RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 002448
(921 letters)
>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 = 87.8 bits (218), Expect = 3e-20
Identities = 42/144 (29%), Positives = 66/144 (45%), Gaps = 15/144 (10%)
Query: 416 QRNSGKQ-----ERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLV 470
Q+ S K +R +R E L A+ +E+ E IK G A+ +K+ LV
Sbjct: 7 QQTSDKAANKITKRLFERYGFPTPEDLAEADEEELRELIKGLGFYRRKAKYIKELARILV 66
Query: 471 REHGSIDLEWLRDVPPDKAKDY-LLSIRGLGLKSVECVRLLTLHH--LAFPVDTNVGRIA 527
+ VP D + LL++ G+G + E V L L + VDT+V R+A
Sbjct: 67 EGYLG-------LVPLDLEELEALLALPGVGRWTAEAVLLFALGRPDVFPAVDTHVRRVA 119
Query: 528 VRLGWVPLQPLPESLQLHLLELYP 551
RLG + +P + ++ L EL+P
Sbjct: 120 KRLGLIDTKPPKKEVERELEELWP 143
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 88.4 bits (220), Expect = 1e-19
Identities = 52/170 (30%), Positives = 78/170 (45%), Gaps = 27/170 (15%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
E L A+ +E+ E IK G+ A+ +K+ L+ + G +VP ++ LL
Sbjct: 62 EDLLNADEEELEELIKSIGLYRNKAKNIKELARILLEKFGG-------EVP--DTREELL 112
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLE 554
S+ G+G K+ V A VDT+V R++ RLG VP PE ++ L++L P
Sbjct: 113 SLPGVGRKTANVVLSFAFGIPAIAVDTHVHRVSNRLGLVP-GKTPEEVEEALMKLIP--- 168
Query: 555 SIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECR 604
K LW +LH+ LI G+ C KP C CP+ C
Sbjct: 169 ---KELW-----------TDLHHWLILHGRYICKARKPRCEECPLADLCP 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 = 80.4 bits (199), Expect = 1e-17
Identities = 44/153 (28%), Positives = 64/153 (41%), Gaps = 26/153 (16%)
Query: 432 LDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKD 491
E L A+ +E+ E I+ G A + + LV E+G PD ++
Sbjct: 22 PTPEDLAAADEEELEELIRGLGFYRRKARYLIELARILVEEYGG--------EVPDDREE 73
Query: 492 YLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 551
LL + G+G K+ V L PVDT+V RIA RLG V + PE ++ L +L P
Sbjct: 74 -LLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP 132
Query: 552 VLESIQKYLWPRLCKLDQRTLYELHYQLITFGK 584
+ EL+ LI FG+
Sbjct: 133 -----------------EEDWRELNLLLIDFGR 148
>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 = 74.6 bits (184), Expect = 1e-15
Identities = 41/117 (35%), Positives = 61/117 (52%), Gaps = 7/117 (5%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
EAL A+ +E+ E I+ G A+ +K+ +V G + L A++ LL
Sbjct: 34 EALAAADEEELRELIRSLGYRRK-AKYLKELARAIVEGFGGLVL------DDPDAREELL 86
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 551
++ G+G K+ V L L AFPVDT+V R+ RLG +P + PE L+ L EL P
Sbjct: 87 ALPGVGRKTANVVLLFALGPDAFPVDTHVRRVLKRLGLIPKKKTPEELEELLEELLP 143
>gnl|CDD|225140 COG2231, COG2231, Uncharacterized protein related to Endonuclease
III [DNA replication, recombination, and repair].
