RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15590
(217 letters)
>gnl|CDD|146632 pfam04099, Sybindin, Sybindin-like family. Sybindin is a
physiological syndecan-2 ligand on dendritic spines, the
small protrusions on the surface of dendrites that
receive the vast majority of excitatory synapses.
Length = 135
Score = 165 bits (421), Expect = 8e-53
Identities = 66/109 (60%), Positives = 79/109 (72%), Gaps = 1/109 (0%)
Query: 102 RMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDT 161
++TTNE LA M + L AI+S+LSP P SSGIE LE DTFKLHC QTLTG+KF++V D
Sbjct: 27 KLTTNEYKLLAGMLHSLHAISSKLSPLPGSSGIESLETDTFKLHCLQTLTGIKFVLVTDP 86
Query: 162 NQS-GLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 209
D +L+K YELY+DY LKNPFYSLEMPIRCELFD L ++
Sbjct: 87 GTGPNRDSLLRKYYELYSDYVLKNPFYSLEMPIRCELFDEKLDQYVRSL 135
Score = 34.2 bits (79), Expect = 0.016
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 3 IYGVYIVSKSGGLIFNYDHNVPKIENAVT 31
I+ +YI +++GGLI+ + + PK E +T
Sbjct: 1 IHSLYIFNRAGGLIYYKEWHRPKQEGKLT 29
>gnl|CDD|227451 COG5122, TRS23, Transport protein particle (TRAPP) complex subunit
[Intracellular trafficking and secretion].
Length = 134
Score = 119 bits (299), Expect = 2e-34
Identities = 48/108 (44%), Positives = 64/108 (59%)
Query: 102 RMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDT 161
+ +NE + LAS + + AI +Q P P SSG VL F + +QT TG KF+ V +
Sbjct: 27 ELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEK 86
Query: 162 NQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 209
L+KIY LY+DY KNPFYS EMPI+C LFD HL+ + + H
Sbjct: 87 RTVNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEGH 134
>gnl|CDD|218183 pfam04628, Sedlin_N, Sedlin, N-terminal conserved region.
Mutations in this protein are associated with the
X-linked spondyloepiphyseal dysplasia tarda syndrome
(OMIM:313400). This family represents an N-terminal
conserved region.
Length = 127
Score = 45.3 bits (108), Expect = 2e-06
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 147 YQTLTGVKFMIVGDT---NQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQ 203
Y T T +KF+++ D+ + ++++ELY + NPFY PIR FD ++
Sbjct: 64 YVTNTHIKFILLHDSSTERDDDIKQFFREVHELYIKTLM-NPFYEPNDPIRSPAFDAKVR 122
Query: 204 NL 205
L
Sbjct: 123 RL 124
>gnl|CDD|188431 TIGR03916, rSAM_link_UDG, putative DNA modification/repair radical
SAM protein. This uncharacterized protein of about 400
amino acids in length contains a radical SAM protein in
the N-terminal half. Members are present in about twenty
percent of prokaryotic genomes, always paired with a
member of the conserved hypothetical protein TIGR03915.
Roughly forty percent of the members of that family
exist as fusions with a uracil-DNA glycosylase-like
region, TIGR03914. In DNA, uracil results from
deamidation of cytosine, forming U/G mismatches that
lead to mutation, and so uracil-DNA glycosylase is a DNA
repair enzyme. This indirect connection, and the
recurring role or radical SAM protein in modification
chemistries, suggest that this protein may act in DNA
modification, repair, or both [Unknown function, Enzymes
of unknown specificity].
Length = 415
Score = 36.5 bits (85), Expect = 0.007
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 156 MIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPI 193
MI+G T ++ ILK LY Y LK FYS +P+
Sbjct: 220 MIIGATGETDYQ-ILKVAESLYQKYGLKRVFYSAYVPV 256
>gnl|CDD|227890 COG5603, TRS20, Subunit of TRAPP, an ER-Golgi tethering complex
[Cell motility and secretion].
