RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4846
(279 letters)
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 104 bits (262), Expect = 2e-25
Identities = 49/179 (27%), Positives = 73/179 (40%), Gaps = 22/179 (12%)
Query: 4 AMLRRHPVPPPANFEPLLHAARRQGFELSVGTGKELATSLDA----------AAVYFSSG 53
+ R H P + L + G L +G K AV +
Sbjct: 467 LLYRTHERPSTEKLQSLREFLQNLGLVLPLGGSKPQPQDYQILLETVKGRPLEAVLQT-- 524
Query: 54 MLQQS---------DFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLD 104
+L +S + H+GLA YTHFTSPIRRY D+IVHR L A + +
Sbjct: 525 LLLRSMKQAEYSPDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTS 584
Query: 105 KKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDE-DGYVLYVRKNALQILIP 162
++ L +++ R+AQ A R + L + + RV +E DG V V + +P
Sbjct: 585 EEELDELAAHISSAERRAQEAERDVIDLLKAEYMKKRVGEEFDGVVTGVTSFGFFVELP 643
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of
ribonuclease II.
Length = 286
Score = 85.4 bits (212), Expect = 2e-19
Identities = 38/112 (33%), Positives = 43/112 (38%), Gaps = 27/112 (24%)
Query: 4 AMLRRHPVPPPAN-FEPLLHAARRQGFELSVGTG-KELATSLDAA--------------- 46
+ R H P P E L G L G G K LA L+
Sbjct: 180 GLYRVHEGPDPEKLAELLKEFLALLGLLLLGGDGPKALAKLLEKIRDSPEERLLELLLLR 239
Query: 47 ----AVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 94
A Y H+GLA YTHFTSPIRRY D+IVHR L A +
Sbjct: 240 SMPHAEYSVDN------SGHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285
>gnl|CDD|216112 pfam00773, RNB, RNB domain. This domain is the catalytic domain of
ribonuclease II.
Length = 322
Score = 77.3 bits (191), Expect = 2e-16
Identities = 33/103 (32%), Positives = 48/103 (46%), Gaps = 11/103 (10%)
Query: 2 DNAMLRRHPVPPPANFEPLLHAARRQGFELSVGTG-----KELATSLDAAAV-YFSSGML 55
+ R HP P + LL +A + +EL S + + L
Sbjct: 220 IPGIYRVHPEPDLEKLQDLLKSALELDLDEEGLESLQKLLEELKDSPERRLLNLLLRRTL 279
Query: 56 QQSDF-----HHYGLATPIYTHFTSPIRRYADIIVHRLLAACI 93
++++ H+GL IYTHFTSPIRRYAD++VHR L A +
Sbjct: 280 PRAEYSTTPAPHFGLGLEIYTHFTSPIRRYADLVVHRQLKALL 322
>gnl|CDD|233703 TIGR02063, RNase_R, ribonuclease R. This family consists of an
exoribonuclease, ribonuclease R, also called VacB. It is
one of the eight exoribonucleases reported in E. coli
and is broadly distributed throughout the bacteria. In
E. coli, double mutants of this protein and
polynucleotide phosphorylase are not viable. Scoring
between trusted and noise cutoffs to the model are
shorter, divergent forms from the Chlamydiae, and
divergent forms from the Campylobacterales (including
Helicobacter pylori) and Leptospira interrogans
[Transcription, Degradation of RNA].
Length = 709
Score = 73.1 bits (180), Expect = 2e-14
Identities = 41/172 (23%), Positives = 69/172 (40%), Gaps = 23/172 (13%)
Query: 4 AMLRRHPVPPPANFEPLLHAARRQGFELSVGTGKE-----LATSLDAA-----AVYFSSG 53
+ R H P + L + G L GT + L+ ++
Sbjct: 467 FIYRVHERPSEEKLQNLREFLKTLGITLKGGTSDKPQPKDFQKLLEKVKGRPEEELINTV 526
Query: 54 ML---QQSDFH-----HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDK 105
+L QQ+ + H+GLA YTHFTSPIRRY D+IVHRL+ + + ++
Sbjct: 527 LLRSMQQAKYSPENIGHFGLALEYYTHFTSPIRRYPDLIVHRLIKKALFGGENTTTEKER 586
Query: 106 KASTA----LCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDE-DGYVLYV 152
+ A + + + R+A A R + ++ +E +G + V
Sbjct: 587 EYLEAKLEEIAEHSSKTERRADEAERDVNDWKKAEYMSEKIGEEFEGVISGV 638
>gnl|CDD|232937 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases
[Transcription, Degradation of RNA].
