RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17672
(319 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 = 233 bits (597), Expect = 5e-78
Identities = 78/124 (62%), Positives = 100/124 (80%)
Query: 165 EAAMEYNPETFGSVVMLYINCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIMRLIDTRWA 224
+ AME++PE+FG V MLYIN ++NG PVKAFVDSGAQ TIMS CAE+C +MRLID R+
Sbjct: 1 QNAMEHHPESFGKVPMLYINVEINGVPVKAFVDSGAQMTIMSKACAEKCGLMRLIDKRFQ 60
Query: 225 GVAKGVGVQQIIGRIHMVQVAIEKDFLTTSLSILEEQPMDMLLGLDMLRRHECCIDLRKN 284
G+AKGVG Q+I+GRIH+ QV I FL S ++LE+ +D L+GLDML+RH+C IDL++N
Sbjct: 61 GIAKGVGTQKILGRIHLAQVKIGNLFLPCSFTVLEDDDVDFLIGLDMLKRHQCVIDLKEN 120
Query: 285 VLRI 288
VLRI
Sbjct: 121 VLRI 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 = 231 bits (590), Expect = 4e-77
Identities = 79/124 (63%), Positives = 102/124 (82%)
Query: 157 QKNVEANMEAAMEYNPETFGSVVMLYINCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIM 216
Q+NV+ N+E AME+ PE FG V MLYINC+VNG PVKAFVDSGAQT+IMS +CAERC IM
Sbjct: 1 QENVDENLEHAMEHTPEAFGRVTMLYINCEVNGVPVKAFVDSGAQTSIMSPRCAERCGIM 60
Query: 217 RLIDTRWAGVAKGVGVQQIIGRIHMVQVAIEKDFLTTSLSILEEQPMDMLLGLDMLRRHE 276
RL+DTR+AG+A+GVG +I+GR+HM + + FL S +++E+Q MD+L GLDML+RH+
Sbjct: 61 RLLDTRFAGIARGVGTAKILGRVHMADLKLGDLFLPCSFTVIEDQDMDLLFGLDMLKRHQ 120
Query: 277 CCID 280
CCID
Sbjct: 121 CCID 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 = 67.0 bits (164), Expect = 3e-14
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 183 INCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIMRLIDTRWAGVAKGVG-VQQIIGRIHM 241
+ K+NG PV+A VDSGA +S A++ + + V G + +G I
Sbjct: 1 LKGKINGVPVRALVDSGASVNFISESLAKKLGLPPRLLPTPLKVKGANGSSVKTLGVILP 60
Query: 242 VQVAIEKDFLTTSLSILEEQPMDMLLGLDMLR 273
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 = 46.8 bits (111), Expect = 6e-07
Identities = 25/103 (24%), Positives = 55/103 (53%), Gaps = 2/103 (1%)
Query: 183 INCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIM-RLIDTRWAGVAKGVGVQ-QIIGRIH 240
++C+ G ++A VD+G Q ++SA C +R + R++ + A + ++IG+I
Sbjct: 1 VSCQCAGKELRALVDTGCQYNLISAACLDRLGLKERVLKAKAEEEAPSLPTSVKVIGQIE 60
Query: 241 MVQVAIEKDFLTTSLSILEEQPMDMLLGLDMLRRHECCIDLRK 283
+ + + + + S ++++ + LGL L+ +C I+L K
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 = 44.6 bits (106), Expect = 2e-06
Identities = 21/90 (23%), Positives = 36/90 (40%), Gaps = 4/90 (4%)
Query: 183 INCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIMRLIDTRWAGVAKGVGVQQIIGRIHMV 242
+ +NG PV+ +D+GA T++S AER + G + +
