RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16316
(335 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 140 bits (356), Expect = 1e-39
Identities = 82/293 (27%), Positives = 129/293 (44%), Gaps = 26/293 (8%)
Query: 17 FRENTDKITSIDYSADGLLLISCSEDDQIVIYDCELGTNKRTVFSKKYGVDLIRFTHAKQ 76
+ +T +T + +S DG LL + S D I ++D E G RT+ V + +
Sbjct: 5 LKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGT 64
Query: 77 AAIHASTKIDDTVRYLSLHDNKYIRYFPGHTKKVNSLCLSPIDDTFISGSYDKTVRLWDL 136
AS D T+R L + +R GHT V+S+ SP S S DKT+++WD+
Sbjct: 65 YL--ASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
Query: 137 RSPNCQ--------GIMHVSGSRPIAAFDPEGLIFGVGVNSDTIKLYDVRSFDKGPFSNF 188
+ C + V AF P+G TIKL+D+R+ +
Sbjct: 123 ETGKCLTTLRGHTDWVNSV-------AFSPDGTFVASSSQDGTIKLWDLRTG--KCVATL 173
Query: 189 KFAAEKECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGFLNNKGCPLEASF 248
+ + FS DG+ +L S++ I+ +D G+CL TL G N +F
Sbjct: 174 TG---HTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENG---VNSVAF 227
Query: 249 TPDSKYVISGSTDGRIHIWNAEKGFKVCVLDADHPSPVQTIQFNPKFNMMASA 301
+PD + SGS DG I +W+ G V L H + V ++ ++P +AS
Sbjct: 228 SPDGYLLASGSEDGTIRVWDLRTGECVQTLSG-HTNSVTSLAWSPDGKRLASG 279
Score = 106 bits (267), Expect = 1e-26
Identities = 69/270 (25%), Positives = 113/270 (41%), Gaps = 58/270 (21%)
Query: 5 DNVIRSYKVAKL-----FRENTDKITSIDYSADGLLLISCSEDDQIVIYDCELGTNKRTV 59
D IR + + +T ++S+ +S DG +L S S D I ++D E G T+
Sbjct: 72 DKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTL 131
Query: 60 FSKKYGVDLIRFTHAKQAAIHASTKIDDTVRYLSLHDNKYIRYFPGHTKKVNSLCLSPID 119
V+ + F+ +S D T++ L K + GHT +VNS+ SP
Sbjct: 132 RGHTDWVNSVAFSPDGTFVASSSQ--DGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDG 189
Query: 120 DTFISGSYDKTVRLWDLRSPNCQGIMHVSGSRPIA-AFDPEGLIFGVGVNSDTIKLYDVR 178
+ +S S D T++LWDL + C G + + + AF P+G + G TI+++D+R
Sbjct: 190 EKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLR 249
Query: 179 SFDKGPFSNFKFAAEKECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGFLN 238
+ G+C+QTL+G N
Sbjct: 250 T-----------------------------------------------GECVQTLSGHTN 262
Query: 239 NKGCPLEASFTPDSKYVISGSTDGRIHIWN 268
+ +++PD K + SGS DG I IW+
Sbjct: 263 SVTS---LAWSPDGKRLASGSADGTIRIWD 289
Score = 98.6 bits (246), Expect = 8e-24
Identities = 53/207 (25%), Positives = 89/207 (42%), Gaps = 12/207 (5%)
Query: 100 IRYFPGHTKKVNSLCLSPIDDTFISGSYDKTVRLWDLRSPNCQGIM--HVSGSRPIAAFD 157
R GHT V + SP +GS D T+++WDL + + H R +AA
Sbjct: 2 RRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASA 61
Query: 158 PEGLIFGVGVNSDTIKLYDVRSFDKGPFSNFKFAAEKECDWTGIKFSADGKYILISTNGS 217
+ + TI+L+D+ + + + + FS DG+ + S+
Sbjct: 62 DGTYLASGSSDK-TIRLWDLETGEC----VRTLTGH-TSYVSSVAFSPDGRILSSSSRDK 115
Query: 218 IIRTFDAYNGQCLQTLAGFLNNKGCPLEASFTPDSKYVISGSTDGRIHIWNAEKGFKVCV 277
I+ +D G+CL TL G + +F+PD +V S S DG I +W+ G V
Sbjct: 116 TIKVWDVETGKCLTTLRG---HTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVAT 172
