RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18197
(144 letters)
>gnl|CDD|133146 cd05479, RP_DDI, RP_DDI; retropepsin-like domain of DNA damage
inducible protein. The family represents the
retropepsin-like domain of DNA damage inducible protein.
DNA damage inducible protein has a retropepsin-like
domain and an amino-terminal ubiquitin-like domain
and/or a UBA (ubiquitin-associated) domain. This CD
represents the retropepsin-like domain of DDI.
Length = 124
Score = 200 bits (510), Expect = 1e-67
Identities = 72/109 (66%), Positives = 87/109 (79%)
Query: 1 MLFINCCVNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRI 60
ML+IN +NGVPVKAFVDSGAQ TIMS CAE+C +MRLID R+ G+AKGVG Q+I+GRI
Sbjct: 16 MLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQGIAKGVGTQKILGRI 75
Query: 61 HMVQVVIEKDFLTTSLSILEEQPMDMLLGLDMLRRHQCCIDLKRNVLRI 109
H+ QV I FL S ++LE+ +D L+GLDML+RHQC IDLK NVLRI
Sbjct: 76 HLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKENVLRI 124
>gnl|CDD|118200 pfam09668, Asp_protease, Aspartyl protease. This family of
eukaryotic aspartyl proteases have a fold similar to
retroviral proteases which implies they function
proteolytically during regulated protein turnover.
Length = 124
Score = 188 bits (479), Expect = 6e-63
Identities = 67/101 (66%), Positives = 84/101 (83%)
Query: 1 MLFINCCVNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRI 60
ML+INC VNGVPVKAFVDSGAQT+IMS CAERC IMRL+DTR+AG+A+GVG +I+GR+
Sbjct: 24 MLYINCEVNGVPVKAFVDSGAQTSIMSPRCAERCGIMRLLDTRFAGIARGVGTAKILGRV 83
Query: 61 HMVQVVIEKDFLTTSLSILEEQPMDMLLGLDMLRRHQCCID 101
HM + + FL S +++E+Q MD+L GLDML+RHQCCID
Sbjct: 84 HMADLKLGDLFLPCSFTVIEDQDMDLLFGLDMLKRHQCCID 124
>gnl|CDD|133136 cd00303, retropepsin_like, Retropepsins; pepsin-like aspartate
proteases. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements, as well as eukaryotic
dna-damage-inducible proteins (DDIs), and bacterial
aspartate peptidases. While fungal and mammalian
pepsins are bilobal proteins with structurally related
N and C-terminals, retropepsins are half as long as
their fungal and mammalian counterparts. The monomers
are structurally related to one lobe of the pepsin
molecule and retropepsins function as homodimers. The
active site aspartate occurs within a motif
(Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral
aspartyl protease is synthesized as part of the POL
polyprotein that contains an aspartyl protease, a
reverse transcriptase, RNase H, and an integrase. The
POL polyprotein undergoes specific enzymatic cleavage
to yield the mature proteins. In aspartate peptidases,
Asp residues are ligands of an activated water molecule
in all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 92
Score = 55.8 bits (135), Expect = 3e-11
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 4 INCCVNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVG-IQRIIGRIHM 62
+ +NGVPV+A VDSGA +S A++ + + V G + +G I
Sbjct: 1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60
Query: 63 VQVVIEKDFLTTSLSILEEQPMDMLLGLDMLR 94
V + I T +L+ D++LG L
Sbjct: 61 VTIGIGGKTFTVDFYVLDLLSYDVILGRPWLE 92
>gnl|CDD|133147 cd05480, NRIP_C, NRIP_C; putative nuclear receptor interacting
protein. Proteins in this family have been described as
probable nuclear receptor interacting proteins. The
C-terminal domain of this family is homologous to the
retroviral aspartyl protease domain. The domain is
structurally related to one lobe of the pepsin molecule.
The conserved active site aspartate occurs within a
motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp
residues are ligands of an activated water molecule in
all examples where catalytic residues have been
identified. This group of aspartate peptidases is
classified by MEROPS as the peptidase family A2
(retropepsin family, clan AA), subfamily A2A.
Length = 103
Score = 42.5 bits (100), Expect = 4e-06
Identities = 24/103 (23%), Positives = 55/103 (53%), Gaps = 2/103 (1%)
Query: 4 INCCVNGVPVKAFVDSGAQTTIMSAECAERCAIM-RLIDTRWAGVAKGVGIQ-RIIGRIH 61
++C G ++A VD+G Q ++SA C +R + R++ + A + ++IG+I
Sbjct: 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIE 60
Query: 62 MVQVVIEKDFLTTSLSILEEQPMDMLLGLDMLRRHQCCIDLKR 104
+ + + + + S ++++ + LGL L+ +C I+L++
Sbjct: 61 RLVLQLGQLTVECSAQVVDDNEKNFSLGLQTLKSLKCVINLEK 103
>gnl|CDD|222288 pfam13650, Asp_protease_2, Aspartyl protease. This family
consists of predicted aspartic proteases, typically
from 180 to 230 amino acids in length, in MEROPS clan
AA. This model describes the well-conserved 121-residue
C-terminal region. The poorly conserved, variable
length N-terminal region usually contains a predicted
transmembrane helix.
