RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7490
(193 letters)
>gnl|CDD|216754 pfam01873, eIF-5_eIF-2B, Domain found in IF2B/IF5. This family
includes the N terminus of eIF-5, and the C terminus of
eIF-2 beta. This region corresponds to the whole of the
archaebacterial eIF-2 beta homologue. The region
contains a putative zinc binding C4 finger.
Length = 125
Score = 193 bits (492), Expect = 5e-64
Identities = 68/123 (55%), Positives = 87/123 (70%)
Query: 35 REKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTS 94
+NPD VAG K +F M PPQV G KT NF++I K L+R P+HLL +LLAELGT
Sbjct: 3 FNQNPDRVAGDKFRFEMPPPQVKIEGKIKTIIVNFSDIAKALNRPPEHLLKYLLAELGTQ 62
Query: 95 GSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGS 154
GS+DG +LI+ GRF K++++VL YIKEYV CH C+SPDT L K+ RL FL+C+ CG+
Sbjct: 63 GSIDGKGRLIVNGRFTPKKLQDVLDDYIKEYVLCHECKSPDTELIKENRLIFLKCKACGA 122
Query: 155 RCS 157
R
Sbjct: 123 RRP 125
>gnl|CDD|214764 smart00653, eIF2B_5, domain present in translation initiation
factor eIF2B and eIF5.
Length = 110
Score = 183 bits (466), Expect = 3e-60
Identities = 64/110 (58%), Positives = 80/110 (72%)
Query: 46 KQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLII 105
+F M PPQV+R G KT NF +I K L+R P H+L FLLAELGT GS+DG +LI+
Sbjct: 1 FYRFKMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGKGRLIV 60
Query: 106 KGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155
GRF K+++++LRRYIKEYV C C SPDT L K+ RLFFL+CE CG+R
Sbjct: 61 NGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFLKCEACGAR 110
>gnl|CDD|224517 COG1601, GCD7, Translation initiation factor 2, beta subunit
(eIF-2beta)/eIF-5 N-terminal domain [Translation,
ribosomal structure and biogenesis].
Length = 151
Score = 153 bits (388), Expect = 5e-48
Identities = 60/151 (39%), Positives = 89/151 (58%), Gaps = 5/151 (3%)
Query: 17 SDRDYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTL 76
S+ + YEELL R + + P+ ++F + P++ R G +T NF +I + L
Sbjct: 2 SEMEDDYEELLERAYS----ELPEKEVKNDERFRIPEPEINREG-NRTIIRNFGDIAEAL 56
Query: 77 HRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDT 136
+R P+HL+ FL ELGT+GS+DG +L+++G+F +I N + RYI EYV C C SPDT
Sbjct: 57 NRDPEHLVKFLKKELGTAGSIDGKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDT 116
Query: 137 ILQKDTRLFFLQCETCGSRCSVASIKSGFQK 167
L K+ RL FL+CE CG+ V +K
Sbjct: 117 ELIKEERLLFLKCEACGAIRPVKLMKEYNLD 147
>gnl|CDD|235189 PRK03988, PRK03988, translation initiation factor IF-2 subunit
beta; Validated.
Length = 138
Score = 141 bits (357), Expect = 2e-43
Identities = 60/142 (42%), Positives = 85/142 (59%), Gaps = 7/142 (4%)
Query: 20 DYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRL 79
Y YEELL R +E + EK K+ +F + P V G + T NF EI L+R
Sbjct: 4 YYDYEELLDRAYEKLPEK-----VFKESRFEVPKPDVRIEGNR-TIIRNFKEIADRLNRD 57
Query: 80 PKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQ 139
PKH+ FLL ELGT+G+++G +LI++G+F + I + RY+KEYV C C SPDT L
Sbjct: 58 PKHVAKFLLKELGTAGNIEGG-RLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLI 116
Query: 140 KDTRLFFLQCETCGSRCSVASI 161
K+ R++ L+CE CG+ V +
Sbjct: 117 KEGRIWVLKCEACGAETPVKPL 138
>gnl|CDD|183451 PRK12336, PRK12336, translation initiation factor IF-2 subunit
beta; Provisional.