Query: 278 LDADHPSPVQTIQFNPKFNMMASACTN 304
L H V ++ F+P + S+ ++
Sbjct: 173 LTG-HTGEVNSVAFSPDGEKLLSSSSD 198
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 94.8 bits (234), Expect = 1e-21
Identities = 91/311 (29%), Positives = 144/311 (46%), Gaps = 21/311 (6%)
Query: 5 DNVIRSYKVAKLFRE------NTDKITSIDYSADGLLLISCSEDD-QIVIYDCELGTNKR 57
D ++ + ++ + +++ +TS+ +S DG LL S S D I ++D G
Sbjct: 133 DGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLS 192
Query: 58 TVFSKKYGVDLIRFTHAKQAAIHASTKIDDTVRYLSLHDNKYIR-YFPGHTKKVNSLCLS 116
T+ V + F+ I AS D T+R L K +R GH+ V S S
Sbjct: 193 TLAGHTDPVSSLAFSPDGGLLI-ASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVS-SFS 250
Query: 117 PIDDTFISGSYDKTVRLWDLRSPNCQGIMHVSGSRPI--AAFDPEGLIFGVGVNSDTIKL 174
P SGS D T+RLWDLRS + S + AF P+G + G + T++L
Sbjct: 251 PDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRL 310
Query: 175 YDVRSFDKGPFSNFKFAAEKECDWTGIKFSADGKYILIS-TNGSIIRTFDAYNGQCLQTL 233
+D+ + G + E + + FS DG ++ ++ IR +D G+ L+TL
Sbjct: 311 WDLET---GKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTL 367
Query: 234 AGFLNNKGCPLEASFTPDSKYVISGSTDGRIHIWNAEKGFKVCVLDADHPSPVQTIQFNP 293
G N L SF+PD + V SGSTDG + +W+ G + LD H S V ++ F+P
Sbjct: 368 EGHSNV----LSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDG-HTSRVTSLDFSP 422
Query: 294 KFNMMASACTN 304
+AS ++
Sbjct: 423 DGKSLASGSSD 433
Score = 91.3 bits (225), Expect = 2e-20
Identities = 77/280 (27%), Positives = 123/280 (43%), Gaps = 17/280 (6%)
Query: 8 IRSYKVAKLFRENTDKITSIDYSADG-LLLISCSEDDQIVIYDCELGTNKRTVFSKKYGV 66
+R+ K +TD ++S+ +S DG LL+ S S D I ++D G R+ S
Sbjct: 185 LRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDS 244
Query: 67 DLIRFTHAKQAAIHASTKIDDTVRYLSLH-DNKYIRYFPGHTKKVNSLCLSPIDDTFISG 125
+ F+ + AS D T+R L + +R GH+ V S+ SP SG
Sbjct: 245 VVSSFSPDGS--LLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
Query: 126 SYDKTVRLWDLRSPNCQGIMHVSGSRPI---AAFDPEGLIFGVGVNSD-TIKLYDVRSFD 181
S D TVRLWDL + + + G +F P+G + G + D TI+L+D+R+
Sbjct: 303 SSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRT-- 360
Query: 182 KGPFSNFKFAAEKECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGFLNNKG 241
P + + + FS DG+ + + +R +D G L+ L G +
Sbjct: 361 GKPLKTLEGHSNV----LSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVT 416
Query: 242 CPLEASFTPDSKYVISGSTDGRIHIWNAEKGFKVCVLDAD 281
F+PD K + SGS+D I +W+ + K D
Sbjct: 417 SL---DFSPDGKSLASGSSDNTIRLWDLKTSLKSVSFSPD 453
Score = 89.4 bits (220), Expect = 9e-20
Identities = 75/307 (24%), Positives = 133/307 (43%), Gaps = 16/307 (5%)
Query: 8 IRSYKVAKLFRENTDKITSIDYSADGLLLISCSEDDQIV-IYDCELGTNKRTVFSKKYG- 65
I+S + + ++S D + +L++ S D V ++D
Sbjct: 101 IKSLEGLHDSSVSKLALSSPDGN---SILLASSSLDGTVKLWDLSTPGKLIRTLEGHSES 157
Query: 66 VDLIRFTHAKQAAIHASTKIDDTVRYLSLHDNKYIRYFPGHTKKVNSLCLSPIDDTFI-S 124
V + F+ + S+ D T++ L K + GHT V+SL SP I S
Sbjct: 158 VTSLAFSPDGKLLASGSSL-DGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIAS 216
