RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2272
(276 letters)
>gnl|CDD|185558 PTZ00329, PTZ00329, eukaryotic translation initiation factor 1A;
Provisional.
Length = 155
Score = 168 bits (427), Expect = 1e-52
Identities = 75/108 (69%), Positives = 89/108 (82%), Gaps = 1/108 (0%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGRLEA CFDG KRLCHIRGK+RK+VWIN GDIIL+ LRD+QD+KADVILKYTPDEA
Sbjct: 41 MLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQDSKADVILKYTPDEA 100
Query: 61 RNLKTYGEFPETVRINDTVTFVEEGYDEDIEFGDEISDDEEGNAVDNL 108
R LK +GE PET +IN+T F +EG D+ IEF D+ SD+E + + NL
Sbjct: 101 RALKQHGELPETAKINETDIFDDEG-DDGIEFQDDESDEEATDEMLNL 147
>gnl|CDD|177798 PLN00208, PLN00208, translation initiation factor (eIF);
Provisional.
Length = 145
Score = 159 bits (403), Expect = 3e-49
Identities = 68/105 (64%), Positives = 76/105 (72%), Gaps = 5/105 (4%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGR EA+C DGTKRLCHIRGK+RKKVWI GDIIL+GLRDYQD KADVILKY PDEA
Sbjct: 41 MLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEA 100
Query: 61 RNLKTYGEFPETVRINDTVTFV-----EEGYDEDIEFGDEISDDE 100
R LK YGE PE R+N+ + + D+ IEF DE D
Sbjct: 101 RLLKAYGELPENTRLNEGIAGDLDEEEDGEGDDYIEFEDEDIDKI 145
>gnl|CDD|240219 cd05793, S1_IF1A, S1_IF1A: Translation initiation factor IF1A,
also referred to as eIF1A in eukaryotes and aIF1A in
archaea, S1-like RNA-binding domain. S1-like
RNA-binding domains are found in a wide variety of
RNA-associated proteins. IF1A is essential for
translation initiation. eIF1A acts synergistically with
eIF1 to mediate assembly of ribosomal initiation
complexes at the initiation codon and maintain the
accuracy of this process by recognizing and
destabilizing aberrant preinitiation complexes from the
mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors. This protein family is only found
in eukaryotes and archaea.
Length = 77
Score = 135 bits (343), Expect = 6e-41
Identities = 48/68 (70%), Positives = 55/68 (80%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGRLE CFDG KRLC IRGK+RK+VWIN+GDI+L+ D+QD KAD+I KYTPDE
Sbjct: 9 MLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEV 68
Query: 61 RNLKTYGE 68
R LK GE
Sbjct: 69 RWLKRKGE 76
>gnl|CDD|128900 smart00652, eIF1a, eukaryotic translation initiation factor 1A.
Length = 83
Score = 118 bits (299), Expect = 3e-34
Identities = 45/70 (64%), Positives = 52/70 (74%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLGNGRLE MC DG +RL I GK+RKKVWI +GDI+L+ D+QD KAD+I KYT DE
Sbjct: 14 MLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEV 73
Query: 61 RNLKTYGEFP 70
R LK GE P
Sbjct: 74 RWLKKEGELP 83
>gnl|CDD|239903 cd04456, S1_IF1A_like, S1_IF1A_like: Translation initiation
factor IF1A-like, S1-like RNA-binding domain. IF1A is
also referred to as eIF1A in eukaryotes and aIF1A in
archaea. S1-like RNA-binding domains are found in a
wide variety of RNA-associated proteins. IF1A is
essential for translation initiation. eIF1A acts
synergistically with eIF1 to mediate assembly of
ribosomal initiation complexes at the initiation codon
and maintain the accuracy of this process by
recognizing and destabilizing aberrant preinitiation
complexes from the mRNA. Without eIF1A and eIF1, 43S
ribosomal preinitiation complexes can bind to the
cap-proximal region, but are unable to reach the
initiation codon. eIF1a also enhances the formation of
5'-terminal complexes in the presence of other
translation initiation factors. This protein family is
only found in eukaryotes and archaea.
Length = 78
Score = 104 bits (261), Expect = 9e-29
Identities = 32/70 (45%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDY-QDAKADVILKYTPDE 59
MLGN R E C DG +RL I GKLRK +WI +GD +++ + +D KAD+I Y D
Sbjct: 9 MLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFVYCKDH 68
Query: 60 ARNLKTYGEF 69
R+LK G
Sbjct: 69 VRSLKKEGFL 78
>gnl|CDD|129614 TIGR00523, eIF-1A, eukaryotic/archaeal initiation factor 1A.
Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A
for Archaea. Also called eIF-4C [Protein synthesis,
Translation factors].
Length = 99
Score = 93.4 bits (232), Expect = 3e-24
Identities = 29/72 (40%), Positives = 45/72 (62%), Gaps = 1/72 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQ-DAKADVILKYTPDE 59
MLG GR++ C DG RL I GKL+K++WI +GD++++ ++Q D K D++ +YT +
Sbjct: 28 MLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIVWRYTKTQ 87
Query: 60 ARNLKTYGEFPE 71
LK G E
Sbjct: 88 VEWLKRKGYLKE 99
>gnl|CDD|216345 pfam01176, eIF-1a, Translation initiation factor 1A / IF-1. This
family includes both the eukaryotic translation factor
eIF-1A and the bacterial translation initiation factor
IF-1.
Length = 65
Score = 87.2 bits (217), Expect = 2e-22
Identities = 27/54 (50%), Positives = 35/54 (64%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILK 54
MLGNGR E DG +RL HI GK RK++WI +GD +L+ L Y K D+I +
Sbjct: 12 MLGNGRFEVELEDGHERLAHIPGKRRKRIWILRGDFVLVELSPYDKTKGDIIYR 65
>gnl|CDD|179708 PRK04012, PRK04012, translation initiation factor IF-1A;
Provisional.
Length = 100
Score = 87.3 bits (217), Expect = 5e-22
Identities = 28/71 (39%), Positives = 45/71 (63%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIGLRDYQDAKADVILKYTPDEA 60
MLG R+ C DG +R+ I GK++K++WI +GD++++ D+QD KAD+I +YT +
Sbjct: 30 MLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWRYTKPQV 89
Query: 61 RNLKTYGEFPE 71
L+ G E
Sbjct: 90 DWLRRKGYISE 100
>gnl|CDD|223438 COG0361, InfA, Translation initiation factor 1 (IF-1)
[Translation, ribosomal structure and biogenesis].
Length = 75
Score = 80.3 bits (199), Expect = 1e-19
Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 1 MLGNGRLEAMCFDGTKRLCHIRGKLRK-KVWINQGDIILIGLRDYQDAKADVILKYTPDE 59
ML NGR +G +RL HI GK+RK ++ I GD++L+ L Y K ++ +Y DE
Sbjct: 16 MLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYKKDE 75
>gnl|CDD|240218 cd05792, S1_eIF1AD_like, S1_eIF1AD_like: eukaryotic translation
initiation factor 1A domain containing protein
(eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is
also known as MGC11102 protein. Little is known about
the function of eIF1AD. S1-like RNA-binding domains are
found in a wide variety of RNA-associated proteins,
including translation initiation factor IF1A (also
referred to as eIF1A in eukaryotes). eIF1A is essential
for translation initiation. eIF1A acts synergistically
with eIF1 to mediate assembly of ribosomal initiation
complexes at the initiation codon and maintain the
accuracy of this process by recognizing and
destabilizing aberrant preinitiation complexes from the
mRNA. Without eIF1A and eIF1, 43S ribosomal
preinitiation complexes can bind to the cap-proximal
region, but are unable to reach the initiation codon.
eIF1a also enhances the formation of 5'-terminal
complexes in the presence of other translation
initiation factors.
Length = 78
Score = 29.7 bits (67), Expect = 0.36
Identities = 19/66 (28%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 3 GNGRLEAMCFDGTKRLCHIRGKLRKKVWINQGDIILIG-LRDYQDAKADVILKYTPDEAR 61
GN E +G++ L + K RK +WI +GD +L+ + + KA+++ T D +
Sbjct: 11 GNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVK 70
Query: 62 NLKTYG 67
+K G
Sbjct: 71 YIKEEG 76
>gnl|CDD|112249 pfam03424, CBM_17_28, Carbohydrate binding domain (family 17/28).
