RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9904
(592 letters)
>gnl|CDD|205691 pfam13513, HEAT_EZ, HEAT-like repeat. The HEAT repeat family is
related to armadillo/beta-catenin-like repeats (see
pfam00514). These EZ repeats are found in subunits of
cyanobacterial phycocyanin lyase and other proteins and
probably carry out a scaffolding role.
Length = 55
Score = 65.5 bits (160), Expect = 1e-13
Identities = 22/55 (40%), Positives = 30/55 (54%)
Query: 111 WEIKESGILALGAIAEGCMNGMVPHLNELVPFLITCLSDKKALVRAITCWTLSRY 165
WE++E+ LALGA+A G + P + EL+P L+ L D VR W L R
Sbjct: 1 WEVREAAALALGALAGGGPELLRPAVPELLPALLPLLKDDDDEVREAAAWALGRI 55
Score = 46.7 bits (111), Expect = 4e-07
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 187 GCMNGMVPHLNELVPFLITCLSDKKALVRAITCWTLSRY 225
G + P + EL+P L+ L D VR W L R
Sbjct: 17 GGPELLRPAVPELLPALLPLLKDDDDEVREAAAWALGRI 55
Score = 33.2 bits (76), Expect = 0.025
Identities = 17/55 (30%), Positives = 25/55 (45%)
Query: 391 PEVRQSSFALLGDLTKACFSHVHPCISDFMPILGQNLNPDLISVCNNATWAIGEI 445
EVR+++ LG L + P + + +P L L D V A WA+G I
Sbjct: 1 WEVREAAALALGALAGGGPELLRPAVPELLPALLPLLKDDDDEVREAAAWALGRI 55
Score = 30.9 bits (70), Expect = 0.17
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 437 NATWAIGEISVKLGEDMRRYVPMVINQLIIIINRPNTPKTLLENTAITIGRL 488
A A+G ++ E +R VP ++ L+ ++ + E A +GR+
Sbjct: 6 AAALALGALAGGGPELLRPAVPELLPALLPLLKDD--DDEVREAAAWALGRI 55
>gnl|CDD|227540 COG5215, KAP95, Karyopherin (importin) beta [Intracellular
trafficking and secretion].
Length = 858
Score = 60.7 bits (147), Expect = 1e-09
Identities = 79/430 (18%), Positives = 161/430 (37%), Gaps = 59/430 (13%)
Query: 57 VEEEDDDLDDDSSLSDWNLRKCSAAALDVLANVFREELLPVLLPILKETLFHHDWEIKES 116
+E++ +D D DWN +++ L + A + ++++ +L +++ + W +E+
Sbjct: 330 LEKQGEDYYGD----DWNPSMAASSCLQLFAQLKGDKIMRPVLGFVEQNIRSESWANREA 385
Query: 117 GILALGAIAEG-CMNGMVPHLNELVPFLITCLSDKKALVRAITCWTLSRYSHWVVSQPHD 175
++A G++ G C + + + + +P + +SD V++ T W + V
Sbjct: 386 AVMAFGSVMHGPCEDCLTKIVPQALPGIENEMSDSCLWVKSTTAWCFGAIADHVAMIISP 445
Query: 176 SYLKPLMTEMLGCMNGMVPHLNELVPFLITCLSDKK--------ALVRAITCWTLSRYSH 227
L + G++ PF S +K VR + + Y
Sbjct: 446 CGHLVLEVS--ASLIGLMDC-----PFRSINCSWRKENLVDHIAKAVREVESFLAKFYLA 498
Query: 228 WVVSQPHDSYLKPLMTEHKNLLILYDAIGTL----ADSVGHHL-NKPEYISLLMPPLIQ- 281
+ + + L + E + L+ A+GTL D+V L +Y S + I
Sbjct: 499 ILNALVKGTELA--LNESNLRVSLFSALGTLILICPDAVSDILAGFYDYTSKKLDECISV 556
