RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8857
(133 letters)
>gnl|CDD|180007 PRK05309, PRK05309, 30S ribosomal protein S11; Validated.
Length = 128
Score = 228 bits (585), Expect = 4e-79
Identities = 84/126 (66%), Positives = 104/126 (82%)
Query: 8 TNARIRKKIKKHITEGVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSRKSTPFAA 67
++KK+KK+I GVAHIHA+FNNTI+TITDR+G +SWAS+G + FKGSRKSTP+AA
Sbjct: 3 KKKTVKKKVKKNIPSGVAHIHATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAA 62
Query: 68 QVAAESAGKIAIEHGIKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRP 127
QVAAE A K A EHG+K +EV +KGPG GRES++RAL G+++T I+DVTPIPHNGCRP
Sbjct: 63 QVAAEDAAKKAKEHGMKTVEVFVKGPGSGRESAIRALQAAGLEVTSIKDVTPIPHNGCRP 122
Query: 128 SKRRRV 133
KRRRV
Sbjct: 123 PKRRRV 128
>gnl|CDD|223178 COG0100, RpsK, Ribosomal protein S11 [Translation, ribosomal
structure and biogenesis].
Length = 129
Score = 192 bits (491), Expect = 7e-65
Identities = 89/124 (71%), Positives = 107/124 (86%)
Query: 10 ARIRKKIKKHITEGVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSRKSTPFAAQV 69
AR +KK+KK+I +GVAHIHASFNNTI+TITD G + WASSG + FKGSRKSTP+AAQ+
Sbjct: 6 ARKKKKVKKNIADGVAHIHASFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQL 65
Query: 70 AAESAGKIAIEHGIKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRPSK 129
AAE A K A EHGIK++EV++KGPGPGRE+++RAL G+KIT+IEDVTPIPHNGCRP K
Sbjct: 66 AAEDAAKKAKEHGIKSVEVKVKGPGPGREAAIRALAAAGLKITRIEDVTPIPHNGCRPPK 125
Query: 130 RRRV 133
RRRV
Sbjct: 126 RRRV 129
>gnl|CDD|188357 TIGR03632, bact_S11, 30S ribosomal protein S11. This model
describes the bacterial 30S ribosomal protein S11.
Cutoffs are set such that the model excludes archaeal
and eukaryotic ribosomal proteins, but many chloroplast
and mitochondrial equivalents of S11 are detected
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 108
Score = 188 bits (480), Expect = 2e-63
Identities = 73/108 (67%), Positives = 91/108 (84%)
Query: 23 GVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSRKSTPFAAQVAAESAGKIAIEHG 82
GVAHIHA+FNNTI+TITD +G LSWAS+G+V FKGS+KSTP+AAQ+AAE A K A E G
Sbjct: 1 GVAHIHATFNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFG 60
Query: 83 IKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRPSKR 130
+K ++V +KGPG GRES++RAL G+++T I+DVTPIPHNGCRP KR
Sbjct: 61 MKTVDVYVKGPGAGRESAIRALQAAGLEVTSIKDVTPIPHNGCRPPKR 108
>gnl|CDD|189537 pfam00411, Ribosomal_S11, Ribosomal protein S11.
Length = 109
Score = 165 bits (421), Expect = 2e-54
Identities = 77/109 (70%), Positives = 90/109 (82%)
Query: 23 GVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSRKSTPFAAQVAAESAGKIAIEHG 82
G+AHI ASFNNTIITITD G + W+S+G FKGSRKSTP+AAQ AAE+A KIA E G
Sbjct: 1 GIAHIQASFNNTIITITDVIGRVVLWSSAGGCGFKGSRKSTPYAAQTAAENAAKIAKEQG 60
Query: 83 IKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRPSKRR 131
IK LEV+IKGPGPGRES++RAL G++IT+I DVTPIPHNGCRP K+R
Sbjct: 61 IKALEVKIKGPGPGRESALRALARSGLRITRIRDVTPIPHNGCRPPKKR 109
>gnl|CDD|176982 CHL00041, rps11, ribosomal protein S11.
Length = 116
Score = 161 bits (411), Expect = 6e-53
Identities = 63/112 (56%), Positives = 87/112 (77%)
Query: 14 KKIKKHITEGVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSRKSTPFAAQVAAES 73
+K K+ I +GV HI ASFNNTI+T+TD +G +SW+S+G+ FKG+RK TPFAAQ AAE+
Sbjct: 5 RKSKRKIPKGVIHIQASFNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAEN 64
Query: 74 AGKIAIEHGIKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGC 125
A + I+ G+K EV IKGPG GR++++RA+ G+K++ I DVTP+PHNGC
Sbjct: 65 AIRTVIDQGMKRAEVMIKGPGLGRDTALRAIRRSGLKLSSIRDVTPMPHNGC 116
>gnl|CDD|236588 PRK09607, rps11p, 30S ribosomal protein S11P; Reviewed.
