RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5 [Candidatus Liberibacter asiaticus str. psy62] (199 letters) >gnl|CDD|179061 PRK00550, rpsE, 30S ribosomal protein S5; Validated. Length = 168 Score = 231 bits (591), Expect = 1e-61 Identities = 86/160 (53%), Positives = 117/160 (73%), Gaps = 1/160 (0%) Query: 13 QNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVR 72 E+ + +++VAINRV+ + GGRRF+FS LVVVGD K +VGF + AREVPEA+R Sbjct: 4 MRIEKNKLELEEKVVAINRVTKVVKGGRRFSFSALVVVGDGKGRVGFGYGKAREVPEAIR 63 Query: 73 KATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132 KA E AK+NMI V L+ G T+ H+ +G+ GA KV+++ A GTGVIAGGA+RAV E+ G+ Sbjct: 64 KAVEDAKKNMIKVPLV-GGTIPHEVIGKFGAAKVLLKPASEGTGVIAGGAVRAVLELAGV 122 Query: 133 HDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 DV+AKS+GS+NP NV+RATF+ L+ P +VA +RG Sbjct: 123 KDVLAKSLGSNNPINVVRATFDALKQLRSPEEVAAKRGKS 162 >gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model. Length = 154 Score = 182 bits (464), Expect = 6e-47 Identities = 79/147 (53%), Positives = 110/147 (74%), Gaps = 1/147 (0%) Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83 +R++A+NRVS + GGRRF+FS LVVVGD K +VGF A+EVP+A++KA E A++N+I Sbjct: 4 ERLIAVNRVSKVVKGGRRFSFSALVVVGDGKGRVGFGFGKAKEVPDAIKKAVEKARKNLI 63 Query: 84 SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143 +V L G T+ H+ +G GA KV+++ A GTGVIAGGA+RA+ E+ G+ D++AKS+GS+ Sbjct: 64 NVPLTKG-TIPHEVIGVSGAAKVLLKPASPGTGVIAGGAVRAILELAGVKDILAKSLGSN 122 Query: 144 NPHNVIRATFEVLRSQSHPRDVANRRG 170 NP NV+RATF+ L P DVA RG Sbjct: 123 NPINVVRATFDALLKLKSPEDVAELRG 149 >gnl|CDD|179727 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed. Length = 211 Score = 71.5 bits (176), Expect = 2e-13 Identities = 51/162 (31%), Positives = 79/162 (48%), Gaps = 13/162 (8%) Query: 22 IVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRN 81 + D ++ IN V GRR F V+VVVG+ VG A++V A+RKA AK N Sbjct: 50 LEDEVLDINMVQRMTDSGRRVRFRVVVVVGNRDGYVGVGQGKAKQVGPAIRKAIRNAKLN 109 Query: 82 MISVSLLDG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132 +I V G ++ G+ G+ +V ++ A G G++AG + V E+ G+ Sbjct: 110 IIKVRRGCGSWECGCGEPHSVPFKVTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAGI 169 Query: 133 HDVVAKSIGSS-NPHNVIRATFEVLRSQS---HPRDVANRRG 170 DV ++ G + N +ATF L++ P D A +RG Sbjct: 170 KDVWTRTFGETRTTVNFAKATFNALKNTYKVRTPPDWAEKRG 211 >gnl|CDD|162160 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5. Length = 212 Score = 65.6 bits (160), Expect = 8e-12 Identities = 42/145 (28%), Positives = 68/145 (46%), Gaps = 10/145 (6%) Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83 + ++ ++ V GRR F VVVG+ VG A+EV A+RKA AK N+I Sbjct: 52 EEVLDVSLVQRMTDSGRRTRFRAFVVVGNRDGYVGLGIGKAKEVAPAIRKAIINAKLNII 111 Query: 84 SVSLLDG---------RTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHD 134 V G ++ G+ G+ +V + A G G++AG + V + G+ D Sbjct: 112 PVRRGCGSWECGCGRPHSVPFKVTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAGIDD 171 Query: 135 VVAKSIGSSNP-HNVIRATFEVLRS 158 V ++ G + N +ATF+ L+ Sbjct: 172 VWTQTRGETRTTVNFAKATFDALKK 196 >gnl|CDD|185425 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional. Length = 257 Score = 55.9 bits (135), Expect = 7e-09 Identities = 44/149 (29%), Positives = 70/149 (46%), Gaps = 8/149 (5%) Query: 18 RDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEA 77 ++ + D ++ I V G+R F VVVGD +G A+EV A+R A A Sbjct: 76 AESKLKDEVMKIMPVQKQTSAGQRTRFKAFVVVGDGNGHIGLGAKVAKEVATAIRGAIIA 135 Query: 78 AKRNMISV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVL 130 AK N++ V + + T+ G+ G+ +V + A GTG++A + + E Sbjct: 136 AKLNLVPVRRGYWGNKIGEPHTVPMKVTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFA 195 Query: 131 GMHDVVAKSIGSSNPH-NVIRATFEVLRS 158 G+ DV S G + N ++ATF LR Sbjct: 196 GVEDVFTSSRGKTRTRGNFLKATFYALRK 224 >gnl|CDD|183859 PRK13103, secA, preprotein translocase subunit SecA; Reviewed. Length = 913 Score = 30.7 bits (69), Expect = 0.24 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 12/76 (15%) Query: 54 KSKVGFAHSTAREVPEAVRKATEAAKRNM----ISVSLLDGRTLHHDGVG--RHGAGKVI 107 K+++ + + +PEA A EA KR M V L+ G TLH + R G GK + Sbjct: 51 KARLAKGETLDQLLPEAFAVAREAGKRVMGMRHFDVQLIGGMTLHEGKIAEMRTGEGKTL 110 Query: 108 MRS------AMAGTGV 117 + + A++G GV Sbjct: 111 VGTLAVYLNALSGKGV 126 >gnl|CDD|183164 PRK11504, tynA, tyramine oxidase; Provisional. Length = 647 Score = 29.1 bits (66), Expect = 0.74 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 2/41 (4%) Query: 