RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8931
(95 letters)
>gnl|CDD|211321 cd11608, eIF2D_C, C-terminal domain of eIF2D and related
proteins. eIF2D translation initiation factor (also
known as ligatin) is involved in the recruitment and
delivery of aminoacyl-tRNAs to the P-site of the
eukaryotic ribosome in a GTP-independent manner.
Length = 85
Score = 102 bits (257), Expect = 2e-30
Identities = 41/85 (48%), Positives = 56/85 (65%), Gaps = 3/85 (3%)
Query: 6 PIDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCINMV---NNAAQVQVQ 62
PID+ R GNKKVTL++ L+ +GID +EF K Q AAST ++ + +VQVQ
Sbjct: 1 PIDITTERRQGNKKVTLISGLESFGIDPEEFAKELQKKCAASTSVSPLPGKKKGVEVQVQ 60
Query: 63 GNQIVFVHNLLTEKFNIQKRFIRGL 87
GNQ+ FV LLTEK+ + K++I GL
Sbjct: 61 GNQVKFVAKLLTEKYGVPKKYIDGL 85
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 61.7 bits (151), Expect = 2e-14
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 2 GKLKPIDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCINMVNNAAQVQV 61
+ + I ++ R G K VT+V L+++GIDLK+ K + V + ++++
Sbjct: 2 KEDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGT---VKDGEEIEI 58
Query: 62 QGNQIVFVHNLLTEKF 77
QG+ V +LL ++
Sbjct: 59 QGDHRDKVKDLLEKEG 74
>gnl|CDD|211320 cd11607, DENR_C, C-terminal domain of DENR and related proteins.
DENR (density regulated protein), together with MCT-1
(multiple copies T cell malignancies), has been shown
to have similar function as eIF2D translation
initiation factor (also known as ligatin), which is
involved in the recruitment and delivery of
aminoacyl-tRNAs to the P-site of the eukaryotic
ribosome in a GTP-independent manner.
Length = 86
Score = 44.9 bits (107), Expect = 1e-07
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 5 KPIDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCIN-MVNNAAQVQVQG 63
+ ++ +R+ K VT V L+ +GIDLK+ KL A + ++ +QG
Sbjct: 1 SKVTIKRISRNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTKGAEGKDEIVIQG 60
Query: 64 NQIVFVHNLLTEKFNI 79
+ + +L+ EK+
Sbjct: 61 DVTDDIVDLILEKWPE 76
>gnl|CDD|211317 cd00474, eIF1_SUI1_like, Eukaryotic initiation factor 1 and
related proteins. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. eIF1 interacts with 18S rRNA in the 40S
ribosomal subunit during eukaryotic translation
initiation. Point mutations in the yeast eIF1 implicate
the protein in maintaining accurate start-site
selection but its mechanism of action is unknown. The
function of non-eukaryotic family members is also
unclear.
Length = 78
Score = 32.0 bits (73), Expect = 0.010
Identities = 20/76 (26%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 7 IDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCINMVNNAAQVQVQGNQI 66
I ++V RSG KKVT V L Y IDL++ + + + ++++QG+
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAY-IDLRKLADELKKKLGCGGSV--EGEKMEIEIQGDHT 58
Query: 67 VFVHNLLTEKFNIQKR 82
+ L EK +
Sbjct: 59 DQIIVALEEKGIDKDW 74
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 29.6 bits (67), Expect = 0.099
Identities = 19/70 (27%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 7 IDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCINMVNNAAQVQVQGNQI 66
+ ++ TR K VT++ LD+ IDLK+ K + A + + ++++QG+
Sbjct: 29 VRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKELKKKCACGGTV--KDG--EIEIQGDHR 84
Query: 67 VFVHNLLTEK 76
V LL +K
Sbjct: 85 DKVKELLIKK 94
>gnl|CDD|233294 TIGR01159, DRP1, density-regulated protein DRP1. This protein
family shows weak but suggestive similarity to
translation initiation factor SUI1 and its prokaryotic
homologs.
