RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3153
(89 letters)
>gnl|CDD|238463 cd00923, Cyt_c_Oxidase_Va, Cytochrome c oxidase subunit Va.
Cytochrome c oxidase (CcO), the terminal oxidase in the
respiratory chains of eukaryotes and most bacteria, is a
multi-chain transmembrane protein located in the inner
membrane of mitochondria and the cell membrane of
prokaryotes. It catalyzes the reduction of O2 and
simultaneously pumps protons across the membrane. The
number of subunits varies from three to five in bacteria
and up to 13 in mammalian mitochondria. Subunits I, II,
and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Found only in
eukaryotes, subunit Va is one of three mammalian
subunits that lacks a transmembrane region. Subunit Va
is located on the matrix side of the membrane and binds
thyroid hormone T2, releasing allosteric inhibition
caused by the binding of ATP to subunit IV and allowing
high turnover at elevated intramitochondrial ATP/ADP
ratios.
Length = 103
Score = 113 bits (284), Expect = 2e-34
Identities = 44/75 (58%), Positives = 60/75 (80%), Gaps = 1/75 (1%)
Query: 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRP 60
+N+L D VP+P +I AAL+A RR+ND+AL +R+LE +++KCG K+ I+PYIL EI+P
Sbjct: 30 LNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAHKE-IYPYILQEIKP 88
Query: 61 TLTELGIETPEDLGY 75
TL ELGI TPE+LGY
Sbjct: 89 TLKELGISTPEELGY 103
>gnl|CDD|111202 pfam02284, COX5A, Cytochrome c oxidase subunit Va. Cytochrome c
oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the
terminal oxidase in the mitochondrial electron transport
chain. This family is composed of cytochrome c oxidase
subunit Va.
Length = 108
Score = 89.2 bits (221), Expect = 6e-25
Identities = 46/77 (59%), Positives = 59/77 (76%), Gaps = 1/77 (1%)
Query: 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRP 60
MN L D VP+P II AAL+A RR+ND+A IR+LE+V++K G K+ I+PY+L E+RP
Sbjct: 33 MNTLVGYDLVPEPKIIEAALRACRRVNDFASAIRILEVVKDKAGPHKE-IYPYVLQELRP 91
Query: 61 TLTELGIETPEDLGYDK 77
TL ELGI TPE+LG DK
Sbjct: 92 TLQELGIPTPEELGLDK 108
>gnl|CDD|221865 pfam12933, FTO_NTD, FTO catalytic domain. This domain is the
catalytic AlkB-like domain from the FTO protein. This
domain catalyzes a demethylase activity with a
preference for 3-methylthymidine.
Length = 252
Score = 27.8 bits (62), Expect = 0.53
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 16 IIAALKAARRLNDYALTIRLLEMVQEKCGKKK 47
+ AA KA RRLND LT R E++++ +K
Sbjct: 98 LSAAYKAVRRLNDA-LTSRSRELLEKLRAPRK 128
>gnl|CDD|129440 TIGR00340, zpr1_rel, ZPR1-related zinc finger protein. This
model describes a strictly archaeal family homologous
to the domain duplicated in the eukaryotic zinc-binding
protein ZPR1. ZPR1 was shown experimentally to bind
approximately two moles of zinc; each copy of the
domain contains a putative zinc finger of the form
CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of
epidermal growth factor receptor, but is displaced by
receptor activation and autophosphorylation after which
it redistributes in part to the nucleus. The proteins
described by This model by analogy may be suggested to
play a role in signal transduction. A model ZPR1_znf
(TIGR00310) has been created to describe the domain
shared by this protein and ZPR1 [Unknown function,
General].
Length = 163
Score = 27.5 bits (61), Expect = 0.72
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 4/63 (6%)
Query: 13 PVIIIAALKAARRLNDYALTIRLLEMVQ--EKCGKKKKVIWPYILGEIRPTLTELGIETP 70
PV LKA D +++ EKCG + + Y L E P + IE
Sbjct: 2 PVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDV--YQLEEKEPVRYIIKIENE 59
Query: 71 EDL 73
+DL
Sbjct: 60 DDL 62
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 27.2 bits (61), Expect = 1.1
Identities = 15/58 (25%), Positives = 21/58 (36%), Gaps = 9/58 (15%)
Query: 16 IIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73
I A K R + LLE + G K++ L +L +T EDL
Sbjct: 471 IRAWFKKQDRDENVEAGRELLEKELSRLGLPKELE---------ELLEKLNFKTVEDL 519
>gnl|CDD|224693 COG1779, COG1779, C4-type Zn-finger protein [General function
prediction only].
