RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5097
(246 letters)
>gnl|CDD|197727 smart00443, G_patch, glycine rich nucleic binding domain. A
predicted glycine rich nucleic binding domain found in
the splicing factor 45, SON DNA binding protein and
D-type Retrovirus- polyproteins.
Length = 47
Score = 68.7 bits (169), Expect = 9e-16
Identities = 27/47 (57%), Positives = 33/47 (70%)
Query: 24 NDSSKFGEKLLRKMGWSDGQGLGVNQQGIKEHIKVKVKQDGKGLGFK 70
+S G KLLRKMGW +GQGLG N+QGI E I ++K+D KGLG
Sbjct: 1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGAV 47
>gnl|CDD|144978 pfam01585, G-patch, G-patch domain. This domain is found in a
number of RNA binding proteins, and is also found in
proteins that contain RNA binding domains. This
suggests that this domain may have an RNA binding
function. This domain has seven highly conserved
glycines.
Length = 45
Score = 64.8 bits (159), Expect = 2e-14
Identities = 26/44 (59%), Positives = 32/44 (72%)
Query: 27 SKFGEKLLRKMGWSDGQGLGVNQQGIKEHIKVKVKQDGKGLGFK 70
S G KLL+KMGW GQGLG N+QGI E I+ K++ D KGLG +
Sbjct: 2 SNIGFKLLQKMGWKPGQGLGKNEQGITEPIEAKIRPDRKGLGAE 45
>gnl|CDD|221692 pfam12656, G-patch_2, DExH-box splicing factor binding site.
Yeast Spp2, a G-patch protein and spliceosome
component, interacts with the ATP-dependent DExH-box
splicing factor Prp2. As this interaction involves the
G-patch sequence in Spp2 and is required for the
recruitment of Prp2 to the spliceosome before the first
catalytic step of splicing, it is proposed that Spp2
might be an accessory factor that confers spliceosome
specificity on Prp2.
Length = 79
Score = 44.3 bits (105), Expect = 2e-06
Identities = 20/45 (44%), Positives = 27/45 (60%)
Query: 27 SKFGEKLLRKMGWSDGQGLGVNQQGIKEHIKVKVKQDGKGLGFKE 71
+FG LLR MGW +GQG+G N +G + + K + G GLG K
Sbjct: 31 EEFGAALLRGMGWKEGQGIGKNNKGDVKPKEPKRRPGGLGLGAKP 75
>gnl|CDD|226724 COG4274, COG4274, Uncharacterized conserved protein [Function
unknown].
Length = 104
Score = 30.1 bits (68), Expect = 0.33
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 86 LLSKLSSQSDKPISDSPTSVEGVNRSLEEQSKKSKARVHYQKFTRG 131
+LS + Q K + ++P V LE +V Q +T G
Sbjct: 13 VLSNFTDQGAKTLKETPKRAAAVRALLE----SMGGKVKEQYWTLG 54
>gnl|CDD|173883 cd08518, PBP2_NikA_DppA_OppA_like_19, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 464
Score = 30.2 bits (69), Expect = 0.90
Identities = 20/81 (24%), Positives = 29/81 (35%), Gaps = 16/81 (19%)
Query: 17 PRGSAWMNDSSKF-------GEKLLRKMGWSDGQGLGVNQQGIKEHIKVKVKQDGKGLGF 69
P G W N + +K+L + GW DG G + G K L +
Sbjct: 282 PDGLPWGNPDAAIYDYDPEKAKKILEEAGWKDGDDGGREKDGQKAEFT---------LYY 332
Query: 70 KENDQVWVEVENEFSSLLSKL 90
DQV ++ +S KL
Sbjct: 333 PSGDQVRQDLAVAVASQAKKL 353
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 30.5 bits (69), Expect = 0.96
Identities = 18/61 (29%), Positives = 33/61 (54%)
Query: 183 EVEGTNTKPNSEEEKSVDNEEQDPNDEEFIEGGAKKKKKRKKAKKRKCENNDVVELNVTE 242
E E + + E+E+ + EE+ + EE ++ +K++K+KK KK K + LN T+
Sbjct: 32 EKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTK 91
Query: 243 A 243
Sbjct: 92 P 92
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 30.4 bits (68), Expect = 1.1
Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 8/82 (9%)
Query: 158 EENENFVQSGNMSDYFKQKKLNIGSEVE--------GTNTKPNSEEEKSVDNEEQDPNDE 209
E+ +++ + + K+ IG ++E T + E+ K D + ++P E
Sbjct: 177 EDQMEYLEPRRLKELIKKHSEFIGYDIELMVEKTTEKEVTDEDEEDTKKADEDGEEPKVE 236
Query: 210 EFIEGGAKKKKKRKKAKKRKCE 231
E EG KKKK KK K+ E
Sbjct: 237 EVKEGDEGKKKKTKKVKEVTKE 258
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 30.0 bits (68), Expect = 1.4
Identities = 21/171 (12%), Positives = 50/171 (29%), Gaps = 2/171 (1%)
Query: 78 EVENEFSSLLSKLSSQSDKPISDSPTSVEGVNRSLEEQSKKSKARVHYQKFTRGKDLSRY 137
+ + S S + D+ P ++ + + + + +
Sbjct: 1211 DKPDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEFSSDDLSKEGK 1270
Query: 138 SKKDLECIFGVSSKSTESKHEENENFVQSGNMSDYFKQKKLNIGSEVEGTNTKPNSEEEK 197
K + + V + S K+K K E+K
Sbjct: 1271 PKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKK 1330
Query: 198 SVDNEEQDPNDEEFI--EGGAKKKKKRKKAKKRKCENNDVVELNVTEAEDT 246
+ ++ ++ + ++ RKK E++D E++ +E ED
Sbjct: 1331 TARKKKSKTRVKQASASQSSRLLRRPRKKKSDSSSEDDDDSEVDDSEDEDD 1381
>gnl|CDD|240388 PTZ00372, PTZ00372, endonuclease 4-like protein; Provisional.
