RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17706
(154 letters)
>gnl|CDD|217282 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 100
Score = 38.8 bits (91), Expect = 1e-04
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 49 PG-FVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
PG VS D+G L V C DG ++L ++ GKK M A DF NG
Sbjct: 57 PGTIVSVDKGG--LLVACGDG-ALLILELQPEGKKAMDAADFLNGA 99
>gnl|CDD|215159 PLN02285, PLN02285, methionyl-tRNA formyltransferase.
Length = 334
Score = 35.4 bits (82), Expect = 0.006
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 50 GFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGYLGK 96
V+F + S L V C G + ++ GKK M A DF NG G+
Sbjct: 288 DAVTFKKDS--LLVPCGGGTWLEVLEVQPPGKKVMKAKDFWNGLRGQ 332
>gnl|CDD|223301 COG0223, Fmt, Methionyl-tRNA formyltransferase [Translation,
ribosomal structure and biogenesis].
Length = 307
Score = 33.7 bits (78), Expect = 0.025
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 42 PITPELTPG-FVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTAVDFKNGY 93
PG ++ D+ K L V C DG ++ +++ AGKK M+A DF NG
Sbjct: 252 EGASNGKPGEILAADK--KGLLVACGDG-ALRLTELQPAGKKAMSAADFLNGR 301
>gnl|CDD|234567 PRK00005, fmt, methionyl-tRNA formyltransferase; Reviewed.
Length = 309
Score = 32.0 bits (74), Expect = 0.086
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 63 VRCVDGKSILCSQITVAGKKKMTAVDFKNG 92
V +G ++ +Q+ GKK M+A DF NG
Sbjct: 271 VATGEG-ALRLTQLQPPGKKPMSAADFLNG 299
>gnl|CDD|115269 pfam06599, DUF1139, Protein of unknown function (DUF1139). This
family consists of several hypothetical Fijivirus
proteins of unknown function.
Length = 309
Score = 31.0 bits (70), Expect = 0.22
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 43 ITPELTPGFV--SFD-RGSKLLRVRCVDGKSILCSQITVAGKKKM 84
I PEL F+ +F + S+LL+V + S++ + + GKK +
Sbjct: 168 IAPELRICFMFRAFKLKPSQLLQVSRILSGSLMFPGLNLIGKKSL 212
>gnl|CDD|232983 TIGR00460, fmt, methionyl-tRNA formyltransferase. The top-scoring
characterized proteins other than methionyl-tRNA
formyltransferase (fmt) itself are
formyltetrahydrofolate dehydrogenases. The mitochondrial
methionyl-tRNA formyltransferases are so divergent that,
in a multiple alignment of bacterial fmt, mitochondrial
fmt, and formyltetrahydrofolate dehydrogenases, the
mitochondrial fmt appears the most different. However,
because both bacterial and mitochondrial fmt are
included in the seed alignment, all credible fmt
sequences score higher than any non-fmt sequence. This
enzyme modifies Met on initiator tRNA to f-Met [Protein
synthesis, tRNA aminoacylation].
Length = 313
Score = 30.1 bits (68), Expect = 0.39
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 3/47 (6%)
Query: 49 PGFVSFDRGSKLLRVRCVDGKSILC-SQITVAGKKKMTAVDFKNGYL 94
PG + + +L IL + GKK M A DF NG
Sbjct: 259 PGEIVYHNKKGILVACG--KDGILLLLSLQPPGKKVMRAEDFYNGSR 303
>gnl|CDD|236142 PRK08051, fre, FMN reductase; Validated.
Length = 232
Score = 29.4 bits (67), Expect = 0.52
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 85 TAVDFKNG-YLGKVKNESDKRYKGMSTCP 112
F+ G YL V E DKR +++ P
Sbjct: 26 APFSFRAGQYLMVVMGEKDKRPFSIASTP 54
>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 = 27.9 bits (63), Expect = 0.58
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 56 RGSKLLRVRCVDGKSILCSQITVAGKKK 83
G+ V DG L + GK++
Sbjct: 13 LGNGRFEVELEDGHERLAH---IPGKRR 37
>gnl|CDD|187732 cd08704, Met_tRNA_FMT_C, C-terminal domain of Formyltransferase
and other enzymes. C-terminal domain of formyl
transferase and other proteins with diverse enzymatic
activities. Proteins found in this family include
methionyl-tRNA formyltransferase, ArnA, and
10-formyltetrahydrofolate dehydrogenase. Methionyl-tRNA
formyltransferases constitute the majority of the
family and also demonstrate greater sequence diversity.
