RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14375
(206 letters)
>gnl|CDD|128904 smart00657, RPOL4c, DNA-directed RNA-polymerase II subunit.
Length = 118
Score = 118 bits (297), Expect = 2e-34
Identities = 60/118 (50%), Positives = 80/118 (67%)
Query: 88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
EF+NA L SEV +LL+ ++ E+ EE+Q S V +KTL Y +F +FKNRE + +V
Sbjct: 1 PEFKNATCLTNSEVQLLLELKRQSKESEEEQQPLSTVMKKTLKYLSKFARFKNREIVRAV 60
Query: 148 RNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKRSLQ 205
R LL KKLHKFE+A + NL PET EEA+ LIPSLE R +EEEL ++LDD+ +
Sbjct: 61 RTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDDLSSLLPFY 118
>gnl|CDD|217775 pfam03874, RNA_pol_Rpb4, RNA polymerase Rpb4. This family includes
the Rpb4 protein. This family also includes C17 (aka
CGRP-RCP) is an essential subunit of RNA polymerase III.
C17 forms a subcomplex with C25 which is likely to be
the counterpart of subcomplex Rpb4/7 in Pol II.
Length = 110
Score = 104 bits (261), Expect = 4e-29
Identities = 41/109 (37%), Positives = 62/109 (56%), Gaps = 2/109 (1%)
Query: 96 LLISEVHMLLQHR--KTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQ 153
L SEV +L+ + + E+ E+ + + +KTL Y +F + KN E+ + L +
Sbjct: 2 LTNSEVLEILKKELEERRRESRYVEENLNTILRKTLEYLNKFSRLKNPESARELVEELKE 61
Query: 154 KKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQILDDIQTKR 202
+L KFE I NL PET +E +A+I SLE RF EE+L +ILD + R
Sbjct: 62 FELTKFEALQIVNLLPETADELRAIIESLESRFSEEQLEEILDILSKYR 110
>gnl|CDD|227575 COG5250, RPB4, RNA polymerase II, fourth largest subunit
[Transcription].
Length = 138
Score = 93.1 bits (231), Expect = 2e-24
Identities = 45/132 (34%), Positives = 74/132 (56%), Gaps = 4/132 (3%)
Query: 78 EEDAGDLQFPKEFENAETLLISEVHMLLQHRKTQNENAEEEQEF----SEVFQKTLTYTE 133
EEDA L+ EFEN + L++SE L++ + + EF +VF+ TL Y +
Sbjct: 7 EEDAAQLKLGPEFENEDMLMLSEARYLIEGQLERRRRETNGAEFRSNDVKVFKSTLGYLD 66
Query: 134 RFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEELRQ 193
F +FK++E ++R L+ H+FE+A + +L ++ EEAK LIPSL + ++ L+
Sbjct: 67 DFCRFKDKEVAEALRTTLSGLGFHEFEIAQLGSLFCQSAEEAKTLIPSLGNKIDDAILQA 126
Query: 194 ILDDIQTKRSLQ 205
IL ++ R Q
Sbjct: 127 ILKELSLLRKFQ 138
>gnl|CDD|184943 PRK14981, PRK14981, DNA-directed RNA polymerase subunit F;
Provisional.
