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= 0021.0021.p (677 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudourid... 949 0.0 gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudou... 69 1e-12 gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudourid... 67 3e-12 gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [H... 64 3e-11 >gi|300312901|ref|YP_003776993.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 560 Score = 949 bits (2454), Expect = 0.0, Method: Compositional matrix adjust. Identities = 560/562 (99%), Positives = 560/562 (99%), Gaps = 2/562 (0%) Query: 116 MDAPAKAKPAKTAKPRGKAKPVEAEQIAAPAPAELPKVIVTVGDEVVAPPVLLDAPADPN 175 MDAPAKAKPAKTAKPRGKAKPVEAEQIAAPAPAELPKVIVTVGDEVVAPPVLLDAPADPN Sbjct: 1 MDAPAKAKPAKTAKPRGKAKPVEAEQIAAPAPAELPKVIVTVGDEVVAPPVLLDAPADPN 60 Query: 176 RNKPARRGVRGPRALRNNRAAQRAAASAEGGVPGKADNGAAPEQQPRGQFGKGHGQGGQN 235 RNKPARRGVRGPRALRNNRAAQRAAASAEGGVPGKADNGAAPEQQPRGQFGKGHGQGGQN Sbjct: 61 RNKPARRGVRGPRALRNNRAAQRAAASAEGGVPGKADNGAAPEQQPRGQFGKGHGQGGQN 120 Query: 236 AQNGQGQQGKKNFDKNGKKPKAPQLGLRAAEPVDDIFSYVTSEAYDRDENPKGGARQPHQ 295 AQNGQGQQGKKNFDKNGKKPKAPQLGLRAAEPVDDIFSYVTSEAYDRDENPKGGARQPHQ Sbjct: 121 AQNGQGQQGKKNFDKNGKKPKAPQLGLRAAEPVDDIFSYVTSEAYDRDENPKGGARQPHQ 180 Query: 296 MRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTD 355 MRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTD Sbjct: 181 MRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTD 240 Query: 356 AVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRL 415 AVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRL Sbjct: 241 AVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRL 300 Query: 416 DYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQF 475 DYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQF Sbjct: 301 DYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQF 360 Query: 476 SRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRW 535 SRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRW Sbjct: 361 SRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRW 420 Query: 536 EELEENAVRNLMAACGLEKQAGEGKSGNGGHAGKGQGNGNGNGPRGNAMQNKGPQKGRGG 595 EELEENAVRNLMAACGLEKQAGEGKSGNGGHAGKGQ GNGNGPRGNAMQNKGPQKGRGG Sbjct: 421 EELEENAVRNLMAACGLEKQAGEGKSGNGGHAGKGQ--GNGNGPRGNAMQNKGPQKGRGG 478 Query: 596 NYGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDAGQRRNNRPQRG 655 NYGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDAGQRRNNRPQRG Sbjct: 479 NYGNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDAGQRRNNRPQRG 538 Query: 656 GNSAPNFMLGGLPGMNRRRGGR 677 GNSAPNFMLGGLPGMNRRRGGR Sbjct: 539 GNSAPNFMLGGLPGMNRRRGGR 560 >gi|300311054|ref|YP_003775146.1| ribosomal small subunit pseudouridine synthase A [Herbaspirillum seropedicae SmR1] Length = 240 Score = 68.9 bits (167), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 66/229 (28%), Positives = 101/229 (44%), Gaps = 9/229 (3%) Query: 314 LHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPP 373 L ++L G GSR+ ELI G V +NGE R P D + + + + R Sbjct: 6 LDRILQSQGFGSRKYCRELIEDGEVVINGEVVD-DYRATP-DTKDLVLTIFEEEWEYREH 63 Query: 374 RVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLA-VGRLDYNTEGLLLFTTSGDLA 432 + +KP I P V LP + + VGRLD++T GLLL + G Sbjct: 64 VYIAINKPPN-IECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFI 122 Query: 433 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRI-ADGGGEGVNKWYR 491 + P+ ++ + YA T + E + +L +GV+L D PA + GE + Sbjct: 123 HAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEPAPLAATRCRQLGENL---LE 179 Query: 492 VTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT-LRRGRWEELE 539 + + +G+ +V+RM A G S L RT G + L L G W L+ Sbjct: 180 IVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLD 228 >gi|300310727|ref|YP_003774819.1| 16S rRNA uridine-516 pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 188 Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust. Identities = 48/143 (33%), Positives = 68/143 (47%), Gaps = 16/143 (11%) Query: 413 GRLDYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGP 472 GRLD ++EGLLL T G L + + HPR + + Y + G+ KL ++L D Sbjct: 38 GRLDADSEGLLLLTDDGKLQHAIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFV 97 Query: 473 AQFSR---IADGGGEGV------------NKWYRVTIGEGRNREVRRMFEAVGLTVSRLI 517 Q S+ I + G W +TI EG+NR+VRRM AVGL RL+ Sbjct: 98 TQGSQARLIQEPGWMWPRNPPIRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLV 157 Query: 518 RTRYGAMTL-PQTLRRGRWEELE 539 R G +L + G W E++ Sbjct: 158 RIAIGPFSLATHPVMPGEWREVD 180 >gi|300311490|ref|YP_003775582.1| RNA pseudouridylate synthase [Herbaspirillum seropedicae SmR1] Length = 248 Score = 64.3 bits (155), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 31/247 (12%) Query: 313 KLHKVLADAGLGSRRDMEELIVAG-RVSVNGEPAHIGQRILPTDAVRINGKLIQRKVS-K 370 +L K +++ GL SRR+ +E I G + +G ++LP V + +R+ S + Sbjct: 6 RLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTV-----ERQASAE 60 Query: 371 RPPRVLVY---------------HKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRL 415 + RV + +KPA +V+ + R + + GRL Sbjct: 61 QAQRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRL 120 Query: 416 DYNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLSGVELDDG 471 D ++ GLL+ T G +A +L+ +++EY VR G+L E ++L G+ +D Sbjct: 121 DIDSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGK 180 Query: 472 PAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLR 531 P + +++ + + R T+ EG+ R++RRM + VGL V L R R G + L + L Sbjct: 181 PLRPAKVVWQNEDQL----RFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGE-LP 235 Query: 532 RGRWEEL 538 G+W L Sbjct: 236 TGQWRYL 242 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.311 0.131 0.380 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,421,328 Number of extensions: 54849 Number of successful extensions: 141 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 136 Number of HSP's successfully gapped: 4 Length of query: 677 Length of database: 1,619,870 Length adjustment: 92 Effective length of query: 585 Effective length of database: 1,184,250 Effective search space: 692786250 Effective search space used: 692786250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 134 (56.2 bits)