RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12660
(294 letters)
>gnl|CDD|221913 pfam13087, AAA_12, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 195
Score = 99.2 bits (248), Expect = 3e-25
Identities = 45/132 (34%), Positives = 66/132 (50%), Gaps = 11/132 (8%)
Query: 21 FQLINVEDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAH-KITILSTYNGQKH 79
I+V+ G E E Y N AEAE V L + G + I I++ Y Q
Sbjct: 67 LVFIDVD---GSEEEEEKSTSYSNEAEAELVVQLVEKLLKSGPEKNKDIGIITPYRAQVR 123
Query: 80 LIRDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIV 136
LI+ ++ + P I +V TVD +QG++ D I+ S VR+ +G L D RRL V
Sbjct: 124 LIKKLLKRKFGGEPDI----EVNTVDGFQGREKDVIIFSTVRSNEKGGIGFLSDPRRLNV 179
Query: 137 AMSRARLGLYVF 148
A++RA+ GL +
Sbjct: 180 ALTRAKRGLIIV 191
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 73.1 bits (179), Expect = 2e-14
Identities = 39/119 (32%), Positives = 57/119 (47%), Gaps = 11/119 (9%)
Query: 42 YQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLIRDVINTRCADNPLIGRPHKV 101
N EAE + + G + I ++S Y Q LIR ++N +V
Sbjct: 622 KLNELEAEIVKVIVDELLKDGLEENDIGVISPYRAQVSLIRRLLNEAGKGV-------EV 674
Query: 102 TTVDKYQGQQNDYILLSLVRTAS----VGHLRDVRRLIVAMSRARLGLYVFARVSLFRN 156
TVD +QG++ D I+LSLVR+ +G L D RRL VA++RA+ L V S +
Sbjct: 675 GTVDGFQGREKDVIILSLVRSNDDKGEIGFLGDPRRLNVALTRAKRKLIVVGSSSTLES 733
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 69.8 bits (171), Expect = 2e-13
Identities = 39/129 (30%), Positives = 66/129 (51%), Gaps = 10/129 (7%)
Query: 22 QLINVEDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLGYPAHKITILSTYNGQKHLI 81
I+ E + N EAE + + +G PA+ I +++ Y+ Q L+
Sbjct: 484 LFIDTSGCELFELKEADSTSKYNPGEAELVSEIIQALVKMGVPANDIGVITPYDAQVDLL 543
Query: 82 RDVINTRCADNPLIGRPHKVTTVDKYQGQQNDYILLSLVRT---ASVGHLRDVRRLIVAM 138
R ++ R D +V++VD +QG++ + I++S VR+ VG L+D+RRL VA+
Sbjct: 544 RQLLEHRHID-------IEVSSVDGFQGREKEVIIISFVRSNRKGEVGFLKDLRRLNVAL 596
Query: 139 SRARLGLYV 147
+RAR L V
Sbjct: 597 TRARRKLIV 605
>gnl|CDD|222209 pfam13538, UvrD_C_2, Family description. This domain is found at
the C-terminus of a wide variety of helicase enzymes.
This domain has a AAA-like structural fold.
Length = 105
Score = 33.9 bits (78), Expect = 0.020
Identities = 11/47 (23%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 101 VTTVDKYQGQQNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGLYV 147
T+ K +G + + + A + R L A++RA+ LY+
Sbjct: 59 ALTIHKAKGSEFPAVFVPDP-DAHAYDMLFRRLLYTAVTRAKKKLYL 104
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 30.5 bits (69), Expect = 0.77
Identities = 17/81 (20%), Positives = 33/81 (40%), Gaps = 12/81 (14%)
Query: 219 MKKEFYSKAKLNADKWKKPGDI-----EEFYSKAKLNADKWKKPGDIEVKDVETHVAIHP 273
M + KL K+K+ + E+ K + K K+ +V + +
Sbjct: 120 MGINKKAGKKLALSKFKRKVGLFTEEEEDIDEKLSMLEKKLKELEAEDVDEEDE------ 173
Query: 274 GGDSDESGDEEEKEEEKMDTE 294
D +E +EEE++E+ D +
Sbjct: 174 -KDEEEEEEEEEEDEDFDDDD 193
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 31.1 bits (70), Expect = 0.79
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 261 EVKDVETHVAIHPGGDSDESGDEEEKEEEKMDTE 294
E K E V G D +S +EEE+EEE+ + E
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEE 877
Score = 30.0 bits (67), Expect = 1.7
Identities = 12/21 (57%), Positives = 17/21 (80%)
Query: 274 GGDSDESGDEEEKEEEKMDTE 294
GGDS+E +EEE+EEE+ + E
Sbjct: 860 GGDSEEEEEEEEEEEEEEEEE 880
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 30.1 bits (69), Expect = 1.4
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 7/33 (21%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRD 130
P K T++KY G +DY++ ASVGH+RD
Sbjct: 10 PAKAKTINKYLG--SDYVVK-----ASVGHIRD 35
>gnl|CDD|223581 COG0507, RecD, ATP-dependent exoDNAse (exonuclease V), alpha
subunit - helicase superfamily I member [DNA
replication, recombination, and repair].