Length = 201
Score = 116 bits (293), Expect = 5e-33
Identities = 50/148 (33%), Positives = 77/148 (52%), Gaps = 7/148 (4%)
Query: 21 YTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLP 80
YE LL R E++ E ++F + P++ G K T NF EI L+R P
Sbjct: 1 MDYESLLDRAMEVLPEPT-----KSGERFSIPEPKIFIEG-KTTILTNFGEIADALNRDP 54
Query: 81 KHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQK 140
HL+ FL ELGT+G ++G + + G+F ++ I+ + Y+ EYV C C PDT L K
Sbjct: 55 DHLMKFLQRELGTAGKIEGG-RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVK 113
Query: 141 DTRLFFLQCETCGSRCSVASIKSGFQKD 168
+ R+ L+C+ CG+ V K+ +
Sbjct: 114 EDRVLMLRCDACGAHRPVKKRKASSETQ 141
>gnl|CDD|129411 TIGR00311, aIF-2beta, translation initiation factor aIF-2, beta
subunit, putative. The trusted cutoff is set high
enough to select only archaeal members. The suggested
cutoff is set to include most eukaryotic members but
largely exclude the related eIF-5 [Protein synthesis,
Translation factors].
Length = 133
Score = 96.5 bits (240), Expect = 6e-26
Identities = 49/139 (35%), Positives = 83/139 (59%), Gaps = 7/139 (5%)
Query: 23 YEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKH 82
YE+LL R + + PD V + ++F + +V G + T NF E+ K L+R +H
Sbjct: 2 YEKLLERAID----QLPDEVF-ETKRFEVPKAYIVIEGNR-TIIQNFREVAKALNRDEQH 55
Query: 83 LLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDT 142
LL +LL ELGT+G+++G +LI++G+F + + Y+++YV C C PDT + K+
Sbjct: 56 LLKYLLKELGTAGNLEG-GRLILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRIIKEG 114
Query: 143 RLFFLQCETCGSRCSVASI 161
R+ L+CE CG++ + +I
Sbjct: 115 RVSLLKCEACGAKAPLRNI 133
>gnl|CDD|99823 cd05780, DNA_polB_Kod1_like_exo, DEDDy 3'-5' exonuclease domain
of Pyrococcus kodakaraensis Kod1 and similar archaeal
family-B DNA polymerases. The 3'-5' exonuclease domain
of archaeal family-B DNA polymerases with similarity to
Pyrococcus kodakaraensis Kod1, including polymerases
from Desulfurococcus (D. Tok Pol) and Thermococcus
gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol
are thermostable enzymes that exhibit both polymerase
and 3'-5' exonuclease activities. They are family-B DNA
polymerases. Their amino termini harbor a DEDDy-type
DnaQ-like 3'-5' exonuclease domain that contains three
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. These motifs are
clustered around the active site and are involved in
metal binding and catalysis. The exonuclease domain of
family B polymerases contains a beta hairpin structure
that plays an important role in active site switching
in the event of nucleotide misincorporation. Members of
this subfamily show similarity to eukaryotic DNA
polymerases involved in DNA replication. Some archaea
possess multiple family-B DNA polymerases. Phylogenetic
analyses of eubacterial, archaeal, and eukaryotic
family-B DNA polymerases support independent gene
duplications during the evolution of archaeal and
eukaryotic family-B DNA polymerases.
Length = 195
Score = 35.0 bits (81), Expect = 0.012
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 13 TWIGSDRDY-----TYEELLSRVFEIMREKNPDMVAG 44
TW D + T +E++ R EI++EK+PD++
Sbjct: 41 TWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVIYT 77
>gnl|CDD|236396 PRK09181, PRK09181, aspartate kinase; Validated.
Length = 475
Score = 32.6 bits (75), Expect = 0.10
Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 14/102 (13%)
Query: 15 IGSDRDYTYEELLSRVFEIMREKNPDMVAG-----KKQKFVMRPPQVVRIGTKKTSFANF 69
D + E L V + M N ++ A + KF+ RI + +
Sbjct: 66 FAKANDEAWREALEAVEQRMLAINAELFADGLDLARADKFIRE-----RIEEARACLIDL 120
Query: 70 TEICKTLH-RLPKHLLDF--LLAELGTSGSVDGNSQLIIKGR 108
+C H L +HLL +LA +G + S N+ L+++ R
Sbjct: 121 QRLCAYGHFSLDEHLLTVREMLASIGEAHSA-FNTALLLQNR 161
>gnl|CDD|236293 PRK08568, PRK08568, preprotein translocase subunit SecY; Reviewed.
Length = 462
Score = 31.3 bits (72), Expect = 0.28
Identities = 15/30 (50%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 99 GNSQLIIKG-RFQQKQIENVLRRYIKEYVT 127
NS + I G R K IE VL RYI VT
Sbjct: 376 QNSGMQIPGFRRNPKVIEKVLERYIP-PVT 404
>gnl|CDD|130625 TIGR01562, FdhE, formate dehydrogenase accessory protein FdhE.
