RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15554
(339 letters)
>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein. This family contains
Sodium, Potassium, Calcium ion channels. This family is
6 transmembrane helices in which the last two helices
flank a loop which determines ion selectivity. In some
sub-families (e.g. Na channels) the domain is repeated
four times, whereas in others (e.g. K channels) the
protein forms as a tetramer in the membrane. A bacterial
structure of the protein is known for the last two
helices but is not the Pfam family due to it lacking the
first four helices.
Length = 194
Score = 68.5 bits (168), Expect = 9e-14
Identities = 33/144 (22%), Positives = 61/144 (42%), Gaps = 3/144 (2%)
Query: 93 YVELACNAWFTFELLVRAVVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDKVQQSDILE 152
++ FT E+L++ + ++ RSP N++D + L ++L + S +L
Sbjct: 1 ILDYVFTVIFTLEMLLKFIALGFKRKYFRSPWNILDFLVVLPSLVSLILFLLGEDSGLLR 60
Query: 153 FFSIIRILRLFKLTRHSPGLKILIHTFKASAK---ELTLLVFFLVLGIVVFASLVYYAER 209
++R+LRL +L R PGL+ L+ + S K L LL+ L+ + ++ E
Sbjct: 61 VLRLLRLLRLLRLLRRFPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAIIGVQLFGGEL 120
Query: 210 LQVSPNIFQFIRSPVNVIDIIATL 233
+ I N L
Sbjct: 121 DKCCDKNENPINGNSNFDSYGEAL 144
Score = 52.3 bits (126), Expect = 4e-08
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 3/103 (2%)
Query: 209 RLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDKVQQSDILEFFSIIRILRLFKLTRH 268
+ ++ RSP N++D + L ++L + S +L ++R+LRL +L R
Sbjct: 17 KFIALGFKRKYFRSPWNILDFLVVLPSLVSLILFLLGEDSGLLRVLRLLRLLRLLRLLRR 76
Query: 269 SPGLKILIHTFKASAK---ELTLLVFFLVLGIVVFASLVYYAE 308
PGL+ L+ + S K L LL+ L+ + ++ E
Sbjct: 77 FPGLRTLLQSLGRSLKSLLNLLLLLLLLLFIFAIIGVQLFGGE 119
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 66.9 bits (164), Expect = 4e-13
Identities = 23/33 (69%), Positives = 27/33 (81%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMV 33
VVN LNDLY+ FD+II + YKV+TIGDAYMV
Sbjct: 59 VVNLLNDLYSRFDQIIDRHGGYKVKTIGDAYMV 91
>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase
catalytic domain.
Length = 184
Score = 58.0 bits (141), Expect = 4e-10
Identities = 20/34 (58%), Positives = 25/34 (73%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMVI 34
+V LNDLYT FD ++ + VYKV+TIGDAYM
Sbjct: 31 LVRLLNDLYTRFDELLDKHGVYKVKTIGDAYMAA 64
>gnl|CDD|143636 cd07302, CHD, cyclase homology domain. Catalytic domains of the
mononucleotidyl cyclases (MNC's), also called cyclase
homology domains (CHDs), are part of the class III
nucleotidyl cyclases. This class includes eukaryotic
and prokaryotic adenylate cyclases (AC's) and guanylate
cyclases (GC's). They seem to share a common catalytic
mechanism in their requirement for two magnesium ions
to bind the polyphosphate moiety of the nucleotide.
Length = 177
Score = 51.8 bits (125), Expect = 5e-08
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMVI 34
+V LN+ ++ FD II+ + +TIGDA M +
Sbjct: 24 LVELLNEYFSAFDEIIERHGGTVDKTIGDAVMAV 57
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.
Class III nucleotidyl cyclases are the largest, most
diverse group of nucleotidyl cyclases (NC's) containing
prokaryotic and eukaryotic proteins. They can be
divided into two major groups; the mononucleotidyl
cyclases (MNC's) and the diguanylate cyclases (DGC's).
The MNC's, which include the adenylate cyclases (AC's)
and the guanylate cyclases (GC's), have a conserved
cyclase homology domain (CHD), while the DGC's have a
conserved GGDEF domain, named after a conserved motif
within this subgroup. Their products, cyclic guanylyl
and adenylyl nucleotides, are second messengers that
play important roles in eukaryotic signal transduction
and prokaryotic sensory pathways.
Length = 133
Score = 42.0 bits (99), Expect = 6e-05
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMVILAVTSVFFICVSVVSFALK 53
LN+L FD +I+ K++TIGD +MV+ + + V+FA
Sbjct: 24 GDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSGLDHPA----AAVAFAED 72
>gnl|CDD|241125 cd12681, RRM_SKAR, RNA recognition motif in S6K1 Aly/REF-like
target (SKAR) and similar proteins. This subgroup
corresponds to the RRM of SKAR, also termed polymerase
delta-interacting protein 3 (PDIP3), 46 kDa DNA
polymerase delta interaction protein (PDIP46), belonging
to the Aly/REF family of RNA binding proteins that have
been implicated in coupling transcription with pre-mRNA
splicing and nucleo-cytoplasmic mRNA transport. SKAR is
widely expressed and localizes to the nucleus. It may be
a critical player in the function of S6K1 in cell and
organism growth control by binding the activated,
hyperphosphorylated form of S6K1 but not S6K2.
