RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8255
(117 letters)
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 88.4 bits (219), Expect = 1e-21
Identities = 47/139 (33%), Positives = 58/139 (41%), Gaps = 26/139 (18%)
Query: 4 DRDKDRERDRRRRSRSRDHKKRSRSR-DRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKA 62
RD+ R R RS +RSR R RRSRS ++ R R RSP ++ + +K
Sbjct: 52 PRDRRRYDSRSPRSLRYSSVRRSRDRPRRRSRSVRSIEQHRRRLRDRSPSNQWRKDDKKR 111
Query: 63 SLYWDVPPPGFEHVSPSQYKAMQAA------------------------AAAAVPVVGST 98
S WD+ PPG+E V+ Q KA Q V
Sbjct: 112 S-LWDIKPPGYELVTADQAKASQVFSVPGTAPRPAMTDPEKLLAEGSIITPLPVLPYQQQ 170
Query: 99 ITRQARRLYVGNIPFGVTE 117
TRQARRLYVG IP E
Sbjct: 171 ATRQARRLYVGGIPPEFVE 189
Score = 39.5 bits (92), Expect = 1e-04
Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 7 KDRERDRRRRSRSRDHKKRSRSRDR-RSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
+D E DR R + RS R R RSR RS+ + R RSR RS R+ ++ R R+
Sbjct: 1 RDEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRHRRSRERSYREDSRPRDRR 56
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors
including the Pad-1 protein (N. crassa), CAPER (M.
musculus) and CC1.3 (H.sapiens). These proteins are
characterized by an N-terminal arginine-rich, low
complexity domain followed by three (or in the case of
4 H. sapiens paralogs, two) RNA recognition domains
(rrm: pfam00706). These splicing factors are closely
related to the U2AF splicing factor family (TIGR01642).
A homologous gene from Plasmodium falciparum was
identified in the course of the analysis of that genome
at TIGR and was included in the seed.
Length = 457
Score = 42.2 bits (99), Expect = 1e-05
Identities = 24/66 (36%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 4 DRDKDRERDRRRRSRSRDHKKRSRSRDRRS--RSRSKDKKRAARSRSRSPRDKTKSRRRK 61
DR++ R R+ RRS + R RSR R R R +D R R RSRS R R
Sbjct: 4 DRERGRLRNDTRRSDKGRERSRRRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPRG 63
Query: 62 ASLYWD 67
Y
Sbjct: 64 DRSYRR 69
Score = 38.7 bits (90), Expect = 2e-04
Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 4 DRDKDRERDRRRRSRS--RDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKT 55
R + R+R RRRR R R + RSRSR R + R+ R R T
Sbjct: 26 RRSRSRDRSRRRRDRDYYRGRRGRSRSRSPNRYYRPR-GDRSYRRDDRRSGRNT 78
Score = 30.2 bits (68), Expect = 0.19
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 9/54 (16%)
Query: 14 RRRSRSRDHKKRSRSRDRRS-----RSRSKDKKRAARSRSRSPRDKTKSRRRKA 62
R R R R R R+ RRS RSR + + R RSR R RD + RR ++
Sbjct: 1 RYRDRER---GRLRNDTRRSDKGRERSRRRSRSR-DRSRRRRDRDYYRGRRGRS 50
Score = 27.2 bits (60), Expect = 2.5
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 23 KKRSRSRDR-RSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWD 67
+ R R R R R+ +R DK R RSR RS RRR Y
Sbjct: 1 RYRDRERGRLRNDTRRSDKGR-ERSRRRSRSRDRSRRRRDRDYYRG 45
>gnl|CDD|240676 cd12230, RRM1_U2AF65, RNA recognition motif 1 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. The subfamily
corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits. U2AF65
specifically recognizes the intron polypyrimidine tract
upstream of the 3' splice site and promotes binding of
U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays
an important role in the nuclear export of mRNA. It
facilitates the formation of a messenger
ribonucleoprotein export complex, containing both the
NXF1 receptor and the RNA substrate. Moreover, U2AF65
interacts directly and specifically with expanded CAG
RNA, and serves as an adaptor to link expanded CAG RNA
to NXF1 for RNA export. U2AF65 contains an N-terminal RS
domain rich in arginine and serine, followed by a
proline-rich segment and three C-terminal RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). The
N-terminal RS domain stabilizes the interaction of U2
snRNP with the branch point (BP) by contacting the
branch region, and further promotes base pair
interactions between U2 snRNA and the BP. The
proline-rich segment mediates protein-protein
interactions with the RRM domain of the small U2AF
subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are
sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The family
also includes Splicing factor U2AF 50 kDa subunit
(dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50
functions as an essential pre-mRNA splicing factor in
flies. It associates with intronless mRNAs and plays a
significant and unexpected role in the nuclear export of
a large number of intronless mRNAs.
