RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5198
(186 letters)
>gnl|CDD|216381 pfam01237, Oxysterol_BP, Oxysterol-binding protein.
Length = 335
Score = 222 bits (568), Expect = 8e-73
Identities = 77/121 (63%), Positives = 95/121 (78%)
Query: 38 PVALNEPLNMLQRMCEELEYSELLDKAAELSDPYERMVYVAAFAVSSYGSSYFRAASKPF 97
PV NEPL++LQR+ E+LEY +LLDKAA+ DP ERM+YVAAFAVS+Y S+ R KPF
Sbjct: 1 PVFFNEPLSLLQRLAEDLEYPDLLDKAAKEDDPLERMLYVAAFAVSTYSSTRKRRTKKPF 60
Query: 98 NPLLGETYECVREDKGFKFVAEQVSHHPPVSVCHAESKNFIFWQDVRIKTKFWGKSMEFQ 157
NPLLGET+E VRED GF+F++EQVSHHPP+S HAESK + W K+KFWGKS+E +
Sbjct: 61 NPLLGETFELVREDGGFRFISEQVSHHPPISAYHAESKGWTLWGSSAPKSKFWGKSIEVK 120
Query: 158 P 158
P
Sbjct: 121 P 121
Score = 41.0 bits (97), Expect = 1e-04
Identities = 15/24 (62%), Positives = 20/24 (83%)
Query: 160 ELNELNAEMKKQIPSTDTRLRPDQ 183
LNEL E+K+++P TD+RLRPDQ
Sbjct: 249 PLNELTPELKEELPPTDSRLRPDQ 272
>gnl|CDD|224328 COG1410, MetH, Methionine synthase I, cobalamin-binding domain
[Amino acid transport and metabolism].
Length = 842
Score = 31.2 bits (71), Expect = 0.34
Identities = 23/114 (20%), Positives = 36/114 (31%), Gaps = 28/114 (24%)
Query: 64 AAELSDPYERMVYVAAFAVSSYGSSYFRAASKPFNPLLGET------------YECVRED 111
A +++ Y+ V Y RA + L+ YE VR
Sbjct: 503 AVKIAPNYKGEVV--------YVKDASRAV-GVMDTLMSAEQRADYSEGFRKEYETVRTQ 553
Query: 112 KGFKFVAEQVSHHPPVSVCHAESKNFIFWQDVRIKT-KFWGKSMEFQPNELNEL 164
A + + P+S+ A W D FWG + + + L EL
Sbjct: 554 H-----ANRKARTRPLSIEAARDNAEAVWADYEPPVPPFWG-TRILKNSSLAEL 601
>gnl|CDD|183119 PRK11403, PRK11403, hypothetical protein; Provisional.
Length = 113
Score = 29.3 bits (66), Expect = 0.54
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 69 DPYERMVYVAAFAVSSYG 86
+ YE ++Y AF V +G
Sbjct: 88 NAYEMVIYPIAFFVCLFG 105
>gnl|CDD|215490 PLN02903, PLN02903, aminoacyl-tRNA ligase.
Length = 652
Score = 30.1 bits (68), Expect = 0.75
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 8/60 (13%)
Query: 31 DLSQVSMPVALNEPLNMLQRMCEEL---EYSELLDKAAELSDPYERMVYVAAFAVSSYGS 87
+ +Q+ M +A PL + ++ E+L + E+ +L +P+ R+ Y A A+S YGS
Sbjct: 294 EFTQLDMELAFT-PLEDMLKLNEDLIRQVFKEIKG--VQLPNPFPRLTY--AEAMSKYGS 348
>gnl|CDD|213298 cd05932, LC_FACS_bac, Bacterial long-chain fatty acid CoA
synthetase (LC-FACS), including Marinobacter
hydrocarbonoclasticus isoprenoid Coenzyme A synthetase.
The members of this family are bacterial long-chain
fatty acid CoA synthetase. Marinobacter
hydrocarbonoclasticus isoprenoid Coenzyme A synthetase
in this family is involved in the synthesis of
isoprenoid wax ester storage compounds when grown on
phytol as the sole carbon source. LC-FACS catalyzes the
formation of fatty acyl-CoA in a two-step reaction: the
formation of a fatty acyl-AMP molecule as an
intermediate, and the formation of a fatty acyl-CoA.
Free fatty acids must be "activated" to their CoA
thioesters before participating in most catabolic and
anabolic reactions.
