RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11412
(290 letters)
>gnl|CDD|218697 pfam05694, SBP56, 56kDa selenium binding protein (SBP56). This
family consists of several eukaryotic selenium binding
proteins as well as three sequences from archaea. The
exact function of this protein is unknown although it is
thought that SBP56 participates in late stages of
intra-Golgi protein transport. The Lotus japonicus
homologue of SBP56, LjSBP is thought to have more than
one physiological role and can be implicated in
controlling the oxidation/reduction status of target
proteins, in vesicular Golgi transport.
Length = 461
Score = 192 bits (490), Expect = 4e-58
Identities = 73/153 (47%), Positives = 94/153 (61%), Gaps = 21/153 (13%)
Query: 1 FYRQSDGTYKADKVIDIPAKQVQGYP------GGDKVPAMVTDILISLDDRYLYTSNWMH 54
+Y+ DG + A+KVI+IPA+ V+G+ G VP +VTDIL+SLDDR+LY S W H
Sbjct: 274 WYKDDDGKWAAEKVIEIPAEPVEGWILPPMLKGFGAVPPLVTDILLSLDDRFLYVSCWGH 333
Query: 55 GDIRQYDIRDTAHPVLVGQIFLGGKIQSDSGVTVIDDPELDKQPDPVIIKGRRFTGSSQM 114
GD+RQYDI D +P L GQ+ LGG I+ +KGRR G QM
Sbjct: 334 GDLRQYDISDPFNPKLTGQVRLGGIIRRA---------------PHPAVKGRRLNGGPQM 378
Query: 115 FQLSLDGKRIYVSSSLFSPWDKEIYPDLVKTDA 147
QLSLDGKR+YV++SL+S WD + YPD VK
Sbjct: 379 VQLSLDGKRLYVTNSLYSAWDDQFYPDGVKKGG 411
Score = 158 bits (402), Expect = 2e-45
Identities = 57/110 (51%), Positives = 70/110 (63%), Gaps = 15/110 (13%)
Query: 181 MVTDILISLDDRYLYTSNWMHGDIRQYDIRDTAHPVLVGQIFLGGKIQSDSGVTVIDDPE 240
+VTDIL+SLDDR+LY S W HGD+RQYDI D +P L GQ+ LGG I+
Sbjct: 313 LVTDILLSLDDRFLYVSCWGHGDLRQYDISDPFNPKLTGQVRLGGIIRRA---------- 362
Query: 241 LDKQPDPVIIKGRRFTGSSQMFQLSLDGKRIYVSSSLFSPWDKEIYPDLV 290
+KGRR G QM QLSLDGKR+YV++SL+S WD + YPD V
Sbjct: 363 -----PHPAVKGRRLNGGPQMVQLSLDGKRLYVTNSLYSAWDDQFYPDGV 407
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 31.0 bits (71), Expect = 0.77
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 52 WMHGDIRQYDIRDTAHPVLVGQIFL 76
W H D+R Y + D +G +L
Sbjct: 351 W-HEDVRLYSVWDADTGEFLGYFYL 374
Score = 31.0 bits (71), Expect = 0.77
Identities = 8/25 (32%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 199 WMHGDIRQYDIRDTAHPVLVGQIFL 223
W H D+R Y + D +G +L
Sbjct: 351 W-HEDVRLYSVWDADTGEFLGYFYL 374
>gnl|CDD|223790 COG0718, COG0718, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 105
Score = 29.1 bits (66), Expect = 0.81
Identities = 17/72 (23%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 103 IKGRRFTGSSQ--MFQLSLDGK----RIYVSSSLFSPWDKEIYPDLVKTDAAFGSD-EIM 155
+ + TG + + ++++GK + + SL P DKE+ DL+ AAF + +
Sbjct: 28 LAQKEVTGKAGGGLVTVTINGKGEVKSVEIDPSLLDPEDKEMLEDLIL--AAFNDAKKKV 85
Query: 156 EFIQRNEMRSMP 167
E ++ +M ++
Sbjct: 86 EETRKEKMGALT 97
>gnl|CDD|220674 pfam10282, Lactonase, Lactonase, 7-bladed beta-propeller. This
entry contains bacterial 6-phosphogluconolactonases
(6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse
6-phosphogluconolactone to 6-phosphogluconate. The entry
also contains the fungal muconate lactonising enzyme
carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and
muconate cycloisomerase (EC:5.5.1.1), which convert
cis,cis-muconates to muconolactones and vice versa as
part of the microbial beta-ketoadipate pathway.
Structures of proteins in this family have revealed a
7-bladed beta-propeller fold.