Sbjct: 1 VPVTINGKPVRFLLDTGASGTLLSRSLAERLGL--KPTKLTIGRVSTANGTVRAALVRLD 58
Query: 243 QVAIEKDFLT-TSLSILEEQPM-DMLLGLD 270
+ 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 = 42.2 bits (100), Expect = 2e-05
Identities = 29/104 (27%), Positives = 45/104 (43%), Gaps = 19/104 (18%)
Query: 180 MLYINCKVNGYPVKAFVDSGAQTTIMSAKCAERCNI-MRLIDTRWAGVAKG------VGV 232
+ +NG PV+ +D+GA TT++S + AER + + L A G V +
Sbjct: 2 HFVVPVTINGQPVRFLLDTGASTTVISEELAERLGLPLTLGGKVTVQTANGRVRAARVRL 61
Query: 233 QQI-IGRIHMVQVAIEKDFLTTSLSILEEQPM--DMLLGLDMLR 273
+ IG I + V +L + D LLG+D LR
Sbjct: 62 DSLQIGGITLRNVPA---------VVLPGDALGVDGLLGMDFLR 96
>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 = 39.1 bits (92), Expect = 3e-04
Identities = 23/103 (22%), Positives = 42/103 (40%), Gaps = 16/103 (15%)
Query: 182 YINCKVNGYPVKAFVDSGAQTTIMSAKCAERCNIMRLIDTRWAGVAKGVGVQQIIGRIHM 241
I KV G P+KA +D+GA T++ + W + I G+I +
Sbjct: 7 RITVKVGGQPIKALLDTGADDTVIPE---------NDLPGSW-PPWGPTTIGGIGGQIRV 56
Query: 242 VQ---VAIEKDFLTTSLS--ILEEQPMDMLLGLDMLRRHECCI 279
Q + +E + +L P++ +LG D+L + +
Sbjct: 57 KQSIQILVEIGGKKFRGTFLVLPSTPVN-ILGRDLLTQLGAKL 98
>gnl|CDD|176391 cd01796, DDI1_N, DNA damage inducible protein 1 ubiquitin-like
domain. DDI1_N DDI1 (DNA damage inducible protein 1)
has an amino-terminal ubiquitin-like domain, an
retroviral protease-like (RVP-like) domain, and a UBA
(ubiquitin-associated) domain. This CD represents the
amino-terminal ubiquitin-like domain of DDI1.
Length = 71
Score = 36.6 bits (85), Expect = 0.001
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 3 VEQFRLICQDECGIDATDMILLNNGKHLLEDGSCLKQAGVRDGDIIL 49
+E F+ +C+ E GI A+ L+ NG+ L+++ L GV+DGD+++
Sbjct: 22 LENFKALCEAESGIPASQQQLIYNGRELVDNKRLLALYGVKDGDLVV 68
>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 = 36.9 bits (86), Expect = 0.001
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 181 LYINCKVNGYPVKAFVDSGAQTTIMSAKCAERCNI 215
+ + + G VKA VD+GA + +S A R +
Sbjct: 9 VTVEVSIGGVEVKALVDTGATHSFISESLAARLGL 43
>gnl|CDD|176364 cd01769, UBL, Ubiquitin-like domain of UBL. UBLs function by
remodeling the surface of their target proteins,
changing their target's half-life, enzymatic activity,
protein-protein interactions, subcellular localization
or other properties. At least 10 different
ubiquitin-like modifications exist in mammals, and
attachment of different ubls to a target leads to
different biological consequences. Ubl-conjugation
cascades are initiated by activating enzymes, which
also coordinate the ubls with their downstream
pathways.