Length = 82
Score = 38.3 bits (90), Expect = 5e-05
Identities = 12/15 (80%), Positives = 14/15 (93%)
Query: 103 ARRLYVGNIPFGVTE 117
ARRLYVGN+P G+TE
Sbjct: 1 ARRLYVGNLPPGITE 15
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 35.5 bits (82), Expect = 0.003
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 1/57 (1%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRR 59
+D DK R + R K RR ++ + R SP +T SR
Sbjct: 21 DDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPW-RTVSRA 76
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 33.5 bits (77), Expect = 0.015
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 2/56 (3%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASL 64
+ RRS S +RSR RRSR + R R +S R+A L
Sbjct: 1 MDDLALRRSSSSL--RRSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAEL 54
Score = 27.4 bits (61), Expect = 1.6
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 4/49 (8%)
Query: 5 RDKDRERDRRRR----SRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSR 49
R + R RR SR R + R RRS +R + R R R
Sbjct: 15 RSRRAARRSRRDGRVGSRGRSRYRSRRRSSRRSSTRRAELADTERDRYR 63
>gnl|CDD|215520 PLN02964, PLN02964, phosphatidylserine decarboxylase.
Length = 644
Score = 32.5 bits (74), Expect = 0.038
Identities = 13/48 (27%), Positives = 20/48 (41%)
Query: 1 MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRS 48
MG ++ + RR + R + K R R R R S + R+ S
Sbjct: 1 MGNGNSREAKESRRSKLRQKLQKFRIRRRHLRCSRGSSSGSVSQRAVS 48
>gnl|CDD|217301 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated
initially from a Japanese patient with hepatitis of
unknown aetiology, has since been found to infect both
healthy and diseased individuals and numerous
prevalence studies have raised questions about its role
in unexplained hepatitis. ORF1 is a large 750 residue
protein. The N-terminal half of this protein
corresponds to the capsid protein.
Length = 525
Score = 31.9 bits (73), Expect = 0.054
Identities = 22/51 (43%), Positives = 28/51 (54%)
Query: 11 RDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
R RRRR R R ++R R RR R R ++R R R R R + + RRRK
Sbjct: 7 RRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRK 57
Score = 29.9 bits (68), Expect = 0.28
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
R R RR R R R ++R R RR R + ++ R R R R + + R+RK
Sbjct: 7 RRRRRRWRGRRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRK 59
Score = 28.4 bits (64), Expect = 0.74
Identities = 15/30 (50%), Positives = 17/30 (56%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSK 38
R R RRRR R ++R R R RR R R K
Sbjct: 31 RRRVRRRRRGRRRRRRRRRRRRRRRRKRKK 60
Score = 27.2 bits (61), Expect = 2.1
Identities = 17/33 (51%), Positives = 19/33 (57%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKK 41
R R RR R R R ++R R R RR R R K KK
Sbjct: 28 RRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKK 60
Score = 26.1 bits (58), Expect = 4.6
Identities = 17/45 (37%), Positives = 23/45 (51%)
Query: 5 RDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSR 49
R + R R R RR R R +R R RR R R + ++R R R +
Sbjct: 16 RRRRRRRRRARRRRRRRRVRRRRRGRRRRRRRRRRRRRRRRKRKK 60
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 31.4 bits (72), Expect = 0.080
Identities = 14/58 (24%), Positives = 23/58 (39%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRR 59
E+ ++D R R R + +R R R R D + R + R + + RR
Sbjct: 164 TEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRR 221
Score = 30.3 bits (69), Expect = 0.17
Identities = 12/58 (20%), Positives = 21/58 (36%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
D++ + R ++R R D R R +++ R R + RRR
Sbjct: 174 RRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRR 231
Score = 29.9 bits (68), Expect = 0.24
Identities = 16/59 (27%), Positives = 24/59 (40%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
G+ D+ E +R R R + + RDRR R D++ R R + RR
Sbjct: 176 GDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRD 234
Score = 29.5 bits (67), Expect = 0.36
Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 3 EDRDKDRERDRRRRSRSR-DHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
+R ++ ERD RRR R D + + +R R R R + + R +
Sbjct: 161 AERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGR 220
Query: 62 A 62
Sbjct: 221 R 221
Score = 29.5 bits (67), Expect = 0.39
Identities = 13/59 (22%), Positives = 21/59 (35%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
E +RDRR R D ++ RD R + ++ +R R+ R
Sbjct: 194 EERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDG 252
Score = 28.7 bits (65), Expect = 0.63
Identities = 15/60 (25%), Positives = 21/60 (35%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
+ RD+ + DRR RD R R RR R ++ R D R+
Sbjct: 203 RDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRR 262
Score = 28.3 bits (64), Expect = 0.83
Identities = 13/61 (21%), Positives = 23/61 (37%), Gaps = 1/61 (1%)
Query: 1 MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
