RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6 [Candidatus Liberibacter asiaticus str. psy62] (135 letters) >gnl|CDD|144734 pfam01250, Ribosomal_S6, Ribosomal protein S6. Length = 92 Score = 111 bits (281), Expect = 5e-26 Identities = 43/90 (47%), Positives = 66/90 (73%) Query: 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYV 61 + YE +F+LR D+S +++K I +Y+ LI+ENGGEV V + G R +AY I+K R+ YYV Sbjct: 1 RKYETMFILRPDLSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYV 60 Query: 62 FMNIASPPAAIHEMKRKMRIDENVLRSLTL 91 +N + P AI E++R++RI+E+VLR LT+ Sbjct: 61 LINFEAEPEAIAELERRLRINEDVLRFLTV 90 >gnl|CDD|30709 COG0360, RpsF, Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]. Length = 112 Score = 100 bits (250), Expect = 1e-22 Identities = 40/106 (37%), Positives = 71/106 (66%) Query: 4 YEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFM 63 YE VF++R D+S +Q+ + +Y+ ++ NGGE+ V + G R +AY I+K R+ +YV M Sbjct: 3 YEIVFIVRPDLSEEQVAALVEKYKGVLTNNGGEIHKVEDWGKRRLAYPIKKLREGHYVLM 62 Query: 64 NIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDR 109 N + PAAI E++R +RI+E+VLR L + V+ ++ + +++ D+ Sbjct: 63 NFEAEPAAIAELERLLRINEDVLRHLIIKVEKAKEELSPMLKKKDQ 108 >gnl|CDD|177046 CHL00123, rps6, ribosomal protein S6; Validated. Length = 97 Score = 58.5 bits (142), Expect = 6e-10 Identities = 26/90 (28%), Positives = 52/90 (57%) Query: 2 KLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYV 61 YE ++LL+ D++ +++ I Y+ L+++ G + V G R ++Y+I K Y+ Sbjct: 6 NKYETMYLLKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGKRKLSYKINKYEDGIYI 65 Query: 62 FMNIASPPAAIHEMKRKMRIDENVLRSLTL 91 MN + ++ +++ +++DENVLR LT Sbjct: 66 QMNYSGNGKLVNSLEKALKLDENVLRYLTF 95 >gnl|CDD|39906 KOG4708, KOG4708, KOG4708, Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis]. Length = 141 Score = 42.6 bits (100), Expect = 3e-05 Identities = 32/98 (32%), Positives = 46/98 (46%), Gaps = 5/98 (5%) Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK----NR 56 M LYE + R + K LI NG VR V LG R + Y+I+K + Sbjct: 3 MPLYELALITRSLSRPELAKLLARTGGHLIDRNG-VVRDVESLGKRELPYKIKKLDQRHY 61 Query: 57 KAYYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVD 94 + + M S PA E+KR ++ D +V+R L + VD Sbjct: 62 RGQHFLMTFYSSPAVQSEIKRILKRDPDVIRWLIVKVD 99 >gnl|CDD|36043 KOG0825, KOG0825, KOG0825, PHD Zn-finger protein [General function prediction only]. Length = 1134 Score = 26.0 bits (56), Expect = 3.1 Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 6/110 (5%) Query: 27 QSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAI--HEMKRKMRIDEN 84 QS+ Q +R V +R IA + F NI + + K ++N Sbjct: 301 QSVKQPEVQLLRHVETERVRAIATC---DTFGSEDFNNIQDSENNLLKNTKLEKSLEEKN 357 Query: 85 VLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRD-RNVDRKQHVSEEKP 133 + + IQ+H +D N+ P + + Q+ SE +P Sbjct: 358 ESLTEHPRSTELPKRHVQQIQKHFSEDNNEMIPMECDSFCSDQNESEVEP 407 >gnl|CDD|185751 cd09238, V_Alix_like_1, Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_Rim20_Bro1_like superfamily also have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind to human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members of the V_Alix_like superfamily also have a proline-rich region (PRR). Length = 339 Score = 25.9 bits (57), Expect = 3.9 Identities = 6/34 (17%), Positives = 18/34 (52%) Query: 64 NIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHE 97 + + A I +M + ++ ++N+L + S++ Sbjct: 206 ALGNERAGIEDMMKALKRNDNILAKVMATTGSYD 239 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 0.320 0.135 0.375 Gapped Lambda K H 0.267 0.0767 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,567,581 Number of extensions: 72757 Number of successful extensions: 179 Number of sequences better than 10.0: 1 Number of HSP's gapped: 177 Number of HSP's successfully gapped: 15 Length of query: 135 Length of database: 6,263,737 Length adjustment: 84 Effective length of query: 51 Effective length of database: 4,448,581 Effective search space: 226877631 Effective search space used: 226877631 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 (21.8 bits) S2: 52 (23.7 bits)