RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8928
(134 letters)
>gnl|CDD|220187 pfam09340, NuA4, Histone acetyltransferase subunit NuA4. The NuA4
histone acetyltransferase (HAT) multisubunit complex is
responsible for acetylation of histone H4 and H2A
N-terminal tails in yeast. NuA4 complexes are highly
conserved in eukaryotes and play primary roles in
transcription, cellular response to DNA damage, and cell
cycle control.
Length = 80
Score = 91.5 bits (228), Expect = 2e-25
Identities = 39/106 (36%), Positives = 56/106 (52%), Gaps = 27/106 (25%)
Query: 14 RSELADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLERQIYAFEGSYLE 73
+ +L +L++KK ++ E LA+LERQIY E YLEDT GN
Sbjct: 1 KQKLKELLQKKKKLEEELAALERQIYDKETEYLEDTTSGGN------------------- 41
Query: 74 DTQLYGNVIRGWDRYLSSNKTNNTNMERNRKFKEAERLFSLSSITS 119
+I+G+D YL S+ + R RKF + +R+FSLSS+TS
Sbjct: 42 -------IIKGFDGYLKSSTNGSAQ-RRKRKFTDDDRIFSLSSVTS 79
>gnl|CDD|220494 pfam09969, DUF2203, Uncharacterized conserved protein (DUF2203).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 120
Score = 29.2 bits (66), Expect = 0.39
Identities = 20/77 (25%), Positives = 31/77 (40%), Gaps = 11/77 (14%)
Query: 13 VRSELADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLERQIYAFEGSYL 72
+R L ++ + KAE+ E LE + E S E L LE QI A +
Sbjct: 15 LRRLLEEVREAKAELEE----LEAALSEGERSLE---ARGLKEELRELEEQIRA----AI 63
Query: 73 EDTQLYGNVIRGWDRYL 89
+ + G ++ D L
Sbjct: 64 AEIEELGIEVKDLDIGL 80
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 29.2 bits (66), Expect = 0.67
Identities = 26/120 (21%), Positives = 47/120 (39%), Gaps = 12/120 (10%)
Query: 11 MNVRSELADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLERQIYAFEGS 70
+ EL +L K+ A++ + LAS ER + + LE + +G+E +I E
Sbjct: 437 EKIEKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDERRT----EIVEEEED 492
Query: 71 YLEDTQL---YGNVI----RGWDRYLSSNKTNNTNMERNRKFKEAERLFSLSSITSSAAV 123
+ED L V+ +G+ + + K KE + L L + +
Sbjct: 493 EIEDEDLIAEEDVVVTLSHKGYIKRV-PLKGYEAQRVSGLGLKEGDFLERLFEANTHDTL 551
>gnl|CDD|193531 cd05654, M20_ArgE_RocB, M20 Peptidase Arginine utilization protein,
RocB. Peptidase M20 family, ArgE RocB (Arginine
utilization protein, RocB; arginine degradation protein,
RocB) subfamily. This group of proteins is possibly
related to acetylornithine deacetylase (ArgE) and may be
involved in the arginine and/or ornithine degradation
pathway. In Bacillus subtilis, RocB is one of the three
genes found in the rocABC operon, which is sigma L
dependent and induced by arginine. The function of
members of this family is as yet unknown, although they
are predicted as deacetylases.
Length = 535
Score = 29.1 bits (66), Expect = 0.69
Identities = 20/111 (18%), Positives = 35/111 (31%), Gaps = 7/111 (6%)
Query: 16 ELADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLERQIYAFEGSYLEDT 75
E+ + +KK A A E I Y + G+ + ++ +E Y E
Sbjct: 304 EVMEKLKKIATEA-----FENTINEAYEKYCRLSNKPGDSL--PWKVKVLTYEELYEEAK 356
Query: 76 QLYGNVIRGWDRYLSSNKTNNTNMERNRKFKEAERLFSLSSITSSAAVSGL 126
+ G + L + R + E L +L + A V
Sbjct: 357 KKGGEKFEKFLEELEKKLLDGELDLREATIRIVEALLALCKDKAPAVVLFF 407
>gnl|CDD|227507 COG5180, PBP1, Protein interacting with poly(A)-binding protein
[RNA processing and modification].
Length = 654
Score = 27.8 bits (61), Expect = 1.9
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 70 SYLEDTQLYGNVIRGWDRYLSSNKTNNTNMERNRKFKEAER 110
S L++ LY V+R D S+ +N +N E NR+ K A
Sbjct: 218 SGLDEEDLYSGVVRRGDECRSAESSNASNKE-NRQEKPAAA 257
>gnl|CDD|226089 COG3559, TnrB3, Putative exporter of polyketide antibiotics [Cell
envelope biogenesis, outer membrane].
