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)