Length = 89
Score = 40.3 bits (95), Expect = 2e-05
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 4/90 (4%)
Query: 4 INCCVNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRIHMV 63
+ +NG PV+ +D+GA T++S AER + G + +
Sbjct: 1 VPVTINGKPVRFLLDTGASGTLLSRSLAERLGL--KPTKLTIGRVSTANGTVRAALVRLD 58
Query: 64 QVVIEKDFLT-TSLSILEEQPM-DMLLGLD 91
+ I L +L+ + D LLG+D
Sbjct: 59 SLKIGGITLRNVPAVVLDLGDLIDGLLGMD 88
>gnl|CDD|133150 cd05483, retropepsin_like_bacteria, Bacterial aspartate
proteases, retropepsin-like protease family. This
family of bacteria aspartate proteases is a subfamily
of retropepsin-like protease family, which includes
enzymes from retrovirus and retrotransposons. While
fungal and mammalian pepsin-like aspartate proteases
are bilobal proteins with structurally related N- and
C-termini, this family of bacteria aspartate proteases
is half as long as their fungal and mammalian
counterparts. The monomers are structurally related to
one lobe of the pepsin molecule and function as
homodimers. The active site aspartate occurs within a
motif (Asp-Thr/Ser-Gly), as it does in pepsin. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where
catalytic residues have been identified. This group of
aspartate proteases is classified by MEROPS as the
peptidase family A2 (retropepsin family, clan AA),
subfamily A2A.
Length = 96
Score = 36.8 bits (86), Expect = 5e-04
Identities = 32/98 (32%), Positives = 45/98 (45%), Gaps = 21/98 (21%)
Query: 8 VNGVPVKAFVDSGAQTTIMSAECAERCAI-MRLIDTRWAGVAKG------VGIQRI-IGR 59
+NG PV+ +D+GA TT++S E AER + + L A G V + + IG
Sbjct: 9 INGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRLDSLQIGG 68
Query: 60 IHMVQV---VIEKDFLTTSLSILEEQPMDMLLGLDMLR 94
I + V V+ D L D LLG+D LR
Sbjct: 69 ITLRNVPAVVLPGDALGV----------DGLLGMDFLR 96
>gnl|CDD|131334 TIGR02281, clan_AA_DTGA, clan AA aspartic protease, TIGR02281
family. This family consists of predicted aspartic
proteases, typically from 180 to 230 amino acids in
length, in MEROPS clan AA. This model describes the
well-conserved 121-residue C-terminal region. The poorly
conserved, variable length N-terminal region usually
contains a predicted transmembrane helix. Sequences in
the seed alignment and those scoring above the trusted
cutoff are Proteobacterial; homologs scroing between
trusted and noise are found in Pyrobaculum aerophilum
str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and
Nostoc sp. PCC 7120 (Cyanobacteria) [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 121
Score = 35.3 bits (82), Expect = 0.002
Identities = 30/104 (28%), Positives = 43/104 (41%), Gaps = 23/104 (22%)
Query: 4 INCCVNGVPVKAFVDSGAQTTIMSAECAERCAI--MRLIDTRWAGVAKG------VGIQR 55
VNG V+ VD+GA + ++ E A+R + RL T A G V + R
Sbjct: 14 ATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANGQIKAARVTLDR 73
Query: 56 I-IG--RIHMVQV-VIEKDFLTTSLSILEEQPMDMLLGLDMLRR 95
+ IG ++ V V E L+ S LLG+ L R
Sbjct: 74 VAIGGIVVNDVDAMVAEGGALSES-----------LLGMSFLNR 106
>gnl|CDD|206145 pfam13975, gag-asp_proteas, gag-polyprotein putative aspartyl
protease. This family of putative aspartyl proteases
is found pre-dominantly in retroviral proteins.
Length = 72
Score = 34.2 bits (79), Expect = 0.003
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 2 LFINCCVNGVPVKAFVDSGAQTTIMSAECAERC 34
+ + + GV VKA VD+GA + +S A R
Sbjct: 9 VTVEVSIGGVEVKALVDTGATHSFISESLAARL 41
>gnl|CDD|116868 pfam08284, RVP_2, Retroviral aspartyl protease. Single domain
aspartyl proteases from retroviruses, retrotransposons,
and badnaviruses (plant dsDNA viruses). These proteases
are generally part of a larger polyprotein; usually pol,
more rarely gag. Retroviral proteases appear to be
homologous to a single domain of the two-domain
eukaryotic aspartyl proteases.