Length = 132
Score = 113 bits (286), Expect = 1e-33
Identities = 56/119 (47%), Positives = 78/119 (65%), Gaps = 9/119 (7%)
Query: 23 GVAHIHASFNNTIITITDRKGC-TLSWASSGSVNFKGSRKSTPFAAQVAAESAGKIAIEH 81
G+AHI+ASFNNTIITITD G T++ +S G V +S+P+AA AAE A + A E
Sbjct: 10 GIAHIYASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEK 69
Query: 82 GIKNLEVRIKG--------PGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRPSKRRR 132
GI + ++++ PGPG ++++RAL G++I +IEDVTPIPH+G RP RR
Sbjct: 70 GITGVHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGTRPPGGRR 128
>gnl|CDD|132667 TIGR03628, arch_S11P, archaeal ribosomal protein S11P. This model
describes exclusively the archaeal ribosomal protein
S11P. It excludes homologous ribosomal proteins S14 from
eukaryotes and S11 from bacteria [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 114
Score = 101 bits (253), Expect = 6e-29
Identities = 51/112 (45%), Positives = 73/112 (65%), Gaps = 9/112 (8%)
Query: 23 GVAHIHASFNNTIITITDRKGC-TLSWASSGSVNFKGSRKSTPFAAQVAAESAGKIAIEH 81
G+AHI++SFNNTIITITD G T++ +S G V +S+P+AA AA A + A E
Sbjct: 3 GIAHIYSSFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKER 62
Query: 82 GIKNLEVRIKGPG--------PGRESSVRALNNLGIKITQIEDVTPIPHNGC 125
GI L ++++ PG PG ++++RAL G++I +IEDVTPIPH+G
Sbjct: 63 GITGLHIKVRAPGGNGQKSPGPGAQAAIRALARAGLRIGRIEDVTPIPHDGT 114
>gnl|CDD|185465 PTZ00129, PTZ00129, 40S ribosomal protein S14; Provisional.
Length = 149
Score = 82.2 bits (203), Expect = 4e-21
Identities = 49/119 (41%), Positives = 68/119 (57%), Gaps = 9/119 (7%)
Query: 23 GVAHIHASFNNTIITITDRKGCTLSWASSGSVNFKGSR-KSTPFAAQVAAESAGKIAIEH 81
GVAHI ASFN+T I +TD G +G + K R +S+P+AA +AA+ E
Sbjct: 29 GVAHIFASFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKEL 88
Query: 82 GIKNLEVRI--------KGPGPGRESSVRALNNLGIKITQIEDVTPIPHNGCRPSKRRR 132
GI L +++ K PGPG ++++RAL G+KI +IEDVTPIP + R RR
Sbjct: 89 GINALHIKLRATGGVRTKTPGPGAQAALRALARAGLKIGRIEDVTPIPTDSTRRKGGRR 147
>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
Length = 409
Score = 29.3 bits (66), Expect = 0.48
Identities = 25/109 (22%), Positives = 35/109 (32%), Gaps = 24/109 (22%)
Query: 45 TLSWASSGSVNFKGSRKSTPFAAQVAAESAGKIAIEHGIKNLEVRIKGPGPGRESS---- 100
T+ A+ F ++ P + E+A +AI + L R K P P
Sbjct: 21 TVDEATFCGWLFNATKLVNPLFRLLDPETAHSLAISAAARGLVPREKRPDPSVLGVEVWG 80
Query: 101 -------------------VRALNNLGIKITQIEDVTPIPHNGCRPSKR 130
V L LG +I VTP+P G P R
Sbjct: 81 RTFSNPIGLAAGFDKNAEAVEGLLGLGFGFVEIGSVTPLPQPG-NPKPR 128
>gnl|CDD|197292 cd09196, PLDc_yTdp1_2, Catalytic domain, repeat 2, of yeast
tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat
2, of yeast tyrosyl-DNA phosphodiesterase (yTdp1, EC
3.1.4.-). yTdp1 is involved in the repair of
topoisomerase I DNA lesions by hydrolyzing the
topoisomerase from the 3'-end of the DNA during
double-strand break repair. Unlike human Tdp1 whose
substrate-binding pocket can accommodate a fairly large
topoisomerase I peptide fragment, yTdp1 has a preference
for substrates containing one to four amino acid
residues. The monomeric yTdp1 contains two copies of a
variant HKD motif (H-x-K-x(4)-D, where x represents any
amino acid residue), which consists of the highly
conserved histidine and lysine residues, but lacks the
aspartate residue that is well conserved in other
phospholipase D (PLD, EC 3.1.4.4) enzymes. Like other
PLD enzymes, yTdp1 may utilize a common two-step general
acid/base catalytic mechanism, involving a DNA-enzyme
intermediate to cleave phosphodiester bonds. A single
active site involved in phosphatidyl group transfer
would be formed by the two variant HKD motifs from the
N- and C-terminal domains in a pseudodimeric way.
