RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6556
(836 letters)
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of the
virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA plus-strand.
lambda1 is an Orthoreovirus core protein, VP3 is the
homologous core protein in Aquareoviruses.
Length = 1166
Score = 39.0 bits (91), Expect = 0.012
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 505 NKHPCNRCNASFSSMVQLSCHQIRAH 530
+ + CN C A FSSM QL+ HQ H
Sbjct: 72 SSYVCNVCMAEFSSMDQLAEHQRTTH 97
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 31.2 bits (71), Expect = 0.10
Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 236 NLQSHIRISHTGERPFQCKYCNYAFK 261
NL+ H+R HTGE+P++C C +F
Sbjct: 1 NLRRHMRT-HTGEKPYKCPVCGKSFS 25
Score = 28.9 bits (65), Expect = 0.60
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 294 NLIQHYRIHTDEKPFNCSLCEKQFRQ 319
NL +H R HT EKP+ C +C K F
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.9 bits (65), Expect = 0.65
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 412 VHMRRHTGFKPYQCKTCNASYAS 434
HMR HTG KPY+C C S++S
Sbjct: 4 RHMRTHTGEKPYKCPVCGKSFSS 26
Score = 28.1 bits (63), Expect = 1.1
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 132 HFKAHLRIHLNIKPYACKYCGNAFAH 157
+ + H+R H KPY C CG +F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
Score = 27.7 bits (62), Expect = 1.7
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 615 LLNHERIHDNHKPYKCTKCNYS 636
L H R H KPYKC C S
Sbjct: 2 LRRHMRTHTGEKPYKCPVCGKS 23
Score = 25.8 bits (57), Expect = 7.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 586 NFNIHMRIHGKDRPFSCLLCNNTFAQ 611
N HMR H ++P+ C +C +F+
Sbjct: 1 NLRRHMRTHTGEKPYKCPVCGKSFSS 26
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 35.1 bits (80), Expect = 0.18
Identities = 62/453 (13%), Positives = 116/453 (25%), Gaps = 35/453 (7%)
Query: 390 FPKQPSICAVCGDTFKTNYNYFVHMRRHTGFKPYQCKTCNASYASMRVL---QHHEITHS 446
+P C C D+F + H+R HTG KP QC + R L +H H+
Sbjct: 29 NAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHLRTHHN 88
Query: 447 KTLKFPCINCGKYFTKLEYMIKHMKRHFNTNKPVCEICSQTMAHNQVLQRHMTLHFTQNK 506
+ +K + + + S + +
Sbjct: 89 NPSDLNSKSLPLSNSKASSSSLSSSSSNSNDNNLLSSHSLPPSSRDPQLPDLLSISNLRN 148
Query: 507 HPCNRCNASFSSMVQLSCHQIRAHGKQKQRFMCHRCGIINLKRKYHVYHLKYECGYTRTL 566
+P N+S + Q + + + +
Sbjct: 149 NPLPGNNSSSVNTPQSNSLHPPLPA--------NSLSKDPSSNLSLLISSNVSTSIPSSS 200
Query: 567 PPELRRQFKHDIVYMDSKTNFNIHMRIHGKDRPFSCLLCNNTFAQLSTLLNHERIHDNHK 626
S + + + + + + + +
Sbjct: 201 ENSPLSSSY-------SIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSSSDS 253
Query: 627 PYKCTKCN-----YSARVLSNKLAHERIYHQDHVFKCHINNCIFSTKFYSCLRRH-RKIF 680
++ ++ S+ + + C S S L RH R +
Sbjct: 254 SSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHLRSVN 313
Query: 681 HSNESYAPAKCKI--CNQSFALFSNLNAHYNKHLKVRRFSCTNCSLNFTYLSNLIRHRRI 738
HS ES P C C + F+ L H H + + + + L
Sbjct: 314 HSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNNEPPQ 373
Query: 739 KHSQHEG-----KYVCNYCGKSYIDKRDYT--NHVSVHMERKSGYTQRCHKCNATFRIKK 791
Q++ K KRD H+ H+ Y + C+ +F
Sbjct: 374 SLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHL-SFRPYNCKNPPCSKSFNRHY 432