Length = 413
Score = 29.3 bits (66), Expect = 2.1
Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 8/82 (9%)
Query: 146 FGVSSKSTESKHEENENFVQSGNMSDYFKQKKLNIGSEVEGTNTKPNSEEEKSVDNEEQD 205
V SK S E EN V + K+ K + +K SE++K E+++
Sbjct: 31 VLVLSKEILSTFSEEENKVA----TTSTKKDKKEDKN----NESKKKSEKKKKKKKEKKE 82
Query: 206 PNDEEFIEGGAKKKKKRKKAKK 227
P E + G K KK KK KK
Sbjct: 83 PKSEGETKLGFKTPKKSKKTKK 104
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 28.6 bits (64), Expect = 2.9
Identities = 11/51 (21%), Positives = 28/51 (54%)
Query: 179 NIGSEVEGTNTKPNSEEEKSVDNEEQDPNDEEFIEGGAKKKKKRKKAKKRK 229
+G + T+ +E + + +Q+ N+++ E + K+KR+K +++K
Sbjct: 384 KLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDERKK 434
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 28.0 bits (63), Expect = 3.6
Identities = 13/47 (27%), Positives = 21/47 (44%)
Query: 52 IKEHIKVKVKQDGKGLGFKENDQVWVEVENEFSSLLSKLSSQSDKPI 98
IK + K+ + G + Q + + EF LL+KL S K +
Sbjct: 83 CLAWIKKQNKKKSERTGGPDTLQGYGLLAEEFIRLLTKLLSALGKNV 129
>gnl|CDD|215527 PLN02976, PLN02976, amine oxidase.
Length = 1713
Score = 28.3 bits (63), Expect = 4.4
Identities = 16/50 (32%), Positives = 20/50 (40%), Gaps = 1/50 (2%)
Query: 150 SKSTESKHEENENFVQSGNMSDYFKQKKLNIGSEVEGTNTKPNSEEEKSV 199
S T+ K EN + S+ K E E N P SEEEK+
Sbjct: 1387 STDTKGKLSSLENVKTDKSKSESLKSVG-RQDIEEEEGNQIPMSEEEKAA 1435
>gnl|CDD|214395 CHL00204, ycf1, Ycf1; Provisional.
Length = 1832
Score = 27.8 bits (62), Expect = 6.5
Identities = 13/74 (17%), Positives = 29/74 (39%), Gaps = 5/74 (6%)
Query: 159 ENENFVQSGNMSDYFKQKKLN-----IGSEVEGTNTKPNSEEEKSVDNEEQDPNDEEFIE 213
+ + N + + N + E + K +SV + ++ +E++ E
Sbjct: 1504 QKKKGFIPSNEKKSIEIENRNQEEKEPAGQGELESDKEKKGNLESVLSNQEKNIEEDYAE 1563
Query: 214 GGAKKKKKRKKAKK 227
KK+K +K+ K
Sbjct: 1564 SDIKKRKNKKQYKS 1577
>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2. This family consists
of several Barren protein homologues from several
eukaryotic organisms. In Drosophila Barren (barr) is
required for sister-chromatid segregation in mitosis.
barr encodes a novel protein that is present in
proliferating cells and has homologues in yeast and
human. Mitotic defects in barr embryos become apparent
during cycle 16, resulting in a loss of PNS and CNS
neurons. Centromeres move apart at the
metaphase-anaphase transition and Cyclin B is degraded,
but sister chromatids remain connected, resulting in
chromatin bridging. Barren protein localises to
chromatin throughout mitosis. Colocalisation and
biochemical experiments indicate that Barren associates
with Topoisomerase II throughout mitosis and alters the
activity of Topoisomerase II. It has been suggested that
this association is required for proper chromosomal
segregation by facilitating the decatenation of
chromatids at anaphase. This family forms one of the
three non-structural maintenance of chromosomes (SMC)
subunits of the mitotic condensation complex along with
Cnd1 and Cnd3.
Length = 719
Score = 27.4 bits (61), Expect = 9.7
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 186 GTNTKPNSEEEKSVDNEEQDPNDEE----FIEGGAKKKKKRKKAKKRK 229
G N E ++ + +D+E E GAKKK K+K+ +K +
Sbjct: 148 GLADSDNKEAPETGREGDDGEDDDEEGSDGEEDGAKKKAKKKRQRKPE 195
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
0.303 0.123 0.337
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,649,897
Number of extensions: 1043405
Number of successful extensions: 1309
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1206
Number of HSP's successfully gapped: 115
Length of query: 246
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 152
Effective length of database: 6,768,326
Effective search space: 1028785552
Effective search space used: 1028785552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 58 (26.0 bits)