RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6898
(111 letters)
>gnl|CDD|189968 pfam01391, Collagen, Collagen triple helix repeat (20 copies).
Members of this family belong to the collagen
superfamily. Collagens are generally extracellular
structural proteins involved in formation of connective
tissue structure. The alignment contains 20 copies of
the G-X-Y repeat that forms a triple helix. The first
position of the repeat is glycine, the second and third
positions can be any residue but are frequently proline
and hydroxyproline. Collagens are post translationally
modified by proline hydroxylase to form the
hydroxyproline residues. Defective hydroxylation is the
cause of scurvy. Some members of the collagen
superfamily are not involved in connective tissue
structure but share the same triple helical structure.
Length = 60
Score = 33.6 bits (78), Expect = 0.002
Identities = 22/46 (47%), Positives = 22/46 (47%)
Query: 29 GRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGKDGIPGTNG 74
G G G G PG PG G PG G G PG G PG G PG G
Sbjct: 7 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPG 52
Score = 33.2 bits (77), Expect = 0.003
Identities = 22/46 (47%), Positives = 22/46 (47%)
Query: 29 GRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGKDGIPGTNG 74
G G G G PG PG G PG G G PG G PG G PG G
Sbjct: 13 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGAPGAPG 58
Score = 33.2 bits (77), Expect = 0.003
Identities = 22/48 (45%), Positives = 22/48 (45%)
Query: 29 GRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGKDGIPGTNGTK 76
G G G G PG PG G PG G G PG G PG G PG G
Sbjct: 1 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPP 48
Score = 31.7 bits (73), Expect = 0.011
Identities = 18/38 (47%), Positives = 18/38 (47%)
Query: 29 GRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGK 66
G G G G PG PG G PG G G PG G PG
Sbjct: 22 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGAPGAPGP 59
Score = 25.1 bits (56), Expect = 2.9
Identities = 20/44 (45%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 28 SGRIGLDGRDGLPGEPGLDGIPGRNGMDGIPGKDGLPGKDGIPG 71
G G G G PG PG G PG G G P G PG G PG
Sbjct: 18 PGPPGPPGPPGPPGPPGPPGPPGPPGPPGPP---GPPGAPGAPG 58
>gnl|CDD|143246 cd05769, IgC_TCR_beta, T cell receptor (TCR) beta chain constant
immunoglobulin domain. IgC_TCR_beta: Constant domain
of the beta chain of alpha/beta T-cell antigen
receptors (TCRs). TCRs mediate antigen recognition by T
lymphocytes, and are composed of alpha and beta, or
gamma and delta, polypeptide chains with variable (V)
and constant (C) regions. This group includes the
variable domain of the beta chain. Alpha/beta TCRs
recognize antigen as peptide fragments presented by
major histocompatibility complex (MHC) molecules. The
antigen binding site is formed by the variable domains
of the alpha and beta chains, located at the N-terminus
of each chain. Alpha/beta TCRs recognize antigens
differently from gamma/delta TCRs.
Length = 115
Score = 27.7 bits (62), Expect = 0.81
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 72 TNGTKTDHYAMGADTKSFS 90
T+G TD A+ +T ++S
Sbjct: 47 TDGVATDPQALRENTSTYS 65
>gnl|CDD|237369 PRK13376, pyrB, bifunctional aspartate carbamoyltransferase
catalytic subunit/aspartate carbamoyltransferase
regulatory subunit; Provisional.
Length = 525
Score = 27.4 bits (61), Expect = 1.9
Identities = 14/31 (45%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 59 GKDGLP--GKDGI-PGTNGTKTDHYAMGADT 86
G G+ GK GI P NGT DH A G
Sbjct: 362 GTKGVQKEGKRGIKPIENGTVIDHIAKGKTP 392
>gnl|CDD|190559 pfam03195, DUF260, Protein of unknown function DUF260.
