RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8285
(507 letters)
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 125 bits (313), Expect = 4e-31
Identities = 91/379 (24%), Positives = 157/379 (41%), Gaps = 19/379 (5%)
Query: 85 SLCSHYLLQQANDETISYREQKKRRHLSFLLHGFEIDRKKVLNQSKRTVSPTQFLRTLGK 144
S LL ++D TI + L L G V + + L
Sbjct: 74 SPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDS--SVSKLALSSPDGNSILLASSS 131
Query: 145 LPRKVKA---KPERILEAPSIINDFYTSGLDW---GYHDTLAVALDTSVYTWNTKTNKTQ 198
L VK L + + L + G +LD ++ W+ +T K
Sbjct: 132 LDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPL 191
Query: 199 LLVEYPTYDNAYISCVAWKPRTTDLAVTNTCTEYIDLWHEQEERLIQ-KLRTHMHQVI-A 256
+ T +S +A+ P L + + I LW +L++ L H V+ +
Sbjct: 192 STLAGHT---DPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSS 248
Query: 257 MCWNGNLLSCGTIGGNILHYDVRTHSDYPTAITREGDVVCGLKWSPNGRYLASGSN-NTV 315
+G+LL+ G+ G I +D+R+ S ++ V + +SP+G+ LASGS+ TV
Sbjct: 249 FSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTV 308
Query: 316 KIWDFRQLDAKRPQVNNQCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKC 375
++WD + + H V ++++ P L++ G D T+RLW+ GK
Sbjct: 309 RLWDLETGK-LLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSD--DGTIRLWDLRTGKPLK 365
Query: 376 HVKTDSQVTSILWSEQYRELVTSHGKQDCSLKMWEYPRLHLIEELKIHQERILSAVLSPD 435
++ S V S+ +S V S G D ++++W+ L+ L H R+ S SPD
Sbjct: 366 TLEGHSNVLSVSFSPD--GRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPD 423
Query: 436 QTCVAAASADETISIWNCF 454
+A+ S+D TI +W+
Sbjct: 424 GKSLASGSSDNTIRLWDLK 442
Score = 85.9 bits (211), Expect = 6e-18
Identities = 78/396 (19%), Positives = 150/396 (37%), Gaps = 24/396 (6%)
Query: 100 ISYREQKKRRHLSFLLHGFEIDRKKVLNQSKRTVSPTQFLRTLGKLPRKVKAKPERILEA 159
S + K + L G ++ +L+ L +
Sbjct: 5 SSTSSENKSKLLKKSELGPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSSLLLRGH 64
Query: 160 PSIINDFYTSGLDWGYHDTLAVALDTSVYTWNTKTNKTQLLVEYPTYDNAYISCVAWKPR 219
I S L+ + D ++ W+ + + +D++ P
Sbjct: 65 EDSITSIAFSPDG---ELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPD 121
Query: 220 TTDLAVTNTCTE-YIDLWHEQEE-RLIQKLRTHMHQVIAMCWNGN---LLSCGTIGGNIL 274
+ + ++ + + LW +LI+ L H V ++ ++ + L S ++ G I
Sbjct: 122 GNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIK 181
Query: 275 HYDVRTHSDYPTAITREGDVVCGLKWSPNGRYLAS--GSNNTVKIWDFRQLDAKRPQVNN 332
+D+RT T V L +SP+G L + S+ T+++WD R ++
Sbjct: 182 LWDLRTGKPLSTLAGHTDPVSS-LAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLS- 239
Query: 333 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN--SMNGKEKCHVKTDSQVTSILWSE 390
H +V ++ + +LLA+G D T+RLW+ S + + S V S+ +S
Sbjct: 240 -GHSDSV--VSSFSPDGSLLASGS--SDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSP 294
Query: 391 QYRELVTSHGKQDCSLKMW--EYPRLHLIEELKIHQERILSAVLSPD-QTCVAAASADET 447
+ L + G D ++++W E +L LK H+ + S SPD V+ S D T
Sbjct: 295 DGKLLAS--GSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGT 352
Query: 448 ISIWNCFPRDKKRKARQVGSGSSLEFAILKQPVSLT 483
I +W+ + + S+ F+ + VS
Sbjct: 353 IRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSG 388
Score = 67.8 bits (164), Expect = 4e-12
