RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028707
(205 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 247 bits (633), Expect = 3e-84
Identities = 112/181 (61%), Positives = 138/181 (76%), Gaps = 1/181 (0%)
Query: 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69
K +V+D + H+LGRLASV+AKELL GQK+VVVRCE++ ISG L R K+KY FLRKRMNT
Sbjct: 4 KVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNT 63
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDAL 129
P GP H RAP+ I WRT+RGM+PHKTKRGAAAL RLK +EGVPAPYDK KR+VIP AL
Sbjct: 64 NPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSAL 123
Query: 130 KVLRLQKGHKYCLLGRLSSEVGWNYYDTI-KVSKKRKERAQVAYERRKQLAKLRVKAEKA 188
+VLRL+ Y +LG LS+ VGW Y D + K+ +KRKERA Y+++ +L K +A K
Sbjct: 124 RVLRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKERAAAYYKKKVKLRKAWKEARKK 183
Query: 189 A 189
A
Sbjct: 184 A 184
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 169 bits (431), Expect = 2e-54
Identities = 82/143 (57%), Positives = 99/143 (69%), Gaps = 1/143 (0%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
V+D H+LGRLASV+AK+LLNG+KVVVV E+I ISG R K+KY FLRKR T P
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 72 SHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKV 131
GP RAP++I RT+RGM+PHKT RG AAL RLK Y G+P DK KR+V+P+AL V
Sbjct: 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-V 119
Query: 132 LRLQKGHKYCLLGRLSSEVGWNY 154
RL KY LG L+ +GW Y
Sbjct: 120 SRLSPTRKYVTLGELAKFLGWKY 142
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 125 bits (316), Expect = 3e-37
Identities = 52/114 (45%), Positives = 64/114 (56%), Gaps = 13/114 (11%)
Query: 12 VVVDARHHMLGRLASVLAKELLN------------GQKVVVVRCEEICISGGLVRQKMKY 59
V+DA+ +LGRLAS +AK LL G VVVV E+I I+G RQK+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 60 MRFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGV 113
P+ GP+H RAP +IL R +RGM+P K K G AAL RLK YEG
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 115 bits (290), Expect = 3e-33
Identities = 48/129 (37%), Positives = 63/129 (48%), Gaps = 15/129 (11%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V+DA+ +LGRLAS +AK L G VVV+ E+I ++G R + KY
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTG-KKRDQKKY 60
Query: 60 MR-FLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
R P+ R P +IL R +RGM+P K K G AAL RLK Y G P P+
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLP-KNKLGRAALKRLKVYAGSPHPHA 119
Query: 119 KTKRMVIPD 127
K V+
Sbjct: 120 AQKPEVLEI 128
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 108 bits (273), Expect = 2e-30
Identities = 59/144 (40%), Positives = 81/144 (56%), Gaps = 3/144 (2%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
VV+DA +LGRLAS +AK LL G++VV+V E+ I+G R KY + + + P
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 72 SHGPIHF-RAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALK 130
+ R P +I RTIRGM+P+K RG AL RLK Y GVP + + VI +A
Sbjct: 65 YRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD- 123
Query: 131 VLRLQKGHKYCLLGRLSSEVGWNY 154
+ RL KY LG +S E+G +
Sbjct: 124 LSRL-STIKYVTLGEVSKELGAKF 146
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 98.1 bits (245), Expect = 3e-26
Identities = 48/138 (34%), Positives = 68/138 (49%), Gaps = 18/138 (13%)
Query: 12 VVVDARHHMLGRLASVLAKELLN------------GQKVVVVRCEEICISGGLVRQKMKY 59
V+DA +LGRLAS +AK L G V+V+ E++ I+G + K Y
Sbjct: 16 YVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYY 75
Query: 60 MRFLRKRMNTKPS-HGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