Length = 173
Score = 28.7 bits (64), Expect = 0.36
Identities = 21/85 (24%), Positives = 34/85 (40%), Gaps = 10/85 (11%)
Query: 2 GKLKPIDLQVAT-----RSGNKKVTLVNNLDVYGIDLKEFCK-LCQHGVAASTCINMVNN 55
GK K Q T R+ K VT++ L+ + IDLK+ K Q + V
Sbjct: 81 GKKKKKLPQKVTIKREPRTKRKFVTVIKGLETFDIDLKKASKTFAQKFATGCSVSKSVTG 140
Query: 56 AAQVQVQGN----QIVFVHNLLTEK 76
++ +QG+ ++H E
Sbjct: 141 KEEIVIQGDVMDDIEDYIHEKWPEV 165
>gnl|CDD|233118 TIGR00761, argB, acetylglutamate kinase. This model describes
N-acetylglutamate kinases (ArgB) of many prokaryotes
and the N-acetylglutamate kinase domains of
multifunctional proteins from yeasts. This enzyme is
the second step in the "acetylated" ornithine
biosynthesis pathway. A related group of enzymes
representing the first step of the pathway contain a
homologous domain and are excluded from this model
[Amino acid biosynthesis, Glutamate family].
Length = 231
Score = 27.6 bits (62), Expect = 0.72
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 51 NMVNNAAQVQVQGNQIVFVH------NLLTEKFNIQKRFIRGLELAPKK 93
++ A ++ G + V VH N L E I F GL + K+
Sbjct: 17 AFASDIAFLRAVGIKPVIVHGGGPEINELLEALGIPPEFKNGLRVTDKE 65
>gnl|CDD|211319 cd11567, YciH_like, Homologs of eIF1/SUI1 including Escherichia
coli YciH. Members of the eIF1/SUI1 (eukaryotic
initiation factor 1) family are found in eukaryotes,
archaea, and some bacteria; eukaryotic members are
understood to play an important role in accurate
initiator codon recognition during translation
initiation. The function of non-eukaryotic family
members is unclear. Escherichia coli YciH is a
non-essential protein and was reported to be able to
perform some of the functions of IF3 in prokaryotic
initiation.
Length = 76
Score = 25.9 bits (58), Expect = 1.7
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 16 GNKKVTLVNNLDVYGIDLKEFCK 38
G K VT++ L + DLKE K
Sbjct: 13 GGKTVTVIEGLPLSEEDLKELAK 35
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 26.0 bits (58), Expect = 2.0
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 7 IDLQVATRSGNKKVTLVNNLDVYGIDLKEFCKLCQHGVAASTCINMVNNAAQVQVQGNQI 66
I ++V R K+VT++ +D IDLKE K + +A C V + ++++QG+
Sbjct: 26 IKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLA---CGGTVKD-GRIELQGDHR 81
Query: 67 VFVHNLLTEK 76
V LL +
Sbjct: 82 ERVKELLIKM 91
>gnl|CDD|204182 pfam09254, Endonuc-FokI_C, Restriction endonuclease FokI, C
terminal. Members of this family are predominantly
found in prokaryotic restriction endonuclease FokI, and
adopt a structure consisting of an alpha/beta/alpha
core containing a five-stranded beta-sheet. They
recognise the double-stranded DNA sequence 5'-GGATG-3'
and cleave DNA phosphodiester groups 9 base pairs away
on this strand and 13 base pairs away on the
complementary strand.
Length = 193
Score = 26.3 bits (57), Expect = 2.8
Identities = 4/27 (14%), Positives = 9/27 (33%)
Query: 68 FVHNLLTEKFNIQKRFIRGLELAPKKK 94
L + + +I +E+A
Sbjct: 7 KKSELRHKLKYVPHEYIELIEIARNST 33
>gnl|CDD|216263 pfam01044, Vinculin, Vinculin family.
Length = 850
Score = 25.8 bits (57), Expect = 3.4
Identities = 6/37 (16%), Positives = 15/37 (40%)
Query: 33 LKEFCKLCQHGVAASTCINMVNNAAQVQVQGNQIVFV 69
+ E C + + +V A + + N+++ V
Sbjct: 500 ILEDVNKCVMAIQNADPQTLVATAGSIAGRANRVLLV 536
>gnl|CDD|236060 PRK07581, PRK07581, hypothetical protein; Validated.
Length = 339
Score = 25.7 bits (57), Expect = 4.0
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 63 GNQIVFVHNLLTEKFNIQK 81
+ + H LLTEKF I++
Sbjct: 106 YDNVRAQHRLLTEKFGIER 124
>gnl|CDD|240350 PTZ00296, PTZ00296, choline kinase; Provisional.
