RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1365
(140 letters)
>gnl|CDD|185469 PTZ00134, PTZ00134, 40S ribosomal protein S18; Provisional.
Length = 154
Score = 234 bits (600), Expect = 5e-81
Identities = 98/140 (70%), Positives = 118/140 (84%), Gaps = 3/140 (2%)
Query: 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR 60
++TN+DGKRKV +ALTAIKG GRRF+ +V KKA ID+ KRAGE + EE++KI+ I+ NP
Sbjct: 18 LNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPL 77
Query: 61 QYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVR 120
Q+KIPDWFLNRQ+D DGK S + + LD+KLREDLERLKKIR HRG+RH+WGLRVR
Sbjct: 78 QFKIPDWFLNRQRDPKDGKNSHLT---SNMLDTKLREDLERLKKIRLHRGLRHHWGLRVR 134
Query: 121 GQHTKTTGRRGRTVGVSKKK 140
GQHTKTTGRRGRTVGVS+KK
Sbjct: 135 GQHTKTTGRRGRTVGVSRKK 154
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 158 bits (403), Expect = 4e-51
Identities = 63/138 (45%), Positives = 93/138 (67%), Gaps = 3/138 (2%)
Query: 3 TNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQY 62
T++DG + V +ALT IKG GRR + + +K +D N + G S+EE++KI + +P +
Sbjct: 15 TDLDGTKPVEYALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALEDPAEE 74
Query: 63 KIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQ 122
IP W LNR+KD G+ ++ + L +RED+ R+KKIR++RG+RH GL+VRGQ
Sbjct: 75 GIPSWMLNRRKDYETGEDLHLI---GSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQ 131
Query: 123 HTKTTGRRGRTVGVSKKK 140
T++TGR G TVGVS+KK
Sbjct: 132 RTRSTGRTGGTVGVSRKK 149
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 143 bits (364), Expect = 3e-45
Identities = 67/140 (47%), Positives = 96/140 (68%), Gaps = 4/140 (2%)
Query: 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR 60
T++DG + V +ALT IKG GRRF+ + +K +D N + G +EE++K+ + N
Sbjct: 9 ADTDLDGNKPVEYALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVEN-Y 67
Query: 61 QYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVR 120
+Y IP W LNR+KD G+ ++ + LD +RED+ R+KKIR++RG+RH GL+VR
Sbjct: 68 EYGIPSWLLNRRKDYETGEDLHLI---GSDLDMTVREDINRMKKIRSYRGIRHELGLKVR 124
Query: 121 GQHTKTTGRRGRTVGVSKKK 140
GQ TK+TGRRGRTVGVS+KK
Sbjct: 125 GQRTKSTGRRGRTVGVSRKK 144
>gnl|CDD|223177 COG0099, RpsM, Ribosomal protein S13 [Translation, ribosomal
structure and biogenesis].
Length = 121
Score = 122 bits (308), Expect = 6e-37
Identities = 53/140 (37%), Positives = 74/140 (52%), Gaps = 27/140 (19%)
Query: 3 TNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQY 62
+I G ++V+ ALT I G GRR + + KKA ID +KR GE +EEE++++
Sbjct: 7 VDIPGNKRVVIALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL---------- 56
Query: 63 KIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQ 122
+D + KY L ++R D++RL KI +RG+RH GL VRGQ
Sbjct: 57 ----------RDAIQNKY-----LVEGDLRREVRMDIKRLMKIGCYRGIRHRRGLPVRGQ 101
Query: 123 HTKTTGRR--GRTVGVSKKK 140
TKT R G GV+KKK
Sbjct: 102 RTKTNARTRKGPRKGVAKKK 121
>gnl|CDD|144128 pfam00416, Ribosomal_S13, Ribosomal protein S13/S18. This family
includes ribosomal protein S13 from prokaryotes and S18
from eukaryotes.
