RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4461
(95 letters)
>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 = 145 bits (369), Expect = 2e-47
Identities = 54/75 (72%), Positives = 66/75 (88%)
Query: 20 RNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQWL 79
RNGRKTLTTVQGL E+DLKKI++A KKEFACNGTV+E PEYGEV+QLQGDQR+NI ++L
Sbjct: 10 RNGRKTLTTVQGLPEEFDLKKILKAFKKEFACNGTVVEDPEYGEVIQLQGDQRKNIKEFL 69
Query: 80 TKTGLAKPEQLKVHG 94
+ G+AK + +KVHG
Sbjct: 70 LEEGIAKKDNIKVHG 84
>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 = 137 bits (346), Expect = 1e-43
Identities = 57/76 (75%), Positives = 66/76 (86%)
Query: 20 RNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQWL 79
RNGRKTLTTVQGL EYDLKKIV+A KKEFACNGTVIE PE GEV+QLQGDQR+N+C++L
Sbjct: 35 RNGRKTLTTVQGLPKEYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFL 94
Query: 80 TKTGLAKPEQLKVHGF 95
GL K +Q+K+HGF
Sbjct: 95 ISQGLLKKDQIKIHGF 110
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 75.2 bits (186), Expect = 1e-19
Identities = 28/65 (43%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 20 RNGRKTLTTVQGL-SSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
R G KT+T V GL DLKK+ + KK+F C GTV + GE +++QGD R+ +
Sbjct: 14 RRGGKTVTVVTGLELFGIDLKKLAKELKKKFGCGGTVKD----GEEIEIQGDHRDKVKDL 69
Query: 79 LTKTG 83
L K G
Sbjct: 70 LEKEG 74
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 65.0 bits (159), Expect = 2e-15
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 7/75 (9%)
Query: 20 RNGRKTLTTVQGL-SSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
R KT+T ++GL + DLKK+ + KK+ AC GTV + GE+ ++QGD R+ + +
Sbjct: 36 RRKGKTVTIIEGLDLKDIDLKKLAKELKKKCACGGTVKD----GEI-EIQGDHRDKVKEL 90
Query: 79 LTKTGLAKPEQLKVH 93
L K G K + + +
Sbjct: 91 LIKKGF-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 = 54.0 bits (130), Expect = 3e-11
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 20 RNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQWL 79
R+G K +T V+GL + DL+K+ KK+ C G+V E E+ ++QGD + I L
Sbjct: 9 RSGGKKVTKVEGLPAYIDLRKLADELKKKLGCGGSVE--GEKMEI-EIQGDHTDQIIVAL 65
Query: 80 TKTGLAK 86
+ G+ K
Sbjct: 66 EEKGIDK 72
>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 = 52.6 bits (127), Expect = 1e-10
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 20 RNGRKTLTTVQGLSSEY-DLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
RN RK +TTV GL + DLKK + K+FAC +V + E + + +QGD ++I
Sbjct: 10 RNKRKFVTTVTGLETFGIDLKKAAKLFAKKFACGASVTKGAEGKDEIVIQGDVTDDIVDL 69
Query: 79 LTKT 82
+ +
Sbjct: 70 ILEK 73
>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 = 49.0 bits (118), Expect = 2e-09
Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 6/65 (9%)
Query: 20 RNGRKTLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
G KT+T ++GL SE DLK++ + KK+ C GTV + ++LQGD RE I +
Sbjct: 11 GRGGKTVTVIEGLPLSEEDLKELAKELKKKCGCGGTVKD-----GEIELQGDHREKIKEL 65
Query: 79 LTKTG 83
L K G
Sbjct: 66 LEKKG 70
>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 = 42.9 bits (102), Expect = 5e-07
Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 20 RNGRKTLTTVQGLSS-EYDLKKIVRACKKEFACNGTV--IEHPEYGEVLQLQGDQRENIC 76
R G K +T + GL S D ++ + +K+ A + +V + + G +Q+QG+Q + +
Sbjct: 9 RQGNKKVTLISGLESFGIDPEEFAKELQKKCAASTSVSPLPGKKKGVEVQVQGNQVKFVA 68
Query: 77 QWLTKTG 83
+ LT+
Sbjct: 69 KLLTEKY 75
>gnl|CDD|179173 PRK00939, PRK00939, translation initiation factor Sui1; Reviewed.