Length = 654
Score = 64.7 bits (158), Expect = 8e-12
Identities = 52/210 (24%), Positives = 79/210 (37%), Gaps = 32/210 (15%)
Query: 4 AMLRRHPVPPPANFEPLLHAARRQGFELSVGTGKELATSLDAAAV-----------YFSS 52
+ R HP P + LL G L G E T+LD A +
Sbjct: 415 GIYRVHPGPSKKKLQSLLEFLAELGLTLPGGN-AENVTTLDGACWLREVKDRPEYEILVT 473
Query: 53 GMLQ---QSDFH-----HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLD 104
+L+ Q+++ H+GL Y HFTSPIRRY D+ HRL+ A + + T
Sbjct: 474 RLLRSLSQAEYSPEPLGHFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTDTERYQ 533
Query: 105 KKAS-TALCYNLNYRNRQAQYAGRASVALHTHLF--------FRSRVQDEDGYVLYVR-- 153
+ + + + R+A+ A R + F + + ++VR
Sbjct: 534 PQDELLQIAEHCSDTERRARDAERDVADWLKCRYLLDKVGTEFSGEISSVTRFGMFVRLD 593
Query: 154 KNALQILIPKSRVQDEDGYVLYVRKNALQI 183
N + LI S + D YV K AL
Sbjct: 594 DNGIDGLIHISTL-HNDYYVFDQEKMALIG 622
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional.
Length = 644
Score = 54.5 bits (132), Expect = 2e-08
Identities = 23/66 (34%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNLNYRNRQ 121
H+GL Y +TSPIR+Y D+I HRLL A I + ++ + L R R
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETA------ERPQDEITVQLAERRRL 538
Query: 122 AQYAGR 127
+ A R
Sbjct: 539 NRMAER 544
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 48.6 bits (116), Expect = 2e-06
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHR 87
H+GLA Y HFTSPIRRY D+ +HR
Sbjct: 555 HFGLALQSYAHFTSPIRRYPDLSLHR 580
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II. This family consists of
exoribonuclease II, the product of the rnb gene, as
found in a number of gamma proteobacteria. In
Escherichia coli, it is one of eight different
exoribonucleases. It is involved in mRNA degradation and
tRNA precursor end processing [Transcription,
Degradation of RNA].
Length = 639
Score = 45.6 bits (108), Expect = 2e-05
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADA 97
H+GL Y +TSPIR+Y D+I HRLL A I +
Sbjct: 481 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGET 516
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription].
Length = 645
Score = 44.8 bits (106), Expect = 3e-05
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI 93
H+GL Y +TSPIR+Y D+I HRLL A I
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVI 516
>gnl|CDD|238981 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
also known as uridine kinase or uridine-cytidine kinase
(UCK), catalyzes the reversible phosphoryl transfer from
ATP to uridine or cytidine to yield UMP or CMP. In the
primidine nucleotide-salvage pathway, this enzyme
combined with nucleoside diphosphate kinases further
phosphorylates UMP and CMP to form UTP and CTP. This
kinase also catalyzes the phosphorylation of several
cytotoxic ribonucleoside analogs such as 5-flurrouridine
and cyclopentenyl-cytidine.
Length = 198
Score = 30.2 bits (69), Expect = 0.77
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 68 PIYTHFTSPIRRYADIIVHR 87
P++ F P +RYAD+I+ R
Sbjct: 161 PMHEQFIEPTKRYADVIIPR 180
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 30.1 bits (69), Expect = 1.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 68 PIYTHFTSPIRRYADIIVHR 87
P++ F P +RYADII+
Sbjct: 168 PMHLQFIEPSKRYADIIIPE 187
>gnl|CDD|143165 cd00096, Ig, Immunoglobulin domain. Ig: immunoglobulin (Ig) domain
found in the Ig superfamily. The Ig superfamily is a
heterogenous group of proteins, built on a common fold
comprised of a sandwich of two beta sheets. Members of
this group are components of immunoglobulin, neuroglia,
cell surface glycoproteins, such as, T-cell receptors,
CD2, CD4, CD8, and membrane glycoproteins, such as,
butyrophilin and chondroitin sulfate proteoglycan core
protein. A predominant feature of most Ig domains is a
disulfide bridge connecting the two beta-sheets with a
tryptophan residue packed against the disulfide bond.