Length = 442
Score = 25.6 bits (56), Expect = 4.3
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 10/66 (15%)
Query: 23 VNNLDVYGIDLKEFCKLCQHGVAASTCINMVNNAAQVQVQGNQIVFVHNLLTEK--FNIQ 80
N++ Y D+ ++ K + I + ++ N IVF HN L E N
Sbjct: 247 YKNIEKYQRDIHKYIK------ESEKFIKFMKVYSKSDNLANDIVFCHNDLQENNIINTN 300
Query: 81 K--RFI 84
K R I
Sbjct: 301 KCLRLI 306
>gnl|CDD|236297 PRK08573, PRK08573, phosphomethylpyrimidine kinase; Provisional.
Length = 448
Score = 25.5 bits (56), Expect = 4.5
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 2/27 (7%)
Query: 30 GI--DLKEFCKLCQHGVAASTCINMVN 54
GI DLK F L HG A T + N
Sbjct: 18 GIEADLKTFAALGVHGAVAITSVTAQN 44
>gnl|CDD|180561 PRK06427, PRK06427, bifunctional hydroxy-methylpyrimidine kinase/
hydroxy-phosphomethylpyrimidine kinase; Reviewed.
Length = 266
Score = 25.5 bits (57), Expect = 5.3
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 30 GI--DLKEFCKLCQHGVAASTCI 50
GI DLK F L +G++A T +
Sbjct: 20 GIQADLKTFQALGVYGMSAITAL 42
>gnl|CDD|239771 cd04238, AAK_NAGK-like, AAK_NAGK-like: N-Acetyl-L-glutamate
kinase (NAGK)-like . Included in this CD are the
Escherichia coli and Pseudomonas aeruginosa type NAGKs
which catalyze the phosphorylation of
N-acetyl-L-glutamate (NAG) by ATP in the second step of
arginine biosynthesis found in bacteria and
photosynthetic organisms using either the acetylated,
noncyclic (NC), or non-acetylated, cyclic (C) route of
ornithine biosynthesis. Also included in this CD is a
distinct group of uncharacterized (UC) bacterial and
archeal NAGKs. Members of this CD belong to the Amino
Acid Kinase Superfamily (AAK).
Length = 256
Score = 25.2 bits (56), Expect = 5.4
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 57 AQVQVQGNQIVFVH------NLLTEKFNIQKRFIRGL 87
++ G V VH N L ++ I+ F+ GL
Sbjct: 24 VLLKQVGINPVIVHGGGPEINELLKRLGIESEFVNGL 60
>gnl|CDD|220082 pfam08960, DUF1874, Domain of unknown function (DUF1874). This
domain is found in a set of hypothetical viral and
bacterial proteins.
Length = 105
Score = 24.6 bits (54), Expect = 7.6
Identities = 8/46 (17%), Positives = 19/46 (41%), Gaps = 5/46 (10%)
Query: 31 IDLKEFCKLCQHG-----VAASTCINMVNNAAQVQVQGNQIVFVHN 71
ID++E +L ++ + +++N V + N+I
Sbjct: 25 IDIEEAKELLENERFISAIGHDATAQLLSNLLGVNIPMNRIQVKLQ 70
>gnl|CDD|225322 COG2602, COG2602, Beta-lactamase class D [Defense mechanisms].
Length = 254
Score = 25.0 bits (55), Expect = 7.8
Identities = 10/41 (24%), Positives = 16/41 (39%), Gaps = 7/41 (17%)
Query: 59 VQVQGNQIVFVHNLLTEKF-------NIQKRFIRGLELAPK 92
V+ N+ VF NL + I + ++ L L K
Sbjct: 214 VETNENKYVFATNLDIDGNEDGPKREEITEAILKELGLLVK 254
>gnl|CDD|234296 TIGR03653, arch_L6P, archaeal ribosomal protein L6P. Members of
this protein family are the archaeal ribosomal protein
L6P. The top-scoring proteins not selected by this model
are eukaryotic cytosolic ribosomal protein L9. Bacterial
ribosomal protein L6 scores lower and is described by a
distinct model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 170
Score = 24.6 bits (54), Expect = 9.0
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 58 QVQVQGNQIVFVHNLLTEKFNIQKRFIRG 86
QV+V+GN++V + N L EK + + G
Sbjct: 93 QVKVEGNKVV-IENFLGEKAPRRAKIPGG 120
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
0.322 0.136 0.392
Gapped
Lambda K H
0.267 0.0504 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,438,062
Number of extensions: 335490
Number of successful extensions: 282
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 27
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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 (21.9 bits)
S2: 53 (24.7 bits)