RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus Liberibacter asiaticus str. psy62] (227 letters) >gnl|CDD|30526 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]. Length = 211 Score = 272 bits (698), Expect = 4e-74 Identities = 102/206 (49%), Positives = 147/206 (71%) Query: 22 PKELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQ 81 K+ EI +P PK EL + + F L+VAV+LSAQ+TD VNKAT LF+ TP+ Sbjct: 3 KKKALEILDRLRELYPEPKTELDFKDPFELLVAVILSAQTTDEVVNKATPALFKRYPTPE 62 Query: 82 KMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGA 141 +L E++L+ I++IG+YR K++NI L+ IL+ +F ++P T E L LPG+GRK A Sbjct: 63 DLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSLPGVGRKTA 122 Query: 142 NVILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLH 201 NV+LS AFGIP I VDTH+ R+SNR+GL PGKTP +VE++L+++IP + + H+WL+LH Sbjct: 123 NVVLSFAFGIPAIAVDTHVHRVSNRLGLVPGKTPEEVEEALMKLIPKELWTDLHHWLILH 182 Query: 202 GRYVCKARKPQCQSCIISNLCKRIKQ 227 GRY+CKARKP+C+ C +++LC + Sbjct: 183 GRYICKARKPRCEECPLADLCPSAGK 208 >gnl|CDD|28938 cd00056, ENDO3c, endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases. Length = 158 Score = 138 bits (349), Expect = 1e-33 Identities = 60/159 (37%), Positives = 94/159 (59%), Gaps = 6/159 (3%) Query: 49 FTLIVAVLLSAQSTDVNVNKATKHLFE-IADTPQKMLAIGEKKLQNYIRTIGIYRKKSEN 107 F ++V+ +LS Q+TD VNKA + LFE TP+ + A E++L+ IR++G YR+K++ Sbjct: 1 FEVLVSEILSQQTTDKAVNKAYERLFERYGPTPEALAAADEEELRELIRSLG-YRRKAKY 59 Query: 108 IISLSHILINEFDNKI---PQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRIS 164 + L+ ++ F + P E L LPG+GRK ANV+L A G VDTH+ R+ Sbjct: 60 LKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVL 119 Query: 165 NRIGLAP-GKTPNKVEQSLLRIIPPKHQYNAHYWLVLHG 202 R+GL P KTP ++E+ L ++P + A+ L+ G Sbjct: 120 KRLGLIPKKKTPEELEELLEELLPKPYWGEANQALMDLG 158 >gnl|CDD|144361 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family. Length = 144 Score = 125 bits (315), Expect = 1e-29 Identities = 53/144 (36%), Positives = 80/144 (55%), Gaps = 8/144 (5%) Query: 53 VAVLLSAQSTDVNVNKATKHLFE--IADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIIS 110 V+ +LS Q++D NK TK LFE TP+ + E++L+ I+ +G YR+K++ I Sbjct: 1 VSAILSQQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKE 60 Query: 111 LSHILINEFDNKIPQT---LEGLTRLPGIGRKGANVILSMAFG--IPTIGVDTHIFRISN 165 L+ IL+ + +P LE L LPG+GR A +L A G VDTH+ R++ Sbjct: 61 LARILVEGYLGLVPLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAK 120 Query: 166 RIGLAPG-KTPNKVEQSLLRIIPP 188 R+GL TP +VE+ L + PP Sbjct: 121 RLGLIKEKPTPEEVERELEELWPP 144 >gnl|CDD|37132 KOG1921, KOG1921, KOG1921, Endonuclease III [Replication, recombination and repair]. Length = 286 Score = 118 bits (297), Expect = 1e-27 Identities = 59/175 (33%), Positives = 96/175 (54%), Gaps = 4/175 (2%) Query: 49 FTLIVAVLLSAQSTDVNVNKATKHLFEIAD-TPQKMLAIGEKKLQNYIRTIGIYRKKSEN 107 F ++V ++LS+Q+ D A L E T + +L I E L I +G Y +K++ Sbjct: 79 FQVLVGLMLSSQTKDEVTAAAMLRLKEYGGLTLEAVLKIDEPTLNELIYPVGFYTRKAKY 138 Query: 108 IISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFG-IPTIGVDTHIFRISNR 166 + + IL ++FD IP T+E L LPG+G K A++ + +A+ I I VDTH+ RI NR Sbjct: 139 LKKTAKILQDKFDGDIPDTVEDLLSLPGVGPKMAHLTMQVAWNKIVGICVDTHVHRICNR 198 Query: 167 IGLAPGKT--PNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIIS 219 +G KT P + +L + +P ++ LV G+ +C R+P+C C++S Sbjct: 199 LGWVDTKTKSPEQTRVALQQWLPKSLWVEINHLLVGFGQTICTPRRPRCGLCLLS 253 >gnl|CDD|31387 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication, recombination, and repair]. Length = 342 Score = 78.8 bits (194), Expect = 1e-15 Identities = 35/155 (22%), Positives = 65/155 (41%), Gaps = 7/155 (4%) Query: 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGR 138 T + + A E ++ +G Y + + N+ + ++ + P E L LPG+G Sbjct: 65 TIKALAAAPEDEVLKAWEGLGYYSR-ARNLHKAAQEVVERHGGEFPDDEEELAALPGVGP 123 Query: 139 KGANVILSMAFGIPTIGVDTHIFRISNRI----GLAPGKTPNKVEQSLLR-IIPPKHQYN 193 A ILS AF P +D ++ R+ +R+ G K L ++ P + Sbjct: 124 YTAGAILSFAFNQPEPVLDGNVKRVLSRLFAISGDIGKPKTKKELWELAEQLLTPDRRPG 183 Query: 194 AHYWLVLH-GRYVCKARKPQCQSCIISNLCKRIKQ 227 ++ G +C A+KP+C C + + C + Sbjct: 184 DFNQAMMDLGATICTAKKPKCSLCPLRDNCAAYRN 218 >gnl|CDD|32412 COG2231, COG2231, Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]. Length = 215 Score = 73.0 bits (179), Expect = 6e-14 Identities = 51/185 (27%), Positives = 91/185 (49%), Gaps = 10/185 (5%) Query: 47 NHFTLIVAVLLSAQSTDVNVNKATKHLFEIADT-PQKMLAIGEKKLQNYIRTIGIYRKKS 105 N +I+ +L+ ++ NV KA ++L +K+L + E++L IR G Y +K+ Sbjct: 29 NKDEIIIGAILTQNTSWKNVEKALENLKNEGILNLKKILKLDEEELAELIRPSGFYNQKA 88 Query: 106 ENIISLSHILINEFDN----KIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIF 161 + + +LS L F N K E L + GIG++ A+ IL A P VD + Sbjct: 89 KRLKALSKNLAKFFINLESFKSEVLREELLSIKGIGKETADSILLYALDRPVFVVDKYTR 148 Query: 162 RISNRIGLAPGKTPNKVEQSLLRIIPPKHQY---NAHYWLVLHGRYVCKARKPQCQSCII 218 R+ +R+G K +++++ + P++ H +V H ++ CK +KP C+ C + Sbjct: 149 RLLSRLGGIEEKKYDEIKELFEENL-PENLRLYQEFHALIVEHAKHFCK-KKPLCEKCPL 206 Query: 219 SNLCK 223 CK Sbjct: 207 KEKCK 211 >gnl|CDD|37668 KOG2457, KOG2457, KOG2457, A/G-specific adenine DNA glycosylase [Replication, recombination and repair]. Length = 555 Score = 56.7 bits (136), Expect = 5e-09 Identities = 35/134 (26%), Positives = 67/134 (50%), Gaps = 11/134 (8%) Query: 98 IGIYRKKSENIISLSHILINEFDNKIPQTLEGLTR-LPGIGRKGANVILSMAFGIPTIGV 156 +G YR+ + ++ + +++ + + P+T L + +PG+G+ A I S+AF T V Sbjct: 176 LGYYRR-ARRLLEGAKMVVAGTEGEFPRTASSLMKGVPGVGQYTAGAIASIAFNQVTGIV 234 Query: 157 DTHIFRISNR---IGLAPGKTPNKVEQSLLR----IIPPKHQYNAHYWLVLHGRYVCKAR 209 D ++ R+ +R I K K QS + ++ P + + L+ G +C + Sbjct: 235 DGNVIRVLSRALAIHSDCSKG--KFFQSSWKLAAQLVDPSRPGDFNQALMELGATLCTPQ 292 Query: 210 KPQCQSCIISNLCK 223 KP C SC +S+ C+ Sbjct: 293 KPSCSSCPVSSQCR 306 >gnl|CDD|30471 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]. Length = 285 Score = 50.4 bits (120), Expect = 4e-07 Identities = 29/114 (25%), Positives = 45/114 (39%), Gaps = 12/114 (10%) Query: 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNK-------IPQTLEGLT 131 TP+++ A E+ L R G+ +K+E IISL+ + + +E LT Sbjct: 146 TPEQLAAADEEAL----RRCGLSGRKAEYIISLARAAAEGELDLSELKPLSDEEAIEELT 201 Query: 132 RLPGIGRKGANVILSMAFGIPTIG-VDTHIFRISNRIGLAPGKTPNKVEQSLLR 184 L GIG A + L G P + D R + + P + E L Sbjct: 202 ALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELA 255 >gnl|CDD|38086 KOG2875, KOG2875, KOG2875, 8-oxoguanine DNA glycosylase [Replication, recombination and repair]. Length = 323 Score = 38.4 bits (89), Expect = 0.001 Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%) Query: 