+ R++ R+ R R R ++ R R R +R D + R + RR
Sbjct: 205 RRDRREQGDRREERGR-RDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRG 263
Query: 61 K 61
+
Sbjct: 264 R 264
Score = 27.9 bits (63), Expect = 1.1
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSR----DRRSRSRSKDKKRAARSRSRSPR 52
E+R +D + RR R + ++ R R DRR R R +D++ A +R R
Sbjct: 193 REERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247
Score = 27.9 bits (63), Expect = 1.2
Identities = 10/52 (19%), Positives = 18/52 (34%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRD 53
+ RD + +R R R R R R +D++ + R+
Sbjct: 233 RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNERE 284
Score = 27.9 bits (63), Expect = 1.3
Identities = 20/59 (33%), Positives = 24/59 (40%), Gaps = 1/59 (1%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
RD R RRRR RD + DR R + R R R R RD+ + RR
Sbjct: 218 RGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGR-RGRRFRDRDRRGRR 275
Score = 27.9 bits (63), Expect = 1.4
Identities = 15/60 (25%), Positives = 21/60 (35%), Gaps = 1/60 (1%)
Query: 2 GEDRDKDRER-DRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
+ R+ DRR R R RD + +R R R R R + + RR
Sbjct: 214 RREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRG 273
Score = 27.6 bits (62), Expect = 1.6
Identities = 14/60 (23%), Positives = 20/60 (33%)
Query: 1 MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
+ +R RR R RD R R R R +++ R R R + R
Sbjct: 179 EDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDA 238
Score = 27.6 bits (62), Expect = 1.7
Identities = 14/59 (23%), Positives = 18/59 (30%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
G DR RRRR R +R + + R R RD+ R
Sbjct: 219 GRRDGGDRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGG 277
Score = 26.8 bits (60), Expect = 2.9
Identities = 7/56 (12%), Positives = 14/56 (25%)
Query: 5 RDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
+ RER R + + ++ R R + R+
Sbjct: 127 ARERRERGEAARRGAARKAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQ 182
Score = 26.8 bits (60), Expect = 3.6
Identities = 7/60 (11%), Positives = 19/60 (31%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
+ +R + ++R DR++ + ++ R + RR +
Sbjct: 152 PATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQ 211
Score = 25.6 bits (57), Expect = 8.0
Identities = 13/62 (20%), Positives = 21/62 (33%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRK 61
GE + D R+ + +R R DR R ++ R R + RR +
Sbjct: 149 GEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDR 208
Query: 62 AS 63
Sbjct: 209 RE 210
>gnl|CDD|223019 PHA03237, PHA03237, envelope glycoprotein M; Provisional.
Length = 424
Score = 30.5 bits (69), Expect = 0.16
Identities = 16/66 (24%), Positives = 23/66 (34%), Gaps = 13/66 (19%)
Query: 22 HKKRS-RSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLY------------WDV 68
H++RS R R + K K+ R R R K+ + L +DV
Sbjct: 354 HRRRSTRFYGRVKTVQQKVKRYLNRVRGGRRRPKSLVEDERGLLLTEDSETDDEEPIYDV 413
Query: 69 PPPGFE 74
FE
Sbjct: 414 VYSEFE 419
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 30.1 bits (67), Expect = 0.27
Identities = 25/93 (26%), Positives = 42/93 (45%), Gaps = 13/93 (13%)
Query: 2 GEDRDKDRERDRRRRSRSRDH--KKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRR 59
GE + K + R + R++ R + S +R RSR+K AA+S R R
Sbjct: 381 GEKKVKRKARLEKMRAKCRRAVGNRMKGSMKKRVRSRAKKFGEAAKSGVR--------RY 432
Query: 60 RKASLYWDVPPPGFEHVSPSQYKAMQAAAAAAV 92
RK + +PP S + Y A+ A+ + ++
Sbjct: 433 RKNIKFVYIPPV---MASLNAYAALMASLSDSI 462
>gnl|CDD|218883 pfam06075, DUF936, Plant protein of unknown function (DUF936).
This family consists of several hypothetical proteins
from Arabidopsis thaliana and Oryza sativa. The function
of this family is unknown.
Length = 564
Score = 29.4 bits (66), Expect = 0.39
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 13 RRRRSRSRDHKKR-SRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
RR R + KK S R+ SRS D K + R+RS S + KS ++ +
Sbjct: 214 RRLRGSASLRKKVAVLSAPRKPGSRSSDCKSSPRARSSSAKSPFKSSIQRKA 265
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 27.2 bits (61), Expect = 0.70
Identities = 7/13 (53%), Positives = 9/13 (69%)
Query: 105 RLYVGNIPFGVTE 117
L+VGN+P TE
Sbjct: 1 TLFVGNLPPDTTE 13
>gnl|CDD|216074 pfam00710, Asparaginase, Asparaginase.
Length = 318
Score = 28.3 bits (64), Expect = 0.76
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 72 GFEHVSPSQYKAMQAAAAAAVPVVGST 98
G +V P+ A++ A A +PVV ++
Sbjct: 240 GAGNVPPALLDALKEAVARGIPVVVAS 266
>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
pylori HP0827 protein and similar proteins. This
subfamily corresponds to the RRM of H. pylori HP0827, a
putative ssDNA-binding protein 12rnp2 precursor,
containing one RNA recognition motif (RRM), also termed
RBD (RNA binding domain) or RNP (ribonucleoprotein
domain). The ssDNA binding may be important in
activation of HP0827. .