Although most proteins with formyltransferase activity
contain the C-terminal domain, some formyltransferases
( for example, prokaryotic glycinamide ribonucleotide
transformylase (GART)) only have the core catalytic
domain, indicating that the C-terminal domain is not a
requirement for catalytic activity and may be involved
in substrate binding. For example, the C-terminal
domain of methionyl-tRNA formyltransferase is involved
in the tRNA binding.
Length = 87
Score = 27.9 bits (63), Expect = 0.73
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 49 PGFVSFDRGSKLLRVRCVDGKSILCSQITVAGKKKMTA 86
++ D+ L V C DG ++ ++ GKK+M+A
Sbjct: 53 GTILAVDKKG--LLVACGDG-ALEILELQPEGKKRMSA 87
>gnl|CDD|128900 smart00652, eIF1a, eukaryotic translation initiation factor 1A.
Length = 83
Score = 26.8 bits (60), Expect = 1.6
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 56 RGSKLLRVRCVDGKSILCS 74
G+ L V C DGK L
Sbjct: 15 LGNGRLEVMCADGKERLAR 33
>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 = 27.1 bits (60), Expect = 1.6
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 57 GSKLLRVRCVDGKSILCS 74
G+ V C DG+ L S
Sbjct: 11 GNNRHEVECADGQRRLVS 28
>gnl|CDD|234504 TIGR04216, halo_surf_glyco, major cell surface glycoprotein.
Members of this family are the S-layer-forming
halobacterial major cell surface glycoprotein. The
highest scores below model cutoffs are fragmentary
paralogs to actual members of the family. Modifications
include at N-linked and O-linked glycosylation, a
C-terminal diphytanylglyceryl modification, and probable
cleavage of the PGF-CTERM tail.
Length = 782
Score = 27.9 bits (62), Expect = 2.2
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 14 TSSKPPSETKEPPERSKEPTDRLTEETNPITPELTPGF 51
T + +ET EP ++EPT+ T ++ TPGF
Sbjct: 731 TGPEETTETAEPTTTTEEPTEETTTGSS------TPGF 762
Score = 26.8 bits (59), Expect = 6.0
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 17 KPPSETKEPPERSKEPTDRLTEETNPITPELTP 49
+P + T E P + PT EET T E T
Sbjct: 713 RPDTTTSEDPTTTTTPTTTGPEETTE-TAEPTT 744
>gnl|CDD|223106 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
formyltransferase (GAR transformylase) [Nucleotide
transport and metabolism].
Length = 394
Score = 26.5 bits (59), Expect = 5.8
Identities = 13/27 (48%), Positives = 14/27 (51%)
Query: 50 GFVSFDRGSKLLRVRCVDGKSILCSQI 76
FV FD LL VR VDG C+ I
Sbjct: 196 EFVKFDFEITLLTVRAVDGTGSFCAPI 222
>gnl|CDD|222648 pfam14283, DUF4366, Domain of unknown function (DUF4366). This
family of proteins is found in bacteria and eukaryotes.
Proteins in this family are typically between 227 and
387 amino acids in length.
Length = 213
Score = 26.5 bits (59), Expect = 5.9
Identities = 10/29 (34%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 18 PPSETKEPPERSKEPTDRLTEETNPITPE 46
P +E +P E EE P+TPE
Sbjct: 32 PQTEATDPSE--VVVETVTEEEGGPLTPE 58
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 26.7 bits (59), Expect = 6.0
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 18 PPSETKEPPERSKEPTDRLTEETNPITPELTP 49
PP PE + D+ T+ + + P
Sbjct: 277 PPPPEPPEPEEEPDEPDQ-TDPDDGEETDQIP 307
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 26.2 bits (58), Expect = 9.4
Identities = 11/42 (26%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 18 PPSETKEPPERSKEPTDRLTEETNPITPELTPGFVSFDRGSK 59
P PP RS +P + FV+F +G K
Sbjct: 426 APPAAAAPPARSADPAAA------ASAGDRWRAFVAFVKGKK 461
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
0.313 0.131 0.391
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: 7,422,171
Number of extensions: 619302
Number of successful extensions: 403
Number of sequences better than 10.0: 1
Number of HSP's gapped: 402
Number of HSP's successfully gapped: 19
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.9 bits)