RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 000431
(1515 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: 1000 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEY 1059
E + ADE E+ + IK G A IKE L+E G PD +E
Sbjct: 60 TPEDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG--------EVPDTREE- 110
Query: 1060 LLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPV 1119
LL + G+G K+ V + A VD +V R++ RLG VP + P
Sbjct: 111 LLSLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-------------GKTP- 156
Query: 1120 MDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECK 1171
++++ 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: 1002 EAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLL 1061
E + ADE E+ + I+ G A + E LVE +G PD +E LL
Sbjct: 25 EDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGG--------EVPDDREE-LL 75
Query: 1062 DIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMD 1121
+ G+G K+ V +L PVD +V RIA RLG V + P ++ L K P
Sbjct: 76 KLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP--- 132
Query: 1122 KIQMYLWPRLCYLDQKTLYELHYQMITFGKI 1152
++ 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: 1000 DWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEY 1059
EA+ ADE E+ + I+ G + A +KE +VE G + L+ PD +E
Sbjct: 32 TPEALAAADEEELRELIRSLGYRRK-AKYLKELARAIVEGFGGLVLDD-----PDAREE- 84
Query: 1060 LLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLP 1106
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: 994 DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPP 1053
++ E + ADE E+ + IK G A IKE LVE + +
Sbjct: 23 ERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILVEGYLGLVPL------D 76
Query: 1054 DKVKEYLLDIEGLGLKSVECVRLLSLQH--IAFPVDVNVGRIAVRLGWVPLQPLPGDLHI 1111
+ E LL + G+G + E V L +L + VD +V R+A RLG + +P ++
Sbjct: 77 LEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVER 136
Query: 1112 HLLKEYP 1118
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: 995 KMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPD 1054
++ + + DE E+A+ I+ G N A R+K L + +++ + +
Sbjct: 57 NEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLE-----SFKSE 111
Query: 1055 KVKEYLLDIEGLGLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLL 1114
++E LL I+G+G ++ + + L +L F VD R+ RLG +
Sbjct: 112 VLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLGGI------------EE 159
Query: 1115 KEYPVMDKIQMYLWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECKH 1172
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: 1007 ADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGL 1066
A E+ + IK G A I LVE +G VP D+ E L+ + G+
Sbjct: 64 AGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG-------EVPEDR--EELVKLPGV 114
Query: 1067 GLKSVECVRLLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMY 1126
G K+ V ++ A VD +V R++ RLG P DK++
Sbjct: 115 GRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSK-GKDP--------------DKVEEE 159
Query: 1127 LWPRLCYLDQKTLYELHYQMITFGKIFCKKRSPNC 1161
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: 978 WDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLV 1037
W L +Y E H E + ADE + + A I
Sbjct: 127 WARLVSLYGNALEIYHSFPTP---EQLAAADEEALRRCGLSGRK----AEYIISLARAAA 179
Query: 1038 ELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVR 1096
E G +DL L+ + ++ E L ++G+G + E L L FP D R A++
Sbjct: 180 E--GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIK 237
Query: 1097 LGWVPLQPLPGDLHIHLLKEY-PVMDKIQMYLW 1128
+ 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: 1038 ELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSLQHI-AFPVDVNVGRIAVR 1096
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: 1153 FCKKRSPNCGACPLRGECKHF 1173
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 = 0.012
Identities = 8/17 (47%), Positives = 8/17 (47%)
Query: 1154 CKKRSPNCGACPLRGEC 1170
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: 1086 VDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRL-CYLDQKTLYELHY 1144
+D NV R+ RL I P K LW L
Sbjct: 141 LDGNVKRVLSRL-----------FAISGDIGKPKTKKE---LWELAEQLLTPDRRPGDFN 186