Length = 78
Score = 27.2 bits (61), Expect = 0.77
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 105 RLYVGNIPFGVTE 117
LYVGN+P+ VTE
Sbjct: 1 NLYVGNLPYNVTE 13
>gnl|CDD|234907 PRK01130, PRK01130, N-acetylmannosamine-6-phosphate 2-epimerase;
Provisional.
Length = 221
Score = 28.2 bits (64), Expect = 0.81
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
+P Q K A AV VVG ITR
Sbjct: 184 TPEQAKKALELGAHAV-VVGGAITR 207
>gnl|CDD|217198 pfam02718, Herpes_UL31, Herpesvirus UL31-like protein. This is a
family of Herpesvirus proteins including UL31, UL53,
and the product of ORF 69 in some strains. The proteins
in this family have no known function.
Length = 262
Score = 28.0 bits (63), Expect = 0.92
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 32 RSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDV 68
RSRS + R+ SRS S + ++ R ++DV
Sbjct: 1 RSRSSVRRLPRSRPSRSSSRKKARRALRLTLREFFDV 37
>gnl|CDD|216553 pfam01528, Herpes_glycop, Herpesvirus glycoprotein M. The
herpesvirus glycoprotein M (gM) is an integral membrane
protein predicted to contain 8 transmembrane segments.
Glycoprotein M is not essential for viral replication.
Length = 374
Score = 26.8 bits (60), Expect = 2.7
Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 3/37 (8%)
Query: 20 RDHKKRSRS---RDRRSRSRSKDKKRAARSRSRSPRD 53
H++RS R R K KR RS+ +
Sbjct: 329 LYHRRRSTRYYALVRTVRETVKSYKRRRRSKLSQASE 365
>gnl|CDD|219406 pfam07420, DUF1509, Protein of unknown function (DUF1509). This
family consists of several uncharacterized viral
proteins from the Marek's disease-like viruses. Members
of this family are typically around 400 residues in
length. The function of this family is unknown.
Length = 377
Score = 26.9 bits (59), Expect = 2.7
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKA 62
ED RR S ++R R R+R S SRS+ + R+ R R R + RR
Sbjct: 304 EDSAGGSHHTMRRPPHSTSGERRGRRRNR-SESRSRSRSRSGSRRYRRRRGRGVPGRRSE 362
Query: 63 S 63
S
Sbjct: 363 S 363
>gnl|CDD|236136 PRK07946, PRK07946, putative monovalent cation/H+ antiporter
subunit C; Reviewed.
Length = 163
Score = 26.5 bits (59), Expect = 2.8
Identities = 9/45 (20%), Positives = 13/45 (28%), Gaps = 1/45 (2%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSR 47
ED + R R S + DH + R + R
Sbjct: 112 EDT-RVALRRRGLASAAPDHDRSDDPETGRQTAEGDAFGPEEFER 155
>gnl|CDD|239806 cd04279, ZnMc_MMP_like_1, Zinc-dependent metalloprotease; MMP_like
sub-family 1. A group of bacterial, archaeal, and fungal
metalloproteinase domains similar to matrix
metalloproteinases and astacin.
Length = 156
Score = 26.7 bits (59), Expect = 2.8
Identities = 10/48 (20%), Positives = 17/48 (35%)
Query: 64 LYWDVPPPGFEHVSPSQYKAMQAAAAAAVPVVGSTITRQARRLYVGNI 111
+Y D P + + S +A++ AAA V +I
Sbjct: 6 VYIDPTPAPPDSRAQSWLQAVKQAAAEWENVGPLKFVYNPEEDNDADI 53
>gnl|CDD|215696 pfam00076, RRM_1, RNA recognition motif. (a.k.a. RRM, RBD, or RNP
domain). The RRM motif is probably diagnostic of an RNA
binding protein. RRMs are found in a variety of RNA
binding proteins, including various hnRNP proteins,
proteins implicated in regulation of alternative
splicing, and protein components of snRNPs. The motif
also appears in a few single stranded DNA binding
proteins. The RRM structure consists of four strands and
two helices arranged in an alpha/beta sandwich, with a
third helix present during RNA binding in some cases The
C-terminal beta strand (4th strand) and final helix are
hard to align and have been omitted in the SEED
alignment The LA proteins have an N terminal rrm which
is included in the seed. There is a second region
towards the C terminus that has some features
characteristic of a rrm but does not appear to have the
important structural core of a rrm. The LA proteins are
one of the main autoantigens in Systemic lupus
erythematosus (SLE), an autoimmune disease.
Length = 70
Score = 25.6 bits (57), Expect = 2.8
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 106 LYVGNIPFGVTE 117
L+VGN+P TE
Sbjct: 1 LFVGNLPPDTTE 12
>gnl|CDD|236944 PRK11642, PRK11642, exoribonuclease R; Provisional.