Length = 536
Score = 27.5 bits (61), Expect = 2.7
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 78 YGNVIRGWDRYLSSNKTNNTNMERNRKFKEAER-----LFSLSSITSSAAV 123
YG+V G +L N +ER E+ LFS+ SI ++A
Sbjct: 314 YGSVFGGLGDFLGDNTAVRQAVERMEGAGALEQAFLVLLFSIISILAAAFA 364
>gnl|CDD|163520 TIGR03808, RR_plus_rpt_1, twin-arg-translocated uncharacterized
repeat protein. Members of this protein family have a
Sec-independent twin-arginine tranlocation (TAT) signal
sequence, which enables tranfer of proteins folded
around prosthetic groups to cross the plasma membrane.
These proteins have four copies of a repeat of about 23
amino acids that resembles the beta-helix repeat.
Beta-helix refers to a structural motif in which
successive beta strands wind around to stack parallel in
a right-handed helix, as in AlgG and related enzymes of
carbohydrate metabolism. The twin-arginine motif
suggests that members of this protein family bind some
unknown cofactor.
Length = 455
Score = 27.1 bits (60), Expect = 3.1
Identities = 18/42 (42%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 43 GSYLE-DTQLYGNETLASLERQIYAFEGSYLEDTQLYGNVIR 83
G Y+E DT + GN + I A G YL D + GNVIR
Sbjct: 350 GIYVEADTAVTGNVVENAPSFGIVAGWGKYLRDVAISGNVIR 391
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 26.7 bits (60), Expect = 4.4
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 18 ADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYG 53
L+++ ++ E + ++ + F S D QLY
Sbjct: 332 LALLRQNPDLREKVVAVFAEAEPFAPSDDVDAQLYD 367
>gnl|CDD|177625 PHA03389, polh, polyhedrin; Provisional.
Length = 246
Score = 26.3 bits (58), Expect = 5.0
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 1 MSSKGGGAPAMNVRSE 16
++ KGGG P MN+ SE
Sbjct: 172 LAKKGGGCPVMNLHSE 187
>gnl|CDD|220821 pfam10602, RPN7, 26S proteasome subunit RPN7. RPN7 (known as the
non ATPase regulatory subunit 6 in higher eukaryotes) is
one of the lid subunits of the 26S proteasome and has
been shown in Saccharomyces cerevisiae to be required
for structural integrity. The 26S proteasome is is
involved in the ATP-dependent degradation of
ubiquitinated proteins.
Length = 174
Score = 25.6 bits (57), Expect = 7.1
Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 101 RNRKFKEAERLF--SLSSITSSAAVS 124
R FKEA +LF SLS+ TS+ +S
Sbjct: 125 AIRDFKEAAKLFLDSLSTFTSTELIS 150
>gnl|CDD|131851 TIGR02804, ExbD_2, TonB system transport protein ExbD, group 2.
Members of this family are Gram-negative bacterial
inner membrane proteins, generally designated ExbD,
related to the TolR family modeled by TIGRFAMs
TIGR02801. Members always are encoded next to a protein
designated ExbB (TIGR02797), related to the TolQ family
modeled by TIGRFAMs TIGR02796. ExbD and ExbB together
form a proton channel through which they can harness
the proton-motive force to energize TonB, which in turn
energizes TonB-dependent receptors in the outer
membrane. TonB-dependent receptors with known
specificity tend to import siderophores or vitamin B12.
A TonB system and Tol-Pal system often will co-exist in
a single bacterial genome.
Length = 121
Score = 25.2 bits (55), Expect = 7.9
Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 24 KAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLE 61
KA A S E + D QLY N+ SLE
Sbjct: 38 KASTAVAFKSDEL---KLLITITADNQLYFNDKPISLE 72
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 25.8 bits (57), Expect = 8.6
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 12/57 (21%)
Query: 12 NVRSELADLVKKKAEIAETLASLERQIYAFEGSYLEDTQLYGNETLASLERQIYAFE 68
++ E+A L KK E + A LE+Q+ + E +ASLE Q+
Sbjct: 42 QIQKEIAALEKKIREQQDQRAKLEKQLKSLE------------TEIASLEAQLIETA 86
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
0.310 0.126 0.340
Gapped
Lambda K H
0.267 0.0800 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,389,465
Number of extensions: 545404
Number of successful extensions: 495
Number of sequences better than 10.0: 1
Number of HSP's gapped: 493
Number of HSP's successfully gapped: 34
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (24.4 bits)