Length = 204
Score = 28.6 bits (64), Expect = 2.6
Identities = 13/56 (23%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 30 WINQGDIILIGLRDY---QDAKADVILKYTPDEARNLKTYGEFPETVRINDTVTFV 82
W N I + +D+ +D +L T ++ NL+ E +N+ + FV
Sbjct: 133 WANPTRSIKVTEKDFVCQEDGTYKALLTITFFDSPNLQDIAVDSEDSLLNNIILFV 188
>gnl|CDD|233041 TIGR00596, rad1, DNA repair protein (rad1). All proteins in this
family for which functions are known are components in a
multiprotein endonuclease complex (usually made up of
Rad1 and Rad10 homologs). This complex is used primarily
for nucleotide excision repair but also for some aspects
of recombinational repair in some species. Most Archaeal
species also have homologs of these genes, but the
function of these Archaeal genes is not known, so we
have set our cutoff to only pick up the eukaryotic
genes.This family is based on the phylogenomic analysis
of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA
metabolism, DNA replication, recombination, and repair].
Length = 814
Score = 28.6 bits (64), Expect = 3.9
Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 4/84 (4%)
Query: 69 FPETVRINDTVTFVEEGYDEDIEFGDEISDDE---EGNAVDNLYLQMHMSKFPWFSIHFK 125
F E + + +E+G ++I ++ E E N +D +Y P HF
Sbjct: 401 FEEDHELEEEGDDLEDGPAQEINAANDSKIFEIIDEENDID-IYSGAEFDNLPQHITHFL 459
Query: 126 LSFLKKVGTVSSIQEARPSYTLQY 149
+ S++E P Y + Y
Sbjct: 460 WGERDEYVLRCSLEELMPRYVIMY 483
>gnl|CDD|185708 cd07897, Adenylation_DNA_ligase_Bac1, Adenylation domain of
putative bacterial ATP-dependent DNA ligases. Bacterial
DNA ligases are divided into two broad classes:
NAD-dependent and ATP-dependent. All bacterial species
have a NAD-dependent DNA ligase (LigA). Some bacterial
genomes contain multiple genes for DNA ligases that are
predicted to use ATP as their cofactor, including
Mycobacterium tuberculosis LigB, LigC, and LigD. This
group is composed of predicted bacterial ATP-dependent
DNA ligases. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three-step reaction mechanism.
The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family,
including this group. The adenylation domain binds ATP
and contains many of the active site residues.
Length = 207
Score = 27.9 bits (63), Expect = 5.2
Identities = 9/34 (26%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 207 NQPFQENKN-LKRVIRHLLAPKLDSSDTLHLDNW 239
P +E + L+ ++ L P+LD S + +W
Sbjct: 130 ALPLRERRARLEALLARLPPPRLDLSPLIAFADW 163
>gnl|CDD|216331 pfam01150, GDA1_CD39, GDA1/CD39 (nucleoside phosphatase) family.
Length = 421
Score = 28.1 bits (63), Expect = 5.8
Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 40 GLRDYQDAKADVILKYTPDEARNLKTYGEFPETVRINDTVTFVEEG 85
G+R + + IL+ + ++L ++ + VRI + EEG
Sbjct: 94 GMRLLPEDAKEKILRALRNGLKSLSSFPVDDQGVRI---IDGAEEG 136
>gnl|CDD|176544 cd08602, GDPD_ScGlpQ1_like, Glycerophosphodiester phosphodiesterase
domain of Streptomycin coelicolor (GlpQ1) and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in a group of putative bacterial and eukaryotic
glycerophosphodiester phosphodiesterases (GP-GDE, EC
3.1.4.46) similar to Escherichia coli periplasmic
phosphodiesterase GlpQ, as well as plant
glycerophosphodiester phosphodiesterases (GP-PDEs), all
of which catalyzes the Ca2+-dependent degradation of
periplasmic glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. The prototypes of this family include putative
secreted phosphodiesterase encoded by gene glpQ1
(SCO1565) from the pho regulon in Streptomyces
coelicolor genome, and in plants, two distinct
Arabidopsis thaliana genes, AT5G08030 and AT1G74210,
coding putative GP-PDEs from the cell walls and
vacuoles, respectively.
Length = 309
Score = 27.6 bits (62), Expect = 6.8
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 119 WFSIHFKLSFLKKVGTVSSIQEARPSYTLQYQ 150
WF+ F L+ LK + + SY Q+
Sbjct: 81 WFTEDFTLAELKTLRARQRLPYRDQSYDGQFP 112
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
0.318 0.137 0.405
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,363,668
Number of extensions: 1392936
Number of successful extensions: 1108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1104
Number of HSP's successfully gapped: 24
Length of query: 276
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 180
Effective length of database: 6,679,618
Effective search space: 1202331240
Effective search space used: 1202331240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.1 bits)