RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy336
(121 letters)
>gnl|CDD|224212 COG1293, COG1293, Predicted RNA-binding protein homologous to
eukaryotic snRNP [Transcription].
Length = 564
Score = 59.3 bits (144), Expect = 1e-11
Identities = 27/65 (41%), Positives = 40/65 (61%), Gaps = 5/65 (7%)
Query: 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTGEAEYHIIVELYDR-----GNIVLTDKDYIIL 55
+RKHLK R+E ++ LG DRI++L+F E IIVEL+ GN++L D++ I+
Sbjct: 81 LRKHLKGARIEKIEQLGFDRILELKFKKDEIGDKIIVELFLEIMGKHGNLILVDEERKII 140
Query: 56 NVLRP 60
LR
Sbjct: 141 EALRH 145
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 57.6 bits (140), Expect = 6e-11
Identities = 23/63 (36%), Positives = 40/63 (63%), Gaps = 4/63 (6%)
Query: 1 MRKHLKNKRLESLKLLGLDRIIDLQFGTG---EAEYHIIVELYDR-GNIVLTDKDYIILN 56
+RKHL+ R+ ++ +G DRI++ +F E EY +IVEL R NI+L D++ I++
Sbjct: 76 LRKHLEGGRIVDIEQIGFDRIVEFEFEKRDGDEIEYTLIVELMGRHSNIILVDENNKIID 135
Query: 57 VLR 59
++
Sbjct: 136 AIK 138
>gnl|CDD|115835 pfam07206, Baculo_LEF-10, Baculovirus late expression factor 10
(LEF-10). This family consists of several Baculovirus
specific late expression factor 10 (LEF-10) sequences.
LEF-10 is thought to be a late expressed structural
protein although its exact function is unknown.
Length = 71
Score = 27.2 bits (61), Expect = 0.71
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 42 RGNIVLTDKDYIILNVLRPHSD 63
+ N+ L D Y+ILNV+ S
Sbjct: 16 KDNLELIDNTYLILNVVDQESG 37
>gnl|CDD|236186 PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional.
Length = 399
Score = 27.9 bits (63), Expect = 1.2
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 84 SGAPTQEMLYELFTKEKYGEQIKKILVPQLGPQAKILV 121
SGA L L T Y E +K+ L +++L+
Sbjct: 343 SGAVGLGALAALMTDPDYQELREKL---GLDEDSRVLL 377
>gnl|CDD|132296 TIGR03252, TIGR03252, uncharacterized HhH-GPD family protein. This
model describes a small, well-conserved bacterial
protein family. Its sequence largely consists of a
domain, HhH-GPD, found in a variety of related base
excision DNA repair enzymes (see pfam00730) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 177
Score = 26.7 bits (59), Expect = 2.7
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 70 YVREKYPVDLAKV-RSGAPT-QEMLYELFTKEKYGEQIKKILVPQLGPQ 116
YV + Y D V G P +E+L L +G+Q KI + LG Q
Sbjct: 90 YVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLGKQ 138
>gnl|CDD|132373 TIGR03330, SAM_DCase_Bsu, S-adenosylmethionine decarboxylase
proenzyme, Bacillus form. Members of this protein
family are the single chain precursor of the two chains
of the mature S-adenosylmethionine decarboxylase as
found in Methanocaldococcus jannaschii, Bacillus
subtilis, and a wide range of other species. It differs
substantially in architecture from the form as found in
Escherichia coli, and lacks any extended homology to
the eukaryotic form (TIGR00535) [Central intermediary
metabolism, Polyamine biosynthesis].