Length = 112
Score = 48.7 bits (117), Expect = 6e-08
Identities = 33/110 (30%), Positives = 51/110 (46%), Gaps = 9/110 (8%)
Query: 88 KEFENAETLLISEVHMLLQHRKTQNENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSV 147
K+ E + I+E +L EEE+E S ++TL Y RF K + E +
Sbjct: 4 KKILEEEYITIAEAKEIL-------SEIEEERELSYELRRTLDYLNRFSKL-DPEDAEEL 55
Query: 148 RNLLTQKKLHKFELAA-IANLCPETPEEAKALIPSLECRFEEEELRQILD 196
L + + K + A IA++ PET +E +A+ EEL +ILD
Sbjct: 56 VEELLELEKMKEKTAVKIADILPETRDELRAIFAKERYTLSPEELDEILD 105
>gnl|CDD|224377 COG1460, COG1460, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 114
Score = 38.5 bits (90), Expect = 3e-04
Identities = 24/84 (28%), Positives = 42/84 (50%)
Query: 113 ENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETP 172
E E+E + ++ L Y E+F K + V LL+ K+ + IA++ P TP
Sbjct: 23 SKVEREEELTYEQREALEYAEKFAKLDPEKARELVEELLSIVKMSEKIAVKIADIMPRTP 82
Query: 173 EEAKALIPSLECRFEEEELRQILD 196
+E ++++ +EEL +ILD
Sbjct: 83 DELRSILAKERVMLSDEELDKILD 106
>gnl|CDD|218607 pfam05494, Tol_Tol_Ttg2, Toluene tolerance, Ttg2. Toluene
tolerance is mediated by increased cell membrane
rigidity resulting from changes in fatty acid and
phospholipid compositions, exclusion of toluene from the
cell membrane, and removal of intracellular toluene by
degradation. Many proteins are involved in these
processes. This family is a transporter which shows
similarity to ABC transporters.
Length = 167
Score = 29.5 bits (67), Expect = 0.72
Identities = 8/29 (27%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 114 NAEEEQEFSEVFQKTL--TYTERFRKFKN 140
+ E+ QEF + F++ L TY + ++
Sbjct: 56 SPEQRQEFVDAFRELLVRTYAKALAEYSG 84
>gnl|CDD|145136 pfam01815, Rop, Rop protein.
Length = 61
Score = 27.0 bits (60), Expect = 1.4
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 150 LLTQKKLHKFELAAIANLCPETPEEAKALIPSLECRFEEEE 190
LL +KL++ +L A+ C + E+A+ L SL R EE
Sbjct: 20 LLLLEKLNELDLDEEADECEKLHEQAEELYRSLSARLGEEG 60
>gnl|CDD|226466 COG3957, COG3957, Phosphoketolase [Carbohydrate transport and
metabolism].
Length = 793
Score = 28.9 bits (65), Expect = 2.3
Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 136 RKFKNRETITSVRNLLTQKKLHKFELAAIA-NLCPETPEEAKALIPSLECRFEEEE 190
++ R T T+ ++ +L +F L A A P+ A L +L+ + E E
Sbjct: 718 EGYRERGTTTTPFDMFVLNRLDRFHLVADAGQRLPQNGLTAAYLAQALKDKLIEHE 773
>gnl|CDD|153306 cd07622, BAR_SNX4, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 4. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX4 is involved in recycling traffic
from the sorting endosome (post-Golgi endosome) back to
the late Golgi. It is also implicated in the regulation
of plasma membrane receptor trafficking and interacts
with receptors for EGF, insulin, platelet-derived growth
factor and leptin. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 201
Score = 28.1 bits (63), Expect = 2.7
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 105 LQHRKTQNENAEEEQ--EFSEVFQKTLTYTERFRKFKNRE 142
L ++K Q E A +E E +E +K L ERF+K K R+
Sbjct: 131 LANKKQQGEEAVKEAKDELNEFVKKALEDVERFKKQKVRD 170
>gnl|CDD|201317 pfam00576, Transthyretin, HIUase/Transthyretin family. This
family includes transthyretin that is a thyroid
hormone-binding protein that transports thyroxine from
the bloodstream to the brain. However, most of the
sequences listed in this family do not bind thyroid
hormones. They are actually enzymes of the purine
catabolism that catalyze the conversion of
5-hydroxyisourate (HIU) to OHCU. HIU hydrolysis is the
original function of the family and is conserved from
bacteria to mammals; transthyretins arose by gene
duplications in the vertebrate lineage. HIUases are
distinguished in the alignment from the conserved
C-terminal YRGS sequence.
