RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 039810
(113 letters)
>gnl|CDD|130228 TIGR01160, SUI1_MOF2, translation initiation factor SUI1,
eukaryotic. Alternate name: MOF2. A similar protein
family (see TIGRFAMs model TIGR01158) is found in
prokaryotes. The human proteins complements a yeast SUI1
mutatation [Protein synthesis, Translation factors].
Length = 110
Score = 175 bits (446), Expect = 9e-59
Identities = 69/110 (62%), Positives = 86/110 (78%), Gaps = 1/110 (0%)
Query: 5 DTQIPSAFDPFAEANAEDSGAGS-KDYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDL 63
Q +FDPFA+A +DS +Y+HIR+QQRNGRK+LTTVQGL KE+ KI+K L
Sbjct: 1 SIQNLKSFDPFADAGDDDSALPGTSNYIHIRIQQRNGRKTLTTVQGLPKEYDLKKIVKAL 60
Query: 64 KKEFCCNGTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKEFIKIHGF 113
KKEF CNGTV++DPE+G+VIQLQGDQRKNV FL+ G++KK+ IKIHGF
Sbjct: 61 KKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQGLLKKDQIKIHGF 110
>gnl|CDD|211318 cd11566, eIF1_SUI1, Eukaryotic initiation factor 1. eIF1/SUI1
(eukaryotic initiation factor 1) plays 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.
Length = 84
Score = 152 bits (387), Expect = 7e-50
Identities = 59/84 (70%), Positives = 70/84 (83%)
Query: 29 DYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
Y+HIR+QQRNGRK+LTTVQGL +EF KILK KKEF CNGTVV+DPE G+VIQLQGD
Sbjct: 1 GYIHIRIQQRNGRKTLTTVQGLPEEFDLKKILKAFKKEFACNGTVVEDPEYGEVIQLQGD 60
Query: 89 QRKNVSTFLVQAGIVKKEFIKIHG 112
QRKN+ FL++ GI KK+ IK+HG
Sbjct: 61 QRKNIKEFLLEEGIAKKDNIKVHG 84
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 79.9 bits (198), Expect = 3e-21
Identities = 28/78 (35%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 25 AGSKDYVHIRVQQRNGRKSLTTVQGL-KKEFSYNKILKDLKKEFCCNGTVVQDPELGQVI 83
+ IR ++R G K++T V GL K+ K+LKK+F C GTV G+ I
Sbjct: 1 KKEDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGTVKD----GEEI 56
Query: 84 QLQGDQRKNVSTFLVQAG 101
++QGD R V L + G
Sbjct: 57 EIQGDHRDKVKDLLEKEG 74
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 76.2 bits (188), Expect = 2e-19
Identities = 32/108 (29%), Positives = 47/108 (43%), Gaps = 8/108 (7%)
Query: 5 DTQIPSAFDPFAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQGL-KKEFSYNKILKDL 63
T P E + V IR + R K++T ++GL K+ K+ K+L
Sbjct: 4 STICGRIGLPKELTCEEVA-KEGDQIVRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKEL 62
Query: 64 KKEFCCNGTVVQDPELGQVIQLQGDQRKNVSTFLVQAGIVKKEFIKIH 111
KK+ C GTV I++QGD R V L++ G K + I I
Sbjct: 63 KKKCACGGTVKDG-----EIEIQGDHRDKVKELLIKKGF-KVKNIGIE 104
>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 = 64.4 bits (157), Expect = 3e-15
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 31 VHIRVQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGDQR 90
+HI+V+QR+G K +T V+GL K+ +LKK+ C G+V I++QGD
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAYIDLRKLADELKKKLGCGGSVE---GEKMEIEIQGDHT 58
Query: 91 KNVSTFLVQAGIVKKEFIKIH 111
+ L + GI K +++
Sbjct: 59 DQIIVALEEKGIDKDW-VELL 78
>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 = 54.9 bits (133), Expect = 2e-11
Identities = 25/88 (28%), Positives = 45/88 (51%), Gaps = 13/88 (14%)
Query: 31 VHIRVQQRNGRKSLTTVQGLK------KEFSYNKILKDLKKEFCCNGTVVQDPEL--GQV 82
+ I ++R G K +T + GL+ +EF+ K+L+K+ + +V P G
Sbjct: 2 IDITTERRQGNKKVTLISGLESFGIDPEEFA-----KELQKKCAASTSVSPLPGKKKGVE 56
Query: 83 IQLQGDQRKNVSTFLVQAGIVKKEFIKI 110
+Q+QG+Q K V+ L + V K++I
Sbjct: 57 VQVQGNQVKFVAKLLTEKYGVPKKYIDG 84
>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 = 49.1 bits (118), Expect = 4e-09
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 31 VHIRVQQRNGRKSLTTVQGLKK-EFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGDQ 89
V I+ RN RK +TTV GL+ K K K+F C +V + E I +QGD
Sbjct: 3 VTIKRISRNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTKGAEGKDEIVIQGDV 62
Query: 90 RKNVSTFLV-QAGIVKKEFIKI 110
++ ++ + + ++ I+I
Sbjct: 63 TDDIVDLILEKWPEIDEDNIEI 84
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 46.5 bits (111), Expect = 6e-08
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 31 VHIRVQQRNGRKSLTTVQGL-KKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGDQ 89
+ I+V +R K +T ++G+ K+ ++ K LK + C GTV I+LQGD
Sbjct: 26 IKIKVDKRRYGKEVTIIEGIDPKDIDLKELAKKLKSKLACGGTVKDG-----RIELQGDH 80
Query: 90 RKNVSTFLVQAG 101
R+ V L++ G
Sbjct: 81 RERVKELLIKMG 92
>gnl|CDD|130226 TIGR01158, SUI1_rel, translation initation factor SUI1, putative,
prokaryotic. This family of archaeal and bacterial
proteins is homologous to the eukaryotic translation
intiation factor SUI1 involved in directing the ribosome
to the proper start site of translation by functioning
in concert with eIF-2 and the initiator tRNA-Met
[Protein synthesis, Translation factors].
