RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15975
(312 letters)
>gnl|CDD|214763 smart00647, IBR, In Between Ring fingers. the domains occurs
between pairs og RING fingers.
Length = 64
Score = 71.7 bits (176), Expect = 2e-16
Identities = 31/63 (49%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 28 KYQHLITNSFVECNRLLRWCPSPDCNNAIKVQ-HVEARPVVC-KCGHRFCFACGENWHDP 85
KY+ L+ S+VE N L+WCP+PDC+ AI V V C KCG FCF C WH P
Sbjct: 2 KYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPWHSP 61
Query: 86 VRC 88
V C
Sbjct: 62 VSC 64
Score = 35.5 bits (82), Expect = 0.003
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 110 ANTKECP--KC--LVTIEKDGGCNHMVCKNQSCKAEFCWVCLGPW 150
+ K CP C + + ++ GCN + C C FC+ C PW
Sbjct: 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTC--PKCGFSFCFRCKVPW 58
>gnl|CDD|216524 pfam01485, IBR, IBR domain. The IBR (In Between Ring fingers)
domain is often found to occur between pairs of ring
fingers (pfam00097). This domain has also been called
the C6HC domain and DRIL (for double RING finger
linked) domain. Proteins that contain two Ring fingers
and an IBR domain (these proteins are also termed RBR
family proteins) are thought to exist in all eukaryotic
organisms. RBR family members play roles in protein
quality control and can indirectly regulate
transcription. Evidence suggests that RBR proteins are
often parts of cullin-containing ubiquitin ligase
complexes. The ubiquitin ligase Parkin is an RBR family
protein whose mutations are involved in forms of
familial Parkinson's disease.
Length = 63
Score = 69.2 bits (169), Expect = 2e-15
Identities = 27/62 (43%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 28 KYQHLITNSFVECNRLLRWCPSPDCNNAIKVQHVEARPVVC-KCGHRFCFACGENWHDPV 86
KY L +VE + L+WCP+PDC N I+ ++ V C KCG FCF+C E WH+ +
Sbjct: 2 KYLKLSLKKYVESPKNLKWCPTPDCGNIIEKTDGGSQNVTCSKCGTEFCFSCKEPWHEGL 61
Query: 87 RC 88
C
Sbjct: 62 TC 63
Score = 31.4 bits (71), Expect = 0.063
Identities = 18/48 (37%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 111 NTKECP--KCLVTIEKDGGCNHMV-CKNQSCKAEFCWVCLGPWEPHGS 155
N K CP C IEK G + V C C EFC+ C PW +
Sbjct: 17 NLKWCPTPDCGNIIEKTDGGSQNVTC--SKCGTEFCFSCKEPWHEGLT 62
>gnl|CDD|215195 PLN02341, PLN02341, pfkB-type carbohydrate kinase family protein.
Length = 470
Score = 32.9 bits (75), Expect = 0.24
Identities = 17/77 (22%), Positives = 29/77 (37%), Gaps = 10/77 (12%)
Query: 121 TIEKDGGCNHMVCKNQSCKAEFCWVCLGPWEPHGSSWYSCNRYDEEEAKVARGAQ---ER 177
+ G + + S + CWV + P + HG C+R D
Sbjct: 162 VVGLIEGTDAGDSSSASYETLLCWVLVDPLQRHG----FCSRADFGPEPAFSWISKLSAE 217
Query: 178 SRAALQ--RYLFYCNRY 192
++ A++ + LF CN Y
Sbjct: 218 AKMAIRQSKALF-CNGY 233
>gnl|CDD|239007 cd02052, PEDF, Pigment epithelium-derived factor (PEDF)_like. PEDF
is non-inhibitory member of the Serpin superfamily. It
exhibits neurotrophic, neuroprotective and
antiangiogenic properties and is widely expressed in the
developing and adult nervous systems. This subgroup
corresponds to clade F1 of the serpin superfamily.
