RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15650
(211 letters)
>gnl|CDD|240292 PTZ00148, PTZ00148, 40S ribosomal protein S8; Provisional.
Length = 205
Score = 175 bits (447), Expect = 7e-56
Identities = 76/170 (44%), Positives = 100/170 (58%), Gaps = 43/170 (25%)
Query: 3 RGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDATP 62
RGGN K+RALR+D GNFSWGS+ +KTRI+DVVYNASNNELVRTKTLVKNAIV IDA P
Sbjct: 49 RGGNFKFRALRLDTGNFSWGSQGIAKKTRILDVVYNASNNELVRTKTLVKNAIVQIDAAP 108
Query: 63 FRQWYETYYALPIGRRKTGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHGD 122
F+QWY +Y + +G++K K
Sbjct: 109 FKQWYAKHYGIDLGKKKKYK---------------------------------------- 128
Query: 123 LNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVEQAIEEQFQTGRILVSILS 172
+ EE KK+S+ +V K + R+K+ K+++A+ EQFQ+GR+L I S
Sbjct: 129 ---KEEENKKAKKKSESLVAKLEVRKKNHKIDKALLEQFQSGRLLARISS 175
>gnl|CDD|211392 cd11380, Ribosomal_S8e_like, Eukaryotic/archaeal ribosomal protein
S8e and similar proteins. This family contains the
eukaryotic/archaeal ribosomal protein S8, a component of
the small ribosomal subunits, as well as the NSA2 gene
product.
Length = 138
Score = 110 bits (278), Expect = 3e-31
Identities = 28/68 (41%), Positives = 36/68 (52%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
RGGN K RALR+D+ N S T+K +I+ V N SNNE VR + K I+ D +
Sbjct: 45 VRGGNIKPRALRLDKANVSHPELGKTKKLKILGVKKNPSNNEYVRRGVITKGTIIETDVS 104
Query: 62 PFRQWYET 69
P E
Sbjct: 105 PLGLVTEE 112
>gnl|CDD|201659 pfam01201, Ribosomal_S8e, Ribosomal protein S8e.
Length = 129
Score = 104 bits (261), Expect = 8e-29
Identities = 33/61 (54%), Positives = 41/61 (67%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
RGGN+K RALR+D+ N SW SE TRK RI+ VVYN +NNE VR + K AI+ D +
Sbjct: 48 VRGGNRKVRALRLDKANVSWPSEGTTRKVRILGVVYNPANNEYVRRNIITKGAIIETDVS 107
Query: 62 P 62
Sbjct: 108 E 108
>gnl|CDD|211394 cd11382, Ribosomal_S8e, Eukaryotic/archaeal ribosomal protein S8e
(RPS8). The eukaryotic/archaeal ribosomal protein S8 is
a component of the small (40S in eukaryotes, 30S in
archaea) ribosomal subunits and interacts tightly with
18S rRNA (16S rRNA in archaea, presumably).
Length = 122
Score = 103 bits (259), Expect = 1e-28
Identities = 36/58 (62%), Positives = 42/58 (72%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVID 59
RGGN K RALR+D GN SW SE T+K +I+DVVYN +NNELVR TL K AI+ D
Sbjct: 44 VRGGNTKVRALRLDTGNVSWPSEGKTKKVKILDVVYNPANNELVRRNTLTKGAIIETD 101
>gnl|CDD|224918 COG2007, RPS8A, Ribosomal protein S8E [Translation, ribosomal
structure and biogenesis].
Length = 127
Score = 70.8 bits (174), Expect = 5e-16
Identities = 26/60 (43%), Positives = 32/60 (53%)
Query: 1 TTRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDA 60
TRGGN K RALR N S T+K +II VV N +N E VR + K AI+ +
Sbjct: 47 RTRGGNFKVRALRAKTANVSDPETGKTKKAKIIGVVENPANPEYVRRNIITKGAIIETEI 106
>gnl|CDD|129407 TIGR00307, S8e, ribosomal protein S8.e. Archaeal and eukaryotic
ribosomal protein S8. This model could easily have been
split into two models, one for eukaryotic S8 and one for
archaeal S8; eukaryotic forms invariably have in insert
of about 80 residues that archaeal forms of S8 do not
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 127
Score = 68.3 bits (167), Expect = 5e-15
Identities = 26/60 (43%), Positives = 30/60 (50%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIVVIDAT 61
TRGGNKK R LR + N S +K I VV N +NN VR + K AIV D
Sbjct: 47 TRGGNKKVRLLRDETANVSDPETGKVKKVEIAGVVENPANNHYVRRNVITKGAIVETDIG 106
>gnl|CDD|235214 PRK04049, PRK04049, 30S ribosomal protein S8e; Validated.
Length = 127
Score = 46.0 bits (110), Expect = 9e-07
Identities = 20/55 (36%), Positives = 29/55 (52%)
Query: 2 TRGGNKKYRALRIDQGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNAIV 56
RGGN+K R LR + N + T+K +I+ VV N +N R + K AI+
Sbjct: 47 VRGGNRKVRLLRANYANVADPKTGKTKKVKILTVVENPANPHYARRNIITKGAII 101
>gnl|CDD|163144 TIGR03123, one_C_unchar_1, probable H4MPT-linked C1 transfer
pathway protein. This protein family was identified, by
the method of partial phylogenetic profiling, as related
to the use of tetrahydromethanopterin (H4MPT) as a C-1
carrier. Characteristic markers of the H4MPT-linked C1
transfer pathway include formylmethanofuran
dehydrogenase subunits, methenyltetrahydromethanopterin
cyclohydrolase, etc. Tetrahydromethanopterin, a
tetrahydrofolate analog, occurs in methanogenic archaea,
bacterial methanotrophs, planctomycetes, and a few other
lineages [Central intermediary metabolism, One-carbon
metabolism].
