RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780779|ref|YP_003065192.1| 30S ribosomal protein S2 [Candidatus Liberibacter asiaticus str. psy62] (278 letters) >gnl|CDD|180001 PRK05299, rpsB, 30S ribosomal protein S2; Provisional. Length = 258 Score = 389 bits (1002), Expect = e-109 Identities = 121/254 (47%), Positives = 175/254 (68%), Gaps = 1/254 (0%) Query: 3 LPQFTIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDT 62 + +++QLLE+GV FGH+ WNPKM+ YIF ERN HIIDL +TVPML +A + D Sbjct: 1 MAVVSMKQLLEAGVHFGHQTRRWNPKMKPYIFGERNGIHIIDLQKTVPMLDEAYNFVRDV 60 Query: 63 VARGGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEEL 122 A GG+ILFV TK QA + + E A+R VN +WLGGM+TN+KT+ +SI++L++LE++ Sbjct: 61 AANGGKILFVGTKKQAQEAIAEEAERCGMPYVNHRWLGGMLTNFKTIRKSIKRLKELEKM 120 Query: 123 L-NKENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLR 181 + + TKKE L + R+ +KL+++L GI+DMGGLPD +FVVD N+E +A++EAR+L Sbjct: 121 EEDGTFEKLTKKEALMLTRELEKLEKSLGGIKDMGGLPDALFVVDPNKEHIAVKEARKLG 180 Query: 182 IPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGADTKSAG 241 IP+VA+VDTN +PD VDY IPGNDD+ RSI L+ +A A ++G + + + + Sbjct: 181 IPVVAIVDTNCDPDGVDYPIPGNDDAIRSIKLYTSKIADAILEGRQGRLAEAAEEEEEEA 240 Query: 242 ETVVHSKEGMQLEE 255 E +E + EE Sbjct: 241 EEEEEEEEEEEAEE 254 >gnl|CDD|183428 PRK12311, rpsB, 30S ribosomal protein S2/unknown domain fusion protein; Provisional. Length = 326 Score = 384 bits (988), Expect = e-107 Identities = 151/230 (65%), Positives = 190/230 (82%), Gaps = 1/230 (0%) Query: 8 IRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARGG 67 +RQLLE+GV FGH++ WNPKM YIF RNN HIIDL+QTVP+L +ALQ +SDTVA+GG Sbjct: 1 MRQLLEAGVHFGHQSHRWNPKMAPYIFGTRNNIHIIDLAQTVPLLHRALQAVSDTVAKGG 60 Query: 68 RILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNK-E 126 R+LFV TK QA D V +AAKRSAQY VNS+WLGG +TNWKT+S SIQ+LR L+E+L+ E Sbjct: 61 RVLFVGTKRQAQDAVADAAKRSAQYFVNSRWLGGTLTNWKTISGSIQRLRKLDEVLSSGE 120 Query: 127 NQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVA 186 G+TKKERL ++R+RDKL RAL GI+DMGGLPDL+FV+DTN+E +AIQEA+RL IP+ A Sbjct: 121 ANGYTKKERLTLQRERDKLDRALGGIKDMGGLPDLLFVIDTNKEDIAIQEAQRLGIPVAA 180 Query: 187 VVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGAD 236 +VDTN +PD + Y +PGNDD+ R+IAL+CDL+A AAIDGI+R +G D Sbjct: 181 IVDTNCDPDGITYPVPGNDDAGRAIALYCDLIARAAIDGISRAQGDLGID 230 >gnl|CDD|130084 TIGR01011, rpsB_bact, ribosomal protein S2, bacterial type. TIGR01012 describes the archaeal and cytosolic forms. Length = 225 Score = 318 bits (818), Expect = 8e-88 Identities = 113/220 (51%), Positives = 162/220 (73%), Gaps = 1/220 (0%) Query: 7 TIRQLLESGVQFGHRNFLWNPKMERYIFCERNNTHIIDLSQTVPMLQKALQVISDTVARG 66 +++ LLE+GV FGH+ WNPKM+ +IF ERN HIIDL +T+ +L++A + D A G Sbjct: 3 SMKDLLEAGVHFGHQTRRWNPKMKPFIFGERNGIHIIDLQKTLQLLKEAYNFVKDVAANG 62 Query: 67 GRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKE 126 G+ILFV TK QA + + E A+R + VN +WLGGM+TN+KT+ +SI+KL+ LE++ Sbjct: 63 GKILFVGTKKQAKEIIKEEAERCGMFYVNQRWLGGMLTNFKTIRKSIKKLKKLEKMEEDG 122 Query: 127 NQ-GFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIV 185 TKKE L + R+++KL+++L GI+DM LPDL+FV+D +EK+A+ EAR+L IP+V Sbjct: 123 