RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7214
(201 letters)
>gnl|CDD|238464 cd00924, Cyt_c_Oxidase_Vb, Cytochrome c oxidase subunit Vb.
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 Vb is one of three
mammalian subunits that lacks a transmembrane region.
Subunit Vb is located on the matrix side of the
membrane and binds the regulatory subunit of protein
kinase A. The abnormally extended conformation is
stable only in the CcO assembly.
Length = 97
Score = 100 bits (252), Expect = 5e-28
Identities = 33/64 (51%), Positives = 43/64 (67%), Gaps = 1/64 (1%)
Query: 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRC-ACGHW 59
D + P K GT++DPNLV SAF R+VGC+CE D + ++WMW+E P+RC CGH
Sbjct: 29 DDFDMKPLKGPFGTKEDPNLVPSAFDKRIVGCICEPDSHDVIWMWLEKGKPKRCPECGHV 88
Query: 60 FKLK 63
FKL
Sbjct: 89 FKLV 92
>gnl|CDD|201667 pfam01215, COX5B, Cytochrome c oxidase subunit Vb.
Length = 136
Score = 69.6 bits (170), Expect = 2e-15
Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 1 DPYYNGPFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYH-IVWMWVEADMPRRC-ACGH 58
DP+ P + GT DP +V S R+VGC D H I+W V +RC CG
Sbjct: 61 DPFDIKPLDASKGTLKDPIIVESIDNYRIVGCTGSPDGSHTIIWFTVHKGEAQRCPECGS 120
Query: 59 WFKLKLI 65
+KLK I
Sbjct: 121 VYKLKPI 127
>gnl|CDD|177931 PLN02294, PLN02294, cytochrome c oxidase subunit Vb.
Length = 174
Score = 51.4 bits (123), Expect = 2e-08
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 7/67 (10%)
Query: 6 GPFKRTSGTRDDPNLVRSAFKSRLVGCVC--EEDQYHIVWMWVEADMPRRC-ACGHWFKL 62
GPF GT++ P +V+S + R+VGC ED++ +VW W+E C C +F+L
Sbjct: 98 GPF----GTKEAPAVVKSYYDKRIVGCPGGEGEDEHDVVWFWLEKGKSFECPVCTQYFEL 153
Query: 63 KLICRGG 69
+++ GG
Sbjct: 154 EVVGPGG 160
>gnl|CDD|218087 pfam04434, SWIM, SWIM zinc finger. This domain is found in
bacterial, archaeal and eukaryotic proteins. It is
predicted to be organised into two N-terminal
beta-strands and a C-terminal alpha helix, thus
possibly adopting a fold similar to that of the C2H2
zinc finger (pfam00096). SWIM is thought to be a
versatile domain that can interact with DNA or proteins
in different contexts.
Length = 38
Score = 29.4 bits (66), Expect = 0.15
Identities = 5/34 (14%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 40 HIVWMWVEADMPRRCACGHWFKLKLICRGGVHVA 73
+ V + ++ + C+C + + C+ H
Sbjct: 1 YRVQLDLDDLVKASCSCPAFQLYGIPCK---HAL 31
>gnl|CDD|220122 pfam09137, Glucodextran_N, Glucodextranase, domain N. Members of
this family, which are uniquely found in bacterial and
archaeal glucoamylases and glucodextranases, adopt a
structure consisting of 17 antiparallel beta-strands.
These beta-strands are divided into two beta-sheets, and
one of the beta-sheets is wrapped by an extended
polypeptide, which appears to stabilise the domain.
Members of this family are mainly concerned with
catalytic activity, hydrolysing alpha-1,6-glucosidic
linkages of dextran to release beta-D-glucose from the
non-reducing end via an inverting reaction mechanism.
Length = 269
Score = 30.8 bits (70), Expect = 0.41
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 66 CRGGVHVAIGSNWSKWILSSVGYLGQSDNLT 96
R V++A+ S+ W S GY+G SD T
Sbjct: 161 ERNSVYLALVSS-LPWKAYSAGYVGVSDGWT 190
>gnl|CDD|149006 pfam07707, BACK, BTB And C-terminal Kelch. This domain is found
associated with pfam00651 and pfam01344. The BACK
domain is found juxtaposed to the BTB domain; they are
separated by as little as two residues. This family
appears to be closely related to the BTB domain (Finn
RD, personal observation).
