RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8393
(98 letters)
>gnl|CDD|216231 pfam00995, Sec1, Sec1 family.
Length = 554
Score = 48.8 bits (117), Expect = 4e-08
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 44 WKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
WK+L+ D+ I+S VL+ +DL E GVTL
Sbjct: 1 WKVLVLDKETTKILSSVLTVSDLLEHGVTLVE 32
>gnl|CDD|227487 COG5158, SEC1, Proteins involved in synaptic transmission and
general secretion, Sec1 family [Intracellular
trafficking and secretion].
Length = 582
Score = 39.7 bits (93), Expect = 6e-05
Identities = 13/47 (27%), Positives = 29/47 (61%), Gaps = 2/47 (4%)
Query: 31 NEVQSKLSSSEP--VWKILIFDRCGQDIISPVLSKNDLRELGVTLFL 75
N++ ++ +P +WK+L+ D+ I+S +++ ++L E G+TL
Sbjct: 10 NKILDEIFLVQPANIWKVLLLDKDTTSILSSLITTSELLEHGITLVD 56
>gnl|CDD|119367 cd01615, CIDE_N, CIDE_N domain, found at the N-terminus of the
CIDE (cell death-inducing DFF45-like effector)
proteins, as well as CAD nuclease (caspase-activated
DNase/DNA fragmentation factor, DFF40) and its
inhibitor, ICAD(DFF45). These proteins are associated
with the chromatin condensation and DNA fragmentation
events of apoptosis; the CIDE_N domain is thought to
regulate the activity of ICAD/DFF45, and the CAD/DFF40
and CIDE nucleases during apoptosis. The CIDE-N domain
is also found in the FSP27/CIDE-C protein.
Length = 78
Score = 27.9 bits (63), Expect = 0.28
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 7/48 (14%)
Query: 54 QDIISPVLSKNDLRELGVTLFLYS--AEVLDEEY-SAL----CLMCLR 94
++++S K L VTL L EV DEEY L LM L
Sbjct: 24 EELLSKACEKLKLPSAPVTLVLEEDGTEVDDEEYFQTLPDNTVLMLLE 71
>gnl|CDD|202090 pfam02017, CIDE-N, CIDE-N domain. This domain is found in CAD
nuclease, and ICAD, the inhibitor of CAD nuclease. The
two proteins interact through this domain.
Length = 78
Score = 27.3 bits (61), Expect = 0.46
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 51 RCGQDIISPVLSKNDLRELGVTLFLYS--AEVLDEEY 85
Q+++S V L + VTL L EV E+Y
Sbjct: 21 SSLQELLSKVCDILQLPDGLVTLVLEEDGTEVDTEDY 57
>gnl|CDD|205676 pfam13498, DUF4122, Domain of unknown function (DUF4122). Based on
Bacteroides thetaiotaomicron gene BT_2607, a putative
uncharacterized protein. As seen in gene expression
experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22
31), it appears to be upregulated in the presence of
host or vs when in culture.
Length = 220
Score = 28.4 bits (63), Expect = 0.58
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 13/74 (17%)
Query: 24 LKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFLYSAEVLDE 83
L++M E Q +L + P + +SPV++ DL LG L + DE
Sbjct: 107 LEEMRMLKEEQEELDAESP----------EVEAVSPVVTPRDLENLGEVLTHLNEAGSDE 156
Query: 84 EYS---ALCLMCLR 94
E S A L +R
Sbjct: 157 EKSMRAARTLHSIR 170
>gnl|CDD|188918 cd09519, SAM_ANKS3, SAM domain of ANKS3 subfamily. SAM (sterile
alpha motif) domain of ANKS3 subfamily is a potential
protein-protein interaction domain. Proteins of this
subfamily have N-terminal ankyrin repeats and a
C-terminal SAM domain. SAM is a widespread domain in
signaling proteins. In many cases it mediates
homo-dimerization/oligomerization.
Length = 64
Score = 26.3 bits (58), Expect = 1.2
Identities = 12/24 (50%), Positives = 18/24 (75%), Gaps = 3/24 (12%)
Query: 54 QDI---ISPVLSKNDLRELGVTLF 74
QDI I L+++DL+E+G+TLF
Sbjct: 26 QDIDLRIFLTLTESDLKEIGITLF 49
>gnl|CDD|188905 cd09506, SAM_Shank1,2,3, SAM domain of Shank1,2,3 family
proteins. SAM (sterile alpha motif) domain of
Shank1,2,3 family proteins is a protein-protein
interaction domain. Shank1,2,3 proteins are scaffold
proteins that are known to interact with a variety of
cytoplasmic and membrane proteins. SAM domains of the
Shank1,2,3 family are prone to homooligomerization.