TFDDLTKKEALMLSREKEKLEKSLGGIKDMKKLPDLLFVIDPVKEKIAVAEARKLGIPVV 182 Query: 186 AVVDTNSNPDLVDYVIPGNDDSSRSIALFCDLVASAAIDG 225 A+VDTN +PDLVDY IPGNDD+ RSI L +L+A A ++G Sbjct: 183 AIVDTNCDPDLVDYPIPGNDDAIRSIRLLTNLIADAVLEG 222 >gnl|CDD|185527 PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional. Length = 249 Score = 62.8 bits (153), Expect = 9e-11 Identities = 48/208 (23%), Positives = 88/208 (42%), Gaps = 51/208 (24%) Query: 8 IRQLLESGVQFGHRNFLWNPKMERYIFCER--NNTHIIDLSQTVPMLQKALQVISDTVAR 65 I+++L G +N M++Y++ +R HII+L++T L+ A +VI+ + Sbjct: 15 IKKMLACKCHIGTKNL--ENAMKKYVY-KRTKEGVHIINLAKTWEKLKLAARVIA-AIEN 70 Query: 66 GGRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNK 125 ++ V+++ V++ A+ + + ++ G TN Q +K Sbjct: 71 PADVVVVSSRPYGQRAVLKFAQYTGASAIAGRFTPGTFTN-----QIQKK---------- 115 Query: 126 ENQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIV 185 F + P L+ V D + AI+EA + IP++ Sbjct: 116 ----FME--------------------------PRLLIVTDPRTDHQAIREASYVNIPVI 145 Query: 186 AVVDTNSNPDLVDYVIPGNDDSSRSIAL 213 A+ DT+S + VD IP N+ SIAL Sbjct: 146 ALCDTDSPLEYVDIAIPCNNRGKESIAL 173 >gnl|CDD|179713 PRK04020, rps2P, 30S ribosomal protein S2; Provisional. Length = 204 Score = 58.7 bits (143), Expect = 2e-09 Identities = 21/55 (38%), Positives = 35/55 (63%) Query: 159 PDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIAL 213 PD++ V D + A++EA + IP+VA+ DT++ VD VIP N+ +++AL Sbjct: 115 PDVVVVTDPRGDAQAVKEAIEVGIPVVALCDTDNLTSNVDLVIPTNNKGRKALAL 169 >gnl|CDD|130085 TIGR01012, Sa_S2_E_A, ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria. Length = 196 Score = 57.1 bits (138), Expect = 5e-09 Identities = 46/207 (22%), Positives = 83/207 (40%), Gaps = 50/207 (24%) Query: 8 IRQLLESGVQFGHRNFLWNPKMERYIFCERNN-THIIDLSQTVPMLQKALQVISDTVARG 66 + + L +GV G +N ME++I+ R++ +++DL +T L+ A + + Sbjct: 6 VDKYLAAGVHIGTQNK--TKDMEKFIYKVRSDGLYVLDLRKTDERLRVAAKFLV--RIEP 61 Query: 67 GRILFVATKSQASDCVMEAAKRSAQYCVNSKWLGGMMTNWKTVSQSIQKLRDLEELLNKE 126 IL V+ + V++ AK + + ++ G TN Sbjct: 62 EDILVVSARIYGQKPVLKFAKVTGARAIAGRFTPGTFTN--------------------- 100 Query: 127 NQGFTKKERLNIERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIVA 186 R+ P+++ V D + A++EA + IPIVA Sbjct: 101 --------------------PMQKAFRE----PEVVVVTDPRADHQALKEASEVGIPIVA 136 Query: 187 VVDTNSNPDLVDYVIPGNDDSSRSIAL 213 + DT++ VD VIP N+ S+AL Sbjct: 137 LCDTDNPLRYVDLVIPTNNKGRHSLAL 163 >gnl|CDD|178013 PLN02389, PLN02389, biotin synthase. Length = 379 Score = 32.1 bits (73), Expect = 0.17 Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 7/54 (12%) Query: 73 ATKSQASDCVMEAAKR-----SAQYCVNSKW--LGGMMTNWKTVSQSIQKLRDL 119 A K + D V+EAAKR S ++C+ + W G TN+ + + ++++R + Sbjct: 112 AQKLMSKDDVLEAAKRAKEAGSTRFCMGAAWRDTVGRKTNFNQILEYVKEIRGM 165 >gnl|CDD|129375 TIGR00274, TIGR00274, N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity. Length = 291 Score = 31.7 bits (72), Expect = 0.24 Identities = 11/71 (15%), Positives = 35/71 (49%) Query: 33 IFCERNNTHIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQY 92 + E + + + +P + A++ I +GGR++++ + V++A++ + Sbjct: 24 LINEEDKLVPLAIESVLPDIAAAVEQIVQAFQQGGRLIYIGAGTSGRLGVLDASECPPTF 83 Query: 93 CVNSKWLGGMM 103 V+ + + G++ Sbjct: 84 