RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy467
(845 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 = 159 bits (403), Expect = 2e-43
Identities = 61/165 (36%), Positives = 88/165 (53%), Gaps = 1/165 (0%)
Query: 4 KVEKAEDFMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVES 63
E H + V+ +A G++L++ DK + +W + C+ +L GH+ V S
Sbjct: 82 TGECVRTLTGHTSYVSSVAF-SPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNS 140
Query: 64 VQFGNGEETLSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSF 123
V F +++ Q G+IK+W+L TL GH + SV F P G+ L S S D
Sbjct: 141 VAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGT 200
Query: 124 IKLWDLRRKGCIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI 168
IKLWDL C+ T RGH +NS+ FSPDG +ASG EDG +R+
Sbjct: 201 IKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRV 245
Score = 151 bits (383), Expect = 8e-41
Identities = 61/156 (39%), Positives = 87/156 (55%), Gaps = 1/156 (0%)
Query: 13 AHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESVQFGNGEET 72
H VN +A G +A+ D + LW L C+ +L+GH+ V SV F E
Sbjct: 133 GHTDWVNSVAFSP-DGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSPDGEK 191
Query: 73 LSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLRRK 132
L + G+IK+W+L+ TL GH++ + SV F P G L SGS D I++WDLR
Sbjct: 192 LLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDLRTG 251
Query: 133 GCIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI 168
C+ T GH+ S+ S+ +SPDG+ +ASG DG +RI
Sbjct: 252 ECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRI 287
Score = 144 bits (366), Expect = 1e-38
Identities = 55/141 (39%), Positives = 80/141 (56%)
Query: 28 GQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESVQFGNGEETLSAGCQSGSIKIWNL 87
G LA+G DK + LW L C+ +L+GH++ V SV F LS+ + +IK+W++
Sbjct: 63 GTYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDV 122
Query: 88 AVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLRRKGCIYTYRGHSKSINS 147
TL GH + SV F P G ++ S S D IKLWDLR C+ T GH+ +NS
Sbjct: 123 ETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNS 182
Query: 148 IRFSPDGQWIASGGEDGVVRI 168
+ FSPDG+ + S DG +++
Sbjct: 183 VAFSPDGEKLLSSSSDGTIKL 203
Score = 142 bits (361), Expect = 8e-38
Identities = 58/158 (36%), Positives = 86/158 (54%), Gaps = 1/158 (0%)
Query: 11 FMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESVQFGNGE 70
H V C+A G++LATG D + +W L + +L GH+ PV V
Sbjct: 5 LKGHTGGVTCVAFSP-DGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADG 63
Query: 71 ETLSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLR 130
L++G +I++W+L RTL GH S ++SV F P G L S S D IK+WD+
Sbjct: 64 TYLASGSSDKTIRLWDLETGECVRTLTGHTSYVSSVAFSPDGRILSSSSRDKTIKVWDVE 123
Query: 131 RKGCIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI 168
C+ T RGH+ +NS+ FSPDG ++AS +DG +++
Sbjct: 124 TGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKL 161
Score = 105 bits (263), Expect = 7e-25
Identities = 64/259 (24%), Positives = 95/259 (36%), Gaps = 61/259 (23%)
Query: 94 RTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLRRKGCIYTYRGHSKSINSIRFSPD 153
RTL GH +T V F P G L +GS D IK+WDL + T +GH+ + + S D
Sbjct: 3 RTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASAD 62
Query: 154 GQWIASGGEDGVVRIGASFHLTNTSIHVVDLSLVHPLGT--PPPQYTSSVPFSHNTSLRK 211
G ++ASG D +R+ DL + T Y SSV FS + +
Sbjct: 63 GTYLASGSSDKTIRL-------------WDLETGECVRTLTGHTSYVSSVAFSPDGRI-- 107
Query: 212 SFTKGRPGGTKAKIDVTRIEENAESEDQAGEEELFATIANPCDYSAIFQPHRSLNRSGTC 271
+ T K+ + C + + H
Sbjct: 108 -LSSSSRDKT-IKV--------------------WDVETGKCLTT--LRGH---TDWVNS 140
Query: 272 VPVSVSRTSLSILPQSPMLCFILTTSSSADRTVNFWDLEKFSLVSTTEKNSSTIRRLTFS 331
V S T ++ SSS D T+ WDL V+T ++ + + FS
Sbjct: 141 VAFSPDGTFVA--------------SSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFS 186
Query: 332 EGGECLL--GGDTEGLKVY 348
GE LL D +K++
Sbjct: 187 PDGEKLLSSSSDGT-IKLW 204
Score = 102 bits (256), Expect = 6e-24
Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 1/118 (0%)
Query: 11 FMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESVQFGNGE 70
H VN +A G+ L + D + LW L C+ +L GH V SV F
