RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4941
(172 letters)
>gnl|CDD|219969 pfam08687, ASD2, Apx/Shroom domain ASD2. This region is found in
the actin binding protein Shroom which mediates apical
contriction in epithelial cells and is required for
neural tube closure.
Length = 274
Score = 157 bits (400), Expect = 1e-48
Identities = 79/169 (46%), Positives = 110/169 (65%), Gaps = 2/169 (1%)
Query: 2 SRLDSKLTLLRSVQVDLNEESRGNDRLGEALATRLASEARPAETAKYKLHVQEVGHITSL 61
S L KL L Q L E+ + N+RLGE + ++ +P E K+++ + ++ + SL
Sbjct: 106 SSLGKKLQDLHEEQESLLEDIQANNRLGEEVEAKVKQACKPNEFEKFRMFIGDLEKVVSL 165
Query: 62 LLGLSGRLARAENALIGLRED--HCDRKSLEEKRDKLASQLEEAKELKENIDRRSTNVAT 119
LL LSGRLAR ENAL L ED +R SL EKR L Q E+AKELKE++DRR V
Sbjct: 166 LLSLSGRLARVENALSRLDEDADPEERASLLEKRKLLTRQHEDAKELKEHVDRRERAVRG 225
Query: 120 LLRKYLSSEEFADYNHFINMKAKLLVDAREISDKIQLGEEQLAALQETM 168
+L +YL +E+ ADY HF+ MKA LL++ RE+ DKI+LGEEQL L++++
Sbjct: 226 ILARYLPAEQLADYQHFVKMKAALLIEQRELEDKIKLGEEQLRCLRDSL 274
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 32.6 bits (75), Expect = 0.092
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 7/85 (8%)
Query: 85 DRKSLEEKRDKLASQLEEAKELKENIDRRSTNVATLLRKYLSSEEFADYNHFINMKAKLL 144
D L+E+ +L +L+E +E E I + L+K KLL
Sbjct: 328 DFPELKEELKELEEELKELEEELEKIKKL-------LKKLPKKARGQLPPEKREQLEKLL 380
Query: 145 VDAREISDKIQLGEEQLAALQETME 169
++S++++ EE+L L+E +E
Sbjct: 381 ETKEKLSEELEELEEELKELKEELE 405
>gnl|CDD|132527 TIGR03488, cas_Cas5p, CRISPR-associated protein Cas5, subtype
PGING. CC Members of this protein family are cas, or
CRISPR-associated, proteins. The two sequences in the
alignment seed are found within cas gene clusters that
are adjacent to CRISPR DNA repeats in two members of the
order Bacteroidales, Porphyromonas gingivalis W83 and
Bacteroides forsythus ATCC 43037. This cas protein
family is unique to the Pgingi (Porphyromonas
gingivalis) subtype, but shows some sequence similarity
to genes of the Cas5 type (see TIGR02593).
Length = 237
Score = 30.7 bits (69), Expect = 0.32
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 4/75 (5%)
Query: 84 CDRKSLEEKRDKLASQLEEAKELKENIDRRSTNVAT-LLRKYLSSEEFADYNHFINMKAK 142
C+ + EE DK+ K KENID AT R+Y+ E +Y I M +
Sbjct: 153 CENERDEENEDKI-DNHALEKFFKENIDFFPFFYATPTNREYIFFE--GNYECPIKMDEQ 209
Query: 143 LLVDAREISDKIQLG 157
L +I D+ +G
Sbjct: 210 LFDLLSDILDQNNIG 224
>gnl|CDD|118696 pfam10168, Nup88, Nuclear pore component. Nup88 can be divided
into two structural domains; the N-terminal two-thirds
of the protein has no obvious structural motifs but is
the region for binding to Nup98, one of the components
of the nuclear pore. the C-terminal end is a predicted
coiled-coil domain. Nup88 is overexpressed in tumour
cells.
Length = 717
Score = 30.6 bits (69), Expect = 0.37
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 85 DRKSLEEKRDKLASQLEEAKELKENIDRR 113
+RKSL E+ +KLA + EEAK +E + R
Sbjct: 587 ERKSLSERAEKLAEKFEEAKYNQELLVNR 615
>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated.
