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= 0514.0004.p (177 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1D8K9.1 B1D8K9_9BACL RNA polymerase, sigma-24 subunit, ECF subf... 194 3e-48 C1P827.1 C1P827_BACCO RNA polymerase, sigma-24 subunit, ECF subf... 163 5e-39 B8D1S9.1 B8D1S9_HALOH RNA polymerase, sigma-24 subunit, ECF subf... 125 2e-27 Q8CXN7.1 Q8CXN7_OCEIH RNA polymerase sigma factor 123 5e-27 C1PU89.1 C1PU89_ALIAC RNA polymerase, sigma subunit, ECF family 123 8e-27 >B1D8K9.1 B1D8K9_9BACL RNA polymerase, sigma-24 subunit, ECF subfamily Length = 179 Score = 194 bits (493), Expect = 3e-48, Method: Compositional matrix adjust. Identities = 97/176 (55%), Positives = 129/176 (73%), Gaps = 4/176 (2%) Query: 1 VVDEKLSLTIDRARRGDQEAFAELVSRYKGIIFRHAFGMLGDRQEAEDASQEIFIKAYLA 60 V E+L I +A+ GDQEA+A LV RYKG ++RHA GMLGDR +AEDA+QE FIKA+ + Sbjct: 3 VASEELKSIILQAKSGDQEAYAALVKRYKGHVYRHALGMLGDRMDAEDAAQEAFIKAFYS 62 Query: 61 LSKLSDVHAFSSWLMRIATNLCKDKLKQRTKAIGTQDMLE---ETIPVDSAADSDLKISM 117 LS L +AFSSW++RI +NLCKD+LK+R KA+ Q++ E E I D+ K+S+ Sbjct: 63 LSSLDTAYAFSSWILRITSNLCKDRLKKRAKAL-EQELKEGHNEDITDPHMPDTLEKVSL 121 Query: 118 QDALARLSVDQREILLLHDVQGYRYEEIAELTDIPIGTVKSRLFSARMSLRKIWNR 173 D L R+S D RE+LLLH+VQGY YEEIA + ++P+GTVKSRLF+AR++LR R Sbjct: 122 ADGLGRISADHREVLLLHEVQGYSYEEIAAILEVPLGTVKSRLFAARINLRNELRR 177 >C1P827.1 C1P827_BACCO RNA polymerase, sigma-24 subunit, ECF subfamily Length = 177 Score = 163 bits (413), Expect = 5e-39, Method: Compositional matrix adjust. Identities = 79/177 (44%), Positives = 124/177 (70%), Gaps = 3/177 (1%) Query: 1 VVDEKLSLTIDRARRGDQEAFAELVSRYKGIIFRHAFGMLGDRQEAEDASQEIFIKAYLA 60 +V++ L+ I +A+ GD +AFA LV+R+KG +FRHA+ M GDR EAED +QE F+KA+ A Sbjct: 1 MVEQDLTQLIRQAKAGDTDAFAVLVARFKGEVFRHAYAMTGDRMEAEDIAQEAFVKAWYA 60 Query: 61 LSKLSDVHAFSSWLMRIATNLCKDKLKQRTKAIGTQDMLEETI---PVDSAADSDLKISM 117 L KL +AF+SW+ +I ++LC D+LK+ K + Q +EE P + +++L+ + Sbjct: 61 LDKLEHAYAFASWMSKIVSHLCYDRLKKMRKKVDLQAEIEEEPLRRPTSNIDNANLRFDI 120 Query: 118 QDALARLSVDQREILLLHDVQGYRYEEIAELTDIPIGTVKSRLFSARMSLRKIWNRG 174 + A+ +LS + R ++L D+QGY YEEIA++ +IP+GTVKSR+ +AR L+K +RG Sbjct: 121 RSAMEKLSPEHRAAIVLRDIQGYSYEEIADILNIPLGTVKSRINTARNILKKELSRG 177 >B8D1S9.1 B8D1S9_HALOH RNA polymerase, sigma-24 subunit, ECF subfamily Length = 195 Score = 125 bits (313), Expect = 2e-27, Method: Compositional matrix adjust. Identities = 68/176 (38%), Positives = 105/176 (59%), Gaps = 15/176 (8%) Query: 16 GDQEAFAELVSRYKGIIFRHAFGMLGDRQEAEDASQEIFIKAYLALSKLSDVHAFSSWLM 75 G++E FA LV +Y+ ++ + MLG+ ++A D +QE FIK + L + +FS+WL Sbjct: 16 GEKELFARLVEKYQRKVYNTTYRMLGNSEDASDLTQEAFIKTFRNLKRFRGKASFSTWLF 75 Query: 