RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4020
(530 letters)
>gnl|CDD|216598 pfam01602, Adaptin_N, Adaptin N terminal region. This family
consists of the N terminal region of various alpha, beta
and gamma subunits of the AP-1, AP-2 and AP-3 adaptor
protein complexes. The adaptor protein (AP) complexes
are involved in the formation of clathrin-coated pits
and vesicles. The N-terminal region of the various
adaptor proteins (APs) is constant by comparison to the
C-terminal which is variable within members of the AP-2
family; and it has been proposed that this constant
region interacts with another uniform component of the
coated vesicles.
Length = 522
Score = 295 bits (758), Expect = 4e-94
Identities = 133/356 (37%), Positives = 192/356 (53%), Gaps = 52/356 (14%)
Query: 21 YPAHFGQLECLKLIASSRFTDKRIGYLGAMLLLDERQDVHLLITNSLKNDLNSSTQFVVG 80
F E +KL+AS+ FT KR+GYL LL +E D+ +L+TNS+K DL S + G
Sbjct: 37 EDISFLFFEVVKLVASNDFTLKRLGYLYLKLLAEESPDLAILVTNSIKKDLQSPNPLIRG 96
Query: 81 LALCTLGAIASPEMSRDLASEVERLMKSSNAYIRKKAALCAYRIILKVPELMEIFL-PAT 139
LAL TL I PE++RDLA ++++L+ + Y+RKKAAL ++ K P+L+ FL P
Sbjct: 97 LALRTLSCIRVPELARDLAPDIKKLLVDRDPYVRKKAALAILKLYRKDPDLVRDFLVPEL 156
Query: 140 RLLLSDKNH-----------------------AIH-----------------QVKILKLL 159
+ LLSDK+ + QVKIL+LL
Sbjct: 157 KELLSDKDPGVVSAAVALLYEIRKNDRLYLNKLLPLLVRRLCNLLTVCNPWLQVKILRLL 216
Query: 160 RILGK-NDVEASEAMNDILAQVATNTETSKNVGNTILYETVLSIMDIKSESGLRVLAVNI 218
+ E E + DIL + N N +LYE V +I+ + E L VLAVN
Sbjct: 217 TRYAPQDPREPKELLEDILNLLQ-------NSNNAVLYEAVKTIIHLDPEPELIVLAVNA 269
Query: 219 LGRFLLNNDKNIRYVALNTLLRTVYIDTSAVQRHRNTILECLK-DPDVSIRRRALELSFA 277
LGR L + D+N+RYVAL L + + AVQ H + I+ CLK D D+SIR RAL+L +
Sbjct: 270 LGRLLSSPDENLRYVALRNLNKILEKHPPAVQ-HLDLIIFCLKTDDDISIRLRALDLLYK 328
Query: 278 LVNSANVRSMMKELLIFL-EKSEPDFKAHCSSNIVLCAERFAPNKRWHLDTLLKVL 332
LV+ +NV+ ++KELL ++ E ++P+FK I AE+F + W +D LL++L
Sbjct: 329 LVDESNVKEIVKELLKYVSEIADPEFKIKLVKAIGRLAEKFPTDAEWCIDVLLELL 384
>gnl|CDD|217268 pfam02883, Alpha_adaptinC2, Adaptin C-terminal domain. Alpha
adaptin is a heterotetramer which regulates clathrin-bud
formation. The carboxyl-terminal appendage of the alpha
subunit regulates translocation of endocytic accessory
proteins to the bud site. This ig-fold domain is found
in alpha, beta and gamma adaptins.
