RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1645
(143 letters)
>gnl|CDD|216037 pfam00637, Clathrin, Region in Clathrin and VPS. Each region is
about 140 amino acids long. The regions are composed of
multiple alpha helical repeats. They occur in the arm
region of the Clathrin heavy chain.
Length = 143
Score = 38.8 bits (91), Expect = 2e-04
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 72 FIKADDPSAYMDVVETSHATESWEDLVRYLQMARKKARESY--IESELIYAYARTNRLAD 129
I+ DP VV+ E+L+ YL+ A K+ +++ L+ YA+
Sbjct: 1 LIELTDPIDISRVVKLFEKRGLLEELIPYLESALKENSRENPALQTALLELYAKYEDPEK 60
Query: 130 LEEFIS 135
LEEF+
Sbjct: 61 LEEFLK 66
Score = 34.5 bits (80), Expect = 0.007
Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 16/96 (16%)
Query: 7 PATHNALAKIYIDSN--NNPERFLK---FFLVD---------HLSKTPFYVLRCNEPGVW 52
PA AL ++Y E FLK + ++ L + + + N G +
Sbjct: 42 PALQTALLELYAKYEDPEKLEEFLKKNNNYDLEKVAKLCEKADLYEEAVILYKKN--GNY 99
Query: 53 SQLAKAQLQKGLVKESIDSFIKADDPSAYMDVVETS 88
+ + L K++I+ +K++DP + ++
Sbjct: 100 KEAISLLKKLKLYKDAIEYAVKSNDPELWEKLLNAL 135
>gnl|CDD|128594 smart00299, CLH, Clathrin heavy chain repeat homology.
Length = 140
Score = 37.6 bits (88), Expect = 5e-04
Identities = 18/72 (25%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 72 FIKADDPSAYMDVVETSHATESWEDLVRYLQMARKKARE-SYIESELIYAYARTNRLADL 130
++ DP +VVE E+L+ YL+ A K E ++++LI YA+ + ++
Sbjct: 1 LLEVSDPIDVSEVVELFEKRNLLEELIPYLESALKLNSENPALQTKLIELYAKYDPQKEI 60
Query: 131 EEFISGEGFFEI 142
E + ++I
Sbjct: 61 ERLDNKSNHYDI 72
Score = 26.1 bits (58), Expect = 5.0
Identities = 6/28 (21%), Positives = 9/28 (32%), Gaps = 2/28 (7%)
Query: 6 EPATHNALAKIYIDSNNNP--ERFLKFF 31
PA L ++Y + ER
Sbjct: 40 NPALQTKLIELYAKYDPQKEIERLDNKS 67
Score = 26.1 bits (58), Expect = 6.0
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 13 LAKIYIDSNNNPERFLKFFLVDHLSKTPFYVLRCNEPGVWSQLAKAQLQK 62
I+ N E+ +++F+ + N P +W+++ KA L K
Sbjct: 101 AIVTLIEHLGNYEKAIEYFV------------KQNNPELWAEVLKALLDK 138
>gnl|CDD|172047 PRK13424, PRK13424, F0F1 ATP synthase subunit gamma; Provisional.
Length = 291
Score = 28.6 bits (64), Expect = 1.2
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 15/78 (19%)
Query: 48 EPGVWSQLA-------KAQLQKGLVKESIDSFIKADDPSAYMDVVETSHATESWEDLVRY 100
EP V LA K Q+ +GL+ S A + +A M ++ +AT + +D++
Sbjct: 211 EPSVEGLLAELLPRFIKVQIYRGLLDTS------ASEHAARMTAMD--NATRNCDDMIGS 262
Query: 101 LQMARKKARESYIESELI 118
L + K R++ I EL+
Sbjct: 263 LTLLYNKTRQASITRELM 280
>gnl|CDD|220013 pfam08777, RRM_3, RNA binding motif. This domain is found in
protein La which functions as an RNA chaperone during
RNA polymerase III transcription, and can also stimulate
translation initiation. It contains a five stranded beta
sheet which forms an atypical RNA recognition motif.
