RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780187|ref|YP_003064600.1| 30S ribosomal protein S4 [Candidatus Liberibacter asiaticus str. psy62] (206 letters) >gnl|CDD|180018 PRK05327, rpsD, 30S ribosomal protein S4; Validated. Length = 203 Score = 291 bits (747), Expect = 1e-79 Identities = 101/208 (48%), Positives = 139/208 (66%), Gaps = 7/208 (3%) Query: 1 MSKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQ-RRKSKPSYFGLQLRAKQKMK 59 M++ K K+ RR+G +L+ K + + Y PG HGQ RRK K S +GLQLR KQK++ Sbjct: 1 MARYTGPKCKLSRRLGVDLFKSGKRCLKRK-YPPGQHGQRRRKPKLSDYGLQLREKQKLR 59 Query: 60 KYYGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHR 119 + YG + EK+FR FKEA R +G+T NL+ LESRLD +VYR F PT ARQ V+H Sbjct: 60 RIYG-VLEKQFRRYFKEAARRKGNTGENLLQLLESRLDNVVYRLGFAPTRRQARQLVSHG 118 Query: 120 HVLVNGRSVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLAE-RDVPEYISVNHDNMVAT 178 H+LVNG+ VNI SYR K GDVIEV++KSK+L + EA +LAE R VP+++ V+ + + T Sbjct: 119 HILVNGKKVNIPSYRVKPGDVIEVREKSKKLPRIKEALELAERRGVPDWLEVDAEKLEGT 178 Query: 179 FVRIPSSLKDVPYPVIMQPNLVVEFYSR 206 F R+P ++ PV + L+VE YS+ Sbjct: 179 FKRLP-EREE--IPVPINEQLIVELYSK 203 >gnl|CDD|130089 TIGR01017, rpsD_bact, ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. Length = 200 Score = 218 bits (557), Expect = 1e-57 Identities = 93/201 (46%), Positives = 134/201 (66%), Gaps = 6/201 (2%) Query: 7 SKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDIS 66 K K+ RR+G NL+G+ + + R Y PG HGQRRK K S +GLQL+ KQK+K YG I+ Sbjct: 5 PKFKLSRRLGVNLFGKSRKLLLKRKYPPGQHGQRRK-KLSDYGLQLQEKQKLKFMYG-IT 62 Query: 67 EKKFRSIFKEADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGR 126 EK+FR FKEA + +G+T NL+ LESRLD +VYR F PT FAARQ V+H H+LVNG+ Sbjct: 63 EKQFRKYFKEAKKLKGNTGENLLRLLESRLDNVVYRLGFAPTRFAARQLVSHGHILVNGK 122 Query: 127 SVNIGSYRCKEGDVIEVKQKSKQLASVLEASQLA-ERDVPEYISVNHDNMVATFVRIPSS 185 V+I SY+ + GD+I +K+KSK++ V E + +R++P ++ V+ + +R+P Sbjct: 123 KVDIPSYQVRPGDIISIKEKSKKIPLVKENLETNGQRNIPSWLEVDKKTLEGKVLRVPE- 181 Query: 186 LKDVPYPVIMQPNLVVEFYSR 206 P+ + +LVVE+YSR Sbjct: 182 --RSQLPLPINESLVVEYYSR 200 >gnl|CDD|128657 smart00363, S4, S4 RNA-binding domain. Length = 60 Score = 66.1 bits (162), Expect = 6e-12 Identities = 21/55 (38%), Positives = 27/55 (49%) Query: 94 SRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148 RLD + R P+ AR+ + V VNG+ V SY K GDVI V+ K Sbjct: 1 RRLDKFLARLGLAPSRSQARKLIEQGRVKVNGKKVTKPSYIVKPGDVISVRGKEL 55 >gnl|CDD|179730 PRK04051, rps4p, 30S ribosomal protein S4P; Validated. Length = 177 Score = 54.9 bits (133), Expect = 1e-08 Identities = 23/44 (52%), Positives = 25/44 (56%) Query: 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133 LE RL TIVYR T ARQF+ H H+ VNGR V SY Sbjct: 99 DILERRLQTIVYRKGLARTPKQARQFIVHGHIAVNGRRVTSPSY 142 >gnl|CDD|130090 TIGR01018, rpsD_arch, ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. Length = 162 Score = 50.1 bits (120), Expect = 4e-07 Identities = 20/43 (46%), Positives = 25/43 (58%) Query: 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133 FLE RL T V++ TI ARQ + H H+ V+GR V SY Sbjct: 101 FLERRLQTQVFKKGLARTIHQARQLIVHGHIAVDGRRVTSPSY 143 >gnl|CDD|177783 PLN00189, PLN00189, 40S ribosomal protein S9; Provisional. Length = 194 Score = 42.4 bits (100), Expect = 9e-05 Identities = 16/44 (36%), Positives = 27/44 (61%) Query: 90 SFLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133 +FLE RL T+V+++ +I AR + RH+ V + VN+ S+ Sbjct: 105 NFLERRLQTLVFKSGMAKSIHHARVLIRQRHIRVGKQIVNVPSF 148 >gnl|CDD|185484 PTZ00155, PTZ00155, 40S ribosomal protein S9; Provisional. Length = 181 Score = 37.8 bits (88), Expect = 0.002 Identities = 15/43 (34%), Positives = 23/43 (53%) Query: 91 FLESRLDTIVYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSY 133 LE RL T V++ +I AR + RH+ V + V+I S+ Sbjct: 104 LLERRLQTKVFKLGLAKSIHHARVLIRQRHIRVGKQIVDIPSF 146 >gnl|CDD|165505 PHA03246, PHA03246, large tegument protein UL36; Provisional. Length = 3095 Score = 29.9 bits (67), Expect = 0.44 