128 EGLTRLPGIGRKGANVILSMAFGIP-TIGVDTHIFRIS 164 E L LPG+G K A+ I M+ + VD HI+RI+ Sbjct: 218 EALCSLPGVGPKVADCICLMSLDKLSAVPVDVHIWRIA 255 >gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. Length = 30 Score = 37.8 bits (89), Expect = 0.002 Identities = 13/29 (44%), Positives = 16/29 (55%) Query: 118 EFDNKIPQTLEGLTRLPGIGRKGANVILS 146 + IP + E L LPG+G K A ILS Sbjct: 1 SLEGLIPASREELLALPGVGPKTAEAILS 29 >gnl|CDD|173750 cd07857, STKc_MPK1, Catalytic domain of the Serine/Threonine Kinase, Fungal Mitogen-Activated Protein Kinase MPK1. Serine/Threonine Kinases (STKs), Fungal Mitogen-Activated Protein Kinase (MAPK) MPK1 subfamily, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MPK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This subfamily is composed of the MAPKs MPK1 from Saccharomyces cerevisiae, Pmk1 from Schizosaccharomyces pombe, and similar proteins. MAPKs are important mediators of cellular responses to extracellular signals. MPK1 (also called Slt2) and Pmk1 (also called Spm1) are stress-activated MAPKs that regulate the cell wall integrity (CWI) pathway, and are therefore important in the maintainance of cell shape, cell wall construction, morphogenesis, and ion homeostasis. MPK1 is activated in response to cell wall stress including heat stimulation, osmotic shock, UV irradiation, and any agents that interfere with cell wall biogenesis such as chitin antagonists, caffeine, or zymolase. MPK1 is regulated by the MAP2Ks Mkk1/2, which are regulated by the MAP3K Bck1. Pmk1 is also activated by multiple stresses including elevated temperatures, hyper- or hypotonic stress, glucose deprivation, exposure to cell-wall damaging compounds, and oxidative stress. It is regulated by the MAP2K Pek1, which is regulated by the MAP3K Mkh1. Length = 332 Score = 29.7 bits (67), Expect = 0.66 Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 2/36 (5%) Query: 72 HLFEIADTPQK--MLAIGEKKLQNYIRTIGIYRKKS 105 + ++ TP + + IG K QNYIR++ KK Sbjct: 221 QILQVLGTPDEETLSRIGSPKAQNYIRSLPNIPKKP 256 >gnl|CDD|38243 KOG3033, KOG3033, KOG3033, Predicted PhzC/PhzF-type epimerase [General function prediction only]. Length = 286 Score = 29.5 bits (66), Expect = 0.73 Identities = 28/118 (23%), Positives = 45/118 (38%), Gaps = 11/118 (9%) Query: 30 YLFSLKWPSPKGELYYVNHFTLIVA-VLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGE 88 FSL+W +P E+ H TL A VL + NVNK K DT +L Sbjct: 62 SRFSLRWFTPTAEVPLCGHATLASAHVLF---NEIGNVNKELKF-----DTLSGILTAKR 113 Query: 89 KKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILS 146 +L + Y S NI + + ++ + P + + + + V+L Sbjct: 114 DELGSIELNFPEYDTTSINISNELEGIFSKAEG--PAFIFDVIKCVTPTPRKLIVVLD 169 >gnl|CDD|143386 cd00141, NT_POLXc, Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family. Length = 307 Score = 29.5 bits (67), Expect = 0.75 Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 6/63 (9%) Query: 95 IRTIG--IYRKKSENIISLSHI-LINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGI 151 + IG I K E I+ + + E +P L L R+PG+G K A + + GI Sbjct: 50 LPGIGKKIAEKIEE-ILETGKLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYEL--GI 106 Query: 152 PTI 154 T+ Sbjct: 107 RTL 109 Score = 27.5 bits (62), Expect = 3.0 Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 10/70 (14%) Query: 75 EIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLP 134 EIAD +++ + E N R YRK + + SL I ++LE +LP Sbjct: 2 EIADILEELADLLELLGGNPFRVRA-YRKAARALESLPE--------PI-ESLEEAKKLP 51 Query: 135 GIGRKGANVI 144 GIG+K A I Sbjct: 52 GIGKKIAEKI 61 >gnl|CDD|31981 COG1796, POL4, DNA polymerase IV (family X) [DNA replication, recombination, and repair]. Length = 326 Score = 27.1 bits (60), Expect = 3.5 Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 20/75 (26%) Query: 73 LFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNK-IPQTLE--G 129 L IAD M GE + I YRK ++++ E + + + E Sbjct: 12 LERIADY---MELEGENPFK-----IRAYRKAAQSL---------ENLTEDLEEIEERGR 54 Query: 130 LTRLPGIGRKGANVI 144 LT LPGIG+ A I Sbjct: 55 LTELPGIGKGIAEKI 69 >gnl|CDD|145578 pfam02514, CobN-Mg_chel, CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis. Length = 1064 Score = 27.1 bits (61), Expect = 4.5 Identities = 9/14 (64%), Positives = 10/14 (71%), Gaps = 1/14 (7%) Query: 186 IPPKHQYNAHY-WL 198 +PP HQY A Y WL Sbjct: 399 LPPTHQYLAFYLWL 412 >gnl|CDD|109238 pfam00172, Zn_clus, Fungal Zn(2)-Cys(6) binuclear cluster domain. Length = 39 Score = 26.5 bits (59), Expect = 6.1 Identities = 7/16 (43%), Positives = 9/16 (56%) Query: 206 CKARKPQCQSCIISNL 221 C +KP C CI + L Sbjct: 13 CDGKKPACSRCIKNGL 28 >gnl|CDD|30702 COG0353, RecR, Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]. Length = 198 Score = 26.7 bits (59), Expect = 6.3 Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 3/31 (9%) Query: 119 FDNKIPQTLEGLTRLPGIGRKGANVILSMAF 149 + I + ++ L +LPG+G K A +AF Sbjct: 3 YPPPIEKLIDALKKLPGVGPKSAQ---RLAF 30 >gnl|CDD|32480 COG2327, WcaK, Uncharacterized conserved protein [Function unknown]. Length = 385 Score = 26.5 bits (58), Expect = 6.6 Identities = 9/36 (25%), Positives = 20/36 (55%), Gaps = 2/36 (5%) Query: 136 IGRKGANVILSMAFGIPTIGVDTH--IFRISNRIGL 169 +G + + I+++AFG+P I + + + +GL Sbjct: 290 VGMRLHSAIMALAFGVPAIAIAYDPKVRGLMQDLGL 325 >gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.. Length = 173 Score = 26.2 bits (58), Expect = 7.6 Identities = 11/35 (31%), Positives = 16/35 (45%) Query: 118 EFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIP 152 F+ + T LT+L G R GA + + G P Sbjct: 134 AFNEALGITGVILTKLDGDARGGAALSIRAVTGKP 168 >gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]. Length = 201 Score = 26.0 bits (57), Expect = 8.1 Identities = 12/36 (33%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Query: 111 LSHILINEFDNKIP-QTLEGLTRLPGIGRKGANVIL 145 LS++ E I + ++ L+++PGIG+K A I+ Sbjct: 90 LSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 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 0.321 0.138 0.411 Gapped Lambda K H 0.267 0.0577 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,735,127 Number of extensions: 138732 Number of successful extensions: 355 Number of sequences better than 10.0: 1 Number of HSP's gapped: 342 Number of HSP's successfully gapped: 28 Length of query: 227 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 137 Effective length of database: 4,318,927 Effective search space: 591692999 Effective search space used: 591692999 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: 56 (25.7 bits)