RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2574
(115 letters)
>gnl|CDD|185434 PTZ00083, PTZ00083, 40S ribosomal protein S27; Provisional.
Length = 85
Score = 137 bits (346), Expect = 1e-43
Identities = 54/70 (77%), Positives = 61/70 (87%)
Query: 6 DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
DLL+P E RKHKLKRLVQ PNSYFMDVKCPGC +ITTVFSHAQ+VV+C GCS+ LCQ
Sbjct: 7 DLLYPDPESEARKHKLKRLVQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66
Query: 66 PTGGRARLTE 75
PTGG+A+LTE
Sbjct: 67 PTGGKAKLTE 76
>gnl|CDD|165774 PLN00209, PLN00209, ribosomal protein S27; Provisional.
Length = 86
Score = 133 bits (337), Expect = 2e-42
Identities = 52/70 (74%), Positives = 60/70 (85%)
Query: 6 DLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65
DLL+P EKRKHKLKRLVQ PNS+FMDVKC GC+ ITTVFSH+Q+VV+C C T+LCQ
Sbjct: 8 DLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67
Query: 66 PTGGRARLTE 75
PTGG+ARLTE
Sbjct: 68 PTGGKARLTE 77
>gnl|CDD|110652 pfam01667, Ribosomal_S27e, Ribosomal protein S27.
Length = 55
Score = 83.7 bits (207), Expect = 6e-23
Identities = 32/48 (66%), Positives = 38/48 (79%)
Query: 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE 75
PNSYF+DVKCPGC ITTVFSHAQ+VV C C +LC+PTGG+ +L
Sbjct: 1 PNSYFLDVKCPGCGNITTVFSHAQTVVKCIICGKVLCEPTGGKGKLKA 48
>gnl|CDD|224962 COG2051, RPS27A, Ribosomal protein S27E [Translation, ribosomal
structure and biogenesis].
Length = 67
Score = 80.1 bits (198), Expect = 2e-21
Identities = 27/61 (44%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 15 EKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLT 74
RK K+ + P S F+ VKCP C VFSHA +VV C C T L +PTGG+A+++
Sbjct: 3 RGRKVKIPK---EPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGKAKIS 59
Query: 75 E 75
Sbjct: 60 G 60
>gnl|CDD|179013 PRK00415, rps27e, 30S ribosomal protein S27e; Reviewed.
Length = 59
Score = 58.0 bits (141), Expect = 8e-13
Identities = 24/50 (48%), Positives = 31/50 (62%)
Query: 24 LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARL 73
L+ P S F+ VKCP C VFSHA +VV C C L +PTGG+A++
Sbjct: 1 LIPQPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKI 50
>gnl|CDD|212569 cd11696, DHR2_DOCK_B, Dock Homology Region 2, a GEF domain, of
Class B Dedicator of Cytokinesis proteins. DOCK
proteins are atypical guanine nucleotide exchange
factors (GEFs) that lack the conventional Dbl homology
(DH) domain. As GEFs, they activate small GTPases by
exchanging bound GDP for free GTP. They are divided
into four classes (A-D) based on sequence similarity
and domain architecture; class B includes Dock3 and 4.
Dock3 is a specific GEF for Rac and it regulates
N-cadherin dependent cell-cell adhesion, cell polarity,
and neuronal morphology. It promotes axonal growth by
stimulating actin polymerization and microtubule
assembly. Dock4 activates the Ras family GTPase Rap1,
probably indirectly through interaction with Rap
regulatory proteins. It plays a role in regulating
dendritic growth and branching in hippocampal neurons,
where it is highly expressed. All DOCKs contain two
homology domains: the DHR-1 (Dock homology region-1),
also called CZH1 (CED-5, Dock180, and MBC-zizimin
homology 1), and DHR-2 (also called CZH2 or Docker).
The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of class B DOCKs,
which contains the catalytic GEF activity for Rac
and/or Cdc42. Class B DOCKs also contain an SH3 domain
at the N-terminal region and a PxxP motif at the
C-terminus.
Length = 391
Score = 29.7 bits (67), Expect = 0.24
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 2 PLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKC-----PGCYKITTVF 47
PL DL HPSQ E +RK L + YF KC P C ++ ++
Sbjct: 40 PLPADLHHPSQPEWQRKEALYLKILQ---YFDRGKCWEKGIPLCRELAELY 87
>gnl|CDD|240998 cd12554, RRM1_RBM15B, RNA recognition motif 1 in putative RNA
binding motif protein 15B (RBM15B) from vertebrate.
