RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780786|ref|YP_003065199.1| ribosome-binding factor A [Candidatus Liberibacter asiaticus str. psy62] (128 letters) >2kzf_A RBFA, ribosome-binding factor A; JCSG, joint center structural genomics, PSI-2, protein struc initiative; NMR {Thermotoga maritima} Length = 106 Score = 87.8 bits (218), Expect = 6e-19 Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 4/102 (3%) Query: 7 KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPLD 65 + R + E++ LM + + +D + +D ++ S V +S D R A VY+S L Sbjct: 3 NPAYRKAMLESEIQKLLMEAL--QQLRDPRLKKDFVTFSRVELSKDKRYADVYVSFLGTP 60 Query: 66 VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSL 107 + LN F R I ++LR L PE+RF D + Sbjct: 61 EERKETVEILNRAKGFFRTFIAKNLR-LYVAPEIRFYEDKGI 101 >1jos_A RBFA, ribosome-binding factor A; RNA binding protein, structure 2 function project, S2F, structural genomics; 1.70A {Haemophilus influenzae} SCOP: d.52.7.1 PDB: 1kkg_A Length = 128 Score = 81.0 bits (200), Expect = 7e-17 Identities = 34/114 (29%), Positives = 63/114 (55%), Gaps = 7/114 (6%) Query: 6 PKNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLD 65 + +R+ RV +E++ + VIL E +D I +++S+V +S DL A ++++ D Sbjct: 2 AREFKRSDRVAQEIQKEIA-VILQREVKDPRIGM--VTVSDVEVSSDLSYAKIFVTFLFD 58 Query: 66 VSP---DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNAL 116 ++ + L +IR +G+++R LR VPE+RF YD SL +++ L Sbjct: 59 HDEMAIEQGMKGLEKASPYIRSLLGKAMR-LRIVPEIRFIYDQSLVEGMRMSNL 111 >1pa4_A Probable ribosome-binding factor A; structural genomics, distant homology, BSGC structure funded by NIH, protein structure initiative, PSI; NMR {Mycoplasma pneumoniae} SCOP: d.52.7.1 Length = 116 Score = 72.9 bits (179), Expect = 2e-14 Identities = 19/110 (17%), Positives = 45/110 (40%), Gaps = 4/110 (3%) Query: 8 NSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVS 67 S + R+ ++ + + +E + + ++ V +S DL TVY+ Sbjct: 2 ASYKKERLENDIIRLINR-TVIHEIYNETVKT--GHVTHVKLSDDLLHVTVYLDCYNREQ 58 Query: 68 PDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117 DRV+ A N + +L L ++ F D ++ + ++ +++ Sbjct: 59 IDRVVGAFNQAKGVFSRVLAHNLY-LAKAVQIHFVKDKAIDNAMRIESII 107 >2e7g_A Putative ribosome-binding factor A; RBFA, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.52.7.1 Length = 129 Score = 72.6 bits (178), Expect = 2e-14 Identities = 19/112 (16%), Positives = 40/112 (35%), Gaps = 3/112 (2%) Query: 7 KNSRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYIS-LPLD 65 ++ R + + AL ++ E L + +S+V ++ D Y Sbjct: 10 EDHARLRALNGLLYKALTDLLCTPEVSQELYDL-NVELSKVSLTPDFSACRAYWKTTLSA 68 Query: 66 VSPDRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTSLQSYWKLNALM 117 + + L + +R + LR VP + F D + +L+ L+ Sbjct: 69 EQNAHMEAVLQRSAAHMRHLLMSQQT-LRNVPPIVFVQDKGNAALAELDQLL 119 >2dyj_A Ribosome-binding factor A; 16S rRNA processing, 17S RNA, KH domain, structural genomics, NPPSFA; 1.84A {Thermus thermophilus HB8} SCOP: d.52.7.1 PDB: 2r1c_A Length = 95 Score = 61.3 bits (149), Expect = 7e-11 Identities = 18/98 (18%), Positives = 41/98 (41%), Gaps = 7/98 (7%) Query: 9 