RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy654
(224 letters)
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 125 bits (317), Expect = 2e-34
Identities = 52/91 (57%), Positives = 65/91 (71%), Gaps = 5/91 (5%)
Query: 14 EETEMIEGEVVEIQI---ERPATGLGS--KVGKLTMKTTEMETSYDLGAKMIEAIGKEKV 68
EE E+ EGEVVE++I E P +G G K GK+T+KTT+ME + LG K+ E + KEKV
Sbjct: 113 EEKEVYEGEVVELEIEEAENPLSGYGKTIKHGKITLKTTKMEKTLKLGPKIYEQLQKEKV 172
Query: 69 QAGDVITIDKATGKITRLGRSFTRARDYDAT 99
QAGDVI IDK TGK+ +LGRSF RA D+D
Sbjct: 173 QAGDVIYIDKNTGKVKKLGRSFARATDFDLE 203
Score = 58.5 bits (142), Expect = 4e-10
Identities = 23/39 (58%), Positives = 27/39 (69%)
Query: 159 VQAGDVITIDKATGKITRLGRSFTRARDYDATGAQTRQC 197
VQAGDVI IDK TGK+ +LGRSF RA D+D + C
Sbjct: 172 VQAGDVIYIDKNTGKVKKLGRSFARATDFDLEATEFVPC 210
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 96.3 bits (240), Expect = 3e-23
Identities = 39/96 (40%), Positives = 53/96 (55%), Gaps = 6/96 (6%)
Query: 14 EETEMIEGEVVEIQIERPATGLGS-----KVGKLTMKTTEMETSYDLGAKMIEAIGKEKV 68
E E+ EGEVVE++I R L +T+KT + E + LG ++ E + KE V
Sbjct: 128 ETREVYEGEVVELEIRRARNPLNPYGKVPSGAIITLKTKDEEKTLRLGPEIAEQLVKEGV 187
Query: 69 QAGDVITIDKATGKITRLGRSFTRARDYDATGAQTR 104
+ GDVI ID TG++ +LGRS RAR D TR
Sbjct: 188 EEGDVIYIDAETGRVKKLGRSKARAR-EDFDLEDTR 222
Score = 44.7 bits (106), Expect = 2e-05
Identities = 19/37 (51%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 159 VQAGDVITIDKATGKITRLGRSFTRARDYDATGAQTR 195
V+ GDVI ID TG++ +LGRS RAR D TR
Sbjct: 187 VEEGDVIYIDAETGRVKKLGRSKARAR-EDFDLEDTR 222
>gnl|CDD|219027 pfam06434, Aconitase_2_N, Aconitate hydratase 2 N-terminus. This
family represents the N-terminal region of several
bacterial Aconitate hydratase 2 proteins and is found in
conjunction with pfam00330.
Length = 204
Score = 32.5 bits (75), Expect = 0.100
Identities = 14/32 (43%), Positives = 19/32 (59%)
Query: 145 EDSGSTVTLHEIVDVQAGDVITIDKATGKITR 176
EDSG+ ++ + GDVITI GKIT+
Sbjct: 110 EDSGALPIEADVSSLNTGDVITIYPYEGKITK 141
Score = 30.1 bits (69), Expect = 0.67
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 51 TSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85
T+ D GA IEA + GDVITI GKIT+
Sbjct: 108 TAEDSGALPIEA-DVSSLNTGDVITIYPYEGKITK 141
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 - 600
residues found from worms to humans. Its function is not
known.
Length = 515
Score = 31.7 bits (72), Expect = 0.31
Identities = 15/75 (20%), Positives = 23/75 (30%), Gaps = 2/75 (2%)
Query: 85 RLGRSFTRARDYDATGAQTRNTLPSRSRHVSSWGVQKDVVQSISNNIICPVVPRPESSRS 144
L R R + T SR + ++ S N SS+
Sbjct: 31 VLAHFLRRRRGKRKMEGEQLGTRRPLSRKIGKCSSRRVRSPSSKPNDTLSGASSKLSSKH 90
Query: 145 EDSGSTVTLHEIVDV 159
SGS+ +L + D
Sbjct: 91 --SGSSHSLASVSDR 103
>gnl|CDD|171871 PRK13142, hisH, imidazole glycerol phosphate synthase subunit HisH;
Provisional.
Length = 192
Score = 30.2 bits (68), Expect = 0.56
Identities = 13/36 (36%), Positives = 14/36 (38%)
Query: 1 MSQMSTHSDTNHIEETEMIEGEVVEIQIERPATGLG 36
M M HSD I G + IQ E P LG
Sbjct: 80 MQLMYEHSDEGDASGLGFIPGNISRIQTEYPVPHLG 115
>gnl|CDD|226664 COG4206, BtuB, Outer membrane cobalamin receptor protein [Coenzyme
metabolism].