Length = 215
Score = 64.7 bits (158), Expect = 1e-11
Identities = 40/178 (22%), Positives = 75/178 (42%), Gaps = 22/178 (12%)
Query: 428 RMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPD 487
L+ + + + +E++E I+ G N A+R+K L + +++ +
Sbjct: 57 NEGILNLKKILKLDEEELAELIRPSGFYNQKAKRLKALSKNLAKFFINLE-----SFKSE 111
Query: 488 KAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLL 547
++ LLSI+G+G ++ + + L L F VD R+ RLG
Sbjct: 112 VLREELLSIKGIGKETADSILLYALDRPVFVVDKYTRRLLSRLG---------------G 156
Query: 548 ELYPVLESIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGECRH 605
+ I++ L + + R E H ++ K FC K KP C CP++ +C+
Sbjct: 157 IEEKKYDEIKELFEENLPE-NLRLYQEFHALIVEHAKHFCKK-KPLCEKCPLKEKCKK 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 = 57.7 bits (140), Expect = 2e-09
Identities = 43/160 (26%), Positives = 70/160 (43%), Gaps = 27/160 (16%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
+AL A ++E+ E IK G+ A+ + LV +G +VP D+ + L+
Sbjct: 59 QALAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGG-------EVPEDREE--LV 109
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLE 554
+ G+G K+ V + A VDT+V R++ RLG P+ ++ LL+L P
Sbjct: 110 KLPGVGRKTANVVLNVAFGIPAIAVDTHVFRVSNRLGLSK-GKDPDKVEEELLKLIP--- 165
Query: 555 SIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNC 594
+ +LH+ LI G+ C KP C
Sbjct: 166 --------------REFWTKLHHWLILHGRYTCKARKPLC 191
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 46.3 bits (110), Expect = 3e-05
Identities = 31/131 (23%), Positives = 52/131 (39%), Gaps = 8/131 (6%)
Query: 433 DYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDY 492
E L A+ EA++ G++ AE + G +DL L+ + ++A +
Sbjct: 146 TPEQLAAADE----EALRRCGLSGRKAEYIISLARAAAE--GELDLSELKPLSDEEAIEE 199
Query: 493 LLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYP 551
L +++G+G + E L L FP D R A++ + E L E +
Sbjct: 200 LTALKGIGPWTAEMFLLFGLGRPDVFPADDLGLRRAIKKLYRLPTRPTEKEVRELAERWG 259
Query: 552 VLESI-QKYLW 561
S YLW
Sbjct: 260 PYRSYAALYLW 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 = 0.002
Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 478 LEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHL-AFPVDTNVGRIAVR 529
L+ +R + A++ L + G+G K +C+ L+ L A PVD +V RIA R
Sbjct: 207 LQQIRGASYEDAREALCELPGVGPKVADCICLMGLDKPQAVPVDVHVWRIANR 259
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 40.8 bits (95), Expect = 0.002
Identities = 41/169 (24%), Positives = 69/169 (40%), Gaps = 27/169 (15%)
Query: 435 EALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDLEWLRDVPPDKAKDYLL 494
A+ V+ + IK G+ N AE + L+ +H +VP D+A L
Sbjct: 62 AAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNG-------EVPEDRAA--LE 112
Query: 495 SIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRLGWVPLQPLPESLQLHLLELYPVLE 554
++ G+G K+ V VDT++ R+ R + P + + E ++ LL++ P
Sbjct: 113 ALPGVGRKTANVVLNTAFGWPTIAVDTHIFRVCNRTQFAPGKNV-EQVEEKLLKVVPAE- 170
Query: 555 SIQKYLWPRLCKLDQRTLYELHYQLITFGKVFCTKSKPNCNACPMRGEC 603
K+D H+ LI G+ C KP C +C + C
Sbjct: 171 ----------FKVD------CHHWLILHGRYTCIARKPRCGSCIIEDLC 203
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 40.0 bits (94), Expect = 0.004
Identities = 30/139 (21%), Positives = 47/139 (33%), Gaps = 27/139 (19%)
Query: 469 LVREHGSIDLEWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLHHLAFP-VDTNVGRIA 527
+V HG P D+ + L ++ G+G + + + P +D NV R+
Sbjct: 100 VVERHGGE-------FPDDEEE--LAALPGVGPYTAGAILSFAFNQ-PEPVLDGNVKRVL 149
Query: 528 VRLGWVPLQPLPESLQLHLLELYPVLESIQKYLWPRL-CKLDQRTLYELHYQ-LITFGKV 585
RL + +K LW L Q ++ G
Sbjct: 150 SRL--------------FAISGDIGKPKTKKELWELAEQLLTPDRRPGDFNQAMMDLGAT 195
Query: 586 FCTKSKPNCNACPMRGECR 604
CT KP C+ CP+R C
Sbjct: 196 ICTAKKPKCSLCPLRDNCA 214
>gnl|CDD|197771 smart00525, FES, iron-sulpphur binding domain in DNA-(apurinic or
apyrimidinic site) lyase (subfamily of ENDO3).