Length = 200
Score = 28.1 bits (63), Expect = 1.1
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 8/53 (15%)
Query: 13 RKKIKKHITEGVAHIHASFNNTII--TITDRKGCTLSWASSGSVNFKGSRKST 63
+ +K H E + I+ T+ + + W S G +FK +R T
Sbjct: 72 IELLKSHQKEHNYKPY------IVYPTVEEIANSPVGWLSGGWFHFKYTRSDT 118
>gnl|CDD|119338 cd06570, GH20_chitobiase-like_1, A functionally uncharacterized
subgroup of the Glycosyl hydrolase family 20 (GH20)
catalytic domain found in proteins similar to the
chitobiase of Serratia marcescens, a
beta-N-1,4-acetylhexosaminidase that hydrolyzes the
beta-1,4-glycosidic linkages in oligomers derived from
chitin. Chitin is degraded by a two step process: i) a
chitinase hydrolyzes the chitin to oligosaccharides and
disaccharides such as di-N-acetyl-D-glucosamine and
chitobiose, ii) chitobiase then further degrades these
oligomers into monomers. This subgroup lacks the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases. The GH20 hexosaminidases are
thought to act via a catalytic mechanism in which the
catalytic nucleophile is not provided by solvent or the
enzyme, but by the substrate itself.
Length = 311
Score = 28.1 bits (63), Expect = 1.1
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 7 NTNARIRKKIKKHITEGVAHIHASFNNTIITITDRKG 43
N N RI+ +K+H + A + A FN + I + G
Sbjct: 164 NENPRIQAFMKEHGLKDAAALQAYFNQRVEKILSKHG 200
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 27.3 bits (61), Expect = 3.0
Identities = 19/49 (38%), Positives = 24/49 (48%), Gaps = 13/49 (26%)
Query: 76 KIAIEHGIKNLEVRIKGP-GPGRESSVRALNNLGIKITQIEDVTPIPHN 123
K A +HGI P GPGR S+ +L +KIT D+ PI H
Sbjct: 350 KWAKDHGI---------PVGPGRGSAAGSLVAYALKIT---DIDPIKHG 386
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 27.2 bits (60), Expect = 3.0
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 2/43 (4%)
Query: 80 EHGIKNLEVRIKGPG--PGRESSVRALNNLGIKITQIEDVTPI 120
E + + E I P ES V L+NL IKI++ E+V PI
Sbjct: 1115 EELMSSHENAIISPVGSSDFESFVSFLSNLLIKISKSENVFPI 1157
>gnl|CDD|173798 cd05562, Peptidases_S53_like, Peptidase domain in the S53 family.
Members of the peptidase S53 (sedolisin) family include
endopeptidases and exopeptidases. The S53 family
contains a catalytic triad Glu/Asp/Ser with an
additional acidic residue Asp in the oxyanion hole,
similar to that of Asn in subtilisin. The stability of
these enzymes may be enhanced by calcium, some members
have been shown to bind up to 4 ions via binding sites
with different affinity. Some members of this clan
contain disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values. Characterized sedolisins include Kumamolisin,
an extracellular calcium-dependent thermostable
endopeptidase from Bacillus. The enzyme is synthesized
with a 188 amino acid N-terminal preprotein region which
is cleaved after the extraction into the extracellular
space with low pH. One kumamolysin paralog,
kumamolisin-As, is believed to be a collagenase. TPP1 is
a serine protease that functions as a tripeptidyl
exopeptidase as well as an endopeptidase. Less is known
about PSCP from Pseudomonas which is thought to be an
aspartic proteinase.
Length = 275
Score = 26.5 bits (59), Expect = 4.3
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 36 ITITDRKGCTLSWASSGSVNFKGSRKSTPFAAQVAA 71
+T D T+ G NF G+ + P AA VAA
Sbjct: 193 VTAPDGVNGTVDGDGDGPPNFFGTSAAAPHAAGVAA 228
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 26.1 bits (58), Expect = 6.7
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 3/42 (7%)
Query: 83 IKNLEVRIKGPGPGRESSVRALNNLGIKITQIEDVTPIPHNG 124
+ N G E RALN L ++I + + VT I NG
Sbjct: 4 LSNATK-TFFKGTPLEK--RALNGLSLEIAEGDFVTVIGSNG 42
>gnl|CDD|237131 PRK12536, PRK12536, RNA polymerase sigma factor; Provisional.
Length = 181
Score = 25.8 bits (57), Expect = 6.7
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 71 AESAGKIAIEHGIKNLEVRIKG 92
+ESA K+ I G+K L +I+G
Sbjct: 158 SESAVKVGIHRGLKALAAKIRG 179
>gnl|CDD|223258 COG0180, TrpS, Tryptophanyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 314
Score = 26.0 bits (58), Expect = 6.9
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 5 LNNTNARIRKKIKKHITEGVAHI 27
L + IRKKIKK T+G I
Sbjct: 210 LLDDPKTIRKKIKKAATDGPTLI 232
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
0.316 0.131 0.376
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: 6,575,678
Number of extensions: 562321
Number of successful extensions: 673
Number of sequences better than 10.0: 1
Number of HSP's gapped: 666
Number of HSP's successfully gapped: 33
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
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: 53 (24.0 bits)