Identities = 62/349 (17%), Positives = 125/349 (35%), Gaps = 36/349 (10%)
Query: 5 HLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVKTDSQ--VTSILWSEQY 62
H S+V +A + + D TV+LW+ + VTS+ +S
Sbjct: 108 HDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDG 167
Query: 63 RESSRSKMVNTDRYVVDRSSYDSLCSH------------------YLLQQANDETISYRE 104
+ + ++ + D + L + + ++D TI +
Sbjct: 168 KLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD 227
Query: 105 QKKRRHLSFLLHGFEIDRKKVLNQSKRTVSPTQFLRTLGKLPRKVK---AKPERILEAPS 161
+ L L G + + SP L G ++ + L
Sbjct: 228 LSTGKLLRSTLSGHS-------DSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTL 280
Query: 162 IINDFYTSGLDW-GYHDTLAVA-LDTSVYTWNTKTNKTQLLVEYPTYDNAYISCVAWKPR 219
+ + + LA D +V W+ +T K + ++ +S +++ P
Sbjct: 281 SGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEGP-VSSLSFSPD 339
Query: 220 TTDLAVTNTCTEYIDLWHEQEERLIQKLRTH-MHQVIAMCWNGNLLSCGTIGGNILHYDV 278
+ L + I LW + + ++ L H ++ +G ++S G+ G + +D+
Sbjct: 340 GSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWDL 399
Query: 279 RTHSDYPTAITREGDVVCGLKWSPNGRYLASGS-NNTVKIWDFRQLDAK 326
T S + V L +SP+G+ LASGS +NT+++WD +
Sbjct: 400 STGSLLRN-LDGHTSRVTSLDFSPDGKSLASGSSDNTIRLWDLKTSLKS 447
>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 = 102 bits (255), Expect = 4e-24
Identities = 70/281 (24%), Positives = 123/281 (43%), Gaps = 33/281 (11%)
Query: 184 DTSVYTWNTKTNKTQLLVEYPTYDNAYISCVAWKPRTTDLAVT---NTCTEYIDLWHEQE 240
D ++ W+ +T + ++ T ++ A LA T LW +
Sbjct: 30 DGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTY---LASGSSDKTIR----LWDLET 82
Query: 241 ERLIQKLRTHMHQVIAMCW--NGNLLSCGTIGGNILHYDVRTHSDYPTAITREG--DVVC 296
++ L H V ++ + +G +LS + I +DV T T G D V
Sbjct: 83 GECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVET---GKCLTTLRGHTDWVN 139
Query: 297 GLKWSPNGRYLASGS-NNTVKIWDFRQLDAKRPQVNNQCHLSAVKAIAWCPWEPTLLATG 355
+ +SP+G ++AS S + T+K+WD R + H V ++A+ P LL++
Sbjct: 140 SVAFSPDGTFVASSSQDGTIKLWDLRTG---KCVATLTGHTGEVNSVAFSPDGEKLLSSS 196
Query: 356 GGICDQTVRLWNSMNGKEKC----HVKTDSQVTSILWSEQYRELVTSHGKQDCSLKMWEY 411
D T++LW+ GK H ++ V S+ +S L+ S G +D ++++W+
Sbjct: 197 S---DGTIKLWDLSTGKCLGTLRGH---ENGVNSVAFSPD-GYLLAS-GSEDGTIRVWDL 248
Query: 412 PRLHLIEELKIHQERILSAVLSPDQTCVAAASADETISIWN 452
++ L H + S SPD +A+ SAD TI IW+
Sbjct: 249 RTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 89.7 bits (223), Expect = 7e-20
Identities = 59/219 (26%), Positives = 102/219 (46%), Gaps = 23/219 (10%)
Query: 243 LIQKLRTHMHQVIAMCWN--GNLLSCGTIGGNILHYDVRTHSDYPTAITREG--DVVCGL 298
L + L+ H V + ++ G LL+ G+ G I +D+ T T +G V +
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELL---RTLKGHTGPVRDV 57
Query: 299 KWSPNGRYLASGS-NNTVKIWDFRQLDAKRPQVNNQCHLSAVKAIAWCPWEPTLLATGGG 357
S +G YLASGS + T+++WD + R H S V ++A+ P + +L++
Sbjct: 58 AASADGTYLASGSSDKTIRLWDLETGECVRTLT---GHTSYVSSVAFSP-DGRILSSSSR 113
Query: 358 ICDQTVRLWNSMNGKEK----CHVKTDSQVTSILWSEQYRELVTSHGKQDCSLKMWEYPR 413
D+T+++W+ GK H V S+ +S V S QD ++K+W+
Sbjct: 114 --DKTIKVWDVETGKCLTTLRGH---TDWVNSVAFS-PDGTFVAS-SSQDGTIKLWDLRT 166
Query: 414 LHLIEELKIHQERILSAVLSPDQTCVAAASADETISIWN 452