Length = 69
Score = 35.3 bits (82), Expect = 0.003
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 1 MDVEQFRLICQDECGIDATDMILLNNGKHLLEDGSCLKQAGVRDGDIILV 50
V + + + G+ L+ GK +L+D L G++DG + +
Sbjct: 18 DTVAELKAKIAAKEGVPPEQQRLIYAGK-ILKDDKTLSDYGIQDGSTLHL 66
>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 = 33.2 bits (76), Expect = 0.057
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 2/95 (2%)
Query: 187 VNGYPVKAFVDSGAQTTIMSAKCAERCNIMRLIDTRWA-GVAKGVGVQQIIGRIHMVQVA 245
VN P DSGA + +S R + + L R V G R V +
Sbjct: 28 VNSIPATVLFDSGASHSFISQAFVGR-HGLPLEALRTPMLVHSPGGDMTATHRCPSVNIE 86
Query: 246 IEKDFLTTSLSILEEQPMDMLLGLDMLRRHECCID 280
I+ +L +L+ + +D++LG+D L +H+ ID
Sbjct: 87 IQGVDFPANLILLDSKDLDVILGMDWLAQHKGVID 121
>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 = 32.6 bits (75), Expect = 0.084
Identities = 26/97 (26%), Positives = 44/97 (45%), Gaps = 7/97 (7%)
Query: 182 YINCKVNGYPVKAFVDSGAQTTIMSAKCAERC--NIMRLIDTRWAGVAKGVGVQQIIGRI 239
Y +VNG V+ VD+GA + ++ + A+R ++ RL T A G Q R+
Sbjct: 13 YATGRVNGRNVRFLVDTGATSVALNEEDAQRLGLDLNRLGYTVTVSTANG---QIKAARV 69
Query: 240 HMVQVAIEKDFLTT--SLSILEEQPMDMLLGLDMLRR 274
+ +VAI + ++ + LLG+ L R
Sbjct: 70 TLDRVAIGGIVVNDVDAMVAEGGALSESLLGMSFLNR 106
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 31.4 bits (72), Expect = 0.087
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 3 VEQFRLICQDECGIDATDMILLNNGKHLLEDGSCLKQAGVRDGDII 48
V + + +D+ GI L+ +GK +LED + L + G++DG +
Sbjct: 18 VSELKEKIEDKEGIPVDQQRLIFSGK-VLEDDTTLSEYGIQDGSTL 62
>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 = 29.5 bits (67), Expect = 0.48
Identities = 6/22 (27%), Positives = 13/22 (59%)
Query: 186 KVNGYPVKAFVDSGAQTTIMSA 207
+NG + +D+GA +I++
Sbjct: 4 YINGKLFEGLLDTGADVSIIAE 25
>gnl|CDD|226106 COG3577, COG3577, Predicted aspartyl protease [General function
prediction only].
Length = 215
Score = 30.4 bits (69), Expect = 0.88
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 182 YINCKVNGYPVKAFVDSGAQTTIMSAKCAER 212
N +VNG V VD+GA + ++ + A R
Sbjct: 107 EANGRVNGKKVDFLVDTGATSVALNEEDARR 137
>gnl|CDD|183035 PRK11199, tyrA, bifunctional chorismate mutase/prephenate
dehydrogenase; Provisional.
Length = 374
Score = 30.6 bits (70), Expect = 1.1
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 79 QDPAHVRDLLLACPDQLALLKQNNPRLSEALST----GKDAFTKVFKE 122
QDP D++++ P+ LAL+K+ R EAL K AF F++
Sbjct: 298 QDPQLYADIIMSSPENLALIKRYYQRFGEALELLEQGDKQAFIDSFRK 345
>gnl|CDD|213301 cd05935, LC_FACS_like, Putative long-chain fatty acid CoA ligase.
The members of this family are putative long-chain
fatty acyl-CoA synthetases, which catalyze the
ATP-dependent activation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. Fatty
acyl-CoA synthetases are responsible for fatty acid
degradation as well as physiological regulation of
cellular functions via the production of fatty acyl-CoA
esters.
Length = 430
Score = 30.4 bits (69), Expect = 1.3
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 35 SCLKQAGVRDGDIILVAMPGRGPTYHVA 62
L++ GVR GD + + M P + +A
Sbjct: 16 GLLQEKGVRKGDRVALYMQN-SPQFVIA 42
>gnl|CDD|219013 pfam06413, Neugrin, Neugrin. This family consists of several mouse
and human neugrin proteins. Neugrin and m-neugrin are
mainly expressed in neurons in the nervous system, and
are thought to play an important role in the process of
neuronal differentiation.
