RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9327
(641 letters)
>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus. This
family represents the C-terminus (approximately 500
residues) of the eukaryotic coatomer alpha subunit.
Coatomer (COPI) is a large cytosolic protein complex
which forms a coat around vesicles budding from the
Golgi apparatus. Such coatomer-coated vesicles have been
proposed to play a role in many distinct steps of
intracellular transport. Note that many family members
also contain the pfam04053 domain.
Length = 421
Score = 170 bits (432), Expect = 8e-47
Identities = 70/131 (53%), Positives = 92/131 (70%), Gaps = 3/131 (2%)
Query: 426 GSFETAFKLLHDQIGVKNFLPYRQMFLNSYLQSRTAYSTLPLLAPVMAFPTR--KGPGIK 483
GSFETA +LLHDQ+GV NF P++ +FL Y SRT+Y LP L V +P R K
Sbjct: 131 GSFETAMRLLHDQLGVVNFAPFKDLFLQLYAGSRTSYRALPGLPSVSIYPERNWSESNSK 190
Query: 484 ENSHPATNIKLEQLIAKIQQCYQLTTSGKFVDAIEKLRNVLISIPLLVVTTKKEIEEAKQ 543
N PA KL QL ++Q YQLTT+GKF +A+EK R++L+SIPL+VV +K+E+ EA+Q
Sbjct: 191 -NGPPAVGFKLSQLAKRLQAAYQLTTNGKFGEAVEKFRSILLSIPLIVVDSKQEVAEAQQ 249
Query: 544 IINICKEYIVG 554
+I IC+EYIVG
Sbjct: 250 LITICREYIVG 260
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 145 bits (368), Expect = 8e-38
Identities = 60/126 (47%), Positives = 77/126 (61%), Gaps = 13/126 (10%)
Query: 230 KHTLHICNRKMEP--------LCNIHE-NTRVKSGAWDESGVFIYTTSNHIKYAIVNGDH 280
K T++I N +E +HE RVKSGAWD VFIYTT NH+KY +VNG+
Sbjct: 161 KDTVYILNYNLEAVAEGVEDAFEVLHEVTERVKSGAWDGD-VFIYTTLNHLKY-LVNGET 218
Query: 281 GIIRTLDLPIYITKIKG--NQVYYLDRECSPHVLRIDPTEFKFKLALINHKYEEVLHIVR 338
GII+ LD P+Y+ N+VY LDR+ + IDPTE +FK AL+ YEEVL I+
Sbjct: 219 GIIKHLDKPMYLLGYLPKDNRVYLLDRDGNVVSYEIDPTELEFKTALLRKDYEEVLRIIA 278
Query: 339 NSRLVG 344
NS L+G
Sbjct: 279 NSNLLG 284
Score = 117 bits (295), Expect = 4e-28
Identities = 44/88 (50%), Positives = 60/88 (68%), Gaps = 3/88 (3%)
Query: 556 NHIKYAIVNGDHGIIRTLDLPIYITKIKG--NQVYYLDRECSPHVLRIDPTEFKFKLALI 613
NH+KY +VNG+ GII+ LD P+Y+ N+VY LDR+ + IDPTE +FK AL+
Sbjct: 208 NHLKY-LVNGETGIIKHLDKPMYLLGYLPKDNRVYLLDRDGNVVSYEIDPTELEFKTALL 266
Query: 614 NHKYEEVLHIVRNSRLVGQSIIAYLQQK 641
YEEVL I+ NS L+GQ II +L++K
Sbjct: 267 RKDYEEVLRIIANSNLLGQKIIRFLEKK 294
Score = 43.3 bits (103), Expect = 3e-04
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 339 NSRLVGEVGERIKILKSCGQTSLAYLTAATHGL 371
N+ +G+V + + IL G+ AYL A T+G
Sbjct: 397 NALYLGDVEKCVDILIKTGRLPEAYLFAKTYGP 429
>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 = 139 bits (352), Expect = 5e-37
Identities = 48/195 (24%), Positives = 80/195 (41%), Gaps = 28/195 (14%)