Length = 504
Score = 29.2 bits (66), Expect = 1.6
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 28 IGKDLSQVSMPVALNEPLNMLQRMCEELEYS--ELLDKAAELSDPYERM 74
+G L Q V L+E + L+R EE+E S + L K + +ER+
Sbjct: 426 VGSGLPQPVALVVLSEAADPLER--EEVEESLQQTLAKVNSELESHERL 472
>gnl|CDD|197337 cd10282, DNase1, Deoxyribonuclease 1. Deoxyribonuclease 1 (DNase1,
EC 3.1.21.1), also known as DNase I, is a Ca2+,
Mg2+/Mn2+-dependent secretory endonuclease, first
isolated from bovine pancreas extracts. It cleaves DNA
preferentially at phosphodiester linkages next to a
pyrimidine nucleotide, producing 5'-phosphate terminated
polynucleotides with a free hydroxyl group on position
3'. It generally produces tetranucleotides. DNase1
substrates include single-stranded DNA, double-stranded
DNA, and chromatin. This enzyme may be responsible for
apoptotic DNA fragmentation. Other deoxyribonucleases in
this subfamily include human DNL1L (human DNase I
lysosomal-like, also known as DNASE1L1, Xib, and DNase X
), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3
(also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and
DNase gamma) . DNASE1L3 is implicated in apoptotic DNA
fragmentation. DNase I is also a cytoskeletal protein
which binds actin. A recombinant form of human DNase1 is
used as a mucoactive therapy in patients with cystic
fibrosis; it hydrolyzes the extracellular DNA in sputum
and reduces its viscosity. Mutations in the gene
encoding DNase1 have been associated with Systemic Lupus
Erythematosus, a multifactorial autoimmune disease. This
subfamily belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 256
Score = 28.7 bits (65), Expect = 1.6
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 12/61 (19%)
Query: 70 PYERMVYVAAFAVSSYGSSYFRAASKPFNPLLGETYECVREDKGFKFVAEQVSHHPPVSV 129
Y+R+V A S S+ ++ F+ + + E+ A VS H PV V
Sbjct: 207 AYDRIV----VAGSLLQSAVVPGSAGVFD--FDKEFGLTEEE------ALAVSDHYPVEV 254
Query: 130 C 130
Sbjct: 255 E 255
>gnl|CDD|169939 PRK09517, PRK09517, multifunctional thiamine-phosphate
pyrophosphorylase/synthase/phosphomethylpyrimidine
kinase; Provisional.
Length = 755
Score = 28.8 bits (64), Expect = 2.2
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 58 SELLDKAAELSDPYERMVYVAAFAVSS-YGSSYFRAASK 95
++KA E + P +R+ AF +S + +F A++
Sbjct: 713 IARVEKALENAGPEQRVDAARAFLSASVHEREFFDQATR 751
>gnl|CDD|235120 PRK03363, fixB, putative electron transfer flavoprotein FixB;
Provisional.
Length = 313
Score = 28.0 bits (62), Expect = 3.3
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 16 ESLSLWNLLCKNIGKDLSQVSMPVALNE 43
E+++L LCK IG +L+ S PVA NE
Sbjct: 209 ENIALAEQLCKAIGAELA-CSRPVAENE 235
>gnl|CDD|239620 cd03561, VHS, VHS domain family; The VHS domain is present in
Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte
growth factor-regulated tyrosine kinase substrate) and
STAM (Signal Transducing Adaptor Molecule). It has a
superhelical structure similar to that of the ARM
(Armadillo) repeats and is present at the N-termini of
proteins involved in intracellular membrane
trafficking. There are four general groups of VHS
domain containing proteins based on their association
with other domains. The first group consists of
proteins of the STAM/EAST/Hbp family which has the
domain composition VHS-SH3-ITAM. The second consists of
proteins with a FYVE domain C-terminal to VHS. The
third consists of GGA proteins with a domain
composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin
ear) domain. The fourth consists of proteins with a VHS
domain alone or with domains other than those mentioned
above. In GGA proteins, VHS domains are involved in
cargo recognition in trans-Golgi, thereby having a
general membrane targeting/cargo recognition role in
vesicular trafficking.
Length = 133
Score = 26.8 bits (60), Expect = 4.3
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 17 SLSLWNLLCKNIGKDLSQVSMPVALNEPLNMLQRMCEE 54
+L+L LL KN GK + VA E L L ++ +
Sbjct: 57 ALTLLELLVKNCGK---PFHLQVADKEFLLELVKIAKN 91
>gnl|CDD|237964 PRK15426, PRK15426, putative diguanylate cyclase YedQ; Provisional.
Length = 570
Score = 27.7 bits (62), Expect = 4.4
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 10/53 (18%)
Query: 55 LEYSELLDKAAELSDPYERMVYV--AAFAVSSY--------GSSYFRAASKPF 97
LE LL A S ER +YV A F VS+Y + Y++ ++P+
Sbjct: 155 LELGYLLRLAHNSSSLVERAMYVSRAGFYVSTYPTLFPSDVPTRYYQYVTQPW 207
>gnl|CDD|223292 COG0214, SNZ1, Pyridoxine biosynthesis enzyme [Coenzyme
metabolism].
