RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12937
(111 letters)
>gnl|CDD|227577 COG5252, COG5252, Uncharacterized conserved protein, contains
CCCH-type Zn-finger protein [General function prediction
only].
Length = 299
Score = 72.0 bits (176), Expect = 2e-16
Identities = 34/90 (37%), Positives = 44/90 (48%), Gaps = 20/90 (22%)
Query: 18 GAKCKFSHDLTIERKAEKRSLYVDMRDDGEDVNETMENWDEDKLKEVVEKKHGEAEKKRP 77
G CKF+H RK EK LY D+RD EDV + ++
Sbjct: 99 GDACKFAHGKEEARKTEKPDLYSDVRDKEEDV--PLG------------------KRPWI 138
Query: 78 TTTIICKYFIEAVENSKYGWFWSCPNGPCT 107
T +CK+FIEA+E+ KYGW W+CPNG
Sbjct: 139 NTDRVCKFFIEAMESGKYGWGWTCPNGNMR 168
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 29.6 bits (67), Expect = 0.22
Identities = 10/38 (26%), Positives = 22/38 (57%)
Query: 44 DDGEDVNETMENWDEDKLKEVVEKKHGEAEKKRPTTTI 81
DD ++ ++ ++WDE++ +E E+K A K + +
Sbjct: 25 DDEDEDDDVKDSWDEEEDEEKEEEKAKVAAKAKAKKAL 62
>gnl|CDD|234778 PRK00484, lysS, lysyl-tRNA synthetase; Reviewed.
Length = 491
Score = 28.1 bits (64), Expect = 0.87
Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 40 VDMRD-----DGEDVNETMENWDEDKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVE 91
+ M D G D ++ +++ + + ++ E EK +I + F E VE
Sbjct: 315 LTMVDAIKEYTGVDFDDM----TDEEARALAKELGIEVEKSWGLGKLINELFEEFVE 367
>gnl|CDD|197366 cd09916, CpxP_like, CpxP component of the bacterial
Cpx-two-component system and related proteins. This
family summarizes bacterial proteins related to CpxP, a
periplasmic protein that forms part of a two-component
system which acts as a global modulator of
cell-envelope stress in gram-negative bacteria. CpxP
aids in combating extracytoplasmic protein-mediated
toxicity, and may also be involved in the response to
alkaline pH. Functioning as a dimer, it inhibits
activation of the kinase CpxA, but also plays a vital
role in the quality control system of P pili. It has
been suggested that CpxP directly interacts with CpxA
via its concave polar surface. Another member of this
family, Spy, is also a periplasmic protein that may be
involved in the response to stress. The homology
between CpxP and Spy suggests similar functions. A
characteristic 5-residue sequence motif LTXXQ is found
repeated twice in many members of this family.
Length = 96
Score = 26.8 bits (60), Expect = 1.4
Identities = 9/47 (19%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 32 KAEKRSLYVDMRDDGEDVNE--TMENWDEDKLKEVVEKKHGEAEKKR 76
+A+ ++L MR E++ T + +DE ++ + + E +++
Sbjct: 20 RAQMKALREQMRAAREELRALLTADTFDEAAVRALAAEMA-ELQQEL 65
>gnl|CDD|214980 smart01024, BCS1_N, This domain is found at the N terminal of the
mitochondrial ATPase BSC1. It encodes the import and
intramitochondrial sorting for the protein.
Length = 170
Score = 27.2 bits (61), Expect = 1.4
Identities = 14/54 (25%), Positives = 23/54 (42%)
Query: 29 IERKAEKRSLYVDMRDDGEDVNETMENWDEDKLKEVVEKKHGEAEKKRPTTTII 82
+ R+ EK + E + T D D KE++E+ A K+ T+I
Sbjct: 95 VTREREKTMADMRTGSPFETLTLTTLGRDRDVFKELLEEARELALKRTEGKTVI 148
>gnl|CDD|239467 cd03370, NADH_oxidase, NADPH_oxidase. Nitroreductase family
containing NADH oxidase and other, uncharacterized
proteins that are similar to nitroreductase.
Nitroreductase catalyzes the reduction of nitroaromatic
compounds such as nitrotoluenes, nitrofurans and
nitroimidazoles. This process requires NAD(P)H as
electron donor in an obligatory two-electron transfer
and uses FMN as cofactor. The enzyme is typically a
homodimer. Members of this family are also called NADH
dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
dihydropteridine reductase.
