RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17313
(197 letters)
>gnl|CDD|240334 PTZ00258, PTZ00258, GTP-binding protein; Provisional.
Length = 390
Score = 287 bits (738), Expect = 1e-97
Identities = 115/181 (63%), Positives = 137/181 (75%), Gaps = 3/181 (1%)
Query: 9 IEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQ 68
IE LN+ LLTAK IYLVN+S KD+I++KNKWL KIKEWV G IIP+S FE +
Sbjct: 209 IEILNEYQLLTAKPMIYLVNMSEKDFIRQKNKWLAKIKEWVGEKGGG-PIIPYSAEFEEE 267
Query: 69 LVDMPDDE-RQRYLDEQKAT-SVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAP 126
L ++ +E R+ YL+E S+LDKII GYK L L +FFTAG DEV+ WTIQKGTKAP
Sbjct: 268 LAELGSEEERKEYLEEYGIKQSMLDKIIKTGYKLLNLIHFFTAGPDEVRCWTIQKGTKAP 327
Query: 127 QAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 186
QAAG IH+DFEKGFI AEVM ++DF E GSEAA +A GKYRQ+G+ Y V+DGDIIFFKFN
Sbjct: 328 QAAGVIHSDFEKGFICAEVMKYEDFLELGSEAAVKAEGKYRQEGKDYVVQDGDIIFFKFN 387
Query: 187 A 187
Sbjct: 388 V 388
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 214 bits (548), Expect = 3e-69
Identities = 81/176 (46%), Positives = 115/176 (65%), Gaps = 4/176 (2%)
Query: 12 LNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVD 71
L L LLTAK +Y+ N+ D + N ++ K++E A GA ++ E ++ +
Sbjct: 191 LKSLQLLTAKPVLYVANVDEDD-LADGNPYVKKVREI--AAKEGAEVVVICAKIEAEIAE 247
Query: 72 MPDDERQRYLDEQKAT-SVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAG 130
+ D+E+ +L+E S LD++I GY+ L L +FTAG EV+AWTI+KGT APQAAG
Sbjct: 248 LDDEEKAEFLEELGLEESGLDRLIRAGYELLGLITYFTAGPKEVRAWTIKKGTTAPQAAG 307
Query: 131 RIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 186
IHTDFEKGFI AEV+ +DD E+GSEA + AGK R +G+ Y V+DGD++ F+FN
Sbjct: 308 VIHTDFEKGFIRAEVISYDDLIEYGSEAGAKEAGKVRLEGKDYIVQDGDVMHFRFN 363
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 194 bits (495), Expect = 3e-61
Identities = 83/179 (46%), Positives = 114/179 (63%), Gaps = 7/179 (3%)
Query: 12 LNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQLVD 71
L LNLLTAK +Y+ N+S D N+++ ++KE A ++P S E +L +
Sbjct: 198 LASLNLLTAKPMLYVANVSEDDL-ANLNEYVKRLKELAAKE--NAEVVPVSAAIELELRE 254
Query: 72 MPD-DERQRYLDE--QKATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAPQA 128
+ D +E+ +L E QK S L+++I GY L LQ +FTAG EV+AWTI+ G+KAP A
Sbjct: 255 LADAEEKGEFLIELGQK-ESGLNELIRAGYGLLGLQTYFTAGVKEVRAWTIKDGSKAPDA 313
Query: 129 AGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFNA 187
AG IH DFEKGFI AEV+ + D +G EAA + AGK R +G+ Y V+DGD+I FKFN
Sbjct: 314 AGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYIVQDGDVIHFKFNV 372
>gnl|CDD|133440 cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS
domain-containing YchF GTP-binding protein, a
universally conserved GTPase whose function is unknown.