Length = 106
Score = 119 bits (300), Expect = 5e-36
Identities = 56/130 (43%), Positives = 74/130 (56%), Gaps = 26/130 (20%)
Query: 1 MSTNIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPR 60
++TN+DG +K+ ALT IKG GRR +N +LKKA +D +KR GE +EEE+D+I I++N
Sbjct: 3 LNTNLDGNKKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN-- 60
Query: 61 QYKIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVR 120
L K+R D+ERLKKIR +RG+RH GL VR
Sbjct: 61 ------------------------YVVENDLRRKIRNDIERLKKIRCYRGLRHIRGLPVR 96
Query: 121 GQHTKTTGRR 130
GQ TKT R
Sbjct: 97 GQRTKTNART 106
>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 = 62.5 bits (153), Expect = 9e-14
Identities = 40/126 (31%), Positives = 62/126 (49%), Gaps = 25/126 (19%)
Query: 4 NIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYK 63
+I ++V ALT I G GR + +L+KA ID +KR + +EEE++ I
Sbjct: 6 DIPNNKRVEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI----------- 54
Query: 64 IPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKKIRAHRGMRHYWGLRVRGQH 123
++ ++ KY L ++ +++RL I +RG+RH GL VRGQ
Sbjct: 55 ---------REEIEAKY-----KVEGDLRREVSLNIKRLMDIGCYRGLRHRRGLPVRGQR 100
Query: 124 TKTTGR 129
TKT R
Sbjct: 101 TKTNAR 106
>gnl|CDD|235358 PRK05179, rpsM, 30S ribosomal protein S13; Validated.
Length = 122
Score = 61.2 bits (150), Expect = 4e-13
Identities = 43/143 (30%), Positives = 68/143 (47%), Gaps = 35/143 (24%)
Query: 4 NIDGKRKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYK 63
+I ++V+ ALT I G GR + +L A ID + R + ++EE+DKI
Sbjct: 8 DIPRNKRVVIALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKI----------- 56
Query: 64 IPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLRE----DLERLKKIRAHRGMRHYWGLRV 119
++ +D Y +++ LR +++RL I +RG+RH GL V
Sbjct: 57 ---------REEIDKNY---------KVEGDLRREVSMNIKRLMDIGCYRGLRHRRGLPV 98
Query: 120 RGQHTKTTGR--RGRTVGVSKKK 140
RGQ TKT R +G ++ KK
Sbjct: 99 RGQRTKTNARTRKGPRKTIAGKK 121
>gnl|CDD|177059 CHL00137, rps13, ribosomal protein S13; Validated.
Length = 122
Score = 46.9 bits (112), Expect = 1e-07
Identities = 39/138 (28%), Positives = 67/138 (48%), Gaps = 35/138 (25%)
Query: 9 RKVMFALTAIKGCGRRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWF 68
+++ +ALT I G G + +L+KA+ID + R + ++E++ +
Sbjct: 13 KRIEYALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISAL---------------- 56
Query: 69 LNRQKDIVDGKYSQILLTSTAQLDSKLRE----DLERLKKIRAHRGMRHYWGLRVRGQHT 124
++I++ Y Q++ LR +++RL +I +RG RH GL VRGQ T
Sbjct: 57 ----REIIEENY---------QVEGDLRRFESLNIKRLMEINCYRGRRHRLGLPVRGQRT 103
Query: 125 KTTGR--RGRTVGVSKKK 140
+T R RG V+ KK
Sbjct: 104 RTNARTRRGAKKTVAGKK 121
>gnl|CDD|173960 cd08550, GlyDH-like, Glycerol_dehydrogenase-like. Families of
proteins related to glycerol dehydrogenases. Glycerol
dehydrogenases (GlyDH) is a key enzyme in the glycerol
dissimilation pathway. In anaerobic conditions, many
microorganisms utilize glycerol as a source of carbon
through coupled oxidative and reductive pathways. One
of the pathways involves the oxidation of glycerol to
dihydroxyacetone with the reduction of NAD+ to NADH
catalyzed by glycerol dehydrogenases. Dihydroxyacetone
is then phosphorylated by dihydroxyacetone kinase and
enters the glycolytic pathway for further degradation.
The activity of GlyDH is zinc-dependent. The zinc ion
plays a role in stabilizing an alkoxide intermediate at
the active site. Some subfamilies have not been
characterized till now.
