RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14758
(134 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 = 83.7 bits (207), Expect = 5e-22
Identities = 39/57 (68%), Positives = 43/57 (75%), Gaps = 5/57 (8%)
Query: 14 DPFADAFKGSEDDVQDG---LVHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKK 67
DPFADA G +D G +HIRIQQRNGRKTLTTVQGL EYDLKKIV+A KK+
Sbjct: 9 DPFADA--GDDDSALPGTSNYIHIRIQQRNGRKTLTTVQGLPKEYDLKKIVKALKKE 63
>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 = 82.6 bits (205), Expect = 7e-22
Identities = 29/38 (76%), Positives = 34/38 (89%)
Query: 30 GLVHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKK 67
G +HIRIQQRNGRKTLTTVQGL E+DLKKI++A KK+
Sbjct: 1 GYIHIRIQQRNGRKTLTTVQGLPEEFDLKKILKAFKKE 38
>gnl|CDD|216391 pfam01253, SUI1, Translation initiation factor SUI1.
Length = 74
Score = 54.0 bits (131), Expect = 7e-11
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 28 QDGLVHIRIQQRNGRKTLTTVQGL-SSEYDLKKIVRACKKK 67
+D + IR ++R G KT+T V GL DLKK+ + KKK
Sbjct: 3 EDQKIRIRREKRRGGKTVTVVTGLELFGIDLKKLAKELKKK 43
>gnl|CDD|223102 COG0023, SUI1, Translation initiation factor 1 (eIF-1/SUI1) and
related proteins [Translation, ribosomal structure and
biogenesis].
Length = 104
Score = 51.1 bits (123), Expect = 2e-09
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 28 QDGLVHIRIQQRNGRKTLTTVQGL-SSEYDLKKIVRACKKK 67
D +V IR + R KT+T ++GL + DLKK+ + KKK
Sbjct: 25 GDQIVRIRRETRRKGKTVTIIEGLDLKDIDLKKLAKELKKK 65
>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 = 44.0 bits (104), Expect = 5e-07
Identities = 16/36 (44%), Positives = 26/36 (72%)
Query: 32 VHIRIQQRNGRKTLTTVQGLSSEYDLKKIVRACKKK 67
+HI+++QR+G K +T V+GL + DL+K+ KKK
Sbjct: 2 IHIKVEQRSGGKKVTKVEGLPAYIDLRKLADELKKK 37
>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 = 38.3 bits (90), Expect = 8e-05
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 32 VHIRIQQRNGRKTLTTVQGLSSEY-DLKKIVRACKK--KRFST 71
V I+ RN RK +TTV GL + DLKK A K K+F+
Sbjct: 3 VTIKRISRNKRKFVTTVTGLETFGIDLKK---AAKLFAKKFAC 42
>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 = 32.5 bits (75), Expect = 0.012
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 32 VHIRIQQRNGRKTLTTVQGLSS-EYDLKKIVRACKKK 67
+ I ++R G K +T + GL S D ++ + +KK
Sbjct: 2 IDITTERRQGNKKVTLISGLESFGIDPEEFAKELQKK 38
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 28.8 bits (65), Expect = 0.80
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 84 KVGTYKIFATETLVTSSELKLSLGNLFQASCLGVNRAGMLLKCFLC 129
K GT K+FA+ + SE K + +LF+ + + RA + C +C
Sbjct: 544 KKGTVKVFASGNIWARSEDKEAAASLFKDAARLLRRAAECVGCGVC 589
>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
Length = 971
Score = 28.7 bits (64), Expect = 0.99
Identities = 26/81 (32%), Positives = 33/81 (40%), Gaps = 16/81 (19%)
Query: 45 LTTVQGLSSEYDLKKIVRACKKKRFSTF--YLSALSKCDPQK--------VGTYKIFATE 94
T++G E LKKI A + K FS F Y+ AL K + VGT+ F
Sbjct: 754 FNTIKGFGDE-LLKKIKSALQNKTFSDFISYIDALKKNNVSLSNIEILINVGTFDSFKLS 812
Query: 95 TLVTSSEL-----KLSLGNLF 110
L + L K SL F
Sbjct: 813 RLFLLNNLPEIFEKTSLNGHF 833
>gnl|CDD|130624 TIGR01561, gde_arch, glycogen debranching enzyme, archaeal type,
putative. The seed for this model is composed of two
uncharacterized archaeal proteins from Methanosarcina
acetivorans and Sulfolobus solfataricus. Trusted cutoff
is set so that essentially only archaeal members hit the
model. The notable exceptions to archaeal membership are
the Gram positive Clostridium perfringens which scores
much better than some other archaea and the