Query: 9 SARVKGLSFHPKRPWILSSLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFHNQQPIFVS 68
+ V ++F P + + +G I++WD LL H GPVR + S
Sbjct: 9 TGGVTCVAFSPDGKLLATGSGDGTIKVWDLETGELLRTLKGHTGPVRDVAASADGTYLAS 68
Query: 69 GGKMIVMAYQGCILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHLDYIRTTF 128
G D I++W+ + +C+ TL GH Y+ +
Sbjct: 69 GS----------------------------SDKTIRLWDLETGECVRTLTGHTSYVSSVA 100
Query: 129 FHHEYPWILSASDDQTIRIWYWQSRNCICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIR 188
F + + S+S D+TI++W ++ C+ L GH +V F P V S+S D TI+
Sbjct: 101 FSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIK 160
Query: 189 VWDISGLRKKNVAPG 203
+WD+ + G
Sbjct: 161 LWDLRTGKCVATLTG 175
Score = 127 bits (321), Expect = 1e-32
Identities = 51/200 (25%), Positives = 77/200 (38%), Gaps = 28/200 (14%)
Query: 12 VKGLSFHPKRPWILSSLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFHNQQPIFVSGGK 71
V ++F P + SS + I++WD L H V + F FV+
Sbjct: 96 VSSVAFSPDGRILSSSSRDKTIKVWDVETGKCLTTLRGHTDWVNSVAFS-PDGTFVASSS 154
Query: 72 MIVMAYQGCILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHLDYIRTTFFHH 131
D IK+W+ + KC+ TL GH + + F
Sbjct: 155 ---------------------------QDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSP 187
Query: 132 EYPWILSASDDQTIRIWYWQSRNCICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWD 191
+ +LS+S D TI++W + C+ L GH + V F P ++ S S D TIRVWD
Sbjct: 188 DGEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWD 247
Query: 192 ISGLRKKNVAPGMGKLVLSM 211
+ G V S+
Sbjct: 248 LRTGECVQTLSGHTNSVTSL 267
Score = 125 bits (317), Expect = 3e-32
Identities = 50/190 (26%), Positives = 78/190 (41%), Gaps = 28/190 (14%)
Query: 2 LTKFETKSARVKGLSFHPKRPWILSSLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFHN 61
LT + V ++F P ++ SS +G I+LWD R + H G V + F
Sbjct: 128 LTTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAFSP 187
Query: 62 QQPIFVSGGKMIVMAYQGCILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHL 121
+S D IK+W+ KC+ TL GH
Sbjct: 188 DGEKLLSS----------------------------SSDGTIKLWDLSTGKCLGTLRGHE 219
Query: 122 DYIRTTFFHHEYPWILSASDDQTIRIWYWQSRNCICVLTGHNHYVMCAQFHPTDDIVVSA 181
+ + + F + + S S+D TIR+W ++ C+ L+GH + V + P + S
Sbjct: 220 NGVNSVAFSPDGYLLASGSEDGTIRVWDLRTGECVQTLSGHTNSVTSLAWSPDGKRLASG 279
Query: 182 SLDQTIRVWD 191
S D TIR+WD
Sbjct: 280 SADGTIRIWD 289
Score = 52.7 bits (127), Expect = 2e-07
Identities = 14/40 (35%), Positives = 19/40 (47%)
Query: 155 CICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWDISG 194
L GH V C F P ++ + S D TI+VWD+
Sbjct: 1 LRRTLKGHTGGVTCVAFSPDGKLLATGSGDGTIKVWDLET 40
>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
only].