Query: 125 GSYDKTVRLWDLRSPNC-QGIMHVSGSRPIAAFDPEGLIFGVGVNSDTIKLYDVRSFDKG 183
GS D T+RLWDL + + + +++F P+G + G + TI+L+D+RS
Sbjct: 217 GSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSL 276
Query: 184 PFSNFKFAAEKECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGFLNNKGCP 243
+ ++ + FS DGK + ++ +R +D G+ L +L ++G
Sbjct: 277 LRTLSGHSSSVLS----VAFSPDGKLLASGSSDGTVRLWDLETGKLLSSL-TLKGHEGPV 331
Query: 244 LEASFTPD-SKYVISGSTDGRIHIWNAEKGFKVCVLDADHPSPVQTIQFNPKFNMMASAC 302
SF+PD S V GS DG I +W+ G + + S V ++ F+P +++S
Sbjct: 332 SSLSFSPDGSLLVSGGSDDGTIRLWDLRTGK--PLKTLEGHSNVLSVSFSPDGRVVSSGS 389
Query: 303 TNLAFWI 309
T+ +
Sbjct: 390 TDGTVRL 396
Score = 85.5 bits (210), Expect = 2e-18
Identities = 74/292 (25%), Positives = 118/292 (40%), Gaps = 55/292 (18%)
Query: 16 LFRENTDKITSIDYSADGLLLISCSEDDQIVIYDCELGTNKRTVFSKKYG---VDLIRFT 72
L R + D ITSI +S DG LL+S S D I ++D + G + L +
Sbjct: 60 LLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSS 119
Query: 73 HAKQAAIHASTKIDDTVRYLSL-HDNKYIRYFPGHTKKVNSLCLSPIDDTFISGS-YDKT 130
+ + AS+ +D TV+ L K IR GH++ V SL SP SGS D T
Sbjct: 120 PDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGT 179
Query: 131 VRLWDLRSPNCQGIMHVSGSRPIAAFDPEGLIFGVGVNSDTIKLYDVRSFDKGPFSNFKF 190
++LWDLR+ +
Sbjct: 180 IKLWDLRTGKPLSTLAGHTDPV-------------------------------------- 201
Query: 191 AAEKECDWTGIKFSADGKYILIS-TNGSIIRTFDAYNGQCLQTLAGFLNNKGCPLEASFT 249
+ + FS DG ++ S ++ IR +D G+ L++ L+ + +SF+
Sbjct: 202 --------SSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRST---LSGHSDSVVSSFS 250
Query: 250 PDSKYVISGSTDGRIHIWNAEKGFKVCVLDADHPSPVQTIQFNPKFNMMASA 301
PD + SGS+DG I +W+ + + H S V ++ F+P ++AS
Sbjct: 251 PDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASG 302
Score = 67.0 bits (162), Expect = 3e-12
Identities = 64/265 (24%), Positives = 104/265 (39%), Gaps = 29/265 (10%)
Query: 5 DNVIRSYKVAK------LFRENTDKITSIDYSADGLLLISCSEDDQIVIYDCELGTNK-R 57
D IR + ++ ++D + S +S DG LL S S D I ++D ++ R
Sbjct: 220 DGTIRLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWDLRSSSSLLR 278
Query: 58 TVFSKKYGVDLIRFTHAKQAAIHASTKIDDTVRYLSLHDNKYIRYFPGHTKKVNSLCLSP 117
T+ V + F+ + S+ + L GH V+SL SP
Sbjct: 279 TLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSP 338
Query: 118 -IDDTFISGSYDKTVRLWDLRSPNCQGIMHVSGSRPIAAFDPEGLIFGVGVNSDTIKLYD 176
GS D T+RLWDLR+ + + +F P+G + G T++L+D
Sbjct: 339 DGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWD 398
Query: 177 VRSFDKGPFSNFKFAAEKECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGF 236
+ + S + T + FS DGK + ++ + IR +D
Sbjct: 399 LST-----GSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDL------------ 441
Query: 237 LNNKGCPLEASFTPDSKYVISGSTD 261
K SF+PD K + S S+D
Sbjct: 442 ---KTSLKSVSFSPDGKVLASKSSD 463
>gnl|CDD|197651 smart00320, WD40, WD40 repeats. Note that these repeats are
permuted with respect to the structural repeats (blades)
of the beta propeller domain.