Sbjct: 173 LTGHTGEVNSVAF-SPDGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDG 231
Query: 71 ETLSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWD 128
L++G + G+I++W+L +TL+GH +S+TS+ + P G L SGS D I++WD
Sbjct: 232 YLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASGSADGTIRIWD 289
Score = 36.9 bits (86), Expect = 0.032
Identities = 19/72 (26%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 279 TSLSILPQSPMLCFILTTSSSADRTVNFWDLEKFSLVSTTEKNSSTIRRLTFSEGGECLL 338
S++ P L SSS+D T+ WDL + T + + + + FS G L
Sbjct: 181 NSVAFSPDGEKLL-----SSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLA 235
Query: 339 GGDTEGLKVYGW 350
G +G + W
Sbjct: 236 SGSEDG-TIRVW 246
Score = 36.9 bits (86), Expect = 0.032
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 279 TSLSILPQSPMLCFILTTSSSADRTVNFWDLEKFSLVSTTEKNSSTIRRLTFSEGGECLL 338
S++ P +L S S D T+ WDL V T +++++ L +S G+ L
Sbjct: 223 NSVAFSPDGYLLA-----SGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLA 277
Query: 339 GG 340
G
Sbjct: 278 SG 279
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 110 bits (276), Expect = 1e-25
Identities = 81/329 (24%), Positives = 126/329 (38%), Gaps = 24/329 (7%)
Query: 5 VEKAEDFMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESV 64
+ H SV LA + + D + LW L + +L+GH+ PV S+
Sbjct: 145 GKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSL 204
Query: 65 QF-GNGEETLSAGCQSGSIKIWNLAV-PTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDS 122
F +G +++G G+I++W+L+ ++ TL+GH S+ S F P G L SGS D
Sbjct: 205 AFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDG 263
Query: 123 FIKLWDLRRKG-CIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI-----GASFHLTN 176
I+LWDLR + T GHS S+ S+ FSPDG+ +ASG DG VR+ G
Sbjct: 264 TIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGTVRLWDLETGKLLSSLT 323
Query: 177 TSIHVVDLSLVHPLGTPPPQYTSSVPFSHNTSLRKSFTKGRPGGTKAKIDVTRIEENAES 236
H V L P S + ++R + K T +
Sbjct: 324 LKGHE---GPVSSLSFSPDGSLLVSGGSDDGTIRLWDLR------TGKPLKTLEGHSNVL 374
Query: 237 EDQAGEEELFATIANPCDYSAIFQPHRSLNRSGTCVPVSVSRTSLSILPQSPMLCFILTT 296
+ + + ++ S SL P L
Sbjct: 375 SVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVT-SLDFSPDGKSLA----- 428
Query: 297 SSSADRTVNFWDLEKFSLVSTTEKNSSTI 325
S S+D T+ WDL+ + + +
Sbjct: 429 SGSSDNTIRLWDLKTSLKSVSFSPDGKVL 457
Score = 110 bits (275), Expect = 2e-25
Identities = 95/348 (27%), Positives = 147/348 (42%), Gaps = 29/348 (8%)
Query: 14 HGASVNCLALGKKSGQVLAT--GGDDKKVNLWAL-GKSNCIMSLSGHSTPVESVQFGNGE 70
H +SV+ LAL G + D V LW L I +L GHS V S+ F
Sbjct: 108 HDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDG 167
Query: 71 ETL-SAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGD-YLCSGSLDSFIKLWD 128
+ L S G+IK+W+L TL GH ++S+ F P G + SGS D I+LWD
Sbjct: 168 KLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD 227
Query: 129 LRRKGCIY-TYRGHSKSINSIRFSPDGQWIASGGEDGVVRIGASFHLTNTSIHVVDLSLV 187
L + T GHS S+ S FSPDG +ASG DG +R+ + L ++S + L
Sbjct: 228 LSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDGTIRL---WDLRSSSSLLRTL--- 280
Query: 188 HPLGTPPPQYTSSVPFSHNTSLRKSFTKGRPGGTKAKIDVTRIEENAESEDQAGEEELFA 247
+ SV FS + L G GT D+ + + + E + +
Sbjct: 281 ----SGHSSSVLSVAFSPDGKL---LASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSS 333
Query: 248 TIANPCDYSAIFQPHRSLNRSGTCVPVSVSRTSLSILPQSPMLCF------ILTTSSSAD 301
+P + S + + + + ++ S +L + +S S D
Sbjct: 334 LSFSPDGSLLVS--GGSDDGTIRLWDLRTGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTD 391
Query: 302 RTVNFWDLEKFSLVSTTEKNSSTIRRLTFSEGGECLL-GGDTEGLKVY 348
TV WDL SL+ + ++S + L FS G+ L G ++++
Sbjct: 392 GTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNTIRLW 439
Score = 82.4 bits (202), Expect = 2e-16
Identities = 55/163 (33%), Positives = 84/163 (51%), Gaps = 13/163 (7%)
Query: 4 KVEKAEDFMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTPVES 63
K+ + H V+ L+ +++ G DD + LW L + +L GHS V S
Sbjct: 317 KLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTLEGHS-NVLS 375
Query: 64 VQFGNGEETLSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSF 123
V F +S+G G++++W+L+ ++ R L+GH S +TS+DF P G L SGS D+
Sbjct: 376 VSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKSLASGSSDNT 435
