RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3800
(133 letters)
>gnl|CDD|239236 cd02908, Macro_Appr_pase_like, Macro domain, Appr-1"-pase_like
family. The macro domain is a high-affinity ADP-ribose
binding module found in a variety of proteins as a
stand-alone domain or in combination with other domains
like in histone macroH2A and some PARPs (poly ADP-ribose
polymerases). Some macro domains recognize poly
ADP-ribose as a ligand. Previously identified as
displaying an Appr-1"-p (ADP-ribose-1"-monophosphate)
processing activity, the macro domain may play roles in
distinct ADP-ribose pathways, such as the
ADP-ribosylation of proteins, an important
post-translational modification which occurs in DNA
repair, transcription, chromatin biology, and long-term
memory formation, among other processes. This family is
composed of uncharacterized proteins that show
similarity to Appr-1"-pase, containing conserved
putative active site residues. Appr-1"-pase is a
phosphatase specific for ADP-ribose-1"-monophosphate.
Length = 165
Score = 133 bits (338), Expect = 4e-41
Identities = 50/85 (58%), Positives = 60/85 (70%), Gaps = 11/85 (12%)
Query: 7 IDGAIHRAAGPQLKEECRTLNGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGE---- 62
+DGAIHRAAGP+L EECR L GC TG+A IT+GYNLP AK+VIHTVGPV
Sbjct: 31 VDGAIHRAAGPELLEECRELRGCPTGEAVITSGYNLP------AKYVIHTVGPVWRGGQH 84
Query: 63 -KPALLKSAYQRSLEVMKQNNLRSI 86
+ LL S Y+ SLE+ ++N LRSI
Sbjct: 85 NEAELLASCYRNSLELARENGLRSI 109
>gnl|CDD|216634 pfam01661, Macro, Macro domain. This domain is an ADP-ribose
binding module. It is found in a number of otherwise
unrelated proteins. It is found at the C-terminus of
the macro-H2A histone protein. This domain is found in
the non-structural proteins of several types of ssRNA
viruses such as NSP3 from alphaviruses. This domain is
also found on its own in a family of proteins from
bacteria, archaebacteria, and eukaryotes.
Length = 117
Score = 101 bits (253), Expect = 7e-29
Identities = 43/89 (48%), Positives = 55/89 (61%), Gaps = 15/89 (16%)
Query: 7 IDGAIHRAAGPQLKEECRTL---NGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVG-- 61
+ GAIHRAAGP L EECR L GC TG+A +T G NLP AK+VIH VGP+
Sbjct: 14 VAGAIHRAAGPALLEECRELKKQGGCPTGEAVVTPGGNLP------AKYVIHAVGPIWRH 67
Query: 62 ----EKPALLKSAYQRSLEVMKQNNLRSI 86
E+ LL SAY+ +LE+ + ++SI
Sbjct: 68 GGGEEEEELLASAYRNALELANELGIKSI 96
>gnl|CDD|234759 PRK00431, PRK00431, RNase III inhibitor; Provisional.
Length = 177
Score = 101 bits (254), Expect = 3e-28
Identities = 44/88 (50%), Positives = 53/88 (60%), Gaps = 15/88 (17%)
Query: 8 DGAIHRAAGPQLKEECRTLN----GCETGDAKITAGYNLPAKLPINAKHVIHTVGPV--- 60
DGAIHRAAGP++ EECR L C TG+A IT+ LP AK+VIHTVGPV
Sbjct: 35 DGAIHRAAGPEILEECRELRQQQGPCPTGEAVITSAGRLP------AKYVIHTVGPVWRG 88
Query: 61 --GEKPALLKSAYQRSLEVMKQNNLRSI 86
+ LL SAY+ SL + + LRSI
Sbjct: 89 GEDNEAELLASAYRNSLRLAAELGLRSI 116
>gnl|CDD|239233 cd02905, Macro_GDAP2_like, Macro domain, GDAP2_like family. The
macro domain is a high-affinity ADP-ribose binding
module found in a variety of proteins as a stand-alone
domain or in combination with other domains like in
histone macroH2A and some PARPs (poly ADP-ribose
polymerases). Some macro domains recognize poly
ADP-ribose as a ligand. Previously identified as
displaying an Appr-1"-p (ADP-ribose-1"-monophosphate)
processing activity, the macro domain may play roles in
distinct ADP-ribose pathways, such as the
ADP-ribosylation of proteins, an important
post-translational modification which occurs in DNA
repair, transcription, chromatin biology, and long-term
memory formation, among other processes. This family
contains proteins similar to human GDAP2, the
ganglioside induced differentiation associated protein
2, whose gene is expressed at a higher level in
differentiated Neuro2a cells compared with
non-differentiated cells. GDAP2 contains an N-terminal
macro domain and a C-terminal Sec14p-like lipid binding
domain. It is specifically expressed in brain and
testis.