+ L H + S SPD + ++S+D TI +W+
Sbjct: 167 GKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWD 205
Score = 36.2 bits (84), Expect = 0.026
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 416 LIEELKIHQERILSAVLSPDQTCVAAASADETISIWNCFPRDKKR 460
L LK H + SPD +A S D TI +W+ + R
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLR 45
Score = 36.2 bits (84), Expect = 0.031
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 5 HLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVKT-DSQVTSILWS 59
H V+ +A L + D+T+RLW+ G+ + S V+S+ +S
Sbjct: 50 HTGPVRDVAASADGTYLASGS---SDKTIRLWDLETGECVRTLTGHTSYVSSVAFS 102
Score = 33.1 bits (76), Expect = 0.28
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 4/57 (7%)
Query: 5 HLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVK-TDSQVTSILWSE 60
H + V ++A+ P L G D T+R+W+ G+ + + VTS+ WS
Sbjct: 218 HENGVNSVAFSPD--GYLLASGSE-DGTIRVWDLRTGECVQTLSGHTNSVTSLAWSP 271
Score = 33.1 bits (76), Expect = 0.29
Identities = 17/62 (27%), Positives = 30/62 (48%), Gaps = 10/62 (16%)
Query: 3 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVKT----DSQVTSILW 58
+ H V ++A+ P + T +A+ D T++LW+ GK V T +V S+ +
Sbjct: 132 RGHTDWVNSVAFSP-DGTFVASSSQ--DGTIKLWDLRTGKC---VATLTGHTGEVNSVAF 185
Query: 59 SE 60
S
Sbjct: 186 SP 187
Score = 31.9 bits (73), Expect = 0.62
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 10/59 (16%)
Query: 5 HLSAVKAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKC----HVKTDSQVTSILWS 59
H V ++A+ P LL++ D T++LW+ GK H ++ V S+ +S
Sbjct: 176 HTGEVNSVAFSPDGEKLLSSSS---DGTIKLWDLSTGKCLGTLRGH---ENGVNSVAFS 228
Score = 29.2 bits (66), Expect = 4.8
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 3 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN 37
H ++V ++AW P + LA+G D T+R+W+
Sbjct: 258 SGHTNSVTSLAWSP-DGKRLASGSA--DGTIRIWD 289
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 40.0 bits (94), Expect = 6e-05
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 293 DVVCGLKWSPNGRYLASGS-NNTVKIWD 319
V + +SP+G LASGS + TV++WD
Sbjct: 12 GPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 35.8 bits (83), Expect = 0.002
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 416 LIEELKIHQERILSAVLSPDQTCVAAASADETISIWN 452
L+ LK H + S SPD +A+ S D T+ +W+
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 32.7 bits (75), Expect = 0.025
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 3 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN 37
+ H V ++A+ P LLA+G D TVR+W+
Sbjct: 8 KGHTGPVTSVAFSPDG-NLLASGSD--DGTVRVWD 39
Score = 32.7 bits (75), Expect = 0.025
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 333 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN 367
+ H V ++A+ P LLA+G D TVR+W+
Sbjct: 8 KGHTGPVTSVAFSPDG-NLLASGSD--DGTVRVWD 39
>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 = 38.8 bits (91), Expect = 2e-04
Identities = 14/28 (50%), Positives = 21/28 (75%), Gaps = 1/28 (3%)
Query: 293 DVVCGLKWSPNGRYLASGS-NNTVKIWD 319
V + +SP+G+YLASGS + T+K+WD
Sbjct: 13 GPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 36.9 bits (86), Expect = 7e-04