Query: 282 KWNILKDEDKDLF-PLLECLSSVATALQAGFLPYCEPVYRRCVSLIEQTLNQHMANSQNP 340
IL ED+ L L V A+ E V + + L + L ++
Sbjct: 557 LGQILATEDQLLVEELQSNYIGVLEAIIRTRRRDIEDVEDQLMELFIRIL-------EST 609
Query: 341 EQFDAPDKDFMIVALDLLSGLAEGLDMHIDSLVSNSNIMHLLYQCMQDPMPEVRQSSFAL 400
+ A + ++ L + L E + + + L + + V S+ L
Sbjct: 610 KPTTAFGDVYTAIS-ALSTSLEERFEQYASKFIP------YLTRALNCTDRFVLNSAVGL 662
Query: 401 LGDLTKACFSHVHPCISDFMPILGQ---------NLNPDLISVCNNATWAIGEISVKLGE 451
+GDL + + M L Q +L P ++SV G+I++ +G
Sbjct: 663 VGDLANTLGTDFNIYADVLMSSLVQCLSSEATHRDLKPAILSV-------FGDIALAIGA 715
Query: 452 DMRRYVPMVI 461
+ Y+ M++
Sbjct: 716 NFESYLDMIM 725
Score = 39.5 bits (92), Expect = 0.005
Identities = 24/105 (22%), Positives = 47/105 (44%), Gaps = 9/105 (8%)
Query: 378 IMHLLYQCMQDPMP-----EVRQSSFALLGDLTKACFSHVHPCISDFMPILGQNLNPDLI 432
+M L + ++ P +V + AL L + + S F+P L + LN
Sbjct: 598 LMELFIRILESTKPTTAFGDVYTAISALSTSLEERFEQYA----SKFIPYLTRALNCTDR 653
Query: 433 SVCNNATWAIGEISVKLGEDMRRYVPMVINQLIIIINRPNTPKTL 477
V N+A +G+++ LG D Y ++++ L+ ++ T + L
Sbjct: 654 FVLNSAVGLVGDLANTLGTDFNIYADVLMSSLVQCLSSEATHRDL 698
Score = 36.5 bits (84), Expect = 0.040
Identities = 36/156 (23%), Positives = 62/156 (39%), Gaps = 17/156 (10%)
Query: 255 IGTLADSVGHHLNKPEYISLLMPPLIQKWNILKDE--DKDLFP-LLECLSSVATALQAGF 311
+G LA+++G N Y +LM L+Q L E +DL P +L +A A+ A F
Sbjct: 663 VGDLANTLGTDFNI--YADVLMSSLVQ---CLSSEATHRDLKPAILSVFGDIALAIGANF 717
Query: 312 LPYCEPVYRRCVSLIEQTLNQHMANSQNPEQFDAPDKDFMIVALDLLSGLAEGLDMHIDS 371
Y + + L+ H S D +V G+ + + S
Sbjct: 718 ESYLDMIMMLFQQA--SELDPH---SDEVYVDDYRKNAVQLV-NCAYVGIGDSSKNRVRS 771
Query: 372 LVSN-SNIMHLLYQCMQDP--MPEVRQSSFALLGDL 404
++ +I H + +DP +++ L+GDL
Sbjct: 772 VLPYVISIFHKIGMIAEDPNGSEAHTRAALGLIGDL 807
>gnl|CDD|237987 cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately
40 amino acid long tandemly repeated sequence motif
first identified in the Drosophila segment polarity gene
armadillo; these repeats were also found in the
mammalian armadillo homolog beta-catenin, the junctional
plaque protein plakoglobin, the adenomatous polyposis
coli (APC) tumor suppressor protein, and a number of
other proteins. ARM has been implicated in mediating
protein-protein interactions, but no common features
among the target proteins recognized by the ARM repeats
have been identified; related to the HEAT domain; three
consecutive copies of the repeat are represented by this
alignment model.