P+ GP+ R P +IL R +RGM+P K G AAL RLK Y G+P P+
Sbjct: 76 RHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLP-KNPLGRAALKRLKVYAGIPHPH- 133
Query: 119 KTKRMVIPDALKVLRLQK 136
P+AL++ L+
Sbjct: 134 ---EAQKPEALELKLLKG 148
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 43.5 bits (104), Expect = 8e-06
Identities = 30/123 (24%), Positives = 53/123 (43%), Gaps = 33/123 (26%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V+DA +LGRLAS +A L G V+V+ E++ ++G + K+ Y
Sbjct: 16 YVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYY 75
Query: 60 --------MRF--LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKA 109
++ + + K P +++ + ++GM+P K G A +LK
Sbjct: 76 RHSGYPGGLKEITFGELLAKK----------PERVIEKAVKGMLP-KNPLGRAMFKKLKV 124
Query: 110 YEG 112
Y G
Sbjct: 125 YAG 127
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 43.1 bits (102), Expect = 1e-05
Identities = 33/122 (27%), Positives = 52/122 (42%), Gaps = 33/122 (27%)
Query: 13 VVDARHHMLGRLASVLAKELLNGQK------------VVVVRCEEICISGGLVRQKMKYM 60
VVDA LGRLAS +A+ L K V+V+ E++ ++G + QK+ Y
Sbjct: 15 VVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR 74
Query: 61 ----------RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAY 110
R + + R P ++L ++GM+P K + G +LK Y
Sbjct: 75 HSGYPGGLKSRTFEEMIA----------RKPERVLEHAVKGMLP-KNRLGRKLFKKLKVY 123
Query: 111 EG 112
G
Sbjct: 124 AG 125
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 40.0 bits (94), Expect = 2e-04
Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 25/118 (21%)
Query: 13 VVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYM 60
++DA+ LGRLA+ +A L G V+V+ E+I ++G
Sbjct: 18 IIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTG-----NKTSQ 72
Query: 61 RFLRKRMNTKPSHGPI------HFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
+F R + +P I R P +I+ + ++GM+P K G +LK Y+G
Sbjct: 73 KFYV-RHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKG 128
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 30.8 bits (71), Expect = 0.50
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 170 VAYERRKQLAKLRVKAEKAAEERLGPQLEIIAP 202
V R ++ K+R KAE+AAEER+ L+ + P
Sbjct: 108 VKMVREEKREKVREKAEEAAEERI---LDALLP 137
>gnl|CDD|233898 TIGR02500, type_III_yscD, type III secretion apparatus protein,
YscD/HrpQ family. This family represents a conserved
protein of bacterial type III secretion systems. Gene
symbols are variable from species to species. Members
are designated YscD in Yersinia, HrpQ in Pseudomonas
syringae, and EscD in enteropathogenic Escherichia coli.
In the Chlamydiae, this model describes the C-terminal
400 residues of a longer protein [Protein fate, Protein
and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 410
Score = 29.7 bits (67), Expect = 1.1
Identities = 21/103 (20%), Positives = 36/103 (34%), Gaps = 15/103 (14%)
Query: 5 SGICAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLR 64
+ R+V A + +LAS+L+ L G V EI +SG L +K ++ L
Sbjct: 267 VPLAGWRIVRVASDVI-AQLASLLSDAGLLGVVTVTESGREIALSGQLDSEKRSRLQELL 325
Query: 65 KRMNTK---------PSHGP---IHFRAPAKILWRTIRGMIPH 95
+ + P + +I G P+
Sbjct: 326 AAFKQRDGVIPDVVLQNIPAADGTSDELPFPV--VSISGSGPN 366
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 28.7 bits (64), Expect = 2.6
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 83 KILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCL 142
+ W ++ G++ + + L L E + D ++R+++P A ++R L
Sbjct: 181 DVFWSSMWGILLNDERLRTGVLNSLMREENNDSHMDWSERLILPHAGLMVR-------AL 233
Query: 143 LGRLSSE 149
L
Sbjct: 234 CAGLGDN 240
>gnl|CDD|236526 PRK09458, pspB, phage shock protein B; Provisional.
