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= 0001.3528.p (560 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase... 542 e-155 gi|134094557|ref|YP_001099632.1| putative pseudouridylate syntha... 74 2e-14 gi|134094904|ref|YP_001099979.1| 16S rRNA pseudouridylate 516 sy... 68 1e-12 gi|134095624|ref|YP_001100699.1| putative pseudouridylate syntha... 67 2e-12 >gi|134095614|ref|YP_001100689.1| putative pseudouridine synthase (Uracil hydrolyase) [Herminiimonas arsenicoxydans] Length = 538 Score = 542 bits (1396), Expect = e-155, Method: Compositional matrix adjust. Identities = 310/496 (62%), Positives = 350/496 (70%), Gaps = 44/496 (8%) Query: 66 KPARRGVRGPRALRNNRAA-------------QRAAAGGAEAAPAQGKGEGDAVPAERHQ 112 KP +RG+RGPR LR R A Q A +A PA G+ + P + Sbjct: 42 KPVKRGLRGPRTLRRARNAPRSGPANHDTPEEQNAVVVETQAVPASGEVRRERNPRRDER 101 Query: 113 PRGQFG--KNNAHAGQAG-QQGKKNFDKNGKKPKAPQLGLRANEPVDDIFSYVTSEAYDR 169 G G K++ +G AG +G K + G DD+FS+VTSEA+D Sbjct: 102 QPGTKGPQKSSGKSGGAGPNRGSKPHSRGGD--------------ADDVFSFVTSEAFDT 147 Query: 170 ---DEGAKAGGRQAHQMRGKNGRRDLTAEDDAPKLHKVLADAGLGSRRDMEELIVAGRVS 226 D+ G R+ Q K+ RRDLTA+DDAPKLHKVLA+AGLGSRRDMEELI+AGRVS Sbjct: 148 LSVDDDKAGGKRRPEQ---KSVRRDLTADDDAPKLHKVLAEAGLGSRRDMEELIIAGRVS 204 Query: 227 VNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPPRVLVYHKPAGEIVSHSDPEGRSSVFD 286 VNGEPAHIGQRILP D VRINGKLIQRKVS +PPRVLVYHKPAGEIVS +DPEGR SVF+ Sbjct: 205 VNGEPAHIGQRILPADQVRINGKLIQRKVSNKPPRVLVYHKPAGEIVSTNDPEGRPSVFE 264 Query: 287 RLPTMKAGKWLAVGRLDFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMR 346 RLPTMKA KWLAVGRLDFNTEGLLLFTTSGDLANRLMHPRY I+REYAVRTLGELEEGMR Sbjct: 265 RLPTMKAAKWLAVGRLDFNTEGLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMR 324 Query: 347 QKLLAGVELDDGPAQFSRIADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRT 406 QKLLAGVEL+DG AQFS+IADGGGEGVNKWYRVTIGEGRNREVRRMFEA+GLTVSRLIRT Sbjct: 325 QKLLAGVELEDGLAQFSKIADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRT 384 Query: 407 RYGAMTLPQTLKRGRWEELEENAVRNLMAACGLEKQAGEAKSGNGGHAGKGQGNGNGNGP 466 RYG +TLP+ LKRGRWEE+EE+AVR+L+A GLEK KS +G G+ NG Sbjct: 385 RYGTLTLPKNLKRGRWEEMEEHAVRDLLAMSGLEK-----KSVDGAPKGRNSPADRQNGN 439 Query: 467 RGNAMQNKG--PQKGRNGGNFGNQGGGNYGNGGNYGGGNKGGQPKSRQPDPLQTALGFPD 524 R + N P+ GN G QG NG GG GQP+SRQPDPLQT+LGFP Sbjct: 440 RAPRVDNGMGLPRSPSQWGNLGGQGRPQGQNGKPAGGRQGQGQPRSRQPDPLQTSLGFPG 499 Query: 525 IGNGQRRGNRPQRGGN 540 +G RR N P RG N Sbjct: 500 MGQ-PRRSNGPNRGPN 514 >gi|134094557|ref|YP_001099632.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 248 Score = 73.9 bits (180), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 79/257 (30%), Positives = 120/257 (46%), Gaps = 47/257 (18%) Query: 200 KLHKVLADAGLGSRRDMEELIVAGRVSVNGEP-AHIGQRILPTDAVRINGKLIQRKVSKR 258 +L K +++ GL SRR+ +E I G V V+G+ + +G +ILPT V + ++ +++ Sbjct: 6 RLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGTKILPTQRVTVE----RQAAAEQ 61 Query: 259 PPRV-LVYHKPAGEI-----------VSHSDPEGRSSVFDRLPT----MKAGKWLAVGRL 302 RV ++ +KP G + V+ E R D PT + + GRL Sbjct: 62 