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= 0541.0062.p (299 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value BS_ypcP [L] COG0258 5'-3' exonuclease (including N-terminal doma... 326 2e-89 lin1994 [L] COG0258 5'-3' exonuclease (including N-terminal doma... 282 5e-76 SA1273 [L] COG0258 5'-3' exonuclease (including N-terminal domai... 280 3e-75 BH3153_1 [L] COG0258 5'-3' exonuclease (including N-terminal dom... 225 7e-59 lin1600_1 [L] COG0258 5'-3' exonuclease (including N-terminal do... 210 2e-54 >BS_ypcP [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) Length = 296 Score = 326 bits (836), Expect = 2e-89, Method: Compositional matrix adjust. Identities = 150/266 (56%), Positives = 196/266 (73%) Query: 1 MIVDGMALLFRAFYATAYGGYIRKTKAGLPTNAVYGFLQYFFDAVSTFEPSHVVCCWDMG 60 ++VDGMALLFRAF+ATA +G+PTN V GFL++ AV TF+P+HVVCCWDMG Sbjct: 7 LLVDGMALLFRAFFATAVHRNFMINDSGVPTNGVNGFLKHLITAVETFQPTHVVCCWDMG 66 Query: 61 KGTFRTEKYDGYKSNRIDAPLELIPQFDLVKEVVAELGVPNIGLAGYEADDCIGTLASCY 120 T+R + + YK+NR P+ELIPQFDL KE AELG+ NIG AGYEADDCIGTLA + Sbjct: 67 SKTYRNDLFQDYKANRSAPPVELIPQFDLAKEAAAELGIMNIGFAGYEADDCIGTLADLF 126 Query: 121 SGESEVYILTGDHDMLQLVSDSVKVVIMKKGRSNYKVYDPAELLEERGLTPAQVIDLKGF 180 + E+++ ++TGD D+LQL++D V V +++KG NYKVY EE G+ P +ID+K Sbjct: 127 ANEADITVVTGDRDLLQLLTDKVSVALLQKGIGNYKVYTKETFYEETGVMPKALIDIKAL 186 Query: 181 MGDTSDNYPGVRGIGEKTALKLLSEYGTVEGVIENLHLLPKGVRAKIEADLDMLHLSREL 240 MGD+SDNYPGV+GIGEKTA KL+ EY T++ ++ENL LLPKG + KI+ L L +SR+L Sbjct: 187 MGDSSDNYPGVKGIGEKTAYKLIREYETIDRLLENLSLLPKGQQGKIQQGLSDLEMSRKL 246 Query: 241 AEIRCDVPVVCTLTECLWELQREKAA 266 AEI C VP+ CTL + L+ LQ E+AA Sbjct: 247 AEIHCSVPLACTLKDALFTLQMEQAA 272 >lin1994 [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) Length = 281 Score = 282 bits (721), Expect = 5e-76, Method: Compositional matrix adjust. Identities = 21/265 (7%), Positives = 45/265 (16%) Query: 1 MIVDGMALLFRAFYATAYGGYIRKTKAGLPTNAVYGFLQYFFDAVSTFEPSHVVCCWDMG 60 + + Y + G I + + E + Sbjct: 9 HPAVACSGIECYPYRLIFKGVIVAVHLLIVDALNLIRRIHAVQGSPCVETCQHALDQLIM 68 Query: 61 KGTFRTEKYDGYKSNRIDAPLELIPQFDLVKEVVAELGVPNIGLAGYEADDCIGTLASCY 120 NR + + A A + G Sbjct: 69 HSQPTHAVAVFDDENRSSGWRHQRLPDYKAGRPPMPEELHDEMPALRAAFEQRGVPCWST 128 Query: 121 SGESEVYILTGDHDMLQLVSDSVKVVIMKKGRSNYKVYDPAELLEERGLTPAQVIDLKGF 180 SG + + +V KG + K F Sbjct: 129 SGNEADDLAATLAVKVTQAGHQATIVSTDKGYCQLLSPTLRIRDYFQKRWLDAPFIDKEF 188 Query: 181 MGDTSDNYPGVRGIGEKTALKLLSEYGTVEGVIENLHLLPKGVRAKIEADLDMLHLSREL 240 G ++ + + L D ++L Sbjct: 189 GVQPQQLPDYWGLAGISSSKVPGVAGIGPKSATQLLVEFQSLEGIYENLDAVAEKWRKKL 248 Query: 241 AEIRCDVPVVCTLTECLWELQREKA 265 + + + +L + Sbjct: 249 ETHKEMAFLCRDIARLQTDLHIDGN 273 >SA1273 [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) Length = 292 Score = 280 bits (715), Expect = 3e-75, Method: Compositional matrix adjust. Identities = 133/259 (51%), Positives = 177/259 (68%), Gaps = 3/259 (1%) Query: 1 MIVDGMALLFRAFYATAYGGYIRKTKAGLPTNAVYGFLQYFFDAVSTFEPSHVVCCWDMG 60 ++VDGMALLFR FYAT+ G+PTN + GF+++ F A+ P+HV CWDMG Sbjct: 6 LLVDGMALLFRHFYATSLHKQFMYNSQGVPTNGIQGFVRHIFSAIHEIRPTHVAVCWDMG 65 Query: 61 KGTFRTEKYDGYKSNRIDAPLELIPQFDLVKEVVAELGVPNIGLAGYEADDCIGTLASCY 120 + TFR + +DGYK NR P ELIPQFD VKE+ + G NIG+ YEADD IGTLA Y Sbjct: 66 QSTFRNDMFDGYKQNRSAPPEELIPQFDYVKEISEQFGFVNIGVKNYEADDVIGTLAQQY 125 Query: 121 SGESEVYILTGDHDMLQLVSDSVKVVIMKKGRSNYKVYDPAELLEERGLTPAQVIDLKGF 180 S +++VYI+TGD D+LQ ++D+V+V ++KKG + Y Y EE L P Q+ID+K F Sbjct: 126 STDNDVYIITGDKDLLQCINDNVEVWLIKKGFNIYNRYTLHRFNEEYALEPQQLIDIKAF 185 Query: 181 MGDTSDNYPGVRGIGEKTALKLLSEYGTVEGVIENLHLLPKGVRAKIEADLDMLHLSREL 240 MGDT+D Y GV+GIGEKTA+KL+ +Y +VE V+EN+ L G R KI +LD L+LS+ L Sbjct: 186 MGDTADGYAGVKGIGEKTAIKLIQQYQSVENVVENIDALSAGQRNKINDNLDELYLSKRL 245 Query: 241 AEIRCDVPVVCTLTECLWE 259 AEI VP+ +E L+E Sbjct: 246 AEIHTQVPID---SEALFE 261 >BH3153_1 [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) Length = 307 Score = 225 bits (573), Expect = 7e-59, Method: Compositional matrix adjust. Identities = 126/302 (41%), Positives = 182/302 (60%), Gaps = 9/302 (2%) Query: 1 MIVDGMALLFRAFYATAYGGYIRKTKAGLPTNAVYGFLQYFFDAVSTFEPSHVVCCWDMG 60 +++DG ++ +RAF+A + G+ TNAVYGF + +P+H+V +D G Sbjct: 5 VLIDGNSIAYRAFFALP----LLNNDKGVYTNAVYGFTMMLLKVLEDEKPTHMVVAFDAG 60 Query: 61 KGTFRTEKYDGYKSNRIDAPLELIPQFDLVKEVVAELGVPNIGLAGYEADDCIGTLASCY 120 K TFR + YD YKS R P EL QF L++E++ + + + +EADD IGTLA Sbjct: 61 KTTFRHDTYDAYKSGRQKTPPELSEQFPLIRELLDAFNIARVEVENFEADDLIGTLAKQA 120 Query: 121 SGES-EVYILTGDHDMLQLVSDSVKVVIMKKGRSNYKVYDPAELLEERGLTPAQVIDLKG 179 S E+ EV I TGD D+LQ+VSD V V + +KG + VYD + E G+TP Q+ID+KG Sbjct: 121 SQENFEVKIFTGDKDLLQIVSDHVTVALTRKGITQIDVYDEKGIEERYGITPEQIIDMKG 