RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9955
(60 letters)
>gnl|CDD|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate
protein-protein interactions in very diverse families
of proteins. The number of ANK repeats in a protein can
range from 2 to over 20 (ankyrins, for example). ANK
repeats may occur in combinations with other types of
domains. The structural repeat unit contains two
antiparallel helices and a beta-hairpin, repeats are
stacked in a superhelical arrangement; this alignment
contains 4 consecutive repeats.
Length = 126
Score = 32.4 bits (74), Expect = 0.004
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 22 LEDAKFWLSSGCLGDVPNPKTGASALHVAAAKGYIKVMK 60
LE K L G + + K G + LH+AA G + V+K
Sbjct: 53 LEIVKLLLEKGADVNARD-KDGNTPLHLAARNGNLDVVK 90
Score = 32.4 bits (74), Expect = 0.005
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 18 ERSMLEDAKFWLSSGCLGDVPNPKTGASALHVAAAKGYIKVMK 60
LE K L +G + + G + LH+AA G+++++K
Sbjct: 16 SNGHLEVVKLLLENGADVNAKD-NDGRTPLHLAAKNGHLEIVK 57
Score = 28.9 bits (65), Expect = 0.069
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 29 LSSGCLGDVPNPKTGASALHVAAAKGYIKVMK 60
L G + + K G + LH+AA G+++V+K
Sbjct: 93 LKHGADVNARD-KDGRTPLHLAAKNGHLEVVK 123
Score = 28.1 bits (63), Expect = 0.18
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 41 KTGASALHVAAAKGYIKVMK 60
+ G + LH+AA+ G+++V+K
Sbjct: 5 EDGRTPLHLAASNGHLEVVK 24
>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction
only].
Length = 235
Score = 30.9 bits (69), Expect = 0.021
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 22 LEDAKFWLSSGCLGDVPNP--KTGASALHVAAAKGYIKVMK 60
+E AK L +G DV N + G + LH AA G +++
Sbjct: 124 IEVAKLLLEAGADLDVNNLRDEDGNTPLHWAALNGDADIVE 164
>gnl|CDD|200936 pfam00023, Ank, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to
24 repeated units, and it mediates most of the
protein's binding activities. Repeats 13-24 are
especially active, with known sites of interaction for
the Na/K ATPase, Cl/HCO(3) anion exchanger,
voltage-gated sodium channel, clathrin heavy chain and
L1 family cell adhesion molecules. The ANK repeats are
found to form a contiguous spiral stack such that ion
transporters like the anion exchanger associate in a
large central cavity formed by the ANK repeat spiral,
while clathrin and cell adhesion molecules associate
with specific regions outside this cavity.
Length = 33
Score = 28.3 bits (64), Expect = 0.035
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 43 GASALHVAAAKGYIKVMK 60
G + LH+AA G+++V+K
Sbjct: 2 GNTPLHLAARNGHLEVVK 19
>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies).
Length = 91
Score = 28.8 bits (65), Expect = 0.059
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 22 LEDAKFWLSSGCLGDVPNPKTGASALHVAAAKGYIKVMK 60
LE K L G DV T +ALH+AA G ++++K
Sbjct: 10 LELVKLLLEKGA--DVNLGDTD-TALHLAARNGNLEIVK 45
Score = 26.8 bits (60), Expect = 0.30
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 41 KTGASALHVAAAKGYIKVMK 60
K G +ALH+AA G ++++K
Sbjct: 59 KDGNTALHLAARNGNLEIVK 78
>gnl|CDD|197603 smart00248, ANK, ankyrin repeats. Ankyrin repeats are about 33
amino acids long and occur in at least four consecutive
copies. They are involved in protein-protein
interactions. The core of the repeat seems to be an
helix-loop-helix structure.
Length = 30
Score = 26.4 bits (59), Expect = 0.18
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 43 GASALHVAAAKGYIKVMK 60
G + LH+AA G ++V+K
Sbjct: 2 GRTPLHLAAENGNLEVVK 19
>gnl|CDD|222277 pfam13637, Ank_4, Ankyrin repeats (many copies).
Length = 54
Score = 26.0 bits (58), Expect = 0.45
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 18 ERSMLEDAKFWLSSGCLGDVPNPKTGASALHVAAAKGYIKVMK 60
LE K+ L G + + + G +ALH+AA G ++V+K
Sbjct: 10 ISGRLELVKYLLEKGVDINRTD-EDGNTALHIAAENGNLEVLK 51
>gnl|CDD|149837 pfam08899, DUF1844, Domain of unknown function (DUF1844). This
family of proteins are functionally uncharacterized.
Length = 74
Score = 25.7 bits (57), Expect = 0.66
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 34 LGDVPNPKTGASALHVAAAKGYIKVM 59
LG++P+P+TG + + AK I ++
Sbjct: 19 LGEIPDPETGETRKDLPLAKHTIDLL 44
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 26.8 bits (59), Expect = 0.71
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 20 SMLEDAKFWLSSGCLGDVPNPKTGASALHVAAAKGY 55
++LE+ L + D+ + K G + LH+AA+KGY
Sbjct: 539 ALLEEL---LKAKLDPDIGDSK-GRTPLHIAASKGY 570
>gnl|CDD|176383 cd01788, ElonginB, Ubiquitin-like domain of Elongin B. Elongin B
is part of an E3 ubiquitin ligase complex called VEC
that activates ubiquitylation by the E2
ubiquitin-conjugating enzyme Ubc5. VEC is composed of
von Hippel-Lindau tumor suppressor protein (pVHL),
elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds
elonginC to form the elonginBC complex which is a
positive regulator of RNA polymerase II elongation
factor Elongin A. The BC complex then binds VHL (von
Hippel-Lindau) tumour suppressor protein to form a VCB
ternary complex. Elongin B has a ubiquitin-llike
domain.
Length = 119
Score = 25.0 bits (54), Expect = 1.9
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 1 MQRFVQGI---NPEDARTFEERSMLEDAKFWLSSGCLGDVPNPKTGAS 45
++R V+GI PED R +++ +L+D K G P+ A+
Sbjct: 27 LKRIVEGILKRPPEDQRLYKDDQLLDDGKTLGDCGFTSQTARPQAPAT 74
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 24.9 bits (55), Expect = 2.4
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 14 RTFEERSMLEDAKFWLSSGCLGDVPNPKTGASALHVAAAK 53
+ FE+R +LE+ +L S + +AL AK
Sbjct: 15 KLFEKRGLLEELIPYLESALKENSRENPALQTALLELYAK 54
>gnl|CDD|236904 PRK11387, PRK11387, S-methylmethionine transporter; Provisional.
Length = 471
Score = 24.8 bits (54), Expect = 2.8
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 28 WLSSGCLGD--VPNPKTGASALHVAAAK 53
+L CLG+ V P+TG A HV AA+
Sbjct: 62 YLVMQCLGELSVAMPETG--AFHVYAAR 87
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
0.318 0.132 0.395
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,051,221
Number of extensions: 204404
Number of successful extensions: 188
Number of sequences better than 10.0: 1
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 15
Length of query: 60
Length of database: 10,937,602
Length adjustment: 31
Effective length of query: 29
Effective length of database: 9,562,628
Effective search space: 277316212
Effective search space used: 277316212
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 (21.7 bits)
S2: 53 (24.1 bits)