Length = 120
Score = 53.1 bits (128), Expect = 1e-08
Identities = 25/131 (19%), Positives = 41/131 (31%), Gaps = 21/131 (16%)
Query: 98 LLPILKETLFHHDWEIKESGILALGAIAEGCMNGMVPHLNEL--VPFLITCLSDKKALVR 155
LP L L D ++ AL ++ G N + + E +P L+ L + V
Sbjct: 8 GLPALVSLLSSSDENVQREAAWALSNLSAG-NNDNIQAVVEAGGLPALVQLLKSEDEEVV 66
Query: 156 AITCWTLSRYSHWVVSQPHDSYLKPLMTEMLGCMNGMVPHLNELVPFLITCLSDKKALVR 215
W L + K ++ E G VP L+ L ++
Sbjct: 67 KAALWALRNLAAGPEDN------KLIVLEAGG------------VPKLVNLLDSSNEDIQ 108
Query: 216 AITCWTLSRYS 226
LS +
Sbjct: 109 KNATGALSNLA 119
Score = 42.7 bits (101), Expect = 5e-05
Identities = 26/105 (24%), Positives = 44/105 (41%), Gaps = 13/105 (12%)
Query: 71 SDWNLRKCSAAAL--------DVLANVFREELLPVLLPILKETLFHHDWEIKESGILALG 122
SD N+++ +A AL D + V LP L+ +LK D E+ ++ + AL
Sbjct: 19 SDENVQREAAWALSNLSAGNNDNIQAVVEAGGLPALVQLLK----SEDEEVVKAALWALR 74
Query: 123 AIAEGC-MNGMVPHLNELVPFLITCLSDKKALVRAITCWTLSRYS 166
+A G N ++ VP L+ L ++ LS +
Sbjct: 75 NLAAGPEDNKLIVLEAGGVPKLVNLLDSSNEDIQKNATGALSNLA 119
Score = 32.3 bits (74), Expect = 0.21
Identities = 19/90 (21%), Positives = 41/90 (45%), Gaps = 2/90 (2%)
Query: 358 LSGLAEGLDMHIDSLVSNSNIMHLLYQCMQDPMPEVRQSSFALLGDLTKACFSHVHPCI- 416
LS L+ G + +I ++V + + L Q ++ EV +++ L +L + +
Sbjct: 31 LSNLSAGNNDNIQAVV-EAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLIVLE 89
Query: 417 SDFMPILGQNLNPDLISVCNNATWAIGEIS 446
+ +P L L+ + NAT A+ ++
Sbjct: 90 AGGVPKLVNLLDSSNEDIQKNATGALSNLA 119
Score = 30.0 bits (68), Expect = 1.3
Identities = 16/101 (15%), Positives = 27/101 (26%), Gaps = 22/101 (21%)
Query: 137 NELVPFLITCLSDKKALVRAITCWTLSRYSHWVVSQPHDSYLKPLMTEMLGCMNGMVPHL 196
+P L++ LS V+ W LS + N + +
Sbjct: 6 AGGLPALVSLLSSSDENVQREAAWALS--------------------NLSAGNNDNIQAV 45
Query: 197 NEL--VPFLITCLSDKKALVRAITCWTLSRYSHWVVSQPHD 235
E +P L+ L + V W L +
Sbjct: 46 VEAGGLPALVQLLKSEDEEVVKAALWALRNLAAGPEDNKLI 86
>gnl|CDD|222285 pfam13646, HEAT_2, HEAT repeats. This family includes multiple
HEAT repeats.
Length = 88
Score = 38.9 bits (91), Expect = 5e-04
Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 18/94 (19%)
Query: 71 SDWNLRKCSAAALDVLANVFREELLPVLLPILKETLFHHDWEIKESGILALGAIAEGCMN 130
D +R AAA L + E LP LL +LK D E++ + ALG + +
Sbjct: 12 PDPEVR---AAAARALGELGDPEALPALLELLK----DPDPEVRRAAAEALGKLGD---- 60
Query: 131 GMVPHLNELVPFLITCL-SDKKALVRAITCWTLS 163
E +P L+ L D A+VRA L+
Sbjct: 61 ------PEALPALLELLQDDDDAVVRAAAASALA 88
Score = 33.9 bits (78), Expect = 0.036
Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 11/68 (16%)
Query: 99 LPILKETLFHH-DWEIKESGILALGAIAEGCMNGMVPHLNELVPFLITCLSDKKALVRAI 157
L L E L D E++ + ALG + E +P L+ L D VR
Sbjct: 1 LEALLEALLSDPDPEVRAAAARALGEL----------GDPEALPALLELLKDPDPEVRRA 50
Query: 158 TCWTLSRY 165
L +
Sbjct: 51 AAEALGKL 58
>gnl|CDD|202500 pfam02985, HEAT, HEAT repeat. The HEAT repeat family is related to
armadillo/beta-catenin-like repeats (see pfam00514).
