RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11838
(78 letters)
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 63.4 bits (155), Expect = 1e-13
Identities = 22/51 (43%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIKIGKS 55
MGELHLEII DR+ E+ +E ++G Q+AY+ET+ + +HK K
Sbjct: 452 MGELHLEIIVDRLKREFGVEVEVGKPQVAYRETIRKKSEVEGKHK-KQSGG 501
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 62.1 bits (152), Expect = 4e-13
Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
MGELHL++ +R+ EY +E + GP Q+ Y+ET+ A HK
Sbjct: 433 MGELHLDVALERLKREYGVEVETGPPQVPYRETIRKKAEGHGRHK 477
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 60.2 bits (147), Expect = 1e-12
Identities = 23/47 (48%), Positives = 32/47 (68%), Gaps = 2/47 (4%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIK 51
MGELHL+II DR+ E+K+EA++G Q+AY+ET+ E K K
Sbjct: 451 MGELHLDIIVDRMKREFKVEANVGAPQVAYRETITKS--VEAEGKYK 495
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 60.1 bits (147), Expect = 2e-12
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
MGELHL+II DR+ E+K+EA++G Q+AY+ET+ +
Sbjct: 454 MGELHLDIIVDRMKREFKVEANVGKPQVAYRETIRKKVEVEGKFV 498
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 55.3 bits (134), Expect = 9e-11
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
MGELHLE+ +R+ E+K+E + G Q+AY+ET+ A + HK
Sbjct: 450 MGELHLEVALERLRREFKLEVNTGKPQVAYRETIRKMAEGVYRHK 494
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 52.9 bits (127), Expect = 8e-10
Identities = 23/49 (46%), Positives = 34/49 (69%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIKIG 53
MGELHL+II DR+ E+K+EA++G Q+AY+ET+ S +H + G
Sbjct: 452 MGELHLDIIVDRMKREFKVEANVGAPQVAYRETIRSKVEVEGKHAKQSG 500
>gnl|CDD|236047 PRK07560, PRK07560, elongation factor EF-2; Reviewed.
Length = 731
Score = 42.5 bits (101), Expect = 3e-06
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETV 38
MGELHLE+I RI +Y IE + Y+ETV
Sbjct: 436 MGELHLEVITYRIKRDYGIEVVTSEPIVVYRETV 469
>gnl|CDD|129581 TIGR00490, aEF-2, translation elongation factor aEF-2. This model
represents archaeal elongation factor 2, a protein more
similar to eukaryotic EF-2 than to bacterial EF-G, both
in sequence similarity and in sharing with eukaryotes
the property of having a diphthamide (modified His)
residue at a conserved position. The diphthamide can be
ADP-ribosylated by diphtheria toxin in the presence of
NAD [Protein synthesis, Translation factors].
Length = 720
Score = 39.5 bits (92), Expect = 3e-05
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIAYKETV 38
MGELHLEII ++I +Y ++ + P + Y+ETV
Sbjct: 436 MGELHLEIIVEKIREDYGLDVETSPPIVVYRETV 469
>gnl|CDD|165622 PLN00044, PLN00044, multi-copper oxidase-related protein;
Provisional.
Length = 596
Score = 28.9 bits (64), Expect = 0.23
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 27 LGPLQIAYKETVLSPAMASHEHKIKIGKSFRLRFRDDKTLAVKTSV 72
GP Q Y ++++ P + + GK++R R + + V TS+
Sbjct: 200 FGPYQ--YNDSLVPPGITYERINVDPGKTYRFRVHN---VGVATSL 240
>gnl|CDD|236157 PRK08126, PRK08126, hypothetical protein; Provisional.
