RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13819
(323 letters)
>gnl|CDD|216423 pfam01301, Glyco_hydro_35, Glycosyl hydrolases family 35.
Length = 318
Score = 236 bits (605), Expect = 2e-76
Identities = 97/233 (41%), Positives = 134/233 (57%), Gaps = 5/233 (2%)
Query: 82 TFRLNEDPFQFVSGSFHYFRAPPGRWCWIMRAMRAAGLNALSTYVEWRSHEVHPGHYHYD 141
+F ++ F+ +SGS HYFR PP W ++ +A GLN + TYV W HE PG Y +
Sbjct: 1 SFLIDGQRFRLISGSIHYFRIPPEMWPDRLQKAKALGLNTIETYVFWNLHEPEPGQYDFS 60
Query: 142 GHRDIEHFLQLAVEEDLYILLRPGPFICGKRDFGGFPPWLLKVAPDILLRQNHPVYQRYV 201
G D+ F++LA E LY++LRPGP+IC + DFGG P WLL+V P I LR + P + V
Sbjct: 61 GILDLVKFIKLAQEAGLYVILRPGPYICAEWDFGGLPAWLLRV-PGIRLRTSDPPFLEAV 119
Query: 202 TRWFQELFPRIQKYLYGNDRPIILVQVENEYGSDAECDPAHAVWLRDLLRTYVQDKAVLY 261
R+ L P+++ N PIILVQ+ENEYGS D A+ LR L R + D AVL+
Sbjct: 120 DRYLTALLPKMKPLQATNGGPIILVQIENEYGSYG-VDKAYLQALRKLYREWGADMAVLF 178
Query: 262 STDGAFDAYLRCTV---DGVYSTVDFTVFKDVNVSFQAQRTRAPQGPLVNAEF 311
+TDG + L+C +Y+T F + F R +P GPL+ +EF
Sbjct: 179 TTDGPWGMCLQCGDLPDPVIYTTNGFGCGANPTSIFGLLRPFSPNGPLMWSEF 231
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 108 bits (270), Expect = 6e-26
Identities = 51/144 (35%), Positives = 84/144 (58%), Gaps = 3/144 (2%)
Query: 92 FVSGSFHYFRAPPGRWCWIMRAMRAAGLNALSTYVEWRSHEVHPGHYHYDGHRDIEHFLQ 151
+SGS HY R+ P W +++ + GL+ + TYV W HE PG+Y+++ D+ F++
Sbjct: 46 LISGSIHYPRSTPEMWPDLIQKAKDGGLDVIQTYVFWNGHEPSPGNYYFEDRYDLVKFIK 105
Query: 152 LAVEEDLYILLRPGPFICGKRDFGGFPPWLLKVAPDILLRQNHPVYQRYVTRWFQELFP- 210
+ LY+ LR GP+IC + +FGGFP W LK P I R ++ ++ + ++ +++
Sbjct: 106 VVQAAGLYVHLRIGPYICAEWNFGGFPVW-LKYVPGIEFRTDNGPFKAAMQKFTEKIVDM 164
Query: 211 -RIQKYLYGNDRPIILVQVENEYG 233
+ +K PIIL Q+ENEYG
Sbjct: 165 MKSEKLFEPQGGPIILSQIENEYG 188
>gnl|CDD|224786 COG1874, LacA, Beta-galactosidase [Carbohydrate transport and
metabolism].
Length = 673
Score = 90.9 bits (226), Expect = 3e-20
Identities = 57/191 (29%), Positives = 82/191 (42%), Gaps = 34/191 (17%)
Query: 79 AGDTFRLNEDPFQFVSGSFHYFRAPPGRWCWIMRAMRAAGLNALST-YVEWRSHEVHPGH 137
G +F + G ++ R P W +R M+A GLN + Y W HE G
Sbjct: 4 DGYSFIRDGRRILLYGGDYYPERWPRETWMDDLRKMKALGLNTVRIGYFAWNLHEPEEGK 63
Query: 138 YHYDGHRDIEHFLQLAVEEDLYILLRPGPFICGKRDFGGFPPWLLKVAPDILL------- 190
+ + D FL+ A + LY++LR GP G P WL K P+IL
Sbjct: 64 FDF-TWLDEI-FLERAYKAGLYVILRTGP-------TGAPPAWLAKKYPEILAVDENGRV 114
Query: 191 -----RQNH----PVYQRYVTRWFQELFPRIQKYLYGNDRPIILVQVENEYGSD----AE 237
R+N PVY+ Y+ R + +I++ LYGN +I Q +NEYG
Sbjct: 115 RSDGARENICPVSPVYREYLDR----ILQQIRERLYGNGPAVITWQNDNEYGGHPCYCDY 170
Query: 238 CDPAHAVWLRD 248
C A +WL+
Sbjct: 171 CQAAFRLWLKK 181
>gnl|CDD|217042 pfam02449, Glyco_hydro_42, Beta-galactosidase. This group of
beta-galactosidase enzymes belong to the glycosyl
hydrolase 42 family. The enzyme catalyzes the hydrolysis
of terminal, non-reducing terminal beta-D-galactosidase
residues.