Length = 31
Score = 33.3 bits (77), Expect = 0.012
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 378 IMHLLYQCMQDPMPEVRQSSFALLGDLTKAC 408
++ LL + + DP PEVR+++ LG L +
Sbjct: 1 LLPLLLELLNDPDPEVREAAAEALGALAEVL 31
Score = 30.2 bits (69), Expect = 0.15
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 139 LVPFLITCLSDKKALVRAITCWTLSR 164
L+P L+ L+D VR L
Sbjct: 1 LLPLLLELLNDPDPEVREAAAEALGA 26
Score = 30.2 bits (69), Expect = 0.15
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 199 LVPFLITCLSDKKALVRAITCWTLSR 224
L+P L+ L+D VR L
Sbjct: 1 LLPLLLELLNDPDPEVREAAAEALGA 26
Score = 30.2 bits (69), Expect = 0.15
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 98 LLPILKETLFHHDWEIKESGILALGAIAEGC 128
LLP+L E L D E++E+ ALGA+AE
Sbjct: 1 LLPLLLELLNDPDPEVREAAAEALGALAEVL 31
>gnl|CDD|227508 COG5181, HSH155, U2 snRNP spliceosome subunit [RNA processing and
modification].
Length = 975
Score = 36.5 bits (84), Expect = 0.044
Identities = 28/92 (30%), Positives = 39/92 (42%), Gaps = 8/92 (8%)
Query: 75 LRKCSAAALDVLANVFR-EELLPVLLPILKETLFH--HDWEIKESGILALGAIAEGCMNG 131
+R + A+ V+A+ EELLP L E L WE + +GI I E
Sbjct: 297 VRNVTGRAVGVVADALGVEELLPFL-----EALCGSRKSWEARHTGIRIAQQICELLGRS 351
Query: 132 MVPHLNELVPFLITCLSDKKALVRAITCWTLS 163
+ HL L+ + L D+ VR T LS
Sbjct: 352 RLSHLGPLLKCISKLLKDRSRFVRIDTANALS 383
Score = 30.3 bits (68), Expect = 3.2
Identities = 35/146 (23%), Positives = 51/146 (34%), Gaps = 31/146 (21%)
Query: 136 LNELVPFLITCLSDKKALVRAITCWTLSRYSHWVVSQPHDSYLKPLMTEMLGCMNGMVPH 195
+ EL+PFL +AL + W + Q + E+LG + H
Sbjct: 314 VEELLPFL-------EALCGSRKSWEARHTGIRIAQQ---------ICELLGR--SRLSH 355
Query: 196 LNELVPFLITCLSDKKALVRAITCWTLSRYSHWVV---SQPHDSYLKPLMTE-----HKN 247
L L+ + L D+ VR T LS + V + D L PL K
Sbjct: 356 LGPLLKCISKLLKDRSRFVRIDTANALSYLAELVGPYGIEQFDEVLCPLWEGASQHRGKE 415
Query: 248 LLILYDAIGTLADSVGHHLNKPEYIS 273
L+ A+G + L PEY
Sbjct: 416 LVSFLKAMGFIIP-----LMSPEYAC 436
>gnl|CDD|193231 pfam12755, Vac14_Fab1_bd, Vacuolar 14 Fab1-binding region. Vac14
is a scaffold for the Fab1 kinase complex, a complex
that allows for the dynamic interconversion of PI3P and
PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids,
that are generated transiently on the cytoplasmic face
of selected intracellular membranes). This
interconversion is regulated by at least five proteins
in yeast: the lipid kinase Fab1p, lipid phosphatase
Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor
Atg18p, and Vac14p, a protein required for the activity
of both Fab1p and Fig4p. This domain appears to be the
one responsible for binding to Fab1. The full length
Vac14 in yeasts is likely to be a protein carrying a
succession of HEAT repeats, most of which have now
degenerated. This regulatory system is crucial for the
proper functioning of the mammalian nervous system.