Furthermore, SKAR functions as a protein partner of the
p50 subunit of DNA polymerase delta. In addition, SKAR
may have particular importance in pancreatic beta cell
size determination and insulin secretion. SKAR contains
a well conserved RNA recognition motif (RRM), also
termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain).
Length = 69
Score = 30.7 bits (70), Expect = 0.16
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 141 LQDKVQQSDILEFFSIIRILRLFKLTRHSPGLKILIHTFKASA 183
L V + DI+E FS I L+ +L R PG+ +++ K A
Sbjct: 8 LHPSVTEDDIVELFSAIGALKRARLVR--PGVAEVVYVRKDDA 48
Score = 30.7 bits (70), Expect = 0.16
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 241 LQDKVQQSDILEFFSIIRILRLFKLTRHSPGLKILIHTFKASA 283
L V + DI+E FS I L+ +L R PG+ +++ K A
Sbjct: 8 LHPSVTEDDIVELFSAIGALKRARLVR--PGVAEVVYVRKDDA 48
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 29.4 bits (66), Expect = 2.4
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMVI 34
+V LN + ++ + V+ IGD ++ +
Sbjct: 69 LVELLNLYFDAVAEVVARHGGRVVKFIGDGFLAV 102
>gnl|CDD|200519 cd11258, Sema_4C, The Sema domain, a protein interacting module, of
semaphorin 4C (Sema4C). Sema4C acts as a Plexin B2
ligand to regulate the development of cerebellar granule
cells and to modulate ureteric branching in the
developing kidney. The binding of Sema4C to Plexin B2
results the phosphorylation of downstream regulator
ErbB-2 and the plexin protein itself. The cytoplasmic
region of Sema4C binds a neurite-outgrowth-related
protein SFAP75, suggesting that Sema4C may also play a
role in neural function. Sema4C 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 = 458
Score = 29.0 bits (65), Expect = 3.7
Identities = 10/47 (21%), Positives = 17/47 (36%)
Query: 293 LVLGIVVFASLVYYAERLQTLDRLYEYSKLEIAIDYTSLKISSFLDV 339
++ V S V+ E LQ D+ S + L S ++
Sbjct: 406 WLIKAVSLGSWVHMIEELQVFDQEPPESLVVSQSSKKLLFAGSRSEL 452
>gnl|CDD|234010 TIGR02781, VirB9, P-type conjugative transfer protein VirB9. The
VirB9 protein is found in the vir locus of Agrobacterium
Ti plasmids where it is involved in a type IV secretion
system. VirB9 is a homolog of the F-type conjugative
transfer system TraK protein (which is believed to be an
outer membrane pore-forming secretin, TIGR02756) as well
as the Ti system TrbG protein [Cellular processes,
Conjugation].
Length = 243
Score = 28.1 bits (63), Expect = 6.4
Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 2/60 (3%)
Query: 185 ELTLLVFFLVLGIVVFASLVYYAERLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDK 244
+L + + L L I +A + I + +P +V+ ++ + + T I D
Sbjct: 1 KLLIALLLLTLAIPAYA--LNTPRGSSYDSRIRTVVYNPDDVVRVVTSYGYSTTIEFADD 58
>gnl|CDD|183874 PRK13165, PRK13165, cytochrome c-type biogenesis protein CcmE;
Reviewed.
Length = 160
Score = 27.3 bits (61), Expect = 9.1
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 284 KELTLLVFFLVLGIVVFASLVYYAERLQTLDRLY 317
K L L ++ G+ + LV YA R +D Y
Sbjct: 7 KRLWLACA-VLAGLALTIGLVLYALR-SNIDLFY 38
>gnl|CDD|185317 PRK15419, PRK15419, proline:sodium symporter PutP; Provisional.
Length = 502
Score = 27.7 bits (61), Expect = 9.8
Identities = 15/59 (25%), Positives = 30/59 (50%)
Query: 204 VYYAERLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDKVQQSDILEFFSIIRILRL 262
V + + +Q S IF I +PV VI + +++ Q ++ D+L+ + + I+ L
Sbjct: 183 VSWTDTVQASLMIFALILTPVIVIISVGGFGDSLEVIKQKSIENVDMLKGLNFVAIISL 241
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
0.331 0.144 0.413
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,697,687
Number of extensions: 1782908
Number of successful extensions: 2965
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2932
Number of HSP's successfully gapped: 96
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 59 (26.5 bits)