This model describes an accessory protein required for
the assembly of formate dehydrogenase of certain
proteobacteria although not present in the final
complex. The exact nature of the function of FdhE in the
assembly of the complex is unknown, but considering the
presence of selenocysteine, molybdopterin, iron-sulfur
clusters and cytochrome b556, it is likely to have
something to do with the insertion of cofactors. The
only sequence scoring between trusted and noise is that
from Aquifex aeolicus, which shows certain structural
differences from the proteobacterial forms in the
alignment. However it is notable that A. aeolicus also
has a sequence scoring above trusted to the alpha
subunit of formate dehydrogenase (TIGR01553).
Length = 305
Score = 30.3 bits (68), Expect = 0.60
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 149 CETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIK 189
C CGS VAS+ K+T L +L C C + +K
Sbjct: 187 CPACGSP-PVASMVRQGGKETGLRYLSCSLCATEWHYVRVK 226
>gnl|CDD|220087 pfam08996, zf-DNA_Pol, DNA Polymerase alpha zinc finger. The DNA
Polymerase alpha zinc finger domain adopts an
alpha-helix-like structure, followed by three turns, all
of which involve proline. The resulting motif is a
helix-turn-helix motif, in contrast to other zinc finger
domains, which show anti-parallel sheet and helix
conformation. Zinc binding occurs due to the presence of
four cysteine residues positioned to bind the metal
centre in a tetrahedral coordination geometry. Function
of this domain is uncertain: it has been proposed that
the zinc finger motif may be an essential part of the
DNA binding domain.
Length = 187
Score = 29.9 bits (68), Expect = 0.61
Identities = 12/55 (21%), Positives = 21/55 (38%)
Query: 134 PDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASI 188
D+ +D L+C +CG+ I + + LQC C + + I
Sbjct: 6 TDSERFRDCARLKLKCPSCGTEFPFEGIFASSGERVTPSGLQCSKCNALIPLLQI 60
>gnl|CDD|223890 COG0820, COG0820, Predicted Fe-S-cluster redox enzyme [General
function prediction only].
Length = 349
Score = 30.0 bits (68), Expect = 0.63
Identities = 23/112 (20%), Positives = 36/112 (32%), Gaps = 16/112 (14%)
Query: 20 DYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVR--IGTKKTSFANFTEICKTL- 76
D T EL + E+ +K R Q+ + F T++ K L
Sbjct: 6 DLTRAELAEWLAELGLKK-------------FRAKQLFKWIYQKGVDDFDEMTDLSKGLR 52
Query: 77 HRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTC 128
+L + LL + S DG + + + IE VL C
Sbjct: 53 AKLKEAFFINLLKVVEVQESSDGTIKWLFEVLPDGTMIETVLIPEKDRNTLC 104
>gnl|CDD|185607 PTZ00422, PTZ00422, glideosome-associated protein 50; Provisional.
Length = 394
Score = 29.4 bits (66), Expect = 1.0
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 62 KKTSFANFTEICKTLHRLPKHLLDFLLA----ELGTSGSVDGNSQLIIK 106
KK S + ++ TL PK D+++ + +SGS G+S L
Sbjct: 192 KKVSERAWQDLKATLEYAPKI-ADYIIVVGDKPIYSSGSSKGDSYLSYY 239
>gnl|CDD|216312 pfam01125, G10, G10 protein.
Length = 145
Score = 28.4 bits (64), Expect = 1.5
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR-CS 157
TC CR P L++ F+QC CG R C+
Sbjct: 117 TC-ICRVPKAKLEEKR---FVQCVHCGCRGCA 144
>gnl|CDD|148309 pfam06626, DUF1152, Protein of unknown function (DUF1152). This
family consists of several hypothetical archaeal
proteins of unknown function.
Length = 297
Score = 28.8 bits (65), Expect = 1.6
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 4 LQELEDESHTWI---GSDRDYTYEELLSRVFEIMREK 37
L +LE+E + GSD + + E LL R+ EI RE
Sbjct: 152 LAKLEEEVVLAVIGPGSDGELSREYLLQRISEIAREG 188
>gnl|CDD|176646 cd05160, DEDDy_DNA_polB_exo, DEDDy 3'-5' exonuclease domain of
family-B DNA polymerases. The 3'-5' exonuclease domain
of family-B DNA polymerases. This domain has a
fundamental role in reducing polymerase errors and is
involved in proofreading activity. Family-B DNA
polymerases contain an N-terminal DEDDy DnaQ-like
exonuclease domain in the same polypeptide chain as the
polymerase domain, similar to family-A DNA polymerases.
