RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17883
(195 letters)
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 68.0 bits (166), Expect = 2e-13
Identities = 47/193 (24%), Positives = 97/193 (50%), Gaps = 5/193 (2%)
Query: 2 YVTALYFTMTCMTSVGFGNVAAETDNEKIFTICMMIIAALLYATIFGHVTTIIQQMTSAT 61
Y++A+Y+++T MT+VG+G++ A E IF I M+ L A + G++T ++ + T T
Sbjct: 251 YISAIYWSITTMTTVGYGDLHAVNTIEMIFIIFYMLFNLGLTAYLIGNMTNLVVEGTRRT 310
Query: 62 AKYHDMLNNVREFMKLHEVPKALSERVMDYVVSTWAMTKGLDTDKVLNYCPKDMKADICV 121
++ + + F+ + +P L ++++ Y+ + + L+ ++++ PK + IC
Sbjct: 311 MEFRNSIEAASNFVGRNRLPPRLKDQILAYMCLRFK-AESLNQQQLIDQLPKSICKSICQ 369
Query: 122 HLNRKVFNEHPAFRLASDGCLRALAMHFTMSHSAPGDLLYHTGESIDSLCFIVTGSLEVI 181
HL V + F+ S L L + P + + E+ D + +V+G +E+I
Sbjct: 370 HLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPPREDVIMQNEAPDDVYIVVSGEVEII 429
Query: 182 ----QDDEVVAIL 190
+ + VV L
Sbjct: 430 DSEGEKERVVGTL 442
>gnl|CDD|237999 cd00038, CAP_ED, effector domain of the CAP family of transcription
factors; members include CAP (or cAMP receptor protein
(CRP)), which binds cAMP, FNR (fumarate and nitrate
reduction), which uses an iron-sulfur cluster to sense
oxygen) and CooA, a heme containing CO sensor. In all
cases binding of the effector leads to conformational
changes and the ability to activate transcription.
Cyclic nucleotide-binding domain similar to CAP are also
present in cAMP- and cGMP-dependent protein kinases
(cAPK and cGPK) and vertebrate cyclic nucleotide-gated
ion-channels. Cyclic nucleotide-monophosphate binding
domain; proteins that bind cyclic nucleotides (cAMP or
cGMP) share a structural domain of about 120 residues;
the best studied is the prokaryotic catabolite gene
activator, CAP, where such a domain is known to be
composed of three alpha-helices and a distinctive
eight-stranded, antiparallel beta-barrel structure;
three conserved glycine residues are thought to be
essential for maintenance of the structural integrity of
the beta-barrel; CooA is a homodimeric transcription
factor that belongs to CAP family; cAMP- and
cGMP-dependent protein kinases (cAPK and cGPK) contain
two tandem copies of the cyclic nucleotide-binding
domain; cAPK's are composed of two different subunits, a
catalytic chain and a regulatory chain, which contains
both copies of the domain; cGPK's are single chain
enzymes that include the two copies of the domain in
their N-terminal section; also found in vertebrate
cyclic nucleotide-gated ion-channels.
Length = 115
Score = 46.6 bits (111), Expect = 4e-07
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 133 AFRLASDGCLRALAMHFTMSHSAPGDLLYHTGESIDSLCFIVTGSLEVIQDDE-----VV 187
F D L LA G+++ G+ DSL +++GS+EV + DE +V
Sbjct: 1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEDGREQIV 60
Query: 188 AIL 190
L
Sbjct: 61 GFL 63
>gnl|CDD|219619 pfam07885, Ion_trans_2, Ion channel. This family includes the
two membrane helix type ion channels found in bacteria.
Length = 74
Score = 44.9 bits (107), Expect = 8e-07
Identities = 14/47 (29%), Positives = 28/47 (59%)
Query: 2 YVTALYFTMTCMTSVGFGNVAAETDNEKIFTICMMIIAALLYATIFG 48
++ ALYF+ +T++G+G++ TD ++FTI ++I L+
Sbjct: 25 FLDALYFSFVTLTTIGYGDIVPLTDAGRLFTIIYILIGIPLFLLFLA 71
>gnl|CDD|197516 smart00100, cNMP, Cyclic nucleotide-monophosphate binding domain.
Catabolite gene activator protein (CAP) is a prokaryotic
homologue of eukaryotic cNMP-binding domains, present in
ion channels, and cNMP-dependent kinases.
Length = 120
Score = 43.2 bits (102), Expect = 7e-06
Identities = 15/52 (28%), Positives = 23/52 (44%)
Query: 134 FRLASDGCLRALAMHFTMSHSAPGDLLYHTGESIDSLCFIVTGSLEVIQDDE 185
F+ LR LA G+++ G+ DS IV+G +EV + E
Sbjct: 2 FKNLDAEELRELADALEPVRYPAGEVIIRQGDVGDSFYIIVSGEVEVYKVLE 53
>gnl|CDD|236711 PRK10537, PRK10537, voltage-gated potassium channel; Provisional.
