RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15011
(334 letters)
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 142 bits (360), Expect = 2e-41
Identities = 50/148 (33%), Positives = 83/148 (56%), Gaps = 2/148 (1%)
Query: 69 MIKLLSRSVPYEPLKEEYLKECWPLVKNALELH-FIKAELDVIEGSMTVFTTRKTWDPYI 127
+ S +V + L W VK A+E +K +D GS+T+ TTRKT DP
Sbjct: 4 FAEKSSEAVKIPKDRIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLA 63
Query: 128 IIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIGNLVQNKQR-FVKRRQRLIGPNGCT 186
++KARD++K + R P E+A+++L+DD ++I + ++V + + R+IG G T
Sbjct: 64 LLKARDVVKAIGRGFPPEKALKLLEDDYYLEVIDLKDVVTLSGDHLRRIKGRIIGREGKT 123
Query: 187 LKSIELLTNCYMLVQGQTVAALGPHKGL 214
++IE LT Y+ V G+TVA +G + +
Sbjct: 124 RRAIEELTGVYISVYGKTVAIIGGFEQV 151
Score = 55.0 bits (133), Expect = 4e-09
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 20 EYLKECWPLVKNALELH-FIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVP 78
L W VK A+E +K +D GS+T+ TTRKT DP ++KARD++K + R P
Sbjct: 20 GVLIGKWGEVKKAIEEKTGVKLRIDSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRGFP 79
Query: 79 YE 80
E
Sbjct: 80 PE 81
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 68.7 bits (169), Expect = 4e-14
Identities = 32/116 (27%), Positives = 59/116 (50%), Gaps = 1/116 (0%)
Query: 94 VKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQD 153
K +E +LD+ + V + DP ++KAR+++K + R E+A+++L D
Sbjct: 19 TKKEIEERT-GVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALKLLDD 77
Query: 154 DISCDIIKIGNLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALG 209
D ++I + ++ + + R+IG G T + IE LT + V G+TV +G
Sbjct: 78 DYMLEVIDLKEYGKSPNALRRIKGRIIGEGGKTRRIIEELTGVSISVYGKTVGIIG 133
Score = 27.5 bits (62), Expect = 7.1
Identities = 12/47 (25%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 29 VKNALELHFIKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSR 75
K +E +LD+ + V + DP ++KAR+++K + R
Sbjct: 19 TKKEIEERT-GVKLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGR 64
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 65.3 bits (160), Expect = 9e-13
Identities = 35/109 (32%), Positives = 59/109 (54%), Gaps = 1/109 (0%)
Query: 103 IKAELDVIEGSMTVFTTRKTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKI 162
+K E+D G + + T DP ++KARD++K + R E+A+R+L DD ++I +
Sbjct: 34 VKLEIDSETGEVIIEPT-DGEDPLAVLKARDIVKAIGRGFSPEKALRLLDDDYVLEVIDL 92
Query: 163 GNLVQNKQRFVKRRQRLIGPNGCTLKSIELLTNCYMLVQGQTVAALGPH 211
+ + + + R+IG G T + IE LT + V G+TVA +G
Sbjct: 93 SDYGDSPNALRRIKGRIIGEGGKTRRIIEELTGVDISVYGKTVAIIGDP 141
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point sequence
(BPS) UACUAAC in the pre-mRNA transcripts during
spliceosome assembly. We show that the KH-QUA2 region of
SF1 defines an enlarged KH (hnRNP K) fold which is
necessary and sufficient for BPS binding. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 120
Score = 31.4 bits (72), Expect = 0.22
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 178 RLIGPNGCTLKSIELLTNCYMLVQG 202
++GP G TLK +E T + ++G
Sbjct: 19 LILGPRGNTLKQLEKETGAKISIRG 43
Score = 28.4 bits (64), Expect = 2.4
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 219 IGPNGCTLKSIELLTNCYMLVQG 241
+GP G TLK +E T + ++G
Sbjct: 21 LGPRGNTLKQLEKETGAKISIRG 43
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 32.2 bits (73), Expect = 0.47
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 231 LLTNCYMLVQGQTVAALGPHKGLLQVRRIVEDTMKNIHPIYNIKALMIKRELAKDPKLKN 290
+TN + QGQ A ++ I ED +I+P+ +AL+ K +L+ D L+
Sbjct: 468 NMTNYFRRSQGQA-ALREIRYQIINDVAIHEDLEVDINPLLVYRALLNKGQLSPDKDLEL 526
Query: 291 E 291
Sbjct: 527 L 527
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 29.2 bits (66), Expect = 0.58
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 173 VKRRQRLIGPNGCTLKSIELLTNCYMLV 200
+ +IG G T+K IE T + +
Sbjct: 11 ADKVGLIIGKGGSTIKKIEEETGVKIDI 38
Score = 26.9 bits (60), Expect = 3.9
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 5/49 (10%)
Query: 219 IGPNGCTLKSIELLTNCYMLVQGQ-----TVAALGPHKGLLQVRRIVED 262
IG G T+K IE T + + G V GP + + + ++ +
Sbjct: 18 IGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILE 66
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the daughter
cell. ASH1 is a specific repressor of transcription that
localizes asymmetrically to the daughter cell nucleus.
