIGYPTPVKTAHDLLPKEF 305 Query: 316 SGDTRFYPPAEITDRLEVYDNLGKRMLAHYNELFLRFKMN 355 + D YPP + D E D +G+ + Y+E F + K+N Sbjct: 306 ANDPSIYPPQSVIDNGEWQDEVGEASVL-YDEYFQKLKVN 344 >STM1222 [E] COG0687 Spermidine/putrescine-binding periplasmic protein Length = 348 Score = 251 bits (642), Expect = 1e-66, Method: Compositional matrix adjust. Identities = 137/331 (41%), Positives = 187/331 (56%), Gaps = 2/331 (0%) Query: 27 SAEGYSGGNTLTIYNWGDYIEPELLKQFEKETGITVIYQTFDSNEAMLTKVEQ-GGTTFD 85 SA S +TL YNW +Y+ P LL+QF KETGI VIY T++SNE M K++ +D Sbjct: 19 SAAHASDNDTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYD 78 Query: 86 VVVPSDYAIAKMREENLLLPLDKSKIPNLANIDSRFMDLSFDPGNVYSVPYFWGTVGIIF 145 +VVPS Y + KMR+E ++ +DKSK+ N N+D ++ FDP N YSVPY WG I Sbjct: 79 LVVPSTYYVDKMRKEGMIQKIDKSKLTNFHNLDPEMLNKPFDPNNDYSVPYIWGATAIGV 138 Query: 146 NPDMTKGMDFSSWDSLWDNRLKNNIFLVDGAREVMGMALNSLHYSVNDQNEEHLQEALAK 205 N D +SW LW KN++ L D AREV MAL L YS N + + ++ A + Sbjct: 139 NSDAIDPKTITSWADLWKPEYKNSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYEE 198 Query: 206 LNRLSPNVKAIVGDEIKMLLANEEAAVGIVWSGDASEIMDENDKLDYVVPKEGSNKWFDN 265 L +L PNV A D E +G+VW+G A L+ V PKEG W D+ Sbjct: 199 LKKLMPNVAAFNSDNPANPYMEGEVNLGMVWNGSAFVARQAGTPLEVVWPKEGGIFWMDS 258 Query: 266 MVVPRTAVNVEGAHKFIDFMLRPDVAAKNAEYVGYSTPNVPALKLLPEEISGDTRFYPPA 325 + +P A N EGA K I+F+LRPDVA + AE +GY TPN+ A KLL E++ D YP A Sbjct: 259 LAIPANAKNKEGALKLINFLLRPDVAKEVAETIGYPTPNLAARKLLSPEVANDKSLYPDA 318 Query: 326 EITDRLEVYDNLGKRMLAHYNELFLRFKMNK 356 + + E +++G A Y E + + K + Sbjct: 319 QTISKGEWQNDVGDAS-AIYEEYYQKLKAGR 348 >ZpotD [E] COG0687 Spermidine/putrescine-binding periplasmic protein Length = 348 Score = 248 bits (632), Expect = 2e-65, Method: Compositional matrix adjust. Identities = 134/331 (40%), Positives = 185/331 (55%), Gaps = 2/331 (0%) Query: 27 SAEGYSGGNTLTIYNWGDYIEPELLKQFEKETGITVIYQTFDSNEAMLTKVEQ-GGTTFD 85 SA NTL YNW +Y+ P LL+QF KETGI VIY T++SNE M K++ +D Sbjct: 19 SAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYD 78 Query: 86 VVVPSDYAIAKMREENLLLPLDKSKIPNLANIDSRFMDLSFDPGNVYSVPYFWGTVGIIF 145 +VVPS Y + KMR+E ++ +DKSK+ N +N+D ++ FDP N YS+PY WG I Sbjct: 79 LVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGV 138 Query: 146 NPDMTKGMDFSSWDSLWDNRLKNNIFLVDGAREVMGMALNSLHYSVNDQNEEHLQEALAK 205 N D +SW LW K ++ L D AREV MAL L YS N + + ++ A + Sbjct: 139 NGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNE 198 Query: 206 LNRLSPNVKAIVGDEIKMLLANEEAAVGIVWSGDASEIMDENDKLDYVVPKEGSNKWFDN 265 L +L PNV A D E +G++W+G A +D V PKEG W D+ Sbjct: 199 LKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDS 258 Query: 266 MVVPRTAVNVEGAHKFIDFMLRPDVAAKNAEYVGYSTPNVPALKLLPEEISGDTRFYPPA 325 + +P A N EGA K I+F+LRPDVA + AE +GY TPN+ A KLL E++ D YP A Sbjct: 259 LAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDA 318 Query: 326 EITDRLEVYDNLGKRMLAHYNELFLRFKMNK 356 E E +++G + Y E + + K + Sbjct: 319 ETIKNGEWQNDVGAAS-SIYEEYYQKLKAGR 348 >potD [E] COG0687 Spermidine/putrescine-binding periplasmic protein Length = 348 Score = 248 bits (632), Expect = 2e-65, Method: Compositional matrix