Length = 140
Score = 79.0 bits (195), Expect = 6e-20
Identities = 35/88 (39%), Positives = 50/88 (56%), Gaps = 12/88 (13%)
Query: 11 IHRAAGPQLKEECRTLNGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGEKPALLKSA 70
I AG +L+EE +TL GC TG+AK+T GYNLP A+ +IHTVGP
Sbjct: 36 IFARAGSELREEIQTLGGCRTGEAKLTKGYNLP------ARFIIHTVGPK------YNVK 83
Query: 71 YQRSLEVMKQNNLRSILEVMKQNNLRSI 98
Y+ + E + R++L++ K+ L SI
Sbjct: 84 YRTAAENALYSCYRNVLQLAKELGLESI 111
>gnl|CDD|235225 PRK04143, PRK04143, hypothetical protein; Provisional.
Length = 264
Score = 81.2 bits (201), Expect = 1e-19
Identities = 38/92 (41%), Positives = 51/92 (55%), Gaps = 18/92 (19%)
Query: 7 IDGAIHRAAGPQLKEECRTL-----NGCETGDAKITAGYNLPAKLPINAKHVIHTVGP-V 60
ID AIH AG QL+ +C + TG AKIT YNLP AK+VIHTVGP +
Sbjct: 119 IDNAIHTFAGVQLRLDCAEIMTEQGRKEATGQAKITRAYNLP------AKYVIHTVGPII 172
Query: 61 GEKPA------LLKSAYQRSLEVMKQNNLRSI 86
++P LL S Y+ L++ ++ L+SI
Sbjct: 173 RKQPVSPIRADLLASCYRSCLKLAEKAGLKSI 204
>gnl|CDD|239234 cd02906, Macro_1, Macro domain, Unknown family 1. The macro domain
is a high-affinity ADP-ribose binding module found in a
variety of proteins as a stand-alone domain or in
combination with other domains like in histone macroH2A
and some PARPs (poly ADP-ribose polymerases). Some macro
domains recognize poly ADP-ribose as a ligand.
Previously identified as displaying an Appr-1"-p
(ADP-ribose-1"-monophosphate) processing activity, the
macro domain may play roles in distinct ADP-ribose
pathways, such as the ADP-ribosylation of proteins, an
important post-translational modification which occurs
in DNA repair, transcription, chromatin biology, and
long-term memory formation, among other processes. This
family is composed of uncharacterized proteins
containing a macro domain, either as a stand-alone
domain or in addition to a C-terminal SIR2 (silent
information regulator 2) domain.
Length = 147
Score = 77.1 bits (190), Expect = 5e-19
Identities = 39/92 (42%), Positives = 49/92 (53%), Gaps = 18/92 (19%)
Query: 7 IDGAIHRAAGPQLKEECRTL-----NGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVG 61
ID IH AGPQL++ C L TG AKIT GYNLP AK+VIHTVGP+
Sbjct: 36 IDNIIHTFAGPQLRQACFELMTKQGREEPTGQAKITPGYNLP------AKYVIHTVGPII 89
Query: 62 EKPA-------LLKSAYQRSLEVMKQNNLRSI 86
E+ LL Y L++ ++ L+SI
Sbjct: 90 ERGLTTPIHRDLLAKCYLSCLDLAEKAGLKSI 121
>gnl|CDD|225021 COG2110, COG2110, Predicted phosphatase homologous to the
C-terminal domain of histone macroH2A1 [General function
prediction only].