Query: 124 IKLWDLRRKGCIYTYRGHSKSINSIRFSPDGQWIASGGEDGVV 166
I+LWDL S+ S+ FSPDG+ +AS D V
Sbjct: 436 IRLWDL------------KTSLKSVSFSPDGKVLASKSSDLSV 466
Score = 67.0 bits (162), Expect = 2e-11
Identities = 81/316 (25%), Positives = 128/316 (40%), Gaps = 35/316 (11%)
Query: 52 MSLSGHSTPVESVQFGNGEETLSAGCQSGSIKIWNL--AVPTVQRTLNGHKSSITSVDF- 108
+ L GH + S+ F E L +G G+IK+W+L ++ H SS++ +
Sbjct: 59 LLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALS 118
Query: 109 HPYGDYL--CSGSLDSFIKLWDLRRKG-CIYTYRGHSKSINSIRFSPDGQWIASGGE-DG 164
P G+ + S SLD +KLWDL G I T GHS+S+ S+ FSPDG+ +ASG DG
Sbjct: 119 SPDGNSILLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGSSLDG 178
Query: 165 VVRIGASFHLTNTSIHVVDLSLVHPLGTPPPQYTSSVPFSHNTSLR-------KSFTKGR 217
+++ S V L P S + ++R K
Sbjct: 179 TIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWDLSTGKLLRSTL 238
Query: 218 PGGTKAKI-DVTRIEENAESEDQAGEEELFATIANPCDYSAIFQPHRSLNRSGTCVPVSV 276
G + + + + S G L+ D + R+L+ + V
Sbjct: 239 SGHSDSVVSSFSPDGSLLASGSSDGTIRLW-------DLRSSSSLLRTLSGHSSSV---- 287
Query: 277 SRTSLSILPQSPMLCFILTTSSSADRTVNFWDLE--KFSLVSTTEKNSSTIRRLTFSEGG 334
S++ P +L S S+D TV WDLE K T + + + L+FS G
Sbjct: 288 --LSVAFSPDGKLL-----ASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDG 340
Query: 335 ECLLGGDTEGLKVYGW 350
L+ G ++ + W
Sbjct: 341 SLLVSGGSDDGTIRLW 356
Score = 63.2 bits (152), Expect = 3e-10
Identities = 60/264 (22%), Positives = 97/264 (36%), Gaps = 27/264 (10%)
Query: 93 QRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLR-RKGCIYTYRG-HSKSINSIRF 150
L GH+ SITS+ F P G+ L SGS D IKLWDL + I + G H S++ +
Sbjct: 58 SLLLRGHEDSITSIAFSPDGELLLSGSSDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLAL 117
Query: 151 -SPDGQWIASGGEDGVVRIGASFHLTNTSIHVVDLSLVHPLGTPPPQYTSSVPFSHNTSL 209
SPDG I + + L+ + L + +S+ FS
Sbjct: 118 SSPDGNSILLASSSLDGTV-KLWDLSTPGKLIRTL-------EGHSESVTSLAFS--PDG 167
Query: 210 RKSFTKGRPGGTKAKIDVTRIEENAESEDQAGE--------EELFATIANPCDYSAIFQP 261
+ + GT D+ + + + + D +
Sbjct: 168 KLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGSSDGTIRLWD 227
Query: 262 HRSLNRSGTCVPVSVSRTSLSILPQSPMLCFILTTSSSADRTVNFWDLE-KFSLVSTTEK 320
+ + + S P +L S S+D T+ WDL SL+ T
Sbjct: 228 LSTGKLLRSTLSGHSDSVVSSFSPDGSLL-----ASGSSDGTIRLWDLRSSSSLLRTLSG 282
Query: 321 NSSTIRRLTFSEGGECLLGGDTEG 344
+SS++ + FS G+ L G ++G
Sbjct: 283 HSSSVLSVAFSPDGKLLASGSSDG 306
Score = 51.2 bits (121), Expect = 2e-06
Identities = 56/256 (21%), Positives = 86/256 (33%), Gaps = 51/256 (19%)
Query: 95 TLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLRRKGCIYTYRGHSKSINSIRFSPDG 154
+ + S+ S+ G L + DS + L DL RGH SI SI FSPDG
Sbjct: 22 GPSLNSLSLLSLGSSESGILLLALLSDSLVSLPDLSS----LLLRGHEDSITSIAFSPDG 77
Query: 155 QWIASGGEDGVVRIGASFHLTNTSIHVVDLSLVHPLGTPPPQYTSSVPFSHNTSLRKSFT 214
+ + SG DG +++ + L N + L +H S + S
Sbjct: 78 ELLLSGSSDGTIKL---WDLDNGEKLIKSLEGLHDS------SVSKLALSSPDGNSILLA 128
Query: 215 KGRPGGTKAKIDVTRIEENAESEDQAGEEELFATIANPCDYSAIFQPHRSLNRSGTCVPV 274
GT D++ + + H
Sbjct: 129 SSSLDGTVKLWDLSTPGKL----------------------IRTLEGHSE---------- 156
Query: 275 SVSRTSLSILPQSPMLCFILTTSSSADRTVNFWDLEKFSLVSTTEKNSSTIRRLTFSEGG 334
S TSL+ P +L + SS D T+ WDL +ST ++ + L FS G
Sbjct: 157 --SVTSLAFSPDGKLLA----SGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDG 210
Query: 335 ECLLGGDTEGLKVYGW 350
L+ + + W
Sbjct: 211 GLLIASGSSDGTIRLW 226
>gnl|CDD|222456 pfam13925, Katanin_con80, con80 domain of Katanin. The con80
domain of katanin is the C-terminal region of the
protein that binds to the N-terminal domain of
katanin-p60, the catalytic ATPase. The complex
associates with a specific subregion of the mitotic
spindle leading to increased microtubule disassembly and
targeting of p60 to the spindle poles. The assembly and
function of the mitotic spindle requires the activity of
a number of microtubule-binding proteins. Katanin, a
heterodimeric microtubule-severing ATPase, is found
localized at mitotic spindle poles. A proposed model is
that katanin is targeted to spindle poles through a
combination of direct microtubule binding by the p60
subunit and through interactions between the WD40 domain
and an unknown protein.
