RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1550
(264 letters)
>gnl|CDD|218726 pfam05742, NRDE, NRDE protein. In eukaryotes this family is
predicted to play a role in protein secretion and Golgi
organisation. In plants this family includes Solanum
habrochaites Cwp, which is involved in water
permeability in the cuticles of fruit. Mouse T10 has
been found to be expressed during early embryogenesis in
mice. This protein contains a conserved NRDE motif.
Length = 267
Score = 145 bits (367), Expect = 2e-42
Identities = 63/233 (27%), Positives = 106/233 (45%), Gaps = 20/233 (8%)
Query: 29 GGTWLATSTNGKLGILLNVLGENSRPNGRDRGPLVVKYVEGQKSAEEYLTDLKKETEENV 88
GGTWL + +GK+ L NV RPN R RG LV ++ SA EYL +LKK E
Sbjct: 53 GGTWLGITKDGKVAALTNVRQPLERPNARSRGELVADFLTSNASALEYLENLKKRAHE-- 110
Query: 89 FNGFHIVLLEL-TLQSTNIYHFSNIAPLDSPSTKVTNVTNKQENKDHVYGFGNSQCTSQP 147
+NGF++V + S +Y+ SN P + + +YG NS + P
Sbjct: 111 YNGFNLVAADKNKTGSDRVYYLSNRPE-KLP---------RIQLAPGIYGLSNSLLDT-P 159
Query: 148 FQKVIFGKEKFAEIVNKFNRKSESQNLIQNILDLMKNKQSNYPDPEIDRKAEADMDEDYK 207
+ KV G++ E + + + + + +IQ +L+++ N + PD ++ + +
Sbjct: 160 WPKVRVGRKLLEERL-EASDELSVETIIQQLLEILANTSAFAPDAQL--PDTGVFVPETE 216
Query: 208 MRYSRVCVDISSIFYGTRTHSIILVDHNNVMDFHEWTL-DYETKKWIHTHIRK 259
S + + YGTR +++LVDH+ + F E + +W
Sbjct: 217 RLLSAIFIRGPR--YGTRASTVVLVDHDGEVTFIERRMGPNGASEWNTGRFEF 267
>gnl|CDD|225869 COG3332, COG3332, Uncharacterized conserved protein [Function
unknown].
Length = 270
Score = 66.4 bits (162), Expect = 6e-13
Identities = 50/220 (22%), Positives = 88/220 (40%), Gaps = 29/220 (13%)
Query: 30 GTWLATSTNGKLGILLNVL--GENSRPNGRDRGPLVVKYVEGQK-SAEEYLTDLKKETEE 86
GTWL + GK L NV E + R RG LV ++ K S E+YL LKK
Sbjct: 56 GTWLGITKEGKFAALTNVRDPSEQNNTKSRSRGELVADFLSIHKASFEDYLNQLKKR--A 113
Query: 87 NVFNGFHIVLLELTLQSTNIYHFSNIAPLDSPSTKVTNVTNKQENKDHVYGFGNSQCTSQ 146
++GF++ L ++++ N ++ YG N S
Sbjct: 114 GHYDGFNL----LYGDRHKLWYYVN------------RSETPRKLLPGYYGLSNGFLDS- 156
Query: 147 PFQKVIFGKEKFAEIVNKFNRKSESQNLIQNILDLMKNKQSNYPDPEIDRKAEADMDEDY 206
P+ KV + AE++ + N + + + +I + L L+ + P+ E
Sbjct: 157 PWPKVKKARAALAELLAE-NIEHDEEKIISSCLQLL---ADSSLAPDGQLPDTGVGVEWE 212
Query: 207 KMRYSRVCVDISSIFYGTRTHSIILVDHNNVMDFHEWTLD 246
++ + + I +YGTR +++ V + + F E
Sbjct: 213 RLLST---IFIPGPYYGTRASTVLRVSKDGTVTFIERVFG 249
>gnl|CDD|182792 PRK10866, PRK10866, outer membrane biogenesis protein BamD;
Provisional.
