RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4856
(654 letters)
>gnl|CDD|189032 cd09862, PIN_Rrp44, PIN domain of yeast exosome subunit Rrp44
endoribonuclease and other eukaryotic homologs. PIN
(PilT N terminus) domain of the Saccharomyces cerevisiae
exosome subunit Rrp44 (Ribosomal RNA-processing protein
44 or Protein Dis3 homolog) and other similar eukaryotic
homologs are included in this family. The eukaryotic
exosome is a conserved macromolecular complex
responsible for many RNA-processing and RNA-degradation
reactions. It is composed of nine core subunits that
directly binds Rrp44. The Rrp44 nuclease is the
catalytic subunit of the exosome and has endonuclease
activity in the PIN domain and an exoribonuclease
activity in its RNase II-like region. Rrp44 binding to
the exosome is mediated mainly by the PIN domain and by
subunits Rrp41-Rrp45, and binding predictions indicate
that the PIN domain active site is positioned on the
outer surface of the exosome. These PIN domains are
structural homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but lack the extensive arch/clamp region
and the H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule. Recombinant Rrp44 was shown to possess
manganese-dependent endonuclease activity in vitro that
was abolished by point mutations in the putative metal
binding residues of its PIN domain.
Length = 182
Score = 127 bits (321), Expect = 7e-34
Identities = 45/88 (51%), Positives = 63/88 (71%), Gaps = 4/88 (4%)
Query: 1 LKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHL-ESAV 59
L+ LI +P ++FYVF NEHH ETYVE+EPGES+NDRNDRA+R W Y EHL + ++
Sbjct: 98 LRALIKDPDKRFYVFSNEHHRETYVEREPGESINDRNDRAIRVATKW---YSEHLPKLSI 154
Query: 60 RVILLSEDVRNRDLATQSGLLTSSIEGY 87
+V+LL+ D NR+ A + G+ +I+ Y
Sbjct: 155 KVVLLTNDRANREKAAEEGITAKTIKEY 182
>gnl|CDD|223631 COG0557, VacB, Exoribonuclease R [Transcription].
Length = 706
Score = 99.8 bits (249), Expect = 1e-21
Identities = 52/203 (25%), Positives = 80/203 (39%), Gaps = 42/203 (20%)
Query: 134 SLLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLE 193
L++G +AS + F + I V ++ LNRA+ GD V V LLP +
Sbjct: 68 DLVEGIVEASAKGFGFLSPDDSKDADDIFV-PKDPLNRALHGDRVLVELLPSDKR----- 121
Query: 194 LVLEDEGSGEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGS 253
R +V I++R G L+P+ G
Sbjct: 122 -----------------------------GRFKEAAVVRILERANSALVGELRPSQGIG- 151
Query: 254 SRHLFVPAERKIP-KIRVETRQIATL-SGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDK 311
+P ++++P I + Q G +VV I WP SR P G V LG +GD
Sbjct: 152 ---RVLPDDKRLPFLIAIPPEQAPGAEEGHLVVVEITRWPDTSRPPFGEVVEVLGDLGDP 208
Query: 312 DTENEVLLLEHDVPHSKFSDLVL 334
+ E +L +H +P +F + VL
Sbjct: 209 GADIEAILRDHGIPS-EFPEKVL 230
Score = 77.4 bits (191), Expect = 8e-15
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 398 ILLFLFQAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATY 457
+L + QA Y + H+GLA YTHFTSPIRRY D+IVHR L A + +
Sbjct: 526 LLRSMKQAEYSPD------NVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIP 579
Query: 458 PSLLDKKASTALCYNL 473
++ L ++
Sbjct: 580 EKKTSEEELDELAAHI 595
Score = 75.1 bits (185), Expect = 5e-14
Identities = 23/59 (38%), Positives = 32/59 (54%)
Query: 474 VSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALCYNL 532
+ H+GLA YTHFTSPIRRY D+IVHR L A + + ++ L ++
Sbjct: 537 PDNVGHFGLALDYYTHFTSPIRRYPDLIVHRQLKALLSGEPIPEKKTSEEELDELAAHI 595
Score = 60.9 bits (148), Expect = 1e-09
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVTY 652
+ EE++ R DLR L + ++DP D+DDA+ L NG +
Sbjct: 240 VPEEDLKGRVDLRDLPIFTIDPEDAKDLDDAVSVEKLRNGGYRLGV 285
Score = 36.2 bits (84), Expect = 0.054
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 533 PGCTDIDDALHCRPLPNGNIEVTY 556
D+DDA+ L NG +
Sbjct: 262 EDAKDLDDAVSVEKLRNGGYRLGV 285
>gnl|CDD|214935 smart00955, RNB, This domain is the catalytic domain of
ribonuclease II.