The N-terminal domain of the YchF protein belongs to the
Obg-like family of GTPases, and some members of the
family contain a C-terminal TGS domain. TGS is a small
domain of about 50 amino acid residues with a
predominantly beta-sheet structure. There is no direct
information on the function of the TGS domain, but its
presence in two types of regulatory proteins (the
GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 83
Score = 172 bits (438), Expect = 3e-56
Identities = 62/83 (74%), Positives = 70/83 (84%)
Query: 103 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRA 162
L FFTAG DEV+AWTI+KGTKAPQAAG IHTDFEKGFI AEVM ++D E GSEAA +
Sbjct: 1 LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60
Query: 163 AGKYRQQGRAYTVEDGDIIFFKF 185
AGKYRQ+G+ Y V+DGDIIFFKF
Sbjct: 61 AGKYRQEGKDYVVQDGDIIFFKF 83
>gnl|CDD|203386 pfam06071, YchF-GTPase_C, Protein of unknown function (DUF933).
This domain is found at the C terminus of the YchF
GTP-binding protein and is possibly related to the
ubiquitin-like and MoaD/ThiS superfamilies.
Length = 84
Score = 161 bits (410), Expect = 4e-52
Identities = 55/84 (65%), Positives = 66/84 (78%)
Query: 103 LQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRA 162
L FFTAG EV+AWTI+KGT APQAAG IH+DFEKGFI AEV+ +DD E+GSEA +
Sbjct: 1 LITFFTAGPKEVRAWTIRKGTTAPQAAGVIHSDFEKGFIRAEVISYDDLIEYGSEAKAKE 60
Query: 163 AGKYRQQGRAYTVEDGDIIFFKFN 186
AGK R +G+ Y V+DGDII F+FN
Sbjct: 61 AGKLRLEGKDYIVQDGDIIHFRFN 84
>gnl|CDD|129200 TIGR00092, TIGR00092, GTP-binding protein YchF. This predicted
GTP-binding protein is found in a single copy in every
complete bacterial genome, and is found in Eukaryotes. A
more distantly related protein, separated from this
model, is found in the archaea. It is known to bind GTP
and double-stranded nucleic acid. It is suggested to
belong to a nucleoprotein complex and act as a
translation factor [Unknown function, General].
Length = 368
Score = 161 bits (410), Expect = 1e-48
Identities = 73/180 (40%), Positives = 101/180 (56%), Gaps = 3/180 (1%)
Query: 10 EHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQ- 68
L K L K I L+ ++DY++ N I EW+ A G + F E
Sbjct: 188 LILIKSLNLLTKKPIILIANVSEDYLRNLNNNYLLIVEWIAAYSKGDPKVVFVCALEESE 247
Query: 69 LVDMPDDERQRYLDE--QKATSVLDKIITQGYKSLQLQYFFTAGQDEVKAWTIQKGTKAP 126
L ++ D+ERQ +L + ++ L+ II YK L L +FFT G++EV+AWT + G AP
Sbjct: 248 LSELDDEERQEFLQKLGLTESAGLNIIIRARYKLLLLSFFFTGGKEEVRAWTRKGGWAAP 307
Query: 127 QAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDIIFFKFN 186
QAAG IHTDFE GFI AEV+ +DDF S + G R +G+ Y V+DGD++FF FN
Sbjct: 308 QAAGIIHTDFETGFIAAEVISWDDFIYKKSSQGAKKGGLMRLEGKYYVVDDGDVLFFAFN 367
>gnl|CDD|206687 cd01900, YchF, YchF GTPase. YchF is a member of the Obg family,
which includes four other subfamilies of GTPases: Obg,
DRG, Ygr210, and NOG1. Obg is an essential gene that is
involved in DNA replication in C. crescentus and
Streptomyces griseus and is associated with the
ribosome. Several members of the family, including YchF,
possess the TGS domain related to the RNA-binding
proteins. Experimental data and genomic analysis suggest
that YchF may be part of a nucleoprotein complex and may
function as a GTP-dependent translational factor.