Length = 74
Score = 27.8 bits (61), Expect = 1.6
Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 196 LRC-----DSPSVSWTYNEKEQSQSCGSVVFHSFDPVTVQLSLDRSNVQHE 241
L C P+++W N K S + V S + +L SNV E
Sbjct: 3 LTCLASGPPPPTITWLKNGKPLPSSVLTRVRSSRGTSSGSSTLTISNVTLE 53
>gnl|CDD|183151 PRK11469, PRK11469, hypothetical protein; Provisional.
Length = 188
Score = 28.4 bits (63), Expect = 3.2
Identities = 25/73 (34%), Positives = 34/73 (46%), Gaps = 7/73 (9%)
Query: 25 RRQGFELSVGTGKELATSLDAAAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADII 84
RR GF L V T +ATSLDA AV LQ + +AT + + I ++
Sbjct: 101 RRHGFWLLVTTA--IATSLDAMAVGVGLAFLQVNI-----IATALAIGCATLIMSTLGMM 153
Query: 85 VHRLLAACIGADA 97
V R + + IG A
Sbjct: 154 VGRFIGSIIGKKA 166
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins
in this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 27.8 bits (62), Expect = 4.8
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 63 YGLATPIYTHFTSPIRRYADIIVHRLLAACIGA 95
Y LA IY F I Y + +V L+ I
Sbjct: 2 YDLANSIYQEFERLIDNYGEEVVKNLMPLVIRV 34
>gnl|CDD|216797 pfam01936, NYN, NYN domain. These domains are found in the
eukaryotic proteins typified by the Nedd4-binding
protein 1 and the bacterial YacP-like proteins
(Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain
shares a common protein fold with two other previously
characterized groups of nucleases, namely the PIN (PilT
N-terminal) and FLAP/5' --> 3' exonuclease
superfamilies. These proteins share a common set of 4
acidic conserved residues that are predicted to
constitute their active site. Based on the conservation
of the acidic residues and structural elements Aravind
and colleagues suggest that PIN and NYN domains are
likely to bind only a single metal ion, unlike the
FLAP/5' --> 3' exonuclease superfamily, which binds two
metal ions. Based on conserved gene neighborhoods
Aravind and colleagues infer that the bacterial members
are likely to be components of the processome/degradsome
that process tRNAs or ribosomal RNAs.
Length = 141
Score = 27.2 bits (61), Expect = 5.5
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 15 ANFEPLLHAARRQGFELSV-GTGKELATSLDAAAVYF 50
+F PLL R +G ++V G + +L AA F
Sbjct: 101 GDFAPLLERLRERGKRVNVLGAEPSTSDALINAADRF 137
>gnl|CDD|224349 COG1432, COG1432, Uncharacterized conserved protein [Function
unknown].
Length = 181
Score = 27.8 bits (62), Expect = 5.7
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 15 ANFEPLLHAARRQGFELSV-GTGKELATSLDAAAVYFS 51
+F PL+ AAR +G + V G ++ L AA Y+
Sbjct: 121 GDFIPLVEAARDKGKRVEVAGIEPMTSSDLRNAADYYI 158
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism].
Length = 218
Score = 27.6 bits (62), Expect = 6.1
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 68 PIYTHFTSPIRRYADIIVHRLLAACIGAD---ATYPSLLDKKASTALCY 113
P+Y F P ++YADII+ + D A S L ++ +T
Sbjct: 170 PMYEQFIEPTKKYADIIIPSGGKNEVAVDLLQAKIASSLSEQNNTNYKE 218
>gnl|CDD|236055 PRK07575, PRK07575, dihydroorotase; Provisional.
Length = 438
Score = 28.1 bits (63), Expect = 6.5
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 6/28 (21%)
Query: 118 RNRQAQYAGRASVALHTHLFFRSRVQDE 145
R R+A++AG + A H S++QDE
Sbjct: 186 RARRAEFAGISDPADH------SQIQDE 207
>gnl|CDD|211372 cd09261, AP-3_Mu3B_Cterm, C-terminal domain of medium Mu3B subunit
in neuron-specific adaptor protein (AP) complex AP-3.