Length = 179
Score = 72.0 bits (177), Expect = 8e-17
Identities = 37/91 (40%), Positives = 51/91 (56%), Gaps = 17/91 (18%)
Query: 7 IDGAIHRAAGPQLKEECRTL------NGCETGDAKITAGYNLPAKLPINAKHVIHTVGPV 60
+ GAIHRAAGPQL+EEC + G+A IT LP AK+VIHTVGP
Sbjct: 34 VAGAIHRAAGPQLEEECAEIAPKRGGGRIPVGEAVITEAGRLP------AKYVIHTVGPS 87
Query: 61 G-----EKPALLKSAYQRSLEVMKQNNLRSI 86
++ LL +AY+ +L + K+ +RS+
Sbjct: 88 WRGGSKDEAELLAAAYRAALRLAKEAGVRSV 118
>gnl|CDD|214701 smart00506, A1pp, Appr-1"-p processing enzyme. Function determined
by Martzen et al. Extended family detected by reciprocal
PSI-BLAST searches (unpublished results, and Pehrson &
Fuji).
Length = 133
Score = 65.4 bits (160), Expect = 1e-14
Identities = 38/88 (43%), Positives = 48/88 (54%), Gaps = 14/88 (15%)
Query: 7 IDGAIHRAAGPQL-KEECRTLNG--CETGDAKITAGYNLPAKLPINAKHVIHTVGPVG-- 61
+ GAI RAAG L KEE R L G C G A +T G NLPA K+VIH VGP
Sbjct: 31 VAGAIARAAGKALSKEEVRKLAGGECPVGTAVVTEGGNLPA------KYVIHAVGPRASG 84
Query: 62 ---EKPALLKSAYQRSLEVMKQNNLRSI 86
E LL++AY+ LE+ + + S+
Sbjct: 85 HSKEGFELLENAYRNCLELAIELGITSV 112
>gnl|CDD|239150 cd02749, Macro, Macro domain, a high-affinity ADP-ribose binding
module found in a variety of proteins as a stand-alone
domain or in combination with other domains like in
histone macroH2A and some PARPs (poly ADP-ribose
polymerases). Some macro domains recognize poly
ADP-ribose as a ligand. Previously identified as
displaying an Appr-1"-p (ADP-ribose-1"-monophosphate)
processing activity, the macro domain may play roles in
distinct ADP-ribose pathways, such as the
ADP-ribosylation of proteins, an important
post-translational modification which occurs in DNA
repair, transcription, chromatin biology, and long-term
memory formation, among other processes.
Length = 147
Score = 59.7 bits (145), Expect = 2e-12
Identities = 30/89 (33%), Positives = 49/89 (55%), Gaps = 14/89 (15%)
Query: 7 IDGAIHRAAGPQLKEECRTL---NGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGEK 63
++ AI + AG +L+EE + L + G+A +T GYNL AK++IH VGP +
Sbjct: 32 VNLAISKKAGKELEEESKKLRKELELQVGEAVLTKGYNLD-----GAKYLIHIVGPKYNQ 86
Query: 64 ------PALLKSAYQRSLEVMKQNNLRSI 86
LLK+AY+ L+ ++ ++SI
Sbjct: 87 GNNKAAFELLKNAYENCLKEAEEKGIKSI 115
>gnl|CDD|239235 cd02907, Macro_Af1521_BAL_like, Macro domain, Af1521- and BAL-like
family. The macro domain is a high-affinity ADP-ribose
binding module found in a variety of proteins as a
stand-alone domain or in combination with other domains
like in histone macroH2A and some PARPs (poly ADP-ribose
polymerases). Some macro domains recognize poly
ADP-ribose as a ligand. Previously identified as an
Appr-1"-p (ADP-ribose-1"-monophosphate) processing
activity, the macro domain may play roles in distinct
ADP-ribose pathways, such as the ADP-ribosylation of
proteins, an important post-translational modification
which occurs in DNA repair, transcription, chromatin
biology, and long-term memory formation, among other
processes. The macro domains in this family show
similarity to Af1521, a protein from Archaeoglobus
fulgidus containing a stand-alone macro domain. Af1521
binds ADP-ribose and exhibits phosphatase activity
toward Appr-1"-p. Also included in this family are the
N-terminal (or first) macro domains of BAL (B-aggressive
lymphoma) proteins which contain multiple macro domains.