Length = 101
Score = 45.0 bits (107), Expect = 2e-07
Identities = 24/73 (32%), Positives = 38/73 (52%), Gaps = 9/73 (12%)
Query: 33 IRVQ-QRNGR--KSLTTVQGL-KKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
+R+Q + GR K +T ++GL + ++ K+LK + C GTV VI++QGD
Sbjct: 26 VRIQRETRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTVKDG-----VIEIQGD 80
Query: 89 QRKNVSTFLVQAG 101
R V L + G
Sbjct: 81 HRDRVKDLLEKKG 93
>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 = 41.3 bits (98), Expect = 4e-06
Identities = 26/77 (33%), Positives = 42/77 (54%), Gaps = 7/77 (9%)
Query: 31 VHIRVQQR-NGRKSLTTVQGLK-KEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
V +R+++R G K++T ++GL E ++ K+LKK+ C GTV I+LQGD
Sbjct: 3 VRVRLEKRGRGGKTVTVIEGLPLSEEDLKELAKELKKKCGCGGTVKDG-----EIELQGD 57
Query: 89 QRKNVSTFLVQAGIVKK 105
R+ + L + G K
Sbjct: 58 HREKIKELLEKKGFKVK 74
>gnl|CDD|236021 PRK07451, PRK07451, translation initiation factor Sui1; Validated.
Length = 115
Score = 34.0 bits (78), Expect = 0.005
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 9/73 (12%)
Query: 33 IRVQ-QRNGR--KSLTTVQGLK-KEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
+RVQ R+GR K++T + G + K + K+LK LK C +G V+D I++QGD
Sbjct: 40 LRVQATRSGRKGKTVTVITGFQHKPETLAKLLKQLKT-QCGSGGTVKDNT----IEIQGD 94
Query: 89 QRKNVSTFLVQAG 101
R+ + L++ G
Sbjct: 95 HRQKILEILIKLG 107
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1; Validated.
Length = 108
Score = 30.3 bits (69), Expect = 0.081
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 9/73 (12%)
Query: 33 IRVQ-QRNGRK--SLTTVQGL-KKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGD 88
+R+Q Q +GRK + + GL + K+ +LKK+ C G V VI++QGD
Sbjct: 33 VRIQRQTSGRKGKGVCLITGLDLDDAELKKLAAELKKKCGCGGAVKDG-----VIEIQGD 87
Query: 89 QRKNVSTFLVQAG 101
+R + + L G
Sbjct: 88 KRDLLKSLLEAKG 100
>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 = 30.2 bits (68), Expect = 0.15
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 1/68 (1%)
Query: 31 VHIRVQQRNGRKSLTTVQGLKK-EFSYNKILKDLKKEFCCNGTVVQDPELGQVIQLQGDQ 89
V I+ + R RK +T ++GL+ + K K ++F +V + + I +QGD
Sbjct: 91 VTIKREPRTKRKFVTVIKGLETFDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDV 150
Query: 90 RKNVSTFL 97
++ ++
Sbjct: 151 MDDIEDYI 158
>gnl|CDD|182523 PRK10530, PRK10530, pyridoxal phosphate (PLP) phosphatase;
Provisional.
Length = 272
Score = 28.5 bits (64), Expect = 0.62
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 68 CCNGTVVQDPELGQVIQ---LQGDQRKNVSTFLVQAGI 102
CCNGT + D + +V++ L Q V L + I
Sbjct: 65 CCNGTYLYDYQAKKVLEADPLPVQQALQVIEMLDEHQI 102
>gnl|CDD|227095 COG4753, COG4753, Response regulator containing CheY-like receiver
domain and AraC-type DNA-binding domain [Signal
transduction mechanisms].