Length = 40
Score = 48.8 bits (117), Expect = 3e-08
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 96 DNKYIRYFPGHTKKVNSLCLSPIDDTFISGSYDKTVRLWD 135
+ ++ GHT V S+ SP SGS D T++LWD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 37.3 bits (87), Expect = 4e-04
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 10 SYKVAKLFRENTDKITSIDYSADGLLLISCSEDDQIVIYD 49
S ++ K + +T +TS+ +S DG L S S+D I ++D
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 36.9 bits (86), Expect = 5e-04
Identities = 18/43 (41%), Positives = 27/43 (62%), Gaps = 3/43 (6%)
Query: 226 NGQCLQTLAGFLNNKGCPLEASFTPDSKYVISGSTDGRIHIWN 268
+G+ L+TL G + G +F+PD KY+ SGS DG I +W+
Sbjct: 1 SGELLKTLKG---HTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 48.1 bits (115), Expect = 4e-08
Identities = 18/38 (47%), Positives = 22/38 (57%)
Query: 98 KYIRYFPGHTKKVNSLCLSPIDDTFISGSYDKTVRLWD 135
K +R GHT V S+ SP + SGS D TVR+WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.6 bits (85), Expect = 6e-04
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 12 KVAKLFRENTDKITSIDYSADGLLLISCSEDDQIVIYD 49
K+ + + +T +TS+ +S DG LL S S+D + ++D
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 35.0 bits (81), Expect = 0.002
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 227 GQCLQTLAGFLNNKGCPLEASFTPDSKYVISGSTDGRIHIWN 268
G+ L+TL G + G +F+PD + SGS DG + +W+
Sbjct: 1 GKLLRTLKG---HTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 42.0 bits (98), Expect = 4e-04
Identities = 41/134 (30%), Positives = 69/134 (51%), Gaps = 8/134 (5%)
Query: 6 NVIRSYKVAKLFRENTDKITSIDYS-ADGLLLISCSEDDQIVIYDCELGTNKRTVFSKKY 64
+V RS V ++ +E+ ++ SIDYS AD LL S S+D + ++ G + T+ +K
Sbjct: 561 DVARSQLVTEM-KEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQGVSIGTIKTKA- 618
Query: 65 GVDLIRFTHAKQAAIHASTKIDDTVRYLSLHDNKY-IRYFPGHTKKVNSLCLSPIDD-TF 122
+ ++F ++ A D V Y L + K + GH+K V+ + +D T
Sbjct: 619 NICCVQFPSESGRSL-AFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRF--VDSSTL 675
Query: 123 ISGSYDKTVRLWDL 136
+S S D T++LWDL
Sbjct: 676 VSSSTDNTLKLWDL 689
Score = 31.6 bits (71), Expect = 0.75
Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 2/101 (1%)
Query: 81 ASTKIDDTVRYLSLHDNKYIRYFPGHTKKVNSLCLSPIDDTFI-SGSYDKTVRLWDLRSP 139
AS+ + V+ + ++ + H K+V S+ S D T + SGS D +V+LW +
Sbjct: 549 ASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKLWSINQG 608
Query: 140 NCQGIMHVSGSRPIAAFDPE-GLIFGVGVNSDTIKLYDVRS 179
G + + F E G G + YD+R+
Sbjct: 609 VSIGTIKTKANICCVQFPSESGRSLAFGSADHKVYYYDLRN 649
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 33.5 bits (76), Expect = 0.16
Identities = 52/225 (23%), Positives = 87/225 (38%), Gaps = 46/225 (20%)
Query: 102 YFPGHTKKVNSLCLSPIDDTFISGSYDKTVRLW------------DLRSPNCQGIMHVSG 149
Y H +NS+ + +T +S + + LW D++ N + + V
Sbjct: 167 YANAHPYHINSISFNSDKETLLSADDLR-INLWNLEIIDGSFNIVDIKPHNMEELTEVIT 225
Query: 150 SRPIAAFDPE-GLIFGVGVNSDTIKLYDVR--SFDKGPFSNFK---------FAAEKECD 197
S A F PE +F + IKL D+R + F+ F E
Sbjct: 226 S---AEFHPEMCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGVDVDFFEEIVSS 282
Query: 198 WTGIKFSADGKYILISTNGSIIRTFDAYNGQ-CLQT--LAGFLNNKGCPL---------- 244
+ KFS +G+YIL S + ++ +D + ++T + L ++ +
Sbjct: 283 ISDFKFSDNGRYIL-SRDYLTVKIWDVNMAKNPIKTIPMHCDLMDELNDVYENDAIFDKF 341
Query: 245 EASFTPDSKYVISGSTDGRIHIW-NAEKGFK---VCVLDADHPSP 285
E SF+ D K+V+SGS I+ GFK V AD +