Length = 286
Score = 80.0 bits (198), Expect = 2e-16
Identities = 25/56 (44%), Positives = 30/56 (53%), Gaps = 6/56 (10%)
Query: 397 FILLFLFQAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 452
+L + A Y H+GLA YTHFTSPIRRY D+IVHR L A +
Sbjct: 236 LLLRSMPHAEYSVDN------SGHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285
Score = 76.2 bits (188), Expect = 4e-15
Identities = 23/38 (60%), Positives = 27/38 (71%)
Query: 474 VSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIG 511
V + H+GLA YTHFTSPIRRY D+IVHR L A +
Sbjct: 248 VDNSGHFGLALDAYTHFTSPIRRYPDLIVHRQLKAALR 285
Score = 61.1 bits (149), Expect = 3e-10
Identities = 15/36 (41%), Positives = 20/36 (55%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
R DLR L + ++DP DIDDA+ L NG +
Sbjct: 1 RVDLRDLPLFTIDPEDAKDIDDAVSVEKLDNGGYRL 36
Score = 39.6 bits (93), Expect = 0.003
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 533 PGCTDIDDALHCRPLPNGNIEV 554
DIDDA+ L NG +
Sbjct: 15 EDAKDIDDAVSVEKLDNGGYRL 36
>gnl|CDD|216112 pfam00773, RNB, RNB domain. This domain is the catalytic domain of
ribonuclease II.
Length = 322
Score = 72.7 bits (179), Expect = 6e-14
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI 451
H+GL IYTHFTSPIRRYAD++VHR L A +
Sbjct: 291 HFGLGLEIYTHFTSPIRRYADLVVHRQLKALL 322
Score = 72.7 bits (179), Expect = 6e-14
Identities = 22/32 (68%), Positives = 26/32 (81%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI 510
H+GL IYTHFTSPIRRYAD++VHR L A +
Sbjct: 291 HFGLGLEIYTHFTSPIRRYADLVVHRQLKALL 322
Score = 56.2 bits (136), Expect = 2e-08
Identities = 16/36 (44%), Positives = 20/36 (55%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
R DLR L ++DP DIDDAL LP+G +
Sbjct: 1 RRDLRDLPFFTIDPETAKDIDDALSVEKLPDGGYRL 36
Score = 36.1 bits (84), Expect = 0.044
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 533 PGCTDIDDALHCRPLPNGNIEV 554
DIDDAL LP+G +
Sbjct: 15 ETAKDIDDALSVEKLPDGGYRL 36
>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 = 66.5 bits (163), Expect = 2e-11
Identities = 21/28 (75%), Positives = 24/28 (85%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLL 447
H+GLA YTHFTSPIRRY D+IVHRL+
Sbjct: 543 HFGLALEYYTHFTSPIRRYPDLIVHRLI 570
Score = 66.5 bits (163), Expect = 2e-11
Identities = 21/28 (75%), Positives = 24/28 (85%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLL 506
H+GLA YTHFTSPIRRY D+IVHRL+
Sbjct: 543 HFGLALEYYTHFTSPIRRYPDLIVHRLI 570
Score = 58.4 bits (142), Expect = 9e-09
Identities = 44/204 (21%), Positives = 78/204 (38%), Gaps = 43/204 (21%)
Query: 135 LLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLEL 194
L++G+ A R+ F G + E D+ + +N A+ GD V VR
Sbjct: 68 LVKGTVIAHRDGF--GFLRPEDDDEDDIFIPPRQMNGAMHGDRVLVR------------- 112