Length = 99
Score = 41.4 bits (98), Expect = 3e-06
Identities = 22/69 (31%), Positives = 37/69 (53%), Gaps = 7/69 (10%)
Query: 24 KTLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQWLTKT 82
K +T ++G+ + DLK++ + K + AC GTV ++LQGD RE + + L K
Sbjct: 37 KEVTIIEGIDPKDIDLKELAKKLKSKLACGGTV-----KDGRIELQGDHRERVKELLIKM 91
Query: 83 GLAKPEQLK 91
G E ++
Sbjct: 92 GF-SEENIE 99
>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 = 41.6 bits (98), Expect = 3e-06
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 8/67 (11%)
Query: 20 RNGR--KTLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENIC 76
GR K +T ++GL S+ DLK++ + K + C GTV + V+++QGD R+ +
Sbjct: 32 TRGRKGKGVTIIEGLDLSDIDLKELAKELKSKCGCGGTVKD-----GVIEIQGDHRDRVK 86
Query: 77 QWLTKTG 83
L K G
Sbjct: 87 DLLEKKG 93
>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 = 38.3 bits (89), Expect = 1e-04
Identities = 18/71 (25%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 20 RNGRKTLTTVQGLSS-EYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
R RK +T ++GL + + DLKK + ++FA +V + E + +QGD ++I +
Sbjct: 98 RTKRKFVTVIKGLETFDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDY 157
Query: 79 LTKTGLAKPEQ 89
+ + ++
Sbjct: 158 IHEKWPEVGDK 168
>gnl|CDD|168689 PRK06824, PRK06824, translation initiation factor Sui1; Validated.
Length = 118
Score = 35.8 bits (83), Expect = 6e-04
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 22 GRKTLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQWLT 80
G KT+T + G+ +E LK++ + K+ GT+ + V+++QGD E + L
Sbjct: 53 GGKTVTVITGVPLAEDALKELAKELKRRCGTGGTLKDG-----VIEIQGDHVELLLAELL 107
Query: 81 KTG 83
K G
Sbjct: 108 KRG 110
>gnl|CDD|181613 PRK09019, PRK09019, translation initiation factor Sui1; Validated.
Length = 108
Score = 35.0 bits (81), Expect = 9e-04
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 8/65 (12%)
Query: 22 GRK--TLTTVQGLS-SEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENICQW 78
GRK + + GL + +LKK+ KK+ C G V + V+++QGD+R+ +
Sbjct: 41 GRKGKGVCLITGLDLDDAELKKLAAELKKKCGCGGAVKDG-----VIEIQGDKRDLLKSL 95
Query: 79 LTKTG 83
L G
Sbjct: 96 LEAKG 100
>gnl|CDD|236021 PRK07451, PRK07451, translation initiation factor Sui1; Validated.
Length = 115
Score = 34.4 bits (79), Expect = 0.002
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 20 RNGR--KTLTTVQGL-SSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQRENIC 76
R+GR KT+T + G L K+++ K + GTV + +++QGD R+ I
Sbjct: 46 RSGRKGKTVTVITGFQHKPETLAKLLKQLKTQCGSGGTVKD-----NTIEIQGDHRQKIL 100
Query: 77 QWLTKTG 83
+ L K G
Sbjct: 101 EILIKLG 107
>gnl|CDD|131424 TIGR02371, ala_DH_arch, alanine dehydrogenase, Archaeoglobus
fulgidus type. This enzyme, a homolog of bacterial
ornithine cyclodeaminases and marsupial mu-crystallins,
is a homodimeric, NAD-dependent alanine dehydrogenase
found in Archaeoglobus fulgidus and several other
Archaea. For a number of close homologs, scoring between
trusted and noise cutoffs, it is not clear at present
what is the enzymatic activity.
Length = 325
Score = 31.4 bits (71), Expect = 0.047
Identities = 17/71 (23%), Positives = 33/71 (46%)
Query: 6 KYLYVCDLLLLSLLRNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEVL 65
KYL D +L ++ GR+ T ++ LS +DL+++ C+ + +Y +
Sbjct: 121 KYLARKDSSVLGIIGAGRQAWTQLEALSRVFDLEEVSVYCRTPSTREKFALRASDYEVPV 180
Query: 66 QLQGDQRENIC 76
+ D RE +
Sbjct: 181 RAATDPREAVE 191
>gnl|CDD|232906 TIGR00287, cas1, CRISPR-associated endonuclease Cas1. This model
identifies CRISPR-associated protein Cas1, the most
universal CRISPR system protein. CRISPR is an acronym
for Clustered Regularly Interspaced Short Palindromic
Repeats, a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA.
Cas1 is a metal-dependent DNA-specific endonuclease
[Mobile and extrachromosomal element functions, Other].
Length = 288
Score = 28.1 bits (63), Expect = 0.56
Identities = 12/64 (18%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 10 VCDLLLLSLLRNGRKTL-----TTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEV 64
+ D L+ SL+ T + E KK ++A ++ T + HP
Sbjct: 206 IVDRLVFSLINRNIITEEDFEKISNGVYLGEEGRKKFLQAFEERLQ---TTVTHPGLNRR 262
Query: 65 LQLQ 68
+
Sbjct: 263 VSYL 266
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 27.7 bits (62), Expect = 0.77
Identities = 10/37 (27%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 15 LLSLLRNGRKTLTTVQGLSSEYDLKKIVRACKKEFAC 51
+ S+ +K L ++G+ SE ++KI A K
Sbjct: 47 VESVAYATKKDLCNIKGI-SEAKVEKIKEAASKLVPM 82
>gnl|CDD|214444 MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 573
Score = 27.4 bits (62), Expect = 0.93
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 12/34 (35%)
Query: 13 LLLLSLLRNGRKTLTT--VQGLSS--EYDLKKIV 42
LLL+SLL T + GL + E+DLKKI+
Sbjct: 246 LLLISLL--------TMFMAGLGANFEFDLKKII 271
>gnl|CDD|225593 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
conversion].