Length = 696
Score = 30.2 bits (68), Expect = 1.6
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 7/51 (13%)
Query: 101 VTTVDKYQGQQNDYILLSLVRTASVGHLRDVRR--LIVAMSRARLGLYVFA 149
T+ K QG + D +++ L H + R L A++RAR L ++
Sbjct: 624 AMTIHKSQGSEFDRVIVLLPS-----HSPMLSRELLYTAITRARDRLILYG 669
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 29.3 bits (66), Expect = 2.0
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 258 GDIEVKDVETHVAIHPGGDSDES 280
G I VK+V+ VA G DES
Sbjct: 171 GGIRVKNVDAMVA--EDGALDES 191
>gnl|CDD|225405 COG2849, COG2849, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 230
Score = 29.3 bits (66), Expect = 2.2
Identities = 7/34 (20%), Positives = 14/34 (41%)
Query: 207 LVYNFYMDKVNGMKKEFYSKAKLNADKWKKPGDI 240
Y++K+ G +K + KL + G+
Sbjct: 27 EEKANYVNKLEGKEKLYDEDGKLLSKLDFSAGEE 60
>gnl|CDD|233249 TIGR01051, topA_bact, DNA topoisomerase I, bacterial. This model
describes DNA topoisomerase I among the members of
bacteria. DNA topoisomerase I transiently cleaves one
DNA strand and thus relaxes negatively supercoiled DNA
during replication, transcription and recombination
events [DNA metabolism, DNA replication, recombination,
and repair].
Length = 610
Score = 29.7 bits (67), Expect = 2.3
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 14/48 (29%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRDVRRLIVAMSRARLGL 145
P K T+ KY G +Y + AS+GH+RD + ++RLG+
Sbjct: 7 PAKAKTIKKYLGD--EYEVE-----ASMGHIRD-------LPKSRLGV 40
>gnl|CDD|235516 PRK05582, PRK05582, DNA topoisomerase I; Validated.
Length = 650
Score = 29.4 bits (67), Expect = 2.3
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 7/33 (21%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRD 130
P K T++KY G +Y ++ AS+GH+RD
Sbjct: 11 PAKAKTIEKYLG--KNYKVV-----ASMGHIRD 36
>gnl|CDD|225798 COG3259, FrhA, Coenzyme F420-reducing hydrogenase, alpha subunit
[Energy production and conversion].
Length = 441
Score = 29.3 bits (66), Expect = 2.8
Identities = 15/78 (19%), Positives = 23/78 (29%), Gaps = 14/78 (17%)
Query: 3 HVGVYAEYQKANAGLVYDFQLINVEDFNGVGESEPNPYFYQNLAEAEYCVALFMYMRLLG 62
H Y +A F ED Y Y Y + LG
Sbjct: 220 HPEPYDGSIRA-YDDREKFDPDEYEDI-------IPESVY------PYSYLKHPYYKDLG 265
Query: 63 YPAHKITILSTYNGQKHL 80
YP +++ L+ +G +
Sbjct: 266 YPDYRVGPLARLDGCPVM 283
>gnl|CDD|184904 PRK14940, PRK14940, DNA polymerase III subunit beta; Provisional.