Length = 102
Score = 27.3 bits (61), Expect = 1.6
Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 60 LQKGLVKESIDSFIKADDPSAYMDVVETSHATESWEDLVRY-LQMARKKARESYIESELI 118
L K +E I Y+D +E E VR+ A KKA E E++L
Sbjct: 9 LNKPTSREDIKEAFSQHGEVKYVDFLEGDK-----EGYVRFKTPEAAKKALEKATEAKLK 63
>gnl|CDD|117454 pfam08887, GAD-like, GAD-like domain. This domain is functionally
uncharacterized, but it appears to be distantly related
to the GAD domain pfam02938.
Length = 109
Score = 26.9 bits (60), Expect = 2.3
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 77 DPSAYMDVVETSHATESWEDLVRYLQMAR 105
+P Y VV++ A D RY +AR
Sbjct: 57 NPQEYKPVVDSWLAGTKLLDADRYHLIAR 85
>gnl|CDD|184515 PRK14111, PRK14111, F0F1 ATP synthase subunit gamma; Provisional.
Length = 290
Score = 27.5 bits (61), Expect = 2.5
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 74 KADDPSAYMDVVETSHATESWEDLVRYLQMARKKARESYIESELI 118
A + SA M V +AT++ ++LVR L + KAR++ I E+
Sbjct: 237 IASEHSARM--VAMRNATDNAKELVRDLTLTYNKARQAAITKEVS 279
>gnl|CDD|107282 cd06287, PBP1_LacI_like_8, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 269
Score = 27.3 bits (61), Expect = 2.6
Identities = 21/99 (21%), Positives = 36/99 (36%), Gaps = 18/99 (18%)
Query: 48 EPGVWSQLAKAQLQKGLVKESIDSFIKADDPSAYMDVVETSHATESWEDLVRYL--QMAR 105
EP Q+G+ SI Y+D+ + + L+ +L Q AR
Sbjct: 64 EPMADDPQVARLRQRGIPVVSIGRPPGDRTDVPYVDL----QSAATARMLLEHLRAQGAR 119
Query: 106 KKA-------RESYIESELIYA-----YARTNRLADLEE 132
+ A R SY+E+E Y + + ++E
Sbjct: 120 QIALIVGSARRNSYLEAEAAYRAFAAEHGMPPVVLRVDE 158
>gnl|CDD|211341 cd02576, PseudoU_synth_ScPUS7, Pseudouridine synthase, TruD family.
This group consists of eukaryotic pseudouridine
synthases similar to Saccharomyces cerevisiae Pus7.
Pseudouridine synthases catalyze the isomerization of
specific uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7
makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in
cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in
yeast U2 snRNA and psi13 in tRNAs are highly
phylogenetically conserved. Psi34 is the mammalian U2
snRNA counterpart of yeast U2 snRNA psi35.
Length = 371
Score = 27.6 bits (62), Expect = 2.8
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 7/64 (10%)
Query: 60 LQKGLVKESIDSFIKADDPSAYMDVVETSHATESW---EDLVRYL-QMARKKARESYIES 115
+ K KE++D +K D+VE A E W D L ++ RKK E +
Sbjct: 168 ILKENWKEAVDLILKPRSELEEGDLVE---AREIWKETGDAKAALKKLPRKKVAEKALLR 224
Query: 116 ELIY 119
L
Sbjct: 225 GLSK 228
>gnl|CDD|238489 cd00989, PDZ_metalloprotease, PDZ domain of bacterial and plant
zinc metalloprotases, presumably membrane-associated or
integral membrane proteases, which may be involved in
signalling and regulatory mechanisms. May be responsible
for substrate recognition and/or binding, as most PDZ
domains bind C-terminal polypeptides, and binding to
internal (non-C-terminal) polypeptides and even to
lipids has been demonstrated. In this subfamily of
protease-associated PDZ domains a C-terminal beta-strand
forms the peptide-binding groove base, a circular
permutation with respect to PDZ domains found in
Eumetazoan signaling proteins.