Length = 111
Score = 27.2 bits (61), Expect = 2.9
Identities = 9/34 (26%), Positives = 12/34 (35%), Gaps = 3/34 (8%)
Query: 67 IIMTHVLDQVVEEDAGDLQ---FPKEFENAETLL 97
+ THVLD + A + F LL
Sbjct: 2 PLTTHVLDTARGKPAAGVAVKLFRLTEGGGWELL 35
>gnl|CDD|220494 pfam09969, DUF2203, Uncharacterized conserved protein (DUF2203).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 120
Score = 27.3 bits (61), Expect = 3.5
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 171 TPEEAKALIPSLECRFEE-EELRQILDDIQTKRS 203
T EEA L+P L EE E + L++++ S
Sbjct: 4 TLEEANELLPELRRLLEEVREAKAELEELEAALS 37
>gnl|CDD|130650 TIGR01589, A_thal_3526, uncharacterized plant-specific domain
TIGR01589. This model represents an uncharacterized
plant-specific domain 57 residues in length. It is
found toward the N-terminus of most proteins that
contain it. Examples include at least 10 proteins from
Arabidopsis thaliana and at least one from Oryza
sativa.
Length = 57
Score = 25.9 bits (57), Expect = 4.1
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 3 CLGLGQNKEKTVSFLLSTSRISPG 26
C+ +KE+TVSFL + ISP
Sbjct: 11 CIQGYMSKEETVSFLFENAGISPK 34
>gnl|CDD|224625 COG1711, COG1711, DNA replication initiation complex subunit, GINS
family [Replication, recombination, and repair].
Length = 223
Score = 27.5 bits (61), Expect = 4.8
Identities = 24/100 (24%), Positives = 35/100 (35%), Gaps = 14/100 (14%)
Query: 113 ENAEEEQEFSEVFQKTLTYTERFRKFKNRETITSVRNLLTQKKLHKFELAAIANLCPETP 172
E+ E + +K L ET S + Q++ K AI ++ ET
Sbjct: 38 EDEAGRAEEARDIEKYLLTDRI-------ETAKSDARSIFQRRYGKIVSRAIYDVPGETI 90
Query: 173 E----EAKALIPSLECRFEEEE---LRQILDDIQTKRSLQ 205
E K L L E+E L I + KR +Q
Sbjct: 91 SNLTPEEKELYEDLVNFIEDERISFLPTIDVIAEEKREIQ 130
>gnl|CDD|237563 PRK13928, PRK13928, rod shape-determining protein Mbl; Provisional.
Length = 336
Score = 27.6 bits (62), Expect = 5.0
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 20/73 (27%)
Query: 29 VVSLFPRKIQPKSNQIKSALS----------KSVPPRTP---YSDRVSIGYIIMT----- 70
+V+ P+ I S +I+ AL KSV RTP +D + G IIMT
Sbjct: 229 LVTGLPKTITVTSEEIREALKEPVSAIVQAVKSVLERTPPELSADIIDRG-IIMTGGGAL 287
Query: 71 -HVLDQVVEEDAG 82
H LD+++ E+
Sbjct: 288 LHGLDKLLAEETK 300
>gnl|CDD|183955 PRK13292, PRK13292, trifunctional NADH dehydrogenase I subunit
B/C/D; Provisional.
Length = 788
Score = 27.4 bits (61), Expect = 5.7
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 132 TERFRKFKNRETITSVRNLLTQKKLHK--FELAAIANLCPETPEEA-KALIPSLECRFEE 188
T F F +RE I + ++T ++H F + +A PE +EA +A + R +E
Sbjct: 523 TPVFYTFTDREKIFDIVEMITGGRMHPAWFRIGGVAEDLPEGWKEAVEAFLRWFPGRLKE 582
Query: 189 EE 190
E
Sbjct: 583 YE 584
>gnl|CDD|215206 PLN02362, PLN02362, hexokinase.
