RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11095
(102 letters)
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 60.1 bits (146), Expect = 1e-13
Identities = 21/47 (44%), Positives = 25/47 (53%)
Query: 16 IKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVNDEIP 62
I PLD E EY LT+ + G L+S ATV I + DVND P
Sbjct: 35 ITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain.
Cadherins are glycoproteins involved in Ca2+-mediated
cell-cell adhesion. The cadherin repeat domains occur
as tandem repeats in the extracellular regions, which
are thought to mediate cell-cell contact when bound to
calcium. They play numerous roles in cell fate,
signalling, proliferation, differentiation, and
migration; members include E-, N-, P-, T-, VE-, CNR-,
proto-, and FAT-family cadherin, desmocollin, and
desmoglein, a large variety of domain architectures
with varying repeat copy numbers. Cadherin-repeat
containing proteins exist as monomers, homodimers, or
heterodimers.
Length = 98
Score = 57.3 bits (139), Expect = 3e-12
Identities = 19/45 (42%), Positives = 24/45 (53%)
Query: 15 DIKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVND 59
+I PLD E Y LT+ + G L+S ATV I + DVND
Sbjct: 53 EITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVND 97
Score = 30.4 bits (69), Expect = 0.061
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 71 TVLEGEPIGSKVTQVNAIDKD 91
+V E P G+ V V+A D D
Sbjct: 5 SVPENAPPGTVVLTVSATDPD 25
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 46.9 bits (112), Expect = 2e-08
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 15 DIKVNHPLDYETIKEYNLTIRVENNGAQQLASEATVHIILE 55
D+ PLD E+I EY LT+ ++G L+S TV I +
Sbjct: 52 DLSTTKPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
Score = 29.6 bits (67), Expect = 0.094
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 71 TVLEGEPIGSKVTQVNAIDKDGT 93
+V E P+G++V V A D D
Sbjct: 4 SVPENAPVGTEVLTVTATDADLG 26
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 28.2 bits (64), Expect = 0.56
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 71 TVLEGEPIGSKVTQVNAIDKDG 92
TV+E P + VTQV ++KDG
Sbjct: 23 TVIEVGP--NVVTQVKTVEKDG 42
>gnl|CDD|234564 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 27.8 bits (63), Expect = 0.83
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 71 TVLEGEPIGSKVTQVNAIDKDG 92
TV+E P + VTQV ++KDG
Sbjct: 26 TVIEAGP--NVVTQVKTVEKDG 45
>gnl|CDD|218462 pfam05140, ResB, ResB-like family. This family includes both ResB
and cytochrome c biogenesis proteins. Mutations in ResB
indicate that they are essential for growth. ResB is
predicted to be a transmembrane protein.
Length = 437
Score = 27.2 bits (61), Expect = 1.5
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 14 ADIKVNHPLDYETIKEY 30
I+VNHPL Y + Y
Sbjct: 235 KTIRVNHPLRYGGVTIY 251
>gnl|CDD|224252 COG1333, ResB, ResB protein required for cytochrome c biosynthesis
[Posttranslational modification, protein turnover,
chaperones].
Length = 478
Score = 26.6 bits (59), Expect = 2.3
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 14 ADIKVNHPLDYETIKEY 30
I+VNHPL Y ++ Y
Sbjct: 246 YTIRVNHPLRYGGVRVY 262
>gnl|CDD|153312 cd07628, BAR_Atg24p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Atg24p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Atg24p is involved in membrane fusion events at the
vacuolar surface during pexophagy. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 185
Score = 25.7 bits (57), Expect = 4.6
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 22 LDYETIKEYNLTIRVENNGAQQLASEATVHIILEDVND 59
LDYE + +Y LT VEN + S+A +L++ +
Sbjct: 114 LDYEELSDYLLTDEVEN---AKETSDAFNKEVLKEYPN 148
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
0.315 0.135 0.388
Gapped
Lambda K H
0.267 0.0710 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,088,063
Number of extensions: 422416
Number of successful extensions: 244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 21
Length of query: 102
Length of database: 10,937,602
Length adjustment: 68
Effective length of query: 34
Effective length of database: 7,921,530
Effective search space: 269332020
Effective search space used: 269332020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.2 bits)