Length = 374
Score = 32.5 bits (74), Expect = 0.25
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 15 TVMRLVRDPKVKLKYQHLITNSFVECNRLLRWCPSPD----CNNAIKVQHVEARPV 66
TV ++ PK+KL Y+ + S E +L SPD + IK+ HV + V
Sbjct: 267 TVKAVLTLPKLKLSYETELLPSLQE-LKLQSLFASPDFTKITSKPIKLSHVHHKAV 321
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 28.6 bits (64), Expect = 0.37
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 65 PVVCKCGHRFCFACGENW 82
PV+ CGH FC +C W
Sbjct: 12 PVILPCGHTFCRSCIRKW 29
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 28.1 bits (63), Expect = 0.65
Identities = 8/23 (34%), Positives = 9/23 (39%)
Query: 60 HVEARPVVCKCGHRFCFACGENW 82
VV CGH F C + W
Sbjct: 11 EPGEEVVVLPCGHVFHKECLDKW 33
>gnl|CDD|221010 pfam11164, DUF2948, Protein of unknown function (DUF2948). This
family of proteins with unknown function appear to be
restricted to Proteobacteria.
Length = 138
Score = 29.5 bits (67), Expect = 1.3
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 160 CNRYDEEEAKVARGAQERSRAALQ 183
NR+ E+A R ER R+AL
Sbjct: 41 LNRFRWEDALRRRRPPERVRSALH 64
>gnl|CDD|216480 pfam01403, Sema, Sema domain. The Sema domain occurs in
semaphorins, which are a large family of secreted and
transmembrane proteins, some of which function as
repellent signals during axon guidance. Sema domains
also occur in the hepatocyte growth factor receptor and
human plexin A-3.
Length = 435
Score = 30.4 bits (69), Expect = 1.3
Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 16/72 (22%)
Query: 48 PSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSNW 107
P+ +C N I+V + CG N PV C+L+ D +
Sbjct: 56 PNTECTNFIRVLQAYNDTHL--------LVCGTNAFQPV-CTLINL------GDRCLFSL 100
Query: 108 IAANTKE-CPKC 118
++ C C
Sbjct: 101 DVDKEEDGCGDC 112
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 29.8 bits (67), Expect = 1.8
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 165 EEEAKVARGAQERSRAALQRYLFYCNRYMNHMQSLKFEHKLYASVKEKM-EEMQQHNMSW 223
++ K+ R E + LQ+Y R H L+ + K +KE E + +
Sbjct: 218 QQLLKLLRAEGESEKQELQQY-----RQKAHR-ILQSKEKRINFLKEGCLFEGLDSSTAQ 271
Query: 224 IEVQFLK 230
IE++ LK
Sbjct: 272 IELEELK 278
>gnl|CDD|227414 COG5082, AIR1, Arginine methyltransferase-interacting protein,
contains RING Zn-finger [Posttranslational modification,
protein turnover, chaperones / Intracellular trafficking
and secretion].
Length = 190
Score = 29.4 bits (66), Expect = 2.0
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 8/70 (11%)
Query: 47 CPSPDCNNAIKVQHVEARPVVCKCGHRFCFACGENWHDPVRCSLLRRWIKKCDDDSETSN 106
CP C N H K C+ CGE H C+ + K C D + T +
Sbjct: 76 CPHSICYNCSWDGHRSNHCPKPK----KCYNCGETGHLSRDCNPSKDQQKSCFDCNSTRH 131
Query: 107 WIAANTKECP 116
++++CP
Sbjct: 132 ----SSEDCP 137
>gnl|CDD|224378 COG1461, COG1461, Predicted kinase related to dihydroxyacetone
kinase [General function prediction only].