Length = 393
Score = 44.2 bits (105), Expect = 1e-05
Identities = 18/52 (34%), Positives = 35/52 (67%), Gaps = 4/52 (7%)
Query: 3 VTALYFTMTCMTSVGFGNVAAETDNEKIFTICMMIIAALLYAT----IFGHV 50
TA YF++ M++VG+G++ +++ ++FTI ++I+ ++AT IFG V
Sbjct: 170 STAFYFSIVTMSTVGYGDIVPVSESARLFTISVIILGITVFATSISAIFGPV 221
>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 = 37.3 bits (87), Expect = 0.002
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 2 YVTALYFTMTCMTSVGFGNV-----AAETDNEKIFTICMMIIAA-LLYATIFGHV 50
Y AL + +T+ G+G+V T KIF + +I+ LL + G +
Sbjct: 140 YGEALLWLFRTLTTEGWGDVMYDTLVPGTVLGKIFFVIFIILGGVLLLNLLIGVI 194
>gnl|CDD|215664 pfam00027, cNMP_binding, Cyclic nucleotide-binding domain.
Length = 91
Score = 33.4 bits (77), Expect = 0.014
Identities = 9/31 (29%), Positives = 20/31 (64%)
Query: 155 APGDLLYHTGESIDSLCFIVTGSLEVIQDDE 185
G++++ G+ DSL +++G ++V + DE
Sbjct: 5 KKGEVIFREGDPADSLYIVLSGKVKVYKLDE 35
>gnl|CDD|223736 COG0664, Crp, cAMP-binding proteins - catabolite gene activator and
regulatory subunit of cAMP-dependent protein kinases
[Signal transduction mechanisms].
Length = 214
Score = 34.8 bits (80), Expect = 0.015
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 127 VFNEHPAFRLASDGCLRALAMHFTMSHSAPGDLLYHTGESIDSLCFIVTGSLEVIQDDE 185
E+P L L LA+ + G++L+ GE DSL I++G +++ + E
Sbjct: 1 ALKENPLLNLLPSELLELLALKLEVRKLPKGEVLFTEGEEADSLYIILSGIVKLYANTE 59
>gnl|CDD|236969 PRK11753, PRK11753, DNA-binding transcriptional dual regulator Crp;
Provisional.
Length = 211
Score = 30.7 bits (70), Expect = 0.39
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 160 LYHTGESIDSLCFIVTGSLEVIQDDE 185
L H GE ++L +IV GS+ V+ DE
Sbjct: 31 LIHAGEKAETLYYIVKGSVAVLIKDE 56
>gnl|CDD|182485 PRK10472, PRK10472, low affinity gluconate transporter;
Provisional.
Length = 445
Score = 29.0 bits (65), Expect = 1.8
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 155 APGDLLYHTGESIDSLCFIVTGSLEVIQDDEVVAIL 190
A G+ L G I CF++ ++ +IQ VA L
Sbjct: 328 ALGEALTGMGLPIAITCFVLAAAVRIIQGSATVACL 363
>gnl|CDD|214001 cd12802, HopAB_PID, Pto-interacting domain of the HopAB family of
Type III Effector proteins. HopAB family members are
type III effector proteins that are secreted by the
plant pathogen Pseudomonas syringae into the host plant
to inhibit its immune system and facilitate the spread
of the pathogen. AvrPtoB, also called HopAB3, is the
best studied member of the family. It suppresses host
basal defenses by interfering with PAMP
(pathogen-associated molecular signature)-triggered
immunity (PTI) through binding and inhibiting BAK1, a
kinase which serves to activate defense signaling. It
also recognizes the kinase Pto to activate
effector-triggered immunity (ETI). AvrPtoB contains an
N-terminal region that contains two kinase-interacting
domains (KID) and a C-terminal E3 ligase domain. The
first KID recognizes the PTI-associated kinase Bti9 as
well as Pto, and is referred to as the Pto-binding
domain (PID). The second KID interacts with BAK1 and
FLS2, which are leucine-rich repeat-containing
receptor-like kinases, and is called the
BAK1-interacting domain (BID). This family also contains
a unique member, HopPmaL, which is shorter and lacks the
C-terminal E3 ligase domain.