76 RIATNLCKDKLKQRTK-------AIGTQDMLE--ETIPVDSAADSDLKI------SMQDA 120 I TNLC+D+L++R + G M E E I +S DL + S+Q A Sbjct: 76 TITTNLCRDELRKRQRRSASPHFPDGQHFMSEDIENIKDNSKVPEDLYMGRETMASIQRA 135 Query: 121 LARLSVDQREILLLHDVQGYRYEEIAELTDIPIGTVKSRLFSARMSLRKIWNRGEG 176 + +L DQ+E+++L D+QG+ Y+EI+E+ +P+GTVKSRL AR SL+K EG Sbjct: 136 INKLPADQKEVIVLRDIQGFSYKEISEIIGVPMGTVKSRLSRARKSLQKHLKNIEG 191 >Q8CXN7.1 Q8CXN7_OCEIH RNA polymerase sigma factor Length = 187 Score = 123 bits (309), Expect = 5e-27, Method: Compositional matrix adjust. Identities = 66/182 (36%), Positives = 110/182 (60%), Gaps = 14/182 (7%) Query: 2 VDEKLSLTIDRARRGDQEAFAELVSRYKGIIFRHAFGMLGDRQEAEDASQEIFIKAYLAL 61 +D+ + I + ++GDQ AFAE+VS Y+ IF+H + MLG++ EAED +QE FI+AY+ + Sbjct: 1 MDQFIIEKIKQVKKGDQSAFAEVVSFYQNKIFQHCYRMLGNKHEAEDIAQEAFIRAYINI 60 Query: 62 SKLSDVHAFSSWLMRIATNLCKDKLKQR-------TKAIGTQ--DMLE-----ETIPVDS 107 + FS+WL RIATNL D++++R + GT+ DM E +P + Sbjct: 61 DSFDEKRKFSTWLYRIATNLTIDRIRKRKPDYYLDAEVKGTEGLDMYSQLASTERLPGEE 120 Query: 108 AADSDLKISMQDALARLSVDQREILLLHDVQGYRYEEIAELTDIPIGTVKSRLFSARMSL 167 +L+ + +++L R I++L ++ + +EI+E+ DIP+GTVK+R+ R +L Sbjct: 121 VESRELQRYIHHEISQLPAKYRSIIMLRYLEEFSLQEISEILDIPLGTVKTRIHRGREAL 180 Query: 168 RK 169 RK Sbjct: 181 RK 182 >C1PU89.1 C1PU89_ALIAC RNA polymerase, sigma subunit, ECF family Length = 177 Score = 123 bits (308), Expect = 8e-27, Method: Compositional matrix adjust. Identities = 70/162 (43%), Positives = 100/162 (61%), Gaps = 6/162 (3%) Query: 10 IDRARRGDQEAFAELVSRYKGIIFRHAFGMLGDRQEAEDASQEIFIKAYLALSKLSDVHA 69 I RAR GD +A +V Y+ ++R A+G+L + +AEDA+QE FI+A+ +L +L + Sbjct: 9 IRRARHGDPQAIETIVRNYQSFVYRTAYGILQNAADAEDATQEAFIRAFRSLGRLREDRT 68 Query: 70 FSSWLMRIATNLCKDKLKQRTKAIGTQDMLEETIPVDSAADSD---LKISMQDALARLSV 126 F +WL RIA + D ++ KA QD EE I A D L+I ++ ALA+LS Sbjct: 69 FPTWLARIAVRISLDMVQ--AKARRAQDPTEE-IHGSVAGGEDAASLRIDLERALAKLSP 125 Query: 127 DQREILLLHDVQGYRYEEIAELTDIPIGTVKSRLFSARMSLR 168 + R +++L G Y+EIAE+ DIPIGTV+SRL ARM LR Sbjct: 126 EHRTVIVLRAFHGLEYDEIAEVLDIPIGTVRSRLHHARMQLR 167 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 0.320 0.134 0.371 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: 900,070,901 Number of extensions: 30861279 Number of successful extensions: 95452 Number of sequences better than 1.0e-05: 4863 Number of HSP's gapped: 92828 Number of HSP's successfully gapped: 4863 Length of query: 177 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 50 Effective length of database: 1,864,227,298 Effective search space: 93211364900 Effective search space used: 93211364900 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 (21.8 bits) S2: 126 (53.1 bits)