RNA localisation is a widespread mechanism for achieving
localised protein synthesis.
Length = 42
Score = 28.3 bits (64), Expect = 0.59
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 177 QRLIGPNGCTLKSIELLTNCYMLV 200
+IG G T+K I T + +
Sbjct: 3 GAIIGKGGETIKEIREETGAKIQI 26
Score = 26.0 bits (58), Expect = 3.6
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 219 IGPNGCTLKSIELLTNCYMLV 239
IG G T+K I T + +
Sbjct: 6 IGKGGETIKEIREETGAKIQI 26
>gnl|CDD|224760 COG1847, Jag, Predicted RNA-binding protein [General function
prediction only].
Length = 208
Score = 29.6 bits (67), Expect = 1.9
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 177 QRLIGPNGCTLKSIELLTNCY 197
RLIG +G TL +++ L N Y
Sbjct: 103 GRLIGKHGKTLDALQYLANLY 123
Score = 28.0 bits (63), Expect = 6.0
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 208 LGPHKGLLQSNIGPNGCTLKSIELLTNCY 236
G G L IG +G TL +++ L N Y
Sbjct: 98 EGEDAGRL---IGKHGKTLDALQYLANLY 123
>gnl|CDD|237031 PRK12273, aspA, aspartate ammonia-lyase; Provisional.
Length = 472
Score = 29.7 bits (68), Expect = 2.5
Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 24/85 (28%)
Query: 224 CTLKSIELLTN-CYML----VQGQT----------------VAALGPHKGLLQVRRIVED 262
+SI +LTN C L + G T V AL P+ G I ++
Sbjct: 370 NLFESISILTNACRTLREKCIDGITANEERCREYVENSIGIVTALNPYIGYENAAEIAKE 429
Query: 263 TMKNIHPIYNI---KALMIKRELAK 284
++ + + + L+ + EL
Sbjct: 430 ALETGKSVRELVLERGLLTEEELDD 454
>gnl|CDD|239097 cd02414, jag_KH, jag_K homology RNA-binding domain. The KH domain
is found in proteins homologous to the Bacillus subtilis
protein Jag, which is associated with SpoIIIJ and is
necessary for the third stage of sporulation. The KH
motif is a beta-alpha-alpha-beta-beta unit that folds
into an alpha-beta structure with a three stranded
beta-sheet interupted by two contiguous helices. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 77
Score = 27.5 bits (62), Expect = 2.6
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 178 RLIGPNGCTLKSIELLTNCYM 198
LIG G TL +++ L N +
Sbjct: 37 LLIGKRGKTLDALQYLANLVL 57
Score = 26.3 bits (59), Expect = 7.2
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 209 GPHKGLLQSNIGPNGCTLKSIELLTNCYM 237
G GLL IG G TL +++ L N +
Sbjct: 32 GDDIGLL---IGKRGKTLDALQYLANLVL 57
>gnl|CDD|218212 pfam04685, DUF608, Protein of unknown function, DUF608. This
family represents a conserved region with a pankaryotic
distribution in a number of uncharacterized proteins.