Length = 813
Score = 27.0 bits (60), Expect = 2.8
Identities = 8/57 (14%), Positives = 21/57 (36%), Gaps = 9/57 (15%)
Query: 9 RERDRRRRSRSRDHKKRSRSRD---------RRSRSRSKDKKRAARSRSRSPRDKTK 56
RE+ ++ + + K+R + R + + +++ P KT+
Sbjct: 739 REKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKAKPKAAKKDARKAKKPSAKTQ 795
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 26.1 bits (58), Expect = 2.9
Identities = 9/45 (20%), Positives = 21/45 (46%)
Query: 22 HKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYW 66
K ++R D+ + + K K+R A + ++ ++ + L W
Sbjct: 43 QKAKAREADKARKQQLKAKQRQAANDDEEDTIESVTQSQSNKLPW 87
>gnl|CDD|184995 PRK15035, PRK15035, cytochrome bd-II oxidase subunit 1;
Provisional.
Length = 514
Score = 26.9 bits (59), Expect = 2.9
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 71 PGFEHVSPSQYKAMQAAAAAAVPVVG 96
P HV+ +QY QAA A+P V
Sbjct: 362 PDMNHVTAAQY---QAAMRGAIPQVA 384
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 26.8 bits (59), Expect = 3.0
Identities = 10/60 (16%), Positives = 28/60 (46%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKA 62
++K++E++++ +++ R R R K K+ ++ + P ++ K R+
Sbjct: 142 PPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAR 201
Score = 26.0 bits (57), Expect = 6.0
Identities = 8/60 (13%), Positives = 26/60 (43%)
Query: 4 DRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
DR+++++R+R R + + +++ ++K+R A + + + +
Sbjct: 159 DREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEERE 218
>gnl|CDD|240080 cd04729, NanE, N-acetylmannosamine-6-phosphate epimerase (NanE)
converts N-acetylmannosamine-6-phosphate to
N-acetylglucosamine-6-phosphate. This reaction is part
of the pathway that allows the usage of sialic acid as a
carbohydrate source. Sialic acids are a family of
related sugars that are found as a component of
glycoproteins, gangliosides, and other
sialoglycoconjugates.
Length = 219
Score = 26.4 bits (59), Expect = 3.1
Identities = 13/25 (52%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
SP Q A AV VVGS ITR
Sbjct: 188 SPEQAAKALELGADAV-VVGSAITR 211
>gnl|CDD|165668 PLN00095, PLN00095, chlorophyllide a oxygenase; Provisional.
Length = 394
Score = 26.6 bits (58), Expect = 3.2
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 5/58 (8%)
Query: 14 RRRSRSRDHKKRSRSRDRRSRSRSKDKKRA----ARSRSRSPRDKTKSRR-RKASLYW 66
R+ +R R R+ +K KK A A +R+R + A +W
Sbjct: 16 MARAEARCAAGARSRAARAQRAGAKAKKGAVDDDASTRARGAPGVDGAGATADARAHW 73
>gnl|CDD|225555 COG3010, NanE, Putative N-acetylmannosamine-6-phosphate epimerase
[Carbohydrate transport and metabolism].
Length = 229
Score = 26.5 bits (59), Expect = 3.5
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 1/25 (4%)
Query: 77 SPSQYKAMQAAAAAAVPVVGSTITR 101
+P Q K A AV VVGS ITR
Sbjct: 191 TPEQAKKAIEIGADAV-VVGSAITR 214
>gnl|CDD|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in
granule-associated RNA binding proteins (p40-TIA-1 and
TIAR), and yeast nuclear and cytoplasmic polyadenylated
RNA-binding protein PUB1. This subfamily corresponds to
the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1
isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin
TIA-1-related protein (TIAR) are granule-associated RNA
binding proteins involved in inducing apoptosis in
cytotoxic lymphocyte (CTL) target cells. They share high
sequence similarity and are expressed in a wide variety
of cell types. TIA-1 can be phosphorylated by a
serine/threonine kinase that is activated during
Fas-mediated apoptosis.TIAR is mainly localized in the
nucleus of hematopoietic and nonhematopoietic cells. It
is translocated from the nucleus to the cytoplasm in
response to exogenous triggers of apoptosis. Both TIA-1
and TIAR bind specifically to poly(A) but not to poly(C)
homopolymers. They are composed of three N-terminal
highly homologous RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a glutamine-rich
C-terminal auxiliary domain containing a
lysosome-targeting motif. TIA-1 and TIAR interact with
RNAs containing short stretches of uridylates and their
RRM2 can mediate the specific binding to uridylate-rich
RNAs. The C-terminal auxiliary domain may be responsible
for interacting with other proteins. In addition, TIA-1
and TIAR share a potential serine protease-cleavage site
(Phe-Val-Arg) localized at the junction between their
RNA binding domains and their C-terminal auxiliary
domains. This subfamily also includes a yeast nuclear
and cytoplasmic polyadenylated RNA-binding protein PUB1,
termed ARS consensus-binding protein ACBP-60, or poly
uridylate-binding protein, or poly(U)-binding protein,
which has been identified as both a heterogeneous
nuclear RNA-binding protein (hnRNP) and a cytoplasmic
mRNA-binding protein (mRNP). It may be stably bound to a
translationally inactive subpopulation of mRNAs within
the cytoplasm. PUB1 is distributed in both, the nucleus
and the cytoplasm, and binds to poly(A)+ RNA (mRNA or
pre-mRNA). Although it is one of the major cellular
proteins cross-linked by UV light to polyadenylated RNAs
in vivo, PUB1 is nonessential for cell growth in yeast.