Length = 466
Score = 100 bits (249), Expect = 2e-22
Identities = 58/279 (20%), Positives = 101/279 (36%), Gaps = 31/279 (11%)
Query: 2 LTKFETKSARVKGLSFHPKRPWILS-SLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFH 60
+ E S V L+F P + S S +G I+LWD R L H PV + F
Sbjct: 148 IRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFS 207
Query: 61 NQQPIFVSGGKMIVMAYQGCILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLL-G 119
+ ++ G D I++W+ K + + L G
Sbjct: 208 PDGGLLIASG---------------------------SSDGTIRLWDLSTGKLLRSTLSG 240
Query: 120 HLDYIRTTFFHHEYPWILSASDDQTIRIWYWQS-RNCICVLTGHNHYVMCAQFHPTDDIV 178
H D + + F + + S S D TIR+W +S + + L+GH+ V+ F P ++
Sbjct: 241 HSDSV-VSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLL 299
Query: 179 VSASLDQTIRVWDISGLRKKNVAPGMGKLVLSMKSKHPIWKYCKPVKYCNPKHTLHICNR 238
S S D T+R+WD+ + + G + R
Sbjct: 300 ASGSSDGTVRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLR 359
Query: 239 KMEPLCNIHENTRVKSGAWDESGVFIYTTSNHIKYAIVN 277
+PL + ++ V S ++ G + + S + +
Sbjct: 360 TGKPLKTLEGHSNVLSVSFSPDGRVVSSGSTDGTVRLWD 398
Score = 88.2 bits (217), Expect = 2e-18
Identities = 54/213 (25%), Positives = 86/213 (40%), Gaps = 19/213 (8%)
Query: 16 SFHPKRPWILSSLHNGVIQLWDYR-MNTLLEKFDEHEGPVRGICFHNQQPIFVSGGK--- 71
SF P + S +G I+LWD R ++LL H V + F + SG
Sbjct: 248 SFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSSDGT 307
Query: 72 --------------MIVMAYQGCILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTL 117
+ + ++G + P + S DD I++W+ + K + TL
Sbjct: 308 VRLWDLETGKLLSSLTLKGHEGPVSSLSFSPDGSLLVSGGSDDGTIRLWDLRTGKPLKTL 367
Query: 118 LGHLDYIRTTFFHHEYPWILSASDDQTIRIWYWQSRNCICVLTGHNHYVMCAQFHPTDDI 177
GH + + F + + S S D T+R+W + + + L GH V F P
Sbjct: 368 EGH-SNVLSVSFSPDGRVVSSGSTDGTVRLWDLSTGSLLRNLDGHTSRVTSLDFSPDGKS 426
Query: 178 VVSASLDQTIRVWDISGLRKKNVAPGMGKLVLS 210
+ S S D TIR+WD+ K GK++ S
Sbjct: 427 LASGSSDNTIRLWDLKTSLKSVSFSPDGKVLAS 459
Score = 77.1 bits (188), Expect = 8e-15
Identities = 62/273 (22%), Positives = 96/273 (35%), Gaps = 45/273 (16%)
Query: 23 WILSSLHNGVIQLWDYR-MNTLLEKFDEHEGPVRGICFHNQQPIFVSGGKMIVMAYQGCI 81
+ SS +G ++LWD L+ + H V + F + SG
Sbjct: 126 LLASSSLDGTVKLWDLSTPGKLIRTLEGHSESVTSLAFSPDGKLLASGS----------- 174
Query: 82 LESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHLDYIRTTFFHHEYPW-ILSAS 140
D IK+W+ + K + TL GH D + + F + I S S
Sbjct: 175 ----------------SLDGTIKLWDLRTGKPLSTLAGHTDPVSSLAFSPDGGLLIASGS 218
Query: 141 DDQTIRIWYWQSRNCI-CVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWDISGLRKK- 198
D TIR+W + + L+GH+ V+ + F P ++ S S D TIR+WD+
Sbjct: 219 SDGTIRLWDLSTGKLLRSTLSGHSDSVVSS-FSPDGSLLASGSSDGTIRLWDLRSSSSLL 277
Query: 199 NVAPGMGKLVLSMKSKHPIWKYCKPVKYCNPKHTLHICNRKMEPLCNI--HENTRVKSGA 256
G VLS+ P K + K+ + HE V S +
Sbjct: 278 RTLSGHSSSVLSVAF-SPDGKLLASGSSDGTVRLWDLETGKLLSSLTLKGHEG-PVSSLS 335
Query: 257 WDESGVFIYTTSNHIKYAIVNGDHGIIRTLDLP 289
+ + + D G IR DL