Length = 357
Score = 29.2 bits (66), Expect = 2.8
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 84 EEYLKECWPLVKNALE 99
+E+LK+ WP VK A++
Sbjct: 110 KEFLKDMWPAVKKAMD 125
Score = 29.2 bits (66), Expect = 3.2
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 20 EYLKECWPLVKNALE 34
E+LK+ WP VK A++
Sbjct: 111 EFLKDMWPAVKKAMD 125
>gnl|CDD|184228 PRK13671, PRK13671, hypothetical protein; Provisional.
Length = 298
Score = 29.3 bits (66), Expect = 2.8
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 271 YNIKALMIKRELAKDPKLKNENWERFLPNFKSKTLSKRKMPKKRKTKSEYTP 322
Y I+ IKR + + E N+ S T RKM + K S+Y+P
Sbjct: 173 YPIQPYCIKRTV-------GFHSENPEDNYASATYL-RKMIFENKDISKYSP 216
>gnl|CDD|221909 pfam13083, KH_4, KH domain.
Length = 71
Score = 27.0 bits (61), Expect = 2.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 178 RLIGPNGCTLKSIELLTNCYM 198
+LIG G TL +++ L +
Sbjct: 41 KLIGKRGRTLDALQTLVSAAA 61
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 26.8 bits (60), Expect = 3.1
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 178 RLIGPNGCTLKSIELLTNC 196
R+IG G T+K I T
Sbjct: 13 RIIGKGGSTIKEIREETGA 31
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 26.4 bits (59), Expect = 3.9
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 178 RLIGPNGCTLKSIELLTNC 196
R+IG G +K I T
Sbjct: 13 RIIGKGGSNIKEIREETGV 31
>gnl|CDD|241253 cd01218, PH_Phafin2-like, Phafin2 (also called EAPF, FLJ13187,
ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain.
Phafin2 is differentially expressed in the liver cancer
cell and regulates the structure and function of the
endosomes through Rab5-dependent processes. Phafin2
modulates the cell's response to extracellular
stimulation by modulating the receptor density on the
cell surface. Phafin2 contains a PH domain and a FYVE
domain. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 123
Score = 27.2 bits (61), Expect = 6.6
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 158 DIIKIGNLVQNKQRFVKRRQRLIGPNGCTLKSIE 191
DI+ G++V NK+++ K QR+I ++ +E
Sbjct: 54 DILVYGSIVINKKKYNK--QRIIPLEDVKIEDLE 85
>gnl|CDD|177928 PLN02291, PLN02291, phospho-2-dehydro-3-deoxyheptonate aldolase.
Length = 474
Score = 27.8 bits (62), Expect = 8.6
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 74 SRSVPYEPLKEEYLKECWPLV--KNALELHFIKAE 106
SR+V ++ L Y C P + +LEL FI AE
Sbjct: 423 SRTVTFDDLSSRYHTHCDPRLNASQSLELAFIIAE 457
>gnl|CDD|215742 pfam00136, DNA_pol_B, DNA polymerase family B. This region of DNA
polymerase B appears to consist of more than one
structural domain, possibly including elongation,
DNA-binding and dNTP binding activities.
Length = 458
Score = 27.7 bits (62), Expect = 9.3
Identities = 20/120 (16%), Positives = 43/120 (35%), Gaps = 11/120 (9%)
Query: 65 KARDMIKLLSRSVPYEPLKEEYLKECWPLVKNALELHFIKAELDVIEGSMTVF----TTR 120
+++ K ++ + ++P+K E+ K V L L K + R
Sbjct: 234 LGKELAKHVTSELFFKPIKLEFEK-----VYKPLLLISKKRYAGLKYDGKGDIKGVDLVR 288
Query: 121 KTWDPYIIIKARDMIKLLSRSVPYEQAVRVLQDDISCDIIKIGNLVQNKQRFVKRRQRLI 180
+ W ++ R ++ LL + E A L+ I + + + + V +I
Sbjct: 289 RDWCEFVKEVIRKVLDLLLKDKDVEDAAPSLKIVIIEILKSLTDKLVQN--KVPLEDLVI 346
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
0.319 0.136 0.408
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,850,014
Number of extensions: 1615518
Number of successful extensions: 1323
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1320
Number of HSP's successfully gapped: 35
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
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 (21.8 bits)
S2: 59 (26.5 bits)