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 415 HLIEELKIHQERILSAVLSPDQTCVAAASADETISIWN 452
L++ LK H + S SPD +A+ S D TI +W+
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 31.9 bits (73), Expect = 0.047
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 3 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN 37
+ H V ++A+ P LA+G D T++LW+
Sbjct: 9 KGHTGPVTSVAFSPDG-KYLASGSD--DGTIKLWD 40
Score = 31.9 bits (73), Expect = 0.047
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 333 QCHLSAVKAIAWCPWEPTLLATGGGICDQTVRLWN 367
+ H V ++A+ P LA+G D T++LW+
Sbjct: 9 KGHTGPVTSVAFSPDG-KYLASGSD--DGTIKLWD 40
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 38.5 bits (89), Expect = 0.007
Identities = 44/176 (25%), Positives = 79/176 (44%), Gaps = 18/176 (10%)
Query: 284 YPTAITREGDVVCGLKWSPNGRYLASGSN--NTVKIWDFRQLDAKRPQVNNQC--HLSAV 339
YP + G+ W+ + + SN V++WD R Q+ + H V
Sbjct: 524 YPVVELASRSKLSGICWNSYIKSQVASSNFEGVVQVWD-----VARSQLVTEMKEHEKRV 578
Query: 340 KAIAWCPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVKTDSQVTSILW-SEQYRELVTS 398
+I + +PTLLA+G D +V+LW+ G +KT + + + + SE R L +
Sbjct: 579 WSIDYSSADPTLLASGSD--DGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSL--A 634
Query: 399 HGKQDCSLKMWEY--PRLHLIEELKIHQERILSAVLSPDQTCVAAASADETISIWN 452
G D + ++ P+L L I + +S V D + + ++S D T+ +W+
Sbjct: 635 FGSADHKVYYYDLRNPKLPLCT--MIGHSKTVSYVRFVDSSTLVSSSTDNTLKLWD 688
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 35.8 bits (82), Expect = 0.047
Identities = 25/84 (29%), Positives = 33/84 (39%), Gaps = 17/84 (20%)
Query: 260 NGNLLSCGTIGGNILHYDVRTHS--DYPT---AITREGDVVCGL----------KWSPNG 304
N+ + G I D+R + D +T +G V K+S NG
Sbjct: 233 MCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGVDVDFFEEIVSSISDFKFSDNG 292
Query: 305 RYLASGSNNTVKIWDFRQLDAKRP 328
RY+ S TVKIWD AK P
Sbjct: 293 RYILSRDYLTVKIWDVNM--AKNP 314
>gnl|CDD|216208 pfam00941, FAD_binding_5, FAD binding domain in molybdopterin
dehydrogenase.
Length = 171
Score = 32.1 bits (74), Expect = 0.40
Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 224 AVTNTCTEYIDLWHEQEERLIQKLRTHMHQVIAMCWNGNLLSCGTIGGNILHYDVRTHSD 283
AVT T + ID + L + + IA + + + TIGGNI + SD
Sbjct: 71 AVTLT--DLID--SPLVAEVFPALAEALRK-IA---SPQIRNVATIGGNIANAS--PISD 120
Query: 284 YPTA 287
P A
Sbjct: 121 LPPA 124
>gnl|CDD|149648 pfam08662, eIF2A, Eukaryotic translation initiation factor eIF2A.
This is a family of eukaryotic translation initiation
factors.
Length = 194
Score = 30.3 bits (69), Expect = 1.7
Identities = 30/125 (24%), Positives = 44/125 (35%), Gaps = 23/125 (18%)
Query: 211 ISCVAWKPRTTDLAVTNTCTEY----IDLWHEQEERLIQKLRTHMHQVIAMCWNGNLLSC 266
I AW P + AV Y I + + +I L I G L+
Sbjct: 62 IHDFAWSPNGKEFAV---IYGYMPAKITFFDLKGN-VIHSLGEQPRNTIFWSPFGRLVLL 117
Query: 267 GTIG---GNILHYDVRTHSDYPTAITREGD-VVCGLKWSPNGRYLASGS-------NNTV 315
G G I +DV+ A + C +WSP+GRY + + +N
Sbjct: 118 AGFGNLAGQIEFWDVKNKKKI--ATAEASNATDC--EWSPDGRYFLTATTSPRLRVDNGF 173
Query: 316 KIWDF 320
KIW +
Sbjct: 174 KIWHY 178
>gnl|CDD|180426 PRK06148, PRK06148, hypothetical protein; Provisional.