adjust. Identities = 134/331 (40%), Positives = 185/331 (55%), Gaps = 2/331 (0%) Query: 27 SAEGYSGGNTLTIYNWGDYIEPELLKQFEKETGITVIYQTFDSNEAMLTKVEQ-GGTTFD 85 SA NTL YNW +Y+ P LL+QF KETGI VIY T++SNE M K++ +D Sbjct: 19 SAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYD 78 Query: 86 VVVPSDYAIAKMREENLLLPLDKSKIPNLANIDSRFMDLSFDPGNVYSVPYFWGTVGIIF 145 +VVPS Y + KMR+E ++ +DKSK+ N +N+D ++ FDP N YS+PY WG I Sbjct: 79 LVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGV 138 Query: 146 NPDMTKGMDFSSWDSLWDNRLKNNIFLVDGAREVMGMALNSLHYSVNDQNEEHLQEALAK 205 N D +SW LW K ++ L D AREV MAL L YS N + + ++ A + Sbjct: 139 NGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNE 198 Query: 206 LNRLSPNVKAIVGDEIKMLLANEEAAVGIVWSGDASEIMDENDKLDYVVPKEGSNKWFDN 265 L +L PNV A D E +G++W+G A +D V PKEG W D+ Sbjct: 199 LKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDS 258 Query: 266 MVVPRTAVNVEGAHKFIDFMLRPDVAAKNAEYVGYSTPNVPALKLLPEEISGDTRFYPPA 325 + +P A N EGA K I+F+LRPDVA + AE +GY TPN+ A KLL E++ D YP A Sbjct: 259 LAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDA 318 Query: 326 EITDRLEVYDNLGKRMLAHYNELFLRFKMNK 356 E E +++G + Y E + + K + Sbjct: 319 ETIKNGEWQNDVGAAS-SIYEEYYQKLKAGR 348 Score = 244 bits (623), Expect = 1e-64, Method: Compositional matrix adjust. Identities = 134/331 (40%), Positives = 185/331 (55%), Gaps = 2/331 (0%) Query: 27 SAEGYSGGNTLTIYNWGDYIEPELLKQFEKETGITVIYQTFDSNEAMLTKVEQ-GGTTFD 85 SA NTL YNW +Y+ P LL+QF KETGI VIY T++SNE M K++ +D Sbjct: 19 SAAHADDNNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYD 78 Query: 86 VVVPSDYAIAKMREENLLLPLDKSKIPNLANIDSRFMDLSFDPGNVYSVPYFWGTVGIIF 145 +VVPS Y + KMR+E ++ +DKSK+ N +N+D ++ FDP N YS+PY WG I Sbjct: 79 LVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGV 138 Query: 146 NPDMTKGMDFSSWDSLWDNRLKNNIFLVDGAREVMGMALNSLHYSVNDQNEEHLQEALAK 205 N D +SW LW K ++ L D AREV MAL L YS N + + ++ A + Sbjct: 139 NGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNE 198 Query: 206 LNRLSPNVKAIVGDEIKMLLANEEAAVGIVWSGDASEIMDENDKLDYVVPKEGSNKWFDN 265 L +L PNV A D E +G++W+G A +D V PKEG W D+ Sbjct: 199 LKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDS 258 Query: 266 MVVPRTAVNVEGAHKFIDFMLRPDVAAKNAEYVGYSTPNVPALKLLPEEISGDTRFYPPA 325 + +P A N EGA K I+F+LRPDVA + AE +GY TPN+ A KLL E++ D YP A Sbjct: 259 LAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDA 318 Query: 326 EITDRLEVYDNLGKRMLAHYNELFLRFKMNK 356 E E +++G + Y E + + K + Sbjct: 319 ETIKNGEWQNDVGAAS-SIYEEYYQKLKAGR 348 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.318 0.136 0.399 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 27,797,339 Number of extensions: 1282733 Number of successful extensions: 5260 Number of sequences better than 1.0e-05: 59 Number of HSP's gapped: 5172 Number of HSP's successfully gapped: 59 Length of query: 357 Length of database: 38,378,431 Length adjustment: 108 Effective length of query: 249 Effective length of database: 25,922,359 Effective search space: 6454667391 Effective search space used: 6454667391 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 116 (49.3 bits)