Sbjct: 342 EISFSGDDKHVLSGSYSNNFGIYPTDSSGFKDVGHVVNLADGSAE 386
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 30.9 bits (71), Expect = 0.41
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 240 KGCPLEASFTPDSKYVISGSTDGRIHIWNAEKGFK 274
+ CP+ DS+YVI+G T IH W G+K
Sbjct: 58 EPCPVL--LYTDSQYVINGITKW-IHGWKK-NGWK 88
>gnl|CDD|241494 cd13340, PH-GRAM_MTMR5, Myotubularian (MTM) related 5 protein
(MTMR5) Pleckstrin Homology-Glucosyltransferases,
Rab-like GTPase activators and Myotubularins (PH-GRAM)
domain. MTMR5 (also called SBF1/SET binding factor 1)
is a catalytically inactive phosphatase that plays a
role as an adapter for the phosphatase myotubularin to
regulate myotubularintracellular location. It lacks
several amino acids in the dsPTPase catalytic pocket
which renders it catalytically inactive as a
phosphatase. MTMR5 is the most well-studied inactive
member of this family and has been implicated in
cellular growth control and oncogenic transformation.
MTMR5 and MTMR13 contain an N-terminal DENN domain, a
PH-GRAM domain, an inactive PTP domain, a SET
interaction domain, a coiled-coil domain, and a
C-terminal PH domain. Myotubularin-related proteins are
a subfamily of protein tyrosine phosphatases (PTPs) that
dephosphorylate D3-phosphorylated inositol lipids.
Mutations in this family cause the human neuromuscular
disorders myotubular myopathy and type 4B
Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs
5, 9-13) contain naturally occurring substitutions of
residues required for catalysis by PTP family enzymes.
Although these proteins are predicted to be
enzymatically inactive, they are thought to function as
antagonists of endogenous phosphatase activity or
interaction modules. Most MTMRs contain a N-terminal
PH-GRAM domain, a Rac-induced recruitment domain (RID)
domain, a PTP domain (which may be active or inactive),
a SET-interaction domain, and a C-terminal coiled-coil
region. In addition some members contain DENN domain
N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH
domains C-terminal to the coiled-coil region. The GRAM
domain, found in myotubularins, glucosyltransferases,
and other putative membrane-associated proteins, is part
of a larger motif with a pleckstrin homology (PH) domain
fold. The PH domain family possesses multiple functions
including the ability to bind phosphoinositides via its
beta1/beta2, beta3/beta4, and beta6/beta7 connecting
loops and to other proteins. However, no
phosphoinositide binding sites have been found for the
MTMRs to date.
Length = 185
Score = 31.0 bits (70), Expect = 0.52
Identities = 18/58 (31%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 7 VIRSYKVAKLFRENTDKITS-ID-YSADGLLLISCSEDDQIVIYDCELGTNKRTVFSK 62
V+RS+ VA L +E + + +D + +GL L SC+ + +D E+ ++ VF K
Sbjct: 93 VVRSFPVASLTKEKRISVQAQVDQFLQEGLQLRSCTFQLLKIAFDEEVASDSAEVFRK 150
>gnl|CDD|183262 PRK11657, dsbG, disulfide isomerase/thiol-disulfide oxidase;
Provisional.
Length = 251
Score = 30.7 bits (70), Expect = 0.85
Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 218 IIRTFDAYNGQCLQTLAGFLNNKGCPLEASFTPDSKYVISGS 259
II+TFDA G L+ A + G + TPD K+ ISG
Sbjct: 37 IIKTFDAPGG--LKGYAAKYQDMGVTIYL--TPDGKHAISGY 74
>gnl|CDD|151789 pfam11348, DUF3150, Protein of unknown function (DUF3150). This
bacterial family of proteins with unknown function
appears to be restricted to Proteobacteria.