Length = 135
Score = 33.5 bits (77), Expect = 0.014
Identities = 25/108 (23%), Positives = 44/108 (40%)
Query: 8 VNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRIHMVQVVI 67
VN +P DSGA + +S R + V G R V + I
Sbjct: 28 VNSIPATVLFDSGASHSFISQAFVGRHGLPLEALRTPMLVHSPGGDMTATHRCPSVNIEI 87
Query: 68 EKDFLTTSLSILEEQPMDMLLGLDMLRRHQCCIDLKRNVLRIGTTGTE 115
+ +L +L+ + +D++LG+D L +H+ ID + + + E
Sbjct: 88 QGVDFPANLILLDSKDLDVILGMDWLAQHKGVIDCANRTVTLTSPKGE 135
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 33.5 bits (77), Expect = 0.020
Identities = 28/85 (32%), Positives = 35/85 (41%), Gaps = 12/85 (14%)
Query: 4 INCCVNGVPVKAFVDSGAQTTIMSAECAERCAI--MRLIDTRWAGVAKG------VGIQR 55
N VNG V VD+GA + ++ E A R I L T A G V + R
Sbjct: 108 ANGRVNGKKVDFLVDTGATSVALNEEDARRLGIDLNSLDYTITVSTANGRARAAPVTLDR 167
Query: 56 I-IGRIHMVQV---VIEKDFLTTSL 76
+ IG I + V V E L SL
Sbjct: 168 VQIGGIRVKNVDAMVAEDGALDESL 192
>gnl|CDD|215697 pfam00077, RVP, Retroviral aspartyl protease. Single domain
aspartyl proteases from retroviruses, retrotransposons,
and badnaviruses (plant dsDNA viruses). These proteases
are generally part of a larger polyprotein; usually pol,
more rarely gag. Retroviral proteases appear to be
homologous to a single domain of the two-domain
eukaryotic aspartyl proteases such as pepsins,
cathepsins, and renins (pfam00026).
Length = 99
Score = 31.8 bits (73), Expect = 0.038
Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 16/98 (16%)
Query: 8 VNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRIH-----M 62
V G P+KA +D+GA T++ + W I I G+I
Sbjct: 12 VGGQPIKALLDTGADDTVIPE---------NDLPGSW-PPWGPTTIGGIGGQIRVKQSIQ 61
Query: 63 VQVVIEKDFLTTSLSILEEQPMDMLLGLDMLRRHQCCI 100
+ V I + +L P++ +LG D+L + +
Sbjct: 62 ILVEIGGKKFRGTFLVLPSTPVN-ILGRDLLTQLGAKL 98
>gnl|CDD|227476 COG5147, REB1, Myb superfamily proteins, including transcription
factors and mRNA splicing factors [Transcription / RNA
processing and modification / Cell division and
chromosome partitioning].
Length = 512
Score = 30.9 bits (70), Expect = 0.20
Identities = 11/45 (24%), Positives = 18/45 (40%)
Query: 79 LEEQPMDMLLGLDMLRRHQCCIDLKRNVLRIGTTGTETRFLSESE 123
+E +G + R C D R+ ++ G T R+ E E
Sbjct: 307 VEHGGSWTEIGKLLGRMPNDCRDRWRDYVKCGDTLKRNRWSIEEE 351
>gnl|CDD|133149 cd05482, HIV_retropepsin_like, Retropepsins, pepsin-like
aspartate proteases. This is a subfamily of
retropepsins. The family includes pepsin-like aspartate
proteases from retroviruses, retrotransposons and
retroelements. While fungal and mammalian pepsins are
bilobal proteins with structurally related N- and
C-termini, retropepsins are half as long as their
fungal and mammalian counterparts. The monomers are
structurally related to one lobe of the pepsin molecule
and retropepsins function as homodimers. The active
site aspartate occurs within a motif (Asp-Thr/Ser-Gly),
as it does in pepsin. Retroviral aspartyl protease is
synthesized as part of the POL polyprotein that
contains an aspartyl protease, a reverse transcriptase,
RNase H, and an integrase. The POL polyprotein
undergoes specific enzymatic cleavage to yield the
mature proteins. In aspartate peptidases, Asp residues
are ligands of an activated water molecule in all
examples where catalytic residues have been identified.
This group of aspartate peptidases is classified by
MEROPS as the peptidase family A2 (retropepsin family,
clan AA), subfamily A2A.