Length = 201
Score = 26.5 bits (59), Expect = 1.4
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 41 EKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGYD 76
E+CG + + L E P L +E+ EDL
Sbjct: 47 ERCGYRSTDV--KTLEEREPRRYTLKVESEEDLSAR 80
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 25.4 bits (55), Expect = 5.0
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 25 RLNDYALTIRLLEMVQEKCGKK-KKVIWPYILG---EIRPTLTELGIETPEDLGYDK-PE 79
RL RL E++ +K GK+ KK I +LG E I+T ++ DK P
Sbjct: 102 RLEGLQFDSRLYEILSKKIGKRLKKTILRGLLGLKDVDDTVSVEANIDTLLEIVEDKWPT 161
Query: 80 LWCK 83
+W
Sbjct: 162 IWKS 165
>gnl|CDD|107278 cd06283, PBP1_RegR_EndR_KdgR_like, Ligand-binding domain of DNA
transcription repressor RegR and other putative
regulators such as KdgR and EndR. Ligand-binding domain
of DNA transcription repressor RegR and other putative
regulators such as KdgR and EndR, all of which are
members of the LacI-GalR family of bacterial
transcription regulators. RegR regulates bacterial
competence and the expression of virulence factors,
including hyaluronidase. The LacI-GalR family repressors
are composed of two functional domains: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
ligand-binding domain, which is homologous to the
sugar-binding domain of ABC-type transport systems that
contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 267
Score = 25.2 bits (56), Expect = 5.5
Identities = 27/87 (31%), Positives = 37/87 (42%), Gaps = 19/87 (21%)
Query: 5 AQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVI-----WPYILGEIR 59
GV + +I I A L RL +++ + KKK I IL E+
Sbjct: 145 EHGIGVNEELIEIDDEDADE------LDERLRQLLNKP--KKKTAIFAANGL--ILLEVL 194
Query: 60 PTLTELGIETPEDLG---YDKPELWCK 83
L ELGI PED+G +D E W +
Sbjct: 195 KALKELGIRIPEDVGLIGFDDTE-WAE 220
>gnl|CDD|222456 pfam13925, Katanin_con80, con80 domain of Katanin. The con80
domain of katanin is the C-terminal region of the
protein that binds to the N-terminal domain of
katanin-p60, the catalytic ATPase. The complex
associates with a specific subregion of the mitotic
spindle leading to increased microtubule disassembly
and targeting of p60 to the spindle poles. The assembly
and function of the mitotic spindle requires the
activity of a number of microtubule-binding proteins.
Katanin, a heterodimeric microtubule-severing ATPase,
is found localized at mitotic spindle poles. A proposed
model is that katanin is targeted to spindle poles
through a combination of direct microtubule binding by
the p60 subunit and through interactions between the
WD40 domain and an unknown protein.
Length = 164
Score = 24.9 bits (55), Expect = 6.1
Identities = 11/32 (34%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 18 AALKAARRLNDYALTIRLLEMVQEKCGKKKKV 49
A+ AARR+ND A+ + +L ++ + KK+ +
Sbjct: 32 GAIAAARRMNDLAVLVDVLSVLT-QSLKKESI 62
>gnl|CDD|216748 pfam01866, Diphthamide_syn, Putative diphthamide synthesis protein.
Human DPH1 is a candidate tumour suppressor gene. DPH2
from yeast, which confers resistance to diphtheria
toxin, has been found to be involved in diphthamide
synthesis. Diphtheria toxin inhibits eukaryotic protein
synthesis by ADP-ribosylating diphthamide, a
posttranslationally modified histidine residue present
in EF2. The exact function of the members of this family
is unknown.
Length = 300
Score = 24.9 bits (55), Expect = 6.9
Identities = 9/46 (19%), Positives = 17/46 (36%), Gaps = 7/46 (15%)
Query: 15 IIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRP 60
II+ R L +++ ++ K + +L EI P
Sbjct: 208 IIVGTKGGQGRP-------DLARRLKKLLKERGKRAYLILLDEINP 246
>gnl|CDD|235529 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 24.8 bits (54), Expect = 6.9
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 10 VPDPVIIIAALKAARRLNDYALTIRL 35
+P PV+I+ L ARR IR+
Sbjct: 177 IPKPVVIVDTLATARRQGVALDDIRI 202
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 24.8 bits (54), Expect = 7.2
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 57 EIRPTLTELGIETP-----EDLGYDKP 78
E T +LG++ P DLGY+KP
Sbjct: 3 EFETTFADLGLKAPILEALNDLGYEKP 29
>gnl|CDD|179554 PRK03204, PRK03204, haloalkane dehalogenase; Provisional.
Length = 286
Score = 24.8 bits (54), Expect = 7.6
Identities = 11/22 (50%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 59 RPTLTELGIETPEDLGYDKPEL 80
RP L L E P LG KP L
Sbjct: 211 RPLLARLAREVPATLG-TKPTL 231
>gnl|CDD|222716 pfam14374, Ribos_L4_asso_C, 60S ribosomal protein L4 C-terminal
domain. This family is found at the very C-terminal of
60 ribosomal L4 proteins.
Length = 80
Score = 24.1 bits (53), Expect = 8.3
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 20 LKAARRLNDYALTIRLLEMVQEKCGKKKK 48
L+A +LN YA R ++ EK KK K
Sbjct: 49 LQAMLKLNPYAKVARRAALLAEKKRKKAK 77
>gnl|CDD|236191 PRK08224, ligC, ATP-dependent DNA ligase; Reviewed.
Length = 350
Score = 24.5 bits (54), Expect = 9.3
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 4 LAQDDGVPDPVIIIAALKAARRLNDYALTIRL 35
L DDG V + +A ARR LT L
Sbjct: 226 LYDDDGQLHHVGVTSAFPMARRR---ELTAEL 254
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 0.140 0.429
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,818,575
Number of extensions: 404540
Number of successful extensions: 464
Number of sequences better than 10.0: 1
Number of HSP's gapped: 462
Number of HSP's successfully gapped: 15
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
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: 53 (24.1 bits)