Length = 21
Score = 34.4 bits (80), Expect = 0.007
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 586 FCTKSKPNCNACPMRGECRHF 606
CT KP C+ CP++ 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 = 31.6 bits (73), Expect = 0.062
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 587 CTKSKPNCNACPMRGEC 603
CT KP C CP+ C
Sbjct: 1 CTARKPKCEECPLADLC 17
>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 = 34.2 bits (78), Expect = 0.38
Identities = 28/80 (35%), Positives = 39/80 (48%), Gaps = 21/80 (26%)
Query: 419 SGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNRLVREHGSIDL 478
S Q+R +M SLD AL +KEI++ IK+R L R G++DL
Sbjct: 302 SKGQKR---KMKSLDESALCIFVLKEINDRIKDR-------------LQSCYRGEGTLDL 345
Query: 479 EWL--RDVPPDKAKDYLLSI 496
WL +D+P A LL+I
Sbjct: 346 AWLKVKDIPCSSA---LLTI 362
>gnl|CDD|153279 cd07595, BAR_RhoGAP_Rich-like, The Bin/Amphiphysin/Rvs (BAR) domain
of Rich-like Rho GTPase Activating Proteins. BAR
domains are dimerization, lipid binding and curvature
sensing modules found in many different proteins with
diverse functions. This subfamily is composed of Rho and
Rac GTPase activating proteins (GAPs) with similarity to
GAP interacting with CIP4 homologs proteins (Rich).
Members contain an N-terminal BAR domain, followed by a
Rho GAP domain, and a C-terminal prolin-rich region.
Vertebrates harbor at least three Rho GAPs in this
subfamily including Rich1, Rich2, and SH3-domain binding
protein 1 (SH3BP1). Rich1 and Rich2 play complementary
roles in the establishment and maintenance of cell
polarity. Rich1 is a Cdc42- and Rac-specific GAP that
binds to polarity proteins through the scaffold protein
angiomotin and plays a role in maintaining the integrity
of tight junctions. Rich2 is a Rac GAP that interacts
with CD317 and plays a role in actin cytoskeleton
organization and the maintenance of microvilli in
polarized epithelial cells. SH3BP1 is a Rac GAP that
inhibits Rac-mediated platelet-derived growth factor
(PDGF)-induced membrane ruffling. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions. The BAR domain of Rich1
has been shown to form oligomers, bind membranes and
induce membrane tubulation.
Length = 244
Score = 33.1 bits (76), Expect = 0.56
Identities = 41/190 (21%), Positives = 74/190 (38%), Gaps = 34/190 (17%)
Query: 292 NASQTRSPPKYDQSCCDIYQHERRTFQCESISIAEQMHHTDLAKEQNVPSGSMLAEKTRN 351
N + QS D ++R + +A+ M + + G +L +
Sbjct: 33 NIHKKLISCLQGQSGEDK---DKRLKKLPEYGLAQSMLESSKELPDDSLLGKVL----KL 85
Query: 352 LGD-DISVANKLSDN-KLIEPNSVEQVLSA-HKVYDETNPNISKSKKRKADGEKKNAIDW 408
G+ ++A +L D+ +E E VLS + + PNI K KKR + K +D
Sbjct: 86 CGEAQNTLARELVDHEMNVE----EDVLSPLQNILEVEIPNIQKQKKRLS----KLVLDM 137
Query: 409 ESLR---KEVQRNSG------KQERSRDRMDSLDY--EALRCANVKEISEAI-KERGMNN 456
+S R ++SG K + +D + + E R A ++ E + KE
Sbjct: 138 DSARSRYNAAHKSSGGQGAAAKVDALKDEYEEAELKLEQCRDALATDMYEFLAKEA---- 193
Query: 457 MLAERMKDFL 466
+A + D +
Sbjct: 194 EIASYLIDLI 203
>gnl|CDD|218076 pfam04417, DUF501, Protein of unknown function (DUF501). Family of
uncharacterized bacterial proteins.