Length = 79
Score = 26.0 bits (58), Expect = 2.9
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 17/52 (32%)
Query: 56 AKAQLQKGLVKESIDSFIKADDPSAYMDVVETSHATESWEDLVRYLQMARKK 107
AKA L+ G D + + +SWEDLV +Q K
Sbjct: 26 AKAGLKAG------DRILAING-----------QKIKSWEDLVDAVQENPGK 60
>gnl|CDD|223502 COG0425, SirA, Predicted redox protein, regulator of disulfide
bond formation [Posttranslational modification, protein
turnover, chaperones].
Length = 78
Score = 25.3 bits (56), Expect = 5.9
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 44 LRCNEPGVWSQLAKAQLQKGLVKESIDSFIKADDPSAYMDV 84
LRC P V ++ A A+L+ G + E + ADDP+A D+
Sbjct: 13 LRCPGPVVETKKALAKLKPGEILE-----VIADDPAAKEDI 48
>gnl|CDD|225586 COG3044, COG3044, Predicted ATPase of the ABC class [General
function prediction only].
Length = 554
Score = 26.4 bits (58), Expect = 6.2
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 2/83 (2%)
Query: 54 QLAKAQLQKGLVKESIDSFIKADDPSAYMDVVETSHATESWEDLVR-YLQMARKKARESY 112
L + V +D + D + M+ TE +L+R YL++AR++
Sbjct: 378 SLRGDLISTIAVTGGLDDLLAVADRAIVMEDHRPKDLTEKRRELIRYYLELARRECETPL 437
Query: 113 I-ESELIYAYARTNRLADLEEFI 134
E+ A +L +F
Sbjct: 438 ARETGRALNCATLQKLLLDGKFR 460
>gnl|CDD|236497 PRK09400, secE, preprotein translocase subunit SecE; Reviewed.
Length = 61
Score = 24.8 bits (55), Expect = 6.3
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 94 WEDLVRYLQMARKKARESYIESELI 118
ED R L++ARK RE ++ +
Sbjct: 14 LEDYKRVLKVARKPTREEFLLVAKV 38
>gnl|CDD|240365 PTZ00333, PTZ00333, triosephosphate isomerase; Provisional.
Length = 255
Score = 26.0 bits (58), Expect = 8.1
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 57 KAQLQKGLVKESIDSFIKADDPSAYMDVV 85
K K +KE IDSF K +DVV
Sbjct: 13 KCNGTKASIKELIDSFNKLKFDPNNVDVV 41
>gnl|CDD|217864 pfam04053, Coatomer_WDAD, Coatomer WD associated region. This
region is composed of WD40 repeats.
Length = 429
Score = 26.0 bits (58), Expect = 8.7
Identities = 9/31 (29%), Positives = 18/31 (58%)
Query: 47 NEPGVWSQLAKAQLQKGLVKESIDSFIKADD 77
++ W +L A L +G +K + +++ KA D
Sbjct: 331 DDEHKWKRLGDAALSQGNIKLAEEAYQKAKD 361
>gnl|CDD|214336 CHL00018, rpoC1, RNA polymerase beta' subunit.
Length = 663
Score = 26.0 bits (58), Expect = 9.2
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 19/63 (30%)
Query: 11 NALAKIYIDSNNNPERFLKFFLVDHLSKTPFYVLRCNEPGVWSQLAKAQLQKGLVKESID 70
N L + I NN L TP ++ C QK L++E++D
Sbjct: 293 NELYRRVIYRNNTLTDLLTTS-----RSTPGELVMC--------------QKKLLQEAVD 333
Query: 71 SFI 73
+ +
Sbjct: 334 ALL 336
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
0.319 0.133 0.388
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,395,194
Number of extensions: 642337
Number of successful extensions: 650
Number of sequences better than 10.0: 1
Number of HSP's gapped: 649
Number of HSP's successfully gapped: 31
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.5 bits)