Query: 195 VLEDEGSGEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSS 254
+ G+ E K+++ R QIVG + G +
Sbjct: 113 ITGKPDGGDRFEARVIKILE----------RANDQIVGTFYIENGI--GFV--------- 151
Query: 255 RHLFVPAERKIP-KIRVETRQIATL-SGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKD 312
+P +++I I + QI G +++V I +P +R G V LG D
Sbjct: 152 ----IPDDKRIYLDIFIPPEQILGAEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPG 207
Query: 313 TENEVLLLEHDVPHSKFSDLVLSY 336
+ +++ +H +P+ F + VL
Sbjct: 208 IDILIIIRKHGIPYE-FPEEVLDE 230
Score = 51.9 bits (125), Expect = 9e-07
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 607 ITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEV 650
+ EEE+ R DLR L ++D D DDA++ L +GN ++
Sbjct: 238 VPEEEIKGRKDLRDLPFVTIDGEDAKDFDDAVYVEKLKDGNYKL 281
Score = 29.9 bits (68), Expect = 5.1
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 537 DIDDALHCRPLPNGNIEV 554
D DDA++ L +GN ++
Sbjct: 264 DFDDAVYVEKLKDGNYKL 281
>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 = 59.7 bits (145), Expect = 3e-09
Identities = 24/60 (40%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 398 ILLFLFQAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATY 457
+L L QA Y + H+GL Y HFTSPIRRY D+ HRL+ A + + T
Sbjct: 475 LLRSLSQAEYSPEPLG------HFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTD 528
Score = 59.3 bits (144), Expect = 4e-09
Identities = 19/38 (50%), Positives = 24/38 (63%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATY 516
H+GL Y HFTSPIRRY D+ HRL+ A + + T
Sbjct: 491 HFGLGLEHYAHFTSPIRRYPDLTNHRLIKAVLAKEQTD 528
Score = 38.9 bits (91), Expect = 0.009
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 605 KSITEEEVARRTDLRHLDVCSVDPPGCTDIDDALHCRPLPNG 646
+ E+ R DL L ++D D+DDA++ + LP+G
Sbjct: 184 FDVDEQAKKYREDLTDLAFVTIDGADAKDLDDAVYVKKLPDG 225
Score = 38.2 bits (89), Expect = 0.016
Identities = 33/202 (16%), Positives = 64/202 (31%), Gaps = 39/202 (19%)
Query: 135 LLQGSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLPESQWSAPLEL 194
L++G +A + F G + + DK + + + GD V L
Sbjct: 16 LVKGVVKAHNKGF--GFLRPDDDDKKDYFIPPPQMKKVMHGDLVEACPL----------- 62
Query: 195 VLEDEGSGEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSS 254
+ E E ++++ + VG + + ++ +P
Sbjct: 63 ---SQPQRGRFEAEVERILE----------PALTRFVGKFLGE-NDFGFVVPDDPRIYLD 108
Query: 255 RHLFVPAERKIPKIRVETRQIATLSGQRIVVAIDSWPRHSRYPQGHFVRALGPIGDKDTE 314
+ VP ++ G ++VV + +P G + LG D
Sbjct: 109 --IIVPKASVKNELA---------EGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIP 157
Query: 315 NEVLLLEHDVPHSKFSDLVLSY 336
V L H++P +F D V
Sbjct: 158 WWVTLARHEIPF-EFPDGVEQQ 178
>gnl|CDD|179920 PRK05054, PRK05054, exoribonuclease II; Provisional.