Length = 128
Score = 30.7 bits (70), Expect = 1.2
Identities = 25/97 (25%), Positives = 35/97 (36%), Gaps = 13/97 (13%)
Query: 442 VKEIS--EA---IKERGMNNMLAERMKDFLNRLVREHGS-IDLEW--LRDVPPDKAKDYL 493
V IS EA +KE + L E ++ V H + W L D +
Sbjct: 36 VAAISRLEAAGVMKE--LQERLDED-EELRAAYVAAHERYLARRWELLSDEFVPELAGV- 91
Query: 494 LSIRGLGLKSVECVRLLTLHHLAFPVDTNVGRIAVRL 530
G+ V+C+ L HHLA P VG +
Sbjct: 92 -GAGGMPDFRVKCLHALVAHHLAGPGVNPVGDEVLER 127
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 32.0 bits (73), Expect = 1.3
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 583 GKVFCTKSKPNCNACPMRGECRHFA 607
G + CT+SKP C CP++ C +A
Sbjct: 188 GAMVCTRSKPKCELCPLQNGCIAYA 212
>gnl|CDD|173813 cd07488, Peptidases_S8_2, Peptidase S8 family domain,
uncharacterized subfamily 2. This family is a member of
the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 247
Score = 31.3 bits (71), Expect = 2.0
Identities = 24/121 (19%), Positives = 39/121 (32%), Gaps = 8/121 (6%)
Query: 127 NGSANFQQVGNATLFQDFYSCINDSSLFQEGYHRFKQAEDGGNFQQESGLESIDNLGSSL 186
N ++ G ++ Y+ I S + G RF A D N E L
Sbjct: 132 NQGKEKEKFGGISIPTLAYNSIVVGSTDRNG-DRFF-ASDVSNAGSEIN---SYGRRKVL 186
Query: 187 TFTQLLNFNSPQNQVGFSSDYE---PHMTSYSELLEAEGSEIYNGECSSWPSISSESSKA 243
N+N P + F S P +T LL Y ++ ++ + S +
Sbjct: 187 IVAPGSNYNLPDGKDDFVSGTSFSAPLVTGIIALLLEFYDRQYKKGNNNLIALRALVSSS 246
Query: 244 K 244
Sbjct: 247 V 247
>gnl|CDD|152115 pfam11679, DUF3275, Protein of unknown function (DUF3275). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 211
Score = 31.0 bits (70), Expect = 2.0
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 644 PMPLPSPEKSSLAEVR--REIGKCEPIIEEPATPEQECTEITESDIEDA 690
P P PSP+ A R R++ + P + P QE + + + EDA
Sbjct: 115 PAPAPSPQSPKPASRRASRDMRRIAPFGMNASAPAQEAAQASSDEDEDA 163
>gnl|CDD|227940 COG5653, COG5653, Protein involved in cellulose biosynthesis (CelD)
[Cell envelope biogenesis, outer membrane].
Length = 406
Score = 31.3 bits (71), Expect = 2.3
Identities = 24/108 (22%), Positives = 33/108 (30%), Gaps = 24/108 (22%)
Query: 409 ESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAERMKDFLNR 468
K ++ K ER + + ++ + A R E+ L R K R
Sbjct: 192 RICDKRRRKKFRKLERRFEEVGAVRFVAARSP--DEVEALF------ATLF-RWK--RLR 240
Query: 469 LVREHGSIDL---EWLRDVPPDKAKDYLLSIRGLGLKSVECVRLLTLH 513
G DL W RD D L + S RL LH
Sbjct: 241 F-ARTGQFDLFRAGWTRDFLRD------LFTQRAEDGS---GRLFGLH 278
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 31.5 bits (71), Expect = 2.5
Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 1/95 (1%)
Query: 167 GGNFQQESGLESIDNLGSSLTFTQLLNFNSPQNQVGFSSDYEPHMTSYSELLEAEGSEIY 226
GG + E+ + ++ S T + N Q+ + T SEL + G+ I+
Sbjct: 55 GGPYDAENVFDDVETKHSRNQSTMASHLNDTQDVGIHARHISSVSTVDSELNDEYGNPIW 114
Query: 227 NGECSSWPSISSESSK-AKNESYARAQQPAEDIGE 260
SW ++ K AK + +AQ P E E
Sbjct: 115 KNRVESWKDKKNKKKKSAKKKEAHKAQIPPEQQME 149
>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 = 30.8 bits (70), Expect = 2.6
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 579 LITFGKVFCTKSKPNCNACPMRGEC 603
L+ G + CT+ KP C+ CP++ C
Sbjct: 180 LMDLGAMICTRKKPKCDLCPLQDFC 204
>gnl|CDD|219562 pfam07766, LETM1, LETM1-like protein. Members of this family are
inner mitochondrial membrane proteins which play a role
in potassium and hydrogen ion exchange. Deletion of
LETM1 is thought to be involved in the development of
Wolf-Hirschhorn syndrome in humans.
