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= 0004.0007.p (166 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value lin0250 [J] COG1098 Predicted RNA binding protein (contains ribo... 153 1e-37 BS_yabR [J] COG1098 Predicted RNA binding protein (contains ribo... 150 9e-37 BH0077 [J] COG1098 Predicted RNA binding protein (contains ribos... 139 2e-33 SA0466 [J] COG1098 Predicted RNA binding protein (contains ribos... 129 2e-30 BH3347 [J] COG1098 Predicted RNA binding protein (contains ribos... 78 6e-15 >lin0250 [J] COG1098 Predicted RNA binding protein (contains ribosomal protein S1 domain) Length = 142 Score = 153 bits (386), Expect = 1e-37, Method: Compositional matrix adjust. Identities = 89/169 (52%), Positives = 107/169 (63%), Gaps = 32/169 (18%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG KL+GKVTGIT+FGAFV+L GG TGLVHISE+ADNYVKD+ND L + D VTVKV Sbjct: 1 MSIEVGNKLQGKVTGITNFGAFVELEGGKTGLVHISEVADNYVKDINDILTVGDEVTVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 +N+ DGKIGLSI++AVD+ Sbjct: 61 MNIGDDGKIGLSIRKAVDRPDRPEKSYDRKPKYSK------------------------- 95 Query: 121 XPFKPAAG--KP--SFEDKMSRFLKDSEERISSIKKNTEGKRGGRGAKR 165 KPA KP SFED MS+FLKDS+ER+++IK+ TE KRGGRGAKR Sbjct: 96 ---KPAGNYVKPAESFEDIMSKFLKDSDERLTTIKRQTESKRGGRGAKR 141 >BS_yabR [J] COG1098 Predicted RNA binding protein (contains ribosomal protein S1 domain) Length = 128 Score = 150 bits (379), Expect = 9e-37, Method: Compositional matrix adjust. Identities = 83/157 (52%), Positives = 102/157 (64%), Gaps = 38/157 (24%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG+KL+GK+TGIT+FGAFV+L GG TGLVHISE+ADNYVKD+NDHLK+ D V VKV Sbjct: 1 MSIEVGSKLQGKITGITNFGAFVELPGGSTGLVHISEVADNYVKDINDHLKVGDQVEVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 INV+KDGKIGLSIK+A D+ Sbjct: 61 INVEKDGKIGLSIKKAKDRPQARPRND--------------------------------- 87 Query: 121 XPFKPAAGKPSFEDKMSRFLKDSEERISSIKKNTEGK 157 F+P K SFE KM++FLKDSE+R+SS+K+NTE K Sbjct: 88 --FRP---KESFEQKMNKFLKDSEDRLSSLKRNTESK 119 >BH0077 [J] COG1098 Predicted RNA binding protein (contains ribosomal protein S1 domain) Length = 137 Score = 139 bits (350), Expect = 2e-33, Method: Compositional matrix adjust. Identities = 79/167 (47%), Positives = 99/167 (59%), Gaps = 49/167 (29%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 MAIEVG+KL+GKVTGIT FGAFV+L GG TGLVHISE+AD+YVKD+N+ L + V VKV Sbjct: 1 MAIEVGSKLQGKVTGITKFGAFVELPGGSTGLVHISEVADHYVKDINELLTVGQEVQVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 +NV+ DGKIGLSI++A+D+ Sbjct: 61 LNVESDGKIGLSIRKALDQ---------------------------------------PE 81 Query: 121 XPFKPAAG----------KPSFEDKMSRFLKDSEERISSIKKNTEGK 157 P +P G PSFEDKM+RFLKDSEER+++IK+ TE K Sbjct: 82 RPKRPHGGGNRGPRTNRPGPSFEDKMARFLKDSEERLATIKRQTESK 128 >SA0466 [J] COG1098 Predicted RNA binding protein (contains ribosomal protein S1 domain) Length = 133 Score = 129 bits (324), Expect = 2e-30, Method: Compositional matrix adjust. Identities = 72/165 (43%), Positives = 96/165 (58%), Gaps = 32/165 (19%) Query: 1 MAIEVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKV 60 M+IEVG KL+GKVTGI FGAFV+L G +GLVHISE+ADNYV++V +HL + D V VKV Sbjct: 1 MSIEVGNKLKGKVTGIKKFGAFVELPEGKSGLVHISEVADNYVENVEEHLSVGDEVDVKV 60 Query: 61 INVDKDGKIGLSIKQAVDKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 120 +++ DGKI LSIK+A D+ Sbjct: 61 LSIADDGKISLSIKKAKDRPRRQHTSKPSHQ----------------------------- 91 Query: 121 XPFKPAAGKPSFEDKMSRFLKDSEERISSIKKNTEGKRGGRGAKR 165 KP FE K+S FLKDSE++++SIK+ TE +RGG+G++R Sbjct: 92 ---KPVQKAEDFEKKLSNFLKDSEDKLTSIKRQTESRRGGKGSRR 133 >BH3347 [J] COG1098 Predicted RNA binding protein (contains ribosomal protein S1 domain) Length = 138 Score = 77.8 bits (190), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 41/72 (56%), Positives = 54/72 (75%), Gaps = 1/72 (1%) Query: 4 EVGTKLEGKVTGITHFGAFVDLSGGVTGLVHISEIADNYVKDVNDHLKIADVVTVKVINV 63 EVG+ +EGKVTGI FGAFV + GLVHISE+A +VKD+ND L + D V VK+++V Sbjct: 5 EVGSIVEGKVTGIKPFGAFVAIDDQKQGLVHISEVAHGFVKDINDVLSVGDEVKVKILSV 64 Query: 64 DKD-GKIGLSIK 74 D++ GKI LSI+ Sbjct: 65 DEESGKISLSIR 76 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 0.314 0.135 0.372 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: 9,283,500 Number of extensions: 308832 Number of successful extensions: 559 Number of sequences better than 1.0e-05: 16 Number of HSP's gapped: 558 Number of HSP's successfully gapped: 22 Length of query: 166 Length of database: 38,378,431 Length adjustment: 98 Effective length of query: 68 Effective length of database: 27,075,699 Effective search space: 1841147532 Effective search space used: 1841147532 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: 42 (21.9 bits) S2: 112 (47.8 bits)