RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12294
(123 letters)
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 115 bits (291), Expect = 4e-33
Identities = 39/53 (73%), Positives = 46/53 (86%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
VTGKCGSV+VRL+PAPRGTGIV AP PKK+L+ AG+ED +TS+RG T T GNF
Sbjct: 162 VTGKCGSVRVRLVPAPRGTGIVAAPTPKKILEFAGVEDVFTSSRGKTRTRGNF 214
>gnl|CDD|233235 TIGR01020, rpsE_arch, ribosomal protein S5(archaeal
type)/S2(eukaryote cytosolic type). This model finds
eukaryotic ribosomal protein S2 as well as archaeal
ribosomal protein S5 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 212
Score = 99.9 bits (249), Expect = 2e-27
Identities = 34/53 (64%), Positives = 41/53 (77%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
VTGKCGSV+VRLIPAPRG G+V V KK+L++AGI+D +T RG T T NF
Sbjct: 134 VTGKCGSVRVRLIPAPRGLGLVAGDVAKKVLRLAGIDDVWTQTRGETRTTVNF 186
>gnl|CDD|235213 PRK04044, rps5p, 30S ribosomal protein S5P; Reviewed.
Length = 211
Score = 83.0 bits (206), Expect = 5e-21
Identities = 30/53 (56%), Positives = 37/53 (69%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
VTGK GSV+V L PAPRG G+V V KK+L++AGI+D +T G T T NF
Sbjct: 134 VTGKAGSVEVTLKPAPRGLGLVAGDVAKKVLELAGIKDVWTRTFGETRTTVNF 186
>gnl|CDD|190724 pfam03719, Ribosomal_S5_C, Ribosomal protein S5, C-terminal
domain.
Length = 74
Score = 78.2 bits (194), Expect = 2e-20
Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
VTGK G+V+V L PAPRGTGI+ + +L++AGI+D + GS N
Sbjct: 1 VTGKFGAVKVLLKPAPRGTGIIAGGAVRAVLELAGIKDVLAKSLGSR-NPINV 52
>gnl|CDD|223176 COG0098, RpsE, Ribosomal protein S5 [Translation, ribosomal
structure and biogenesis].
Length = 181
Score = 74.1 bits (183), Expect = 9e-18
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
V GK G+V+V L PAP GTGI+ + +L++AGI+D + GS N
Sbjct: 99 VIGKHGAVKVLLKPAPEGTGIIAGGAVRAVLELAGIKDVLAKSLGSR-NPINV 150
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 43.9 bits (105), Expect = 2e-06
Identities = 19/48 (39%), Positives = 30/48 (62%), Gaps = 2/48 (4%)
Query: 29 VTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
V GK G+ +V L PA GTG++ G V + +L++AG++D + GS
Sbjct: 87 VIGKFGAAKVLLKPASEGTGVIAGGAV-RAVLELAGVKDVLAKSLGSN 133
>gnl|CDD|130093 TIGR01021, rpsE_bact, ribosomal protein S5, bacterial/organelle
type. This model finds chloroplast ribosomal protein S5
as well as bacterial ribosomal protein S5. A candidate
mitochondrial form (Saccharomyces cerevisiae YBR251W and
its homolog) differs substantially and is not included
in this model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 154
Score = 42.7 bits (101), Expect = 5e-06
Identities = 18/49 (36%), Positives = 30/49 (61%), Gaps = 2/49 (4%)
Query: 28 IVTGKCGSVQVRLIPAPRGTGIV-GAPVPKKLLQMAGIEDCYTSARGST 75
V G+ G+ +V L PA GTG++ G V + +L++AG++D + GS
Sbjct: 75 EVIGRSGAAKVLLKPASPGTGVIAGGAV-RAILELAGVKDILAKSLGSN 122
>gnl|CDD|237294 PRK13186, lpxC, UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine
deacetylase; Reviewed.
Length = 295
Score = 29.3 bits (67), Expect = 0.45
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 30 TGKCGSVQVRLIPAPRGTGIV 50
+GK V + L PAP TGIV
Sbjct: 20 SGK--KVTLTLRPAPANTGIV 38
>gnl|CDD|109982 pfam00947, Pico_P2A, Picornavirus core protein 2A. This protein is
a protease, involved in cleavage of the polyprotein.
Length = 127
Score = 28.1 bits (63), Expect = 0.74
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 16 GILFCQHKVLGLIVTGKCGSV 36
GIL C+H V+G++ G G V
Sbjct: 94 GILRCEHGVIGIVTAGGEGHV 114
>gnl|CDD|235715 PRK06147, PRK06147, 3-oxoacyl-(acyl carrier protein) synthase;
Validated.
