RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000414
(1541 letters)
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 96.9 bits (242), Expect = 2e-22
Identities = 49/172 (28%), Positives = 73/172 (42%), Gaps = 27/172 (15%)
Query: 1026 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEY 1085
E + ADE E+ + IK G A IKE L+E G PD +E
Sbjct: 60 TPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG--------EVPDTREE- 110
Query: 1086 LLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPV 1145
LL + G+G K+ V + A VD +V R++ RLG VP + P
Sbjct: 111 LLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-------------GKTP- 156
Query: 1146 MDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECK 1197
++++ L + ++ +LH+ +I G+ CK R P C CPL C
Sbjct: 157 -EEVEEALMKLI---PKELWTDLHHWLILHGRYICKARKPRCEECPLADLCP 204
>gnl|CDD|214684 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 70.0 bits (172), Expect = 8e-14
Identities = 43/151 (28%), Positives = 63/151 (41%), Gaps = 26/151 (17%)
Query: 1028 EAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLL 1087
E + ADE E+ + I+ G A + E LVE +G PD +E LL
Sbjct: 25 EDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGG--------EVPDDREE-LL 75
Query: 1088 DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1147
+ G+G K+ V +L PVD +V RIA RLG V + P ++ L K P
Sbjct: 76 KLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP--- 132
Query: 1148 KIQMYLWPRLCYLDQKTLYELHYQMITFGKI 1178
++ EL+ +I FG+
Sbjct: 133 --------------EEDWRELNLLLIDFGRT 149
>gnl|CDD|238013 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 = 68.4 bits (168), Expect = 3e-13
Identities = 38/107 (35%), Positives = 56/107 (52%), Gaps = 7/107 (6%)
Query: 1026 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEY 1085
EA+ ADE E+ + I+ G + A +KE +VE G + L+ PD +E
Sbjct: 32 TPEALAAADEEELRELIRSLGYRRK-AKYLKELARAIVEGFGGLVLDD-----PDAREE- 84
Query: 1086 LLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLP 1132
LL + G+G K+ V L +L AFPVD +V R+ RLG +P + P
Sbjct: 85 LLALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTP 131
>gnl|CDD|216088 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 = 66.6 bits (163), Expect = 1e-12
Identities = 35/127 (27%), Positives = 56/127 (44%), Gaps = 8/127 (6%)
Query: 1020 DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPP 1079
++ E + ADE E+ + IK G A IKE LVE + +
Sbjct: 23 ERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLGLVPL------D 76
Query: 1080 DKVKEYLLDIEGLGLKSVECVRLLSLQH--IAFPVDVNVGRIAVRLGWVPLQPLPGDLHI 1137
+ E LL + G+G + E V L +L + VD +V R+A RLG + +P ++
Sbjct: 77 LEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVER 136
Query: 1138 HLLKEYP 1144
L + +P
Sbjct: 137 ELEELWP 143
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease III
[DNA replication, recombination, and repair].
Length = 215
Score = 62.4 bits (152), Expect = 1e-10
Identities = 43/178 (24%), Positives = 79/178 (44%), Gaps = 22/178 (12%)
Query: 1021 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPD 1080
++ + + DE E+A+ I+ G N A R+K L + +++ + +
Sbjct: 57 NEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLE-----SFKSE 111
Query: 1081 KVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLL 1140
++E LL I+G+G ++ + + L +L F VD R+ RLG +
Sbjct: 112 VLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGI------------EE 159
Query: 1141 KEYPVMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKH 1198
K+Y + ++ P + + E H ++ K FCKK+ P C CPL+ +CK
Sbjct: 160 KKYDEIKELFEENLPE----NLRLYQEFHALIVEHAKHFCKKK-PLCEKCPLKEKCKK 212
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes nth
members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 48.9 bits (117), Expect = 4e-06
Identities = 42/155 (27%), Positives = 64/155 (41%), Gaps = 27/155 (17%)
Query: 1033 ADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGL 1092
A E+ + IK G A I LVE +G VP D+ E L+ + G+
Sbjct: 64 AGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG-------EVPEDR--EELVKLPGV 114
Query: 1093 GLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMY 1152
G K+ V ++ A VD +V R++ RLG P DK++
Sbjct: 115 GRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSK-GKDP--------------DKVEEE 159
Query: 1153 LWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNC 1187
L L + ++ +LH+ +I G+ CK R P C
Sbjct: 160 L---LKLIPREFWTKLHHWLILHGRYTCKARKPLC 191
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and repair].