Length = 101
Score = 28.7 bits (65), Expect = 0.83
Identities = 7/26 (26%), Positives = 12/26 (46%), Gaps = 1/26 (3%)
Query: 32 CVCEEDQ-YHIVWMWVEADMPRRCAC 56
V E++ + V WV+ D+ R
Sbjct: 55 NVPSEEEVFEAVIKWVKHDVENRKKH 80
>gnl|CDD|143632 cd07430, GH15_N, Glycoside hydrolase family 15, N-terminal domain.
Members of this family are N-terminal domains uniquely
found in bacterial and archaeal glucoamylases and
glucodextranases. Glucoamylase (glucan
1,4-alpha-glucosidase; 4-alpha-D-glucan glucohydrolase;
amyloglucosidase; exo-1,4-alpha-glucosidase;
gamma-amylase; lysosomal alpha-glucosidase; EC 3.2.1.3)
hydrolyzes beta-1,4-glucosidic linkages of starch,
glycogen and malto-oligosaccharides, releasing
beta-D-glucose from the non-reducing end.
Glucodextranase (glucan 1,6-alpha-glucosidase;
exo-1,6-alpha-glucosidase; EC 3.2.1.70) uses an
inverting reaction mechanism to hydrolyze
alpha-1,6-glucosidic linkages of dextran and related
oligosaccharides, releasing beta-D-glucose from the
non-reducing end. These N-terminal domains adopt a
structure consisting of antiparallel beta-strands,
divided into two beta-sheets, with one sheet wrapped by
an extended polypeptide, which appears to stabilize the
domain. The function of these domains in the enzymes is
as yet unknown. However, it is suggested that domain N
of bacterial GA is involved in folding and/or the
thermostability of the A domain that forms an
(alpha/alpha)6-barrel structure.
Length = 260
Score = 28.7 bits (65), Expect = 2.1
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 67 RGGVHVAIGSNWSKWILSSVGYLGQSDNLT 96
RG V +A+ ++ + +SVGY+G SD
Sbjct: 159 RGSVALALKAS-IPFTRASVGYVGVSDGWQ 187
>gnl|CDD|223049 PHA03334, PHA03334, putative DNA polymerase catalytic subunit;
Provisional.
Length = 1545
Score = 28.3 bits (63), Expect = 3.8
Identities = 12/67 (17%), Positives = 23/67 (34%)
Query: 7 PFKRTSGTRDDPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKLKLIC 66
P R S R + K + ED + + ++ P C + LK +
Sbjct: 1224 PKNRVSRDRSRGRAHPTVLKHAVSLHYLTEDTNFLAHVLLDRACPTSCYIPDGWPLKAML 1283
Query: 67 RGGVHVA 73
+ G+ +
Sbjct: 1284 QSGLAMI 1290
>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated.
Length = 367
Score = 27.6 bits (62), Expect = 5.0
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 17/59 (28%)
Query: 131 QLDMALESLLPTPGSLLSKLVLGRDPKVHHFNRFRIRFGSGGNRTERLQGKGNVFQATR 189
QL+ L++L R+ V R+RFG RT L+ G VF TR
Sbjct: 298 QLEDVLDTLTD------------REENV-----LRLRFGLDDGRTRTLEEVGKVFGVTR 339
>gnl|CDD|202885 pfam04095, NAPRTase, Nicotinate phosphoribosyltransferase
(NAPRTase) family. Nicotinate phosphoribosyltransferase
(EC:2.4.2.11) is the rate limiting enzyme that catalyzes
the first reaction in the NAD salvage synthesis. This
family also includes Pre-B cell enhancing factor that is
a cytokine. This family is related to Quinolinate
phosphoribosyltransferase pfam01729.