Length = 608
Score = 30.5 bits (69), Expect = 0.77
Identities = 25/110 (22%), Positives = 42/110 (38%), Gaps = 21/110 (19%)
Query: 63 IGKEKVQAGDVITIDKATGKIT-RLGRSFTRARDYDATGAQTRNTLPSRSRHVSSWGVQK 121
IGK +++ G T + TG +T + +D A T NTLP R+RH+ + +
Sbjct: 470 IGKARIK-GVEATAEFDTGGLTHTASYDYKDPQD-----ASTGNTLPRRARHMVKYELDW 523
Query: 122 DVVQ---SISNNIICPVVPRPESSRSEDSGSTVTLHEIVDVQAGDVITID 168
++ + R + S +TV L G +D
Sbjct: 524 AFYDFDWGLTYQY---LGTRYDGDYSTYPANTVKL--------GGYSLLD 562
>gnl|CDD|224781 COG1868, FliM, Flagellar motor switch protein [Cell motility and
secretion].
Length = 332
Score = 29.6 bits (67), Expect = 1.3
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 148 GSTVTLHEIVDVQAGDVITIDK 169
++TL EI+ ++ GDVI ++K
Sbjct: 263 EISLTLREILRLEVGDVIPLEK 284
>gnl|CDD|236424 PRK09238, PRK09238, bifunctional aconitate hydratase
2/2-methylisocitrate dehydratase; Validated.
Length = 835
Score = 29.8 bits (68), Expect = 1.3
Identities = 19/51 (37%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 35 LGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85
LG K+ + T E D GA IE K+ GDVI I GKI
Sbjct: 264 LGGKIAPIFFNTME-----DSGALPIEL-DVSKLNMGDVIDIYPYKGKIRN 308
Score = 28.2 bits (64), Expect = 4.5
Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 145 EDSGSTVTLHEIVDVQA---GDVITIDKATGKITR 176
EDSG+ L +DV GDVI I GKI
Sbjct: 277 EDSGA---LPIELDVSKLNMGDVIDIYPYKGKIRN 308
>gnl|CDD|235849 PRK06666, fliM, flagellar motor switch protein FliM; Validated.
Length = 337
Score = 29.4 bits (67), Expect = 1.6
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 149 STVTLHEIVDVQAGDVITIDK 169
+TL EI++++ GDVI ++K
Sbjct: 269 IKLTLSEILNLKVGDVIPLEK 289
>gnl|CDD|233589 TIGR01828, pyru_phos_dikin, pyruvate, phosphate dikinase. This
model represents pyruvate,phosphate dikinase, also
called pyruvate,orthophosphate dikinase. It is similar
in sequence to other PEP-utilizing enzymes [Energy
metabolism, Other].
Length = 856
Score = 29.6 bits (67), Expect = 1.6
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 63 IGKEKVQAGDVITIDKATGKI 83
IG GD+I+ID +TG+I
Sbjct: 481 IGGRVFHEGDIISIDGSTGEI 501
>gnl|CDD|223978 COG1049, AcnB, Aconitase B [Energy production and conversion].
Length = 852
Score = 29.3 bits (66), Expect = 2.0
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 6/51 (11%)
Query: 35 LGSKVGKLTMKTTEMETSYDLGAKMIEAIGKEKVQAGDVITIDKATGKITR 85
LG K+ + T E D GA IE ++ GDVI I GKI
Sbjct: 265 LGGKIAPIFFNTME-----DAGALPIEV-DVSNLEMGDVIDIYPYEGKIRN 309
Score = 28.9 bits (65), Expect = 2.4
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 145 EDSGSTVTLHEIVDVQAGDVITIDKATGKITR 176
ED+G+ ++ +++ GDVI I GKI
Sbjct: 278 EDAGALPIEVDVSNLEMGDVIDIYPYEGKIRN 309
>gnl|CDD|201573 pfam01052, SpoA, Surface presentation of antigens (SPOA). This
family includes the C-terminal region of flagellar motor
switch proteins FliN and FliM. It is associated with
family FliM, pfam02154.
Length = 77
Score = 27.1 bits (61), Expect = 2.4
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 150 TVTLHEIVDVQAGDVITIDKATGKITRL---GRSFTRAR 185
+TL E+++++ GDVI +DK L GR R
Sbjct: 20 ELTLGELLNLKVGDVIPLDKPADDPVTLYVNGRPIFRGE 58
>gnl|CDD|236446 PRK09279, PRK09279, pyruvate phosphate dikinase; Provisional.