Length = 644
Score = 51.8 bits (125), Expect = 8e-07
Identities = 21/41 (51%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 459
H+GL Y +TSPIR+Y D+I HRLL A I G A P
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ 525
Score = 51.8 bits (125), Expect = 8e-07
Identities = 21/41 (51%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYPS 518
H+GL Y +TSPIR+Y D+I HRLL A I G A P
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETAERPQ 525
Score = 37.5 bits (88), Expect = 0.021
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651
R DL LD ++D D+DDAL+ LP+G +++T
Sbjct: 190 REDLTALDFVTIDSASTEDMDDALYVEKLPDGGLQLT 226
Score = 29.1 bits (66), Expect = 8.6
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 537 DIDDALHCRPLPNGNIEVT 555
D+DDAL+ LP+G +++T
Sbjct: 208 DMDDALYVEKLPDGGLQLT 226
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 49.0 bits (117), Expect = 7e-06
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHR 445
H+GLA Y HFTSPIRRY D+ +HR
Sbjct: 555 HFGLALQSYAHFTSPIRRYPDLSLHR 580
Score = 49.0 bits (117), Expect = 7e-06
Identities = 17/26 (65%), Positives = 20/26 (76%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHR 504
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 = 46.4 bits (110), Expect = 4e-05
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 2/71 (2%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYPSLLDKKASTALC--YNLPGCT 536
H+GL Y +TSPIR+Y D+I HRLL A I + D A N
Sbjct: 481 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRPQEDITVQLAERRRLNRIAER 540
Query: 537 DIDDALHCRPL 547
D+ D L+ R L
Sbjct: 541 DVADWLYARFL 551
Score = 45.6 bits (108), Expect = 8e-05
Identities = 18/36 (50%), Positives = 23/36 (63%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADA 455
H+GL Y +TSPIR+Y D+I HRLL A I +
Sbjct: 481 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGET 516
Score = 38.7 bits (90), Expect = 0.009
Identities = 15/37 (40%), Positives = 21/37 (56%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651
R DL LD ++D D+DDAL LPNG +++
Sbjct: 186 REDLTALDFVTIDSESTKDMDDALFAEALPNGKLQLI 222
>gnl|CDD|227117 COG4776, Rnb, Exoribonuclease II [Transcription].
Length = 645
Score = 44.8 bits (106), Expect = 1e-04
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 420 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI 451
H+GL Y +TSPIR+Y D+I HRLL A I
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVI 516
Score = 44.8 bits (106), Expect = 1e-04
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 479 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI 510
H+GL Y +TSPIR+Y D+I HRLL A I
Sbjct: 485 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVI 516
Score = 34.7 bits (80), Expect = 0.16
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 615 RTDLRHLDVCSVDPPGCTDIDDALHCRPLPNGNIEVT 651
R DL LD ++D D+DDAL+ PLP+G+ ++
Sbjct: 190 REDLTALDFVTIDSESTEDMDDALYAEPLPDGDWQLI 226
>gnl|CDD|189024 cd09854, PIN_VapC-Smg6_family, PIN domains of VapC and Smg6
ribonucleases, ribosome assembly factor NOB1,
rRNA-processing protein Fcf1, Archaeoglobus fulgidus
AF0591 protein, and homologs. PIN (PilT N terminus)
domains of such ribonucleases as the toxins of
prokaryotic toxin/antitoxin operons FitAB and VapBC, as
well as, eukaryotic ribonucleases such as Smg6, ribosome
assembly factor NOB1, exosome subunit Rrp44
endoribonuclease and, rRNA-processing protein Fcf1, are
included in this family. Also included are the PIN
domains of the Pyrobaculum aerophilum Pea0151 and
Archaeoglobus fulgidus AF0591 proteins and other similar
archaeal homologs. These PIN domains are structural
homologs of flap endonuclease-1 (FEN1)-like PIN domains,
but lack the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains typically contain three or four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule.
Length = 125
Score = 37.7 bits (87), Expect = 0.003
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 8 PSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWY 48
++F F E T+VE+ P E++ND +D A+ +
Sbjct: 60 DHKRFICFHKEFSEHTFVERLPNETINDADDCAINKTCMHR 100
>gnl|CDD|222278 pfam13638, PIN_4, PIN domain. Members of this family of bacterial
domains are predicted to be RNases (from similarities to
5'-exonucleases).