Length = 136
Score = 33.3 bits (76), Expect = 0.029
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 147 YQTLTGVKFMIV-GDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNL 205
Y +G+KF+ + + ++ L++++ELYA L +PFY + PIR + FD ++
Sbjct: 73 YIMPSGMKFLFIHQNQSRKNARSFLQEVHELYAK-TLMSPFYEPDEPIRSQAFDDGVREA 131
Query: 206 LQQH 209
+
Sbjct: 132 ARVC 135
>gnl|CDD|214570 smart00228, PDZ, Domain present in PSD-95, Dlg, and ZO-1/2. Also
called DHR (Dlg homologous region) or GLGF (relatively
well conserved tetrapeptide in these domains). Some PDZs
have been shown to bind C-terminal polypeptides; others
appear to bind internal (non-C-terminal) polypeptides.
Different PDZs possess different binding specificities.
Length = 85
Score = 31.6 bits (72), Expect = 0.062
Identities = 16/67 (23%), Positives = 25/67 (37%), Gaps = 10/67 (14%)
Query: 41 TPENKKIVVSF------GQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPV 94
E +VVS + G+ VG V+ VN ++ + ++ L K V
Sbjct: 22 KDEGGGVVVSSVVPGSPAAKAGLRVGDVILEVNGTSVEGLTHL---EAVDLLKKAGG-KV 77
Query: 95 KLTFTRP 101
LT R
Sbjct: 78 TLTVLRG 84
>gnl|CDD|114274 pfam05543, Peptidase_C47, Staphopain peptidase C47. Staphopains
are one of four major families of proteinases secreted
by the Gram-positive Staphylococcus aureus. These
staphylococcal cysteine proteases are secreted as
preproenzymes that are proteolytically cleaved to
generate the mature enzyme.
Length = 174
Score = 30.3 bits (68), Expect = 0.44
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 39 KLTPENKKIVV---SFGQRDGILVGHVLTAVNDAVIKNGQ 75
+LT NK I + R+GI GH + V +A + NGQ
Sbjct: 95 QLTKNNKGIAILGSRVESRNGIHAGHAMAVVGNAKLNNGQ 134
>gnl|CDD|226727 COG4277, COG4277, Predicted DNA-binding protein with the
Helix-hairpin-helix motif [General function prediction
only].
Length = 404
Score = 30.9 bits (70), Expect = 0.48
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 156 MIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPI 193
MIVG ++ D IL + LY Y+LK +YS P+
Sbjct: 222 MIVGADGETDED-ILSRSENLYGRYSLKRVYYSAFSPV 258
>gnl|CDD|177430 PHA02605, 54, baseplate subunit; Provisional.
Length = 305
Score = 28.3 bits (63), Expect = 3.2
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 13/52 (25%)
Query: 1 MVIYGVYIVSKSGGLIFNYDHNVPKIENAVTFQFPLNIKLT-PENKKIVVSF 51
++IY V + G +Y+HN P NI++T E +V+SF
Sbjct: 123 LLIYSVKMPENRLGYEMDYNHNSP------------NIRITGREYDPLVLSF 162
>gnl|CDD|235788 PRK06372, PRK06372, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 253
Score = 28.0 bits (62), Expect = 4.2
Identities = 40/162 (24%), Positives = 65/162 (40%), Gaps = 27/162 (16%)
Query: 39 KLTPENKKIVVSFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTF 98
L P+N K+ + + + + + H ND+VI G + + F+S E +K +
Sbjct: 60 NLRPKNLKLGIE--KHEKMAIEHAKPLFNDSVI--GTISSSQVLKAFISSSEK--IKSVY 113
Query: 99 TRPRMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIV 158
E I +A + SGI+V+ + + + V +IV
Sbjct: 114 ILESRPMLEGIDMAKLL--------------VKSGIDVVLLTDASM--CEAVLNVDAVIV 157
Query: 159 G-DTNQSGLDLILKK---IYELYADYALKNPFYSLEMPIRCE 196
G D+ LI K L A Y LK PFYSL + ++ E
Sbjct: 158 GSDSVLYDGGLIHKNGTFPLALCARY-LKKPFYSLTISMKIE 198
>gnl|CDD|99935 cd05503, Bromo_BAZ2A_B_like, Bromodomain, BAZ2A/BAZ2B_like
subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and
2B (BAZ2B) were identified as a novel human bromodomain
gene by cDNA library screening. BAZ2A is also known as
Tip5 (Transcription termination factor I-interacting
protein 5) and hWALp3. The proteins may play roles in
transcriptional regulation. Human Tip5 is part of a
complex termed NoRC (nucleolar remodeling complex),
which induces nucleosome sliding and may play a role in
the regulation of the rDNA locus. Bromodomains are 110
amino acid long domains, that are found in many
chromatin associated proteins. Bromodomains can
interact specifically with acetylated lysine.