Length = 97
Score = 31.8 bits (73), Expect = 0.20
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 117 GILALGAIAEGCMNGMVPHLNELVPFLITCLSDKKALVRAITC 159
G++ L A+A + P+L+E++P ++ C +D+ + VR C
Sbjct: 6 GLIGLAAVAIALGKDIAPYLDEIIPPVLACFTDQDSRVRYYAC 48
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 32.4 bits (74), Expect = 0.44
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 10/68 (14%)
Query: 13 KGDVEEDEMIPDRDEDIRPRFHKSKRSVKAEGENMNMG------ENGGEEVEEEDDDLDD 66
K + +E D D + + K + E E+++ E EE E+ED D DD
Sbjct: 138 KVGLFTEEEE---DIDEKLSMLEKKLK-ELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDD 193
Query: 67 DSSLSDWN 74
D D+N
Sbjct: 194 DDDDDDYN 201
>gnl|CDD|217246 pfam02834, LigT_PEase, LigT like Phosphoesterase. Members of this
family are bacterial and archaeal RNA ligases that are
able to ligate tRNA half molecules containing
2',3'-cyclic phosphate and 5' hydroxyl termini to
products containing the 2',5' phosphodiester linkage.
Each member of this family contains an internal
duplication, each of which contains an HXTX motif that
defines the family. The structure of a related protein
is known. They belong to the 2H phosphoesterase
superfamily. They share a common active site,
characterized by two conserved histidines, with
vertebrate myelin-associated 2',3' phosphodiesterases,
plant Arabidopsis thaliana CPDases and several several
bacteria and virus proteins.
Length = 87
Score = 30.1 bits (68), Expect = 0.72
Identities = 12/50 (24%), Positives = 18/50 (36%), Gaps = 1/50 (2%)
Query: 483 ITIGRLGYVCPHDVAPLCSSLRNI-RDNEEKDSAFRGMCAMITVNPGGVV 531
IT+ LG V V L +L NI + G+ + V+
Sbjct: 37 ITLAFLGEVDEEKVPELLEALANIAFGFPPFELKVDGVGLFPSTLRPRVI 86
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The
CAF-1 or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression
in addition to DNA-based checkpoints.
Length = 76
Score = 29.5 bits (67), Expect = 0.83
Identities = 14/25 (56%), Positives = 17/25 (68%), Gaps = 3/25 (12%)
Query: 43 EGENMNMGENGGEEVEEEDDDLDDD 67
EGE++ E+ EE EEEDDD D D
Sbjct: 53 EGEDL---ESEDEEDEEEDDDDDMD 74
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 32.0 bits (73), Expect = 1.00
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 41 KAEGENMNMGENGG---EEVEEEDDDLDDDSSLSDWNLRKCS 79
K EG++++ + E E+EDDD DDD + W LRK
Sbjct: 317 KIEGKSVSEEDEDEDSDSEEEDEDDDEDDDDGENPWMLRKKL 358
>gnl|CDD|224331 COG1413, COG1413, FOG: HEAT repeat [Energy production and
conversion].
