RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11634
(178 letters)
>gnl|CDD|185458 PTZ00120, PTZ00120, D-tyrosyl-tRNA(Tyr) deacylase; Provisional.
Length = 154
Score = 185 bits (473), Expect = 5e-61
Identities = 70/139 (50%), Positives = 93/139 (66%)
Query: 31 VDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKYEI 90
V+ V+ SIG GL +L+GI DT +D DYI+ K LKL+++ +E GK W SV DK YE+
Sbjct: 15 VEGEVVGSIGKGLVLLVGIHEEDTWEDADYIIRKCLKLRLWPDEGGKMWDRSVKDKDYEV 74
Query: 91 LCISQFTLYHGLKGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHMSVN 150
L +SQFTL++ KGN FH AM D+ YNKF+EK K Y K+K GKFG +M+V+
Sbjct: 75 LVVSQFTLFNVKKGNKPDFHLAMSPEDALPLYNKFVEKFKKEYAPEKIKTGKFGQYMNVS 134
Query: 151 IVNDGPVTIPLESPSEKSN 169
+VNDGPVTI L+S +
Sbjct: 135 LVNDGPVTIILDSKEKNLA 153
>gnl|CDD|238316 cd00563, Dtyr_deacylase, D-Tyrosyl-tRNAtyr deacylases; a class of
tRNA-dependent hydrolases which are capable of
hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing
the level of cellular D-Tyrosine while recycling the
peptidyl-tRNA; found in bacteria and in eukaryotes but
not in archea; beta barrel-like fold structure; forms
homodimers in which two surface cavities serve as the
active site for tRNA binding.
Length = 145
Score = 181 bits (461), Expect = 3e-59
Identities = 64/134 (47%), Positives = 84/134 (62%), Gaps = 4/134 (2%)
Query: 31 VDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKYEI 90
VD V+ +IG GL +L+G++ DTE+D +Y+ KIL L+IFE+EEGK SV D EI
Sbjct: 15 VDGEVVGAIGQGLLVLVGVTHDDTEEDAEYLARKILNLRIFEDEEGKMN-LSVKDVNGEI 73
Query: 91 LCISQFTLYHGL-KGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHMSV 149
L +SQFTLY KG +F A +E Y F+E L+ KV+ G FGA M V
Sbjct: 74 LVVSQFTLYADTKKGRRPSFSAAAPPDKAEPLYESFVELLREKGI--KVETGVFGAMMQV 131
Query: 150 NIVNDGPVTIPLES 163
++VNDGPVTI L+S
Sbjct: 132 SLVNDGPVTIILDS 145
>gnl|CDD|202294 pfam02580, Tyr_Deacylase, D-Tyr-tRNA(Tyr) deacylase. This family
comprises of several D-Tyr-tRNA(Tyr) deacylase proteins.
Cell growth inhibition by several d-amino acids can be
explained by an in vivo production of d-aminoacyl-tRNA
molecules. Escherichia coli and yeast cells express an
enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling
such d-aminoacyl-tRNA molecules into free tRNA and
d-amino acid. Accordingly, upon inactivation of the
genes of the above deacylases, the toxicity of d-amino
acids increases. Orthologues of the deacylase are found
in many cells.
Length = 144
Score = 167 bits (425), Expect = 8e-54
Identities = 67/136 (49%), Positives = 90/136 (66%), Gaps = 4/136 (2%)
Query: 29 CLVDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKY 88
VD V+ SIG GL +L+G+++ DTE+D+ Y+V KIL L+IFE+EEGK S+ D
Sbjct: 12 VSVDGEVVGSIGRGLLVLVGVTKDDTEEDLRYLVEKILNLRIFEDEEGK-MNLSLKDVGG 70
Query: 89 EILCISQFTLYHGL-KGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHM 147
EIL +SQFTLY KG +FH A ++E Y KF++ L+ A KV+ G FGA M
Sbjct: 71 EILIVSQFTLYGDTKKGRRPSFHAAAKPDEAEELYEKFVQLLREAG--IKVETGTFGADM 128
Query: 148 SVNIVNDGPVTIPLES 163
V++VNDGPVTI L+S
Sbjct: 129 QVSLVNDGPVTILLDS 144
>gnl|CDD|235383 PRK05273, PRK05273, D-tyrosyl-tRNA(Tyr) deacylase; Provisional.