Length = 274
Score = 100 bits (253), Expect = 3e-26
Identities = 37/94 (39%), Positives = 51/94 (54%), Gaps = 4/94 (4%)
Query: 9 IEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDANDPGATIIPFSGVFEHQ 68
I+ L L LLTAK IY+ N+S D I+ NK L K A GA +IP S E +
Sbjct: 184 IKILKSLQLLTAKPVIYVANVSEDDLIRGNNKVL---KVREIAAKEGAEVIPISAKLEAE 240
Query: 69 LVDMPDDERQRYLDEQKAT-SVLDKIITQGYKSL 101
L ++ ++E +L+E S LDK+I GY+ L
Sbjct: 241 LAELDEEEAAEFLEELGLEESGLDKLIRAGYELL 274
>gnl|CDD|133441 cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of
Obg-like GTPases such as those present in DRG
(developmentally regulated GTP-binding protein), and
GTP-binding proteins Ygr210 and YchF. The TGS domain
(named after the ThrRS, GTPase, and SpoT proteins where
it occurs) is a small domain of about 50 amino acid
residues with a predominantly beta-sheet structure.
There is no direct information on the function of the
TGS domain, but its presence in two types of regulatory
proteins (the GTPases and guanosine polyphosphate
phosphohydrolases/synthetases) suggests a ligand (most
likely nucleotide)-binding, regulatory role.
Length = 76
Score = 47.0 bits (112), Expect = 1e-07
Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 18/87 (20%)
Query: 99 KSLQLQYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEA 158
K++ + G ++KGT A +IH D EKGFI A
Sbjct: 8 KNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------------- 54
Query: 159 ACRAAGKYRQQGRAYTVEDGDIIFFKF 185
G+ R +G+ + DI+ FK
Sbjct: 55 -----GRRRLEGKDVILGKNDILKFKT 76
>gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and
SpoT/RelA proteins where it occurs, is structurally
similar to ubiquitin. TGS is a small domain of about 50
amino acid residues with a predominantly beta-sheet
structure. There is no direct information on the
function of the TGS domain, but its presence in two
types of regulatory proteins (the GTPases and guanosine
polyphosphate phosphohydrolases/synthetases) suggests a
ligand (most likely nucleotide)-binding, regulatory
role.
Length = 60
Score = 40.4 bits (95), Expect = 2e-05
Identities = 22/80 (27%), Positives = 29/80 (36%), Gaps = 22/80 (27%)
Query: 104 QYFFTAGQDEVKAWTIQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAA 163
FT A + KG A A +IHTD KGFI A V
Sbjct: 1 MIIFTPDG---SAVELPKGATAMDFALKIHTDLGKGFIGALVNG---------------- 41
Query: 164 GKYRQQGRAYTVEDGDIIFF 183
+ +YT++DGD +
Sbjct: 42 ---QLVDLSYTLQDGDTVSI 58
>gnl|CDD|133439 cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of
Ygr210 GTP-binding protein which is a member of Obg-like
family of GTPases, and present in archaea. Several
Obg-like family members possess a C-terminal RNA-binding
domain, the TGS domain, which is also present in
threonyl-tRNA synthetase and in bacterial guanosine
polyphosphatase SpoT. TGS is a small domain of about 50
amino acid residues with a predominantly beta-sheet
structure. There is no direct information on the
function of the TGS domain, but its presence in two
types of regulatory proteins (the GTPases and guanosine
polyphosphate phosphohydrolases/synthetases) suggests a
ligand (most likely nucleotide)-binding, regulatory
role.
Length = 76
Score = 28.0 bits (63), Expect = 0.79
Identities = 15/46 (32%), Positives = 19/46 (41%), Gaps = 13/46 (28%)
Query: 110 GQDEVKAWTIQKGTKAPQA------------AGRIHTDFEKGFIMA 143
+DE K T ++G P A A IHTD GF+ A
Sbjct: 7 VEDENK-LTDKEGNVLPDAFLLPKGSTARDLAYAIHTDIGDGFLHA 51
>gnl|CDD|219151 pfam06725, 3D, 3D domain. This short presumed domain contains
three conserved aspartate residues, hence the name 3D.