Length = 285
Score = 41.7 bits (98), Expect = 0.002
Identities = 33/153 (21%), Positives = 52/153 (33%), Gaps = 11/153 (7%)
Query: 1004 WDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLV 1063
W L +Y E H E + ADE + + A I
Sbjct: 127 WARLVSLYGNALEIYHSFPTP---EQLAAADEEALRRCGLSGRK----AEYIISLARAAA 179
Query: 1064 ELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVR 1122
E G +DL L+ + ++ E L ++G+G + E L L FP D R A++
Sbjct: 180 E--GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIK 237
Query: 1123 LGWVPLQPLPGDLHIHLLKEY-PVMDKIQMYLW 1154
+ L + + P +YLW
Sbjct: 238 KLYRLPTRPTEKEVRELAERWGPYRSYAALYLW 270
>gnl|CDD|211589 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg). All proteins in
this family for which functions are known are
8-oxo-guanaine DNA glycosylases that function in base
excision repair. This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University). This family is distantly realted to the
Nth-MutY superfamily [DNA metabolism, DNA replication,
recombination, and repair].
Length = 310
Score = 41.4 bits (97), Expect = 0.003
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 1064 ELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVR 1122
E G L+ +R + +E L ++ G+G K +C+ L+ L A PVDV+V RIA R
Sbjct: 200 EQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANR 259
>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or
apyrimidinic site) lyase (subfamily of ENDO3).
Length = 21
Score = 36.0 bits (84), Expect = 0.003
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 1179 FCKKRSPNCGACPLRGECKHF 1199
C R P C CPL+ C +
Sbjct: 1 ICTARKPRCDECPLKDLCPAY 21
>gnl|CDD|204516 pfam10576, EndIII_4Fe-2S, Iron-sulfur binding domain of endonuclease
III. Escherichia coli endonuclease III (EC 4.2.99.18) is
a DNA repair enzyme that acts both as a DNA
N-glycosylase, removing oxidized pyrimidines from DNA,
and as an apurinic/apyrimidinic (AP) endonuclease,
introducing a single-strand nick at the site from which
the damaged base was removed. Endonuclease III is an
iron-sulfur protein that binds a single 4Fe-4S cluster.
The 4Fe-4S cluster does not seem to be important for
catalytic activity, but is probably involved in the
proper positioning of the enzyme along the DNA strand.
The 4Fe-4S cluster is bound by four cysteines which are
all located in a 17 amino acid region at the C-terminal
end of endonuclease III. A similar region is also present
in the central section of mutY and in the C-terminus of
ORF-10 and of the Micro-coccus UV endonuclease.
Length = 17
Score = 34.3 bits (80), Expect = 0.011
Identities = 8/17 (47%), Positives = 8/17 (47%)
Query: 1180 CKKRSPNCGACPLRGEC 1196
C R P C CPL C
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 39.2 bits (92), Expect = 0.015
Identities = 23/87 (26%), Positives = 27/87 (31%), Gaps = 16/87 (18%)
Query: 1112 VDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRL-CYLDQKTLYELHY 1170
+D NV R+ RL I P K LW L
Sbjct: 141 LDGNVKRVLSRL-----------FAISGDIGKPKTKKE---LWELAEQLLTPDRRPGDFN 186
Query: 1171 Q-MITFGKIFCKKRSPNCGACPLRGEC 1196
Q M+ G C + P C CPLR C
Sbjct: 187 QAMMDLGATICTAKKPKCSLCPLRDNC 213
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 34.2 bits (78), Expect = 0.32
Identities = 36/156 (23%), Positives = 59/156 (37%), Gaps = 27/156 (17%)
Query: 1042 IKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1101
IK G N A + + L+E H VP D+ L + G+G K+ V
Sbjct: 76 IKTIGLYNSKAENVIKTCRILLEQHNG-------EVPEDR--AALEALPGVGRKTANVVL 126
Query: 1102 LLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLD 1161
+ VD ++ R+ R + P + + + LLK P K+
Sbjct: 127 NTAFGWPTIAVDTHIFRVCNRTQFAPGKNVE-QVEEKLLKVVPAEFKV------------ 173
Query: 1162 QKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECK 1197
+ H+ +I G+ C R P CG+C + C+
Sbjct: 174 -----DCHHWLILHGRYTCIARKPRCGSCIIEDLCE 204
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 34.7 bits (80), Expect = 0.36
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 153 TRSNRRSRRRRRLNILFMRNLPVGQGQYPRRKRRLRRATRRCNLT 197
RS R +RR RR + R + RR+ R +TRR L
Sbjct: 14 RRSRRAARRSRRDGRVGSRGRSRYRS---RRRSSRRSSTRRAELA 55
>gnl|CDD|226024 COG3493, CitS, Na+/citrate symporter [Energy production and
conversion].