Length = 147
Score = 156 bits (396), Expect = 2e-49
Identities = 63/136 (46%), Positives = 84/136 (61%), Gaps = 6/136 (4%)
Query: 31 VDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKYEI 90
VD V+ IG GL +L+G+ + DTE+D DY+ KIL L+IFE+EEGK SV D EI
Sbjct: 15 VDGEVVGEIGKGLLVLVGVEKGDTEEDADYLAEKILNLRIFEDEEGK-MNLSVQDVGGEI 73
Query: 91 LCISQFTLYHG--LKGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHMS 148
L +SQFTLY KG +F A ++E Y+ F+E L+ V+ G+FGA M
Sbjct: 74 LVVSQFTLY-ADTRKGRRPSFSAAAPPEEAEPLYDYFVEALRAQG--VPVETGRFGADMQ 130
Query: 149 VNIVNDGPVTIPLESP 164
V++VNDGPVT L+S
Sbjct: 131 VSLVNDGPVTFLLDSK 146
>gnl|CDD|224407 COG1490, Dtd, D-Tyr-tRNAtyr deacylase [Translation, ribosomal
structure and biogenesis].
Length = 145
Score = 155 bits (394), Expect = 3e-49
Identities = 65/134 (48%), Positives = 85/134 (63%), Gaps = 4/134 (2%)
Query: 31 VDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKYEI 90
VD V+ +IG GL +L+G++ DTE+D DY+ KIL L+IFE+EEGK SV D EI
Sbjct: 15 VDGEVVGAIGQGLLVLVGVTHDDTEEDADYLAEKILNLRIFEDEEGK-MNLSVQDVGGEI 73
Query: 91 LCISQFTLYHGL-KGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHMSV 149
L +SQFTLY KG +F A +E Y F+E L+ KV+ G+FGA M V
Sbjct: 74 LVVSQFTLYADTKKGRRPSFSKAAKPDQAEELYEYFVELLRELGI--KVETGRFGADMQV 131
Query: 150 NIVNDGPVTIPLES 163
++VNDGPVTI L+S
Sbjct: 132 SLVNDGPVTILLDS 145
>gnl|CDD|129358 TIGR00256, TIGR00256, D-tyrosyl-tRNA(Tyr) deacylase. This
homodimeric enzyme appears able to cleave any D-amino
acid (and glycine, which does not have distinct D/L
forms) from charged tRNA. The name reflects
characterization with respect to D-Tyr on tRNA(Tyr) as
established in the literature, but substrate specificity
seems much broader [Protein synthesis, tRNA
aminoacylation].
Length = 145
Score = 116 bits (291), Expect = 1e-33
Identities = 49/134 (36%), Positives = 70/134 (52%), Gaps = 4/134 (2%)
Query: 31 VDSNVISSIGMGLCILIGISRHDTEKDMDYIVNKILKLKIFENEEGKRWASSVSDKKYEI 90
V+ VI IG GL +L+G+ + D E+ D + K+L +IF + EGK +V EI
Sbjct: 15 VEGEVIGEIGAGLLVLLGVEKDDDEQKADKLAEKVLNYRIFSDSEGK-MNLNVQQAGGEI 73
Query: 91 LCISQFTLYHGL-KGNGLTFHHAMGGADSEVFYNKFLEKLKTAYDLSKVKDGKFGAHMSV 149
L +SQFTL KG +F +E Y F+E + KV+ G+F A M V
Sbjct: 74 LSVSQFTLAADTKKGMRPSFSKGASPDRAEELYEYFVELCREKGM--KVQTGRFAADMQV 131
Query: 150 NIVNDGPVTIPLES 163
++ NDGPVT L+
Sbjct: 132 SLTNDGPVTFWLDV 145
>gnl|CDD|220265 pfam09491, RE_AlwI, AlwI restriction endonuclease. This family
includes the AlwI (recognises GGATC), Bsp6I (recognises
GC^NGC), BstNBI (recognises GASTC), PleI(recognises
GAGTC) and MlyI (recognises GAGTC) restriction
endonucleases.