Length = 879
Score = 28.5 bits (65), Expect = 3.6
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 63 IGKEKVQAGDVITIDKATGKI 83
+G ++ GDVITID +TG++
Sbjct: 487 VGGGTLKEGDVITIDGSTGEV 507
Score = 28.2 bits (64), Expect = 4.7
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 157 VDVQAGDVITIDKATGKI 174
++ GDVITID +TG++
Sbjct: 490 GTLKEGDVITIDGSTGEV 507
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1). All proteins
in this family with known functions are ATP-dependent
DNA ligases. Functions include DNA repair, DNA
replication, and DNA recombination (or any process
requiring ligation of two single-stranded DNA sections).
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 514
Score = 28.1 bits (63), Expect = 4.5
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 156 IVDVQAGDVITIDKATGKITRLGRSFTRARDYD 188
I+D G+++ ID TGK R R YD
Sbjct: 242 ILD---GEMVAIDPETGKPLPFQTLLRRKRKYD 271
>gnl|CDD|237193 PRK12764, PRK12764, hypothetical protein; Provisional.
Length = 500
Score = 27.8 bits (62), Expect = 5.4
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 21 GEVVEIQIERPATGLGSKVGKLTMKTTEMETSY-DLGAK 58
G+VVE++++ PA G G+L + E T + D GA+
Sbjct: 202 GDVVEVEVDAPADG-APSTGRLVTRVVEGTTPFADFGAQ 239
>gnl|CDD|220827 pfam10627, CsgE, Curli assembly protein CsgE. Curli are a class
highly aggregated surface fibres that are part of a
complex extracellular matrix. They promote biofilm
formation in addition to other activities. CsgE is a
non-structural protein involved in curli biogenesis.
CsgE forms an outer membrane complex with the curli
assembly proteins CsgG and CsgF.
Length = 107
Score = 26.5 bits (59), Expect = 6.3
Identities = 7/27 (25%), Positives = 12/27 (44%)
Query: 141 SSRSEDSGSTVTLHEIVDVQAGDVITI 167
G +T+ E +AG +IT+
Sbjct: 27 RDIPPTLGFNLTIKERPTARAGSLITV 53
>gnl|CDD|240935 cd12491, RRM2_RBM47, RNA recognition motif 2 in vertebrate
RNA-binding protein 47 (RBM47). This subgroup
corresponds to the RRM2 of RBM47, a putative RNA-binding
protein that shows high sequence homology with
heterogeneous nuclear ribonucleoprotein R (hnRNP R) and
heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its
biological function remains unclear. Like hnRNP R and
hnRNP Q, RBM47 contains two well-defined and one
degenerated RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains). .
Length = 89
Score = 26.2 bits (57), Expect = 6.4
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 58 KMIEAIGKEKVQAGDVITIDKATGKITRLGRSFTRARDYDATGAQTRNTLPSRSRHVSSW 117
+++E I K DVI A K+ G +F + A R +P R + W
Sbjct: 17 EILEEISKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMARRKLMPGR---IQLW 73
Query: 118 GVQ 120
G Q
Sbjct: 74 GHQ 76
>gnl|CDD|234762 PRK00439, leuD, 3-isopropylmalate dehydratase small subunit;
Reviewed.
Length = 163
Score = 26.7 bits (60), Expect = 6.6
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 66 EKVQAGDVITIDKATGKITRLGRS 89
+K++ GD + +D TG IT L
Sbjct: 107 DKIEDGDEVEVDLETGVITNLTTG 130
>gnl|CDD|132847 cd07208, Pat_hypo_Ecoli_yjju_like, Hypothetical patatin similar to
yjju protein of Escherichia coli. Patatin-like
phospholipase similar to yjju protein of Escherichia
coli. This family predominantly consists of bacterial
patatin glycoproteins, and some representatives from
eukaryotes and archaea. The patatin protein accounts
for up to 40% of the total soluble protein in potato
tubers. Patatin is a storage protein, but it also has
the enzymatic activity of a lipid acyl hydrolase,
catalyzing the cleavage of fatty acids from membrane
lipids. Members of this family have also been found in
vertebrates.
Length = 266
Score = 27.2 bits (61), Expect = 7.7
Identities = 15/54 (27%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 7 HSDTNH-IEETEMIEGEVVEIQIERPATGLGSKVGKLTMKTTEMETSYDLGAKM 59
HS N +E +E E I KV +L ++E YDLG +
Sbjct: 215 HSRYNETLEFIRRLEAEGKIFVIAPEKP---LKVSRLERDPEKLEALYDLGYED 265
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 27.3 bits (61), Expect = 7.8
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 67 KVQAGDVITIDKATGKITRLGRSFTRARDYD 97
V+ GD +TI +G + ++ T R +D
Sbjct: 660 PVKVGDTVTIGTVSGTVRKISVRATTIRTFD 690
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
0.313 0.128 0.353
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,777,163
Number of extensions: 976300
Number of successful extensions: 798
Number of sequences better than 10.0: 1
Number of HSP's gapped: 796
Number of HSP's successfully gapped: 46
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)