Length = 156
Score = 27.0 bits (60), Expect = 1.6
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 53 MENWDEDKLKEVV 65
M +DE+K+KE +
Sbjct: 112 MTGFDEEKVKEAL 124
>gnl|CDD|225094 COG2183, Tex, Transcriptional accessory protein [Transcription].
Length = 780
Score = 27.2 bits (61), Expect = 1.8
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 44 DDGEDVNETMENWDEDKLKEVVEKKHGEAEK-KRPTTTIICK 84
D GE + + N + KLK + ++ + PT I
Sbjct: 587 DLGEADPDLIGNRERAKLKSLNLEEFADELDFGLPTLEDIIL 628
>gnl|CDD|215847 pfam00305, Lipoxygenase, Lipoxygenase.
Length = 667
Score = 27.0 bits (60), Expect = 2.2
Identities = 19/62 (30%), Positives = 22/62 (35%), Gaps = 17/62 (27%)
Query: 62 KEVVEKKHGEAEKKRP--------------TTTII--CKYFIEAVENSKYGWFWSCPNGP 105
KEVVE HG+ K P T II AV +Y + PN P
Sbjct: 493 KEVVEVGHGDK-KDEPWWPKLQTREQLIEFCTIIIWTASALHAAVNFGQYDYGGWIPNRP 551
Query: 106 CT 107
T
Sbjct: 552 TT 553
>gnl|CDD|225404 COG2848, COG2848, Uncharacterized conserved protein [Function
unknown].
Length = 445
Score = 27.1 bits (60), Expect = 2.4
Identities = 8/30 (26%), Positives = 14/30 (46%)
Query: 37 SLYVDMRDDGEDVNETMENWDEDKLKEVVE 66
SL + D E++ E + K ++VE
Sbjct: 28 SLLDCISSDIEELAENIYEKITTKALKLVE 57
>gnl|CDD|238439 cd00862, ProRS_anticodon_zinc, ProRS Prolyl-anticodon binding
domain, long version found predominantly in eukaryotes
and archaea. ProRS belongs to class II aminoacyl-tRNA
synthetases (aaRS). This alignment contains the
anticodon binding domain, which is responsible for
specificity in tRNA-binding, so that the activated amino
acid is transferred to a ribose 3' OH group of the
appropriate tRNA only, and an additional C-terminal
zinc-binding domain specific to this subfamily of aaRSs.
Length = 202
Score = 26.5 bits (59), Expect = 2.5
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 30 ERKAEKRSLYVDMRDDGEDVNETMENWDE---DKLKEVVEKKHGEAEKKRPTTTIICKY- 85
R EK ++ + RD GE + E + L E+ E + A + R T I+ +
Sbjct: 76 PRDLEKNTVVIVRRDTGEKKTVPLAELVEKVPELLDEIQEDLYERALEFRDATRIVDTWE 135
Query: 86 -FIEAVENSKY 95
F EA+
Sbjct: 136 EFKEALNEKGI 146
>gnl|CDD|218422 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyze the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 26.7 bits (60), Expect = 3.0
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 31 RKAEKRSLYVDMRDDGEDVNETMENWDEDKLKEVVEKKHGEA 72
R VD+ + + E +W ED+L++ + + GE
Sbjct: 393 RVDPGAEPDVDVAELEARLAEAARSW-EDRLQDALLEAFGEE 433
>gnl|CDD|178144 PLN02529, PLN02529, lysine-specific histone demethylase 1.
Length = 738
Score = 26.4 bits (58), Expect = 3.4
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 53 MENWDEDKLKEVVEKKHGEAEKKRPTTT 80
++N+DE+ + E++EK G + KK+ T
Sbjct: 21 LKNYDENLMDELIEKHLGGSFKKKNRTK 48
>gnl|CDD|215258 PLN02465, PLN02465, L-galactono-1,4-lactone dehydrogenase.