Sbjct: 336 F---------SPDGSLLVSGGSDDGTIRLWDLR 359
Score = 76.3 bits (186), Expect = 1e-14
Identities = 57/289 (19%), Positives = 102/289 (35%), Gaps = 45/289 (15%)
Query: 12 VKGLSFHPKRPWILSSLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFHNQQPIFVSGG- 70
+ L +L+ L + ++ L D HE + I F + +SG
Sbjct: 30 LLSLGSSESGILLLALLSDSLVSLPDLSSLL----LRGHEDSITSIAFSPDGELLLSGSS 85
Query: 71 --KMIVMAYQG-----CILESRNEPCLFRIKSVLGD-----------DYKIKVWNY-KQR 111
+ + LE ++ + ++ D D +K+W+
Sbjct: 86 DGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTPG 145
Query: 112 KCIFTLLGHLDYIRTTFFHHEYPWILSASD-DQTIRIWYWQSRNCICVLTGHNHYVMCAQ 170
K I TL GH + + + F + + S S D TI++W ++ + L GH V
Sbjct: 146 KLIRTLEGHSESVTSLAFSPDGKLLASGSSLDGTIKLWDLRTGKPLSTLAGHTDPVSSLA 205
Query: 171 FHPTDD-IVVSASLDQTIRVWDISGLRKKNVAPGMGKLVLSMKSKHPIWKYCKPVKY--- 226
F P ++ S S D TIR+WD+S GKL+ S S H
Sbjct: 206 FSPDGGLLIASGSSDGTIRLWDLS----------TGKLLRSTLSGHSDSVVSSFSPDGSL 255
Query: 227 ---CNPKHTLHICNRKMEPLC---NIHENTRVKSGAWDESGVFIYTTSN 269
+ T+ + + + ++ V S A+ G + + S+
Sbjct: 256 LASGSSDGTIRLWDLRSSSSLLRTLSGHSSSVLSVAFSPDGKLLASGSS 304
Score = 47.4 bits (111), Expect = 2e-05
Identities = 42/198 (21%), Positives = 71/198 (35%), Gaps = 15/198 (7%)
Query: 81 ILESRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHLDYIRTTFFHHEYPWILSAS 140
L S + L D + + + L GH D I + F + +LS S
Sbjct: 29 SLLSLGSSESGILLLALLSDSLVSLPDLSSL----LLRGHEDSITSIAFSPDGELLLSGS 84
Query: 141 DDQTIRIWYWQ-SRNCICVLTG-HNHYVMCAQFHPTDD---IVVSASLDQTIRVWDISGL 195
D TI++W I L G H+ V D ++ S+SLD T+++WD+S
Sbjct: 85 SDGTIKLWDLDNGEKLIKSLEGLHDSSVSKLALSSPDGNSILLASSSLDGTVKLWDLSTP 144
Query: 196 RK-KNVAPGMGKLVLSMKSKHPIWKYCKPVKYCNPKHTLHICNRKMEPLCNIHENTR--V 252
K G + V S+ P K + T+ + + + + V
Sbjct: 145 GKLIRTLEGHSESVTSLAF-SPDGKLL--ASGSSLDGTIKLWDLRTGKPLSTLAGHTDPV 201
Query: 253 KSGAWDESGVFIYTTSNH 270
S A+ G + + +
Sbjct: 202 SSLAFSPDGGLLIASGSS 219
>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 = 53.9 bits (130), Expect = 9e-10
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 152 SRNCICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWD 191
S + L GH V F P + S S D TI++WD
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 43.5 bits (103), Expect = 4e-06
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 110 QRKCIFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRIW 148
+ + TL GH + + F + ++ S SDD TI++W
Sbjct: 1 SGELLKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLW 39
Score = 31.1 bits (71), Expect = 0.096
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 2 LTKFETKSARVKGLSFHPKRPWILSSLHNGVIQLWD 37
L + + V ++F P ++ S +G I+LWD
Sbjct: 5 LKTLKGHTGPVTSVAFSPDGKYLASGSDDGTIKLWD 40
Score = 30.7 bits (70), Expect = 0.15
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 42 TLLEKFDEHEGPVRGICFHNQQPIFVSGGK 71
LL+ H GPV + F SG
Sbjct: 3 ELLKTLKGHTGPVTSVAFSPDGKYLASGSD 32
>gnl|CDD|201208 pfam00400, WD40, WD domain, G-beta repeat.