Length = 257
Score = 30.7 bits (70), Expect = 0.94
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 11/63 (17%)
Query: 148 SGSRPIAAFDPEGLIFGVGVNSDTIKLYD---VRSFDKG---PFSNFKFAAEKECDWTGI 201
SG + ++A D G+G KL + D PFS K AE+ C G+
Sbjct: 16 SGRKKLSAED-----LGLGDKLPPEKLASLGSKKIIDPEALKPFSKLKSRAERLCLKVGV 70
Query: 202 KFS 204
+F
Sbjct: 71 RFL 73
>gnl|CDD|140297 PTZ00271, PTZ00271, hypoxanthine-guanine phosphoribosyltransferase;
Provisional.
Length = 211
Score = 28.8 bits (64), Expect = 2.8
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 16/84 (19%)
Query: 190 FAAEKEC------DWTGIKFSADGK-YILISTNGSIIRTFDAYNGQCLQTLAGFLNNKGC 242
+AA +C D+ K + + Y+L GS I T D LA FL ++G
Sbjct: 34 WAATAKCAKKIAEDYRSFKLTTENPLYLLCVLKGSFIFTAD---------LARFLADEGV 84
Query: 243 PLEASFTPDSKYVISGSTDGRIHI 266
P++ F S Y T G++ +
Sbjct: 85 PVKVEFICASSYGTGVETSGQVRM 108
>gnl|CDD|215384 PLN02724, PLN02724, Molybdenum cofactor sulfurase.
Length = 805
Score = 29.5 bits (66), Expect = 3.5
Identities = 9/41 (21%), Positives = 15/41 (36%), Gaps = 7/41 (17%)
Query: 108 KKVNSLCLSPIDDTFISGSYDKTVRLWDLRSPNCQGIMHVS 148
KKV +C I+ D +R+P C + +
Sbjct: 565 KKVPEMC-------LITTFIDLESGKLVVRAPRCDHKLEIP 598
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 28.5 bits (64), Expect = 4.7
Identities = 9/58 (15%), Positives = 18/58 (31%), Gaps = 4/58 (6%)
Query: 215 NGSIIRTFDAYNGQCLQTLAGFLNNKGCPLEASFTPDSKYVISGSTDGRIHIWNAEKG 272
++ DA G+ L + G + D + + G + +A G
Sbjct: 1 ADGVVAALDAATGKVLWRVDLGGTALGGGV----AVDGGRLYVATGKGELVALDAATG 54
>gnl|CDD|163615 cd00839, MPP_PAPs, purple acid phosphatases of the
metallophosphatase superfamily, metallophosphatase
domain. Purple acid phosphatases (PAPs) belong to a
diverse family of binuclear metallohydrolases that have
been identified and characterized in plants, animals,
and fungi. PAPs contain a binuclear metal center and
their characteristic pink or purple color derives from a
charge-transfer transition between a tyrosine residue
and a chromophoric ferric ion within the binuclear
center. PAPs catalyze the hydrolysis of a wide range of
activated phosphoric acid mono- and di-esters and
anhydrides. PAPs are distinguished from the other
phosphatases by their insensitivity to L-(+) tartrate
inhibition and are therefore also known as tartrate
resistant acid phosphatases (TRAPs). While only a few
copies of PAP-like genes are present in mammalian and
fungal genomes, multiple copies are present in plant
genomes. PAPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 294
Score = 28.4 bits (64), Expect = 4.7
Identities = 13/34 (38%), Positives = 14/34 (41%), Gaps = 6/34 (17%)
Query: 39 CSEDDQIVIYDCELGTNKRTVFSK---KYGVDLI 69
CS D DC G R KYGVDL+
Sbjct: 167 CSNTDH---DDCIEGEKMRAALEDLFYKYGVDLV 197
>gnl|CDD|226855 COG4447, COG4447, Uncharacterized protein related to plant
photosystem II stability/assembly factor [General
function prediction only].