Length = 164
Score = 86.5 bits (215), Expect = 1e-19
Identities = 29/65 (44%), Positives = 45/65 (69%)
Query: 781 DNVWNLELCSAILPVIQDLLQSKYEMYITTACDTLNLILRTFGPVIKNNMKWSGGSIGVD 840
L+LC +LP++++LLQSKYE +I +TL IL+ FGPVI++ + + S+GVD
Sbjct: 59 KESITLDLCVDLLPLVEELLQSKYERHILVGLETLRSILKKFGPVIRSALSAAPSSVGVD 118
Query: 841 ISKEE 845
+S+EE
Sbjct: 119 LSREE 123
Score = 43.0 bits (102), Expect = 1e-04
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 12/82 (14%)
Query: 455 GHDKMMAVLRNRQRSLGLVYMAVNNKNMEAGIDTALSMNDGTVMIDLFKSMLGQGYKK-- 512
HD M++VL +R L +V +++ I A MND V++D+ S+L Q KK
Sbjct: 3 DHDTMLSVLSSRLTKLKVVRTLWRQNDIKGAIAAARRMNDLAVLVDVL-SVLTQSLKKES 61
Query: 513 -----CVKVYNALMPVKSVLLK 529
CV L+P+ LL+
Sbjct: 62 ITLDLCV----DLLPLVEELLQ 79
Score = 35.7 bits (83), Expect = 0.042
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 486 IDTALSMNDGTVMIDLFKSMLGQGYKKCVKVYNALMPVKSVLLKKQTVQGKLGQTFRDLL 545
I +ALS +V +DL + + +KC K L +K ++ +G +G+ R+L
Sbjct: 104 IRSALSAAPSSVGVDLSRE---ERLQKCQKCKQQLKKIKQIVKLLARRKGSVGELARELQ 160
Query: 546 AEI 548
E+
Sbjct: 161 LEL 163
>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 = 55.4 bits (134), Expect = 3e-10
Identities = 14/35 (40%), Positives = 26/35 (74%)
Query: 134 CIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI 168
+ T +GH+ + S+ FSPDG+++ASG +DG +++
Sbjct: 4 LLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKL 38
Score = 53.9 bits (130), Expect = 1e-09
Identities = 21/35 (60%), Positives = 23/35 (65%)
Query: 94 RTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWD 128
+TL GH +TSV F P G YL SGS D IKLWD
Sbjct: 6 KTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 38.8 bits (91), Expect = 2e-04
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 47 KSNCIMSLSGHSTPVESVQFGNGEETLSAGCQSGSIKIWN 86
+ +L GH+ PV SV F + L++G G+IK+W+
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 35.4 bits (82), Expect = 0.004
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 11 FMAHGASVNCLALGKKSGQVLATGGDDKKVNLW 43
H V +A G+ LA+G DD + LW
Sbjct: 8 LKGHTGPVTSVAFSP-DGKYLASGSDDGTIKLW 39
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 55.1 bits (133), Expect = 5e-10
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 134 CIYTYRGHSKSINSIRFSPDGQWIASGGEDGVVRI 168
+ T +GH+ + S+ FSPDG +ASG +DG VR+
Sbjct: 3 LLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRV 37
Score = 54.7 bits (132), Expect = 6e-10
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 91 TVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWD 128
+ RTL GH +TSV F P G+ L SGS D +++WD
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.9 bits (86), Expect = 0.001
Identities = 12/38 (31%), Positives = 22/38 (57%)
Query: 49 NCIMSLSGHSTPVESVQFGNGEETLSAGCQSGSIKIWN 86
+ +L GH+ PV SV F L++G G++++W+
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 36.2 bits (84), Expect = 0.002
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 11 FMAHGASVNCLALGKKSGQVLATGGDDKKVNLW 43
H V +A G +LA+G DD V +W
Sbjct: 7 LKGHTGPVTSVAF-SPDGNLLASGSDDGTVRVW 38
Score = 27.3 bits (61), Expect = 2.8
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 5/30 (16%)
Query: 279 TSLSILPQSPMLCFILTTSSSADRTVNFWD 308
TS++ P +L S S D TV WD
Sbjct: 15 TSVAFSPDGNLLA-----SGSDDGTVRVWD 39
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 52.6 bits (126), Expect = 6e-07
Identities = 26/89 (29%), Positives = 48/89 (53%), Gaps = 10/89 (11%)
Query: 51 IMSLSGHSTPVESVQFGNG-EETLSAGCQSGSIKIWNL--------AVPTVQRTLNGHKS 101
++ L GH++ + +QF E L++G + +I++W + + Q L GHK