Length = 373
Score = 29.4 bits (66), Expect = 1.1
Identities = 22/94 (23%), Positives = 36/94 (38%), Gaps = 10/94 (10%)
Query: 15 QVDLNEESRGNDRLGEALATRLASEARPAETAKYKLHVQEVGHITSLLLGLSGRLARAEN 74
+ +E + +ALA + ++++QE+G I RL R +
Sbjct: 32 SSENADELSEKEAKAKALARIKIGPKKVYTEDSIRVYLQEIGRI---------RLLRPDE 82
Query: 75 ALIGLREDHCDRKSLEEKRDKLASQLEEAKELKE 108
I L D LEE R++ S+L KE
Sbjct: 83 E-IELARKIADLLELEELREQFESELGREPSDKE 115
>gnl|CDD|237178 PRK12705, PRK12705, hypothetical protein; Provisional.
Length = 508
Score = 29.3 bits (66), Expect = 1.1
Identities = 28/139 (20%), Positives = 48/139 (34%), Gaps = 5/139 (3%)
Query: 26 DRLGEALATRLASEARPAETAKYKLHVQEVGHITSLLLGLSGRLARAENALIGLREDHCD 85
+ E EA+ + QE L RL + E L R + D
Sbjct: 43 QKEAEEKLEAALLEAKELLLRERNQQRQEARREREELQREEERLVQKEEQL-DARAEKLD 101
Query: 86 RKS--LEEKRDKLASQLEEAKELKENIDRRSTNVATLLRKYLSSEEFADYNHFINMKAKL 143
LEE+ L+++ E +EL++ +D VA L + + + +
Sbjct: 102 NLENQLEEREKALSARELELEELEKQLDNELYRVAGLTPEQARKLLLKLLDAELEEEKAQ 161
Query: 144 LVDAREISDKIQLGEEQLA 162
V I ++ L E+ A
Sbjct: 162 RVKK--IEEEADLEAERKA 178
>gnl|CDD|216295 pfam01093, Clusterin, Clusterin.
Length = 434
Score = 28.9 bits (65), Expect = 1.3
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 8/41 (19%)
Query: 73 ENALIGLREDHCDRKSL----EEKRDKLASQLEEAKELKEN 109
+NALIG+++ K+L EE+ L S LE+ K+ KE
Sbjct: 19 KNALIGVKQ----MKTLMERTEEEHKNLMSTLEKTKKEKEE 55
>gnl|CDD|215507 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 29.1 bits (65), Expect = 1.5
Identities = 25/99 (25%), Positives = 44/99 (44%), Gaps = 20/99 (20%)
Query: 71 RAENALIGLREDHCDRKSLEEKRDKLASQLEEAKELKENIDRRSTNVATLLRKYLSSEEF 130
+ E A + L ++ L +K DKL + L+EA N+ + S+ LL++ L
Sbjct: 315 QVEKAALVLDQNQ----DLRDKVDKLEASLKEA-----NVSKFSSYKVELLQQKLKL--- 362
Query: 131 ADYNHFINMKAKLLVDAREISDKIQLGEEQLAALQETME 169
++ +L EI IQL +E + Q+T+
Sbjct: 363 --------LEERLQASDHEIHSYIQLYQESIKEFQDTLS 393
>gnl|CDD|110514 pfam01517, HDV_ag, Hepatitis delta virus delta antigen. The
hepatitis delta virus (HDV) encodes a single protein,
the hepatitis delta antigen (HDAg). The central region
of this protein has been shown to bind RNA. Several
interactions are also mediated by a coiled-coil region
at the N terminus of the protein.
Length = 194
Score = 28.3 bits (63), Expect = 1.5
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 80 REDHCDRKSLEEKRDKLAS--------QLEEAKELKENIDRRSTNVA 118
R DH RK+LE K+ +L+S + EE + L E + R VA
Sbjct: 98 RRDHRRRKALENKKKQLSSGGKHLSREEEEELRRLTEEDEERERRVA 144
>gnl|CDD|153086 cd01677, PFL2_DhaB_BssA, Pyruvate formate lyase 2 and related
enzymes. This family includes pyruvate formate lyase 2
(PFL2), B12-independent glycerol dehydratase (DhaB) and
the alpha subunit of benzylsuccinate synthase (BssA),
all of which have a highly conserved ten-stranded
alpha/beta barrel domain, which is similar to those of
PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide
reductase). Pyruvate formate lyase catalyzes a key step
in anaerobic glycolysis, the conversion of pyruvate and
CoenzymeA to formate and acetylCoA. DhaB catalyzes the
first step in the conversion of glycerol to
1,3-propanediol while BssA catalyzes the first step in
the anaerobic mineralization of both toluene and
m-xylene.