Length = 129
Score = 36.4 bits (85), Expect = 0.011
Identities = 16/83 (19%), Positives = 30/83 (36%), Gaps = 12/83 (14%)
Query: 1 LKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYVKYEEHLESAVR 60
L +L+ + S + V + + D+ND + A +E L
Sbjct: 57 LDELLEDGSGRIRVQTLDERLP--------PEIEDKNDDRILDCALLL---QEEL-PDRP 104
Query: 61 VILLSEDVRNRDLATQSGLLTSS 83
V+L++ D+ R A G+
Sbjct: 105 VVLVTNDINLRIKAKALGIPAED 127
>gnl|CDD|203875 pfam08206, OB_RNB, Ribonuclease B OB domain. This family includes
the N-terminal OB domain found in ribonuclease B
proteins in one or two copies.
Length = 58
Score = 32.1 bits (74), Expect = 0.081
Identities = 11/47 (23%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 138 GSFQASRENFLEGQVNCEGYDKPILVQGREGLNRAIDGDTVAVRLLP 184
G+ + ++ F G + + + I + E + +A+ GD V VR+
Sbjct: 1 GTVRGHKKGF--GFLIPDDEEDDIFI-PPEQMKKAMHGDRVLVRITK 44
>gnl|CDD|218386 pfam05021, NPL4, NPL4 family. The HRD4 gene was identical to NPL4,
a gene previously implicated in nuclear transport. Using
a diverse set of substrates and direct ubiquitination
assays, analysis revealed that HRD4/NPL4 is required for
a poorly characterized step in ER-associated degradation
after ubiquitination of target proteins but before their
recognition by the 26S proteasome. Npl4p physically
associates with Cdc48p via Ufd1p to form a
Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex
functions in the recognition of several
polyubiquitin-tagged proteins and facilitates their
presentation to the 26S proteasome for processive
degradation or even more specific processing.
Length = 306
Score = 31.9 bits (73), Expect = 0.93
Identities = 17/59 (28%), Positives = 21/59 (35%), Gaps = 9/59 (15%)
Query: 368 VGLEQGFPSLLKPRTTFVFYDFPRTTRTNFILLFLFQAV--YFSS-----GMLQQSDFH 419
V L GFP P F FP R +A+ Y S + + SDFH
Sbjct: 202 VTLTHGFP--EDPSPLFKSSTFPIENREAMGESQDLRALAKYLKSHKPKPFLERLSDFH 258
>gnl|CDD|212036 cd10326, SLC5sbd_NIS-like, Na(+)/iodide (NIS) and
Na(+)/multivitamin (SMVT) cotransporters, and related
proteins; solute binding domain. NIS (product of the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. SMVT (product of the SLC5A6 gene)
transports biotin, pantothenic acid and lipoate. This
subfamily also includes SMCT1 and 2. SMCT1(the product
of the SLC5A8 gene) is a high-affinity transporter of
various monocarboxylates including lactate and pyruvate,
short-chain fatty acids, ketone bodies, nicotinate and
its structural analogs, pyroglutamate, benzoate and its
derivatives, and iodide. SMCT2 (product of the SLC5A12
gene) is a low-affinity transporter for short-chain
fatty acids, lactate, pyruvate, and nicotinate. This
subfamily belongs to the solute carrier 5 (SLC5)
transporter family.