Length = 268
Score = 30.0 bits (68), Expect = 5.7
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 3/43 (6%)
Query: 428 RMD-SLDYEALRCANVKEISEAIKERGMN--NMLAERMKDFLN 467
D ++ E + + +E+ A + RGM + ER++D L
Sbjct: 207 ADDRAIAREGVHSLSPEELQYACRARGMRALGLSEERLRDQLQ 249
>gnl|CDD|223142 COG0064, GatB, Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit
(PET112 homolog) [Translation, ribosomal structure and
biogenesis].
Length = 483
Score = 30.2 bits (69), Expect = 6.0
Identities = 20/74 (27%), Positives = 27/74 (36%), Gaps = 32/74 (43%)
Query: 574 ELHYQLITFGKVFC------TKSKPNCNACPMRGECRHFASAFASARLALPGPEEKSIVS 627
E+H QL T K+F ++PN N CP+ C L LPG
Sbjct: 13 EVHVQLNTKTKLFSGCSTDFGGAEPNTNVCPV---C-----------LGLPG-------- 50
Query: 628 STMPTMAERNPSVV 641
+P + N V
Sbjct: 51 -ALPVL---NKEAV 60
>gnl|CDD|205692 pfam13514, AAA_27, AAA domain. This domain is found in a number of
double-strand DNA break proteins. This domain contains a
P-loop motif.
Length = 1118
Score = 30.1 bits (68), Expect = 6.4
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 402 KKNAIDWESLRKEVQRNSGKQERSRDRMDSLDYEALRCANVKEISEAIKERGMNNMLAER 461
+K A + E KEV + + + R+ +L A RC ++E+ A++ L +R
Sbjct: 811 EKLAEEIEEAEKEVSEAAAALDEAEARLTAL-LRAARCTTIEELLAAVERSDTYRELRKR 869
Query: 462 MKDFLNRLVREHGSIDLEWLRD 483
+ LVR G + LE L
Sbjct: 870 IAALERTLVRAGGGLSLEALVA 891
>gnl|CDD|212686 cd11736, HSPA12B_like_NBD, Nucleotide-binding domain of HSPA12B and
similar proteins. Human HSPA12B (also known as 70-kDa
heat shock protein-12B, chromosome 20 open reading frame
60/C20orf60, dJ1009E24.2; the gene encoding HSPA12B maps
to 20p13) belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly, and can direct incompetent "client" proteins
towards degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs). No
co-chaperones have yet been identified for HSPA12B.
HSPA12B is predominantly expressed in endothelial cells,
is required for angiogenesis, and may interact with
known angiogenesis mediators. HSPA12B may be important
for host defense in microglia-mediated immune response.
HSPA12B expression is up-regulated in lipopolysaccharide
(LPS)-induced inflammatory response in the spinal cord,
and mostly located in active microglia; this induced
expression may be regulated by activation of MAPK-p38,
ERK1/2 and SAPK/JNK signaling pathways. Overexpression
of HSPA12B also protects against LPS-induced cardiac
dysfunction and involves the preserved activation of the
PI3K/Akt signaling pathway.
Length = 468
Score = 30.0 bits (67), Expect = 7.5
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 731 LVALNPDAASIPAPKLKNVSRLRTEHQVYELPDSHPLLEGMDRREPDDPS 780
L+AL P+AASI KL RL HQ+ +L +D D S
Sbjct: 178 LIALEPEAASIYCRKL----RL---HQLTDLSQRAVTNFDIDGSRSIDSS 220
>gnl|CDD|219987 pfam08719, DUF1768, Domain of unknown function (DUF1768). This is
a domain of unknown function. It is alpha helical in
structure. The GO annotation for this protein suggests
it is involved in nematode larval development and has a
positive regulation on growth rate.
Length = 146
Score = 28.7 bits (65), Expect = 7.8
Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 12/57 (21%)
Query: 371 NSVEQVLSAHKVYDE------------TNPNISKSKKRKADGEKKNAIDWESLRKEV 415
+VE A K +P +K RK + DW+ ++ +V
Sbjct: 29 PTVEHYFQAQKFRLFGDREIAAKILAAKSPAEAKKLGRKVRNFDEARKDWDKVKVDV 85
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
0.314 0.130 0.384
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: 45,413,562
Number of extensions: 4363641
Number of successful extensions: 2849
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2833
Number of HSP's successfully gapped: 40
Length of query: 921
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 815
Effective length of database: 6,236,078
Effective search space: 5082403570
Effective search space used: 5082403570
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 64 (28.3 bits)