Length = 225
Score = 29.5 bits (66), Expect = 2.2
Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 1/79 (1%)
Query: 103 PRLSEALSTGKDAFTKVFKEQLVEREKRQ-KQKIKLMNAHPFDTHAQRLIAEEIRQKNVE 161
PRL+E D +V K + V +R+ KQ K++ +L K +
Sbjct: 33 PRLAEGFDVSTDVIRRVLKSKFVPTLERKLKQDQKVLKKAGLARQILQLPGPGPGPKLLP 92
Query: 162 ANMEAAMEYNPETFGSVVM 180
A + ++ GS++M
Sbjct: 93 AGQQDRLKLPGSVSGSLLM 111
>gnl|CDD|225862 COG3325, ChiA, Chitinase [Carbohydrate transport and metabolism].
Length = 441
Score = 29.3 bits (66), Expect = 3.0
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 3/62 (4%)
Query: 86 DLLLACPDQLALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQ---KQKIKLMNAHP 142
D L L LK P L +S G + + F + + R+ K ++ M +
Sbjct: 108 DPLKGHFGALFDLKATYPDLKTLISIGGWSDSGGFSDMAADDASRENFAKSAVEFMRTYG 167
Query: 143 FD 144
FD
Sbjct: 168 FD 169
>gnl|CDD|147008 pfam04639, Baculo_E56, Baculoviral E56 protein, specific to ODV
envelope. This family represents the E56 protein, which
is localises to the occlusion derived virus (ODV)
envelope, but not to the budded virus (BV) envelope.
Length = 308
Score = 28.8 bits (65), Expect = 3.3
Identities = 15/59 (25%), Positives = 21/59 (35%), Gaps = 11/59 (18%)
Query: 57 PTYHVAQSRHTAPHRSFMTAQLQDPAHVRDLLLACPDQLALLKQNNPRLSEALSTGKDA 115
T H Q+R A + + P V + L NPRL++ L K A
Sbjct: 69 ATLHSLQTRKNAVKNNHPETNTRTPEGVENAL-----------NQNPRLNDYLQNLKTA 116
>gnl|CDD|129230 TIGR00124, cit_ly_ligase, [citrate (pro-3S)-lyase] ligase. ATP is
cleaved to AMP and pyrophosphate during the reaction.
The carboxyl end is homologous to a number of
cytidyltransferases that also release pyrophosphate
[Energy metabolism, Fermentation, Protein fate, Protein
modification and repair].
Length = 332
Score = 29.0 bits (65), Expect = 3.5
Identities = 19/74 (25%), Positives = 31/74 (41%), Gaps = 16/74 (21%)
Query: 88 LLACPDQLALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQKQKIK--LMNAHPFDT 145
L DQ LL+ + RL ST + + + KI +MNA+PF T
Sbjct: 107 LAEAKDQGVLLENSATRLKRYCST-------------LPKPRTPGNKIGSIVMNANPF-T 152
Query: 146 HAQRLIAEEIRQKN 159
+ R + E+ ++
Sbjct: 153 NGHRYLIEQAARQC 166
>gnl|CDD|180481 PRK06231, PRK06231, F0F1 ATP synthase subunit B; Validated.
Length = 205
Score = 28.3 bits (63), Expect = 4.5
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 5/80 (6%)
Query: 95 LALLKQNNPRLSEALSTGKDAFTKVFKEQL-----VEREKRQKQKIKLMNAHPFDTHAQR 149
LL+ R AL+ K+ + E L +E+E ++ + + A +R
Sbjct: 99 QQLLENAKQRHENALAQAKEIIDQANYEALQLKSELEKEANRQANLIIFQARQEIEKERR 158
Query: 150 LIAEEIRQKNVEANMEAAME 169
+ E++++++VE M AA E
Sbjct: 159 ELKEQLQKESVELAMLAAEE 178
>gnl|CDD|214753 smart00636, Glyco_18, Glyco_18 domain.