Length = 542
Score = 29.6 bits (67), Expect = 2.4
Identities = 16/63 (25%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 255 KNNQSVLFEDNQKDLESATEKLSEYLERDITSENLANIKQQVQDKYRLVEI------QLK 308
++ + L + +K L+ +E ++ Y +D T E +++++++KY VE+ Q
Sbjct: 475 EDLEDALKKTLEKLLDEDSEIVTIYYGKDATEEEAEELEKKIEEKYPDVEVEIYEGGQPL 534
Query: 309 YSY 311
YSY
Sbjct: 535 YSY 537
>gnl|CDD|234714 PRK00286, xseA, exodeoxyribonuclease VII large subunit; Reviewed.
Length = 438
Score = 29.4 bits (67), Expect = 2.7
Identities = 27/136 (19%), Positives = 58/136 (42%), Gaps = 19/136 (13%)
Query: 165 EEEAKVARGAQERSRAALQRYLFYCNRYMNHMQ-SLKFEH--KLYASVKEKMEEMQQHNM 221
E + + Q+R A++R L + ++ + LKF+ +L A +++++ +QQ
Sbjct: 263 AELLQRLQQLQQRLARAMRRRLEQKRQRLDQLARRLKFQSPERLLAQQQQRLDRLQQRLQ 322
Query: 222 SWIEVQFLKKAVDILCQCRQTLMYTYVFAYYLRKNNQSVLFEDNQKDLESATEKLSEYLE 281
+E + L +Q L + L++ N E Q+ LE ++L +
Sbjct: 323 RALERR--------LRLAKQRLER---LSQRLQQQNPQRRIERAQQRLEQLEQRLRRAMR 371
Query: 282 RDITSENLANIKQQVQ 297
R L +Q+++
Sbjct: 372 R-----QLKRKRQRLE 382
>gnl|CDD|235978 PRK07234, PRK07234, putative monovalent cation/H+ antiporter
subunit D; Reviewed.
Length = 470
Score = 29.5 bits (67), Expect = 2.7
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 170 VARGAQERSRAALQRYLFYCNRYMN 194
VA +R+ RYLFY N M
Sbjct: 134 VAYPRTDRAIWVGLRYLFYSNVAML 158
>gnl|CDD|216016 pfam00602, Flu_PB1, Influenza RNA-dependent RNA polymerase subunit
PB1. Two GTP binding sites exist in this protein.
Length = 740
Score = 29.4 bits (66), Expect = 2.8
Identities = 9/42 (21%), Positives = 19/42 (45%)
Query: 205 LYASVKEKMEEMQQHNMSWIEVQFLKKAVDILCQCRQTLMYT 246
L +++E+ + +M + + D L + RQT +T
Sbjct: 93 LINNLEEEHPGSFEKSMEEAMEELMNMEFDKLTKGRQTYDWT 134
>gnl|CDD|216059 pfam00685, Sulfotransfer_1, Sulfotransferase domain.
Length = 254
Score = 28.8 bits (65), Expect = 2.8
Identities = 19/112 (16%), Positives = 38/112 (33%), Gaps = 30/112 (26%)
Query: 184 RYLFYCNRYMNHMQSLKFEHKLYASVKEKMEEMQQHNMSWIEVQFLKKAVDILCQCRQTL 243
Y F+ + FE +E+ ++
Sbjct: 109 YYHFFRMAKILKAPGTPFEF---------VEDFLNGKVNC------------------GS 141
Query: 244 MYTYVFAYYLRKNNQSVLF---EDNQKDLESATEKLSEYLERDITSENLANI 292
+ +V ++ + ++LF ED +KD +K++E+L +T E L I
Sbjct: 142 YFDHVKGWWKLRPPGNILFLRYEDLKKDPRGEIKKIAEFLGIPLTEEELDKI 193
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 29.2 bits (66), Expect = 3.2
Identities = 20/109 (18%), Positives = 46/109 (42%), Gaps = 13/109 (11%)
Query: 196 MQSLKFEHKLYASVKEKMEEMQQHNMSWIEVQFLKKAVD----ILCQCRQTLMYTYVFAY 251
Q + +K+K++E+Q ++ L A+D I+ + +
Sbjct: 291 TQQISEGPDRITKIKDKLKELQH------SLEKLDTAIDELEEIMDEFNEQSKKLLELKN 344
Query: 252 YLRKNNQSVLFEDNQ-KDLESATEKLSEYLERDITSENLANIKQQVQDK 299
+ N QS++ ++ K +++A E+L E +E LA ++ ++
Sbjct: 345 KISTNKQSLITLVDKAKKVKAAIEELQA--EFVDNAEELAKLQDELDKI 391
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 26.3 bits (58), Expect = 3.7
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 66 VVCKCGHRFCFACGENW 82
V+ CGH FC +C + W
Sbjct: 14 VLLPCGHVFCRSCIDKW 30
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 28.5 bits (63), Expect = 3.9