Query: 792 FLTRHMKTHLI-QYRCTRCNKTFKQNTSFIRHS 823
L H K H K+F+++ H
Sbjct: 433 NLIPHKKIHTNHAPLLCSILKSFRRDLDLSNHG 465
Score = 33.9 bits (77), Expect = 0.36
Identities = 78/456 (17%), Positives = 126/456 (27%), Gaps = 40/456 (8%)
Query: 11 MPHESQDERTYHCPLCSKQFSKLTTLKRHVGIHMKTQPVRCGYCGQFFLDLGRLNAHIRQ 70
+ S R CP C+ FS+L L RH+ H +P +C Y G L
Sbjct: 24 LKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRPLELSRHL 83
Query: 71 RHTSNKKIYYKCDKCNKTYKSKYKFERHKNTHVTENSEYPCIYCRNIYPCSFCAYRGRYR 130
R N S K + + NS S + R
Sbjct: 84 RTHHNNPSDLNSKSL---PLSNSKASSSSLSSSSSNSNDN-------NLLSSHSLPPSSR 133
Query: 131 YHFKAHLRIHLNIKPYACKYCGNAFAHKSSRDAHQNIHTDLKPYLCLTCGQSFRTFNLMK 190
L N++ ++ + ++H L S + +
Sbjct: 134 DPQLPDLLSISNLRNNPLPGNNSSSVN---TPQSNSLHPPLPANSLSKDPSSNLSLLISS 190
Query: 191 RH----------NLCDHQDVRNYLCNFCNKTYKDRKTLDNHILGHVDIKPYKQL-SNLQS 239
+ + N Q S+L S
Sbjct: 191 NVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSQSPSSLSS 250
Query: 240 HIRISHTGERPFQCKYCNYAFKEKHHLETHVNLHLGKTKSFNCNVCNYSSSLKWNLIQHY 299
S E P + + E+ + G + CN S S L +H
Sbjct: 251 SDSSSSASESPRSSL-PTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPLTRHL 309
Query: 300 R--IHTDE--KPFNC--SLCEKQFRQKIHVKNHLRIIHNMNF-----CDHCFKFVGPEQE 348
R H+ E KPF+C SLC K F + +K H+ + +++ + KF
Sbjct: 310 RSVNHSGESLKPFSCPYSLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLLNN 369
Query: 349 LNIFRHCEVCDKSNNSYLLC-WKCGFKTSVLNELKAHIKSHHFPKQPS--ICAVCGDTFK 405
+ D N+ + + + H +P C +F
Sbjct: 370 EPPQSLQQYKDLKNDKKSETLSNSCIRNFKRDSNLSLHIITHLSFRPYNCKNPPCSKSFN 429
Query: 406 TNYNYFVHMRRHTGFKPYQCKTCNASYASMRVLQHH 441
+YN H + HT P C S+ L +H
Sbjct: 430 RHYNLIPHKKIHTNHAPLLCSILK-SFRRDLDLSNH 464
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.2 bits (73), Expect = 0.33
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 20 TYHCPLCSKQFSKLTTLKRHVGIHMKTQPVRCGYCGQFFLDLGRLNAHIRQRH 72
Y CPLC FS +LK+H I C CG+ F + H+ ++H
Sbjct: 73 PYVCPLCLMPFSSSVSLKQH--IRYTEHSKVCPVCGKEFRNTDSTLDHVCKKH 123
>gnl|CDD|227225 COG4888, COG4888, Uncharacterized Zn ribbon-containing protein
[General function prediction only].
Length = 104
Score = 30.6 bits (69), Expect = 1.1
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 4/41 (9%)
Query: 18 ERTYHCPLCSKQFSKLTTLKRHVGIHMKTQPVRCGYCGQFF 58
+T+ CP C + T+K+ V I CG CG F
Sbjct: 20 PKTFTCPRCGHEKVSSCTVKKTVNIGT----AVCGNCGLSF 56
>gnl|CDD|213736 TIGR02773, addB_Gpos, helicase-exonuclease AddAB, AddB subunit. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RexAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
Nevertheless, the partner is designated AddB in both
systems. This model describes the AddB protein as found
Bacillus subtilis and related species. Although the RexB
protein of Streptococcus and Lactococcus is considered to
be orthologous, functionally equivalent, and merely named
differently, all members of this protein family have a
P-loop nucleotide binding motif GxxGxGK[ST] at the
N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif
at the C-terminus, both of which may be relevant to
function [DNA metabolism, DNA replication, recombination,
and repair].