Length = 1013
Score = 30.8 bits (70), Expect = 2.4
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 171 LDWGYHDTLAVALDTSVYTWNTKTNKTQ 198
LD YH T +D S Y +N K K +
Sbjct: 712 LDHAYHGTTTELIDLSPYKFNRKGGKGR 739
>gnl|CDD|240577 cd12950, RRP7_Rrp7p, RRP7 domain ribosomal RNA-processing protein 7
(Rrp7p) and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C
gene from Saccharomyces cerevisiae. It is an essential
yeast protein involved in pre-rRNA processing and
ribosome assembly. Rrp7p contains an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 128
Score = 28.8 bits (65), Expect = 3.4
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 103 REQKKRRHLSFLLHGFEIDRKKV 125
RE+KK + LL FE D+++V
Sbjct: 100 REKKKEE-QADLLKKFEEDKERV 121
>gnl|CDD|240576 cd12932, RRP7_like, RRP7 domain ribosomal RNA-processing protein 7
(Rrp7p), ribosomal RNA-processing protein 7 homolog A
(Rrp7A), and similar proteins. This CD corresponds to
the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by
YCL031C gene from Saccharomyces cerevisiae. It is an
essential yeast protein involved in pre-rRNA processing
and ribosome assembly, and is speculated to be required
for correct assembly of rpS27 into the pre-ribosomal
particle. Rrp7A, also termed gastric cancer antigen
Zg14, is the Rrp7p homolog mainly found in Metazoans.
The cellular function of Rrp7A remains unclear
currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain), and a
C-terminal RRP7 domain.
Length = 118
Score = 28.4 bits (64), Expect = 4.4
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 102 YREQ---KKRRHLSFLLHGFEIDRKKV 125
YR Q KK+ L+ L FE D+K++
Sbjct: 92 YRFQIREKKKEELAELRKKFEEDKKRI 118
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 29.0 bits (65), Expect = 6.1
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 388 WSEQY-RELVTSHGKQDCSLKMWEYPRLHLIEELKIHQERILSAVLSPD 435
+ +Y RE V D +L+ +Y ++ L Q I AV
Sbjct: 190 SAWEYAREYVEEKLGGDEALQYSDYAQIAL-----GQQRYIDYAVRHAH 233
>gnl|CDD|223257 COG0179, MhpD, 2-keto-4-pentenoate
hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
(catechol pathway) [Secondary metabolites biosynthesis,
transport, and catabolism].
Length = 266
Score = 28.8 bits (65), Expect = 6.1
Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 7/63 (11%)
Query: 345 CPWEPTLLATGGGICDQTVRLWNSMNGKEKCHVKTDSQVTSILWSEQYRELVTSHGKQDC 404
P P ++ Q + L +NG+ + T + SI EL+ ++ +
Sbjct: 171 APVGPWIVTKDEISDPQNLPLSLRVNGEVRQRGNTSDMIFSI------PELI-AYLSRFM 223
Query: 405 SLK 407
+L+
Sbjct: 224 TLE 226
>gnl|CDD|233424 TIGR01466, cobJ_cbiH, precorrin-3B C17-methyltransferase. This
model represents precorrin-3B C17-methyltransferase, one
of two methyltransferases commonly referred to as
precorrin-3 methylase (the other is precorrin-4
C11-methyltransferase, EC 2.1.1.133). This enzyme
participates in the pathway toward the biosynthesis of
cobalamin and related products. Members of this family
may appear as fusion proteins with other enzymes of
cobalamin biosynthesis [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 239
Score = 28.4 bits (64), Expect = 6.8
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 6/38 (15%)
Query: 428 LSAVLSP----DQTCVAAASADETISIWNCFPRDKKRK 461
LS +L+P ++ AAA AD I+I+N PR K+R
Sbjct: 131 LSDLLTPWPEIEKRLRAAAEADFVIAIYN--PRSKRRP 166
>gnl|CDD|221857 pfam12923, RRP7, Ribosomal RNA-processing protein 7 (RRP7). RRP7
is an essential protein in yeast that is involved in
pre-rRNA processing and ribosome assembly. It is
speculated to be required for correct assembly of rpS27
into the pre-ribosomal particle.
Length = 131
Score = 27.6 bits (62), Expect = 7.4
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 102 YREQ---KKRRHLSFLLHGFEIDRKKV--LNQSKR 131
YR Q KK+ L+ L FE D+K++ L +++
Sbjct: 93 YRFQIREKKKEELAELRKKFEEDKKRIEQLKAARK 127
>gnl|CDD|187833 cd09702, Csx1_III-U, CRISPR/Cas system-associated protein Csx1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Protein of this family often fused to HTH domain; Some
proteins could have an additional fusion with
RecB-family nuclease domain; Core domain appears to have
a Rossmann-like fold; loosely associated with CRISPR/Cas
systems; also known as TIGR02710 family.