Length = 245
Score = 27.4 bits (61), Expect = 5.2
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 159 HHF--NRFRIRFGSGGNRTERLQGKGNVFQ--ATRLVVVKKEIS 198
H N F I FG G N T+ L F T L +V K +
Sbjct: 168 EHLKGNGFNIAFGIGTNLTQDLNRDTLGFAYKLTPLNIVIKLVE 211
>gnl|CDD|216830 pfam01987, AIM24, Mitochondrial biogenesis AIM24. In eukaryotes,
this domain is involved in mitochondrial biogenesis. Its
function in prokaryotes in unknown.
Length = 206
Score = 26.8 bits (60), Expect = 6.3
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 160 HFNRFRIRFGSGGNRTERLQGKGNVFQATRLVVVKKEIS 198
F F FG G +L G G VF ++ +V+ E++
Sbjct: 112 KFQGFLGGFGGEGLFLLKLSGTGLVFLSSYGAIVEIELA 150
>gnl|CDD|197943 smart00875, BACK, BTB And C-terminal Kelch. The BACK domain is
found juxtaposed to the BTB domain; they are separated
by as little as two residues.
Length = 101
Score = 25.8 bits (57), Expect = 7.1
Identities = 10/46 (21%), Positives = 17/46 (36%), Gaps = 2/46 (4%)
Query: 17 DPNLVRSAFKSRLVGCVCEEDQYHIVWMWVEADMPRRCACGHWFKL 62
+ S + EE+ + V WV+ D +R H +L
Sbjct: 41 PLEQLLELLSSDDLNVSSEEEVFEAVLRWVKHDPEKRRE--HLPEL 84
>gnl|CDD|224241 COG1322, COG1322, Predicted nuclease of restriction
endonuclease-like fold, RmuC family [General function
prediction only].
Length = 448
Score = 27.0 bits (60), Expect = 7.1
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 98 KDSNEQSVKPIQQMTRTKSTKFSTQLKAST 127
+ N+Q++K + + R KF QL+
Sbjct: 123 AELNQQNLKQLLKPLREVLEKFREQLEQRI 152
>gnl|CDD|151038 pfam10472, CReP_N, eIF2-alpha phosphatase phosphorylation
constitutive repressor. This is the conserved
N-terminal domain of CReP, constitutive repressor of
eIF2-alpha phosphorylation/protein phosphatase 1,
catalytic subunit. It functions in the dephosphorylation
of eIF2-alpha under basal conditions in the absence of
stress. In response to translation inhibition, there is
reduced synthesis of the labile CReP that contributes to
elevated levels of eIF2-alpha phosphorylation. The
C-terminus, family PP1c, is shared with the
apoptosis-associated protein Gadd34 and herpes simplex
virus.
Length = 411
Score = 27.0 bits (59), Expect = 8.6
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 6/82 (7%)
Query: 87 GY--LGQSDNLTKKDSNEQSVKPIQQMT----RTKSTKFSTQLKASTLCGQLDMALESLL 140
GY L + NL + D P Q + +T+ T+ K L ++ +ALE
Sbjct: 321 GYHSLEEEHNLLRMDPKHCRDNPAQAVPAAADIPGNTQEPTEEKIELLIQEVPLALEEES 380
Query: 141 PTPGSLLSKLVLGRDPKVHHFN 162
P G L ++ + ++ + H N
Sbjct: 381 PQEGCLFCEIPMEKECEEDHIN 402
>gnl|CDD|211960 TIGR04237, seadorna_VP9, seadornavirus/coltivirus VP9 protein.
This model, broader than related pfam08978, describes
proteins VP9 in Coltivirus, and proteins with various
designations in the seadornavirus group: VP9 in Banna
virus, VP10 in Liao ning virus, and VP11 in Kadipiro
virus.
Length = 280
Score = 26.5 bits (58), Expect = 9.0
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 6/40 (15%)
Query: 136 LESLLPTPGSLLSKLVLGRDPKV------HHFNRFRIRFG 169
+E L T + KL P + H FN RF
Sbjct: 39 VEKLAVTKKEMKDKLAQCNLPSIELNTREHTFNGDFARFM 78
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
0.321 0.136 0.428
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,753,497
Number of extensions: 831090
Number of successful extensions: 553
Number of sequences better than 10.0: 1
Number of HSP's gapped: 550
Number of HSP's successfully gapped: 16
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
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 (21.9 bits)
S2: 56 (25.4 bits)