Length = 115
Score = 97.0 bits (242), Expect = 3e-24
Identities = 38/111 (34%), Positives = 66/111 (59%), Gaps = 3/111 (2%)
Query: 422 SVKAYDNHGVVINLLLDSQTPGDSVTIVTMQATNENLTLVSDFLFQAAVPKTFQLQMLPP 481
V Y+++G+ I + + I T+ TN++ + +++F FQAAVPK+ +LQ+ PP
Sbjct: 2 PVVLYESNGLQIGFSFEKPRRPGQIRI-TLTFTNKSSSPITNFSFQAAVPKSLKLQLQPP 60
Query: 482 SDTNIPP--GSQVTQTLRVAKANNNVQASLRMRIKVSYNVNGTFIQDQAEI 530
S +PP G Q+TQ L V + + LR+R+K+SYN+NG + + ++
Sbjct: 61 SSNTLPPFGGGQITQVLLVENFSEPGKKPLRLRVKISYNINGQQVLELGDV 111
>gnl|CDD|197886 smart00809, Alpha_adaptinC2, Adaptin C-terminal domain. Adaptins
are components of the adaptor complexes which link
clathrin to receptors in coated vesicles.
Clathrin-associated protein complexes are believed to
interact with the cytoplasmic tails of membrane
proteins, leading to their selection and concentration.
Gamma-adaptin is a subunit of the golgi adaptor. Alpha
adaptin is a heterotetramer that regulates clathrin-bud
formation. The carboxyl-terminal appendage of the alpha
subunit regulates translocation of endocytic accessory
proteins to the bud site. This Ig-fold domain is found
in alpha, beta and gamma adaptins and consists of a
beta-sandwich containing 7 strands in 2 beta-sheets in a
greek-key topology.. The adaptor appendage contains an
additional N-terminal strand.
Length = 104
Score = 95.4 bits (238), Expect = 8e-24
Identities = 36/106 (33%), Positives = 67/106 (63%), Gaps = 6/106 (5%)
Query: 425 AYDNHGVVINLLLDSQTPGDSVTIVTMQATNENLTLVSDFLFQAAVPKTFQLQMLPPSDT 484
AY+ +G+ I + + + +T+ TN++ + +++F FQAAVPK+ +LQ+ PPS
Sbjct: 1 AYEKNGLQIGFKFERR---PGLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSP 57
Query: 485 NIPPGSQVTQTLRVAKANNNVQASLRMRIKVSYNVNGTFIQDQAEI 530
+PPG Q+TQ L+V N + LR+R+++SY + G+ + +Q ++
Sbjct: 58 TLPPGGQITQVLKVE---NPGKFPLRLRLRLSYLLGGSAVTEQGDV 100
>gnl|CDD|227427 COG5096, COG5096, Vesicle coat complex, various subunits
[Intracellular trafficking and secretion].
Length = 757
Score = 45.1 bits (107), Expect = 8e-05
Identities = 25/90 (27%), Positives = 47/90 (52%)
Query: 31 LKLIASSRFTDKRIGYLGAMLLLDERQDVHLLITNSLKNDLNSSTQFVVGLALCTLGAIA 90
+K +A+ KR+ YL + ++ LL N+++ DL + + G AL TL +
Sbjct: 61 IKNVATRDVELKRLLYLYLERYAKLKPELALLAVNTIQKDLQDPNEEIRGFALRTLSLLR 120
Query: 91 SPEMSRDLASEVERLMKSSNAYIRKKAALC 120
E+ ++ +++L+ +AY+RK AAL
Sbjct: 121 VKELLGNIIDPIKKLLTDPHAYVRKTAALA 150
>gnl|CDD|219941 pfam08623, TIP120, TATA-binding protein interacting (TIP20).
TIP120 (also known as cullin-associated and
neddylation-dissociated protein 1) is a TATA binding
protein interacting protein that enhances transcription.
Length = 169
Score = 31.8 bits (73), Expect = 0.44
Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 196 YETVLSIMDI-KSESGLRVLAVNIL-GRFLLNNDKNIRYVALNTLLRTVYIDTSAVQRHR 253
YET+ +++D S + I G L+++ +I+ +AL L + + V
Sbjct: 48 YETMYTLLDSCFSRLDIPEFLDRIEAG---LSDEHDIKMLALLMLSKLAVLAPEEVLARL 104
Query: 254 NTILECLK 261
+ + E L+
Sbjct: 105 DRLAEPLR 112
>gnl|CDD|221797 pfam12830, Nipped-B_C, Sister chromatid cohesion C-terminus. This
domain lies towards the C-terminus of nipped-B or sister
chromatid cohesion proteins.