Length = 348
Score = 28.4 bits (64), Expect = 0.86
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 33 CGSVQVRLIPAPRGTGIVGAPVP--------KKLLQMA--GIEDC 67
+ R I P G ++GAPVP ++L +MA I +
Sbjct: 32 DNFQETRFIDPPGGEWLIGAPVPLPPPWRGPERLAEMAAPAIAEA 76
>gnl|CDD|239476 cd03381, PAP2_glucose_6_phosphatase, PAP2_like proteins,
glucose-6-phosphatase subfamily. Glucose-6-phosphatase
converts glucose-6-phosphate into free glucose and is
active in the lumen of the endoplasmic reticulum, where
it is bound to the membrane. The generation of free
glucose is an important control point in metabolism, and
stands at the end of gluconeogenesis and the release of
glucose from glycogen. Deficiency of
glucose-6-phosphatase leads to von Gierke's disease.
Length = 235
Score = 27.3 bits (61), Expect = 1.7
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 8 WGHLMVTSGILFCQHKVLGLIVTGKCGSVQVRLIP 42
GH M T+ +L L + G+ S +R++
Sbjct: 76 SGHAMGTTAVLLVMVTALLSHLAGRKRSRFLRVML 110
>gnl|CDD|238715 cd01434, EFG_mtEFG1_IV, EFG_mtEFG1_IV: domains similar to domain
IV of the bacterial translational elongation factor
(EF) EF-G. Included in this group is a domain of
mitochondrial Elongation factor G1 (mtEFG1) proteins
homologous to domain IV of EF-G. Eukaryotic cells
harbor 2 protein synthesis systems: one localized in
the cytoplasm, the other in the mitochondria. Most
factors regulating mitochondrial protein synthesis are
encoded by nuclear genes, translated in the cytoplasm,
and then transported to the mitochondria. The
eukaryotic system of elongation factor (EF) components
is more complex than that in prokaryotes, with both
cytoplasmic and mitochondrial elongation factors and
multiple isoforms being expressed in certain species.
During the process of peptide synthesis and tRNA site
changes, the ribosome is moved along the mRNA a
distance equal to one codon with the addition of each
amino acid. In bacteria this translocation step is
catalyzed by EF-G_GTP, which is hydrolyzed to provide
the required energy. Thus, this action releases the
uncharged tRNA from the P site and transfers the newly
formed peptidyl-tRNA from the A site to the P site.
Eukaryotic mtEFG1 proteins show significant homology to
bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects
and a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 116
Score = 26.6 bits (60), Expect = 2.2
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 31 GKCGSVQVRLIPAPRGTG------IVGAPVPKKLLQ--MAGIEDC 67
G+ G V + + P PRG+G IVG +PK+ + G +
Sbjct: 23 GQYGHVVLEIEPLPRGSGFEFVNKIVGGAIPKEYIPAVEKGFREA 67
>gnl|CDD|224906 COG1995, PdxA, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 332
Score = 26.8 bits (60), Expect = 2.8
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 13/73 (17%)
Query: 48 GIVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNFGECNTQHETSSYTETQCMQ---VLVS 104
IV AP+ K+ L AGI Y G T L + + LV+
Sbjct: 116 AIVTAPINKEALNDAGIP--YP---GHTEFLAELSGTH-----DPVMMLAVPELRVALVT 165
Query: 105 SHFPISESLNTIS 117
+H P+ + + I+
Sbjct: 166 THIPLKDVPDAIT 178
>gnl|CDD|223845 COG0774, LpxC, UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell
envelope biogenesis, outer membrane].
Length = 300
Score = 26.8 bits (60), Expect = 3.3
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 30 TGKCGSVQVRLIPAPRGTGIV 50
+GK V + L PAP TGIV
Sbjct: 20 SGK--KVTLTLRPAPANTGIV 38
>gnl|CDD|224234 COG1315, COG1315, Uncharacterized conserved protein [Function
unknown].
Length = 543
Score = 26.6 bits (59), Expect = 4.2
Identities = 13/38 (34%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 23 KVLGLIVTGKCGSVQVRLIPAPRGT---GIVGAPVPKK 57
K LG + G V R IPA +G + G P+ K
Sbjct: 177 KSLGFVNNVDEGEVLARRIPATKGEDGYTVFGNPIKPK 214
>gnl|CDD|237185 PRK12739, PRK12739, elongation factor G; Reviewed.