Length = 39
Score = 52.4 bits (126), Expect = 3e-09
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 153 RNCICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWD 191
+ L GH V F P +++ S S D T+RVWD
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 43.5 bits (103), Expect = 4e-06
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 111 RKCIFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRIW 148
K + TL GH + + F + + S SDD T+R+W
Sbjct: 1 GKLLRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVW 38
Score = 33.5 bits (77), Expect = 0.015
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 2 LTKFETKSARVKGLSFHPKRPWILSSLHNGVIQLWD 37
L + + V ++F P + S +G +++WD
Sbjct: 4 LRTLKGHTGPVTSVAFSPDGNLLASGSDDGTVRVWD 39
Score = 31.2 bits (71), Expect = 0.087
Identities = 9/30 (30%), Positives = 11/30 (36%)
Query: 42 TLLEKFDEHEGPVRGICFHNQQPIFVSGGK 71
LL H GPV + F + SG
Sbjct: 2 KLLRTLKGHTGPVTSVAFSPDGNLLASGSD 31
>gnl|CDD|177776 PLN00181, PLN00181, protein SPA1-RELATED; Provisional.
Length = 793
Score = 50.1 bits (119), Expect = 3e-06
Identities = 41/173 (23%), Positives = 72/173 (41%), Gaps = 33/173 (19%)
Query: 24 ILSSLHNGVIQLWDYRMNTLLEKFDEHEGPVRGICFHNQQPIFVSGGKMIVMAYQGCILE 83
+ SS GV+Q+WD + L+ + EHE V I + + P ++ G
Sbjct: 548 VASSNFEGVVQVWDVARSQLVTEMKEHEKRVWSIDYSSADPTLLASGS------------ 595
Query: 84 SRNEPCLFRIKSVLGDDYKIKVWNYKQRKCIFTLLGHLDYIRTTFFHHEYPWILSASDDQ 143
DD +K+W+ Q I T+ + F + S D
Sbjct: 596 ---------------DDGSVKLWSINQGVSIGTIKTKANICCVQFPSESGRSLAFGSADH 640
Query: 144 TIRIWYWQSRNC---ICVLTGHNHYVMCAQFHPTDDIVVSASLDQTIRVWDIS 193
+++Y+ RN +C + GH+ V +F + +V S+S D T+++WD+S
Sbjct: 641 --KVYYYDLRNPKLPLCTMIGHSKTVSYVRFVDSSTLV-SSSTDNTLKLWDLS 690
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 42.2 bits (99), Expect = 8e-04
Identities = 41/170 (24%), Positives = 74/170 (43%), Gaps = 22/170 (12%)
Query: 103 IKVWNYKQRKCIFTLLGHLDYIRTTFFHHEYPWIL-SASDDQTIRIW--------YWQSR 153
I++ N ++ + L GH I F+ + IL S S+D TIR+W + +
Sbjct: 56 IRLENQMRKPPVIKLKGHTSSILDLQFNPCFSEILASGSEDLTIRVWEIPHNDESVKEIK 115
Query: 154 NCICVLTGHNHYVMCAQFHPTDD-IVVSASLDQTIRVWDISGLRKKNVAPGMGKLVLSMK 212
+ C+L GH + ++P + I+ S+ D + +WDI K+ M K + S+K
Sbjct: 116 DPQCILKGHKKKISIIDWNPMNYYIMCSSGFDSFVNIWDIEN-EKRAFQINMPKKLSSLK 174
Query: 213 SKHPIWKYCKPV--KYCNPKHTLHICNRKMEPLCN---IHENTRVKSGAW 257
W + C KH +HI + + + + + IH+ + W
Sbjct: 175 -----WNIKGNLLSGTCVGKH-MHIIDPRKQEIASSFHIHDGGKNTKNIW 218
>gnl|CDD|235010 PRK02186, PRK02186, argininosuccinate lyase; Provisional.
Length = 887
Score = 31.7 bits (72), Expect = 1.4
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 1/37 (2%)
Query: 374 EAAELESNLRTADPNATLPTVHPEAQ-LLRPPAPVAE 409
A + L A A P + PEAQ ++ P
Sbjct: 397 GDAARAAALNDAGAGAARPGLPPEAQAIVYGPGASEA 433
>gnl|CDD|173756 cd08216, PK_STRAD, Pseudokinase domain of STE20-related kinase
adapter protein. Protein Kinase family, STE20-related
kinase adapter protein (STRAD) subfamily, pseudokinase
domain. The STRAD subfamily is part of a larger
superfamily that includes the catalytic domains of
serine/threonine kinases (STKs), protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
pseudokinase domain shows similarity to protein kinases
but lacks crucial residues for catalytic activity. STRAD
forms a complex with the scaffolding protein MO25, and
the STK, LKB1, resulting in the activation of the
kinase. In the complex, LKB1 phosphorylates and
activates adenosine monophosphate-activated protein
kinases (AMPKs), which regulate cell energy metabolism
and cell polarity. LKB1 is a tumor suppressor linked to
the rare inherited disease, Peutz-Jeghers syndrome,
which is characterized by a predisposition to benign
polyps and hyperpigmentation of the buccal mucosa. There
are two forms of STRAD, alpha and beta, that complex
with LKB1 and MO25. The structure of STRAD-alpha is
available and shows that this protein binds ATP, has an
ordered activation loop, and adopts a closed
conformation typical of fully active protein kinases. It
does not possess activity due to nonconservative
substitutions of essential catalytic residues. ATP
binding enhances the affinity of STRAD for MO25. The
conformation of STRAD-alpha stabilized through ATP and
MO25 may be needed to activate LKB1.