Most BAL proteins also contain a C-terminal PARP active
site and are also named as PARPs. Human BAL1 (or
PARP-9) was originally identified as a risk-related gene
in diffuse large B-cell lymphoma that promotes malignant
B-cell migration. Some BAL family proteins exhibit PARP
activity. Poly (ADP-ribosyl)ation is an immediate
DNA-damage-dependent post-translational modification of
histones and other nuclear proteins. BAL proteins may
also function as transcription repressors.
Length = 175
Score = 59.6 bits (145), Expect = 5e-12
Identities = 30/88 (34%), Positives = 40/88 (45%), Gaps = 16/88 (18%)
Query: 9 GAIHRAAGPQLKEEC----RTLNGCETGDAKITAGYNLPAKLPINAKHVIHTVGPV---- 60
AI +A GP+++EE R TG+ +T+ LP K +VIH VGP
Sbjct: 35 LAIVKAGGPEIQEESDEYVRKNGPVPTGEVVVTSAGKLPCK------YVIHAVGPRWSGG 88
Query: 61 --GEKPALLKSAYQRSLEVMKQNNLRSI 86
E LK A SL ++ LRSI
Sbjct: 89 EAEECVEKLKKAILNSLRKAEELGLRSI 116
>gnl|CDD|239231 cd02903, Macro_BAL_like, Macro domain, BAL_like family. The macro
domain is a high-affinity ADP-ribose binding module
found in a variety of proteins as a stand-alone domain
or in combination with other domains like in histone
macroH2A and some PARPs (poly ADP-ribose polymerases).
Some macro domains recognize poly ADP-ribose as a
ligand. Previously identified as displaying an Appr-1"-p
(ADP-ribose-1"-monophosphate) processing activity, the
macro domain may play roles in distinct ADP-ribose
pathways, such as the ADP-ribosylation of proteins, an
important post-translational modification which occurs
in DNA repair, transcription, chromatin biology, and
long-term memory formation, among other processes.
Members of this family show similarity to BAL
(B-aggressive lymphoma) proteins, which contain one to
three macro domains. Most BAL family macro domains
belong to this family except for the most N-terminal
domain in multiple-domain containing proteins. Most BAL
proteins also contain a C-terminal PARP active site and
are also named as PARPs. Human BAL1 (or PARP-9) was
originally identified as a risk-related gene in diffuse
large B-cell lymphoma that promotes malignant B-cell
migration. Some BAL family proteins exhibit PARP
activity. Poly (ADP-ribosyl)ation is an immediate
DNA-damage-dependent post-translational modification of
histones and other nuclear proteins. BAL proteins may
also function as transcription repressors.
Length = 137
Score = 49.6 bits (119), Expect = 1e-08
Identities = 28/80 (35%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 10 AIHRAAGPQLKEECRTLN-GCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGEKPAL-- 66
AI R AGP+L++E G G +T G NLP K+V H V P AL
Sbjct: 36 AILRKAGPELQKELDKAKLGQTVGSVIVTKGGNLP------CKYVYHVVLPNWSNGALKI 89
Query: 67 LKSAYQRSLEVMKQNNLRSI 86
LK LE ++ + SI
Sbjct: 90 LKDIVSECLEKCEELSYTSI 109
>gnl|CDD|239446 cd03330, Macro_2, Macro domain, Unknown family 2. The macro domain
is a high-affinity ADP-ribose binding module found in a
variety of proteins as a stand-alone domain or in
combination with other domains like in histone macroH2A
and some PARPs (poly ADP-ribose polymerases). Some macro
domains recognize poly ADP-ribose as a ligand.
Previously identified as displaying an Appr-1"-p
(ADP-ribose-1"-monophosphate) processing activity, the
macro domain may play roles in distinct ADP-ribose
pathways, such as the ADP-ribosylation of proteins, an
important post-translational modification which occurs
in DNA repair, transcription, chromatin biology, and
long-term memory formation, among other processes. This
family is composed of uncharacterized proteins
containing a stand-alone macro domain.