Length = 691
Score = 26.3 bits (59), Expect = 5.3
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 6/32 (18%)
Query: 31 GKCGSVQVRLIPAPRGTG------IVGAPVPK 56
G+ G V + P G G IVG +PK
Sbjct: 502 GQYGDVWIEFEPNEEGKGFEFVNKIVGGVIPK 533
>gnl|CDD|234569 PRK00007, PRK00007, elongation factor G; Reviewed.
Length = 693
Score = 26.2 bits (59), Expect = 5.3
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 6/33 (18%)
Query: 30 TGKCGSVQVRLIPAPRGTG------IVGAPVPK 56
G+ G V + P G G IVG +PK
Sbjct: 504 RGQYGHVVIEFEPNEPGKGYEFVNKIVGGVIPK 536
>gnl|CDD|233112 TIGR00746, arcC, carbamate kinase. In most species, carbamate
kinase works in arginine catabolism and consumes
carbamoyl phosphate to convert ADP into ATP. In the
pathway in Pyrococcus furiosus, the enzyme acts instead
to generate carbamoyl phosphate.The seed alignment for
this model includes experimentally confirmed examples
from a set of phylogenetically distinct species. In a
neighbor-joining tree constructed from an alignment of
candidate carbamate kinases and several acetylglutamate
kinases, the latter group forms a clear outgroup which
roots the tree of carbamate kinase-like proteins. This
analysis suggests that in E. coli, the ArcC paralog YqeA
may be a second isozyme, while the paralog YahI branches
as an outlier and is less likely to be an authentic
carbamate kinase. The homolog from Mycoplasma pneumoniae
likewise branches outside the set containing known
carbamate kinases and also scores below the trusted
cutoff [Energy metabolism, Amino acids and amines].
Length = 309
Score = 26.3 bits (58), Expect = 5.4
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 39 RLIPAPRGTGIVGAPVPKKLLQ 60
R++P+PR IV A K L++
Sbjct: 158 RVVPSPRPKDIVEAETIKTLVE 179
>gnl|CDD|181674 PRK09148, PRK09148, aminotransferase; Validated.
Length = 405
Score = 26.2 bits (58), Expect = 5.5
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 41 IPAPRGTGIVGAPVPKKLLQMAGIE 65
IP P + AP+P+ + +E
Sbjct: 315 IPPPAASMFAWAPIPEAFRHLGSLE 339
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 25.7 bits (57), Expect = 7.8
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 9/54 (16%)
Query: 34 GSVQVRLIPAPRGTG------IVGAPVPKKLLQMAGIEDCYTSARGSTGTLGNF 81
G V +R+ P RG G +VG +P++L + +E A ++G L +
Sbjct: 504 GEVHLRVEPLERGAGFIFVSKVVGGAIPEEL--IPAVEKGIREAL-ASGPLAGY 554
>gnl|CDD|147898 pfam05989, Chordopox_A35R, Chordopoxvirus A35R protein. This
family consists of several Chordopoxvirus sequences
homologous to the Vaccinia virus A35R protein. The
function of this family is unknown.
Length = 176
Score = 25.4 bits (56), Expect = 7.9
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 53 PVPKKLLQMAGIEDCYTSARG 73
P+P L+ ++DCY + G
Sbjct: 48 PIPVNLINQRDLQDCYIAYNG 68
>gnl|CDD|236831 PRK11052, malQ, 4-alpha-glucanotransferase; Provisional.
Length = 695
Score = 25.6 bits (57), Expect = 8.1
Identities = 6/18 (33%), Positives = 8/18 (44%)
Query: 56 KKLLQMAGIEDCYTSARG 73
+ AGI Y +A G
Sbjct: 7 DQAALAAGIAPSYINAHG 24
>gnl|CDD|183998 PRK13359, PRK13359, beta-ketoadipyl CoA thiolase; Provisional.
Length = 400
Score = 25.5 bits (56), Expect = 8.6
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 43 APRGTGIVGAPVPKKLLQMAGI 64
PR GI AP +KLL G+
Sbjct: 290 EPRVMGIGPAPATQKLLARLGM 311
>gnl|CDD|233023 TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.
This model represents PdxA, an NAD+-dependent
4-hydroxythreonine 4-phosphate dehydrogenase (EC
1.1.1.262) active in pyridoxal phosphate biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridoxine].
Length = 320
Score = 25.5 bits (57), Expect = 8.8
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 48 GIVGAPVPKKLLQMAGI 64
+V AP+ K + AG
Sbjct: 110 ALVTAPIHKGAINQAGF 126
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
0.320 0.135 0.409
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,790,207
Number of extensions: 476141
Number of successful extensions: 369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 29
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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 (24.2 bits)