RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5937
(201 letters)
>gnl|CDD|190614 pfam03366, YEATS, YEATS family. We have named this family the
YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF
small subunit'. This family also contains the GAS41
protein. All these proteins are thought to have a
transcription stimulatory activity.
Length = 84
Score = 96.5 bits (241), Expect = 2e-26
Identities = 34/69 (49%), Positives = 47/69 (68%), Gaps = 1/69 (1%)
Query: 109 THDWEVFVRGVDNA-DIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGFTLPIEV 167
TH W VFVRG+DN D+ FI KV F LHE+FP P R + +PP+ V E+G+ F +PI++
Sbjct: 1 THKWTVFVRGLDNEGDLSYFIKKVTFKLHESFPNPVRTVTKPPFEVTETGWGEFEIPIKI 60
Query: 168 YLKNNNEPR 176
Y ++NE
Sbjct: 61 YFVDSNEKP 69
Score = 90.3 bits (225), Expect = 4e-24
Identities = 32/61 (52%), Positives = 43/61 (70%), Gaps = 1/61 (1%)
Query: 28 THDWEVFVRGVDNA-DIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGFTLPIEV 86
TH W VFVRG+DN D+ FI KV F LHE+FP P R + +PP+ V E+G+ F +PI++
Sbjct: 1 THKWTVFVRGLDNEGDLSYFIKKVTFKLHESFPNPVRTVTKPPFEVTETGWGEFEIPIKI 60
Query: 87 Y 87
Y
Sbjct: 61 Y 61
>gnl|CDD|227366 COG5033, TFG3, Transcription initiation factor IIF, auxiliary
subunit [Transcription].
Length = 225
Score = 76.8 bits (189), Expect = 2e-17
Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 12 IGHEASVRN--KRTPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPP 69
I EA +R P TH W VFVR DI + KV+F LH TF P R ++ PP
Sbjct: 17 IPGEAKPLGNEERFPVRHTHIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPP 76
Query: 70 YVVKESGYAGFTLPIEVY 87
+ +KE+G+ F + I+++
Sbjct: 77 FEIKETGWGEFDIQIKIF 94
Score = 76.4 bits (188), Expect = 3e-17
Identities = 26/75 (34%), Positives = 39/75 (52%)
Query: 109 THDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESGYAGFTLPIEVY 168
TH W VFVR DI + KV+F LH TF P R ++ PP+ +KE+G+ F + I+++
Sbjct: 35 THIWLVFVRAPGKEDIATIVKKVIFKLHPTFSNPTRTIESPPFEIKETGWGEFDIQIKIF 94
Query: 169 LKNNNEPRKIRRKHT 183
+ I
Sbjct: 95 FAEKAGEKTIHFYLH 109
>gnl|CDD|183221 PRK11595, PRK11595, DNA utilization protein GntX; Provisional.
Length = 227
Score = 30.0 bits (68), Expect = 0.59
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 5/59 (8%)
Query: 140 PKPKRILKEPPYVVK--ESGYAGFTL---PIEVYLKNNNEPRKIRRKHTTPPSRHLSSR 193
KP RI+ P + + G+ L P+ +L + + + R T LS+R
Sbjct: 111 QKPDRIISVPLHQRRHWRRGFNQSDLLCRPLARWLGCDYDSEALTRTRATATQHFLSAR 169
>gnl|CDD|153076 cd00716, creatine_kinase_like, Phosphagen (guanidino) kinases
such as creatine kinase and similar enzymes.
Eukaryotic creatine kinase-like phosphagen (guanidino)
kinases are enzymes that transphosphorylate a high
energy phosphoguanidino compound, like phosphocreatine
(PCr) in the case of creatine kinase (CK), which is
used as an energy-storage and -transport metabolite, to
ADP, thereby creating ATP. The substrate binding site
is located in the cleft between the N and C-terminal
domains, but most of the catalytic residues are found
in the larger C-terminal domain. In higher eukaryotes,
CKs are found as tissue-specific (muscle, brain), as
well as compartment-specific (mitochondrial, cytosolic,
and flagellar) isoforms. Mitochondrial and cytoplasmic
CKs are dimeric or octameric, while the flagellar
isoforms are trimers with three CD domains fused as a
single protein chain. CKs are either coupled to
glycolysis (cytosolic form) or oxidative
phosphorylation (mitochondrial form). Besides CK, one
of the most studied members of this family, this model
also represents other phosphagen kinases with different
substrate specificities, like glycocyamine kinase (GK),
lombricine kinase (LK), taurocyamine kinase (TK), and
echinoderm arginine kinase (AK).
Length = 357
Score = 28.8 bits (65), Expect = 2.1
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 16 ASVRNKRTPEGFTHDWEVFVRGVDNADIHNFIDKV 50
A +R+K TP G T D + GVDN H FI V
Sbjct: 25 AKLRDKVTPNGVTLD-KCIQTGVDNPG-HPFIKTV 57
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 28.8 bits (64), Expect = 2.2
Identities = 25/162 (15%), Positives = 46/162 (28%), Gaps = 29/162 (17%)
Query: 17 SVRNKRTPEGFTHDWEVFVRGVDNADIHNFIDKVVFHLHETFPKPKRILKEPPYVVKESG 76
S N + D+E FV + N I + VF + + I + S
Sbjct: 1120 SHENAIISPVGSSDFESFVSFLSNLLIKISKSENVFPIMDLNDIVGDIFCDKEMAAGGSV 1179
Query: 77 YAGFTLPIEVYGDLIVPKSKRTTYIFIKPEGFTHD--WEVFVRGVDNADIHNFI-DKVVF 133
+ F G +H + + ++ + F K +
Sbjct: 1180 GSAFLSA-----------------------GVSHLKVYYILEELIEQSKDRLFFLIKEMT 1216
Query: 134 HLHETFPKPKRILKEP--PYVVKE-SGYAGFTLPIEVYLKNN 172
L + + + +K+ Y F P+E Y K
Sbjct: 1217 WLIKEWYHSDMSFRARILLEDIKKLKNYNEFYDPVEKYCKRK 1258
>gnl|CDD|131884 TIGR02837, spore_II_R, stage II sporulation protein R. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage II
sporulation protein R [Cellular processes, Sporulation
and germination].