SRRALRVGEEVRSALMWVILNNEFQDRLISRDVISISEVCMSVDLRVATVYISLPLDVSP 68 + + +++ AL I +D + +++ V +S D V +VY+ Sbjct: 2 AYGKAHLEAQLKRALAEEI--QALEDPRLFL--LTVEAVRLSKDGSVLSVYVEA--FREE 55 Query: 69 DRVISALNCNIKFIRGRIGRSLRNLRYVPELRFRYDTS 106 + + AL+ + + + R +R +R +P L F + Sbjct: 56 EGALRALSRAERRLVAALARRVR-MRRLPRLEFLPWRA 92 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 34.5 bits (79), Expect = 0.007 Identities = 26/141 (18%), Positives = 43/141 (30%), Gaps = 59/141 (41%) Query: 7 KNSRRALRV----GEEVRSALMWVILNNEFQDRLISRDVISISE-------VCM-SV-DL 53 + R+A+ V G VR + + + ++ S M S+ +L Sbjct: 294 VSVRKAITVLFFIG--VRC-------YEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL 344 Query: 54 RVATV--YI-----SLPLDVSPDRVISALNCNIKFIRGRIGRSLRNLRYV----PELRFR 102 V Y+ LP + + I + G +NL V P+ Sbjct: 345 TQEQVQDYVNKTNSHLP----AGKQVE-----ISLVNGA-----KNL--VVSGPPQ---- 384 Query: 103 YDTSLQSYWKLNALMCLPKIP 123 SL LN + K P Sbjct: 385 ---SLYG---LNLTLRKAKAP 399 Score = 34.1 bits (78), Expect = 0.008 Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 28/104 (26%) Query: 40 DVISISEVCMSVDLRVATVYISLPLD-----------VSPDRVISALNCN-IKFIRGRIG 87 DV+SI + V R T+ +++P D ++P RV ++ + ++++ R+G Sbjct: 1775 DVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYGMIAINPGRVAASFSQEALQYVVERVG 1834 Query: 88 R-----------SLRNLRYVP--ELRFRYD--TSLQSYWKLNAL 116 + ++ N +YV +LR D T++ ++ KL + Sbjct: 1835 KRTGWLVEIVNYNVENQQYVAAGDLR-ALDTVTNVLNFIKLQKI 1877 Score = 28.0 bits (62), Expect = 0.64 Identities = 19/105 (18%), Positives = 31/105 (29%), Gaps = 27/105 (25%) Query: 19 VRSALMWVILNNEFQDR-LISRDV-------ISISEVCMSVDLRVATVY---ISLPLDVS 67 + L EF++ L D+ + ++ + + Y + Sbjct: 84 LNLCL------TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPF 137 Query: 68 PDRVISAL-------NCNIKFIRGRIGRSLRNLRYVPELRFRYDT 105 + SAL N + I G G Y ELR Y T Sbjct: 138 DKKSNSALFRAVGEGNAQLVAIFGGQGN---TDDYFEELRDLYQT 179 >2oem_A 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; rubisco-like protein, isomerase; HET: KCX 1AE; 1.70A {Geobacillus kaustophilus} PDB: 2oel_A* 2oek_A* 2oej_A Length = 413 Score = 24.8 bits (54), Expect = 5.7 Identities = 16/85 (18%), Positives = 28/85 (32%), Gaps = 10/85 (11%) Query: 25 WVILNNEFQDRLISRD--VISISEV--------CMSVDLRVATVYISLPLDVSPDRVISA 74 W L Q++L V++I E+ L+ A V I+ P + + Sbjct: 32 WTDLPALEQEQLRKHKGEVVAIEELGESERVNAYFGKRLKRAIVKIAYPTVNFSADLPAL 91 Query: 75 LNCNIKFIRGRIGRSLRNLRYVPEL 99 L + L +L + E Sbjct: 92 LVTTFGKLSLDGEVRLLDLEFPDEW 116 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.325 0.138 0.406 Gapped Lambda K H 0.267 0.0604 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,072,319 Number of extensions: 43348 Number of successful extensions: 159 Number of sequences better than 10.0: 1 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 12 Length of query: 128 Length of database: 5,693,230 Length adjustment: 82 Effective length of query: 46 Effective length of database: 3,705,222 Effective search space: 170440212 Effective search space used: 170440212 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (23.7 bits)