Length = 509
Score = 27.5 bits (61), Expect = 6.0
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 57 PYSDRVSIGYIIMTHVLDQVVEEDAGDLQFPKEFENA----ETLLISEVHM 103
P S R+S +++ T + + E+D+ +LQ E A ETL ISEV +
Sbjct: 343 PVSSRLSTPFVLRTPSVAAMHEDDSPELQ-----EVARILKETLGISEVPL 388
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily
of calcium sensors and calcium signal modulators; most
examples in this alignment model have 2 active canonical
EF hands. Ca2+ binding induces a conformational change
in the EF-hand motif, leading to the activation or
inactivation of target proteins. EF-hands tend to occur
in pairs or higher copy numbers.
Length = 63
Score = 25.2 bits (56), Expect = 7.9
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 171 TPEEAKALIPSLECRFEEEELRQILDDI 198
+ +E KA + SL EEE+ +++ ++
Sbjct: 18 SADELKAALKSLGEGLSEEEIDEMIREV 45
>gnl|CDD|193548 cd05673, M20_Acy1L2_AbgB, M20 Peptidase Aminoacylase 1-like protein
2 aminobenzoyl-glutamate utilization protein B
subfamily. Peptidase M20 family, ACY1L2
aminobenzoyl-glutamate utilization protein B (AbgB)
subfamily. This group contains mostly bacterial
amidohydrolases, including gene products of abgB that
catalyze the cleavage of p-aminobenzoyl-glutamate, a
folate catabolite in Escherichia coli, to
p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate
is a natural end product of folate catabolism, and its
utilization is initiated by the abg region gene product,
AbgT, by enabling uptake of its into the cell in a
concentration-dependent, saturable manner. It is
subsequently cleaved by AbgA and AbgB (sometimes
referred to as AbgAB).
Length = 434
Score = 26.7 bits (60), Expect = 8.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 116 EEEQEFSEVFQKTLTYTER 134
EEEQ F++ Q+TL R
Sbjct: 312 EEEQAFAKEIQETLGEEAR 330
>gnl|CDD|173688 cd05597, STKc_DMPK_like, Catalytic domain of Myotonic Dystrophy
protein kinase-like Protein Serine/Threonine Kinases.
Serine/Threonine Kinases (STKs), Myotonic Dystrophy
protein kinase (DMPK)-like subfamily, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The DMPK-like subfamily
is part of a larger superfamily that includes the
catalytic domains of other protein STKs, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. The DMPK-like subfamily is composed of DMPK
and DMPK-related cell division control protein 42
(Cdc42) binding kinase (MRCK). Three isoforms of MRCK
are known, named alpha, beta and gamma. The DMPK gene is
implicated in myotonic dystrophy 1 (DM1), an inherited
multisystemic disorder with symptoms that include muscle
hyperexcitability, progressive muscle weakness and
wasting, cataract development, testicular atrophy, and
cardiac conduction defects. The genetic basis for DM1 is
the mutational expansion of a CTG repeat in the 3'-UTR
of DMPK. DMPK is expressed in skeletal and cardiac
muscles, and in central nervous tissues. The functional
role of DMPK is not fully understood. It may play a role
in the signal transduction and homeostasis of calcium.
MRCK is activated via interaction with the small GTPase
Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent
cell motility. MRCKgamma is expressed in heart and
skeletal muscles, unlike MRCKalpha and MRCKbeta, which
are expressed ubiquitously.
Length = 331
Score = 26.7 bits (59), Expect = 9.0
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 169 PETPEEAKALIPSLECRFEEEELRQILDDIQT 200
+ EEAK LI L C E R L D +
Sbjct: 234 TDVSEEAKDLIRRLICSPETRLGRNGLQDFKD 265
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
0.316 0.131 0.362
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,101,939
Number of extensions: 920060
Number of successful extensions: 1051
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1048
Number of HSP's successfully gapped: 45
Length of query: 206
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 114
Effective length of database: 6,857,034
Effective search space: 781701876
Effective search space used: 781701876
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 (21.6 bits)
S2: 57 (25.8 bits)