Length = 438
Score = 32.3 bits (74), Expect = 2.3
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 372 GKTLPFPGHFISGLPQLNIGV------LGLLPELSIGAVEPFLDQSNSSLEFF 418
GK +P +I G L + V LLP I AV F+ +SN L+F+
Sbjct: 65 GKRIPIVNKYIGGGAILALFVAAYLVFYNLLPSNVIKAVTNFMGKSN-FLDFY 116
>gnl|CDD|236776 PRK10856, PRK10856, cytoskeletal protein RodZ; Provisional.
Length = 331
Score = 31.5 bits (72), Expect = 3.1
Identities = 21/114 (18%), Positives = 36/114 (31%), Gaps = 11/114 (9%)
Query: 749 KALQENGDIKVMTDAVPSQAFDTSSVQSLDRTQLFPTGNSKADVASSTKTSNAESFITQF 808
KA QE +I M D Q+ S+ S + Q P S ++T A T
Sbjct: 137 KAQQE--EITTMAD----QS---SAELSQNSGQSVPLDTSTTTDPATTPAPAAPVDTTPT 187
Query: 809 SHTGNLKKNSVNQLFPTVNSKADVASPSQNHITQSSVTQFWPTGNSTADVASPS 862
+ + + V +PSQ ++ ++ P+
Sbjct: 188 NSQTP--AVATAPAPAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLPT 239
>gnl|CDD|234230 TIGR03491, TIGR03491, RecB family nuclease, putative, TM0106 family.
Members of this uncharacterized protein family are found
broadly but sporadically among bacteria. The N-terminal
region is homologous to the Cas4 protein of CRISPR
systems, although this protein family shows no signs of
association with CRISPR repeats.
Length = 457
Score = 31.5 bits (72), Expect = 3.5
Identities = 18/89 (20%), Positives = 31/89 (34%), Gaps = 16/89 (17%)
Query: 1014 GEERSH----DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSI 1069
EE + + S + E+E + + I+E L R V++H
Sbjct: 327 TEELAWQQFLQLLQSYPDAPIYHYGETEKDSLRRLAKRYGTPEAEIEELLKRFVDIH--- 383
Query: 1070 DLEWLRNVPPDKVKEYLLDIEGLGLKSVE 1098
+R ++L IE LKS+
Sbjct: 384 --TIVRR-------SWILPIESYSLKSIA 403
>gnl|CDD|226718 COG4268, McrC, McrBC 5-methylcytosine restriction system component
[Defense mechanisms].
Length = 439
Score = 31.3 bits (71), Expect = 4.4
Identities = 13/87 (14%), Positives = 27/87 (31%), Gaps = 6/87 (6%)
Query: 382 ISGLPQLNIGVLGLLPELSIGAVEPFLDQSNSSLEFFPRQAQAINSQAEFLKEQV----- 436
P G +L I + + N+ +E P+ + + EF+ E
Sbjct: 47 YFISPNDTTGSFDGDKDLKIFNYVGQIIKPNAVIEILPKTQERLTISMEFIDESRRNLFY 106
Query: 437 MYR-LDQLRKQINGPSSQLQEQNRVIQ 462
M L + +S + + +
Sbjct: 107 MLTYLKGYLFEATQAASLQSSKMPLYE 133
>gnl|CDD|200535 cd11274, Sema_plexin_A4, The Sema domain, a protein interacting
module, of Plexin A4. Plexin A4 forms a receptor complex
with neuropilins (NRPs) and transduces signals for class
3 semaphorins in the nervous system. It regulates facial
nerve development by functioning as a receptor for
Sema3A/NRP1. Both plexins A3 and A4 are essential for
normal sympathetic development. They function both
cooperatively, to regulate the migration of sympathetic
neurons, and differentially, to guide sympathetic axons.
Plexin A4 is also expressed in lymphoid tissues and
functions in the immune system. It negatively regulates T
lymphocyte responses. The Sema domain is located at the
N-terminus and contains four disulfide bonds formed by
eight conserved cysteine residues. It serves as a
ligand-recognition and -binding module.