Length = 79
Score = 27.1 bits (60), Expect = 2.0
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 49 HVTTIIQQMTSATAKYHDMLNNVREFMKLHEVPKALSERVMDYVVSTWA--MTKGLDTDK 106
H I+QQ+ A A ++ +R M V ALS + + + + G+ D
Sbjct: 5 HANRIVQQLVEAGADLANIRTMLRNAMNGDAV--ALSRVEQNILRQHFPNMLMCGISRDS 62
Query: 107 VL 108
L
Sbjct: 63 EL 64
>gnl|CDD|148689 pfam07230, Phage_T4_Gp20, Bacteriophage T4-like capsid assembly
protein (Gp20). This family consists of several
bacteriophage T4-like capsid assembly (or portal)
proteins. The exact mechanism by which the
double-stranded (ds) DNA bacteriophages incorporate the
portal protein at a unique vertex of the icosahedral
capsid is unknown. In phage T4, there is evidence that
this vertex, constituted by 12 subunits of gp20, acts
as an initiator for the assembly of the major capsid
protein and the scaffolding proteins into a prolate
icosahedron of precise dimensions. The regulation of
portal protein gene expression is an important
regulator of prohead assembly in bacteriophage T4.
Length = 500
Score = 28.5 bits (64), Expect = 2.7
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 66 DMLNNVREFMKLHEVPKALSERVMDYVVS 94
+++ RE EV A+ E V + +V
Sbjct: 67 ELIRRYRELALYPEVDNAIDEIVNEAIVY 95
>gnl|CDD|114140 pfam05399, EVI2A, Ectropic viral integration site 2A protein
(EVI2A). This family contains several mammalian
ectropic viral integration site 2A (EVI2A) proteins. The
function of this protein is unknown although it is
thought to be a membrane protein and may function as an
oncogene in retrovirus induced myeloid tumours.
Length = 227
Score = 27.3 bits (60), Expect = 5.4
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 21 VAAETDNEKIFTICMMIIAALLYATIFGHVTTII 54
V E + IC++IIAAL F ++T++
Sbjct: 120 VCEENTSNFAMLICLIIIAALFLICTFLFLSTVV 153
>gnl|CDD|221888 pfam13001, Ecm29, Proteasome stabiliser. The proteasome consists
of two subunits, and the capacity of the proteasome to
degrade protein depends crucially on the interaction
between these two subunits. This interaction is affected
by a wide range of factors including metabolites, such
as ATP, and proteasome-associated proteins such as
Ecm29. Ecm29 stabilises the interaction between the two
subunits.
Length = 497
Score = 27.2 bits (61), Expect = 5.6
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 14/71 (19%)
Query: 106 KVLNYCPKDMKADICVHLNRKVFNEHPAFRLASDGC---LRALAMHFTM------SHSAP 156
K+L+ K + A ++ + L SD L+ L + F H+AP
Sbjct: 299 KILSLLCKSILAATSFPAILQIIFDG----LYSDNTNSKLKQLGLQFITWSVWVLKHAAP 354
Query: 157 GDLLYHTGESI 167
DL+ I
Sbjct: 355 -DLIKLLRPFI 364
>gnl|CDD|217575 pfam03464, eRF1_2, eRF1 domain 2. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif
at an exposed tip of domain 2 suggests that the Gln
residue coordinates a water molecule to mediate the
hydrolytic activity at the peptidyl transferase centre.
A conserved groove on domain 1, 80 A from the GGQ
motif, is proposed to form the codon recognition site.
This family also includes other proteins for which the
precise molecular function is unknown. Many of them are
from Archaebacteria. These proteins may also be
involved in translation termination but this awaits
experimental verification.
Length = 129
Score = 26.1 bits (58), Expect = 8.2
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 42 LYATIFGHVTTIIQQMTSATAKYHDMLN-NVREFM-KLHEVPKALSERVMDYV 92
L + G+ I+ ++T H + R F K HE + ++E Y
Sbjct: 13 LIGLLTGYGIEILGKITVGLPGKHGRGGQSARRFEEKRHEFYRKVAEAANQYF 65
>gnl|CDD|187757 cd09317, TDT_Mae1_like, C4-dicarboxylate transporter/malic acid
transport protein family includes Mae1. This family
contains eukaryotic homologs of C4-dicarboxylate
transporter/malic acid transport proteins which are part
of the Tellurite-resistance/Dicarboxylate Transporter
(TDT) family. This includes the MAE1 gene in
Schizosaccharomyces pombe gene that encodes malate
permease, Mae1, which functions by proton symport and
transports C4-dicarboxylates (malate, fumarate,
succinate, oxaloacetate, etc.), but not K-ketoglutarate.
Length = 330
Score = 26.4 bits (59), Expect = 9.6
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 30 IFTICMMIIAALLYATIFGHVTTIIQQMTSA 60
I+ +I+A Y +F T + MT A
Sbjct: 107 IYVALSLIVAIGQYLLLFSTHTFPLTTMTPA 137
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
0.326 0.136 0.413
Gapped
Lambda K H
0.267 0.0685 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,667,410
Number of extensions: 869673
Number of successful extensions: 1155
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1153
Number of HSP's successfully gapped: 27
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 56 (25.4 bits)