Length = 367
Score = 28.7 bits (64), Expect = 3.9
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 159 ELTPAFNQLMIRPQ------QLHIVPHETFPTSRLNTSRVPNSVAIQDMVHM 204
EL QL+I P QL + HE+FP N V ++ +D+ M
Sbjct: 87 ELELCDEQLVITPPNKKISFQLKTISHESFPCFPENEGGVSFAIPTKDLREM 138
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 28.6 bits (64), Expect = 4.6
Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 12/80 (15%)
Query: 225 SKAKLN------ADKWKKPGDIE----EFYSKAKLNADKWKKPGDIEVKDVETHVAIHPG 274
SKAKL+ +K+ K ++ +F K K+K+ D+ D+E ++
Sbjct: 828 SKAKLDNLKTLVPEKYNKETNLLTVQDKFVKLVKNFISKFKELNDL--TDLEEYLISQFQ 885
Query: 275 GDSDESGDEEEKEEEKMDTE 294
+ D+ DE+E ++E D +
Sbjct: 886 ENEDDDADEDEDQDEDEDED 905
>gnl|CDD|183731 PRK12766, PRK12766, 50S ribosomal protein L32e; Provisional.
Length = 232
Score = 27.9 bits (62), Expect = 5.6
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 10/48 (20%)
Query: 247 AKLNADKWKKPGDIEVKDVETHVAIHPGGDSDESGDEEEKEEEKMDTE 294
A++ AD G +EV + ET + DE G+EEE+E+ ++TE
Sbjct: 50 ARIKADV----GGLEVSE-ETEAEVE-----DEGGEEEEEEDADVETE 87
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 27.9 bits (62), Expect = 5.6
Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 15/96 (15%)
Query: 214 DKVNGMKKEFYSKAKLNADKWKKPGD---IEEFYSK------------AKLNADKWKKPG 258
+ + K + + N +EE+Y K K + K KK
Sbjct: 189 EPEDDPKDSLGNGSSTNGLPDSSQDKNKSLEEYYEKESSDAAASQDDGPKGSDVKNKKSD 248
Query: 259 DIEVKDVETHVAIHPGGDSDESGDEEEKEEEKMDTE 294
D E D + DE +E E+EEE+ D +
Sbjct: 249 DEEDDDQDGDYVEEKELKEDEEEEETEEEEEEEDED 284
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 27.2 bits (60), Expect = 6.2
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 12/70 (17%)
Query: 225 SKAKLNADKWKKPGDIEEFYSKAKLNADKWKKPGDIEVKDVETHVAIHPGGDSDESGDEE 284
SK + N D ++ D+E W + G E A + E+ D +
Sbjct: 35 SKCEKNYDLGREARDLE------------WTEAGRAEKGPAAAATAAAEAAEEAEAADAD 82
Query: 285 EKEEEKMDTE 294
E +E + +
Sbjct: 83 EDADEAAEAD 92
>gnl|CDD|235840 PRK06599, PRK06599, DNA topoisomerase I; Validated.
Length = 675
Score = 28.3 bits (64), Expect = 6.3
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 98 PHKVTTVDKYQGQQNDYILLSLVRTASVGHLRD 130
P K T+ KY G DY +L AS GH+RD
Sbjct: 11 PAKAKTIKKYLG--KDYKVL-----ASFGHVRD 36
>gnl|CDD|240541 cd13136, MATE_DinF_like, DinF and similar proteins, a subfamily of
the multidrug and toxic compound extrusion (MATE)-like
proteins. Escherichia coli DinF is a membrane protein
that has been found to protect cells against oxidative
stress and bile salts. The expression of DinF is
regulated as part of the SOS system. It may act by
detoxifying oxidizing molecules that have the potential
to damage DNA. Some member of this family have been
reported to enhance the virulence of plant pathogenic
bacteria by enhancing their ability to grow in the
presence of toxic compounds. Proteins from the MATE
family are involved in exporting metabolites across the
cell membrane and are often responsible for multidrug
resistance (MDR).
Length = 424
Score = 27.5 bits (62), Expect = 8.2
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 116 LLSLVRTASVGHLRDVRRL 134
LL LV TA VGHL L
Sbjct: 21 LLGLVDTAVVGHLGSAAYL 39
>gnl|CDD|224416 COG1499, NMD3, NMD protein affecting ribosome stability and mRNA
decay [Translation, ribosomal structure and biogenesis].
Length = 355
Score = 27.4 bits (61), Expect = 9.9
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 257 PGDIEVKDVETHVAIHPGGDSDESGDE 283
P I+V D ET+ A G S E GDE
Sbjct: 312 PSAIQVLDPETYEARTVKGPSLEEGDE 338
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 0.135 0.399
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,049,901
Number of extensions: 1434985
Number of successful extensions: 1313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1286
Number of HSP's successfully gapped: 39
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
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 (21.7 bits)
S2: 59 (26.6 bits)