Sbjct: 67 VIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIKDPQCILKGHKK 126
Query: 102 SITSVDFHPYGDY-LCSGSLDSFIKLWDL 129
I+ +D++P Y +CS DSF+ +WD+
Sbjct: 127 KISIIDWNPMNYYIMCSSGFDSFVNIWDI 155
Score = 41.9 bits (98), Expect = 0.001
Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 16/102 (15%)
Query: 80 GSIKIWN-LAVPTVQRTLNGHKSSITSVDFHP-YGDYLCSGSLDSFIKLWDLRRKG---- 133
G+I++ N + P V + L GH SSI + F+P + + L SGS D I++W++
Sbjct: 54 GAIRLENQMRKPPVIK-LKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVK 112
Query: 134 ------CIYTYRGHSKSINSIRFSPDGQWI-ASGGEDGVVRI 168
CI +GH K I+ I ++P +I S G D V I
Sbjct: 113 EIKDPQCI--LKGHKKKISIIDWNPMNYYIMCSSGFDSFVNI 152
Score = 30.7 bits (69), Expect = 4.3
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 278 RTSLSILPQSPMLCFILTTSSSADRTVNFWDLE 310
+ +SI+ +PM +I+ SS D VN WD+E
Sbjct: 125 KKKISIIDWNPMNYYIMC-SSGFDSFVNIWDIE 156
Score = 29.5 bits (66), Expect = 9.8
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 118 GSLDSFIKLWDLRRKGCIYTYRGHSKSINSIRFSP-DGQWIASGGEDGVVRI 168
G L I+L + RK + +GH+ SI ++F+P + +ASG ED +R+
Sbjct: 50 GGLIGAIRLENQMRKPPVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRV 101
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 44.1 bits (104), Expect = 2e-04
Identities = 30/124 (24%), Positives = 51/124 (41%), Gaps = 9/124 (7%)
Query: 54 LSGHSTPVESVQFGNGEET-LSAGCQSGSIKIWNLAVPTVQRT-------LNGHKSSITS 105
L G P+ V F + L + G+I W + + + L GH +
Sbjct: 71 LLGQEGPIIDVAFNPFDPQKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGI 130
Query: 106 VDFHPYG-DYLCSGSLDSFIKLWDLRRKGCIYTYRGHSKSINSIRFSPDGQWIASGGEDG 164
V FHP + L S D + +WD+ R + + HS I S+ ++ DG + + +D
Sbjct: 131 VSFHPSAMNVLASAGADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDK 190
Query: 165 VVRI 168
+ I
Sbjct: 191 KLNI 194
Score = 35.6 bits (82), Expect = 0.12
Identities = 28/112 (25%), Positives = 46/112 (41%), Gaps = 10/112 (8%)
Query: 29 QVLATGGDDKKVNLWALG----KSNC---IMSLSGHSTPVESVQFGNGEETL--SAGCQS 79
Q L T +D + W + N I+ L GH+ V V F + SAG
Sbjct: 89 QKLFTASEDGTIMGWGIPEEGLTQNISDPIVHLQGHTKKVGIVSFHPSAMNVLASAGADM 148
Query: 80 GSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLRR 131
+ +W++ + H ITS++++ G LC+ S D + + D R
Sbjct: 149 -VVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNIIDPRD 199
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 43.9 bits (103), Expect = 4e-04
Identities = 38/141 (26%), Positives = 68/141 (48%), Gaps = 10/141 (7%)
Query: 30 VLATGGDDKKVNLWALGKSNCIMSLSGHSTPVESVQF-GNGEETLSAGCQSGSIKIWNLA 88
+LA+G DD V LW++ + I ++ + + VQF +L+ G + ++L
Sbjct: 590 LLASGSDDGSVKLWSINQGVSIGTIKTKAN-ICCVQFPSESGRSLAFGSADHKVYYYDLR 648
Query: 89 VPTVQR-TLNGHKSSITSVDFHPYGDYLCSGSLDSFIKLWDLR------RKGCIYTYRGH 141
P + T+ GH +++ V F L S S D+ +KLWDL + ++++ GH
Sbjct: 649 NPKLPLCTMIGHSKTVSYVRFVD-SSTLVSSSTDNTLKLWDLSMSISGINETPLHSFMGH 707
Query: 142 SKSINSIRFSPDGQWIASGGE 162
+ N + S +IA+G E
Sbjct: 708 TNVKNFVGLSVSDGYIATGSE 728
Score = 34.3 bits (78), Expect = 0.36
Identities = 36/169 (21%), Positives = 69/169 (40%), Gaps = 35/169 (20%)
Query: 1 MRAKVEKAEDFMAHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNCIMSLSGHSTP 60
+R K + + + + +++ C + G+ AT G +KK+ ++ + I+ G
Sbjct: 468 LRVKADLKQGDLLNSSNLVCAIGFDRDGEFFATAGVNKKIKIF---ECESIIK-DGRDIH 523
Query: 61 VESVQFGNGEETLSAGCQSGSIKIWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLCSGSL 120
V+ LS C WN + KS + S +F
Sbjct: 524 YPVVELA-SRSKLSGIC-------WNSYI----------KSQVASSNF------------ 553
