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= 0001.2027.p (248 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134094557|ref|YP_001099632.1| putative pseudouridylate syntha... 412 e-116 gi|134094298|ref|YP_001099373.1| putative ribosomal large subuni... 199 1e-52 gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase... 73 1e-14 gi|134095624|ref|YP_001100699.1| putative pseudouridylate syntha... 66 2e-12 gi|134094904|ref|YP_001099979.1| 16S rRNA pseudouridylate 516 sy... 64 6e-12 >gi|134094557|ref|YP_001099632.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 248 Score = 412 bits (1058), Expect = e-116, Method: Compositional matrix adjust. Identities = 199/248 (80%), Positives = 225/248 (90%) Query: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVERQASAE 60 MTEP+RLSKRMSELGLCSRREADEWI +GWVRVDG+VVS LG+K+LP Q+VTVERQA+AE Sbjct: 1 MTEPLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGTKILPTQRVTVERQAAAE 60 Query: 61 QAQRVTILINKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Q++RVTILINKPMGYVSGQAEDGYKPAV LV +SRW ED + +FHP QL+SLVPAGRL Sbjct: 61 QSKRVTILINKPMGYVSGQAEDGYKPAVALVKAESRWKEDTSPTQFHPTQLRSLVPAGRL 120 Query: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPEADLKRLNHGLIMDGK 180 DIDSVGLLVLTQDGRIAK LIGE+S+V+KEYLVRVQY +PGKLPEADL+RLNHGL++DGK Sbjct: 121 DIDSVGLLVLTQDGRIAKHLIGENSSVEKEYLVRVQYIKPGKLPEADLQRLNHGLMLDGK 180 Query: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 L PA+V WQNEDQL F LREGKKRQIRRMCD+VGLKV+GLKRVRIG VKLG+LP G+WR Sbjct: 181 KLLPAQVKWQNEDQLSFILREGKKRQIRRMCDIVGLKVVGLKRVRIGRVKLGDLPVGEWR 240 Query: 241 YLRPDEKF 248 YL E+F Sbjct: 241 YLAEGEQF 248 >gi|134094298|ref|YP_001099373.1| putative ribosomal large subunit pseudouridine synthase [Herminiimonas arsenicoxydans] Length = 237 Score = 199 bits (506), Expect = 1e-52, Method: Compositional matrix adjust. Identities = 104/248 (41%), Positives = 155/248 (62%), Gaps = 11/248 (4%) Query: 1 MTEPVRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVERQASAE 60 MT+ +RL+KR+++ CSRREA+++IE GWV VDG V+ G +V P Q + + A+ Sbjct: 1 MTDSIRLAKRVADAVPCSRREAEQYIEGGWVTVDGVVIEEPGHRVSPQQAIHLSPDATLV 60 Query: 61 QAQRVTILINKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 VTIL++KP G + A A+ L+ ++ +AED++ +RF + L P L Sbjct: 61 AINPVTILLHKPAG-IDADA------ALRLITPENLYAEDRSGIRFLKKHTSELKPVDVL 113 Query: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPEADLKRLNHGLIMDGK 180 + + GL+V TQD +A++L+ + + V++EY+ V G L L LNHGL +GK Sbjct: 114 ETYASGLMVFTQDWHVARKLVDDAATVEQEYIAEVS----GDLIPNGLALLNHGLNFNGK 169 Query: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQWR 240 PL P KV WQNE +LRF L+ G++ QI MC+MVGLK++ LKR+RI + + LP GQWR Sbjct: 170 PLAPIKVSWQNETRLRFALKAGRRGQIAHMCEMVGLKLLNLKRIRIARLPMASLPAGQWR 229 Query: 241 YLRPDEKF 248 YL+ E+F Sbjct: 230 YLKGYERF 237 >gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase (Uracil hydrolyase) [Herminiimonas arsenicoxydans] Length = 538 Score = 72.8 bits (177), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 67/246 (27%), Positives = 121/246 (49%), Gaps = 29/246 (11%) Query: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVE----RQASAEQ 61 +L K ++E GL SRR+ +E I G V V+G+ + G ++LP +V + ++ + + Sbjct: 178 