RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17656
(85 letters)
>gnl|CDD|220215 pfam09379, FERM_N, FERM N-terminal domain. This domain is the
N-terminal ubiquitin-like structural domain of the FERM
domain.
Length = 79
Score = 67.6 bits (166), Expect = 6e-17
Identities = 23/53 (43%), Positives = 39/53 (73%)
Query: 27 ITLLDGSLLDVTIERKAKGEDLFDRVCDHLNLLERDYFGLTYDNKYDPQCWLE 79
+ LLDG+ L+ T+++ A G++L D+VC L L E+DYFGL +++K + + WL+
Sbjct: 1 VRLLDGTQLEFTVDKSATGQELLDQVCQRLGLREKDYFGLQFNDKKNERIWLD 53
>gnl|CDD|214604 smart00295, B41, Band 4.1 homologues. Also known as
ezrin/radixin/moesin (ERM) protein domains. Present in
myosins, ezrin, radixin, moesin, protein tyrosine
phosphatases. Plasma membrane-binding domain. These
proteins play structural and regulatory roles in the
assembly and stabilization of specialized
plasmamembrane domains. Some PDZ domain containing
proteins bind one or more of this family. Now includes
JAKs.
Length = 201
Score = 56.9 bits (138), Expect = 1e-11
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 24 VAHITLLDGSLLDVTIERKAKGEDLFDRVCDHLNLLERDYFGL-TYDNKYDPQCWLEM 80
V + LLDG+ L+ ++ E+L + VC L + E +YFGL D D + WL+
Sbjct: 1 VLKVYLLDGTTLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLRHWLDP 58
>gnl|CDD|234357 TIGR03797, NHLM_micro_ABC2, NHLM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal leader
sequence cleavage domain, and an HlyD homolog
(TIGR03794). In a number of genomes, members of protein
families related to nitrile hydratase alpha subunit or
to nif11 have undergone paralogous family expansions,
with members possessing a putative bacteriocin cleavage
region ending with a classic Gly-Gly motif. Those sets
of putative bacteriocins, members of this protein family
and its partners TIGR03794 and TIGR03796, and
cyclodehydratase/docking scaffold fusion proteins of
thiazole/oxazole biosynthesis frequently show correlated
species distribution and co-clustering within many of
those genomes [Transport and binding proteins, Amino
acids, peptides and amines, Cellular processes,
Biosynthesis of natural products].
Length = 686
Score = 28.8 bits (65), Expect = 0.28
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 2 TMTEIDTESAPPKTKPLKGKIEVAHITLL---DGSLL--DVTIERKAKGE 46
+ E+D P L G IEV +T DG L+ DV+++ + GE
Sbjct: 434 ALPEVDEAKTDPG--KLSGAIEVDRVTFRYRPDGPLILDDVSLQIEP-GE 480
>gnl|CDD|129357 TIGR00255, TIGR00255, TIGR00255 family protein. The apparent
ortholog from Aquifex aeolicus as reported is split into
two consecutive reading frames [Hypothetical proteins,
Conserved].
Length = 291
Score = 26.3 bits (58), Expect = 1.6
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 21 KIEVAHITLLDGSLLDVTIERKAKGEDLFDRVCDHLNLLERD 62
I + L+ +LLD R+ +GE+L + L+L+ER+
Sbjct: 128 AIYALILGALEEALLDFINMREFEGENLKSDIVQRLDLIERE 169
>gnl|CDD|240299 PTZ00164, PTZ00164, bifunctional dihydrofolate
reductase-thymidylate synthase; Provisional.
Length = 514
Score = 26.6 bits (59), Expect = 1.7
Identities = 17/60 (28%), Positives = 24/60 (40%), Gaps = 19/60 (31%)
Query: 9 ESAPPKTKPLKGKIEVAHITLLDGSLLDVTIERKAKGED------LFDRVCDHLNLLERD 62
ES P K +PLK +I +V + R E+ +F + D L LL D
Sbjct: 69 ESIPKKFRPLKNRI-------------NVVLSRTLTEEEADPGVLVFGSLEDALRLLAED 115
>gnl|CDD|148950 pfam07614, DUF1577, Protein of unknown function (DUF1577). A
family of hypothetical proteins in Leptospira
interrogans.