Length = 187
Score = 30.0 bits (68), Expect = 2.3
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 246 TSAVQRHRNTILECLKDPDVSIRRRALEL 274
+S VQR+ ILE + +R ALEL
Sbjct: 3 SSLVQRYLKDILELCLSSNDKVRLLALEL 31
>gnl|CDD|118166 pfam09632, Rac1, Rac1-binding domain. The Rac1-binding domain is
the C-terminal portion of YpkA from Yersinia. It is an
all-helical molecule consisting of two distinct
subdomains connected by a linker. the N-terminal end,
residues 434-615, consists of six helices organised into
two three-helix bundles packed against each other. This
region is involved with binding to GTPases. The
C-terminal end, residues 705-732. is a novel and
elongated fold consisting of four helices clustered into
two pairs, and this fold carries the helix implicated in
actin activation. Rac1-binding domain mimics host
guanidine nucleotide dissociation inhibitors (GDIs) of
the Rho GTPases, thereby inhibiting nucleotide exchange
in Rac1 and causing cytoskeletal disruption in the host.
It is usually found downstream of pfam00069.
Length = 297
Score = 30.0 bits (67), Expect = 2.7
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 401 RWHLDTLLKVLVAVSENKDKVSVKAYD 427
HL+TLL+VLV +S+ VS + YD
Sbjct: 131 HKHLETLLEVLVTLSQQGQPVSSETYD 157
>gnl|CDD|220417 pfam09812, MRP-L28, Mitochondrial ribosomal protein L28. Members
of this family are components of the mitochondrial large
ribosomal subunit. Mature mitochondrial ribosomes
consist of a small (37S) and a large (54S) subunit. The
37S subunit contains at least 33 different proteins and
1 molecule of RNA (15S). The 54S subunit contains at
least 45 different proteins and 1 molecule of RNA (21S).
Length = 146
Score = 28.5 bits (64), Expect = 4.6
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 451 MQATNENLTLVSDFLFQAAV---PKTFQLQMLPPSDTNIPP 488
Q E L L S L++AA+ P F L++ P+DT PP
Sbjct: 101 QQEALEELKLESPELYEAAIAPDPGLFPLELRGPTDT--PP 139
>gnl|CDD|227439 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase
[Transcription].
Length = 1117
Score = 29.6 bits (66), Expect = 5.6
Identities = 26/92 (28%), Positives = 36/92 (39%), Gaps = 3/92 (3%)
Query: 26 GQLECLKLIASSRFTDKRIGYLGAMLLLDERQDVHLLITNSLKNDLNSSTQFVVGLALCT 85
G LE L AS KR+ Y + L D + HL I DL S ++ G+ L
Sbjct: 308 GLLEALLAEASLGKAGKRLTYGPYLKLADLDKVAHLTIRELF--DLVSMRRYDRGMRLTP 365
Query: 86 LGAIASPEMSRDLASE-VERLMKSSNAYIRKK 116
L + + SE + K + RKK
Sbjct: 366 LSIRLGAMVEDEFFSEQFKGHEKDAYEDARKK 397
>gnl|CDD|178473 PLN02885, PLN02885, nicotinate phosphoribosyltransferase.
Length = 545
Score = 28.9 bits (65), Expect = 7.1
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 29 ECLKLIASSRFTDKRIGYL 47
ECL+ IA+ +FTD I +L
Sbjct: 59 ECLRFIANFKFTDDDIDFL 77
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
0.320 0.133 0.369
Gapped
Lambda K H
0.267 0.0764 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,996,175
Number of extensions: 2539103
Number of successful extensions: 2121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2110
Number of HSP's successfully gapped: 26
Length of query: 530
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 429
Effective length of database: 6,457,848
Effective search space: 2770416792
Effective search space used: 2770416792
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 (21.9 bits)
S2: 61 (27.2 bits)