KLHKVLAEAGLGSRRDMEELIIAGRVSVNGEPAHI-GQRILPADQVRINGKLIQRKVSNK 236 Query: 62 AQRVTILINKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121 RV ++ +KP G + + +P+V R + + GRLD Sbjct: 237 PPRV-LVYHKPAGEIVSTNDPEGRPSVF--------------ERLPTMKAAKWLAVGRLD 281 Query: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPEADLKRLNHGLIMDGKP 181 ++ GLL+ T G +A +L+ +D+EY VR G+L E ++L G+ ++ Sbjct: 282 FNTEGLLLFTTSGDLANRLMHPRYGIDREYAVRTL----GELEEGMRQKLLAGVELEDGL 337 Query: 182 LRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE-LPT 236 + +K+ + + R T+ EG+ R++RRM + +GL V L R R G + L + L Sbjct: 338 AQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGTLTLPKNLKR 397 Query: 237 GQWRYL 242 G+W + Sbjct: 398 GRWEEM 403 >gi|134095624|ref|YP_001100699.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 186 Score = 66.2 bits (160), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 54/148 (36%), Positives = 71/148 (47%), Gaps = 19/148 (12%) Query: 111 LKSLVPAGRLDIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPEADLKR 170 + + PAGRLD DS GLL+LT DG++ + D K YL +V+ P A L+ Sbjct: 31 IPDIYPAGRLDADSEGLLLLTDDGKLQHAISHPDHKQTKTYLAQVEGI-PHTEALARLRA 89 Query: 171 -LNHG-LIMDG---KPLRPAKVVWQNEDQLR-----------FTLREGKKRQIRRMCDMV 214 LN G I G K ++ +W +R TL EGK RQ+RRM V Sbjct: 90 PLNLGDFITQGCEVKRVQEPDWLWPRNPPIRERAQVPTSWLAITLAEGKNRQVRRMTGAV 149 Query: 215 GLKVIGLKRVRIGGVKLGELP--TGQWR 240 GL + L R+ IG + L P GQWR Sbjct: 150 GLPTLRLIRIAIGPISLQSHPLLPGQWR 177 >gi|134094904|ref|YP_001099979.1| 16S rRNA pseudouridylate 516 synthase [Herminiimonas arsenicoxydans] Length = 244 Score = 64.3 bits (155), Expect = 6e-12, Method: Compositional matrix adjust. Identities = 62/244 (25%), Positives = 94/244 (38%), Gaps = 26/244 (10%) Query: 5 VRLSKRMSELGLCSRREADEWIEKGWVRVDGQVVSVLGSKVLPHQKVTVERQASAE---Q 61 + L + + G +R+ IE G V ++G VV + V +E E Sbjct: 4 LTLDRILQSQGFGTRKYCRGLIEDGEVSINGVVVDNFKTAV---DTTDLEFTIFDEVWRY 60 Query: 62 AQRVTILINKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLD 121 + V I++NKP + + + + L+ EQ W + L P GRLD Sbjct: 61 REHVYIVLNKPANFECSRKPSHHPGVLTLLPEQFTW--------------RDLQPVGRLD 106 Query: 122 IDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPEADLKRLNHGLIMD-GK 180 D+ G+L+++ DG + K Y V T PE + L + D Sbjct: 107 HDTTGMLLMSDDGPFIHAQSSPKRHIPKIY---VATTHDPVTPELIAQLLGGVQLHDEPA 163 Query: 181 PLRPAKVVWQNEDQLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE--LPTGQ 238 PL E Q+ L +GK Q++RM G L R IG + L L G+ Sbjct: 164 PLAAQTCRMLAEHQIEIVLEQGKYHQVKRMLAAAGNHCSALNRAEIGELTLESLGLEEGE 223 Query: 239 WRYL 242 W YL Sbjct: 224 WTYL 227 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 Lambda K H 0.319 0.137 0.403 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 3295 Number of Hits to DB: 493,777 Number of extensions: 20007 Number of successful extensions: 62 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 54 Number of HSP's successfully gapped: 5 Length of query: 248 Length of database: 1,000,347 Length adjustment: 79 Effective length of query: 169 Effective length of database: 740,042 Effective search space: 125067098 Effective search space used: 125067098 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 (21.7 bits) S2: 127 (53.5 bits)