Length = 344
Score = 30.3 bits (69), Expect = 1.1
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 37 DILISLDDRYLYTSNWMHGDIRQYDI-RDTAHPVLVGQIFLGGK 79
I IS D R+LY SN H I + + LV ++ G
Sbjct: 248 AIRISPDGRFLYVSNRGHDSIAVFAVDEAGGTLTLVERVSTEGD 291
Score = 30.3 bits (69), Expect = 1.1
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 184 DILISLDDRYLYTSNWMHGDIRQYDI-RDTAHPVLVGQIFLGGK 226
I IS D R+LY SN H I + + LV ++ G
Sbjct: 248 AIRISPDGRFLYVSNRGHDSIAVFAVDEAGGTLTLVERVSTEGD 291
>gnl|CDD|226956 COG4590, COG4590, ABC-type uncharacterized transport system,
permease component [General function prediction only].
Length = 733
Score = 29.9 bits (67), Expect = 1.9
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 18/115 (15%)
Query: 31 VPAMVTDILISLDDRYLYTSNWMHGDI-----RQYDIR--------DTAHPVLVG-QIFL 76
+ V+ +L++ D + LY + R IR D+ H V +
Sbjct: 219 PFSDVSQLLLTPDGKTLYVRTGSELVVALLDKRSLQIRKLVDDSPGDSRHQVTEQLYLLS 278
Query: 77 GGK----IQSDSGVTVIDDPELDKQPDPVIIKGRRFTGSSQMFQLSLDGKRIYVS 127
GG + D V+ D D QP I+ + + F L ++ + S
Sbjct: 279 GGFSLLVVHEDGLVSQWFDVRRDGQPHLNHIRNFKLAPAEVQFLLPETNRKGFYS 333
>gnl|CDD|198456 cd10466, FimH_man-bind, Mannose binding domain of FimH and related
proteins. This family, restricted to
gammaproteobacteria, includes FimH, a mannose-specific
adhesin of uropathogenic Escherichia coli strains. The
domain appears to bind specifically to D-mannose and
mediates cellular adhesion to mannosylated proteins, a
prerequisite to colonization and subsequent invasion of
epithelial tissues.
Length = 160
Score = 28.8 bits (65), Expect = 2.2
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 107 RFTGSSQMFQLSLDGKRIYVSSSLFSPWDKEIYPDLVKTDAAFG 150
F GS+ F L D K I SS + P ++Y L AA G
Sbjct: 76 DFYGSTYPFPLQSDTKVIVYSSGTWKPLPLKLY--LTPVSAAGG 117
Score = 27.7 bits (62), Expect = 5.7
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 254 RFTGSSQMFQLSLDGKRIYVSSSLFSPWDKEIY 286
F GS+ F L D K I SS + P ++Y
Sbjct: 76 DFYGSTYPFPLQSDTKVIVYSSGTWKPLPLKLY 108
>gnl|CDD|218383 pfam05014, Nuc_deoxyrib_tr, Nucleoside 2-deoxyribosyltransferase.
Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6
catalyzes the cleavage of the glycosidic bonds of
2`-deoxyribonucleosides.
Length = 112
Score = 27.5 bits (62), Expect = 3.9
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 124 IYVSSSLFSPWDKEIYPDLVKTDAAFGSD 152
IY++ FSP + L A G +
Sbjct: 1 IYLAGPFFSPDQRARVARLRALLEANGFE 29
>gnl|CDD|131094 TIGR02039, CysD, sulfate adenylyltransferase, small subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules [Central intermediary
metabolism, Sulfur metabolism].
Length = 294
Score = 28.2 bits (63), Expect = 4.9
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 50 SNWMHGDIRQYDIRDTAHPVLVGQIFLGGK---IQSDSGVTVIDDPELDKQPDPVI 102
SNW DI +Y + + + ++ K +Q D + ++DD + P V+
Sbjct: 179 SNWTELDIWRYIAAEN---IPIVPLYFAAKRPVVQRDGMLIMVDDVRMPLAPGEVV 231
Score = 28.2 bits (63), Expect = 4.9
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 197 SNWMHGDIRQYDIRDTAHPVLVGQIFLGGK---IQSDSGVTVIDDPELDKQPDPVI 249
SNW DI +Y + + + ++ K +Q D + ++DD + P V+
Sbjct: 179 SNWTELDIWRYIAAEN---IPIVPLYFAAKRPVVQRDGMLIMVDDVRMPLAPGEVV 231
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 0.139 0.417
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,621,767
Number of extensions: 1541333
Number of successful extensions: 1203
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1199
Number of HSP's successfully gapped: 25
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
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 (21.7 bits)
S2: 58 (26.0 bits)