Query: 121 DSFIKLWDLRRKGCIYTYRGHSKSINSIRF-SPDGQWIASGGEDGVVRI 168
+ +++WD+ R + + H K + SI + S D +ASG +DG V++
Sbjct: 554 EGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGSDDGSVKL 602
Score = 33.5 bits (76), Expect = 0.59
Identities = 29/111 (26%), Positives = 51/111 (45%), Gaps = 8/111 (7%)
Query: 16 ASVNCLALGKKSGQVLATGGDDKKVNLWALGKSNC-IMSLSGHSTPVESVQFGNGEETLS 74
A++ C+ +SG+ LA G D KV + L + ++ GHS V V+F + TL
Sbjct: 618 ANICCVQFPSESGRSLAFGSADHKVYYYDLRNPKLPLCTMIGHSKTVSYVRFVD-SSTLV 676
Query: 75 AGCQSGSIKIWNLAVP------TVQRTLNGHKSSITSVDFHPYGDYLCSGS 119
+ ++K+W+L++ T + GH + V Y+ +GS
Sbjct: 677 SSSTDNTLKLWDLSMSISGINETPLHSFMGHTNVKNFVGLSVSDGYIATGS 727
>gnl|CDD|233801 TIGR02251, HIF-SF_euk, Dullard-like phosphatase domain. This model
represents the putative phosphatase domain of a family
of eukaryotic proteins including "Dullard" , and the NLI
interacting factor (NIF)-like phosphatases. This domain
is a member of the haloacid dehalogenase (HAD)
superfamily by virtue of a conserved set of three
catalytic motifs and a conserved fold as predicted by
PSIPRED. The third motif in this family is distinctive
(hhhhDNxPxxa) and aparrently lacking the last aspartate.
This domain is classified as a "Class III" HAD, since
there is no large "cap" domain found between motifs 1
and 2 or motifs 2 and 3. This domain is related to
domains found in FCP1-like phosphatases (TIGR02250), and
together both are detected by the pfam03031.
Length = 162
Score = 31.9 bits (73), Expect = 0.67
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 679 RKPLERDVDE-LVYISPFGQEKPSVDFEVPTKES-EIYPTYVRKGP 722
+K L D+DE LV+ S F K DF+VP +I P YV K P
Sbjct: 1 KKTLVLDLDETLVH-STFKMPKVDADFKVPVLIDGKIIPVYVFKRP 45
>gnl|CDD|149288 pfam08149, BING4CT, BING4CT (NUC141) domain. This C terminal
domain is found in the BING4 family of nucleolar WD40
repeat proteins.
Length = 80
Score = 29.9 bits (68), Expect = 0.87
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 95 TLNGHKSSITSVDFHPYGDYLCSGSLDSF 123
T N S I+SV F P+ D L G F
Sbjct: 4 THNKPGSKISSVRFCPFEDVLGIGHSGGF 32
>gnl|CDD|227498 COG5170, CDC55, Serine/threonine protein phosphatase 2A, regulatory
subunit [Signal transduction mechanisms].
Length = 460
Score = 32.3 bits (73), Expect = 1.0
Identities = 34/155 (21%), Positives = 59/155 (38%), Gaps = 29/155 (18%)
Query: 13 AHGASVNCLALGKKSGQVLATGGDDKKVNLWALGKSN---CIMSLSGHSTP-----VESV 64
AH +N ++ +L+ DD ++NLW L + I+ + H+ + S
Sbjct: 170 AHPYHINSISFNSDKETLLSA--DDLRINLWNLEIIDGSFNIVDIKPHNMEELTEVITSA 227
Query: 65 QFGNGE-ETLSAGCQSGSIKIWNL--------AVPTVQRTLNGHK--------SSITSVD 107
+F G IK+ +L + + T++G SSI+
Sbjct: 228 EFHPEMCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGVDVDFFEEIVSSISDFK 287
Query: 108 FHPYGDYLCSGSLDSFIKLWDLRR-KGCIYTYRGH 141
F G Y+ S + +K+WD+ K I T H
Sbjct: 288 FSDNGRYILSRDYLT-VKIWDVNMAKNPIKTIPMH 321
Score = 31.5 bits (71), Expect = 2.2
Identities = 34/136 (25%), Positives = 52/136 (38%), Gaps = 28/136 (20%)
Query: 50 CIMSLSGHSTPVESVQFGNGEET-LSAGCQSGSIKIWNLAVPTVQRTL---NGHKSS--- 102
C + + H + S+ F + +ET LSA I +WNL + + H
Sbjct: 164 CRVYANAHPYHINSISFNSDKETLLSA--DDLRINLWNLEIIDGSFNIVDIKPHNMEELT 221
Query: 103 --ITSVDFHPYGDYLCSGSLDS-FIKLWDLRRKGCIYT----------------YRGHSK 143
ITS +FHP + S IKL DLR+ +
Sbjct: 222 EVITSAEFHPEMCNVFMYSSSKGEIKLNDLRQSALCDNSKKLFELTIDGVDVDFFEEIVS 281
Query: 144 SINSIRFSPDGQWIAS 159
SI+ +FS +G++I S
Sbjct: 282 SISDFKFSDNGRYILS 297
>gnl|CDD|224423 COG1506, DAP2, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases
[Amino acid transport and metabolism].