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 65 PVVCKCGHRFCFACGENW 82
PVV CGH FC+ C W
Sbjct: 31 PVVTLCGHLFCWPCIHKW 48
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 25.5 bits (56), Expect = 6.2
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 66 VVCKCGHRFCFACGENW 82
V+ CGH FC C +
Sbjct: 17 VLTPCGHVFCRECILRY 33
>gnl|CDD|184886 PRK14892, PRK14892, putative transcription elongation factor Elf1;
Provisional.
Length = 99
Score = 26.6 bits (59), Expect = 6.3
Identities = 8/32 (25%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 114 ECPKC---LVTIEKDGGCNHMVCKNQSCKAEF 142
ECP+C ++++ + C N EF
Sbjct: 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54
>gnl|CDD|233304 TIGR01180, aman2_put, alpha-1,2-mannosidase, putative. The
identification of members of this family as putative
alpha-1,2-mannosidases is based on an unpublished
characterization of the aman2 gene in Bacillus sp. M-90
by Maruyama,Y., Nakajima,M. and Nakajima,T. (Genbank
accession BAA76709, pid g4587313). Most members of this
family appear to have signal sequences. Members from the
dental pathogen Porphyromonas gingivalis have been
described as immunoreactive with periodontitis patient
serum [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 750
Score = 28.3 bits (63), Expect = 6.8
Identities = 10/60 (16%), Positives = 16/60 (26%), Gaps = 8/60 (13%)
Query: 196 MQSLKFEHKLYASVKEKMEEMQQHNMSWIEVQFLKKA-VDILCQCRQTLMYTYVFAYYLR 254
+ K H +S K + V Q ++L Y +AY
Sbjct: 434 YHATKAVHPKISSTGRKPWR-------TDNDLYYVLGYVPADEQAARSLSYALEYAYDDW 486
>gnl|CDD|219523 pfam07697, 7TMR-HDED, 7TM-HD extracellular. This entry represents
the extracellular domain of the 7TM-HD (7TM Receptors
with HD hydrolase).
Length = 218
Score = 27.6 bits (62), Expect = 6.9
Identities = 11/49 (22%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 263 EDNQKDLESAT-EKLSEYLERDITSENLANIKQQVQDKYRLVEIQLKYS 310
+++ K LE A L L + I L K++ ++QL+
Sbjct: 100 DEDLKLLEDAIRTALDRILSQGIREGLLIEAKEEA------AKLQLESL 142
>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma
subunit [Transcription].
Length = 247
Score = 27.3 bits (61), Expect = 8.7
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 5/60 (8%)
Query: 252 YLRKNNQSVL---FEDNQKDLESATEKLSEYLERDITSENLANIKQQVQDKYRLVEIQLK 308
YLRKN+ + + + +E A ++L + L R+ T E +A +++Y +E L
Sbjct: 92 YLRKNDSVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEY--IEALLA 149
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
0.322 0.134 0.437
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,154,349
Number of extensions: 1356859
Number of successful extensions: 1478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1472
Number of HSP's successfully gapped: 41
Length of query: 312
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 215
Effective length of database: 6,635,264
Effective search space: 1426581760
Effective search space used: 1426581760
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 (22.0 bits)
S2: 59 (26.6 bits)