Length = 349
Score = 29.8 bits (67), Expect = 0.37
Identities = 18/54 (33%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 5 IDGKRKVMFALTAIKGCGRRFSNIVLKKADI--DLNKRAGECSEEEVDKIITIM 56
K V+ T +K RF L K+ I D+ GECS EEV K +
Sbjct: 21 FGSKVAVVGGKTVLKKSRPRFEA-ALAKSIIVVDVIVFGGECSTEEVVKALCGA 73
>gnl|CDD|130916 TIGR01857, FGAM-synthase, phosphoribosylformylglycinamidine
synthase, clade II. This model represents a
single-molecule form of
phosphoribosylformylglycinamidine synthase, also called
FGAM synthase, an enzyme of purine de novo biosynthesis.
This model represents a second clade of these enzymes
found in Clostridia, Bifidobacteria and Streptococcus
species. This enzyme performs the fourth step in IMP
biosynthesis (the precursor of all purines) from PRPP
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 1239
Score = 30.2 bits (68), Expect = 0.41
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 42 GECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQILLTSTAQ---LDSKLRED 98
G+ +EE++KI NP +R+KD+ GK + S + L D
Sbjct: 121 GDLDDEELNKIKNYYINPVD--------SREKDLTTGKALEEFSESPKEVETLTGFESYD 172
Query: 99 LERLKKIRAHRGM 111
E L K +A +G+
Sbjct: 173 AEDLAKFKAEQGL 185
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 29.1 bits (66), Expect = 0.71
Identities = 9/36 (25%), Positives = 24/36 (66%)
Query: 23 RRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTN 58
+R + ++L++ ID + A + S++E+ K++ ++ N
Sbjct: 296 KRLAELLLEQLGIDPDLPAAQLSKKEIKKLVQLLKN 331
>gnl|CDD|239623 cd03565, VHS_Tom1, VHS domain family, Tom1 subfamily; The VHS
domain is an essential part of Tom1 (Target of myb1 -
retroviral oncogene) protein. The VHS domain has a
superhelical structure similar to the structure of the
ARM repeats and is present at the very N-termini of
proteins. It is a right-handed superhelix of eight
alpha helices. The VHS domain has been found in a
number of proteins, some of which have been implicated
in intracellular trafficking and sorting. The VHS
domain of the Tom1 protein is essential for the
negative regulation of Interleukin-1 and Tumor Necrosis
Factor-induced signaling pathways.
Length = 141
Score = 27.8 bits (62), Expect = 1.4
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 9 RKVMFALT----AIKGCGRRFSNIVLKK 32
++VM LT +K CG RF +V KK
Sbjct: 54 KEVMLTLTVLETCVKNCGHRFHVLVAKK 81
>gnl|CDD|181843 PRK09423, gldA, glycerol dehydrogenase; Provisional.
Length = 366
Score = 27.9 bits (63), Expect = 2.1
Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 30 LKKADIDLNKRA--GECSEEEVDKIITI 55
LK+A + + GECS+ E+D+++ I
Sbjct: 52 LKEAGLTVVFEVFNGECSDNEIDRLVAI 79
>gnl|CDD|227013 COG4667, COG4667, Predicted esterase of the alpha-beta hydrolase
superfamily [General function prediction only].
Length = 292
Score = 27.3 bits (61), Expect = 3.0
Identities = 12/27 (44%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 43 ECSEEEVDKIITIMTNPRQY-KIPDWF 68
E DKI+ I T P Y K P WF
Sbjct: 179 EAIRLGADKIVVIRTRPSDYYKTPQWF 205
>gnl|CDD|217133 pfam02598, Methyltrn_RNA_3, Putative RNA methyltransferase. This
family has a TIM barrel-like fold with a deep C-terminal
trefoil knot. The arrangement of its hydrophilic and
hydrophobic surfaces are opposite to that of the classic
TIM barrel proteins. It is likely to bind RNA, and may
function as a methyltransferase.
Length = 283
Score = 26.9 bits (60), Expect = 3.2
Identities = 14/62 (22%), Positives = 20/62 (32%), Gaps = 10/62 (16%)
Query: 69 LNRQKDIVDGKYSQILLTSTAQLDSKLRE------DLERLKKIRAH----RGMRHYWGLR 118
+ K Y I L +LDS + ++ K G YWG +
Sbjct: 120 IRMSKPGGKTSYVNIGLDKPVELDSLVPPGTRVTVRIKSQKGKVVSPAEPYGEGLYWGYK 179
Query: 119 VR 120
VR
Sbjct: 180 VR 181
>gnl|CDD|223844 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
biogenesis, outer membrane].