Length = 378
Score = 28.7 bits (64), Expect = 7.6
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 5/71 (7%)
Query: 54 TSILWSEQYRESSRSKMVNTD---RYVVDRSSYDSLC--SHYLLQQANDETISYREQKKR 108
+ Y ES+R+ + D ++ +++YD L L Q+ E + +
Sbjct: 287 DDDINPAGYPESTRAALALRDGKKSHLALKNAYDLLECEGDDLAQRLFGEDNRLLDLLQI 346
Query: 109 RHLSFLLHGFE 119
R+ S L HGF
Sbjct: 347 RNHSILAHGFR 357
>gnl|CDD|238160 cd00257, Fascin, Fascin-like domain; members include
actin-bundling/crosslinking proteins facsin,
histoactophilin and singed; identified in sea urchin,
Drosophila, Xenopus, rodents, and humans; The
fascin-like domain adopts a beta-trefoil topology and
contains an internal threefold repeat; the fascin
subgroup contains four copies of the domain;
Structurally similar to fibroblast growth factor (FGF).
Length = 119
Score = 27.6 bits (62), Expect = 7.6
Identities = 19/84 (22%), Positives = 31/84 (36%), Gaps = 13/84 (15%)
Query: 234 DLWH-EQEERLIQKLRTHMHQVIAMCWNGNLLSCGTIGGNILHYDVRTHSDYPTAITREG 292
+ + E + LR+H +G LS + GG L + +G
Sbjct: 34 ETFTLEFDNTGKYALRSH---------DGKYLSADSDGGVQLEGHPNADCRFTLEFHGDG 84
Query: 293 DVVCGLKWSPNGRYLASGSNNTVK 316
L+ + NGRYL + T+K
Sbjct: 85 KWA--LR-AENGRYLGGDGSGTLK 105
>gnl|CDD|173651 cd05095, PTKc_DDR2, Catalytic domain of the Protein Tyrosine
Kinase, Discoidin Domain Receptor 2. Protein Tyrosine
Kinase (PTK) family; mammalian Discoidin Domain Receptor
2 (DDR2) and homologs; catalytic (c) domain. The PTKc
family is part of a larger superfamily that includes the
catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. DDR2 is a
member of the DDR subfamily, which are receptor tyr
kinases (RTKs) containing an extracellular discoidin
homology domain, a transmembrane segment, an extended
juxtamembrane region, and an intracellular catalytic
domain. The binding of the ligand, collagen, to DDRs
results in a slow but sustained receptor activation.
DDR2 binds mostly to fibrillar collagens. More recently,
it has been reported to also bind collagen X. DDR2 is
widely expressed in many tissues with the highest levels
found in skeletal muscle, skin, kidney and lung. It is
important in cell proliferation and development. Mice,
with a deletion of DDR2, suffer from dwarfism and
delayed healing of epidermal wounds. DDR2 also
contributes to collagen (type I) regulation by
inhibiting fibrillogenesis and altering the morphology
of collagen fibers. It is also expressed in immature
dendritic cells (DCs), where it plays a role in DC
activation and function.
Length = 296
Score = 28.3 bits (63), Expect = 9.2
Identities = 31/102 (30%), Positives = 38/102 (37%), Gaps = 18/102 (17%)
Query: 310 GSNNTVKIWDF---RQL---DAKRPQVNNQCHLSAVKAIAWCPWEPTLLA---TGGGICD 360
G N T+KI DF R L D R Q AV I W WE LL T +
Sbjct: 164 GKNYTIKIADFGMSRNLYSGDYYRIQGR------AVLPIRWMSWESILLGKFTTASDVWA 217
Query: 361 QTVRLWNSMNGKEKCHVKTDSQVTSILWSEQYRELVTSHGKQ 402
V LW + C + SQ++ E E G+Q
Sbjct: 218 FGVTLWEILT---LCKEQPYSQLSDEQVIENTGEFFRDQGRQ 256
>gnl|CDD|148235 pfam06504, RepC, Replication protein C (RepC). This family
consists of several bacterial replication protein C
(RepC) sequences.
Length = 283
Score = 28.3 bits (63), Expect = 9.3
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 80 RSSYDSLCSHYLLQQANDETISYREQKKRRHLSFL 114
R D+LC + +AN E + R Q R+ L L
Sbjct: 225 RVELDTLCGYVWPDEANGEAMKKRRQTARKALPEL 259
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
0.318 0.131 0.414
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: 24,699,703
Number of extensions: 2269047
Number of successful extensions: 1762
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1696
Number of HSP's successfully gapped: 43
Length of query: 507
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 406
Effective length of database: 6,457,848
Effective search space: 2621886288
Effective search space used: 2621886288
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 (21.8 bits)
S2: 61 (27.3 bits)