GVSPELVKGII 94 >gnl|CDD|149105 pfam07851, TMPIT, TMPIT-like protein. A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. Length = 330 Score = 29.7 bits (67), Expect = 0.77 Identities = 11/54 (20%), Positives = 26/54 (48%), Gaps = 1/54 (1%) Query: 107 KTVSQSIQKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGIRDM-GGLP 159 +++ ++L+ L L K + T ++ +E+ +++K + DM LP Sbjct: 39 SAIARQRKRLKQLIVSLKKLKKSLTPEDSELVEQLEEQIKERKNQFFDMESFLP 92 >gnl|CDD|181250 PRK08140, PRK08140, enoyl-CoA hydratase; Provisional. Length = 262 Score = 29.1 bits (66), Expect = 1.3 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 13/67 (19%) Query: 155 MGGLPDLMFVVDTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPGNDDSSRSIALF 214 G +PDL ++T L ++ R L +P++A V+ V G + ++AL Sbjct: 74 GGAMPDLGESIETFYNPL-VRRLRALPLPVIAAVNG---------VAAG---AGANLALA 120 Query: 215 CDLVASA 221 CD+V +A Sbjct: 121 CDIVLAA 127 >gnl|CDD|172646 PRK14158, PRK14158, heat shock protein GrpE; Provisional. Length = 194 Score = 28.7 bits (64), Expect = 1.9 Identities = 16/58 (27%), Positives = 29/58 (50%) Query: 193 NPDLVDYVIPGNDDSSRSIALFCDLVASAAIDGIARQHSYMGADTKSAGETVVHSKEG 250 N L+ ++P D+ R++ + SA I+GI S + + K G T V +++G Sbjct: 89 NESLILEILPAVDNMERALDHADEESMSAIIEGIRMTLSMLLSTLKKFGVTPVEAEKG 146 >gnl|CDD|162195 TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso- diaminopimelate ligase (murein tripeptide ligase) is described by TIGR01081. Length = 448 Score = 27.3 bits (61), Expect = 4.7 Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 3/20 (15%) Query: 166 DTNREKLAIQEARRLRIPIV 185 D N E I EA+ IP++ Sbjct: 70 DDNPE---IVEAKERGIPVI 86 >gnl|CDD|183692 PRK12704, PRK12704, phosphodiesterase; Provisional. Length = 520 Score = 27.0 bits (61), Expect = 5.0 Identities = 9/39 (23%), Positives = 22/39 (56%), Gaps = 1/39 (2%) Query: 114 QKLRDLEELLNKENQGFTKKERLNIERKRDKLKRALDGI 152 ++L EE L+++ + K+E +E+K +L++ + Sbjct: 89 KRLLQKEENLDRKLELLEKREE-ELEKKEKELEQKQQEL 126 >gnl|CDD|179218 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase; Validated. Length = 451 Score = 26.6 bits (60), Expect = 6.6 Identities = 7/13 (53%), Positives = 9/13 (69%) Query: 177 ARRLRIPIVAVVD 189 A+ L P+V VVD Sbjct: 110 AKLLGAPVVLVVD 122 >gnl|CDD|132204 TIGR03160, cobT_DBIPRT, nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Members of this family are nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, an enzyme of cobalamin biosynthesis. Length = 333 Score = 26.7 bits (60), Expect = 7.0 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 16/75 (21%) Query: 138 IERKRDKLKRALDGIRDMGGLPDLMFVVDTNREKLAIQEARRLRIPIV---------AVV 188 + R R LD + +GG ++ + AI A RIP++ A+V Sbjct: 208 LARHRPNAGDPLDVLAKVGGF-EIAAMAG------AILGAAARRIPVLVDGFISTAAALV 260 Query: 189 DTNSNPDLVDYVIPG 203 P + DY+I Sbjct: 261 AVRLAPGVRDYLIAS 275 >gnl|CDD|180192 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated. Length = 1135 Score = 26.6 bits (60), Expect = 7.9 Identities = 7/21 (33%), Positives = 13/21 (61%), Gaps = 2/21 (9%) Query: 168 NREKLA--IQEARRLRIPIVA 186 N +K+A + E RR+ I ++ Sbjct: 781 NTDKVAVYLDECRRMGIKVLP 801 >gnl|CDD|161715 TIGR00113, queA, S-adenosylmethionine:tRNA