Length = 473
Score = 31.1 bits (70), Expect = 4.8
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 1000 VQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 1059
V D D+L ++S G++R KM S+D A+ EI D IK+R L
Sbjct: 290 VGPDDDILFTVFSKGQKR---KMKSLDESALCIFVLKEINDRIKDR-------------L 333
Query: 1060 NRLVELHGSIDLEWLR 1075
G++DL WL+
Sbjct: 334 QSCYRGEGTLDLAWLK 349
>gnl|CDD|226904 COG4521, TauA, ABC-type taurine transport system, periplasmic
component [Inorganic ion transport and metabolism].
Length = 334
Score = 31.0 bits (70), Expect = 5.3
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 2/81 (2%)
Query: 355 FQEQKIDSLAPFPGQSSGKTLPFPGHFISGLPQLNIGVLGLLPELSIGAVEPFLDQSNSS 414
F + +D+ A + +S L +L+ +PEL G P + S
Sbjct: 232 FAKVALDAQADYLANPDVWLADSEQ--VSKLARLSGVPEEDVPELLKGNTFPTPQEQTSD 289
Query: 415 LEFFPRQAQAINSQAEFLKEQ 435
E +AI AEFLKEQ
Sbjct: 290 KELGGGVVKAIADTAEFLKEQ 310
>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated
initially from a Japanese patient with hepatitis of
unknown aetiology, has since been found to infect both
healthy and diseased individuals and numerous prevalence
studies have raised questions about its role in
unexplained hepatitis. ORF1 is a large 750 residue
protein. The N-terminal half of this protein corresponds
to the capsid protein.
Length = 525
Score = 31.1 bits (71), Expect = 5.8
Identities = 15/40 (37%), Positives = 16/40 (40%), Gaps = 15/40 (37%)
Query: 154 RSNRRSRRRRRLNILFMRNLPVGQGQYPRRKRRLRRATRR 193
R RR RRRRR RR+R RR RR
Sbjct: 23 RRARRRRRRRR---------------VRRRRRGRRRRRRR 47
Score = 30.7 bits (70), Expect = 6.5
Identities = 17/46 (36%), Positives = 19/46 (41%), Gaps = 16/46 (34%)
Query: 148 RENNKTRSNRRSRRRRRLNILFMRNLPVGQGQYPRRKRRLRRATRR 193
R + R RR RRRRR RR+RR RR RR
Sbjct: 8 RRRRRWRGRRRRRRRRR----------------ARRRRRRRRVRRR 37
Score = 30.3 bits (69), Expect = 9.6
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 154 RSNRRSRRRRRLNILFMRNLPVGQGQYPRRKRRLRRATRR 193
R RR RRRR R + + RR+RR RR +R
Sbjct: 19 RRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKR 58
>gnl|CDD|240050 cd04694, Nudix_Hydrolase_35, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU,
where U = I, L or V), which functions as a metal binding
and catalytic site. Substrates of nudix hydrolases
include intact and oxidatively damaged nucleoside
triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the nucleotide
pools and to maintain cell viability, thereby serving as
surveillance & "house-cleaning" enzymes. Substrate
specificity is used to define families within the
superfamily. Differences in substrate specificity are
determined by the N-terminal extension or by residues in
variable loop regions. Mechanistically, substrate
hydrolysis occurs by a nucleophilic substitution
reaction, with variation in the numbers and roles of
divalent cations required.
Length = 143
Score = 29.8 bits (67), Expect = 6.5
Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 25/79 (31%)
Query: 1316 VMLQDSSALVALTAEAASVPTRKLKRCAHLRTEHHVYVLPDAH-----ELLRGFDRR--- 1367
V+LQ S + LT +R + LR +V+V P H LL R
Sbjct: 6 VLLQSSDQKLLLT-----------RRASSLRIFPNVWVPPGGHVELGENLLEAGLRELNE 54
Query: 1368 ------DPDDPSPYLLAIW 1380
DP D S +L +W
Sbjct: 55 ETGLTLDPIDKSWQVLGLW 73
>gnl|CDD|219248 pfam06978, POP1, Ribonucleases P/MRP protein subunit POP1. This
family represents a conserved region approximately 150
residues long located towards the N-terminus of the POP1
subunit that is common to both the RNase MRP and RNase P
ribonucleoproteins (EC:3.1.26.5). These RNA-containing
enzymes generate mature tRNA molecules by cleaving their
5' ends.