Length = 513
Score = 27.0 bits (60), Expect = 1.3
Identities = 17/76 (22%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 20 RNGRKTLTTVQGLSSEYDLKKIVRACKKEFACNGTVIEHPEYGEVLQLQGDQ-RENICQW 78
R G + V + ++ K + A C+ ++EH + G V ++ R + +
Sbjct: 75 RGGDLVVNMVMDVIAKMGFKNLTLASSSLSDCHAPLVEHIKNGVVTRIYSSGLRGPLGEE 134
Query: 79 LTKTGLAKPEQLKVHG 94
+++ LA+P Q+ HG
Sbjct: 135 ISRGLLAEPVQIHSHG 150
>gnl|CDD|227913 COG5626, COG5626, Uncharacterized small conserved protein
[Function unknown].
Length = 97
Score = 25.7 bits (56), Expect = 2.4
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 13/48 (27%)
Query: 53 GTVIEHPEYGEVLQ-------------LQGDQRENICQWLTKTGLAKP 87
+I H V+Q + GD RE + W+++ ++KP
Sbjct: 18 AELIPHAARDAVIQVDAALDLLEVGEAIAGDDREKVAAWISEGLISKP 65
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 26.0 bits (57), Expect = 3.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 22 GRKTLTTVQGLSSEYDLKKIVRACKKE 48
GR+ T+ QG S++YD+ I C +
Sbjct: 642 GREKCTSKQGSSNKYDVSYIYIECGPQ 668
>gnl|CDD|151554 pfam11110, Phage_hub_GP28, Baseplate hub distal subunit. These
baseplate proteins are also referred to as Gp28. Gp28
is the structural component of the central part of the
bacteriophage T4 baseplate, which possesses a
hydrophobic region and is membrane bound. Gp28 forms a
complex with gp27 which is another structural component
of the baseplate.
Length = 151
Score = 25.5 bits (56), Expect = 3.9
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 12 DLLLLSLLR-NGR-KTLTTVQGLSSEYDLKKIVRACKKEFACNGTVI 56
D ++L LL NG+ KT+ G YDL + + EF G
Sbjct: 39 DFVILHLLAFNGKLKTVQEKDGF--TYDLDDVYICQRTEFQFQGKTF 83
>gnl|CDD|236048 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 25.5 bits (57), Expect = 4.5
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 46 KKEFACNGTVIEHPEYGEVLQLQ 68
+ V EHPE G +Q +
Sbjct: 694 LGLLSLPRPVGEHPECGSEIQAK 716
>gnl|CDD|182912 PRK11028, PRK11028, 6-phosphogluconolactonase; Provisional.
Length = 330
Score = 25.3 bits (56), Expect = 6.5
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 1 MTPCLKYLYVCD 12
+TP ++LY CD
Sbjct: 235 ITPDGRHLYACD 246
>gnl|CDD|214436 MTH00151, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 565
Score = 24.8 bits (55), Expect = 7.8
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 10/33 (30%)
Query: 13 LLLLSLLRNGRKTLTTV-QGLSS--EYDLKKIV 42
LL +SLL T + G+S+ E DLKKI+
Sbjct: 243 LLFISLL-------TLLMAGISACYENDLKKII 268
>gnl|CDD|213992 cd07437, PHP_HisPPase_Ycdx_like, Polymerase and Histidinol
Phosphatase domain of Ycdx like. PHP Ycdx-like is a
stand alone PHP domain similar to Ycdx E. coli protein
with an unknown physiological role. The PHP (also called
histidinol phosphatase-2/HIS2) domain is associated with
several types of DNA polymerases, such as PolIIIA and
family X DNA polymerases, stand alone histidinol
phosphate phosphatases (HisPPases), and a number of
uncharacterized protein families. The PHP domain has
four conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination. It
has also been shown that the PHP domain functions in DNA
repair. The PHP structures have a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel. YcdX may be
involved in swarming.
Length = 233
Score = 24.7 bits (55), Expect = 8.4
Identities = 5/23 (21%), Positives = 11/23 (47%), Gaps = 4/23 (17%)
Query: 35 EYDLKKIVRACKKEFACNGTVIE 57
D + +V+A K+ ++E
Sbjct: 137 PIDYEAVVKAAKE----YNVLLE 155
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
0.321 0.138 0.425
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,619,461
Number of extensions: 359887
Number of successful extensions: 342
Number of sequences better than 10.0: 1
Number of HSP's gapped: 330
Number of HSP's successfully gapped: 28
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 (24.3 bits)