Length = 314
Score = 30.8 bits (70), Expect = 2.0
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 2/68 (2%)
Query: 407 VAEAETNWPLLTVSKSFFEGSFETAFKLLHDQIGVKNFLPYRQMFLNSYLQSRTAYSTLP 466
+A+ + L+ V K + + KLL +I L + + Y+ S S L
Sbjct: 18 LAKHKPTNTLVAVKKINLDSCSKEDLKLLQQEIITSRQLQHPN--ILPYVTSFIVDSELY 75
Query: 467 LLAPVMAF 474
+++P+MA+
Sbjct: 76 VVSPLMAY 83
>gnl|CDD|239021 cd02070, corrinoid_protein_B12-BD, B12 binding domain of corrinoid
proteins. A family of small methanogenic corrinoid
proteins that bind methyl-Co(III)
5-hydroxybenzimidazolylcobamide as a cofactor. They play
a role on the methanogenesis from trimethylamine,
dimethylamine or monomethylamine, which is initiated by
a series of corrinoid-dependent methyltransferases.
Length = 201
Score = 30.3 bits (69), Expect = 2.1
Identities = 10/39 (25%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 512 KFVDAIEKLRNVLISIPLLVVTTKKEIEEAKQIINICKE 550
+FV+A+++ + ++ + L+ TT ++E +I KE
Sbjct: 124 EFVEAVKEHKPDILGLSALMTTTMGGMKE---VIEALKE 159
>gnl|CDD|223875 COG0804, UreC, Urea amidohydrolase (urease) alpha subunit [Amino
acid transport and metabolism].
Length = 568
Score = 30.8 bits (70), Expect = 2.4
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 5/74 (6%)
Query: 386 DPNATLPTVHPEAQLLRPP-APVAEAETNWPLLTVSKSFFEGSFETAFKLLHDQIGVKNF 444
DPNA++PT P+ RP +A T + VS++ + L VKN
Sbjct: 461 DPNASIPT--PQPVHYRPMFGAYGKALTATSVTFVSQAALDAGVAERLGLEKQVAAVKNC 518
Query: 445 --LPYRQMFLNSYL 456
+ M LNS
Sbjct: 519 RNVGKADMKLNSAT 532
>gnl|CDD|173611 PTZ00421, PTZ00421, coronin; Provisional.
Length = 493
Score = 30.6 bits (69), Expect = 3.0
Identities = 19/107 (17%), Positives = 41/107 (38%), Gaps = 9/107 (8%)
Query: 98 GDDYKIKVWNYKQRKCIFTLLGHLDYIRTTFFHHEYPWILSASDDQTIRIWYWQSRNCIC 157
G D + VW+ ++ K + + H D I + ++ + + + S D+ + I R+
Sbjct: 145 GADMVVNVWDVERGKAVEVIKCHSDQITSLEWNLDGSLLCTTSKDKKLNI--IDPRDGTI 202
Query: 158 VLTGHNHY-------VMCAQFHPTDDIVVSASLDQTIRVWDISGLRK 197
V + H + + + S S + I +WD +
Sbjct: 203 VSSVEAHASAKSQRCLWAKRKDLIITLGCSKSQQRQIMLWDTRKMAS 249
>gnl|CDD|99919 cd05536, POLBc_B3, DNA polymerase type-B B3 subfamily catalytic
domain. Archaeal proteins that are involved in DNA
replication are similar to those from eukaryotes. Some
members of the archaea also possess multiple family B
DNA polymerases (B1, B2 and B3). So far there is no
specific function(s) has been assigned for different
members of the archaea type B DNA polymerases.