Length = 112
Score = 26.0 bits (58), Expect = 3.2
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 33 YHIIVELYDRGNIVLTDKDYII 54
H+IV+LY L D ++I
Sbjct: 5 RHLIVDLYGCDPEKLDDVEFIE 26
>gnl|CDD|197563 smart00187, INB, Integrin beta subunits (N-terminal portion of
extracellular region). Portion of beta integrins that
lies N-terminal to their EGF-like repeats. Integrins are
cell adhesion molecules that mediate cell-extracellular
matrix and cell-cell interactions. They contain both
alpha and beta subunits. Beta integrins are proposed to
have a von Willebrand factor type-A "insert" or "I"
-like domain (although this remains to be confirmed).
Length = 423
Score = 26.5 bits (59), Expect = 3.5
Identities = 12/26 (46%), Positives = 13/26 (50%), Gaps = 7/26 (26%)
Query: 58 LRPHSDGEEVRFYVR----EKYPVDL 79
LRP GE F + E YPVDL
Sbjct: 80 LRP---GEPQNFTLTVRQAEDYPVDL 102
>gnl|CDD|215878 pfam00362, Integrin_beta, Integrin, beta chain. Integrins have
been found in animals and their homologues have also
been found in cyanobacteria, probably due to horizontal
gene transfer. The sequences repeats have been trimmed
due to an overlap with EGF.
Length = 424
Score = 26.4 bits (59), Expect = 3.8
Identities = 14/26 (53%), Positives = 14/26 (53%), Gaps = 7/26 (26%)
Query: 58 LRPHSDGEEVRF--YVR--EKYPVDL 79
LRP GE F VR E YPVDL
Sbjct: 81 LRP---GEPQTFNLKVRQAEDYPVDL 103
>gnl|CDD|202344 pfam02675, AdoMet_dc, S-adenosylmethionine decarboxylase. This
family contains several S-adenosylmethionine
decarboxylase proteins from bacterial and
archaebacterial species. S-adenosylmethionine
decarboxylase (AdoMetDC), a key enzyme in the
biosynthesis of spermidine and spermine, is first
synthesised as a proenzyme, which is cleaved post
translationally to form alpha and beta subunits. The
alpha subunit contains a covalently bound pyruvoyl
group derived from serine that is essential for
activity.
Length = 107
Score = 25.2 bits (56), Expect = 6.2
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 34 HIIVELYDRGNIVLTDKDYI 53
H+I +LY +L D + +
Sbjct: 1 HLIADLYGCDADLLNDAERL 20
>gnl|CDD|237267 PRK13012, PRK13012, 2-oxoacid dehydrogenase subunit E1;
Provisional.
Length = 896
Score = 26.0 bits (58), Expect = 6.3
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 41 DRGNIVLTDKDYIILNVLRPHSDGEEVRFYVREK 74
DR + L+D+ L +P D E+R Y+ +
Sbjct: 433 DRFRLPLSDEQLEQLPFYKPAEDSPEMR-YLHAR 465
>gnl|CDD|214612 smart00314, RA, Ras association (RalGDS/AF-6) domain. RasGTP
effectors (in cases of AF6, canoe and RalGDS); putative
RasGTP effectors in other cases. Kalhammer et al. have
shown that not all RA domains bind RasGTP. Predicted
structure similar to that determined, and that of the
RasGTP-binding domain of Raf kinase. Predicted RA
domains in PLC210 and nore1 found to bind RasGTP.
Included outliers (Grb7, Grb14, adenylyl cyclases
etc.).
Length = 90
Score = 25.0 bits (55), Expect = 7.5
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 32 EYHIIVELYDRGNIVLTDKDYIILNVLRPHSDGEEVRFYVREKY 75
EY ++ L D VL D + + G +RF +R++
Sbjct: 47 EYVLVEVLPDGKERVLPDDENPLQLQKLWPRRGPNLRFVLRKRD 90
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
0.320 0.142 0.400
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,478,046
Number of extensions: 603800
Number of successful extensions: 575
Number of sequences better than 10.0: 1
Number of HSP's gapped: 572
Number of HSP's successfully gapped: 32
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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 (21.8 bits)
S2: 53 (24.2 bits)