Length = 459
Score = 27.2 bits (61), Expect = 3.8
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 111 MRHYWGLRVRGQHTKTT 127
MR + V G H KTT
Sbjct: 104 MRFRTSIAVAGTHGKTT 120
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 26.8 bits (60), Expect = 4.5
Identities = 11/37 (29%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 29 VLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIP 65
+L+KA +D NK+ E + EE+++++ ++YK
Sbjct: 277 ILEKAGLDPNKKPKELTREELERLVEAF---KKYKFM 310
>gnl|CDD|235393 PRK05294, carB, carbamoyl phosphate synthase large subunit;
Reviewed.
Length = 1066
Score = 26.6 bits (60), Expect = 5.6
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 63 KIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKK 104
KI WFL + ++IV+ + L + LD E L K+
Sbjct: 454 KIDPWFLEQIEEIVE--LEEELKENGLPLD---AELLREAKR 490
>gnl|CDD|173929 cd08170, GlyDH, Glycerol dehydrogenases (GlyDH) catalyzes
oxidation of glycerol to dihydroxyacetone in glycerol
dissmilation. Glycerol dehydrogenases (GlyDH) is a key
enzyme in the glycerol dissimilation pathway . In
anaerobic conditions, many microorganisms utilize
glycerol as a source of carbon through coupled
oxidative and reductive pathways. One of the pathways
involves the oxidation of glycerol to dihydroxyacetone
with the reduction of NAD+ to NADH catalyzed by
glycerol dehydrogenases. Dihydroxyacetone is then
phosphorylated by dihydroxyacetone kinase and enters
the glycolytic pathway for further degradation. The
activity of GlyDH is zinc-dependent. The zinc ion plays
a role in stabilizing an alkoxide intermediate at the
active site.
Length = 351
Score = 26.3 bits (59), Expect = 5.8
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 30 LKKADIDLN--KRAGECSEEEVDKIITIM 56
L A ID GEC+ E++++ I
Sbjct: 45 LAAAGIDARFEVFGGECTRAEIERLAEIA 73
>gnl|CDD|217231 pfam02787, CPSase_L_D3, Carbamoyl-phosphate synthetase large chain,
oligomerisation domain. Carbamoyl-phosphate synthase
catalyzes the ATP-dependent synthesis of
carbamyl-phosphate from glutamine or ammonia and
bicarbonate. The carbamoyl-phosphate synthase (CPS)
enzyme in prokaryotes is a heterodimer of a small and
large chain.
Length = 122
Score = 25.2 bits (56), Expect = 8.4
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 63 KIPDWFLNRQKDIVDGKYSQILLTSTAQLDSKLREDLERLKK 104
KI WFL + K+IV+ L + L E L + KK
Sbjct: 34 KIDPWFLEKIKEIVE------LEKELKKGLPLLDELLRKAKK 69
>gnl|CDD|221427 pfam12114, Period_C, Period protein 2/3C-terminal region. This
domain is found in eukaryotes. This domain is typically
between 164 to 200 amino acids in length. This domain is
found associated with pfam08447.
Length = 190
Score = 25.5 bits (56), Expect = 9.0
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 91 LDSKLREDLERLKKIRAHR 109
L+ L+ED E+LK ++ +
Sbjct: 113 LEEVLKEDREKLKSMQKQQ 131
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. The seed alignment is built from bacterial
sequences only. Eukaryotic homologs include Nop2, a
protein required for processing pre-rRNA, that is likely
also a rRNA methyltransferase, although the fine
specificity may differ. Cutoff scores are set to avoid
treating archaeal and eukaroytic homologs automatically
as functionally equivalent, although they may have very
similar roles [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 26.0 bits (57), Expect = 9.5
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 11/61 (18%)
Query: 23 RRFSNIVLKKADIDLNKRAGECSEEEVDKIITIMTNPRQYKIPDWFLNRQKDIVDGKYSQ 82
+ N VL++ +R E E + +Y P+W + R + G++
Sbjct: 107 KGLVNGVLRRF-----QREQEELLAEFNA------LDARYLHPEWLVKRLQKAYPGQWQS 155
Query: 83 I 83
I
Sbjct: 156 I 156
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 0.136 0.396
Gapped
Lambda K H
0.267 0.0865 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,172,964
Number of extensions: 647263
Number of successful extensions: 753
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 45
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.3 bits)