Length = 87
Score = 28.4 bits (64), Expect = 0.53
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 8 VNGVPVKAFVDSGAQTTIMSAE 29
+NG + +D+GA +I++
Sbjct: 5 INGKLFEGLLDTGADVSIIAEN 26
>gnl|CDD|133151 cd05484, retropepsin_like_LTR_2, Retropepsins_like_LTR,
pepsin-like aspartate proteases. Retropepsin of
retrotransposons with long terminal repeats are
pepsin-like aspartate proteases. While fungal and
mammalian pepsins are bilobal proteins with
structurally related N- and C-termini, retropepsins are
half as long as their fungal and mammalian
counterparts. The monomers are structurally related to
one lobe of the pepsin molecule and retropepsins
function as homodimers. The active site aspartate
occurs within a motif (Asp-Thr/Ser-Gly), as it does in
pepsin. Retroviral aspartyl protease is synthesized as
part of the POL polyprotein that contains an aspartyl
protease, a reverse transcriptase, RNase H, and an
integrase. The POL polyprotein undergoes specific
enzymatic cleavage to yield the mature proteins. In
aspartate peptidases, Asp residues are ligands of an
activated water molecule in all examples where
catalytic residues have been identified. This group of
aspartate peptidases is classified by MEROPS as the
peptidase family A2 (retropepsin family, clan AA),
subfamily A2A.
Length = 91
Score = 27.9 bits (63), Expect = 0.81
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 2/87 (2%)
Query: 8 VNGVPVKAFVDSGAQTTIMSAECAERCAIMRLIDTRWAGVAKGVGIQRIIGRIHMVQVVI 67
VNG P+K +D+G+ T++S + + L T+ ++G+I V V
Sbjct: 7 VNGKPLKFQLDTGSAITVISEKTWRKLGSPPLKPTKKRLRTATGTKLSVLGQIL-VTVKY 65
Query: 68 EKDFLTTSLSILEEQPMDMLLGLDMLR 94
+L +++ + ++ LLG D L
Sbjct: 66 GGKTKVLTLYVVKNEGLN-LLGRDWLD 91
>gnl|CDD|225735 COG3194, DAL3, Ureidoglycolate hydrolase [Nucleotide transport
and metabolism].
Length = 168
Score = 27.7 bits (62), Expect = 1.6
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 73 TTSLSILEEQPMDMLLGLDMLRRHQC 98
T ++I QP L + ML RH
Sbjct: 53 RTLINIFRAQPAVHPLTISMLERHPL 78
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 28.1 bits (63), Expect = 1.7
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 103 KRNVLRIGTTGTETRFLSESELPVCARLT 131
+RN+ + G + R LS EL + + L
Sbjct: 179 RRNIKKAEKKGVKVRRLSREELDLFSELM 207
>gnl|CDD|215556 PLN03064, PLN03064, alpha,alpha-trehalose-phosphate synthase
(UDP-forming); Provisional.
Length = 934
Score = 27.1 bits (60), Expect = 3.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 38 RLIDTRWAGVAKGVGIQRIIGRI 60
R ++ R GV KG I RI+G I
Sbjct: 758 RSVEVRPVGVTKGAAIDRILGEI 780
>gnl|CDD|183464 PRK12352, PRK12352, putative carbamate kinase; Reviewed.
Length = 316
Score = 26.3 bits (58), Expect = 5.9
Identities = 26/104 (25%), Positives = 40/104 (38%), Gaps = 17/104 (16%)
Query: 32 ERCAIMRLIDTRWAGVAKGVG----IQRIIGRIHMVQVVIEKDFLTTSLSILEEQPMDML 87
E AI LI + + G G ++ G V VI+KD T L+ E D+L
Sbjct: 175 EAPAIKALIQQGFVVIGAGGGGIPVVRTDAGDYQSVDAVIDKDLSTALLA--REIHADIL 232
Query: 88 L---GLDMLRRHQCCIDL-KRNVLRIGTTGTE--TRFLSESELP 125
+ G++ + CI K + TR++ E P
Sbjct: 233 VITTGVE-----KVCIHFGKPQQQALDRVDIATMTRYMQEGHFP 271
>gnl|CDD|173409 PTZ00117, PTZ00117, malate dehydrogenase; Provisional.
Length = 319
Score = 25.8 bits (57), Expect = 9.0
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 6 CCVNGVPVKAFVDSGAQTTIMSAECAERCAIM 37
C VNG+P+ FV GA T E ++ M
Sbjct: 189 CTVNGIPLSDFVKKGAITEKEINEIIKKTRNM 220
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
0.327 0.140 0.420
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,197,180
Number of extensions: 645006
Number of successful extensions: 544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 542
Number of HSP's successfully gapped: 27
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (24.5 bits)