Length = 620
Score = 32.5 bits (74), Expect = 1.1
Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 7/102 (6%)
Query: 84 IWNLAVPTVQRTLNGHKSSITSVDFHPYGDYLC--SGSLDSFIKLWDLRRKGCIYTYRGH 141
+W TV+ G ++ + + P G L S +L+ + G I
Sbjct: 45 LWVSDGKTVRLLTFG--GGVSELRWSPDGSVLAFVSTDGGRVAQLYLVDVGGLITK---T 99
Query: 142 SKSINSIRFSPDGQWIASGGEDGVVRIGASFHLTNTSIHVVD 183
+ ++ R+SPDG IA +G + HL + V
Sbjct: 100 AFGVSDARWSPDGDRIAFLTAEGASKRDGGDHLFVDRLPVWF 141
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 32.7 bits (74), Expect = 1.2
Identities = 26/119 (21%), Positives = 55/119 (46%), Gaps = 11/119 (9%)
Query: 559 KFLSSRNLREKEDRIGE---SQPFRGRTLSVQDKIYFGFDFRSGQSLSSTFFENFALNID 615
KFL + L+E+E+RI S+ + L D Y F + + + ++ L I+
Sbjct: 593 KFLCTHYLKEREERICFIQNSEHWDNLVLGSSDLYYS---FSNEKKSNKN--KSLKLIIE 647
Query: 616 IVRLNSGGVSELNNISKLYISSPSPASRGSSRTASPRRTLPPASPSYSTGSVDMATTSP 674
+++N G + N K Y++ + SS+ + +T + S ++ + + ++TS
Sbjct: 648 KLKINEQG-GQKKNSKKEYMNPAQTTT--SSKAKTHSKTKNDHNKSKTSKNKEPSSTSF 703
>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane
glycoprotein G.
Length = 408
Score = 31.2 bits (70), Expect = 2.2
Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 8/83 (9%)
Query: 636 SSPSPASRGSSRTASPRRTLPPASPSYSTGSVDMATTSPHPLP-----RKPLERDVDELV 690
+S ++ G + + RR P P+ S +T +P P +P R
Sbjct: 254 TSQDQSTTGDGQEHTQRRKTP---PATSNRRSPHSTATPPPTTKRQETGRPTPRPTATTQ 310
Query: 691 YISPFGQEKPSVDFEVPTKESEI 713
S P PT ++ +
Sbjct: 311 SGSSPPHSSPPGVQANPTTQNLV 333
>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional.
Length = 943
Score = 31.6 bits (71), Expect = 2.3
Identities = 32/148 (21%), Positives = 51/148 (34%), Gaps = 32/148 (21%)
Query: 638 PSPASRGSSRTASPRRTLPPASPSYSTGSVDMATTSPHPLPRKPLERDVDELVYISPFGQ 697
P R S SP+R PP PS P +P + + SP
Sbjct: 621 PKSPKRPESPK-SPKRPPPPQRPSS---------------PERPEGPKIIK----SPKPP 660
Query: 698 EKPSVDFEVPTKESEIYPTYVRKGPDMYGPQSQYAPTKENDYGSQSGDSMLGDHEAETHE 757
+ P F+ P + + Y Y+ ++ TK +S +S+L + ET
Sbjct: 661 KSPKPPFD-PKFKEKFYDDYLDAA-------AKSKETKTTVVLDESFESILKETLPETPG 712
Query: 758 PSRYSMKPI----PYSPSTPREYAKEPD 781
+ +P+ P P E +PD
Sbjct: 713 TPFTTPRPLPPKLPRDEEFPFEPIGDPD 740
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 31.3 bits (71), Expect = 2.6
Identities = 17/94 (18%), Positives = 27/94 (28%), Gaps = 12/94 (12%)
Query: 636 SSPSPASRGSSRTASPRRTLPPASPSYSTGSVDMATTSPHPLPRKPLERDVDELVYIS-- 693
SPSP+ S R P S + S+ A ++ P R+ V
Sbjct: 349 RSPSPSRPPPPADPSSPRKRPRPSRAPSSP----AASAGRPTRRRA-RAAVAGRARRRDA 403
Query: 694 --PFGQEKPSVDFEVPTKESEIYPTYVRKGPDMY 725
F +P P + + P +
Sbjct: 404 TGRFPAGRPRP---SPLDAGAASGAFYARYPLLT 434
>gnl|CDD|237605 PRK14086, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 617
Score = 30.6 bits (69), Expect = 4.0
Identities = 25/147 (17%), Positives = 38/147 (25%), Gaps = 22/147 (14%)
Query: 638 PSPASRGSSRTASPRRTLPP--ASPSYSTGSVDMATTSPHPLPRKPLERDVDELVYISPF 695
P+P + RT+ P P Y D + P R
Sbjct: 95 PAPPPPHARRTSEPELPRPGRRPYEGYGGPRADDRPPGLPRQDQLPTAR----------- 143
Query: 696 GQEKPSVDFEVPTKESEIYPTYVRKGPDMYGPQSQ-YAPTKENDYGSQSGDSMLGDHEAE 754
P+ E +P + D YG Q Q Y S + + + + E
Sbjct: 144 ----PAYPAYQQRPEPGAWP----RAADDYGWQQQRLGFPPRAPYASPASYAPEQERDRE 195
Query: 755 THEPSRYSMKPIPYSPSTPREYAKEPD 781
++ R PR P
Sbjct: 196 PYDAGRPEYDQRRRDYDHPRPDWDRPR 222
>gnl|CDD|179569 PRK03359, PRK03359, putative electron transfer flavoprotein FixA;
Reviewed.