PUB1 also binds to T-rich single stranded DNA (ssDNA);
however, there is no strong evidence implicating PUB1 in
the mechanism of DNA replication. PUB1 contains three
RRMs, and a GAR motif (glycine and arginine rich
stretch) that is located between RRM2 and RRM3. .
Length = 73
Score = 25.3 bits (56), Expect = 3.9
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 106 LYVGNIPFGVTE 117
+YVGN+P G+TE
Sbjct: 3 VYVGNLPHGLTE 14
>gnl|CDD|177566 PHA03242, PHA03242, envelope glycoprotein M; Provisional.
Length = 428
Score = 26.3 bits (58), Expect = 4.1
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 13 RRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDVPPPG 72
RR RSR H + +R R R R + R +R + AS + P
Sbjct: 352 RRHRSRFYGHVRDARHRARSYIRRVRSSMRNSREAPYAGESDVGRDDDYASTDGE---PI 408
Query: 73 FEHVSPSQ 80
++ V+P +
Sbjct: 409 YDEVAPDE 416
>gnl|CDD|234941 PRK01315, PRK01315, putative inner membrane protein translocase
component YidC; Provisional.
Length = 329
Score = 26.2 bits (58), Expect = 4.1
Identities = 7/59 (11%), Positives = 26/59 (44%), Gaps = 6/59 (10%)
Query: 9 RERDRRRRSRSRDHK----KRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
ER ++ + + + + + R + K++ + + P+ +++++R+K
Sbjct: 270 EERLAKKGKDHGESEGKVVAPEGAVAQTTEVREQTKRQTVQRQQ--PKRQSRAKRQKGG 326
>gnl|CDD|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate
RNA-binding protein RBM23, RBM39 and similar proteins.
This subfamily corresponds to the RRM2 of RBM39 (also
termed HCC1), a nuclear autoantigen that contains an
N-terminal arginine/serine rich (RS) motif and three RNA
recognition motifs (RRMs), also termed RBDs (RNA binding
domains) or RNPs (ribonucleoprotein domains). An
octapeptide sequence called the RS-ERK motif is repeated
six times in the RS region of RBM39. Although the
cellular function of RBM23 remains unclear, it shows
high sequence homology to RBM39 and contains two RRMs.
It may possibly function as a pre-mRNA splicing factor.
.
Length = 73
Score = 25.3 bits (56), Expect = 4.2
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 106 LYVGNIPFGVTE 117
LYVGN+ F +TE
Sbjct: 1 LYVGNLHFNITE 12
>gnl|CDD|223747 COG0675, COG0675, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 364
Score = 26.2 bits (57), Expect = 4.3
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 15 RRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
R+ R K + R ++SRS+ + K + +R R + K +
Sbjct: 203 RKLLKRLKKAQKRLSRKKSRSKRRKKAKLKLARLRERIRNRRKDFHKLA 251
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 26.5 bits (59), Expect = 4.5
Identities = 14/65 (21%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 2 GEDRDKDRERDRRRRSRSRDHKKRSRSR-----DRRSRSRSKDKKRAARSRSRSPRDKTK 56
E RD R RR +R+ +R+R + S+ + AR++ + +
Sbjct: 618 NERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTEKARTQDEQQQAPRR 677
Query: 57 SRRRK 61
R+R+
Sbjct: 678 ERQRR 682
Score = 25.4 bits (56), Expect = 9.2
Identities = 16/63 (25%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 3 EDRDKDR-----ERDRRRRSRSRDHKKRSR-SRDRRSRSRSKDKKRAARSRSRSPRDKTK 56
+DR K R +R+ RR +R ++ R +R+ R+R + +++ A +R + T+
Sbjct: 604 QDRRKPRQNNRRDRNERRDTRDNRTRREGRENREENRRNRRQAQQQTAETRESQQAEVTE 663
Query: 57 SRR 59
R
Sbjct: 664 KAR 666
>gnl|CDD|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear
cap-binding protein subunit 2 (CBP20) and similar
proteins. This subfamily corresponds to the RRM of
CBP20, also termed nuclear cap-binding protein subunit 2
(NCBP2), or cell proliferation-inducing gene 55 protein,
or NCBP-interacting protein 1 (NIP1). CBP20 is the small
subunit of the nuclear cap binding complex (CBC), which
is a conserved eukaryotic heterodimeric protein complex
binding to 5'-capped polymerase II transcripts and plays
a central role in the maturation of pre-mRNA and
uracil-rich small nuclear RNA (U snRNA). CBP20 is most
likely responsible for the binding of capped RNA. It
contains an RNA recognition motif (RRM), also termed RBD
(RNA binding domain) or RNP (ribonucleoprotein domain),
and interacts with the second and third domains of
CBP80, the large subunit of CBC. .
Length = 78
Score = 25.2 bits (56), Expect = 4.5
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 106 LYVGNIPFGVTE 117
LYVGN+ F TE
Sbjct: 1 LYVGNLSFYTTE 12
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 -
600 residues found from worms to humans. Its function
is not known.