Length = 376
Score = 64.2 bits (157), Expect = 2e-11
Identities = 40/173 (23%), Positives = 64/173 (36%), Gaps = 39/173 (22%)
Query: 103 PPGRWCWIMRAMRAAGLNALS-TYVEWRSHEVHPGHYHYDGHRDIEHFLQLAVEEDLYIL 161
P W +R M+ AG+N + W E G Y + ++ + L + + ++
Sbjct: 8 PEETWEEDIRLMKEAGVNVVRLGIFAWAKLEPEEGKYDFGW---LDEIIDLLAKAGIKVI 64
Query: 162 LRPGPFICGKRDFGGFPPWLLKVAPDILL------------RQN----HPVYQRYVTRWF 205
L P WL K P+IL R + PVY+ Y R
Sbjct: 65 LATPT--------AAPPAWLAKKHPEILPVDADGRRRGFGSRHHYCPSSPVYREYAARIV 116
Query: 206 QELFPRIQKYLYGNDRPIILVQVENEYG---SDAECDPAHA---VWLRDLLRT 252
+ L R YG+ +I ++NEYG S+ C+ WL++ T
Sbjct: 117 EALAER-----YGDHPALIGWHIDNEYGCHVSECYCETCQQAFRKWLKNRYGT 164
>gnl|CDD|222076 pfam13364, BetaGal_dom4_5, Beta-galactosidase jelly roll domain.
This domain is found in beta galactosidase enzymes. It
has a jelly roll fold.
Length = 109
Score = 30.7 bits (70), Expect = 0.31
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 3 RWSKGVLFANGRHWGRYWSEVGPQYSLFVPEEFLKVGTNRITI 45
R S L+ NG G Y +GPQ + VPE L T+
Sbjct: 62 RAS---LWVNGYQLGSYVGHIGPQTTFPVPEGILNYRNTVATV 101
>gnl|CDD|224037 COG1112, COG1112, Superfamily I DNA and RNA helicases and helicase
subunits [DNA replication, recombination, and repair].
Length = 767
Score = 30.3 bits (68), Expect = 1.6
Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 3/66 (4%)
Query: 40 TNRITIFELTRAPDKYDVDFVDKISQRRARMSRTFAIDLAGDTFRLNEDPFQFVSGSFHY 99
T I F + + ++D +D+ SQ A L D Q F
Sbjct: 475 TLSIAGFSILKK-YEFDYVIIDEASQ--ATEPSALIALSRAKKVILVGDHKQLPPTVFFK 531
Query: 100 FRAPPG 105
+P G
Sbjct: 532 ESSPEG 537
>gnl|CDD|220074 pfam08925, DUF1907, Domain of Unknown Function (DUF1907). The
structure of this domain displays an
alpha-beta-beta-alpha four layer topology, with an
HxHxxxxxxxxxH motif that coordinates a zinc ion, and an
acetate anion at a site that likely supports the
enzymatic activity of an ester hydrolase.
Length = 283
Score = 29.6 bits (67), Expect = 2.4
Identities = 13/31 (41%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 130 SHEVHPGHYHYDGHRD-IEHFLQLAVEEDLY 159
SH GHYHYD D +E+ E LY
Sbjct: 251 SHHGEGGHYHYDTTPDTVEYEGYFNPAERLY 281
>gnl|CDD|212511 cd09015, Ureohydrolase, Ureohydrolase superfamily includes
arginase, formiminoglutamase, agmatinase and
proclavaminate amidinohydrolase (PAH). This family,
also known as arginase-like amidino hydrolase family,
includes Mn-dependent enzymes: arginase (Arg, EC
3.5.3.1), formimidoylglutamase (HutG, EC 3.5.3.8 ),
agmatinase (SpeB, EC 3.5.3.11), guanidinobutyrase (Gbh,
EC=3.5.3.7), proclavaminate amidinohydrolase (PAH, EC
3.5.3.22) and related proteins. These enzymes catalyze
hydrolysis of amide bond. They are involved in control
of cellular levels of arginine and ornithine (both
involved in protein biosynthesis, and production of
creatine, polyamines, proline and nitric acid), in
histidine and arginine degradation, and in clavulanic
acid biosynthesis.