Length = 243
Score = 30.1 bits (68), Expect = 1.0
Identities = 16/77 (20%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 135 VYGFGNSQCTSQPFQKVIFGKEKFAE----IVNKFNRKSESQNLIQNILDLMKNKQSNYP 190
V G+ NSQ T+ ++++F K++ A+ + + ++ ++ + +++ +YP
Sbjct: 151 VRGYPNSQYTTDATKRLVFLKDRLAKYELSVAEYYTKRGAYVAVVNRVEQMLR----DYP 206
Query: 191 DPEIDRKAEADMDEDYK 207
D + R A M+ Y+
Sbjct: 207 DTQATRDALPLMENAYR 223
>gnl|CDD|182368 PRK10306, PRK10306, zinc/cadmium-binding protein; Provisional.
Length = 216
Score = 29.0 bits (65), Expect = 2.2
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 20/66 (30%)
Query: 186 QSNYP-------DPEIDRKAEADMD---EDYKMRYSRVCVDISSIFYGTRTHSIILVDHN 235
QS YP DP +KA+ D E+ K Y + Y T I + N
Sbjct: 63 QSVYPYLQSGKLDPVFQKKAKKDKTKTFEEIKAYYRK--------GYATDVEMIGI--EN 112
Query: 236 NVMDFH 241
+++FH
Sbjct: 113 GIVEFH 118
>gnl|CDD|235005 PRK02122, PRK02122, glucosamine-6-phosphate deaminase-like protein;
Validated.
Length = 652
Score = 29.2 bits (66), Expect = 2.8
Identities = 16/56 (28%), Positives = 28/56 (50%), Gaps = 12/56 (21%)
Query: 157 KFAEIVNKFNRK-----SESQNLIQNILDLMKNKQSNYPD-PEID------RKAEA 200
+FA+ +N FN+ E + + I++ +KNK+ D PE+ R+ EA
Sbjct: 419 RFADFINDFNQIFGISSDELKKKYEEIIEFLKNKKPGEIDSPEVRKLKGLIRRGEA 474
>gnl|CDD|163686 cd07767, MPN, Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also
known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are
found in the N-terminal termini of proteins with a
variety of functions; they are components of the
proteasome regulatory subunits, the signalosome (CSN),
eukaryotic translation initiation factor 3 (eIF3)
complexes, and regulators of transcription factors.
These domains are isopeptidases that release ubiquitin
from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. Catalytically active MPN domains contain a
metalloprotease signature known as the JAB1/MPN/Mov34
metalloenzyme (JAMM) motif. For example, Rpn11 (also
known as POH1 or PSMD14), a subunit of the 19S
proteasome lid is involved in the ATP-dependent
degradation of ubiquitinated proteins, contains the
conserved JAMM motif involved in zinc ion coordination.
Poh1 is a regulator of c-Jun, an important regulator of
cell proliferation, differentiation, survival and death.
JAB1 is a component of the COP9 signalosome (CSN), a
regulatory particle of the ubiquitin (Ub)/26S proteasome
system occurring in all eukaryotic cells; it cleaves the
ubiquitin-like protein NEDD8 from the cullin subunit of
the SCF (Skp1, Cullins, F-box proteins) family of E3
ubiquitin ligases. AMSH (associated molecule with the
SH3 domain of STAM, also known as STAMBP), a member of
JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves
Lys 63-linked polyubiquitin (poly-Ub) chains, thus
facilitating the recycling and subsequent trafficking of
receptors to the cell surface. Similarly, BRCC36, part
of the nuclear complex that includes BRCA1 protein and
is targeted to DNA damage foci after irradiation,
specifically disassembles K63-linked polyUb. BRCC36 is
aberrantly expressed in sporadic breast tumors,
indicative of a potential role in the pathogenesis of
the disease. Some variants of the JAB1/MPN domains lack
key residues in their JAMM motif and are unable to
coordinate a metal ion. Comparisons of key catalytic and
metal binding residues explain why the MPN-containing
proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the
translation initiation factor 3 subunits f (p47) and h
(p40) do not show catalytic isopeptidase activity. It
has been proposed that the MPN domain in these proteins
has a primarily structural function.