Length = 1160
Score = 32.4 bits (74), Expect = 1.4
Identities = 22/103 (21%), Positives = 36/103 (34%), Gaps = 42/103 (40%)
Query: 204 LCNFCNKTYKDRKTLDNHILGHVDIKPYKQLSNLQSHIRISHTGERPFQCKYCNYAFKEK 263
L + ++ + +N G V I+PYK + P C+YCN++
Sbjct: 1085 LRKHVRRKFQ--EAGENITDGRVSIEPYK------------MKKQTP--CQYCNFS---- 1124
Query: 264 HHLETHVNLHLGKTKSFNCNVCNYSSSLKWNLIQHYRIHTDEK 306
+VC + +SL+ N YR EK
Sbjct: 1125 -------------------SVCQFDTSLEEN---EYRHLEAEK 1145
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.9 bits (73), Expect = 1.5
Identities = 9/41 (21%), Positives = 12/41 (29%), Gaps = 12/41 (29%)
Query: 716 RFSCTNCSLNFTYLSNLIRHRRIKHSQHEGKYVCNYCGKSY 756
C NC T + G+ C+YCG
Sbjct: 444 IAECPNCDSPLTL------------HKATGQLRCHYCGYQE 472
>gnl|CDD|223601 COG0527, LysC, Aspartokinases [Amino acid transport and
metabolism].
Length = 447
Score = 31.5 bits (72), Expect = 1.8
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 40 VGIHMKTQPVRCGYCGQFFLDLGRLNAHIRQRHTSNKKI 78
VG M++ P G + F L N +I +S I
Sbjct: 389 VGAGMRSNP---GVAARIFQALAEENINIIMISSSEISI 424
>gnl|CDD|218352 pfam04962, KduI, KduI/IolB family. This family includes the 5-keto
4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is
involved in pectin degradation. This family aldo
includes bacterial Myo-inositol catabolism (IolB)
proteins. The Bacillus subtilis inositol operon
(iolABCDEFGHIJ) is involved in myo-inositol catabolism.
Glucose repression of the iol operon induced by inositol
is exerted through catabolite repression mediated by
CcpA and the iol induction system mediated by IolR. The
exact function of IolB is unknown. Members of this
family possess a Cupin like structure.
Length = 261
Score = 30.7 bits (70), Expect = 2.7
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 4 HQHEEQCMPHESQDERTYH 22
H+H++ +P E+ E TY+
Sbjct: 169 HKHDQDNLPDETYLEETYY 187
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.3 bits (58), Expect = 5.7
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 80 YKCDKCNKTYKSKYKFERHKNTH 102
Y+C +C K +KSK H TH
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 30.1 bits (68), Expect = 6.2
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 239 SHIRISHTGERPFQ--CKYCNYAFKEK 263
+HIRI + G+RP+ C CN+ +K
Sbjct: 644 NHIRIINGGKRPWDLGCPQCNFIEWQK 670
>gnl|CDD|184989 PRK15029, PRK15029, arginine decarboxylase; Provisional.
Length = 755
Score = 29.8 bits (67), Expect = 6.7
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 9/74 (12%)
Query: 457 GKYFTKLEYMIKHMKRHFNTNKPVCEICSQTMAHNQVLQRHMTLH--------FTQNKHP 508
GK+ T + + KRH++ N P+ ++ + + +M +H + + +P
Sbjct: 589 GKWGTLVNTLCS-FKRHYDANTPLAQVMPELVEQYPDTYANMGIHDLGDTMFAWLKENNP 647
Query: 509 CNRCNASFSSMVQL 522
R N ++S +
Sbjct: 648 GARLNEAYSGLPVA 661
>gnl|CDD|215459 PLN02854, PLN02854, 3-ketoacyl-CoA synthase.
Length = 521
Score = 29.5 bits (66), Expect = 9.0
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 281 NCNVCNYSSSLKWNLIQHYRIHTDEKPFN 309
NC++ N + SL ++ HY++ TD K +N
Sbjct: 216 NCSLFNPTPSLSAMIVNHYKLRTDIKSYN 244
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
0.327 0.136 0.458
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 39,414,164
Number of extensions: 3587893
Number of successful extensions: 5144
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5061
Number of HSP's successfully gapped: 179
Length of query: 836
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 731
Effective length of database: 6,280,432
Effective search space: 4590995792
Effective search space used: 4590995792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 63 (28.1 bits)