Length = 573
Score = 26.4 bits (58), Expect = 3.6
Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 22/87 (25%)
Query: 7 YSGYLPCLFQSGAKCKFSHDLTIERKAEKRSLYVDMRDDGEDVNETMENW---------- 56
Y GY L S A +S K +K + T+ NW
Sbjct: 47 YLGYAALLLFSAAATYYSFPFPENAKHKKA-------APLPEDLHTVSNWSGTHEVQTRR 99
Query: 57 -----DEDKLKEVVEKKHGEAEKKRPT 78
++L+++V++ H + + RP
Sbjct: 100 YHQPESLEELEDIVKEAHEKGRRIRPV 126
>gnl|CDD|233107 TIGR00734, hisAF_rel, hisA/hisF family protein. This model
models a family of proteins found so far in three
archaeal species: Methanobacterium thermoautotrophicum,
Methanococcus jannaschii, and Archaeoglobus fulgidus.
This protein is homologous to
phosphoribosylformimino-5-aminoimidazole carboxamide
ribotide isomerase (HisA) and, with lower similarity,
to the cyclase HisF, both of which are enzymes of
histidine biosynthesis. Each species with this protein
also encodes HisA. The function of this protein is
unknown [Unknown function, General].
Length = 221
Score = 26.0 bits (57), Expect = 4.0
Identities = 7/25 (28%), Positives = 9/25 (36%)
Query: 60 KLKEVVEKKHGEAEKKRPTTTIICK 84
K V K GE E P ++
Sbjct: 10 KDGIAVAGKSGERESYPPLESVSRL 34
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated.
Length = 822
Score = 26.1 bits (58), Expect = 5.1
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 5/44 (11%)
Query: 43 RDDGEDVNETMENWDEDKLKEVVEKKHGE-----AEKKRPTTTI 81
D +E + WDE++ +E+ EK G + K+ TI
Sbjct: 235 YRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTI 278
>gnl|CDD|224693 COG1779, COG1779, C4-type Zn-finger protein [General function
prediction only].
Length = 201
Score = 25.4 bits (56), Expect = 6.0
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 5/42 (11%)
Query: 47 EDVNETMENWDED-----KLKEVVEKKHGEAEKKRPTTTIIC 83
+V ET ED K +E++++ E KR T II
Sbjct: 119 YEVLETAIKLAEDDESKKKAEELLKRIDEAIEGKRKFTLIIE 160
>gnl|CDD|224164 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 25.8 bits (57), Expect = 6.6
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 13/55 (23%)
Query: 57 DEDKLKEVVEKKHGEAEKKRPTTTIICKYFIEAVENSKYGWFWSCPNGPCTFENG 111
E++L+E++ +K P TI + AV S +G CP+G C F G
Sbjct: 46 PEERLREILRRK--------PVRTISGVAVV-AVMTSPHG----CPHGRCVFCPG 87
>gnl|CDD|226795 COG4345, COG4345, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 181
Score = 25.2 bits (55), Expect = 6.9
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 32 KAEKRSLYVDMRDDGEDVNETMENWDE--DKLKEVVEKKHGEAEKKRPTTTII 82
+A + V ++ E + + ME + ++E+V + A K + T +I
Sbjct: 110 EALTIGIEVYPKELEEKLADAMEEVERIEKTIEELVSELESLANKLKEVTDVI 162
>gnl|CDD|180895 PRK07228, PRK07228, N-ethylammeline chlorohydrolase; Provisional.
Length = 445
Score = 25.7 bits (57), Expect = 7.0
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 42 MRDDGEDVNETMENWDEDKLKEVV---EKKHG 70
M D G+DV E ++ E L E V EK HG
Sbjct: 147 MMDYGDDVPEGLQEDTEASLAESVRLLEKWHG 178
>gnl|CDD|237501 PRK13777, PRK13777, transcriptional regulator Hpr; Provisional.
Length = 185
Score = 25.0 bits (55), Expect = 9.9
Identities = 10/29 (34%), Positives = 21/29 (72%), Gaps = 1/29 (3%)
Query: 31 RKAEKRSLYVDMRDDGEDV-NETMENWDE 58
++ +KR+ Y+++ + GE++ ETME +D
Sbjct: 94 KEDDKRNTYIELTEKGEELLLETMEEYDP 122
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 0.134 0.424
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,464,503
Number of extensions: 449419
Number of successful extensions: 564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 37
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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 (21.6 bits)
S2: 53 (24.1 bits)