RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15518
(195 letters)
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 61.8 bits (150), Expect = 2e-11
Identities = 40/130 (30%), Positives = 60/130 (46%), Gaps = 19/130 (14%)
Query: 19 PEYKLQTPRIHKWTILHYSPFKA---VWDWLILILVVYTAIFTPYVAAFLLNEPDFTNRT 75
P Y W I SP + W+ L+++LV Y+A P+ AFL P R
Sbjct: 40 PSYNQNHIGSDGWII---SPMDSRYRWWETLMVVLVAYSAWVYPFEVAFLNASP---KRG 93
Query: 76 RNIRRYSDPIVFVDLIVDVTFIVDIAINFRTTYVNANDEV-VSNPGLIALHYLRGWFIID 134
I D +VD+ F VDI + F Y++ ++ V + IA+ YL WF++D
Sbjct: 94 LEI---------ADNVVDLFFAVDIVLTFFVAYIDPRTQLLVRDRKKIAVRYLSTWFLMD 144
Query: 135 LVAAIPFDLL 144
+ + IPF L
Sbjct: 145 VASTIPFQAL 154
>gnl|CDD|149466 pfam08412, Ion_trans_N, Ion transport protein N-terminal. This
metazoan domain is found to the N-terminus of pfam00520
in voltage- and cyclic nucleotide-gated K/Na ion
channels.
Length = 77
Score = 30.5 bits (69), Expect = 0.12
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 31 WTILHYSPFKAVWDWLILILVVYTAIFTPYVAAFLLNE 68
W I YS F+ WD +L+L++ I P F +E
Sbjct: 37 WIIHPYSDFRFYWDLCMLLLMMGNLIILPVGITFFKDE 74
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 30.3 bits (69), Expect = 0.46
Identities = 20/112 (17%), Positives = 32/112 (28%), Gaps = 24/112 (21%)
Query: 87 FVDLIVDVTFIVDIAINFRTTYVNANDEVVSNPGLIALHYLR-GWFIIDLVAAIPFDLLI 145
+D + V F +++ + F Y R W I+D + +P + +
Sbjct: 1 ILDYVFTVIFTLEMLLKFIALG-------------FKRKYFRSPWNILDFLVVLPSLVSL 47
Query: 146 FGSETEETLDS----------RELPLSMSIEMHFKLLTSVMTKWIGLKRLTL 187
E R L L LL S+ L L L
Sbjct: 48 ILFLLGEDSGLLRVLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLL 99
>gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional.
Length = 815
Score = 30.2 bits (68), Expect = 0.70
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 150 TEETLDSRELPLSMSIEMHFKLLTSVMTKWI 180
E LDS +LP+ M + H K V+ ++
Sbjct: 477 MEMGLDSPDLPMGMLSDFHLKRCEEVLLEFA 507
>gnl|CDD|176572 cd08767, Cdt1_c, The C-terminal fold of replication licensing
factor Cdt1 is essential for Cdt1 activity and directly
interacts with MCM2-7 helicase. Cdt1 is a replication
licensing factor in eukaryotes that recruits the
Minichromosome Maintenance Complex (MCM2-7) to the
Origin Recognition Complex (ORC). The Cdt1 protein is
divided into three regions based on sequence comparison
and biochemical analyses: the N-terminal region (Cdt1_n)
binds DNA in a sequence-, strand-, and
conformation-independent manner; the middle winged helix
fold (Cdt1_m) binds geminin to inhibit both binding of
the MCM complex to origins of replication and DNA; and
the C-terminal region (Cdt1_c) is essential for Cdt1
activity and directly interacts with the MCM2-7
helicase. Precise duplication of chromosomal DNA is
required for genomic stability during replication.
Assembly of replication factors to start DNA replication
in eukaryotes must occur only once per cell cycle. To
form a pre-replicative complex on replication origins in
the G phase, ORC first binds origin DNA and triggers the
binding of Cdc6 and Cdt1. These two factors recruit a
putative replicative helicase and the MCM2-7. The MCM2-7
complex promotes the unwinding of DNA origins, and the
binding of additional factors to initiate the DNA
replication in S-phase. Cdt1 is present during G1 and
early S phase of the cell cycle and is degraded during
the late S, G2, and M phases. The winged helix fold
structure of Cdt1_m is similar to the structures of
Cdt1_c and archaeal homologues of the eukaryotic
replication initiator, without apparent sequence
similarity.
Length = 126
Score = 27.2 bits (61), Expect = 3.4
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 8/62 (12%)
Query: 127 LRGWFIIDLVAAIPFDLLI--FGSETEETLDSRELPLSMSIEMHFKLLTSVMTKWIGLKR 184
LR F+ + +P + L+ + L E +E H +LL + WI K
Sbjct: 50 LRNIFVSEKKTVLPLEELVYKLQASYPSILSRGE------VEEHLRLLAELAPDWISEKS 103
Query: 185 LT 186
L
Sbjct: 104 LR 105
>gnl|CDD|226055 COG3524, KpsE, Capsule polysaccharide export protein [Cell
envelope biogenesis, outer membrane].
Length = 372
Score = 26.7 bits (59), Expect = 9.0
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 20 EYKLQTPRIHKWTILHYSPFKAVWDWLILILVVYTAIFTP 59
E K + + K +I SP W +I+ILV + +
Sbjct: 3 ETKAERKKPKKKSIKKLSPL--FWVTVIIILVYFGLFASD 40
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
0.329 0.143 0.442
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,478,699
Number of extensions: 1028046
Number of successful extensions: 1258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1253
Number of HSP's successfully gapped: 39
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.2 bits)