Query: 1145 Q-MITFGKIFCKKRSPNCGACPLRGEC 1170
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 = 0.31
Identities = 36/156 (23%), Positives = 59/156 (37%), Gaps = 27/156 (17%)
Query: 1016 IKERGQQNIIAGRIKEFLNRLVELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVR 1075
IK G N A + + L+E H VP D+ L + G+G K+ V
Sbjct: 76 IKTIGLYNSKAENVIKTCRILLEQHNG-------EVPEDR--AALEALPGVGRKTANVVL 126
Query: 1076 LLSLQHIAFPVDVNVGRIAVRLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLD 1135
+ VD ++ R+ R + P + + + LLK P K+
Sbjct: 127 NTAFGWPTIAVDTHIFRVCNRTQFAPGKNVE-QVEEKLLKVVPAEFKV------------ 173
Query: 1136 QKTLYELHYQMITFGKIFCKKRSPNCGACPLRGECK 1171
+ 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|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: 723 KALQENGDIKVMTDAVPSQAFDTSSVQSLDRTQLFPTGNSKADVASSTKTSNAESFITQF 782
KA QE +I M D Q+ S+ S + Q P S ++T A T
Sbjct: 137 KAQQE--EITTMAD----QS---SAELSQNSGQSVPLDTSTTTDPATTPAPAAPVDTTPT 187
Query: 783 SHTGNLKKNSVNQLFPTVNSKADVASPSQNHITQSSVTQFWPTGNSTADVASPS 836
+ + + 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: 988 GEERSH----DKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFLNRLVELHGSI 1043
EE + + S + E+E + + I+E L R V++H
Sbjct: 327 TEELAWQQFLQLLQSYPDAPIYHYGETEKDSLRRLAKRYGTPEAEIEELLKRFVDIH--- 383
Query: 1044 DLEWLRNVPPDKVKEYLLDIEGLGLKSVE 1072
+R ++L IE LKS+
Sbjct: 384 --TIVRR-------SWILPIESYSLKSIA 403
>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 = 4.7
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 16/76 (21%)
Query: 974 VQQDWDLLRRIYSTGEERSHDKMDSVDWEAVRCADESEIADAIKERGQQNIIAGRIKEFL 1033
V D D+L ++S G++R KM S+D A+ EI D IK+R L
Sbjct: 290 VGPDDDILFTVFSKGQKR---KMKSLDESALCIFVLKEINDRIKDR-------------L 333
Query: 1034 NRLVELHGSIDLEWLR 1049
G++DL WL+
Sbjct: 334 QSCYRGEGTLDLAWLK 349
>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 = 6.6
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 = 9.5
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 = 6.0
Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 25/79 (31%)
Query: 1290 VMLQDSSALVALTAEAASVPTRKLKRCAHLRTEHHVYVLPDAH-----ELLRGFDRR--- 1341
V+LQ S + LT +R + LR +V+V P H LL R
Sbjct: 6 VLLQSSDQKLLLT-----------RRASSLRIFPNVWVPPGGHVELGENLLEAGLRELNE 54
Query: 1342 ------DPDDPSPYLLAIW 1354
DP D S +L +W
Sbjct: 55 ETGLTLDPIDKSWQVLGLW 73
>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 = 7.5
Identities = 32/136 (23%), Positives = 51/136 (37%), Gaps = 26/136 (19%)
Query: 1037 VELHGSIDLEWLRNVPPDKVKEYLLDIEGLGLKSVECVRLLSL-QHIAFPVDVNVGRIAV 1095
VE G P D E L + G+G + + +L + +D NV R+
Sbjct: 93 VEEFGG-------EFPQDF--EDLAALPGVGRYTAGAILSFALNKPYPI-LDGNVKRVLS 142
Query: 1096 RLGWVPLQPLPGDLHIHLLKEYPVMDKIQMYLWPRLCYLDQKTLYELHYQ-MITFGKIFC 1154
RL ++ +P K++ LW L K E Q ++ G + C
Sbjct: 143 RL--------------FAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMIC 188
Query: 1155 KKRSPNCGACPLRGEC 1170
++ 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 = 7.6
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 498 FKDLTIRDG------GSQLPLQCNKADGPSNVHNAVVPYQVGPSSEHGALV 542
F DLT++ G+ P ADGP N++NAV S+ G LV
Sbjct: 124 FLDLTVKSDKPVVIVGAMRPSTSVSADGPMNLYNAVSVAANPKSAGRGVLV 174
>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 = 8.0
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|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 = 9.8
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 395 QAQAINSQAEFLKEQVMYRLDQLRKQINGPSSQLQEQNRVIQRK 438
+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
0.315 0.132 0.391
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: 75,460,304
Number of extensions: 7359171
Number of successful extensions: 6586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6493
Number of HSP's successfully gapped: 37
Length of query: 1515
Length of database: 10,937,602
Length adjustment: 109
Effective length of query: 1406
Effective length of database: 6,103,016
Effective search space: 8580840496
Effective search space used: 8580840496
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)