Length = 334
Score = 28.4 bits (64), Expect = 4.9
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 94 QLALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQK---QKIKLMNAHPFD 144
QL LK+ NP L LS G + F L + R+K + + + FD
Sbjct: 56 QLKALKKKNPGLKVLLSIGGWTESDNFSSMLSDPASRKKFIDSIVSFLKKYGFD 109
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 26.3 bits (58), Expect = 5.7
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 1 MDVEQFRLICQDECGIDATDMILLNNGKHLLEDGSCLKQAGVRDGDIILVAMP 53
V + + G+ LL NGK L D L+ G++DGD +++
Sbjct: 18 TTVADLKEKLAKKLGLPPEQQRLLVNGKIL-PDSLTLEDYGLQDGDELVLVPR 69
>gnl|CDD|233654 TIGR01953, NusA, transcription termination factor NusA. This model
describes NusA, or N utilization substance protein A, a
bacterial transcription termination factor. It binds to
RNA polymerase alpha subunit and promotes termination at
certain RNA hairpin structures. It is named for the
interaction in E. coli of phage lambda antitermination
protein N with the N-utilization substance, consisting
of NusA, NusB, NusE (ribosomal protein S10), and nusG.
This model represents a region of NusA shared in all
bacterial forms, and including an S1 (pfam00575) and a
KH (pfam00013) RNA binding domains. Proteobacterial
forms have an additional C-terminal region, not included
in this model, with two repeats of 50-residue domain
rich in acidic amino acids [Transcription, Transcription
factors].
Length = 341
Score = 28.4 bits (64), Expect = 6.0
Identities = 16/92 (17%), Positives = 41/92 (44%), Gaps = 3/92 (3%)
Query: 96 ALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQKQKIKLMNAHPFDTHAQRLIAEEI 155
AL K+ + + ++A + +K+ +++ + I + + ++ + EE+
Sbjct: 8 ALAKEKGISIETVIEAIEEALEQAYKKTF-GQDENVEVNIDRKTGD-INVYRRKEVVEEV 65
Query: 156 RQKNVEANMEAAMEYNPET-FGSVVMLYINCK 186
++E ++E A E +P+ G V I +
Sbjct: 66 EDPSLEISLEDAREIDPDVQIGDEVKKEIPPE 97
>gnl|CDD|148143 pfam06353, DUF1062, Protein of unknown function (DUF1062). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 142
Score = 27.3 bits (61), Expect = 6.1
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 6/60 (10%)
Query: 95 LALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQKQKIKLMNAHPFDTHAQRLIAEE 154
LA+L++N L E ++ K L +I+L PF RL+AEE
Sbjct: 59 LAVLRRNRAELDEFPE------FEIAKRLLTGIASHAAIEIQLRLEFPFSLRLDRLLAEE 112
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 27.4 bits (62), Expect = 6.2
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 12/61 (19%)
Query: 118 KVFKEQLVEREKRQKQKIKLMNAHPFDTHAQRLIAEEIRQKNVEANMEAAMEYNPETFGS 177
K + + E E + +++ A+ L AE++ V +A + FGS
Sbjct: 45 KQLEARRAELEAKAAEELA---------EAEAL-AEKLEGLTVTIKAKAGEDGK--LFGS 92
Query: 178 V 178
V
Sbjct: 93 V 93
>gnl|CDD|225735 COG3194, DAL3, Ureidoglycolate hydrolase [Nucleotide transport and
metabolism].
Length = 168
Score = 27.7 bits (62), Expect = 6.4
Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 15/54 (27%)
Query: 252 TTSLSILEEQPMDMLLGLDMLRRHECCIDLRKNVLRIGTTGTETKFLPERELPS 305
T ++I QP L + ML RH G++ F+P P
Sbjct: 53 RTLINIFRAQPAVHPLTISMLERHPL--------------GSQA-FIPLSGRPF 91
>gnl|CDD|163647 cd07404, MPP_MS158, Microscilla MS158 and related proteins,
metallophosphatase domain. MS158 is an uncharacterized
Microscilla protein with a metallophosphatase domain.