Length = 97
Score = 26.6 bits (59), Expect = 4.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 27 ENAVTFQFPLNIKLTPENKKIV 48
E+A F P+N KL P +KI+
Sbjct: 16 EDAWPFLEPVNTKLVPGYRKII 37
>gnl|CDD|238488 cd00988, PDZ_CTP_protease, PDZ domain of C-terminal processing-,
tail-specific-, and tricorn proteases, which function in
posttranslational protein processing, maturation, and
disassembly or degradation, in Bacteria, Archaea, and
plant chloroplasts. May be responsible for substrate
recognition and/or binding, as most PDZ domains bind
C-terminal polypeptides, and binding to internal
(non-C-terminal) polypeptides and even to lipids has
been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 85
Score = 26.4 bits (59), Expect = 4.5
Identities = 15/70 (21%), Positives = 32/70 (45%), Gaps = 9/70 (12%)
Query: 38 IKLTPENKKIVVS---FG---QRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPES 91
++L ++ +V++ G + GI G ++ A++ + L+ DV++ L
Sbjct: 6 LELKYDDGGLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLE---DVVKLLRGKAG 62
Query: 92 FPVKLTFTRP 101
V+LT R
Sbjct: 63 TKVRLTLKRG 72
>gnl|CDD|236483 PRK09364, moaC, molybdenum cofactor biosynthesis protein MoaC;
Provisional.
Length = 159
Score = 26.7 bits (60), Expect = 7.1
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 1 MVIYGVYIVSKSGG 14
MVI V ++ KSGG
Sbjct: 137 MVIGDVRLLEKSGG 150
>gnl|CDD|221961 pfam13180, PDZ_2, PDZ domain.
Length = 81
Score = 25.7 bits (57), Expect = 7.2
Identities = 9/52 (17%), Positives = 21/52 (40%), Gaps = 6/52 (11%)
Query: 54 RDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSK-PESFPVKLTFTRPRMT 104
+ G+ G ++ +++ + T+++E + VKLT R
Sbjct: 28 KAGLKPGDIILSIDGKKVN-----SLTELIEVILNGKPGDTVKLTVYRDGKK 74
>gnl|CDD|201332 pfam00595, PDZ, PDZ domain (Also known as DHR or GLGF). PDZ
domains are found in diverse signaling proteins.
