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= 0101.0017.p (185 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value A9KRY5.1 A9KRY5_CLOPH RNA polymerase sigma factor 114 3e-24 A9III5.1 A9III5_BORPD RNA polymerase sigma factor 90 9e-17 C0N4S3.1 C0N4S3_9GAMM RNA polymerase sigma factor RpoE 90 1e-16 Q3KGK1.1 Q3KGK1_PSEPF RNA polymerase sigma factor 88 3e-16 C3KE31.1 C3KE31_PSEFS Alternative ECF subfamily sigma factor 88 3e-16 >A9KRY5.1 A9KRY5_CLOPH RNA polymerase sigma factor Length = 204 Score = 114 bits (286), Expect = 3e-24, Method: Compositional matrix adjust. Identities = 70/168 (41%), Positives = 97/168 (57%), Gaps = 7/168 (4%) Query: 14 GDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRETYQPSHAFNT 73 GD A+EELV+KH+ + I F V +L AED+ Q+ FV +H+E Y +F T Sbjct: 35 GDMEAFEELVIKHKDRLIYFIQRLVNNLTIAEDLAQDAFVEVL---VHKERYHFQVSFKT 91 Query: 74 YLFTIIRNSCIDYLRSRQASRSFSSEAVPELSDHTTP-EEILASRENTKLIYEVLDDLQI 132 YLFTI RN IDY+R + R E PE D EE + +E +KL+Y+ + L+ Sbjct: 92 YLFTIGRNKAIDYIRKNK--RMMLVEDYPESYDEENRMEENIIRKEESKLLYDAMKKLKP 149 Query: 133 DYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKKF-KLQYKE 179 DYK A+ L + SY + A ++KKS Q+K+L+YRARK KL KE Sbjct: 150 DYKAAISLIDLEQMSYAEAAKVLKKSDAQMKVLIYRARKSLAKLMEKE 197 >A9III5.1 A9III5_BORPD RNA polymerase sigma factor Length = 230 Score = 89.7 bits (221), Expect = 9e-17, Method: Compositional matrix adjust. Identities = 59/190 (31%), Positives = 99/190 (52%), Gaps = 17/190 (8%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D EL+ARVQ GDK A++ LVLK++ K + + D ED+ QE F+ Y Sbjct: 38 DAELVARVQRGDKKAFDLLVLKYQRKILRLLGRMIRDPAEIEDVAQEAFIKA---YRALP 94 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE------------LSDHTTPE 111 ++ AF T+L+ I N+ ++L S A R S+ E L+D +TPE Sbjct: 95 QFRGESAFYTWLYRIAVNTARNWLAS--AGRRPSAPNAIETEDGETFNETDNLTDISTPE 152 Query: 112 EILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 ++ASRE + + V+++L + +TA+ L + SY+DIA M + ++ ++RAR+ Sbjct: 153 SMVASREIAETVNAVIEELPEELRTAIVLREIEGMSYEDIAQSMGCPIGTVRSRIFRARE 212 Query: 172 KFKLQYKELM 181 + + L+ Sbjct: 213 AIATRLRPLL 222 >C0N4S3.1 C0N4S3_9GAMM RNA polymerase sigma factor RpoE Length = 192 Score = 89.7 bits (221), Expect = 1e-16, Method: Compositional matrix adjust. Identities = 64/193 (33%), Positives = 95/193 (49%), Gaps = 16/193 (8%) Query: 4 DNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHRE 63 D EL+ RVQAGDK A++ L++K++ + I FV D A D+ QE F+ Y Sbjct: 4 DQELVRRVQAGDKKAFDLLIMKYQQRIIHVITGFVHDPVEAMDVAQEAFIKA---YRALP 60 Query: 64 TYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAV-----------PELSDHTTPEE 112 ++ AF T+L+ I N+ +YL + ASR V PEL + TPE Sbjct: 61 GFRGDSAFYTWLYRIAINTSKNYLTA--ASRRPPVSDVDAMDATIYYDAPELKEFETPES 118 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARKK 172 L S E + I+ + DL D TA+ L SY++IA M + ++ ++RAR+ Sbjct: 119 SLMSDELKQAIHLAIQDLPEDTATAIKLREFEGLSYEEIAQAMDCPIGTVRSRIFRAREA 178 Query: 173 FKLQYKELMVNEE 185 Q K +M EE Sbjct: 179 IDKQVKAVMGGEE 191 >Q3KGK1.1 Q3KGK1_PSEPF RNA polymerase sigma factor Length = 193 Score = 88.2 bits (217), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 60/179 (33%), Positives = 91/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED +L+ RVQ GDK A++ LVLK++ K + FV D + A+D+ QE F+ Y Sbjct: 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ +YL SR R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNYLVSR-GRRPPDSDVSSEDAEFYDGDHGLKDLESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 L E ++ + L D +TAL L SY+DIAS+M+ V ++ ++RAR+ Sbjct: 122 ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 >C3KE31.1 C3KE31_PSEFS Alternative ECF subfamily sigma factor Length = 193 Score = 88.2 bits (217), Expect = 3e-16, Method: Compositional matrix adjust. Identities = 60/179 (33%), Positives = 91/179 (50%), Gaps = 14/179 (7%) Query: 3 EDNELMARVQAGDKGAYEELVLKHRLKAIAFANSFVCDLYTAEDIVQECFVXXXXXYIHR 62 ED +L+ RVQ GDK A++ LVLK++ K + FV D + A+D+ QE F+ Y Sbjct: 6 EDQQLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFI---KAYRAL 62 Query: 63 ETYQPSHAFNTYLFTIIRNSCIDYLRSRQASRSFSSEAVPE----------LSDHTTPEE 112 ++ AF T+L+ I N+ +YL SR R S+ E L D +PE Sbjct: 63 GNFRGDSAFYTWLYRIAINTAKNYLVSR-GRRPPDSDVSSEDAEFYDGDHGLKDLESPER 121 Query: 113 ILASRENTKLIYEVLDDLQIDYKTALYLYAVADFSYKDIASIMKKSVPQIKILLYRARK 171 L E ++ + L D +TAL L SY+DIAS+M+ V ++ ++RAR+ Sbjct: 122 ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.321 0.134 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 940,912,118 Number of extensions: 32626554 Number of successful extensions: 89349 Number of sequences better than 1.0e-05: 1350 Number of HSP's gapped: 90192 Number of HSP's successfully gapped: 1350 Length of query: 185 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 58 Effective length of database: 1,864,227,298 Effective search space: 108125183284 Effective search space used: 108125183284 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 127 (53.5 bits)