Length = 432
Score = 28.5 bits (64), Expect = 0.24
Identities = 19/57 (33%), Positives = 22/57 (38%), Gaps = 13/57 (22%)
Query: 6 GELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIKIGKSFRLRFRD 62
G LE IR R+ TE I P+ A LSP E G+ FRD
Sbjct: 199 GRRKLEQIRQRLYTE--ITGRRDPVPPA-----LSPHWQGAEP----GR--LRSFRD 242
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 27.9 bits (63), Expect = 0.38
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 5 MGELHLEIIRDRILTEYKIE 24
+G LH+EII++R+ E+ ++
Sbjct: 348 LGLLHMEIIQERLEREFDLD 367
>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
Length = 600
Score = 27.3 bits (62), Expect = 0.78
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 6 GELHLEIIRDRILTEYKIE 24
G LH+EII++R+ E+ ++
Sbjct: 347 GLLHMEIIQERLEREFDLD 365
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 26.5 bits (59), Expect = 1.3
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 5 MGELHLEIIRDRILTEYKIE 24
+G LH+EII++R+ E+ ++
Sbjct: 342 LGLLHMEIIQERLEREFNLD 361
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation
releasing factor, RF-3 (prfC) was originally described
as stop codon-independent, in contrast to peptide chain
release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and
RF-2 are closely related to each other, while RF-3 is
similar to elongation factors EF-Tu and EF-G; RF-1 is
active at UAA and UAG and RF-2 is active at UAA and UGA.
More recently, RF-3 was shown to be active primarily at
UGA stop codons in E. coli. All bacteria and organelles
have RF-1. The Mycoplasmas and organelles, which
translate UGA as Trp rather than as a stop codon, lack
RF-2. RF-3, in contrast, seems to be rare among bacteria
and is found so far only in Escherichia coli and some
other gamma subdivision Proteobacteria, in Synechocystis
PCC6803, and in Staphylococcus aureus [Protein
synthesis, Translation factors].
Length = 527
Score = 26.0 bits (57), Expect = 2.0
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 5 MGELHLEIIRDRILTEYKIEADLGPLQIA 33
+G L +++ R+ EY +EA P+ +A
Sbjct: 439 VGVLQFDVVVYRLKEEYNVEARYEPVNVA 467
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 26.0 bits (58), Expect = 2.2
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 2 KKRMGELHLEIIRDRILTEYKIE 24
K + GE L IRD LTE ++E
Sbjct: 159 KGKPGEWKLVKIRDEPLTEEELE 181
>gnl|CDD|133056 cd06434, GT2_HAS, Hyaluronan synthases catalyze polymerization of
hyaluronan. Hyaluronan synthases (HASs) are
bi-functional glycosyltransferases that catalyze
polymerization of hyaluronan. HASs transfer both GlcUA
and GlcNAc in beta-(1,3) and beta-(1,4) linkages,
respectively to the hyaluronan chain using UDP-GlcNAc
and UDP-GlcUA as substrates. HA is made as a free
glycan, not attached to a protein or lipid. HASs do not
need a primer for HA synthesis; they initiate HA
biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA,
and Mg2+. Hyaluronan (HA) is a linear
heteropolysaccharide composed of (1-3)-linked
beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can
be found in vertebrates and a few microbes and is
typically on the cell surface or in the extracellular
space, but is also found inside mammalian cells.
Hyaluronan has several physiochemical and biological
functions such as space filling, lubrication, and
providing a hydrated matrix through which cells can
migrate.
Length = 235
Score = 25.3 bits (56), Expect = 3.6
Identities = 11/55 (20%), Positives = 17/55 (30%), Gaps = 10/55 (18%)
Query: 32 IAYKETVLSPAMASHEHKIKIGKSFRLRFRDDKTL----------AVKTSVAECE 76
AY+ +L + E + RL DD+ L V +E
Sbjct: 157 AAYRTEILKDFLFLEEFTNETFMGRRLNAGDDRFLTRYVLSHGYKTVYQYTSEAY 211
>gnl|CDD|179105 PRK00741, prfC, peptide chain release factor 3; Provisional.