Length = 429
Score = 28.5 bits (64), Expect = 1.8
Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 19/96 (19%)
Query: 17 YFKQLVKH---TPFVCLVDSNVISSIGMGLCILI------GISRHD---------TEKDM 58
+ KQL+K+ +P+ + I L +L +S+ + + D+
Sbjct: 36 FLKQLLKYQIPSPYSKSCELFDIRPFRFLLKLLNELELESYLSKEEIALFVLTITDDNDI 95
Query: 59 DYIVNKILKLKIFENEEGKRWASSVSDKKYEILCIS 94
D IVN+ILK + E + K +S + +E C S
Sbjct: 96 DEIVNRILKFRK-ERLKNKDNIKKLSKEYFEKECYS 130
>gnl|CDD|235228 PRK04155, PRK04155, chaperone protein HchA; Provisional.
Length = 287
Score = 27.7 bits (62), Expect = 3.1
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 102 LKGNGLTFHH-AMGGADSEV--FYNKFLEKLKTAYDLSKV 138
L GN + F + AM D V FY K+ K K L+ V
Sbjct: 98 LSGNPVKFEYWAMPHEDEAVMGFYEKYKSKFKQPKKLADV 137
>gnl|CDD|192488 pfam10228, DUF2228, Uncharacterized conserved protein (DUF2228).
This is a family of conserved proteins of approximately
700 residues found from worms to humans.
Length = 253
Score = 27.0 bits (60), Expect = 5.9
Identities = 23/78 (29%), Positives = 34/78 (43%), Gaps = 2/78 (2%)
Query: 68 LKIFENEEGKRWASSVSDKKYEILCISQFTLYHGLKGNGLTFHHAMGGADSEVFYNKFLE 127
LK E E K D+ E++ QF G GL + + S+ F+ L+
Sbjct: 177 LKTIEEAEDKEERDKAFDELQELMTFVQFANDECDYGMGLELGIDLFCSGSKYFHKVMLQ 236
Query: 128 KLKTAYDLSKVKDGKFGA 145
L TAY+L +K +F A
Sbjct: 237 LLPTAYNL--LKRPQFAA 252
>gnl|CDD|234092 TIGR03023, WcaJ_sugtrans, Undecaprenyl-phosphate glucose
phosphotransferase. This family of proteins encompasses
the E. coli WcaJ protein involved in colanic acid
biosynthesis , the Methylobacillus EpsB protein involved
in methanolan biosynthesis , as well as the GumD protein
involved in the biosynthesis of xanthan. All of these
are closely related to the well-characterized WbaP
(formerly RfbP) protein which is the first enzyme in
O-antigen biosynthesis in Salmonella typhimurium. The
enzyme transfers galactose from UDP-galactose (NOTE: not
glucose) to a polyprenyl carrier (utilizing the highly
conserved C-terminal sugar transferase domain,
pfam02397) a reaction which takes place at the
cytoplasmic face of the inner membrane. The N-terminal
hydrophobic domain is then believed to facilitate the
"flippase" function of transferring the liposaccharide
unit from the cytoplasmic face to the periplasmic face
of the inner membrane. Most of these genes are found
within large operons dedicated to the production of
complex exopolysaccharides such as the enterobacterial
O-antigen. Colanic acid biosynthesis utilizes a
glucose-undecaprenyl carrier , knockout of EpsB
abolishes incorporation of UDP-glucose into the lipid
phase and the C-terminal portion of GumD has been shown
to be responsible for the glucosyl-1-transferase
activity.
Length = 451
Score = 26.8 bits (60), Expect = 7.2
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 7 SVTGPRP----YVKYFKQLVKH 24
S+ GPRP + + +++L+
Sbjct: 363 SIVGPRPHAVAHNEQYRKLIPG 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
0.319 0.137 0.414
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,947,558
Number of extensions: 790653
Number of successful extensions: 734
Number of sequences better than 10.0: 1
Number of HSP's gapped: 719
Number of HSP's successfully gapped: 14
Length of query: 178
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 87
Effective length of database: 6,901,388
Effective search space: 600420756
Effective search space used: 600420756
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: 56 (25.5 bits)