Length = 477
Score = 31.7 bits (73), Expect = 1.3
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 5/47 (10%)
Query: 361 ISTGVISVGLEQGFPSLLK-----PRTTFVFYDFPRTTRTNFILLFL 402
+ +ISV L G + R+ +D T+R F F+
Sbjct: 190 LVIIIISVKLGGGLGEIWSTASESGRSRIFDFDPDPTSRHTFWKQFI 236
>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 = 2.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 426 PIYTHFTSPIRRYADIIVHR 445
P++ F P +RYAD+I+ R
Sbjct: 161 PMHEQFIEPTKRYADVIIPR 180
Score = 30.2 bits (69), Expect = 2.6
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 485 PIYTHFTSPIRRYADIIVHR 504
P++ F P +RYAD+I+ R
Sbjct: 161 PMHEQFIEPTKRYADVIIPR 180
>gnl|CDD|218885 pfam06080, DUF938, Protein of unknown function (DUF938). This
family consists of several hypothetical proteins from
both prokaryotes and eukaryotes. The function of this
family is unknown.
Length = 201
Score = 29.7 bits (67), Expect = 3.4
Identities = 15/51 (29%), Positives = 19/51 (37%)
Query: 337 LPPMPWEKSTGRPWCSGTSIGLSQISTGVISVGLEQGFPSLLKPRTTFVFY 387
PP P E + + SI + IS GL +G LL P Y
Sbjct: 87 RPPWPVEAPAPASYDAIFSINMIHISPWSCVEGLFRGAGRLLPPGGVLYIY 137
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 29.7 bits (68), Expect = 3.6
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 426 PIYTHFTSPIRRYADIIVHR 445
P++ F P +RYADII+
Sbjct: 168 PMHLQFIEPSKRYADIIIPE 187
Score = 29.7 bits (68), Expect = 3.6
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 485 PIYTHFTSPIRRYADIIVHR 504
P++ F P +RYADII+
Sbjct: 168 PMHLQFIEPSKRYADIIIPE 187
>gnl|CDD|238025 cd00070, GLECT, Galectin/galactose-binding lectin. This domain
exclusively binds beta-galactosides, such as lactose,
and does not require metal ions for activity. GLECT
domains occur as homodimers or tandemly repeated
domains. They are developmentally regulated and may be
involved in differentiation, cell-cell interaction and
cellular regulation.
Length = 127
Score = 28.4 bits (64), Expect = 5.5
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 5 ISNPSRKFYVFVNEHHYETYVEQEPGESVN 34
I KF +FVN H+ ++ + P ES++
Sbjct: 84 ILVEEDKFQIFVNGQHFFSFPHRLPLESID 113
>gnl|CDD|176559 cd08622, PI-PLCXDc_CG14945_like, Catalytic domain of Drosophila
melanogaster CG14945-like proteins similar to
phosphatidylinositol-specific phospholipase C, X domain
containing. This subfamily corresponds to the catalytic
domain present in uncharacterized metazoan Drosophila
melanogaster CG14945-like proteins, which are similar to
eukaryotic phosphatidylinositol-specific phospholipase
C, X domain containing proteins (PI-PLCXD). The typical
eukaryotic phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11) has a multidomain organization
that consists of a PLC catalytic core domain, and
various regulatory domains. The catalytic core domain is
assembled from two highly conserved X- and Y-regions
split by a divergent linker sequence. In contrast,
eukaryotic PI-PLCXDs contain a single TIM-barrel type
catalytic domain, X domain, and are more closely related
to bacterial PI-PLCs, which participate in
Ca2+-independent PI metabolism, hydrolyzing the membrane
lipid phosphatidylinositol (PI) to produce
phosphorylated myo-inositol and diacylglycerol (DAG).
Although the biological function of eukaryotic PI-PLCXDs
still remains unclear, it may distinct from that of
typical eukaryotic PI-PLCs.