AP complexes participate in the formation of
intracellular coated transport vesicles and select cargo
molecules for incorporation into the coated vesicles in
the late secretory and endocytic pathways. There are
four AP complexes, AP-1, AP-2, AP-3, and AP-4, described
in various eukaryotic organisms. Each AP complex
consists of four subunits: two large chains (one each of
gamma/alpha/delta/epsilon and beta1-4, respectively), a
medium mu chain (mu1-4), and a small sigma chain
(sigma1-4). Each of the four subunits from the different
AP complexes exhibits similarity with each other. This
subfamily corresponds to the C-terminal domain of
heterotetrameric adaptor protein complex 3 (AP-3) medium
mu3B subunit encoded by ap3m2 gene. Mu3B is specifically
expressed in neurons and neuroendocrine cells.
Neuron-specific AP-3 appears to be involved in synaptic
vesicle biogenesis from endosomes in neurons and plays
an important role in synaptic transmission in the
central nervous system. Unlike AP-1 and AP-2, which
function in conjunction with clathrin which is a
scaffolding protein participating in the formation of
coated vesicles, the nature of the outer shell of
neuron-specific AP-3 containing coats remains to be
elucidated. Membrane-anchored cargo molecules interact
with adaptors through short sorting signals in their
cytosolic segments. Tyrosine-based endocytotic signals
are one of the most important sorting signals. They are
of the form Y-X-X-Phi, where Y is tyrosine, X is any
amino acid and Phi is a bulky hydrophobic residue that
can be Leu, Ile, Met, Phe, or Val. These kinds of
sorting signals can be recognized by the C-terminal
domain of AP-3 mu3B subunit, also known as Y-X-X-Phi
signal-binding domain that contains two hydrophobic
pockets, one for the tyrosine-binding and one for the
bulky hydrophobic residue-binding.
Length = 254
Score = 27.7 bits (61), Expect = 6.7
Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 9/57 (15%)
Query: 222 HSFDPVTVQLSLDRSNVQHEKLVLRLVRPVIEGFSVSSAGEQGEEKMEEGETRSLYC 278
++FDPVT LS D + +KL P ++G S + + G K +E T +L
Sbjct: 166 YTFDPVTKLLSWDVGKINPQKL------PSLKG---SMSLQAGASKPDENPTINLQF 213
>gnl|CDD|233126 TIGR00785, dass, anion transporter. The Divalent Anion:Na+
Symporter (DASS) Family (TC 2.A.47) Functionally
characterized proteins of the DASS family transport (1)
organic di- and tricarboxylates of the Krebs Cycle as
well as dicarboxylate amino acid, (2) inorganic sulfate
and (3) phosphate. The animal NaDC-1 cotransport 3 Na+
with each dicarboxylate. Protonated tricarboxylates are
also cotransported with 3Na+ [Transport and binding
proteins, Anions, Transport and binding proteins,
Cations and iron carrying compounds].
Length = 444
Score = 27.7 bits (62), Expect = 7.5
Identities = 11/56 (19%), Positives = 17/56 (30%), Gaps = 8/56 (14%)
Query: 10 PVPPPANFEPLLHAARRQGFELSVGTGKELATSLDAAAVYFSSGMLQQSDFHHYGL 65
+P L +A GF T A+ + SG ++ D G
Sbjct: 379 GIPLELLALALALSASLMGFLTPYATP--------PNAIAYGSGYVKIKDMWRVGA 426
>gnl|CDD|191473 pfam06214, SLAM, Signaling lymphocytic activation molecule (SLAM)
protein. This family consists of several mammalian
signaling lymphocytic activation molecule (SLAM)
proteins. Optimal T cell activation and expansion
require engagement of the TCR plus co-stimulatory
signals delivered through accessory molecules. SLAM, a
70-kDa co-stimulatory molecule belonging to the Ig
superfamily, is defined as a human cell surface molecule
that mediates CD28-independent proliferation of human T
cells and IFN-gamma production by human Th1 and Th2
clones. SLAM has also been recognised as a receptor for
measles virus.
Length = 126
Score = 26.7 bits (59), Expect = 8.2
Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 145 EDGYVLYVRKNALQILIPKSRVQDEDGYVLYVRKN 179
EDGY ++ +L+IL +SR +DE Y + + +N
Sbjct: 93 EDGYKFHLENLSLRIL--ESRKEDEGWYFMTLEEN 125
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 0.135 0.398
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,224,799
Number of extensions: 1340457
Number of successful extensions: 1176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1173
Number of HSP's successfully gapped: 28
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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 (21.8 bits)
S2: 58 (26.1 bits)