Length = 318
Score = 30.0 bits (68), Expect = 0.81
Identities = 37/152 (24%), Positives = 53/152 (34%), Gaps = 33/152 (21%)
Query: 40 SNNELVRTKTLVKNAIVVIDATPFR-QWYET---YYALPIGRRKTGKLDVQQLTPSLDPE 95
ELV T L + P +W Y+A+ T DV +L + E
Sbjct: 162 KTGELVYTGVLRTPISALAREVPLEGEWTRVSSEYFAI------TA--DVYRLLGEITEE 213
Query: 96 EYTLYVPVVVTRSTELSV--LTRAISHGDLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKV 153
+YT P +S E + L R + DL EE V N + K Y Q ++
Sbjct: 214 DYTCDTPDGKGKSIEECMRRLARMVC-ADLEELGEEDVRN------LAKYYYEAQL-EQL 265
Query: 154 EQAIEEQFQ-----------TGRILVSILSER 174
+AIEE + G L + R
Sbjct: 266 TEAIEEVLERYGLKTVVAAGAGEFLAKEAAAR 297
>gnl|CDD|220489 pfam09952, DUF2186, Uncharacterized protein conserved in bacteria
(DUF2186). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 143
Score = 28.9 bits (65), Expect = 0.98
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 66 WYETYYALPIGRRKTGKLDVQQLTPSLDPEEYTLYVP 102
W+ G G+ +LTP L P TLYV
Sbjct: 36 WWFDVNLEAAGAAWGGEAAAAKLTPYLKPGSATLYVS 72
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 29.1 bits (65), Expect = 2.1
Identities = 23/79 (29%), Positives = 32/79 (40%), Gaps = 5/79 (6%)
Query: 116 RAISHGDLNTEAEEAVLNKKRSKKVVKKYKSRQKHAKVE-----QAIEEQFQTGRILVSI 170
RAI L +E E L KK + KY ++ + E Q E + I
Sbjct: 440 RAILEKILKSERELNQLVKKEIQADATKYGLARRSSLEEREEAKQVSEIDMIPKEPVTII 499
Query: 171 LSERTAVRQAKFHAVDSGS 189
LS+ VR AK H +D +
Sbjct: 500 LSKMGWVRSAKGHDIDLST 518
>gnl|CDD|183625 PRK12617, flgA, flagellar basal body P-ring biosynthesis protein
FlgA; Reviewed.
Length = 214
Score = 28.0 bits (62), Expect = 3.1
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 73 LPIGRRKTGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHGDLNTEAE 128
+ + + TG V+ P P + L+VP+ V R+ ++ VL R I+ G+ + A+
Sbjct: 55 IALQAQPTGTNTVEVACP--QPAGWRLFVPLKVRRNQDVLVLRRGITAGETISLAD 108
>gnl|CDD|221933 pfam13144, SAF_2, SAF-like. The members of this family are similar
to those in the SAF family, and include flagellar
basal-body proteins and pilus-assembly proteins.
Length = 196
Score = 27.5 bits (62), Expect = 4.0
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 71 YALPIGRRKTGKLDVQQLTPSLDPEEYTLYVPVVVTRSTELSVLTRAISHGDL 123
+LP GRR G V P+ +T+YVPV V + + V R ++ G++
Sbjct: 39 ISLPSGRRLRGNGTVG--VRCDGPQPWTVYVPVRVEVTGPVVVAARPLARGEV 89
>gnl|CDD|224371 COG1454, EutG, Alcohol dehydrogenase, class IV [Energy production
and conversion].
Length = 377
Score = 27.6 bits (62), Expect = 5.8
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 92 LDPEEYTLYVPVVVTRSTELSVLTRAI 118
LDPE TL +P +T +T + LT AI
Sbjct: 173 LDPE-LTLGMPPSLTAATGMDALTHAI 198
>gnl|CDD|221408 pfam12072, DUF3552, Domain of unknown function (DUF3552). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, archaea and eukaryotes.
This domain is about 200 amino acids in length. This
domain is found associated with pfam00013, pfam01966.
This domain has a single completely conserved residue A
that may be functionally important.
Length = 201
Score = 26.7 bits (60), Expect = 8.5
Identities = 11/37 (29%), Positives = 21/37 (56%)
Query: 126 EAEEAVLNKKRSKKVVKKYKSRQKHAKVEQAIEEQFQ 162
E +E L +K + ++ + +K ++E+ IEEQ Q
Sbjct: 102 EKKEESLEEKEKELAARQQQLEEKEEELEELIEEQQQ 138
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
0.315 0.128 0.366
Gapped
Lambda K H
0.267 0.0800 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,318,182
Number of extensions: 932724
Number of successful extensions: 991
Number of sequences better than 10.0: 1
Number of HSP's gapped: 990
Number of HSP's successfully gapped: 22
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)