Length = 526
Score = 25.1 bits (56), Expect = 3.8
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 6 GELHLEIIRDRILTEYKIEADLGPLQIA 33
G+L E++ R+ EY +EA P+ +A
Sbjct: 439 GQLQFEVVAHRLKNEYNVEAIYEPVGVA 466
>gnl|CDD|236869 PRK11168, glpC, sn-glycerol-3-phosphate dehydrogenase subunit C;
Provisional.
Length = 396
Score = 25.2 bits (56), Expect = 3.9
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 2/53 (3%)
Query: 2 KKRMGELHLEIIRDRILTEYKIEADLG-PL-QIAYKETVLSPAMASHEHKIKI 52
+ + +RDRIL+ + L P + T L P E + I
Sbjct: 80 RAKYVTERGPPLRDRILSHTDLMGSLATPFAPLVNAATGLKPVRWLLEKTLGI 132
>gnl|CDD|101884 PRK05640, PRK05640, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 151
Score = 25.2 bits (55), Expect = 4.0
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 15 DRILTEYKIEADLG----PLQIAYKETVLSPAMASHEHKIKI 52
+ E KI+ LG PL +A T ++ S+E +K
Sbjct: 69 EETREEIKIDLPLGLAVIPLALALLRTRITVNSLSYEAYLKA 110
>gnl|CDD|237242 PRK12874, ubiA, prenyltransferase; Reviewed.
Length = 291
Score = 25.0 bits (55), Expect = 4.2
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 21 YKIEADLGPLQIAYKETVLSPAMASHEHKI------KIGKSF 56
+ A LG AY ++S + +EH + KI K+F
Sbjct: 230 FVWCAHLG--LFAYLGVIVSALILLYEHYLVRKDFKKIDKAF 269
>gnl|CDD|177407 PHA02578, 53, baseplate wedge subunit; Provisional.
Length = 181
Score = 24.7 bits (54), Expect = 4.9
Identities = 7/32 (21%), Positives = 11/32 (34%)
Query: 3 KRMGELHLEIIRDRILTEYKIEADLGPLQIAY 34
+ +I L Y I P Q+A+
Sbjct: 21 RNYRAYFNRVIPSYTLRTYYITGSPRPEQLAH 52
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 24.4 bits (54), Expect = 5.4
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 3/28 (10%)
Query: 3 KRMGEL---HLEIIRDRILTEYKIEADL 27
KR+GEL +E +RD I +Y +E DL
Sbjct: 43 KRVGELTEEEIERLRDAIQNKYLVEGDL 70
>gnl|CDD|213840 TIGR03631, bact_S13, 30S ribosomal protein S13. This model
describes bacterial ribosomal protein S13, to the
exclusion of the homologous archaeal S13P and
eukaryotic ribosomal protein S18. This model identifies
some (but not all) instances of chloroplast and
mitochondrial S13, which is of bacterial type [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 113
Score = 24.0 bits (53), Expect = 8.6
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 3 KRMGEL---HLEIIRDRILTEYKIEADL 27
KR+ +L L IR+ I +YK+E DL
Sbjct: 41 KRVKDLTEEELNAIREEIEAKYKVEGDL 68
>gnl|CDD|184898 PRK14905, PRK14905, triosephosphate isomerase/PTS system
glucose/sucrose-specific transporter subunit IIB;
Provisional.
Length = 355
Score = 24.2 bits (52), Expect = 10.0
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 10 LEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIKIG 53
L ++ ++Y IE + P IA K+ V + A + KIKIG
Sbjct: 27 LLAFAEKFKSDYDIELFVIPSYIALKDAVEAAASETGHPKIKIG 70
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
0.319 0.135 0.372
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,801,985
Number of extensions: 292847
Number of successful extensions: 226
Number of sequences better than 10.0: 1
Number of HSP's gapped: 226
Number of HSP's successfully gapped: 29
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
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 (21.8 bits)
S2: 53 (24.0 bits)