Length = 276
Score = 29.2 bits (66), Expect = 6.4
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 10/59 (16%)
Query: 10 RKFYVFVN---EHHYE--TYVEQEPGESVNDRNDRALRRVATWYVKYEEHLESAVRVIL 63
+F V + E H E + + QE G+ + R+ R W E RVI+
Sbjct: 105 HRFPVGFHSHPEVHDELISLLRQELGDLILRRS-----RNYGWGPTLSEIWARRKRVII 158
>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 = 28.5 bits (64), Expect = 7.0
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 421 YGLATPIYTHFTSPIRRYADIIVHRLLAACIGA 453
Y LA IY F I Y + +V L+ I
Sbjct: 2 YDLANSIYQEFERLIDNYGEEVVKNLMPLVIRV 34
Score = 28.5 bits (64), Expect = 7.0
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 480 YGLATPIYTHFTSPIRRYADIIVHRLLAACIGA 512
Y LA IY F I Y + +V L+ I
Sbjct: 2 YDLANSIYQEFERLIDNYGEEVVKNLMPLVIRV 34
>gnl|CDD|146915 pfam04513, Baculo_PEP_C, Baculovirus polyhedron envelope protein,
PEP, C terminus. Polyhedra are large crystalline
occlusion bodies containing nucleopolyhedrovirus
virions, and surrounded by an electron-dense structure
called the polyhedron envelope or polyhedron calyx. The
polyhedron envelope (associated) protein PEP is thought
to be an integral part of the polyhedron envelope. PEP
is concentrated at the surface of polyhedra, and is
thought to be important for the proper formation of the
periphery of polyhedra. It is thought that PEP may
stabilise polyhedra and protect them from fusion or
aggregation.
Length = 140
Score = 28.1 bits (63), Expect = 7.2
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 64 LSEDVRNRDLATQSGL--LTSSIEGYISTLSN 93
L + +RN S L LTSS+ STL+N
Sbjct: 79 LQDTLRNELTNLNSILNNLTSSVTNINSTLNN 110
>gnl|CDD|235104 PRK03103, PRK03103, DNA polymerase IV; Reviewed.
Length = 409
Score = 29.2 bits (66), Expect = 8.6
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 17/73 (23%)
Query: 566 KDIQACLLELGYNLNYRNRQAQYAGRASVAL--------HTHLFFRRKSITEE------- 610
++I+ LLEL + R R Y GR +V++ F R+ ++ E
Sbjct: 264 EEIKVVLLELCEEVCRRARAKGYMGR-TVSVSLRGADFDWPTGFSRQMTLPEPTNLAMEV 322
Query: 611 -EVARRTDLRHLD 622
E A + RH D
Sbjct: 323 YEAACKLFHRHWD 335
>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator. This protein is
found in a wide range of eukaryotes. It is a nuclear
protein and is suggested to be DNA binding. In plants,
this family is essential for correct circadian clock
functioning by acting as a light-quality regulator
coordinating the activities of blue and red light
signalling pathways during plant growth - inhibiting
growth in red light but promoting growth in blue light.
Length = 233
Score = 28.5 bits (64), Expect = 8.7
Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 7/73 (9%)
Query: 202 GEDEEGEDGKLIKGNKTVPPAERRPTGQIVGIIKRKWRQYCGILQPNPLAGSSRHLFVPA 261
G+D+E ED + K VP P V K+K + NP +S
Sbjct: 14 GDDDEEEDEDEGEDEKKVPKESSEPDEANVNPNKKK-------IGKNPSVDTSFLPDKAR 66
Query: 262 ERKIPKIRVETRQ 274
E K ++R E R+
Sbjct: 67 EEKEAELREELRE 79
>gnl|CDD|238102 cd00175, SNc, Staphylococcal nuclease homologues. SNase homologues
are found in bacteria, archaea, and eukaryotes. They
contain no disufide bonds.
Length = 129
Score = 27.6 bits (62), Expect = 9.0
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 171 RAIDGDTVAVRLLPESQWSAPLELV----LEDEGSGEDEEGE 208
R IDGDT+ VRL P + L + G+ E E
Sbjct: 1 RVIDGDTIRVRLPPGPLITVRLSGIDAPETARPNKGKSETDE 42
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
0.319 0.137 0.414
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: 33,998,594
Number of extensions: 3388308
Number of successful extensions: 2586
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2581
Number of HSP's successfully gapped: 64
Length of query: 654
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 551
Effective length of database: 6,369,140
Effective search space: 3509396140
Effective search space used: 3509396140
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: 62 (27.6 bits)