Length = 515
Score = 26.3 bits (58), Expect = 4.7
Identities = 16/51 (31%), Positives = 21/51 (41%)
Query: 13 RRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
RRRR + + ++ +R SR K R RS S P D K S
Sbjct: 37 RRRRGKRKMEGEQLGTRRPLSRKIGKCSSRRVRSPSSKPNDTLSGASSKLS 87
>gnl|CDD|215814 pfam00242, DNA_pol_viral_N, DNA polymerase (viral) N-terminal
domain.
Length = 379
Score = 26.3 bits (58), Expect = 4.8
Identities = 10/52 (19%), Positives = 16/52 (30%), Gaps = 1/52 (1%)
Query: 13 RRRRSRSRDHKKRSRSRDRRS-RSRSKDKKRAARSRSRSPRDKTKSRRRKAS 63
++ RS + R S RR S S +S R+ +
Sbjct: 261 HGQQGRSGSIRGRKHSTTRRPFGVEPSSSGVTTNRASSSSSCFHQSAVRETA 312
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 26.3 bits (58), Expect = 5.0
Identities = 15/89 (16%), Positives = 26/89 (29%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDV 68
R + K++SRS S S R + +R P ++ +
Sbjct: 804 RSGPAADAASRTASKRKSRSHTPDGGSESSGPARPPGAAARPPPARSSESSKSKPAAAGG 863
Query: 69 PPPGFEHVSPSQYKAMQAAAAAAVPVVGS 97
G + +A AA P +
Sbjct: 864 RARGKNGRRRPRPPEPRARPGAAAPPKAA 892
>gnl|CDD|221937 pfam13148, DUF3987, Protein of unknown function (DUF3987). A
family of uncharacterized proteins found by clustering
human gut metagenomic sequences.
Length = 379
Score = 26.1 bits (58), Expect = 5.2
Identities = 9/63 (14%), Positives = 20/63 (31%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRRKASLYWDV 68
E + R + K + + K ++ A+ + +D+ L +
Sbjct: 64 EEIEEELREEYEEELKEYEAEKEIWEAEKKGLEKKAKKAIKKGKDEEALAEELLELEAEE 123
Query: 69 PPP 71
P P
Sbjct: 124 PEP 126
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 26.2 bits (57), Expect = 5.4
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 3 EDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTK 56
E R+K +DR + R +D +++ R S R+K+++ + + R R +
Sbjct: 1010 ECREKHEIKDRIVKERIKDQEEKER---MESLQRAKEEEIGKKEKEREQRIRKT 1060
>gnl|CDD|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily. RRM,
also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), is a highly abundant domain
in eukaryotes found in proteins involved in
post-transcriptional gene expression processes including
mRNA and rRNA processing, RNA export, and RNA stability.
This domain is 90 amino acids in length and consists of
a four-stranded beta-sheet packed against two
alpha-helices. RRM usually interacts with ssRNA, but is
also known to interact with ssDNA as well as proteins.
RRM binds a variable number of nucleotides, ranging from
two to eight. The active site includes three aromatic
side-chains located within the conserved RNP1 and RNP2
motifs of the domain. The RRM domain is found in a
variety heterogeneous nuclear ribonucleoproteins
(hnRNPs), proteins implicated in regulation of
alternative splicing, and protein components of small
nuclear ribonucleoproteins (snRNPs).
Length = 72
Score = 25.0 bits (55), Expect = 5.5
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 106 LYVGNIPFGVTE 117
L+VGN+P TE
Sbjct: 1 LFVGNLPPDTTE 12
>gnl|CDD|227413 COG5081, COG5081, Predicted membrane protein [Function unknown].
Length = 180
Score = 26.0 bits (57), Expect = 5.5
Identities = 8/21 (38%), Positives = 9/21 (42%)
Query: 54 KTKSRRRKASLYWDVPPPGFE 74
RRR +SL V FE
Sbjct: 3 SDHRRRRSSSLISHVEKETFE 23
>gnl|CDD|234729 PRK00331, PRK00331, glucosamine--fructose-6-phosphate
aminotransferase; Reviewed.
Length = 604
Score = 25.8 bits (58), Expect = 6.3
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 82 KAMQAAAAAAVPVVGSTITRQA 103
K + A A V GSTI R++
Sbjct: 360 KELGAKTLAICNVPGSTIARES 381
>gnl|CDD|199208 cd08964, L-asparaginase_II, Type II (periplasmic) bacterial
L-asparaginase. Asparaginases (amidohydrolases, E.C.
3.5.1.1) are enzymes that catalyze the hydrolysis of
asparagine to aspartic acid and ammonia. In bacteria,
there are two classes of amidohydrolases. This model
represents type II L-asparaginases, which tend to be
highly specific for asparagine and localized to the
periplasm. They are potent antileukemic agents and have
been used in the treatment of acute lymphoblastic
leukemia (ALL), but not without severe side effects.