Length = 256
Score = 25.9 bits (57), Expect = 3.0
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 24 VAHITLLDGSLLDVTIERKAKGEDLFDRV-CDHLNLLERDYFGLTYDNKYD 73
++ TL+D +L ++ K D ++ + +L D FG D K++
Sbjct: 111 ISSKTLIDANLFNIPTLVKVNFNDYKRKLKQKYPDLRLVDIFGSDLDKKFE 161
>gnl|CDD|212679 cd10237, HSPA13-like_NBD, Nucleotide-binding domain of human HSPA13
and similar proteins. Human HSPA13 (also called 70-kDa
heat shock protein 13, STCH, "stress 70 protein
chaperone, microsome-associated, 60kD", "stress 70
protein chaperone, microsome-associated, 60kDa"; the
gene encoding HSPA13 maps to 21q11.1) belongs to the
heat shock protein 70 (HSP70) family of chaperones that
assist in protein folding and assembly and can direct
incompetent "client" proteins towards degradation.
Typically, HSP70s have a nucleotide-binding domain (NBD)
and a substrate-binding domain (SBD). The nucleotide
sits in a deep cleft formed between the two lobes of the
NBD. The two subdomains of each lobe change conformation
between ATP-bound, ADP-bound, and nucleotide-free
states. ATP binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs). STCH contains an NBD but lacks an SBD.
STCH may function to regulate cell proliferation and
survival, and modulate the TRAIL-mediated cell death
pathway. The HSPA13 gene is a candidate stomach cancer
susceptibility gene; a mutation in the NBD coding region
of HSPA13 has been identified in stomach cancer cells.
The NBD of HSPA13 interacts with the ubiquitin-like
proteins Chap1 and Chap2, implicating HSPA13 in
regulating cell cycle and cell death events. HSPA13 is
induced by the Ca2+ ionophore A23187.
Length = 417
Score = 25.5 bits (56), Expect = 4.1
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 17/75 (22%)
Query: 18 LKGKIEVAHITLLD--GSLLDVTI---------------ERKAKGEDLFDRVCDHLNLLE 60
L K +V ++ ++D G LDV++ + G+D R+ +L
Sbjct: 204 LHKKQDVFNVLVVDLGGGTLDVSLLNKQGGMFLTRAMAGNNRLGGQDFNQRLLQYLYQKI 263
Query: 61 RDYFGLTYDNKYDPQ 75
+ +G DNK D Q
Sbjct: 264 YEKYGKVPDNKEDIQ 278
>gnl|CDD|236981 PRK11783, rlmL, 23S rRNA m(2)G2445 methyltransferase; Provisional.
Length = 702
Score = 25.1 bits (56), Expect = 4.9
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 59 LERDYFGLTYDNKYDPQCWLEMVN 82
L R+ +G + +D W E++
Sbjct: 219 LHRERWGFSGWLGHDEALWQELLE 242
>gnl|CDD|200520 cd11259, Sema_4D, The Sema domain, a protein interacting module, of
semaphorin 4D (Sema4D, also known as CD100).
Sema4D/CD100 is expressed in immune cells and plays
critical roles in immune response; it is thus termed an
"immune semaphorin". It is expressed by lymphocytes and
promotes the aggregation and survival of B lymphocytes
and inhibits cytokine-induced migration of immune cells
in vitro. Sema4D/CD100 knock-out mice demonstrate that
Sema4D is required for normal activation of B and T
lymphocytes. Sema4D increases B-cell and DC function
using either Plexin B1 or CD72 as receptors. The
function of Sema4D in immune response implicates its
role in infectious and noninfectious diseases. Sema4D
belongs to the class 4 transmembrane semaphorin family
of proteins. Semaphorins are regulatory molecules in the
development of the nervous system and in axonal
guidance. They also play important roles in other
biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 471
Score = 24.8 bits (54), Expect = 6.0
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 45 GEDLFDRVCDHLNLLERDYFGLTYDNK----YDP 74
G + F CD+LNL G D K +DP
Sbjct: 97 GTNAFQPTCDYLNLTSFRLLGKNEDGKGRCPFDP 130
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 24.6 bits (53), Expect = 8.8
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 12 PPKTKPLKGKIEVAHITLLDGSLLDVTIERKAKGEDLFDRVCDHLNLLER 61
PP+ K K KIE++ ++D +D T K + + + D L+L R
Sbjct: 114 PPEGKGTKQKIELSVEKVIDVGTVDPTKYPLPKTKLTLEFLRDVLHLRSR 163
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
0.319 0.139 0.420
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,354,229
Number of extensions: 350400
Number of successful extensions: 294
Number of sequences better than 10.0: 1
Number of HSP's gapped: 294
Number of HSP's successfully gapped: 14
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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 (21.7 bits)
S2: 53 (24.2 bits)