Cyanobacterium Nostoc sp. which scores just above the
trusted cutoff. Noise cutoff is set to exclude the
characterized eukaryotic glycogen debranching enzyme in
S. cerevisiae. These cutoffs leave the prokaryotes
Porphyromonas gingivalis and Deinococcus radiodurans
below trusted but above noise. Multiple alignments
including these last two species exhibit sequence
divergence which may suggest a subtly different function
for these prokaryotic proteins [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 575
Score = 27.7 bits (61), Expect = 2.2
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 51 LSSEYDLKKIVRACKKKRFSTFYLSALSKCDPQKVGTYK 89
+ E K I+ +K F L +LS+ DP G YK
Sbjct: 509 IDDESIAKAILDLIEKDLLRPFGLKSLSRDDPLYKGQYK 547
>gnl|CDD|182755 PRK10816, PRK10816, DNA-binding transcriptional regulator PhoP;
Provisional.
Length = 223
Score = 27.4 bits (61), Expect = 2.3
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 4 RVWSSDLFMLDPFADA-FKGSED-DVQDGLVHIRIQQRNGRKTLTTVQGLSSEYDLK 58
+V S D ML + DA + S DV G + +IQ + ++ +TTV+G +DL+
Sbjct: 167 KVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQGYRFDLR 223
>gnl|CDD|221753 pfam12753, Nro1, Nuclear pore complex subunit Nro1. In fission
yeast, this protein is a positive regulator of the
stability of Sre1N, the sterol regulatory
element-binding protein which is an ER membrane-bound
transcription factor that controls adaptation to low
oxygen-growth. In addition, the fission yeast Nro1 is a
direct inhibitor of a protein that inhibits SreN1
degradation, Ofd1 (an oxoglutamate deoxygenase). The
outcome of this reactivity is that Ofd1 acts as an
oxygen sensor that regulates the binding of Nro1 to Ofd1
to control the stability of Sre1N. Solution of the
structure of Nro1 reveals it to be made up of a number
of TPR coils.
Length = 401
Score = 26.8 bits (59), Expect = 4.6
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 93 TETLVTSSELKLSLGNLFQ 111
ET V +E + LGNL+
Sbjct: 347 PETWVDVAEAMIDLGNLYD 365
>gnl|CDD|184856 PRK14854, nhaA, pH-dependent sodium/proton antiporter; Provisional.
Length = 383
Score = 26.0 bits (57), Expect = 7.7
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 90 IFATETLVTSSELKLSLGNLFQASCLGVNR 119
IF T++L S L LSLG LF + + NR
Sbjct: 169 IFYTKSL---SLLSLSLGTLFILAMIICNR 195
>gnl|CDD|213830 TIGR03576, pyridox_MJ0158, pyridoxal phosphate enzyme, MJ0158
family. Members of this archaeal protein family are
pyridoxal phosphate enzymes of unknown function.
Sequence similarity to SelA, a bacterial enzyme of
selenocysteine biosynthesis, has led to some members
being misannotated as functionally equivalent, but
selenocysteine is made on tRNA in Archaea by a two-step
process that does not involve a SelA homolog [Unknown
function, Enzymes of unknown specificity].
Length = 346
Score = 25.9 bits (57), Expect = 8.7
Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 54 EYDLKKIVRACKKKRFSTFYLSALSKCDPQKVGTYKIFATETLVTSSELKLSL 106
E++L +I A K+K YL K + ++ T + E+ L L
Sbjct: 249 EFELSRIRDAFKRKE--EVYLRLFDKLNVERTPTGFVIKGVEEEKLIEIGLDL 299
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 0.135 0.400
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,350,949
Number of extensions: 525624
Number of successful extensions: 388
Number of sequences better than 10.0: 1
Number of HSP's gapped: 386
Number of HSP's successfully gapped: 19
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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 (22.0 bits)
S2: 54 (24.8 bits)