It has been shown to be part of the catalytic double psi
beta barrel domain of MltA.
Length = 72
Score = 27.2 bits (61), Expect = 1.5
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 147 HFDDFKEHGSEAACRAAGKYRQQGRAYTVE 176
D + G EA AG YR+ GR Y +
Sbjct: 44 RIDLYFGTGDEA-GNLAGLYRKTGRVYILL 72
>gnl|CDD|202551 pfam03142, Chitin_synth_2, Chitin synthase. Members of this family
are fungal chitin synthase EC:2.4.1.16 enzymes. They
catalyze chitin synthesis as follows:
UDP-N-acetyl-D-glucosamine +
{(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP +
{(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).
Length = 527
Score = 28.9 bits (65), Expect = 1.9
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 8 RIEHLNKLNLLTAKTQIYLVNLSAKDYIKKKNKWLPKIKEWVDAND 53
++ L+K NLL YL L K + K+K K++P+ A D
Sbjct: 313 VVDTLHKKNLLLLGEDRYLTTLMLKTFPKRKTKFVPQAVCKTIAPD 358
>gnl|CDD|185418 PTZ00054, PTZ00054, 60S ribosomal protein L23; Provisional.
Length = 139
Score = 28.2 bits (63), Expect = 1.9
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 168 QQGRAYTVEDGDIIFFKFNAGAGLNPK 194
+Q +A+ +DG I+F+ NAG +NPK
Sbjct: 82 RQRKAWRRKDGVFIYFEDNAGVIVNPK 108
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 28.2 bits (64), Expect = 2.5
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 17/61 (27%)
Query: 121 KGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQGRAYTVEDGDI 180
KG+ A A +IHTD +GF+ A D + R+ G Y ++DGD+
Sbjct: 347 KGSTARDLAYKIHTDIGEGFLYAI-----DARTK------------RRIGEDYELKDGDV 389
Query: 181 I 181
I
Sbjct: 390 I 390
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 28.0 bits (63), Expect = 3.8
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 16/65 (24%)
Query: 119 IQKGTKAPQAAGRIHTDFEKGFIMAEVMHFDDFKEHGSEAACRAAGKYRQQ--GRAYTVE 176
+++G+ +IH D + F A V G K+ Q G + +E
Sbjct: 310 LRRGSTVGDVCRKIHRDLVENFRYARVW--------GKSV------KHPGQRVGLDHVLE 355
Query: 177 DGDII 181
D DI+
Sbjct: 356 DEDIV 360
>gnl|CDD|219974 pfam08696, Dna2, DNA replication factor Dna2. Dna2 is a DNA
replication factor with single-stranded DNA-dependent
ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease)
and helicase activities. It is required for Okazaki
fragment processing and is involved in DNA repair
pathways.
Length = 209
Score = 26.8 bits (60), Expect = 5.7
Identities = 7/27 (25%), Positives = 15/27 (55%)
Query: 24 IYLVNLSAKDYIKKKNKWLPKIKEWVD 50
+YL+ S + ++ + LP I+ W +
Sbjct: 130 LYLLGESQDEVREEVMEHLPAIEGWAE 156
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 26.9 bits (60), Expect = 7.5
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 36 KKKNKWLPKIKEWVDANDPGATII 59
K+ N W K+K +++ GA +I
Sbjct: 138 KRSNPWFDKVKNFLEKE--GARVI 159
>gnl|CDD|234838 PRK00784, PRK00784, cobyric acid synthase; Provisional.
Length = 488
Score = 26.6 bits (60), Expect = 9.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 28 NLSAKDYIKKKNKWLPKIKE 47
N+ A+DY K + L + E
Sbjct: 98 NMDARDYHDYKPRLLEAVLE 117
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
0.320 0.136 0.407
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,340,349
Number of extensions: 962318
Number of successful extensions: 949
Number of sequences better than 10.0: 1
Number of HSP's gapped: 933
Number of HSP's successfully gapped: 34
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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 (25.3 bits)