ribosyltransferase-isomerase. This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine. Length = 344 Score = 26.6 bits (59), Expect = 7.9 Identities = 14/55 (25%), Positives = 29/55 (52%), Gaps = 4/55 (7%) Query: 41 HIIDLSQTVPMLQKALQVISDTVARGGRILFVATKSQASDCVMEAAKRSAQYCVN 95 H++ ++ + Q+ ++ ++ T GGRI+ V T S S +E+A + A + Sbjct: 224 HVMH-AEYYEVPQETVEALNKTRENGGRIIAVGTTSVRS---LESAAQEADGLIE 274 >gnl|CDD|163312 TIGR03535, DapD_actino, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. Alternate name: tetrahydrodipicolinate N-succinyltransferase. Length = 319 Score = 26.6 bits (59), Expect = 8.1 Identities = 23/59 (38%), Positives = 29/59 (49%), Gaps = 10/59 (16%) Query: 149 LDGIRDMGGLPDLMFVVDTNREKLAIQ--EARRLRIP---IVAVVDTNSNPDLVDYVIP 202 LDGI G LP+ VV TN A+ E R R+ V V + P +VDYV+P Sbjct: 98 LDGI--FGLLPN---VVWTNHGPCAVDDFELTRARLRARGPVTVYSVDKFPRMVDYVVP 151 >gnl|CDD|119297 pfam10777, YlaC, Extracytoplasmic function sigma factor YlaC. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis. Length = 156 Score = 26.2 bits (58), Expect = 8.9 Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 1/32 (3%) Query: 134 ERLNIERKRD-KLKRALDGIRDMGGLPDLMFV 164 ER+N E KRD K + + IR L M Sbjct: 13 ERINREEKRDNKPRFSSSFIRKHPYLFLAMLA 44 >gnl|CDD|150862 pfam10256, Erf4, Golgin subfamily A member 7/ERF4 family. This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4. Length = 118 Score = 26.4 bits (59), Expect = 9.0 Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 9/56 (16%) Query: 92 YCVNSKW--LGGMM-------TNWKTVSQSIQKLRDLEELLNKENQGFTKKERLNI 138 + S L G++ + + + L LE+ + + N+ L I Sbjct: 50 FEPISWRNLLEGILGCLTLYLWSLILKTHYKRTLAKLEKYIEELNERLYHPRGLKI 105 >gnl|CDD|182860 PRK10949, PRK10949, protease 4; Provisional. Length = 618 Score = 26.2 bits (58), Expect = 9.5 Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 6/34 (17%) Query: 214 FCDLVASA------AIDGIARQHSYMGADTKSAG 241 F LVA + ID IA+ H + G D K+ G Sbjct: 488 FITLVADSRHKTPEQIDKIAQGHVWTGQDAKANG 521 >gnl|CDD|180089 PRK05447, PRK05447, 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional. Length = 385 Score = 26.2 bits (59), Expect = 9.8 Identities = 28/91 (30%), Positives = 34/91 (37%), Gaps = 15/91 (16%) Query: 148 ALDGIRDMGGLPDLMFVV----DTNREKLAIQEARRLRIPIVAVVDTNSNPDLVDYVIPG 203 LD IR PD VV N E LA Q AR R V V D + +L + + Sbjct: 17 TLDVIRR---NPDRFRVVALSAGKNVELLAEQ-AREFRPKYVVVADEEAAKELKEALAAA 72 Query: 204 NDDSSRSIALFCDLVAS-------AAIDGIA 227 + C+L A AAI G A Sbjct: 73 GIEVLAGEEGLCELAALPEADVVVAAIVGAA 103 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 0.317 0.132 0.372 Gapped Lambda K H 0.267 0.0670 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,411,810 Number of extensions: 277149 Number of successful extensions: 682 Number of sequences better than 10.0: 1 Number of HSP's gapped: 679 Number of HSP's successfully gapped: 40 Length of query: 278 Length of database: 5,994,473 Length adjustment: 92 Effective length of query: 186 Effective length of database: 4,006,537 Effective search space: 745215882 Effective search space used: 745215882 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: 56 (25.5 bits)