Length = 335
Score = 31.4 bits (71), Expect = 1.1
Identities = 22/96 (22%), Positives = 35/96 (36%), Gaps = 15/96 (15%)
Query: 72 DWNLRKCSAAALDVLANVFREELLPVLLPILKETLFHHDWEIKESGILALGAIAEGCMNG 131
++R +A AL L + P +P+L E L D +++ + ALG +
Sbjct: 162 LLDVRAAAAEALGELGD-------PEAIPLLIELLEDEDADVRRAAASALGQLGS----- 209
Query: 132 MVPHLNELVPFLITCLSDKKALVRAITCWTLSRYSH 167
E L+ LSD+ VR L
Sbjct: 210 ---ENVEAADLLVKALSDESLEVRKAALLALGEIGD 242
>gnl|CDD|227396 COG5064, SRP1, Karyopherin (importin) alpha [Intracellular
trafficking and secretion].
Length = 526
Score = 31.8 bits (72), Expect = 1.2
Identities = 34/157 (21%), Positives = 64/157 (40%), Gaps = 23/157 (14%)
Query: 82 ALDVLANVFREELLPVL----LPILKETLFHHDWEIKESGILALGAIAEGCMNGMVPHLN 137
A+ L++ E++ VL L E L H +I+ + ++G I G + +N
Sbjct: 266 AISYLSDGPNEKIQAVLDVGIPGRLVELLSHESAKIQTPALRSVGNIVTGSDDQTQVIIN 325
Query: 138 -ELVPFLITCLSDKKALVRAITCWTLSRYSHWVVSQPHDSYLKPLMTEMLGCMNGMVPHL 196
+ + LS K +R CWT+S + Q ++ ++ N
Sbjct: 326 CGALKAFRSLLSSPKENIRKEACWTISNITAGNTEQ-----IQAVID-----AN------ 369
Query: 197 NELVPFLITCLSDKKALVRAITCWTLSRYSHWVVSQP 233
L+P LI LS + ++ CW +S + +++P
Sbjct: 370 --LIPPLIHLLSSAEYKIKKEACWAISNATSGGLNRP 404
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 31.5 bits (71), Expect = 1.5
Identities = 12/57 (21%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 13 KGDVEEDEMIPDRDEDIRPRFHK-SKRSVKAEGENMNMGENGGEEVEEEDDDLDDDS 68
K ++E+DE + +E+ SK+ K + ++ + DD D D
Sbjct: 311 KPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDSDDSDI 367
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 31.3 bits (71), Expect = 1.5
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 8/46 (17%)
Query: 35 KSKRSVKAEGENMNMGENGGE--------EVEEEDDDLDDDSSLSD 72
SKR A+ + ++ + G +E + DD DDD S D
Sbjct: 235 SSKRRTIAQIDGIDSDDEGDGSDDDDDEDAIESDLDDSDDDVSDED 280
>gnl|CDD|221583 pfam12449, DUF3684, Protein of unknown function (DUF3684). This
domain family is found in eukaryotes, and is typically
between 1072 and 1090 amino acids in length.
Length = 1084
Score = 31.1 bits (71), Expect = 1.9
Identities = 13/46 (28%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 53 GGEEVEEEDDDLDDDSSLSDWNLRKCSAAAL--DVLA-NVFREELL 95
E++DDD D+D+ + +W L K S + D + +F++ +L
Sbjct: 983 KASTSEDDDDDEDEDAGIKEWQLAKASDIVIVDDYNSYQLFKDSIL 1028
>gnl|CDD|223136 COG0058, GlgP, Glucan phosphorylase [Carbohydrate transport and
metabolism].
Length = 750
Score = 30.7 bits (70), Expect = 2.3
Identities = 19/94 (20%), Positives = 40/94 (42%), Gaps = 17/94 (18%)
Query: 118 ILALGAIAEGCMNGMVPHLNE-----LVPFLITCLSDKKAL--------VRAITCWTLSR 164
ILA G + ++ + HLN+ +P L+ L D++ L VR +T
Sbjct: 252 ILARGHLEHHDLDVLADHLNDTHPALAIPELMRLLIDEEGLSWDEAWEIVRKTFVYT--- 308
Query: 165 YSHWVVSQPHDSYLKPLMTEMLGCMNGMVPHLNE 198
+H + + +++ L ++L ++ +N
Sbjct: 309 -NHTPLPEALETWPVELFKKLLPRHLQIIYEINA 341
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 30.6 bits (69), Expect = 2.6
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 13/79 (16%)
Query: 15 DVEEDEMIPDRDEDIRPRFHKSKRSVKAEGENMNMGENGGEEVEEEDDDLDDDSSLSDWN 74
D EEDE D E K +A + +N+ + E+++ +DD+ +
Sbjct: 681 DGEEDEQ-EDDAEANEGVVPIDKAVRRALPKVLNLPDALDGGDSEDEEGMDDEQMM---- 735
Query: 75 LRKCSAAALDV-LANVFRE 92
LD LA +F+E
Sbjct: 736 -------RLDTYLAQIFKE 747
>gnl|CDD|168632 PRK06633, PRK06633, acetyl-CoA acetyltransferase; Provisional.