Length = 781
Score = 28.0 bits (63), Expect = 2.8
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 86 RKSLEEKRDKLASQLEEAKELKENIDRRSTNVATLLRKYLSSEEFADYNHFINM 139
++ +EE R E A EL E + N +R S++ FA YN F N+
Sbjct: 288 KQDIEEGRL----TREGAIELLECL-WIKINEINKVRSGASAKYFAGYNTFQNL 336
>gnl|CDD|220229 pfam09418, DUF2009, Protein of unknown function (DUF2009). This is
a eukaryotic family of proteins with unknown function.
Length = 458
Score = 27.7 bits (62), Expect = 3.7
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 11/46 (23%)
Query: 105 ELKENIDRRSTNVATLLRKYLSSE-----------EFADYNHFINM 139
+++ I ++ V TL +KY SS+ ADYN ++N
Sbjct: 171 QIQRAIKQKERAVETLAKKYSSSKLSKEDVRQCLYSLADYNAYLNA 216
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 27.0 bits (60), Expect = 7.3
Identities = 27/91 (29%), Positives = 36/91 (39%), Gaps = 11/91 (12%)
Query: 79 LREDHCDRKSLEEKRDKLASQLEEAKELKENID---RRSTNVATLLRKYLSSEEFADYNH 135
++E R SL E+R LA QL E + E + R L RK L E A
Sbjct: 804 MQETWLHRDSLREERPNLAIQLRELESSAEELQQELTRLIKDTKLRRKKLEQERKA---- 859
Query: 136 FINMKAKLLVDAREISDKIQLGEEQLAALQE 166
K L E+ ++ QLA L+E
Sbjct: 860 ----LEKQLDQLDELLRGLRDEMRQLAELKE 886
>gnl|CDD|237110 PRK12472, PRK12472, hypothetical protein; Provisional.
Length = 508
Score = 26.8 bits (59), Expect = 7.7
Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 12/89 (13%)
Query: 33 ATRLASEARPAETAKYKLHVQEVGHITSLLLGLSGRLARAENALIGLREDHCDRKSLEEK 92
A R A EA+ A A + E + + L L ARA+ L D+ K
Sbjct: 202 AARAADEAKTAAAAAAR----EAAPLKASLRKLERAKARADAELK-----RADKALAAAK 252
Query: 93 RDKLASQLEEAKELKENIDRRSTNVATLL 121
D+ ++ EE ++ +++ AT L
Sbjct: 253 TDEAKARAEER---QQKAAQQAAEAATQL 278
>gnl|CDD|238324 cd00580, CHMI, 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI)
is a trimeric enzyme catalyzing the isomerization of the
unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate
to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is
one step in the homoprotocatechuate pathway, one of the
microbial meta-fission pathways that degrade aromatic
carbon sources to citric acid cycle intermediates.
Despite the structural similarity of CHMI with
4-oxalocrotonate tautomerase (4-OT) and macrophage
migration inhibitory factor (MIF), there is no
significant sequence similarity among these protein
families, and therefore, they are not combined in one
hierarchy.
Length = 113
Score = 25.6 bits (57), Expect = 8.1
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 134 NHFINMKAKLLVDAREISDKIQLGEEQLAALQETMEGE 171
+ FI++ ++L R K +L E LAAL+ +
Sbjct: 58 DAFIHVTLRIL-AGRSEEQKQELSEALLAALRAHLAPV 94
>gnl|CDD|227247 COG4910, PduE, Propanediol dehydratase, small subunit [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 170
Score = 26.1 bits (57), Expect = 8.8
Identities = 16/37 (43%), Positives = 18/37 (48%)
Query: 93 RDKLASQLEEAKELKENIDRRSTNVATLLRKYLSSEE 129
R LA E A EL E D R + LR Y SS+E
Sbjct: 95 RPTLALNFERAAELTEVPDDRILEIYNALRPYRSSKE 131
>gnl|CDD|169692 PRK09174, PRK09174, F0F1 ATP synthase subunit B'; Validated.
Length = 204
Score = 25.9 bits (57), Expect = 9.9
Identities = 9/23 (39%), Positives = 16/23 (69%)
Query: 89 LEEKRDKLASQLEEAKELKENID 111
+E +RD++A L++A LK+ D
Sbjct: 82 IETRRDRIAQDLDQAARLKQEAD 104
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
0.311 0.128 0.330
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,432,887
Number of extensions: 784461
Number of successful extensions: 1248
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1196
Number of HSP's successfully gapped: 177
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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 (21.8 bits)
S2: 55 (25.0 bits)