Phylogenetic analyses of eubacterial, archaeal, and
eukaryotic family B DNA polymerases are support
independent gene duplications during the evolution of
archaeal and eukaryotic family B DNA polymerases.
Structural comparison of the thermostable DNA polymerase
type B to its mesostable homolog suggests several
adaptations to high temperature such as shorter loops,
disulfide bridges, and increasing electrostatic
interaction at subdomain interfaces.
Length = 371
Score = 30.0 bits (68), Expect = 3.6
Identities = 28/104 (26%), Positives = 41/104 (39%), Gaps = 15/104 (14%)
Query: 512 KFV-DAIEKLRNVLISIPLLVV--TTKKEIEE----------AKQIINICKEYIVGTNHI 558
K V + IEKL+ + LV+ K++ E AK++ + GT I
Sbjct: 257 KIVKEVIEKLKRGEVPPEKLVIWKQLTKDLSEYKATGPHVAAAKKLAKRGYKVRPGTK-I 315
Query: 559 KYAIVNGDHGIIRTLDLPIYITKIKGNQV-YYLDRECSPHVLRI 601
Y IV G I + + YY+D + P VLRI
Sbjct: 316 GYVIVKGSGKISDRAYPYDMVDEKHKYDAEYYIDNQVLPAVLRI 359
>gnl|CDD|234368 TIGR03835, termin_org_DnaJ, terminal organelle assembly protein
TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ
homolog and probable assembly protein of the Mycoplasma
terminal organelle. The terminal organelle is involved
in both cytadherence and gliding motility [Cellular
processes, Chemotaxis and motility].
Length = 871
Score = 30.6 bits (68), Expect = 3.7
Identities = 36/182 (19%), Positives = 52/182 (28%), Gaps = 38/182 (20%)
Query: 365 TAATHGLSEEAAELESN---------LRTADPNATLPTVHPEAQLLRPPAPVAEAETNWP 415
AT +E + + L + + E Q+ P PV E +
Sbjct: 404 NWATDYQLDEPTQSNIDWYKQEDPKDLEQLVQDQATLEITEENQI--SPEPVEEQPS--- 458
Query: 416 LLTVSKSFFEGSFETAFKLLHDQIGVKNFLPYRQMFLNSYLQSRTAYSTLPLLAPVMAFP 475
V + E A K + + K F + Q S LL P P
Sbjct: 459 ---VESTAPEDQVVEAIKEEEELLEQKK----AAEFAELFGQPTPTTSIEELLNPEQTQP 511
Query: 476 TRKGPGIKENSHPATNIKLEQLIAKIQQCYQLTTSGKFVDAIEKLRNVLISIPLLVVTTK 535
T I EN+ + Q YQL D +K N I L + +
Sbjct: 512 TEFDEIIIENNLD-------NVSVADDQNYQLK------DDNKKFIN----ISLPTIVSS 554
Query: 536 KE 537
E
Sbjct: 555 NE 556
>gnl|CDD|238088 cd00156, REC, Signal receiver domain; originally thought to be
unique to bacteria (CheY, OmpR, NtrC, and PhoB), now
recently identified in eukaroytes ETR1 Arabidopsis
thaliana; this domain receives the signal from the
sensor partner in a two-component systems; contains a
phosphoacceptor site that is phosphorylated by histidine
kinase homologs; usually found N-terminal to a DNA
binding effector domain; forms homodimers.
Length = 113
Score = 27.9 bits (63), Expect = 6.9
Identities = 7/41 (17%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 514 VDAIEKLRNVLISIPLLVVTTKKEIEEAKQIINI-CKEYIV 553
++ + ++R IP++ +T + E+A + + +Y+
Sbjct: 57 LELLRRIRKRGPDIPIIFLTAHGDDEDAVEALKAGADDYLT 97
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
0.322 0.138 0.427
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: 32,329,178
Number of extensions: 3161218
Number of successful extensions: 2685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2645
Number of HSP's successfully gapped: 47
Length of query: 641
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 538
Effective length of database: 6,369,140
Effective search space: 3426597320
Effective search space used: 3426597320
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: 62 (27.7 bits)