Length = 168
Score = 27.0 bits (60), Expect = 5.4
Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 11/67 (16%)
Query: 54 LHETFPKPKRILKEPPYVVKESG--------YAGFTLPIEVYGDLIVPKSKRTTYIFIKP 105
+ E P+ +RI + V+K G ++ P ++YG++++P + +
Sbjct: 85 IRENLPEIERIAES---VIKAEGADYKVRVELGKYSFPTKLYGNIVLPAGEYEALRILIG 141
Query: 106 EGFTHDW 112
EG +W
Sbjct: 142 EGAGANW 148
>gnl|CDD|224108 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and
related pseudouridylate synthases [Translation,
ribosomal structure and biogenesis].
Length = 248
Score = 27.2 bits (61), Expect = 6.0
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 63 RILKEPPYVVKESGYAGFTLPIEVYGDLIVPKSKRTTYIFIKPEG 107
++ VV +EV G I K +R + KP G
Sbjct: 34 KVATLGGVVVDPDD-----DVVEVDGKRIELKEERVYLLLNKPRG 73
>gnl|CDD|234655 PRK00133, metG, methionyl-tRNA synthetase; Reviewed.
Length = 673
Score = 27.0 bits (61), Expect = 8.7
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 9/47 (19%)
Query: 12 IGHEASVRN---KRTPEGFTHDWEVFVRGVDNADIHNFI--DKVVFH 53
IG+ +S +N KR DW+ + + + ++++FI D + FH
Sbjct: 256 IGYISSTKNLCDKRGGL----DWDEYWKKDSDTELYHFIGKDIIYFH 298
>gnl|CDD|185718 cd08772, GH43_62_32_68, Glycosyl hydrolase families: GH43, GH62,
GH32, GH68. Members of the glycosyl hydrolase families
32, 43, 62 and 68 (GH32, GH43, GH62, GH68) all possess
5-bladed beta-propeller domains and comprise clans F and
J, as classified by the carbohydrate-active enzymes
database (CAZY). Clan F consists of families GH43 and
GH62. GH43 includes beta-xylosidases, beta-xylanases,
alpha-L-arabinases, and alpha-L-arabinofuranosidases,
using aryl-glycosides as substrates, while family GH62
contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that
specifically cleave either alpha-1,2 or
alpha-1,3-L-arabinofuranose sidechains from xylans.
These are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Clan J
consists of families GH32 and GH68. GH32 comprises
sucrose-6-phosphate hydrolases, invertases, inulinases,
levanases, eukaryotic fructosyltransferases, and
bacterial fructanotransferases while GH68 consists of
frucosyltransferases (FTFs) that include levansucrase
(EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26);
inulosucrase (EC 2.4.1.9), while GH68 consists of
frucosyltransferases (FTFs) that include levansucrase
(EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26);
inulosucrase (EC 2.4.1.9), all of which use sucrose as
their preferential donor substrate. Members of this clan
are retaining enzymes (i.e. they retain the
configuration at anomeric carbon atom of the substrate)
that catalyze hydrolysis in two steps involving a
covalent glycosyl enzyme intermediate: an aspartate
located close to the N-terminus acts as the catalytic
nucleophile and a glutamate acts as the general
acid/base; a conserved aspartate residue in the
Arg-Asp-Pro (RDP) motif stabilizes the transition state.
Structures of all families in the two clans manifest a
funnel-shaped active site that comprises two subsites
with a single route for access by ligands.
Length = 286
Score = 26.6 bits (59), Expect = 8.9
Identities = 11/35 (31%), Positives = 13/35 (37%), Gaps = 3/35 (8%)
Query: 22 RTPEGFTHDWEVFVRGVDN---ADIHNFIDKVVFH 53
G D+ DN AD+ NF D VF
Sbjct: 95 EDGNGPWTDYIGGPVLPDNPPAADVSNFRDPFVFE 129
>gnl|CDD|185150 PRK15235, PRK15235, outer membrane fimbrial usher protein SefC;
Provisional.
Length = 814
Score = 27.0 bits (59), Expect = 9.1
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 9/62 (14%)
Query: 69 PYVVKESGYAGFTLPI----EVYGDLIVPKSKRTTYIFIKPEGFTHDWEVFVRGVDNADI 124
P + GY+ +++ I EV D I P TYI+ P GFT GV A+I
Sbjct: 328 PVLSLPDGYSKYSVTIGRYREVNNDYIDPVFFEGTYIYGLPYGFT-----LFGGVQWANI 382
Query: 125 HN 126
+N
Sbjct: 383 YN 384
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
0.321 0.140 0.435
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,872,849
Number of extensions: 1048332
Number of successful extensions: 780
Number of sequences better than 10.0: 1
Number of HSP's gapped: 776
Number of HSP's successfully gapped: 27
Length of query: 201
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 109
Effective length of database: 6,857,034
Effective search space: 747416706
Effective search space used: 747416706
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: 56 (25.2 bits)