Length = 475
Score = 28.5 bits (64), Expect = 0.74
Identities = 19/56 (33%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 30 YVHIRVQQRNGRKSLTTV-QGLKKEFSYNKILKDLKKEFCCNGTVVQDPELGQVIQ 84
YV V+ G + V + K FS N LKDL K F N LGQ+ +
Sbjct: 360 YVIQSVENIEGSSLIQKVLDYIHKHFSENLTLKDLAKVFHINPV-----YLGQLFK 410
>gnl|CDD|235394 PRK05297, PRK05297, phosphoribosylformylglycinamidine synthase;
Provisional.
Length = 1290
Score = 28.6 bits (65), Expect = 0.78
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 78 ELGQVIQLQGDQRKNVSTFLVQAGI 102
ELG VIQ++ R V L + G+
Sbjct: 920 ELGAVIQVRAADRDAVEAILAEHGL 944
>gnl|CDD|236674 PRK10364, PRK10364, sensor protein ZraS; Provisional.
Length = 457
Score = 26.7 bits (59), Expect = 3.1
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 7 QIPSAFDPFAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQG 49
Q+ + F P+ AE +G G VH V+Q G + + +G
Sbjct: 396 QLEAIFTPYFTTKAEGTGLGLA-VVHNIVEQHGGTIQVASQEG 437
>gnl|CDD|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large
nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa
subunit (U2AF65) and similar proteins. This subfamily
corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65,
also termed U2AF2, is the large subunit of U2 small
nuclear ribonucleoprotein (snRNP) auxiliary factor
(U2AF), which has been implicated in the recruitment of
U2 snRNP to pre-mRNAs and is a highly conserved
heterodimer composed of large and small subunits.
U2AF65 specifically recognizes the intron
polypyrimidine tract upstream of the 3' splice site and
promotes binding of U2 snRNP to the pre-mRNA
branchpoint. U2AF65 also plays an important role in the
nuclear export of mRNA. It facilitates the formation of
a messenger ribonucleoprotein export complex,
containing both the NXF1 receptor and the RNA
substrate. Moreover, U2AF65 interacts directly and
specifically with expanded CAG RNA, and serves as an
adaptor to link expanded CAG RNA to NXF1 for RNA
export. U2AF65 contains an N-terminal RS domain rich in
arginine and serine, followed by a proline-rich segment
and three C-terminal RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). The N-terminal RS domain
stabilizes the interaction of U2 snRNP with the branch
point (BP) by contacting the branch region, and further
promotes base pair interactions between U2 snRNA and
the BP. The proline-rich segment mediates
protein-protein interactions with the RRM domain of the
small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2
are sufficient for specific RNA binding, while RRM3 is
responsible for protein-protein interactions. The
family also includes Splicing factor U2AF 50 kDa
subunit (dU2AF50), the Drosophila ortholog of U2AF65.
dU2AF50 functions as an essential pre-mRNA splicing
factor in flies. It associates with intronless mRNAs
and plays a significant and unexpected role in the
nuclear export of a large number of intronless mRNAs.
Length = 89
Score = 25.6 bits (57), Expect = 3.5
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 46 TVQGLKKEFSYNKILKDLKKEFCCNGTVVQ 75
T + L+ + Y +IL+D+K+E G V+
Sbjct: 11 TPEELEDDEEYEEILEDVKEECGKYGKVLS 40
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 26.2 bits (58), Expect = 4.5
Identities = 13/65 (20%), Positives = 25/65 (38%)
Query: 3 EFDTQIPSAFDPFAEANAEDSGAGSKDYVHIRVQQRNGRKSLTTVQGLKKEFSYNKILKD 62
+ D Q F F + D A S + ++ G+ +TT+Q K +++
Sbjct: 314 DLDDQTSDEFQSFGKVAFNDPKAESTSELKELLEDGKGKIIVTTIQKFNKAVKEDELELL 373
Query: 63 LKKEF 67
+K
Sbjct: 374 KRKNV 378
>gnl|CDD|152015 pfam11579, DUF3238, Protein of unknown function (DUF3238). This
family of proteins with unknown function appears to be
restricted to Bacillus cereus.
Length = 193
Score = 25.7 bits (56), Expect = 5.5
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 74 VQDPELGQVIQLQGDQRK 91
++DP G+VIQ +GD R+
Sbjct: 20 IKDPATGRVIQFEGDSRE 37
>gnl|CDD|236168 PRK08156, PRK08156, type III secretion system protein SpaS;
Validated.
Length = 361
Score = 25.4 bits (56), Expect = 7.5
Identities = 10/27 (37%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 42 KSLTTVQGLKKEFSYNKILKDLKKEFC 68
+L V+GLKK FS + +K+ K
Sbjct: 114 SALNPVKGLKKIFSL-RTVKEFVKALL 139
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
0.317 0.135 0.382
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,558,546
Number of extensions: 455675
Number of successful extensions: 365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 23
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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: 53 (24.5 bits)