SKRVTILINKPMGYVSGQAEDGYKPAVALVKAESRWK-EDTSPTQFHPTQLRSLVPAGRL 120 Query: 303 DFNTEGLLLFTTSGDLANRLMHPRYNIEREYAVRTL----GELEEGMRQKLLAGVELDDG 358 D ++ GLL+ T G +A L+ ++E+EY VR G+L E Q+L G+ LD Sbjct: 121 DIDSVGLLVLTQDGRIAKHLIGENSSVEKEYLVRVQYIKPGKLPEADLQRLNHGLMLDGK 180 Query: 359 ---PAQFSRIADGGGEGVNKW-----YRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGA 410 PAQ KW + EG+ R++RRM + VGL V L R R G Sbjct: 181 KLLPAQV------------KWQNEDQLSFILREGKKRQIRRMCDIVGLKVVGLKRVRIGR 228 Query: 411 MTLPQTLKRGRWEELEE 427 + L L G W L E Sbjct: 229 VKLGD-LPVGEWRYLAE 244 >gi|134094904|ref|YP_001099979.1| 16S rRNA pseudouridylate 516 synthase [Herminiimonas arsenicoxydans] Length = 244 Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 63/228 (27%), Positives = 95/228 (41%), Gaps = 7/228 (3%) Query: 201 LHKVLADAGLGSRRDMEELIVAGRVSVNGEPAHIGQRILPTDAVRINGKLIQRKVSKRPP 260 L ++L G G+R+ LI G VS+NG + D + + R Sbjct: 6 LDRILQSQGFGTRKYCRGLIEDGEVSING--VVVDNFKTAVDTTDLEFTIFDEVWRYREH 63 Query: 261 RVLVYHKPAGEIVSHSDPEGRSSVFDRLPTMKAGKWLA-VGRLDFNTEGLLLFTTSGDLA 319 +V +KPA S P V LP + L VGRLD +T G+LL + G Sbjct: 64 VYIVLNKPANFECSRK-PSHHPGVLTLLPEQFTWRDLQPVGRLDHDTTGMLLMSDDGPFI 122 Query: 320 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVELDDGPAQFSRIADGGGEGVNKWYRV 379 + P+ +I + Y T + + +LL GV+L D PA + A + Sbjct: 123 HAQSSPKRHIPKIYVATTHDPVTPELIAQLLGGVQLHDEPAPLA--AQTCRMLAEHQIEI 180 Query: 380 TIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQT-LKRGRWEELE 426 + +G+ +V+RM A G S L R G +TL L+ G W L+ Sbjct: 181 VLEQGKYHQVKRMLAAAGNHCSALNRAEIGELTLESLGLEEGEWTYLD 228 >gi|134095624|ref|YP_001100699.1| putative pseudouridylate synthase [Herminiimonas arsenicoxydans] Length = 186 Score = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 55/188 (29%), Positives = 85/188 (45%), Gaps = 23/188 (12%) Query: 262 VLVYHKPAGEIVSHSDPEGRSSVFDRL--PTMKAGKWLAVGRLDFNTEGLLLFTTSGDLA 319 +++++KP + S R+S+ D L P + GRLD ++EGLLL T G L Sbjct: 3 LILFNKPFQVMCQFSPHPTRASLADYLDIPDIYPA-----GRLDADSEGLLLLTDDGKLQ 57 Query: 320 NRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVELDDGPAQ---FSRIADGG------- 369 + + HP + + Y + G +L A + L D Q R+ + Sbjct: 58 HAISHPDHKQTKTYLAQVEGIPHTEALARLRAPLNLGDFITQGCEVKRVQEPDWLWPRNP 117 Query: 370 -----GEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTL-PQTLKRGRWE 423 + W +T+ EG+NR+VRRM AVGL RLIR G ++L L G+W Sbjct: 118 PIRERAQVPTSWLAITLAEGKNRQVRRMTGAVGLPTLRLIRIAIGPISLQSHPLLPGQWR 177 Query: 424 ELEENAVR 431 E+ +R Sbjct: 178 EVSAAELR 185 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 0.313 0.135 0.398 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: 803,061 Number of extensions: 30906 Number of successful extensions: 81 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 73 Number of HSP's successfully gapped: 4 Length of query: 560 Length of database: 1,000,347 Length adjustment: 87 Effective length of query: 473 Effective length of database: 713,682 Effective search space: 337571586 Effective search space used: 337571586 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 (21.9 bits) S2: 131 (55.1 bits)