Length = 133
Score = 41.7 bits (98), Expect = 1e-05
Identities = 25/90 (27%), Positives = 38/90 (42%), Gaps = 15/90 (16%)
Query: 9 GAIHRAAGPQLKEECRTLNGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGEKPALLK 68
GAI RA G ++ E G+A IT +LP A++VIH E+P
Sbjct: 33 GAIKRAGGSVIEREAVRKAPIPVGEAVITGAGDLP------ARYVIHA--ATMEEPG--- 81
Query: 69 SAYQRSLEVMKQNNLRSILEVMKQNNLRSI 98
RS E + R+ L + + + S+
Sbjct: 82 ----RSSEESVRKATRAALALADELGIESV 107
>gnl|CDD|215334 PLN02623, PLN02623, pyruvate kinase.
Length = 581
Score = 28.4 bits (63), Expect = 1.1
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 7/56 (12%)
Query: 30 ETGDAKITAGYNLPAKLPINAKHVIHTVG-------PVGEKPALLKSAYQRSLEVM 78
E DA + +G K P+ A V+HTV P G P L A++ + M
Sbjct: 409 EGADAVMLSGETAHGKFPLKAVKVMHTVALRTEATLPEGTTPPNLGQAFKNHMSEM 464
>gnl|CDD|213736 TIGR02773, addB_Gpos, helicase-exonuclease AddAB, AddB subunit.
DNA repair is accomplished by several different systems
in prokaryotes. Recombinational repair of
double-stranded DNA breaks involves the RecBCD pathway
in some lineages, and AddAB (also called RexAB) in
other. The AddA protein is conserved between the
firmicutes and the alphaproteobacteria, while the
partner protein is not. Nevertheless, the partner is
designated AddB in both systems. This model describes
the AddB protein as found Bacillus subtilis and related
species. Although the RexB protein of Streptococcus and
Lactococcus is considered to be orthologous,
functionally equivalent, and merely named differently,
all members of this protein family have a P-loop
nucleotide binding motif GxxGxGK[ST] at the N-terminus,
unlike RexB proteins, and a CxxCxxxxxC motif at the
C-terminus, both of which may be relevant to function
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1160
Score = 27.8 bits (62), Expect = 2.0
Identities = 20/92 (21%), Positives = 37/92 (40%), Gaps = 5/92 (5%)
Query: 20 KEECRTLNGCETGDAKITAGYNLPAKLPINAKHVIHTVGPVGEKPALLKSAYQRSLEVMK 79
K R + + L + P K + H +PA+ + Q SL + +
Sbjct: 251 KTYYRLKQLAKELGIDVEEPIFLNTERPTKNKELAHLEKQFDARPAIAYAEKQESLSIFQ 310
Query: 80 QNNLRSILEVMKQNNLRSIDILKGRQQKWRYR 111
NN R+ +E + + LR + R + +RY+
Sbjct: 311 ANNRRAEVEGVAREILRLV-----RDKGYRYK 337
>gnl|CDD|227441 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 26.0 bits (57), Expect = 7.0
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 43 PAKLPINAKHVIHTVGPVGEKPALLKSAYQRSLEVMKQNNLRSILEVMKQNNLRS----I 98
P K+ + ++TVG G P + + V+ + R+ L+ + N S +
Sbjct: 810 PIKVNVRVGQAVNTVGQAGR-PKKITGWQTHTTPVLLSHKERAELDTDEYNVCTSYIEGV 868
Query: 99 DILK 102
ILK
Sbjct: 869 VILK 872
>gnl|CDD|185317 PRK15419, PRK15419, proline:sodium symporter PutP; Provisional.
Length = 502
Score = 25.7 bits (56), Expect = 8.3
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 87 LEVMKQNNLRSIDILKG 103
LEV+KQ ++ ++D+LKG
Sbjct: 216 LEVIKQKSIENVDMLKG 232
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 0.407
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,613,452
Number of extensions: 549005
Number of successful extensions: 482
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 24
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
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 (21.8 bits)
S2: 53 (24.2 bits)