Length = 158
Score = 29.6 bits (67), Expect = 7.5
Identities = 11/46 (23%), Positives = 21/46 (45%)
Query: 144 AREQRENNKTRSNRRSRRRRRLNILFMRNLPVGQGQYPRRKRRLRR 189
RE ++N R + +RL L + P +Y +R++R +
Sbjct: 56 KREMAKDNTPTKLSRKKPSKRLLRLALARPPNLSRKYRKRQKRKKW 101
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase. This equivalog
model identifies mutY members of the pfam00730
superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro
rich loop followed by a conserved aspartate). The major
members of the superfamily are nth and mutY [DNA
metabolism, DNA replication, recombination, and repair].
Length = 275
Score = 30.5 bits (69), Expect = 7.6
Identities = 32/136 (23%), Positives = 51/136 (37%), Gaps = 26/136 (19%)
Query: 1063 VELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSL-QHIAFPVDVNVGRIAV 1121
VE G P D E L + G+G + + +L + +D NV R+
Sbjct: 93 VEEFGG-------EFPQDF--EDLAALPGVGRYTAGAILSFALNKPYPI-LDGNVKRVLS 142
Query: 1122 RLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLDQKTLYELHYQ-MITFGKIFC 1180
RL ++ +P K++ LW L K E Q ++ G + C
Sbjct: 143 RL--------------FAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMIC 188
Query: 1181 KKRSPNCGACPLRGEC 1196
++ P C CPL+ C
Sbjct: 189 TRKKPKCDLCPLQDFC 204
>gnl|CDD|129611 TIGR00520, asnASE_II, L-asparaginase, type II. Two related
families of asparaginase (L-asparagine amidohydrolase,
EC 3.5.1.1) are designated type I and type II according
to the terminology in E. coli, which has both:
L-asparaginase I is a low-affinity enzyme found in the
cytoplasm, while L-asparaginase II is a high-affinity
periplasmic enzyme synthesized with a cleavable signal
sequence. This model describes L-asparaginases related
to type II of E. coli. Both the cytoplasmic and the cell
wall asparaginases of Saccharomyces cerevisiae belong to
this set. Members of this set from Acinetobacter
glutaminasificans and Pseudomonas fluorescens are
described as having both glutaminase and asparaginase
activitities. All members are homotetrameric [Energy
metabolism, Amino acids and amines].
Length = 349
Score = 30.5 bits (69), Expect = 7.7
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 524 FKDLTIRDG------GSQLPLQCNKADGPSNVHNAVVPYQVGPSSEHGALV 568
F DLT++ G+ P ADGP N++NAV S+ G LV
Sbjct: 124 FLDLTVKSDKPVVIVGAMRPSTSVSADGPMNLYNAVSVAANPKSAGRGVLV 174
>gnl|CDD|197361 cd09803, UBAN, polyubiquitin binding domain of NEMO and related
proteins. NEMO (NF-kappaB essential modulator) is a
regulatory subunit of the kinase complex IKK, which is
involved in the activation of NF-kappaB via
phosporylation of inhibitory IkappaBs. This mechanism
requires the binding of NEMO to ubiquinated substrates.
Binding is achieved via the UBAN motif (ubiquitin
binding in ABIN and NEMO), which is described in this
model. This region of NEMO has also been named CoZi (for
coiled-coil 2 and leucine zipper). ABINs (A20-binding
inhibitors of NF-kappaB) are sensors for ubiquitin that
are involved in regulation of apoptosis, ABIN-1 is
presumed to inhibit signalling via the NF-kappaB route.
The UBAN motif is also found in optineurin, the product
of a gene associated with glaucoma, which has been
characterized as a negative regulator of NF-kappaB as
well.
Length = 87
Score = 28.1 bits (63), Expect = 8.4
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 421 QAQAINSQAEFLKEQVMYRLDQLRKQINGPSSQLQEQNRVIQRK 464
+AQA +++F E R R++++ QL EQ +QR+
Sbjct: 45 KAQAEIYKSDFEAE----RAA--REKLHQEKEQLAEQLEYLQRE 82
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.132 0.393
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 77,010,024
Number of extensions: 7531737
Number of successful extensions: 6705
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6612
Number of HSP's successfully gapped: 40
Length of query: 1541
Length of database: 10,937,602
Length adjustment: 110
Effective length of query: 1431
Effective length of database: 6,058,662
Effective search space: 8669945322
Effective search space used: 8669945322
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 (21.6 bits)
S2: 66 (29.1 bits)