Length = 392
Score = 30.0 bits (67), Expect = 3.6
Identities = 15/35 (42%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 81 AALDVLANVFREELLPVLLPILKET-LFHHDWEIK 114
AA LA +F++E+LP+ + I K T LF HD ++
Sbjct: 186 AAKAQLAGIFKDEILPIEVTIKKTTSLFDHDETVR 220
>gnl|CDD|235089 PRK02946, aceK, bifunctional isocitrate dehydrogenase
kinase/phosphatase protein; Validated.
Length = 575
Score = 30.2 bits (69), Expect = 4.0
Identities = 10/43 (23%), Positives = 15/43 (34%)
Query: 547 PKEDLKEMFHKILHGFRTQVGDENWQRFADQFPDQLRDRLSAM 589
P L +IL F ++ E+ R LR+ L
Sbjct: 145 PDGGLAATLERILSDFPLRLPFEDLDRDIAYIAAALREALGPF 187
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 29.3 bits (66), Expect = 4.7
Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 17 EEDEMIPDRDEDIRPRFHKSKRSVKAEGENMNMGENGGEEVEEEDDDLDDD 67
E DE + DE R R + R+ A+ + + + ++ DDD +D
Sbjct: 94 EGDEDDDEEDEIKRKRIEEDARNSDADDSDSS--SDSDSSDDDSDDDDSED 142
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 28.8 bits (65), Expect = 4.8
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 44 GENMNMGENGGEEVEEEDDDLDDDSSLSD 72
+ ++ E+ EEEDD+ DDD S+
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESE 136
>gnl|CDD|227943 COG5656, SXM1, Importin, protein involved in nuclear import
[Posttranslational modification, protein turnover,
chaperones].
Length = 970
Score = 29.4 bits (66), Expect = 6.2
Identities = 26/170 (15%), Positives = 59/170 (34%), Gaps = 16/170 (9%)
Query: 199 LVPFLITCLSDKKALVRAITCWTLSRYS-HW----VVSQPHDSYLKPLMTEHKNLLI-LY 252
+V +I +++ C +S + ++ + +++ L H ++I
Sbjct: 461 IVNHVIPAFRSNYGFLKSRACEFISTIEEDFKDNGILLEAYENTHNCLKNNHLPVMIEAA 520
Query: 253 DAIGTLADSVGHHLNKPEYISLLMPPLIQKWNILK-DEDKDLFPLLECLSSVATALQAGF 311
A+ + H E S +P ++K +L ++ PL + S
Sbjct: 521 LALQFFIFNEQSH----EKFSAHVPETMEK--LLSLSNTFEIDPLSMVMESFVEYFSEEL 574
Query: 312 LPYCEPVYRRCVSLIEQTLNQHMANSQNPEQFDAPDKDFMIVALDLLSGL 361
P+ + SL+ Q L + +N + D + A +L +
Sbjct: 575 SPFAPELAG---SLVRQFLKIAQSLLENSSDTSSVVDDKQMAASGILRTI 621
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 0.425
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,856,192
Number of extensions: 3065062
Number of successful extensions: 2891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2843
Number of HSP's successfully gapped: 54
Length of query: 592
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 490
Effective length of database: 6,413,494
Effective search space: 3142612060
Effective search space used: 3142612060
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)