Length = 339
Score = 28.7 bits (64), Expect = 5.0
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 201 IKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAG 235
I SAD Y+ + GS T+ A GQ + G
Sbjct: 176 IARSADNGYVAVGARGSFFSTWGA--GQTVWLPHG 208
>gnl|CDD|236469 PRK09331, PRK09331, Sep-tRNA:Cys-tRNA synthetase; Provisional.
Length = 387
Score = 28.0 bits (63), Expect = 7.3
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 65 GVDLIRFTH----AKQAAIHASTKIDDTV 89
G+D R TH K A +H+ K D V
Sbjct: 77 GMDEARVTHGAREGKFAVMHSLCKKGDYV 105
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a
homologue of the Fer4_NifH superfamily. Like the other
members of the superfamily, MRP contains a ATP-binding
domain at the N-termini. It is found in bacteria as a
membrane-spanning protein and functions as a Na+/H+
antiporter.
Length = 169
Score = 27.4 bits (62), Expect = 7.7
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 269 AEKGFKVCVLDAD 281
A+ G+KV +LDAD
Sbjct: 25 AKLGYKVGLLDAD 37
>gnl|CDD|222638 pfam14269, Arylsulfotran_2, Arylsulfotransferase (ASST).
Length = 301
Score = 27.7 bits (62), Expect = 7.9
Identities = 15/78 (19%), Positives = 26/78 (33%), Gaps = 7/78 (8%)
Query: 24 ITSIDYSADGLLLISCSEDDQIVIYDCELGTNKRTVFSKKYG----VDLIRFTHAKQAAI 79
+ S++ DG LIS + + G + G F++ A
Sbjct: 147 LNSVEKFGDGDYLISLRYYCSLFLIRPSNGKVMWQLNGPTGGDFELGPNSTFSYQHDARF 206
Query: 80 HASTKIDDTVRYLSLHDN 97
T +D +SL +N
Sbjct: 207 VNQT--EDDQV-ISLFNN 221
>gnl|CDD|227444 COG5113, UFD2, Ubiquitin fusion degradation protein 2
[Posttranslational modification, protein turnover,
chaperones].
Length = 929
Score = 28.0 bits (62), Expect = 8.0
Identities = 20/113 (17%), Positives = 36/113 (31%), Gaps = 15/113 (13%)
Query: 148 SGSRPIAAFDPEGLIFG--VGVNS-DTIKLYDVRSFDKGPFS----NFKFAAE------- 193
+ P F I G + NS D I L + + FS + KF +
Sbjct: 21 ADMDPYELFKEAECIRGSYLTNNSSDNILLTLLPRYKNNTFSYLQESAKFLIQTIKRIVK 80
Query: 194 -KECDWTGIKFSADGKYILISTNGSIIRTFDAYNGQCLQTLAGFLNNKGCPLE 245
E + A + + GS+ + +N + + + G P+
Sbjct: 81 NPEMAGSAHSPVALIPLLTNTYGGSVFDVMECFNSEKISEIEGMARKMLLPMI 133
>gnl|CDD|217275 pfam02897, Peptidase_S9_N, Prolyl oligopeptidase, N-terminal
beta-propeller domain. This unusual 7-stranded
beta-propeller domain protects the catalytic triad of
prolyl oligopeptidase (see pfam00326), excluding larger
peptides and proteins from proteolysis in the cytosol.
Length = 412
Score = 28.0 bits (63), Expect = 8.4
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 198 WTGIKFSADGKYILIS----TNGSIIRTFDAYNGQCLQT 232
+ G + S DGKY+ IS T+ + + D +
Sbjct: 229 YLGAERSDDGKYLFISSASGTDVNELYVLDLAQEKDGPL 267
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 27.6 bits (62), Expect = 9.7
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 9 RSYKVAKLFRENTDKITSIDYSADGL----LLISCSEDDQIVIYD 49
+ K+ K F+E+ K + YS D + LL SE + YD
Sbjct: 87 GTVKIFKNFKESVTKSIKLPYSVDKIFGGALLGVKSE-SFVSFYD 130
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
0.321 0.137 0.423
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,895,142
Number of extensions: 1592603
Number of successful extensions: 1320
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1261
Number of HSP's successfully gapped: 42
Length of query: 335
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 238
Effective length of database: 6,635,264
Effective search space: 1579192832
Effective search space used: 1579192832
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 (21.9 bits)
S2: 59 (26.5 bits)