Identities = 24/85 (28%), Positives = 34/85 (40%), Gaps = 12/85 (14%) Query: 2 SKRESSKHKIDRRIGENLWGRPKSPVNTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKY 61 S+ +S+HK RR W P S N S GP R+ S+ S L L Sbjct: 456 SRGSNSRHK--RR--RPSWTPPSSSENVSSDGPTFSQSRKPSRKSKRALDLD-------- 503 Query: 62 YGDISEKKFRSIFKEADRSRGDTSH 86 YG +S + + +D G S+ Sbjct: 504 YGHLSNEPSDVDGENSDSPAGAISN 528 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 29.9 bits (67), Expect = 0.49 Identities = 13/21 (61%), Positives = 17/21 (80%), Gaps = 1/21 (4%) Query: 58 MKKYYGDISEKKFRSIFKEAD 78 M KYYG+ SE++ R IFKEA+ Sbjct: 249 MSKYYGE-SEERLREIFKEAE 268 >gnl|CDD|162487 TIGR01687, moaD_arch, MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable. Length = 88 Score = 29.7 bits (67), Expect = 0.52 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 10/86 (11%) Query: 60 KYYGDISEKKFRSIFK-EADRSRGDTSHNLISFLESRLDTIVYRAKFVPTIFAARQFVNH 118 KY+ + + + + E + G T +L++ L +R Y +F V + Sbjct: 4 KYFATLRDITGKKSEEIEIE---GKTVGDLLNELMAR-----YPKEFSELFKEGLGLVPN 55 Query: 119 RHVLVNGRSVNIG-SYRCKEGDVIEV 143 +LVNGR+V+ G K+GDV+ + Sbjct: 56 VIILVNGRNVDWGLGTELKDGDVVAI 81 >gnl|CDD|177682 PLN00051, PLN00051, RNA-binding S4 domain-containing protein; Provisional. Length = 267 Score = 27.4 bits (61), Expect = 2.8 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 13/60 (21%) Query: 95 RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQKSK 148 RLD + + R+K V I + V VN R V K GDV+ V K + Sbjct: 193 RLDALASAGFRMSRSKLVDLISSG-------DVRVNWREVTKNGTTLKTGDVVSVSGKGR 245 >gnl|CDD|184784 PRK14667, uvrC, excinuclease ABC subunit C; Provisional. Length = 567 Score = 27.4 bits (61), Expect = 2.9 Identities = 12/46 (26%), Positives = 25/46 (54%), Gaps = 1/46 (2%) Query: 34 PGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDI-SEKKFRSIFKEAD 78 PG++ ++K + Y G K ++ ++Y ++ K R+IF E+ Sbjct: 17 PGVYLFKKKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESS 62 >gnl|CDD|165244 PHA02933, PHA02933, unchracterized protein; Provisional. Length = 149 Score = 26.5 bits (58), Expect = 4.5 Identities = 14/36 (38%), Positives = 20/36 (55%) Query: 62 YGDISEKKFRSIFKEADRSRGDTSHNLISFLESRLD 97 Y ISE +F+S+ D D + LI FLE +L+ Sbjct: 114 YKKISESRFQSLGNITDLMTDDNINILILFLEKKLN 149 >gnl|CDD|180858 PRK07139, PRK07139, amidase; Provisional. Length = 439 Score = 26.6 bits (59), Expect = 4.8 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 6/49 (12%) Query: 28 NTRSYGPGLHGQRRKSKPSYFGLQLRAKQKMKKYYGDISEKKFRSIFKE 76 NTRS G G Q+R SYF ++ +KY+ + KK R + K Sbjct: 304 NTRSEGFGKMVQKRLILGSYF----LEEENQEKYF--LKAKKVRRVIKN 346 >gnl|CDD|132113 TIGR03069, PS_II_S4, photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium. Length = 257 Score = 26.1 bits (58), Expect = 6.5 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 13/58 (22%) Query: 95 RLDTI------VYRAKFVPTIFAARQFVNHRHVLVNGRSVNIGSYRCKEGDVIEVKQK 146 R+D I + R+K V I A R + +N ++V S K GD ++++ K Sbjct: 185 RIDAIASAGFGLSRSKIVDQIKAGR-------LRLNWKTVTQPSRELKVGDRLQLRGK 235 >gnl|CDD|179455 PRK02645, ppnK, inorganic polyphosphate/ATP-NAD kinase; Provisional. Length = 305 Score = 25.6 bits (57), Expect = 9.6 Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 5/27 (18%) Query: 180 VRIPSSLKDVPYPVIM-----QPNLVV 201 + PS KD PYPV + +L + Sbjct: 36 LMGPSGPKDNPYPVFLASASELIDLAI 62 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.319 0.134 0.384 Gapped Lambda K H 0.267 0.0733 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,269,490 Number of extensions: 193724 Number of successful extensions: 417 Number of sequences better than 10.0: 1 Number of HSP's gapped: 407 Number of HSP's successfully gapped: 21 Length of query: 206 Length of database: 5,994,473 Length adjustment: 89 Effective length of query: 117 Effective length of database: 4,071,361 Effective search space: 476349237 Effective search space used: 476349237 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 (21.7 bits) S2: 55 (25.0 bits)