RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13 [Candidatus Liberibacter asiaticus str. psy62] (155 letters) >gnl|CDD|144239 pfam00572, Ribosomal_L13, Ribosomal protein L13. Length = 128 Score = 188 bits (479), Expect = 7e-49 Identities = 72/129 (55%), Positives = 92/129 (71%), Gaps = 1/129 (0%) Query: 16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75 W ++DAKG I+GRLAS++A LRGK+KPTYTP D GD+VV++NA K+ +GKK DQK Y Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVVNAEKIVLTGKKRDQKKY 60 Query: 76 YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHE 135 YRHTGYPGG+K TAK L P IL++A+ MLP+ L R +K L +YA HPH Sbjct: 61 YRHTGYPGGLKNPTAKGPLE-RKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHA 119 Query: 136 AQKPVFMDI 144 AQKP ++I Sbjct: 120 AQKPEVLEI 128 >gnl|CDD|30451 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]. Length = 148 Score = 184 bits (468), Expect = 9e-48 Identities = 77/146 (52%), Positives = 102/146 (69%) Query: 4 TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63 TF K SEVE+KW ++DA+G ++GRLAS++A RLRGK+KPTYTP D GD+V++INA KV Sbjct: 3 TFTAKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKV 62 Query: 64 AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123 +GKK K YYRH+GYPGG+K T LA P IL++A+ MLP+ PL R +K Sbjct: 63 VITGKKLTDKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKR 122 Query: 124 LHIYAEDHHPHEAQKPVFMDIAKMNP 149 L +YA HPHEAQKP +++ + Sbjct: 123 LKVYAGIPHPHEAQKPEALELKLLKG 148 >gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated. Length = 143 Score = 158 bits (402), Expect = 5e-40 Identities = 69/144 (47%), Positives = 93/144 (64%), Gaps = 1/144 (0%) Query: 1 MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60 M TF +KW ++DAK +GRLA++IA LRGKNKP+Y PS D GD+V++INA Sbjct: 1 MNKTFIPSKDYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINA 60 Query: 61 SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120 K+ +G K QK Y RH+G PGG+K T +E L P I++KA+ MLP+GPL RK Sbjct: 61 EKIKVTGNKTSQKFYVRHSGRPGGLKIETFEE-LQNRLPNRIIEKAVKGMLPKGPLGRKL 119 Query: 121 MKNLHIYAEDHHPHEAQKPVFMDI 144 L +Y + HPH AQKP+ ++I Sbjct: 120 FTKLKVYKGESHPHVAQKPIKINI 143 >gnl|CDD|88313 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.. Length = 114 Score = 150 bits (381), Expect = 1e-37 Identities = 59/113 (52%), Positives = 80/113 (70%), Gaps = 1/113 (0%) Query: 16 WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75 W ++DAKG ++GRLAS++A L GK+KPTYTP D GD+VV++NA K+ +GKK+ QK Y Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60 Query: 76 YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYA 128 YRHTGYPGG+K TA + +P ILK+A+ MLP+ L R +K L +Y Sbjct: 61 YRHTGYPGGLKNPTAGPLHP-RAPERILKRAVRGMLPKNKLGRAALKRLKVYE 112 >gnl|CDD|38413 KOG3203, KOG3203, KOG3203, Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis]. Length = 165 Score = 142 bits (359), Expect = 4e-35 Identities = 65/134 (48%), Positives = 89/134 (66%), Gaps = 7/134 (5%) Query: 12 VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYD 71 + W +VDAK +GRLASQIA L+GK+KP Y PS D GDHVV+ N K+AFSGKK++ Sbjct: 19 FARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWE 78 Query: 72 QKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDH 131 QK Y H+GYPGG+K+TTA + LA P I++ A+ MLP+ L R++M+ LH++ + Sbjct: 79 QKIYRSHSGYPGGLKQTTADQ-LADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEE 137 Query: 132 HP------HEAQKP 139 HP E +P Sbjct: 138 HPEKVNIGSELHQP 151 >gnl|CDD|73075 cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.. Length = 440 Score = 26.0 bits (57), Expect = 5.2 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 12/63 (19%) Query: 38 RGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGA 97 RGK YT S +D HV + + K Y Y I ++ +I Sbjct: 41 RGKGSHAYTHSLEDNHHVFLNLET----------LKFYCLPDNYE--IIDSSLDDIKYVL 88 Query: 98 SPT 100 +PT Sbjct: 89 NPT 91 >gnl|CDD|34498 COG4889, COG4889, Predicted helicase [General function prediction only]. Length = 1518 Score = 25.3 bits (55), Expect = 6.8 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 9/54 (16%) Query: 104 KKAIARMLPRGPL---------ARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMN 148 K +A+ PR L K++ +LH+ E ++ K ++ A+M+ Sbjct: 1371 KNDLAKEAPRIALSEDFKELSMLGKELADLHLNYESGEMWDSIKHNKLEAAEMD 1424 >gnl|CDD|37314 KOG2103, KOG2103, KOG2103, Uncharacterized conserved protein [Function unknown]. Length = 910 Score = 25.3 bits (55), Expect = 7.1 Identities = 20/77 (25%), Positives = 25/77 (32%), Gaps = 12/77 (15%) Query: 59 NASKVAFSGKKYDQKTYYRHTG---YPGGIK-----KT----TAKEILAGASPTNILKKA 106 N F T +P IK T T+K IL G IL+ Sbjct: 732 NKLSNVFDSLSAPPLPGQVQTQSYIFPQIIKTMSVTITEQGITSKHILIGLPSGQILEIP 791 Query: 107 IARMLPRGPLARKQMKN 123 A + PR P A + K Sbjct: 792 KALLDPRRPPAPTEKKR 808 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.317 0.133 0.386 Gapped Lambda K H 0.267 0.0756 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,872,910 Number of extensions: 91150 Number of successful extensions: 207 Number of sequences better than 10.0: 1 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 11 Length of query: 155 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 69 Effective length of database: 4,405,363 Effective search space: 303970047 Effective search space used: 303970047 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (24.1 bits)