This subfamily corresponds to the RRM1 of RBM15B, also
termed one twenty-two 3 (OTT3), a paralog of RNA
binding motif protein 15 (RBM15), also known as
One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has
post-transcriptional regulatory activity. It is a
nuclear protein sharing with RBM15 the association with
the splicing factor compartment and the nuclear
envelope as well as the binding to mRNA export factors
NXF1 and Aly/REF. RBM15B belongs to the Spen (split
end) protein family, which shares a domain architecture
comprising of three N-terminal RNA recognition motifs
(RRMs), also known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralog and ortholog C-terminal) domain. .
Length = 81
Score = 26.7 bits (59), Expect = 1.3
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 9 HPSQAEEKRKHKLKRLV 25
HP A E R K +RL+
Sbjct: 53 HPEDAREARHAKSRRLL 69
>gnl|CDD|212577 cd11704, DHR2_DOCK3, Dock Homology Region 2, a GEF domain, of
Class B Dedicator of Cytokinesis 3. Dock3, also called
modifier of cell adhesion (MOCA), is an atypical
guanine nucleotide exchange factor (GEF) that lacks the
conventional Dbl homology (DH) domain. As a GEF, it
activates small GTPases by exchanging bound GDP for
free GTP. Dock3 is a specific GEF for Rac. It regulates
N-cadherin dependent cell-cell adhesion, cell polarity,
and neuronal morphology. It promotes axonal growth by
stimulating actin polymerization and microtubule
assembly. DOCK proteins are divided into four classes
(A-D) based on sequence similarity and domain
architecture; class B includes Dock3 and 4. All DOCKs
contain two homology domains: the DHR-1 (Dock homology
region-1), also called CZH1 (CED-5, Dock180, and
MBC-zizimin homology 1), and DHR-2 (also called CZH2 or
Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock3, which
contains the catalytic GEF activity for Rac and/or
Cdc42. Class B DOCKs also contain an SH3 domain at the
N-terminal region and a PxxP motif at the C-terminus.
Length = 392
Score = 27.7 bits (61), Expect = 1.6
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 2 PLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKC 37
PL + L +PSQ+E +RK L R + H YF K
Sbjct: 40 PLREFLHYPSQSEWQRKEGLCRKIIH---YFNKGKS 72
>gnl|CDD|220377 pfam09747, DUF2052, Coiled-coil domain containing protein
(DUF2052). This entry is of sequences of two conserved
domains separated by a region of low complexity,
spanning some 200 residues. The function is unknown.
Length = 178
Score = 25.8 bits (57), Expect = 4.9
Identities = 6/19 (31%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 16 KRKHKLKRLVQHPNSYFMD 34
+R L+RL++ YF +
Sbjct: 2 RRYAYLQRLIEEGE-YFSE 19
>gnl|CDD|185123 PRK15201, PRK15201, fimbriae regulatory protein FimW;
Provisional.
Length = 198
Score = 25.4 bits (55), Expect = 6.6
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 39 GCYKITTVFSHAQSVVICAGC 59
GCY+I H V+IC C
Sbjct: 58 GCYQIPMHTQHQLRVIICNKC 78
>gnl|CDD|131677 TIGR02629, L_rham_iso_rhiz, L-rhamnose catabolism isomerase,
Pseudomonas stutzeri subtype. Members of this family
are isomerases in the pathway of L-rhamnose catabolism
as found in Pseudomonas stutzeri and in a number of the
Rhizobiales. This family differs from the L-rhamnose
isomerases of Escherichia coli (see TIGR01748). This
enzyme catalyzes the isomerization step in rhamnose
catabolism. Genetic evidence in Rhizobium leguminosarum
bv. trifolii suggests phosphorylation occurs first, then
isomerization of the the phosphorylated sugar, but
characterization of the recombinant enzyme from
Pseudomonas stutzeri does show L-rhamnose isomerase
activity. The name given is deliberately vague because
the relative order of phosphorylation and isomerization
is unclear [Energy metabolism, Sugars].
Length = 412
Score = 25.8 bits (56), Expect = 6.9
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 7/36 (19%)
Query: 87 CALDSG--TPTTDTE-----LIRMSHCGGFYFDDSQ 115
C +D G P + E LI+ GGF+F+DS+
Sbjct: 242 CLVDLGHHAPNVNIEMIVARLIQFKKLGGFHFNDSK 277
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
0.321 0.135 0.425
Gapped
Lambda K H
0.267 0.0676 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,581,316
Number of extensions: 434482
Number of successful extensions: 363
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 17
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
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 (21.9 bits)
S2: 53 (24.3 bits)