Microscilla proteins MS152, and MS153 are also included
in this family. The domain present in members of this
family belongs to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 166
Score = 27.6 bits (62), Expect = 6.6
Identities = 13/48 (27%), Positives = 16/48 (33%), Gaps = 8/48 (16%)
Query: 55 RGPTYHVAQSRHTAPHRSFMTAQLQDP-----AHVRDLLLACPDQLAL 97
RG T V + H AP + Q D V L D + L
Sbjct: 96 RGKT--VVVT-HHAPSPLSLAPQYGDSLVNAAFAVDLDDLILADPIDL 140
>gnl|CDD|235730 PRK06187, PRK06187, long-chain-fatty-acid--CoA ligase; Validated.
Length = 521
Score = 27.8 bits (63), Expect = 8.5
Identities = 25/122 (20%), Positives = 36/122 (29%), Gaps = 40/122 (32%)
Query: 36 CLKQAGVRDGDIILVAMPGRGPTYHVAQSRHTAPHRSFMTAQLQ------DPAHVRDLLL 89
+ D+ LV +P +HV P+ + M Q DP ++ DL+
Sbjct: 199 VCAWLKLSRDDVYLVIVPM----FHVHAW--GLPYLALMAGAKQVIPRRFDPENLLDLIE 252
Query: 90 --------ACPDQL-ALLKQNNPR----------------LSEALSTGKDAFTKVFKEQL 124
A P LLK L AL F + F L
Sbjct: 253 TERVTFFFAVPTIWQMLLKAPRAYFVDFSSLRLVIYGGAALPPALL---REFKEKFGIDL 309
Query: 125 VE 126
V+
Sbjct: 310 VQ 311
>gnl|CDD|176407 cd01812, BAG1_N, Ubiquitin-like domain of BAG1. BAG1_N
N-terminal ubiquitin-like (Ubl) domain of the BAG1
protein. This domain occurs together with the BAG
domain and is closely related to the Ubl domain of a
family of deubiquitinases that includes Rpn11, UBP6
(USP14), USP7 (HAUSP).
Length = 71
Score = 25.7 bits (57), Expect = 8.9
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 15 GIDATDMILLNNGKHLLEDGSCLKQAGVRDGDIILVA 51
G++ D L+ GK +D L +GV+DG +++
Sbjct: 34 GVEPRDQKLIFKGKER-DDAETLDMSGVKDGSKVMLL 69
>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein. This
model represents a group of paralogous families in
plasmodium species alternately annotated as reticulocyte
binding protein, 235-kDa family protein and rhoptry
protein. Rhoptry protein is localized on the cell surface
and is extremely large (although apparently lacking in
repeat structure) and is important for the process of
invasion of the RBCs by the parasite. These proteins are
found in P. falciparum, P. vivax and P. yoelii.
Length = 2757
Score = 28.1 bits (62), Expect = 9.7
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 93 DQLALLKQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQKQKIKLMNAHPFDTHAQRLIA 152
D+ +L + LS + GK +F E++ E +K+ + IK M A+ D
Sbjct: 1205 DKTSLEEVKGINLSYGKNLGK-----LFLEKIDEEKKKSEHMIKAMEAYIEDL------- 1252
Query: 153 EEIRQKN--VEANMEAAMEYNPE 173
+EI++K+ +E M M+ E
Sbjct: 1253 DEIKEKSPEIENEMGIEMDIKAE 1275
>gnl|CDD|235621 PRK05842, flgD, flagellar basal body rod modification protein;
Reviewed.
Length = 295
Score = 27.7 bits (61), Expect = 9.8
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 99 KQNNPRLSEALSTGKDAFTKVFKEQLVEREKRQKQKIKLMNAHPFDTHAQRLIAEEIRQK 158
K+ P ++ L K+AF K+F EQL + + M T +L E++++
Sbjct: 18 KKEQPTIANGLD--KNAFMKLFLEQL-----KNQDPTAPMETDKIITQTAQLTQVEMQEE 70
Query: 159 NVEANME--AAMEYNPET 174
N + E +AM+ N ET
Sbjct: 71 NKKTMQEVASAMKSNKET 88
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 0.135 0.395
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,223,178
Number of extensions: 1564764
Number of successful extensions: 1496
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1489
Number of HSP's successfully gapped: 42
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
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: 59 (26.5 bits)