This domain contains three sequence motifs termed ExoI,
ExoII and ExoIII, with a specific YX(3)D pattern at
ExoIII. These motifs are clustered around the active
site and contain four conserved acidic residues that
serve as ligands for the two metal ions required for
catalysis. The exonuclease domain of family B
polymerase also contains a beta hairpin structure that
plays an important role in active site switching in the
event of nucleotide misincorporation. Members include
Escherichia coli DNA polymerase II, some eubacterial
phage DNA polymerases, nuclear replicative DNA
polymerases (alpha, delta, epsilon and zeta), and
eukaryotic viral and plasmid-borne enzymes. Nuclear DNA
polymerases alpha and zeta lack the four conserved
acidic metal-binding residues. Family-B DNA polymerases
are predominantly involved in DNA replication and DNA
repair.
Length = 199
Score = 28.5 bits (64), Expect = 1.8
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 10 ESHTWIGSDRDYTYEELLSRVFEIMREKNPDMVAG 44
E I + +ELL R F+I+RE +PD++ G
Sbjct: 50 EFIDGIEVEYFADEKELLKRFFDIIREYDPDILTG 84
>gnl|CDD|237145 PRK12583, PRK12583, acyl-CoA synthetase; Provisional.
Length = 558
Score = 28.6 bits (64), Expect = 2.5
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 39 PDMVAGKKQKFVMRPPQVVRIGTKK 63
P V GK QKF MR + +
Sbjct: 534 PMTVTGKVQKFRMREISIEELALPV 558
>gnl|CDD|226521 COG4034, COG4034, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 328
Score = 28.2 bits (63), Expect = 3.0
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 16 GSDRDYTYEELLSRVFEIMRE 36
GSD + + E LL R+ EI RE
Sbjct: 182 GSDGELSREYLLRRISEIARE 202
>gnl|CDD|237788 PRK14687, PRK14687, hypothetical protein; Provisional.
Length = 173
Score = 27.7 bits (61), Expect = 3.4
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 21 YTYEELLSRVFEIMREKNPDMVAGKKQK 48
Y E+LSR+ ++M P M+ KQ+
Sbjct: 4 YDNSEMLSRLIDVMANDKPLMLTSPKQR 31
>gnl|CDD|217123 pfam02585, PIG-L, GlcNAc-PI de-N-acetylase. Members of this family
are related to PIG-L an
N-acetylglucosaminylphosphatidylinositol de-N-acetylase
(EC:3.5.1.89) that catalyzes the second step in GPI
biosynthesis.
Length = 115
Score = 26.5 bits (59), Expect = 4.6
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 19 RDYTYEELLSRVFEIMREKNPDMV 42
R++ EELL+ + ++RE PD+V
Sbjct: 81 REWDLEELLAALARLIREIRPDVV 104
>gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor
biosynthesis protein NifE/NifN; Provisional.
Length = 917
Score = 27.4 bits (61), Expect = 5.3
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 31 FEIMREKNPDM-VAGKKQKFV 50
+MREK PD+ VAG K KF+
Sbjct: 382 LRVMREKMPDLIVAGGKTKFL 402
>gnl|CDD|147564 pfam05451, Phytoreo_Pns, Phytoreovirus nonstructural protein
Pns10/11. This family consists of Phytoreovirus
nonstructural proteins Pns10 and Pns11. Genome segment
S11 of rice gall dwarf virus (RGDV), a member of
Phytoreovirus encodes a putative protein of 40 kDa that
exhibits approximately 37% homology at the amino acid
level to the nonstructural proteins Pns10 of rice dwarf
and wound tumour viruses, which are other members of
Phytoreovirus.
Length = 344
Score = 27.1 bits (60), Expect = 6.7
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 1 MSTLQELEDESHTWIGSD---RDYT 22
S L+ +S +I SD RD T
Sbjct: 50 FSKLRNFARKSEAYIASDLAERDLT 74
>gnl|CDD|234308 TIGR03682, arCOG04112, diphthamide biosynthesis enzyme Dph2.
Members of this family are the archaeal protein Dph2,
members of the universal archaeal protein family
designated arCOG04112. The chemical function of this
protein is analogous to the radical SAM family
(pfam04055), although the sequence is not homologous.
The chemistry involves [4Fe-4S]-aided formation of a
3-amino-3-carboxypropyl radical rather than the
canonical 5'-deoxyadenosyl radical of the radical SAM
family.
Length = 308
Score = 26.5 bits (59), Expect = 8.5
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 23 YEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQV 56
+ LL +V EI+ E+ ++V GK V P QV
Sbjct: 108 HVHLLEKVKEILEERGIEVVIGKGDGRVTYPGQV 141
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
0.323 0.136 0.406
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: 9,548,385
Number of extensions: 863798
Number of successful extensions: 905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 898
Number of HSP's successfully gapped: 31
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.3 bits)