Length = 80
Score = 25.7 bits (57), Expect = 7.3
Identities = 10/48 (20%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 50 SFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLT 97
+ G+ G + ++N ++N D+ L K V LT
Sbjct: 35 GAAEAGGLQEGDRILSINGQDLENLSHDEAVLAL----KGSGGEVTLT 78
>gnl|CDD|238080 cd00136, PDZ, PDZ domain, also called DHR (Dlg homologous region)
or GLGF (after a conserved sequence motif). Many PDZ
domains bind C-terminal polypeptides, though binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. Heterodimerization
through PDZ-PDZ domain interactions adds to the
domain's versatility, and PDZ domain-mediated
interactions may be modulated dynamically through
target phosphorylation. Some PDZ domains play a role in
scaffolding supramolecular complexes. PDZ domains are
found in diverse signaling proteins in bacteria,
archebacteria, and eurkayotes. This CD contains two
distinct structural subgroups with either a N- or
C-terminal beta-strand forming the peptide-binding
groove base. The circular permutation placing the
strand on the N-terminus appears to be found in
Eumetazoa only, while the C-terminal variant is found
in all three kingdoms of life, and seems to co-occur
with protease domains. PDZ domains have been named
after PSD95(post synaptic density protein), DlgA
(Drosophila disc large tumor suppressor), and ZO1, a
mammalian tight junction protein.
Length = 70
Score = 25.3 bits (56), Expect = 8.1
Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 34 FPLNIKLTPENKKIVV-------SFGQRDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFL 86
L + + VV S +R G+ G V+ AVN +KN L+ DV E L
Sbjct: 1 GGLGFSIRGGTEGGVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLE---DVAELL 57
Query: 87 SKPESFPVKLTF 98
K V LT
Sbjct: 58 KKEVGEKVTLTV 69
>gnl|CDD|233695 TIGR02037, degP_htrA_DO, periplasmic serine protease, Do/DeqQ
family. This family consists of a set proteins various
designated DegP, heat shock protein HtrA, and protease
DO. The ortholog in Pseudomonas aeruginosa is designated
MucD and is found in an operon that controls mucoid
phenotype. This family also includes the DegQ (HhoA)
paralog in E. coli which can rescue a DegP mutant, but
not the smaller DegS paralog, which cannot. Members of
this family are located in the periplasm and have
separable functions as both protease and chaperone.
Members have a trypsin domain and two copies of a PDZ
domain. This protein protects bacteria from thermal and
other stresses and may be important for the survival of
bacterial pathogens.// The chaperone function is
dominant at low temperatures, whereas the proteolytic
activity is turned on at elevated temperatures [Protein
fate, Protein folding and stabilization, Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 428
Score = 26.8 bits (60), Expect = 8.9
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 24/89 (26%)
Query: 40 LTPENKKIVVSFGQRDGILV----------------GHVLTAVNDAVIKNGQLDDGTDVL 83
L+PE +K + G G++V G V+ +VN + + + + VL
Sbjct: 347 LSPEIRKELRLKGDVKGVVVTKVVSGSPAARAGLQPGDVILSVNQQPVSS--VAELRKVL 404
Query: 84 EFLSKPESFPVKLTFTRPRMTTNEKIFLA 112
K V L R IF+
Sbjct: 405 ARAKKGGR--VALLILR----GGATIFVT 427
>gnl|CDD|177681 PLN00049, PLN00049, carboxyl-terminal processing protease;
Provisional.
Length = 389
Score = 27.0 bits (60), Expect = 9.3
Identities = 25/93 (26%), Positives = 37/93 (39%), Gaps = 9/93 (9%)
Query: 54 RDGILVGHVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLAS 113
R GI G V+ A++ + L + D L+ PE V+LT R T + L
Sbjct: 117 RAGIRPGDVILAIDGTSTEGLSLYEAADRLQ---GPEGSSVELTLRRGPET--RLVTLTR 171
Query: 114 MFYPLFAIASQL----SPEPKSSGIEVLEADTF 142
L + S+L P S I ++ TF
Sbjct: 172 EKVSLNPVKSRLCEVPGPGAGSPKIGYIKLTTF 204
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 0.139 0.401
Gapped
Lambda K H
0.267 0.0695 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,036,062
Number of extensions: 1041220
Number of successful extensions: 904
Number of sequences better than 10.0: 1
Number of HSP's gapped: 902
Number of HSP's successfully gapped: 28
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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: 57 (25.8 bits)