Length = 101
Score = 26.0 bits (58), Expect = 3.0
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 1 MGRVQGMLQVLEVHDRRDIGRAI 23
V +L+ L R D R++
Sbjct: 39 ASNVTKLLKALPPEQRDDAMRSL 61
>gnl|CDD|226518 COG4031, COG4031, Predicted metal-binding protein [General function
prediction only].
Length = 227
Score = 26.0 bits (57), Expect = 5.0
Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 1/65 (1%)
Query: 3 RVQGMLQVLEVHDRRDIGRAISTVISGRIGLDGRDGLPGEPGLDG-IPGRNGMDGIPGKD 61
R +L +E +G + ST+I GR G + P + IPG G G
Sbjct: 113 RKDRLLDNVENPPEEKLGGSHSTIIGGRSGKKLILLVAQHPYVKKVIPGVISAKGSAGGG 172
Query: 62 GLPGK 66
G+ K
Sbjct: 173 GVRLK 177
>gnl|CDD|188629 cd00344, FBP_aldolase_I, Fructose-bisphosphate aldolase class I.
Fructose-bisphosphate aldolase class I.
Fructose-1,6-bisphosphate aldolase is an enzyme of the
glycolytic and gluconeogenic pathways found in
vertebrates, plants, and bacteria. The enzyme catalyzes
the cleavage of fructose 1,6-bisphosphate to
glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate (DHAP). Mutations in the aldolase genes in
humans cause hemolytic anemia and hereditary fructose
intolerance. The enzyme is a member of the class I
aldolase family, which utilizes covalent catalysis
through a Schiff base formed between a lysine residue of
the enzyme and ketose substrates. Although structurally
similar, the class II aldolases use a different
mechanism and are believed to have an independent
evolutionary origin.
Length = 328
Score = 25.9 bits (56), Expect = 5.1
Identities = 14/79 (17%), Positives = 25/79 (31%), Gaps = 10/79 (12%)
Query: 38 GLPGEPGLDGIPGRNGMDGIPGKDGL---PGKDGIPGTNGTK-------TDHYAMGADTK 87
G+ + G+ + G NG G DGL + G + K +H
Sbjct: 94 GIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIM 153
Query: 88 SFSDGVLPSVQRAIAAGLV 106
++ + G+V
Sbjct: 154 ENANVLARYASICQQNGIV 172
>gnl|CDD|150536 pfam09876, DUF2103, Predicted metal-binding protein (DUF2103).
This domain, found in various putative metal binding
prokaryotic proteins, has no known function.
Length = 103
Score = 25.1 bits (55), Expect = 6.7
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 12 EVHDRRDIGRAISTVISGRIGLDGRDGLPGEPGLDG-IPGRNGMDGIPGKDGLPGKDGIP 70
E + +G + ST+I GR G + + P + IPG G GL K
Sbjct: 2 EKPPKEKLGGSHSTLIGGRSGRKLLETIAQHPEVKKVIPGVISAKGSRSGGGLRAKVTRA 61
Query: 71 GTNG 74
NG
Sbjct: 62 DANG 65
>gnl|CDD|235677 PRK06029, PRK06029, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase;
Provisional.
Length = 185
Score = 25.2 bits (56), Expect = 7.8
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 13 VHDRRDIGRAISTVISGRIGLDG 35
VHD RDIG +I+ SG G DG
Sbjct: 62 VHDVRDIGASIA---SGSFGTDG 81
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 25.5 bits (56), Expect = 8.3
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 54 MDGIPGKDGLPGKDGIP 70
MDGI K GL G+ IP
Sbjct: 343 MDGIMNKFGLSGRAFIP 359
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
0.318 0.144 0.434
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,956,716
Number of extensions: 539501
Number of successful extensions: 438
Number of sequences better than 10.0: 1
Number of HSP's gapped: 422
Number of HSP's successfully gapped: 24
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
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: 41 (21.6 bits)
S2: 53 (24.3 bits)