Length = 296
Score = 27.3 bits (61), Expect = 4.6
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 40 ALNEPLNMLQRMCEELEYSELLDKAAELSDPYERMVYVA 78
+N + LQ M E+ EL A EL PYE + VA
Sbjct: 168 KINGEIRRLQSMTED----ELYVVAKELQAPYELVKEVA 202
>gnl|CDD|225271 COG2407, FucI, L-fucose isomerase and related proteins
[Carbohydrate transport and metabolism].
Length = 470
Score = 27.4 bits (61), Expect = 4.6
Identities = 11/61 (18%), Positives = 27/61 (44%)
Query: 19 SLWNLLCKNIGKDLSQVSMPVALNEPLNMLQRMCEELEYSELLDKAAELSDPYERMVYVA 78
S+ ++ K L ++ + V + + +R+ E E +++A + + R+ V
Sbjct: 176 SMGFASVRDSEKLLERLGVEVEAVDLEEIFRRVDNESVDDERVERALKWLEKNFRVGQVP 235
Query: 79 A 79
A
Sbjct: 236 A 236
>gnl|CDD|227649 COG5345, COG5345, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 358
Score = 26.7 bits (59), Expect = 7.4
Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 12/83 (14%)
Query: 80 FAVSSYG-----SSYFRAASKPFNPLLGETYECV-----REDKGFKFVAEQVSH-HPPVS 128
F +S +G S++RAA++ G+ C+ R D +FV + +
Sbjct: 188 FGLSPFGPKTPTPSFYRAAARNLRNFNGDLATCLASFDQRADNLVQFVDRIATDIGNTSA 247
Query: 129 VCHAESKNF-IFWQDVRIKTKFW 150
+ ++N W D R +FW
Sbjct: 248 ILPERAENVNEGWFDTRADDRFW 270
>gnl|CDD|219218 pfam06888, Put_Phosphatase, Putative Phosphatase. This family
contains a number of putative eukaryotic acid
phosphatases. Some family members represent the products
of the PSI14 phosphatase family in Lycopersicon
esculentum (Tomato).
Length = 234
Score = 26.6 bits (59), Expect = 7.5
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 51 MCEELEYSELLDKAAELSDPYERMVYV 77
MC+ E++ A YER++YV
Sbjct: 149 MCKGKVLDEIVASQAREGVRYERVIYV 175
>gnl|CDD|222645 pfam14280, DUF4365, Domain of unknown function (DUF4365). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria, eukaryotes and
viruses. Proteins in this family are typically between
182 and 530 amino acids in length. There is a single
completely conserved residue D that may be functionally
important.
Length = 139
Score = 26.2 bits (58), Expect = 7.9
Identities = 21/80 (26%), Positives = 29/80 (36%), Gaps = 10/80 (12%)
Query: 102 GETYECVREDKGFKFVAEQVSH------HP-PV-SVCHAESKNFIFWQDVRIKTK-FWGK 152
GE+Y GF F E H HP PV V S +WQD+ +
Sbjct: 54 GESYFYEETGGGFSFRLE-REHLNYWLNHPLPVILVLVDPSDKKAYWQDITDNLIDSTKE 112
Query: 153 SMEFQPNELNELNAEMKKQI 172
+ + N L+AE +
Sbjct: 113 GRTIEIPKSNVLDAESLDAL 132
>gnl|CDD|179769 PRK04180, PRK04180, pyridoxal biosynthesis lyase PdxS; Provisional.
Length = 293
Score = 26.6 bits (60), Expect = 8.6
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 40 ALNEPLNMLQRMCEELEYSELLDKAAELSDPYERMVYVA 78
+N + L M E+ EL A EL PYE + VA
Sbjct: 165 QINGEIRRLTSMSED----ELYTAAKELQAPYELVKEVA 199
>gnl|CDD|240078 cd04727, pdxS, PdxS is a subunit of the pyridoxal 5'-phosphate
(PLP) synthase, an important enzyme in deoxyxylulose
5-phosphate (DXP)-independent pathway for de novo
biosynthesis of PLP, present in some eubacteria, in
archaea, fungi, plants, plasmodia, and some metazoa.
Together with PdxT, PdxS forms the PLP synthase, a
heteromeric glutamine amidotransferase (GATase), whereby
PdxT produces ammonia from glutamine and PdxS combines
ammonia with five- and three-carbon phosphosugars to
form PLP. PLP is the biologically active form of vitamin
B6, an essential cofactor in many biochemical processes.
PdxS subunits form two hexameric rings.
Length = 283
Score = 26.4 bits (59), Expect = 8.9
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 40 ALNEPLNMLQRMCEELEYSELLDKAAELSDPYERMVYVA 78
A+N + LQ M EE EL A E+ PYE + A
Sbjct: 156 AVNGEIRKLQSMSEE----ELYAVAKEIQAPYELVKETA 190
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
0.317 0.131 0.396
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,151,408
Number of extensions: 804156
Number of successful extensions: 665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 25
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.4 bits)