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= 0188.0029.p (182 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value C2YJE1.1 C2YJE1_BACCE Prophage LambdaBa01, positive control fact... 117 6e-25 B7GIM3.1 B7GIM3_ANOFW DNA-directed RNA polymerase specialized si... 116 1e-24 B9J6L2.1 B9J6L2_BACCQ Possible positive control factor Xpf 109 9e-23 C3AW01.1 C3AW01_BACMY Prophage LambdaBa01, positive control fact... 109 1e-22 Q81XW4.1 Q81XW4_BACAN Prophage LambdaBa01, positive control fact... 105 2e-21 >C2YJE1.1 C2YJE1_BACCE Prophage LambdaBa01, positive control factor Xpf Length = 166 Score = 117 bits (292), Expect = 6e-25, Method: Compositional matrix adjust. Identities = 58/158 (36%), Positives = 96/158 (60%), Gaps = 6/158 (3%) Query: 29 DMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNKRGIERRAGY 88 +++ Y+ +L+ E + A D ++I MISD EY +EW+ T ++PGN+RGIERRA Y Sbjct: 3 ELIKQYKETLKQLELSKKDATEKDAEIIGEMISDIEYAIEWMCTAKKPGNRRGIERRAAY 62 Query: 89 EREILLEPMRMQIFTRHT------HTNAVNSEGLSEDQQLRLEYIMALLSKRERECYMLA 142 +RE +P+ MQ +TR T V +SE +++LE ++ L++RE+E Y+++ Sbjct: 63 QRERPCDPLLMQRYTRSTVMPVYVWDTEVKESVISEWDRIQLEDALSTLTEREKEIYVMS 122 Query: 143 NGEGFSHVAIAEMLTISAGSVSEYIQRAQRKICSIMNG 180 G GF+ I+ L + +V EY++RA +KI +NG Sbjct: 123 RGHGFTQEKISNYLGVKRTTVQEYLKRADKKIGERLNG 160 >B7GIM3.1 B7GIM3_ANOFW DNA-directed RNA polymerase specialized sigma subunit Length = 166 Score = 116 bits (290), Expect = 1e-24, Method: Compositional matrix adjust. Identities = 62/154 (40%), Positives = 98/154 (63%), Gaps = 7/154 (4%) Query: 27 VDDMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNKRGIERRA 86 +D++L +Y+ +L+ ++L A DK +I +I D E+V+EWL+TGR PG+KRGIERRA Sbjct: 1 MDELLREYKQTLKDTKKLLERAPEQDKTIIRQIIVDLEFVIEWLTTGRHPGHKRGIERRA 60 Query: 87 GYEREILLEPMRMQIFTRHTHT------NAVNSEGLSEDQQLRLEYIMALLSKRERECYM 140 Y+RE +P+ MQ + R T + S S D++ R+E +++L++RERE Y+ Sbjct: 61 AYQREKPFDPLLMQKYFRSTEPTYEWDDHEKESVITSWDRE-RIEDALSVLTEREREVYL 119 Query: 141 LANGEGFSHVAIAEMLTISAGSVSEYIQRAQRKI 174 ++ G ++ IA L IS+ SV I+RA+RKI Sbjct: 120 MSRGYCLTYSEIANYLCISSSSVQTMIERAERKI 153 >B9J6L2.1 B9J6L2_BACCQ Possible positive control factor Xpf Length = 166 Score = 109 bits (273), Expect = 9e-23, Method: Compositional matrix adjust. Identities = 61/159 (38%), Positives = 93/159 (58%), Gaps = 8/159 (5%) Query: 29 DMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNKRGIERRAGY 88 D++ Y + + E A D +I GMISD Y +EW+ T +QPG KRGIERRA Y Sbjct: 3 DLMKQYTETRKRLEASKVGATEKDISIINGMISDINYALEWMRTAKQPGKKRGIERRAAY 62 Query: 89 EREILLEPMRMQIFTRHTH-------TNAVNSEGLSEDQQLRLEYIMALLSKRERECYML 141 +RE +P+ MQ +TR T T A S +SE +++LE ++ L++RE+E Y++ Sbjct: 63 QRERPCDPLLMQRYTRSTEMPIYEWDTEAKES-VISEWDRIQLEDALSTLTEREKEIYVM 121 Query: 142 ANGEGFSHVAIAEMLTISAGSVSEYIQRAQRKICSIMNG 180 + G GF+ I+ L + +V EY++RA RKI ++G Sbjct: 122 SRGYGFTQDKISNYLNVKRTTVQEYLKRADRKIGERLSG 160 >C3AW01.1 C3AW01_BACMY Prophage LambdaBa01, positive control factor Xpf Length = 167 Score = 109 bits (272), Expect = 1e-22, Method: Compositional matrix adjust. Identities = 55/157 (35%), Positives = 91/157 (57%), Gaps = 6/157 (3%) Query: 29 DMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNKRGIERRAGY 88 D++ Y +LR + ++ A +D KV+ MISD Y +EW+ R+PGN+RGIER A Y Sbjct: 3 DLIKQYNTTLRKLREAHKDAKEEDVKVLTDMISDITYSLEWMKKARRPGNRRGIERLAAY 62 Query: 89 EREILLEPMRMQIFTR------HTHTNAVNSEGLSEDQQLRLEYIMALLSKRERECYMLA 142 +RE +P+ MQ + R + N + E ++RLE ++LL++RE+E Y+++ Sbjct: 63 QRETACDPLLMQRYFRSMDDNLYEWDNHQQEHAIGEWDKIRLEDALSLLTEREKEVYLMS 122 Query: 143 NGEGFSHVAIAEMLTISAGSVSEYIQRAQRKICSIMN 179 G ++ IA L I+ +V I+RA++KI +N Sbjct: 123 RGYCLTYREIARYLKITCSTVQSMIERAEKKIARQVN 159 >Q81XW4.1 Q81XW4_BACAN Prophage LambdaBa01, positive control factor Xpf, putative Length = 167 Score = 105 bits (262), Expect = 2e-21, Method: Compositional matrix adjust. Identities = 54/157 (34%), Positives = 90/157 (57%), Gaps = 6/157 (3%) Query: 29 DMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNKRGIERRAGY 88 D++ Y +LR + + A +D KV+ MISD Y +EW+ R+PGN+RG+ER A Y Sbjct: 3 DLIKQYNTTLRQLREAQKDAKEEDVKVLTDMISDITYSLEWMKKARRPGNRRGVERLAAY 62 Query: 89 EREILLEPMRMQIFTR------HTHTNAVNSEGLSEDQQLRLEYIMALLSKRERECYMLA 142 +RE +P+ MQ + R + N + E ++RLE ++LL++RE+E Y+++ Sbjct: 63 QRERACDPLLMQRYFRSMDDNLYEWDNHQQEHSIGEWDKVRLEDALSLLTEREKEVYLMS 122 Query: 143 NGEGFSHVAIAEMLTISAGSVSEYIQRAQRKICSIMN 179 G ++ IA L I+ +V I+RA++KI +N Sbjct: 123 RGYCLTYREIARYLDITCSTVQSMIERAEKKIARQVN 159 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 0.136 0.391 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: 1,060,487,561 Number of extensions: 39392743 Number of successful extensions: 85197 Number of sequences better than 1.0e-05: 36 Number of HSP's gapped: 85164 Number of HSP's successfully gapped: 36 Length of query: 182 Length of database: 3,060,696,203 Length adjustment: 127 Effective length of query: 55 Effective length of database: 1,864,227,298 Effective search space: 102532501390 Effective search space used: 102532501390 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)