Length = 270
Score = 28.5 bits (64), Expect = 4.8
Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 7/82 (8%)
Query: 209 FPRIQKYLYGNDRPIILVQVENEYGSDAECDPAHAVWLRDLLRTYVQDKAV--LYSTDGA 266
F ++ + L + + I+ + V + PA + R L YV V L
Sbjct: 132 FRQLLEELQQSPKHIVCIGV-----RGLDPGPALFEYARKLGVKYVTMDEVDKLGLGGVL 186
Query: 267 FDAYLRCTVDGVYSTVDFTVFK 288
+ D VY +VD
Sbjct: 187 EQLFHYDDGDNVYLSVDVDGLD 208
>gnl|CDD|200568 cd10943, CE4_NodB, Putative catalytic domain of rhizobial NodB
chitooligosaccharide N-deacetylase and its bacterial
homologs. This family corresponds to rhizobial NodB
chitooligosaccharide N-deacetylase (EC 3.5.1.-), encoded
by nodB gene from the nodulation (nod) gene cluster that
is responsible for the biosynthesis of bacterial
nodulation signals, termed Nod factors. NodB is involved
in de-N-acetylating the nonreducing N-acetylglucosamine
residue of chitooligosaccharides to allow for the
attachment of the fatty acyl group by the
acyltransferase NodA. The monosaccharide
N-acetylglucosamine cannot be deacetylated by NodB. NodB
is composed of a 6-stranded barrel catalytic domain with
detectable sequence similarity to the 7-stranded barrel
homology domain of polysaccharide deacetylase (DCA)-like
proteins in the larger carbohydrate esterase 4 (CE4)
superfamily.
Length = 193
Score = 27.9 bits (62), Expect = 5.1
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 95 GSFHYFRAPPGRWC-WIMRAMRAAGLNALSTYVEWR 129
S YFRAP G W ++ A AGL L V+ R
Sbjct: 92 ASVRYFRAPYGAWSEEVLTASNKAGLAPLHWSVDPR 127
>gnl|CDD|235324 PRK04968, PRK04968, SecY interacting protein Syd; Provisional.
Length = 181
Score = 27.5 bits (62), Expect = 6.6
Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%)
Query: 198 QRYVTRWFQEL--FPRIQKYLYGNDRPIILVQVENE 231
QRY W +E PR + LYG P I+ E+
Sbjct: 12 QRYCDAWQEEHGELPRSE-ELYGVPSPCIIETSEDA 46
>gnl|CDD|224799 COG1887, TagB, Putative glycosyl/glycerophosphate transferases
involved in teichoic acid biosynthesis
TagF/TagB/EpsJ/RodC [Cell envelope biogenesis, outer
membrane].
Length = 388
Score = 28.1 bits (63), Expect = 6.8
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 128 WRSHEVHPGHYHYDGHRDIEHFLQLAVEEDLYILLRPGPFICGKRDF 174
+R ++V G ++ DIE + E + I+++P P I K D
Sbjct: 217 FRDNDVLIGTQFFNLDIDIEKLKEKLGENEYVIIVKPHPLISDKIDK 263
>gnl|CDD|221813 pfam12860, PAS_7, PAS fold. The PAS fold corresponds to the
structural domain that has previously been defined as
PAS and PAC motifs. The PAS fold appears in archaea,
eubacteria and eukarya.
Length = 115
Score = 26.7 bits (60), Expect = 7.0
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 32 PEEFLKVGTNRITIFELTRAPDKYDVDFVDKISQRRARMSRTF 74
P+E L+VGT + +Y V+ +RR +R
Sbjct: 31 PDELLQVGTPFEDLIRYNAERGEYGPGDVEAHVERRLAQARAG 73
>gnl|CDD|117743 pfam09189, DUF1952, Domain of unknown function (DUF1952). Members
of this family are found in various Thermus thermophilus
proteins. Their exact function has not, as yet, been
determined.
Length = 78
Score = 26.2 bits (57), Expect = 7.3
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 171 KRDFGGFPPWLLK 183
+R FG FPPWLL+
Sbjct: 3 ERTFGAFPPWLLE 15
>gnl|CDD|153085 cd01676, RNR_II_monomer, Class II ribonucleotide reductase,
monomeric form. Ribonucleotide reductase (RNR)
catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophage, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class II RNRs are found in bacteria that
can live under both aerobic and anaerobic conditions.
Many, but not all members of this class, are found to be
homodimers. This particular subfamily is found to be
active as a monomer. Adenosylcobalamin interacts
directly with an active site cysteine to form the
reactive cysteine radical.
Length = 658
Score = 27.9 bits (62), Expect = 8.4
Identities = 11/38 (28%), Positives = 13/38 (34%), Gaps = 6/38 (15%)
Query: 102 APPGRWCWIM-----RAMRAAGL-NALSTYVEWRSHEV 133
PPGR W+ R R A L N E +
Sbjct: 68 LPPGRGLWLGGTDYSRQRRFASLNNCAFVSTEDVVYPF 105
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
0.326 0.142 0.471
Gapped
Lambda K H
0.267 0.0762 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,611,457
Number of extensions: 1735759
Number of successful extensions: 1932
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1921
Number of HSP's successfully gapped: 28
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.4 bits)