They are highly enriched in the postsynaptic density,
acting as scaffolds to organize assembly of
postsynaptic proteins. SAM domains of Shank3 proteins
can form large sheets of helical fibers. Shank genes
show distinct patterns of expression, in rat Shank1
mRNA is found almost exclusively in brain, Shank2 in
brain, kidney and liver, and Shank3 in heart, brain and
spleen.
Length = 66
Score = 25.4 bits (56), Expect = 2.3
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 59 PVLSKNDLRELGVT 72
P L K DL ELGVT
Sbjct: 37 PNLDKEDLTELGVT 50
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 26.0 bits (57), Expect = 3.0
Identities = 9/45 (20%), Positives = 20/45 (44%)
Query: 19 QKSYALKQMMNFNEVQSKLSSSEPVWKILIFDRCGQDIISPVLSK 63
QK+Y + + + + ++ IFD GQ++ S ++
Sbjct: 28 QKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSAGQELFSDMVEN 72
>gnl|CDD|233070 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ.
All proteins in this family are 5'-3' single-strand DNA
exonucleases. These proteins are used in some aspects
of mismatch repair, recombination, and recombinational
repair [DNA metabolism, DNA replication, recombination,
and repair].
Length = 539
Score = 25.7 bits (57), Expect = 5.2
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 45 KILIFDRCGQD-IISPVLSKNDLRELGVTLFLYSAEVLDEEY 85
KILIF D I S + L++LGV + Y + E Y
Sbjct: 56 KILIFGDYDVDGITSTAILVEFLKDLGVNVDYYIPNRITEGY 97
>gnl|CDD|227934 COG5647, COG5647, Cullin, a subunit of E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 773
Score = 25.1 bits (55), Expect = 6.8
Identities = 9/56 (16%), Positives = 17/56 (30%), Gaps = 9/56 (16%)
Query: 44 WKILIFDRCGQDIISPVLSKNDLRELGVTLFLYSAEVLDEEYSALCL-MCLRMNCY 98
KI F +I+P+L + + +D +Y M +
Sbjct: 160 EKIESFRLIVDSLINPLLYYVERYRAL--------QSIDRKYIEDAKDMLESLERP 207
>gnl|CDD|183481 PRK12376, PRK12376, putative translaldolase; Provisional.
Length = 236
Score = 24.9 bits (55), Expect = 9.2
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 39 SSEPVWKILIFDRCGQDIIS---PVLSKNDLRELGVTLFLYSAE 79
S V+ I+ D+ G DII+ VL K L LG L S E
Sbjct: 178 SPREVYNIIQADQLGCDIITVTPDVLKK--LPLLGKDLEELSLE 219
>gnl|CDD|153314 cd07630, BAR_SNX_like, The Bin/Amphiphysin/Rvs (BAR) domain of
uncharacterized Sorting Nexins. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions. This subfamily is composed of
uncharacterized proteins with similarity to sorting
nexins (SNXs), which 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. BAR domains form dimers that bind to membranes,
induce membrane bending and curvature, and may also be
involved in protein-protein interactions.
Length = 198
Score = 24.8 bits (54), Expect = 9.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 60 VLSKNDLRELGVTLFLYS 77
V++ N+ LG+TL LYS
Sbjct: 82 VVAGNNENTLGLTLDLYS 99
>gnl|CDD|224230 COG1311, HYS2, Archaeal DNA polymerase II, small subunit/DNA
polymerase delta, subunit B [DNA replication,
recombination, and repair].
Length = 481
Score = 24.7 bits (54), Expect = 9.8
Identities = 15/71 (21%), Positives = 23/71 (32%), Gaps = 8/71 (11%)
Query: 28 MNFNEVQSKLS-------SSEPVWKILIFDRCGQDIISPVLSKNDLRELGVTLFLYSAEV 80
F + KLS + V I G D+ + ND+RE F+ S E
Sbjct: 106 PYFRDRYEKLSRIIREREEARYVSPIKKDLEGGSDV-KIIGEVNDVRETKNGHFIISLED 164
Query: 81 LDEEYSALCLM 91
+ +
Sbjct: 165 TTGVVTVVLGK 175
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
0.324 0.138 0.410
Gapped
Lambda K H
0.267 0.0587 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,751,889
Number of extensions: 382500
Number of successful extensions: 396
Number of sequences better than 10.0: 1
Number of HSP's gapped: 395
Number of HSP's successfully gapped: 15
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.5 bits)