132 MHDVVAKSIGSSNPH-NVIRATFEVLRSQSH-PRDVANRRG 170 + V +G NPH N +L ++S RD G Sbjct: 458 EVNSVPVPMGPDNPHGNAFYTRETLLETESEAARDADPSTG 498 >gnl|CDD|149298 pfam08161, NUC173, NUC173 domain. This is the central domain of of novel family of hypothetical nucleolar proteins. Length = 198 Score = 29.1 bits (66), Expect = 0.87 Identities = 8/38 (21%), Positives = 16/38 (42%), Gaps = 8/38 (21%) Query: 141 GSSNPH--NVIRATFEVLRSQSHP------RDVANRRG 170 ++ V+ A FE L +S+P + + + R Sbjct: 14 QAAWKEVLQVLSALFEKLGERSNPLLLKVLKTLGDLRT 51 >gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog; Provisional. Length = 606 Score = 28.9 bits (65), Expect = 0.91 Identities = 21/59 (35%), Positives = 27/59 (45%), Gaps = 8/59 (13%) Query: 44 FSVLVVVGDTKSKVGFAHS--TAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGR 100 F +VV +T VG S T+R +P A R +I V+ LDG H D GR Sbjct: 196 FECVVVDAETGLPVGHPQSILTSRVIP-----APSPTPRRLIQVNGLDG-MGHLDLDGR 248 >gnl|CDD|134348 PRK00694, PRK00694, 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated. Length = 606 Score = 28.7 bits (64), Expect = 0.94 Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 1/27 (3%) Query: 125 AVCEVLGMHDVVAKSIGSSNPHNVIRA 151 VCE L DVV S+ SSNP ++ A Sbjct: 194 EVCEKLDYRDVVF-SMKSSNPKVMVAA 219 >gnl|CDD|130763 TIGR01702, CO_DH_cata, carbon-monoxide dehydrogenase, catalytic subunit. This model represents the carbon-monoxide dehydrogenase catalytic subunit. This protein is related to prismane (also called hybrid cluster protein), a complex whose activity is not yet fully described; the two share similar sets of ligands to unusual metal-containing clusters. Length = 621 Score = 28.2 bits (63), Expect = 1.6 Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 14/90 (15%) Query: 47 LVVVGDTKSKVGFAH-STAREVPE---AVRKATEAAKRNMISVSLLDGRTLHHDGVGRHG 102 + G K V S + + V E KRN++ ++ G Sbjct: 425 AIASGKIKGVVLVVGCSNLKNGGQDSSTVTLTKELIKRNILVLAT---------GCSNGA 475 Query: 103 AGKVIMRSAMAGTGVIAGGAIRAVCEVLGM 132 K + + +AG ++ VC+ LG+ Sbjct: 476 LEKAGLMT-PEAAEELAGEGLKGVCKALGI 504 >gnl|CDD|184511 PRK14106, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional. Length = 450 Score = 28.0 bits (63), Expect = 1.6 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 8/42 (19%) Query: 46 VLVVVGDTKS-------KVGFAHST-AREVPEAVRKATEAAK 79 L+++G+T K GF + A + EAV+KA E AK Sbjct: 375 KLILLGETAQEIAEAARKYGFDNILFAETLEEAVKKAYEIAK 416 >gnl|CDD|117463 pfam08896, DUF1842, Domain of unknown function (DUF1842). This domain is found at the N-terminus of proteins that are functionally uncharacterized. Length = 114 Score = 27.2 bits (61), Expect = 2.5 Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 1/33 (3%) Query: 31 RVSTALPGGRRFAFSVLVVVGDTKSKVGFAHST 63 RV T LPG ++LV D KS G A T Sbjct: 9 RVGTGLPGAPVLTLNLLVYTPD-KSVSGTAVIT 40 >gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated. Length = 232 Score = 26.7 bits (59), Expect = 4.1 Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 4/48 (8%) Query: 116 GVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPR 163 G A RA+ +V+ +H V + +G +P V +++L HPR Sbjct: 139 GFEENQAHRALDDVITLHRVFSALVGDLSPQQV----YDLLNESCHPR 182 >gnl|CDD|163120 TIGR03055, photo_alph_chp2, putative photosynthetic complex assembly protein 2. This uncharacterized protein family was identified, by the method of partial phylogenetic profiling, as having a matching phylogenetic distribution to that of the photosynthetic reaction center of the alpha-proteobacterial type. It is nearly always encoded near other photosynthesis-related genes, including puhA. Length = 245 Score = 26.3 bits (58), Expect = 6.0 Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 4/31 (12%) Query: 93 LHHDGVGRHGAGKVIMRSAMAGTGVIAGGAI 123 D +GR +RS +AG ++ GG Sbjct: 19 WLLDSLGRS----THLRSVVAGLPLLTGGLW 45 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 0.316 0.129 0.359 Gapped Lambda K H 0.267 0.0656 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,140,817 Number of extensions: 196882 Number of successful extensions: 465 Number of sequences better than 10.0: 1 Number of HSP's gapped: 461 Number of HSP's successfully gapped: 26 Length of query: 199 Length of database: 5,994,473 Length adjustment: 89 Effective length of query: 110 Effective length of database: 4,071,361 Effective search space: 447849710 Effective search space used: 447849710 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: 55 (25.1 bits)