Length = 116
Score = 27.9 bits (62), Expect = 2.9
Identities = 9/47 (19%), Positives = 13/47 (27%)
Query: 214 CVDISSIFYGTRTHSIILVDHNNVMDFHEWTLDYETKKWIHTHIRKT 260
VD V +DF + W HTH + +
Sbjct: 30 DVDEVIAVPFDEGDKDDNVWFLMYLDFKKLNAGLRIVGWYHTHPKPS 76
>gnl|CDD|224541 COG1626, TreA, Neutral trehalase [Carbohydrate transport and
metabolism].
Length = 558
Score = 28.6 bits (64), Expect = 3.5
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 195 DRKAEADMDEDYKMRYSRVCVDISSIFYGTRTHSIILVDHNNVMDFHEWTLD 246
D +A + D+ R+ V ++SI RT SI+ VD N ++ E +
Sbjct: 321 DDRAGRESGWDFSSRWLGVPAPLASI----RTTSILPVDLNALLYKLEEIIA 368
>gnl|CDD|218004 pfam04283, CheF-arch, Chemotaxis signal transduction system protein
F from archaea. This is a family of proteins that are
archaea-specific components of the bacterial-like
chemotaxis signal transduction system of archaea. In H.
salinarum, the CheF proteins interact with the
chemotaxis proteins CheY, CheD and CheC2 as well as the
flagella-accessory proteins FlaCE and FlaD, and are
essential for any tactic response. CheF probably
functions at the interface between the bacterial-like
chemotaxis signal transduction system and the archaeal
flagellar apparatus.
Length = 220
Score = 27.7 bits (62), Expect = 6.1
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 4/56 (7%)
Query: 27 VKGGTWLATSTNGKLGILLNVLGENSR----PNGRDRGPLVVKYVEGQKSAEEYLT 78
A S + I ++ +G+ R +G+ R L V++VE S YL
Sbjct: 138 TDEAVKFARSDGQFVRIDISNVGDVEREEREVDGKQRPVLKVEHVEDGTSVTSYLA 193
>gnl|CDD|211409 cd11568, FAT-like_CASS4_C, C-terminal FAT-like Four helix bundle
domain, also called DUF3513, of CAS (Crk-Associated
Substrate) scaffolding protein family member 4; a
protein interaction module. CASS4, also called HEPL
(HEF1-EFS-p130Cas-like), localizes to focal adhesions
and plays a role in regulating FAK activity, focal
adhesion integrity, and cell spreading. It is most
abundant in blood cells and lung tissue, and is also
found in high levels in leukemia and ovarian cell lines.
CAS proteins function as molecular scaffolds to regulate
protein complexes that are involved in many cellular
processes. They share a common domain structure
containing protein interaction modules that enable their
scaffolding function, including an N-terminal SH3
domain, an unstructured substrate domain that contains
many YxxP motifs, a serine-rich four-helix bundle, and a
FAT-like C-terminal domain, which binds to the
C-terminal domain of NSPs (novel SH2-containing
proteins) to form multidomain signaling modules that
mediate cell migration and invasion.
Length = 123
Score = 26.7 bits (59), Expect = 7.1
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 174 LIQNILDLMKNKQSNYPDPEIDRKAEADMDEDYK 207
L++N+ KN YP P R+ + DE K
Sbjct: 80 LLKNLALATKNAALQYPSPAALRELQDIADELAK 113
>gnl|CDD|235450 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 27.4 bits (62), Expect = 8.0
Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 53 RP-NGRDRGPLVVKYVEGQKSAEEYLTDL 80
RP G D V YV Q EE+L +
Sbjct: 201 RPLTGLD--KPVADYVLAQPEVEEFLDKI 227
>gnl|CDD|218855 pfam06017, Myosin_TH1, Myosin tail.
Length = 199
Score = 26.9 bits (60), Expect = 9.4
Identities = 12/63 (19%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 145 SQPFQKVIFGKEK-----FAEIVNKFNRKSESQNLI-----QNILDLMKNKQSNYPDPEI 194
+ QK + +E FA+ VNK NR + + + + + K + +
Sbjct: 34 NPKLQKAVGSEEGNEKVLFADKVNKVNRSGKPSKRDLLLTDKALYLVGREKVKDQKTYVL 93
Query: 195 DRK 197
R+
Sbjct: 94 KRR 96
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 0.132 0.384
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,915,827
Number of extensions: 1178377
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 777
Number of HSP's successfully gapped: 23
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
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: 58 (26.1 bits)