Length = 256
Score = 30.1 bits (68), Expect = 4.5
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 381 VGTWSHQDSGFSTLDSYSAGSPVSTMGRERDQIV 414
V WS D GF+ ++S + RER +IV
Sbjct: 203 VQVWSAADIGFNAEPAWSEQQVAAPKQRERQRIV 236
>gnl|CDD|235351 PRK05137, tolB, translocation protein TolB; Provisional.
Length = 435
Score = 29.9 bits (68), Expect = 5.7
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 12/38 (31%)
Query: 149 RFSPDGQWIA-SGGEDGVVRIGASFHLTNTSIHVVDLS 185
RFSPDG+ + S + G NT I+ +DL
Sbjct: 252 RFSPDGRKVVMSLSQGG-----------NTDIYTMDLR 278
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 30.1 bits (67), Expect = 7.0
Identities = 29/136 (21%), Positives = 38/136 (27%), Gaps = 14/136 (10%)
Query: 638 PSPASRGSSRTASPRRTLPPASPSYSTGSVDM--ATTSPHPLPRKPLERDVDELVYISPF 695
+ S S +TAS T P S + + + A S P DE V F
Sbjct: 449 TAQTSAKSIQTASEAETPPENQVSKNKAADNETDAPLSEVPSENPIQATPNDEAVETETF 508
Query: 696 GQEKPSVDFEVPTKESEIYPTYVRKGPDMYGPQSQYAPTKENDYGSQSGDSMLGDHEAET 755
E P+ P Y PD P A D+ + G E
Sbjct: 509 AHEAPA------------EPFYGYGFPDNDCPPEDGAEIPPPDWEHAAPADTAGGGADEE 556
Query: 756 HEPSRYSMKPIPYSPS 771
E P +P
Sbjct: 557 AEAGGIGGNNTPSAPP 572
>gnl|CDD|202558 pfam03159, XRN_N, XRN 5'-3' exonuclease N-terminus. This family
aligns residues towards the N-terminus of several
proteins with multiple functions. The members of this
family all appear to possess 5'-3' exonuclease activity
EC:3.1.11.-. Thus, the aligned region may be necessary
for 5' to 3' exonuclease function. The family also
contains several Xrn1 and Xrn2 proteins. The 5'-3'
exoribonucleases Xrn1p and Xrn2p/Rat1p function in the
degradation and processing of several classes of RNA in
Saccharomyces cerevisiae. Xrn1p is the main enzyme
catalyzing cytoplasmic mRNA degradation in multiple
decay pathways, whereas Xrn2p/Rat1p functions in the
processing of rRNAs and small nucleolar RNAs (snoRNAs)
in the nucleus.
Length = 237
Score = 29.2 bits (66), Expect = 7.4
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 424 LDMEQFLPKSYQTHQGKSSMSESELMSTIFNGHDKMMAVLRNRQRSLGLVYMAV 477
LDM + +E E+ IF D++ ++R R+ L+YMA+
Sbjct: 35 LDMNGIIHPCSHPEDKPFPETEDEMFVAIFEYIDRLFNIVRPRK----LLYMAI 84
>gnl|CDD|226036 COG3505, VirD4, Type IV secretory pathway, VirD4 components
[Intracellular trafficking and secretion].
Length = 596
Score = 29.3 bits (66), Expect = 10.0
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 818 ILRTFGPVIKNNMKWSGGSIGVDISKE 844
+ G VI N +K+ G + +D E
Sbjct: 164 SGKGVGFVIPNLLKYPGSVVVLDPKGE 190
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 0.131 0.386
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: 41,651,660
Number of extensions: 3982312
Number of successful extensions: 2385
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2342
Number of HSP's successfully gapped: 67
Length of query: 845
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 740
Effective length of database: 6,280,432
Effective search space: 4647519680
Effective search space used: 4647519680
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: 42 (22.0 bits)
S2: 63 (28.0 bits)