Length = 75
Score = 26.4 bits (59), Expect = 3.7
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 163 KRKERAQVAYERRKQLAKLRVKAEKAAE 190
KR+ ++ E +++LA+L KAE+ E
Sbjct: 29 KRQGSQGLSQEEQQRLAQLTEKAERMRE 56
>gnl|CDD|119400 cd06661, GGCT_like, GGCT-like domains, also called AIG2-like
family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes
the formation of pyroglutamic acid (5-oxoproline) from
dipeptides containing gamma-glutamyl, and is a dimeric
protein. In Homo sapiens, the protein is encoded by the
gene C7orf24, and the enzyme participates in the
gamma-glutamyl cycle. Hereditary defects in the
gamma-glutamyl cycle have been described for some of the
genes involved, but not for C7orf24. The synthesis and
metabolism of glutathione
(L-gamma-glutamyl-L-cysteinylglycine) ties the
gamma-glutamyl cycle to numerous cellular processes;
glutathione acts as a ubiquitous reducing agent in
reductive mechanisms involved in protein and DNA
synthesis, transport processes, enzyme activity, and
metabolism. AIG2 (avrRpt2-induced gene) is an
Arabidopsis protein that exhibits RPS2- and
avrRpt2-dependent induction early after infection with
Pseudomonas syringae pv maculicola strain ES4326
carrying avrRpt2. avrRpt2 is an avirulence gene that can
convert virulent strains of P. syringae to avirulence on
Arabidopsis thaliana, soybean, and bean. The family also
includes bacterial tellurite-resistance proteins (trgB);
tellurium (Te) compounds are used in industrial
processes and had been used as antimicrobial agents in
the past. Some members have been described proteins
involved in cation transport (chaC).
Length = 99
Score = 26.5 bits (59), Expect = 4.0
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 101 AAALARLKAYEGVPAPYDKTKRMVIPDALKVLR 133
LARL A+EGVP Y + + V + + +
Sbjct: 61 PEDLARLDAFEGVPGGYRREEVEVELEDGEGVE 93
>gnl|CDD|222242 pfam13584, BatD, Oxygen tolerance. This family of proteins carries
up to three membrane spanning regions and is involved in
tolerance to oxygen in in Bacteroides spp.
Length = 488
Score = 27.2 bits (61), Expect = 6.1
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 162 KKRKERAQVAYERRKQLAKLRVKAEKAAEERLG 194
K+R A VA R K+ KL K K A++ L
Sbjct: 451 KRRARNADVAGNRTKKANKLAKKRLKEAKKALA 483
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 27.2 bits (61), Expect = 7.1
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 170 VAYERRKQLAKLRVKAEKAAEERL 193
V R +++ K++ KAE+ AEER+
Sbjct: 108 VKLVREEKIEKVKDKAEELAEERI 131
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 26.0 bits (58), Expect = 7.5
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 21 LGRLASVLAKELLNGQKVVVV 41
GR+ LA+EL G VVV
Sbjct: 6 YGRVGRSLAEELREGGPDVVV 26
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 26.9 bits (60), Expect = 9.9
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 6/56 (10%)
Query: 152 WNYYD--TIKVSKKRKERAQVAYERRKQLAKLRVKAEKAAEERLGPQLEIIAPIKY 205
W D ++ K+ KE A + +K+L KL+ + EK +E + I P ++
Sbjct: 545 WKLDDKEELQREKEEKE----ALKEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEF 596
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
0.323 0.137 0.402
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,592,577
Number of extensions: 1002587
Number of successful extensions: 1303
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1282
Number of HSP's successfully gapped: 50
Length of query: 205
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 113
Effective length of database: 6,857,034
Effective search space: 774844842
Effective search space used: 774844842
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)