Tumor cells appear to have a heightened dependence on
exogenous L-aspartate, and depleting their surroundings
of L-aspartate may starve cancerous ALL cells. Type II
L-asparaginase acts as a tetramer, which is actually a
dimer of two tightly bound dimers. A conserved threonine
residue is thought to supply the nucleophile
hydroxy-group that attacks the amide bond. Many
bacterial L-asparaginases have both L-asparagine and
L-glutamine hydrolysis activities, to a different
degree, and some of them are annotated as
asparaginase/glutaminase.
Length = 319
Score = 25.5 bits (57), Expect = 6.9
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
+V P+ +A++ A A +PVV S+
Sbjct: 243 NVPPALVEALERAVAKGIPVVRSS 266
>gnl|CDD|205235 pfam13054, DUF3915, Protein of unknown function (DUF3915). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are approximately 120 amino acids in
length.
Length = 116
Score = 24.9 bits (54), Expect = 7.9
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 8 DRERDRRRRSRSRDHKKRSRSRDRRSR 34
D RD R ++R R R++ +
Sbjct: 9 DNFRDCHHHEREDFEREREREREKEPQ 35
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 25.6 bits (56), Expect = 8.0
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 8 DRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAAR 45
D +R R RD + DR R +D+ R R
Sbjct: 443 DAPMRPKREFRDRDDRGPRDRNDRGPRGDREDRPRRER 480
>gnl|CDD|150369 pfam09681, Phage_rep_org_N, N-terminal phage replisome organiser
(Phage_rep_org_N). This entry represents the N-terminal
domain of a small family of phage proteins. The protein
contains a region of low-complexity sequence that
reflects DNA direct repeats able to function as an
origin of phage replication. The region is N-terminal to
the low-complexity region.
Length = 121
Score = 24.9 bits (55), Expect = 8.5
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 3 EDRDKDRERDRRRRSRSR 20
E + RER+RRR+ + R
Sbjct: 103 ESLEARRERNRRRKQKHR 120
>gnl|CDD|217037 pfam02443, Circo_capsid, Circovirus capsid protein. Circoviruses
are small circular single stranded viruses. This family
is the capsid protein from viruses such as porcine
circovirus and beak and feather disease virus. These
proteins are about 220 amino acids long.
Length = 237
Score = 25.5 bits (56), Expect = 8.5
Identities = 15/41 (36%), Positives = 18/41 (43%)
Query: 9 RERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSR 49
R R RRR R R ++R R RR R R R +R
Sbjct: 1 RFRIRRRYRRPRRRRRRRRHWRRRYRRRRLHINRRRHRTNR 41
>gnl|CDD|216147 pfam00844, Gemini_coat, Geminivirus coat protein/nuclear export
factor BR1 family. It has been shown that the 104
N-terminal amino acids of the maize streak virus coat
protein bind DNA non- specifically. This family also
includes various geminivirus movement proteins that are
nuclear export factors or shuttles. One member BR1
facilitates the export of both ds and ss DNA form the
nucleus.
Length = 244
Score = 25.3 bits (56), Expect = 9.0
Identities = 14/47 (29%), Positives = 19/47 (40%), Gaps = 3/47 (6%)
Query: 13 RRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRR 59
RRR + RSR+R RS +K + + R R R R
Sbjct: 1 RRRLNFDSR---RSRARAPTRRSTNKKRGWSKRPMRRKGRSYRMYRS 44
>gnl|CDD|214873 smart00870, Asparaginase, Asparaginase, found in various plant,
animal and bacterial cells. Asparaginase catalyses the
deamination of asparagine to yield aspartic acid and an
ammonium ion, resulting in a depletion of free
circulatory asparagine in plasma. The enzyme is
effective in the treatment of human malignant lymphomas,
which have a diminished capacity to produce asparagine
synthetase: in order to survive, such cells absorb
asparagine from blood plasma..- if Asn levels have been
depleted by injection of asparaginase, the lymphoma
cells die.
Length = 323
Score = 25.2 bits (56), Expect = 9.2
Identities = 7/24 (29%), Positives = 14/24 (58%)
Query: 75 HVSPSQYKAMQAAAAAAVPVVGST 98
+V P +A++ A +PVV ++
Sbjct: 248 NVPPDLLEALKEALERGIPVVRTS 271
>gnl|CDD|236394 PRK09169, PRK09169, hypothetical protein; Validated.
Length = 2316
Score = 25.4 bits (56), Expect = 9.8
Identities = 9/64 (14%), Positives = 12/64 (18%)
Query: 1 MGEDRDKDRERDRRRRSRSRDHKKRSRSRDRRSRSRSKDKKRAARSRSRSPRDKTKSRRR 60
D R R R+ S R S ++ R
Sbjct: 14 AAAPADPRPRRRPRLGDAPAPRTARADSGATPRGRPRAGADREPTSEQLRDYERWLDRAA 73
Query: 61 KASL 64
L
Sbjct: 74 AGQL 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
0.316 0.127 0.362
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,051,598
Number of extensions: 524130
Number of successful extensions: 2814
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2139
Number of HSP's successfully gapped: 396
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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 (24.0 bits)