180 Query: 180 FMGDTSDNYPGVRGIGEKTALKLLSEYGTVEGVIENLHLLP-KGVRAKIEADLDMLHLSR 238 MGD+SDN PGV GIGEKTALKLL EYG+VE V+E++ + K ++ ++E D +S+ Sbjct: 181 LMGDSSDNIPGVPGIGEKTALKLLKEYGSVEKVLESIDEISGKKMKERLEEHRDQALMSK 240 Query: 239 ELAEIRCDVPVVCTLTECLW-ELQREKAARKFQELEFGSLLHLVGPVKDEQGIVQIELGD 297 +LA I + PV + E +++ + F+EL+F SLL V D +GI + EL Sbjct: 241 KLATIYLEAPVTLDADSFTFGEYDKKEVVKLFKELDFNSLLDKVDA--DGEGIEKEELQS 298 Query: 298 LG 299 L Sbjct: 299 LN 300 >lin1600_1 [L] COG0258 5'-3' exonuclease (including N-terminal domain of PolI) Length = 316 Score = 210 bits (535), Expect = 2e-54, Method: Compositional matrix adjust. Identities = 117/282 (41%), Positives = 166/282 (58%), Gaps = 8/282 (2%) Query: 1 MIVDGMALLFRAFYATAYGGYIRKTKAGLPTNAVYGFLQYFFDAVSTFEPSHVVCCWDMG 60 +++DG ++ RAFYA + G+ TNAVYGF + + +PSHV+ +D G Sbjct: 5 VLIDGNSIANRAFYALP----LLNNDKGVYTNAVYGFAMMLMNVLEKEKPSHVLVAFDAG 60 Query: 61 KGTFRTEKYDGYKSNRIDAPLELIPQFDLVKEVVAELGVPNIGLAGYEADDCIGTLASCY 120 K TFR + GYK R P EL QF ++E++ +P LA YEADD IGTL Sbjct: 61 KTTFRHTTFKGYKGGRQKTPSELSEQFPFIRELLTAYDIPQYELANYEADDIIGTLTKKA 120 Query: 121 SGES-EVYILTGDHDMLQLVSDSVKVVIMKKGRSNYKVYDPAELLEERGLTPAQVIDLKG 179 + EV I+TGD D+ QL S V I KKG ++ + P L E+ LTP+Q+ID+KG Sbjct: 121 EADGMEVAIITGDRDLTQLASRKTTVYITKKGIADMETNTPETLKEKYDLTPSQIIDMKG 180 Query: 180 FMGDTSDNYPGVRGIGEKTALKLLSEY-GTVEGVIENLHLLP-KGVRAKIEADLDMLHLS 237 MGD+SDN PG+ G+GEKTALKLL E+ GTVE V+E+ + K ++ K+ + ++ LS Sbjct: 181 LMGDSSDNIPGIPGVGEKTALKLLHEFGGTVESVLEHAEEISGKKLKEKVLENKELAILS 240 Query: 238 RELAEIRCDVPVVCTLTECLWE-LQREKAARKFQELEFGSLL 278 +ELA I D P+ CT+ ++ Q EK +E+ F +LL Sbjct: 241 KELATINVDSPIECTVESTKYDGYQTEKVIPLLKEMNFTTLL 282 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 0.320 0.140 0.416 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: 22,894,407 Number of extensions: 978614 Number of successful extensions: 4196 Number of sequences better than 1.0e-05: 485 Number of HSP's gapped: 3677 Number of HSP's successfully gapped: 485 Length of query: 299 Length of database: 38,378,431 Length adjustment: 106 Effective length of query: 193 Effective length of database: 26,153,027 Effective search space: 5047534211 Effective search space used: 5047534211 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: 115 (48.9 bits)