RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029588
(191 letters)
>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
Provisional.
Length = 191
Score = 319 bits (819), Expect = e-113
Identities = 157/191 (82%), Positives = 175/191 (91%), Gaps = 1/191 (0%)
Query: 2 QKALAGLRRINLEGLRWRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLN 61
+KALAGLRRINLEGLRWRVFDAKGQVLGRLASQ++TV+QGKDKPTYAPNRDDGD+CIVLN
Sbjct: 1 KKALAGLRRINLEGLRWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLN 60
Query: 62 AKDICVTGRKLKNKVYYWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDR 121
AKDI VTGRKL +K Y WHTGYIGHLKER+LK+QM +DPTE IRKAVLRMLPRN+LRDDR
Sbjct: 61 AKDISVTGRKLTDKFYRWHTGYIGHLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDDR 120
Query: 122 DRKLRIFPGSEHPFGDRPLEPYVMPPRRVRELRPRVRRAMIREQKKAEMQ-QSNKDMRKN 180
DRKLRIF GSEHPFGD+PLEP+VMPPR+VRE+RPR RRAMIR QKKAE + Q+ + RK
Sbjct: 121 DRKLRIFAGSEHPFGDKPLEPFVMPPRQVREMRPRARRAMIRAQKKAEQREQAANEKRKG 180
Query: 181 RKKEVEAEVTA 191
+KKEVE EVTA
Sbjct: 181 KKKEVEVEVTA 191
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 172 bits (440), Expect = 8e-56
Identities = 59/117 (50%), Positives = 84/117 (71%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W V DA+G+VLGRLAS+VA++++GK KPT+ P+ D GD IV+NA+ + +TG+KL +K+Y
Sbjct: 15 WYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIY 74
Query: 78 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 134
Y H+GY G LKE T E + + P I KAV MLP+N L +KL+++ G+EHP
Sbjct: 75 YRHSGYPGGLKEITFGELLAKKPERVIEKAVKGMLPKNPLGRAMFKKLKVYAGAEHP 131
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 164 bits (418), Expect = 7e-53
Identities = 61/126 (48%), Positives = 82/126 (65%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W V DAKGQ+LGRLAS+VA +++GK KPTY P+ D GD +V+NA+ I +TG+K K Y
Sbjct: 1 WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTGKKRDQKKY 60
Query: 78 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPFGD 137
Y HTGY G LK T K +ER P + +AV MLP+NKL ++L+++ GS HP
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHAA 120
Query: 138 RPLEPY 143
+ E
Sbjct: 121 QKPEVL 126
>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 = 158 bits (402), Expect = 2e-50
Identities = 57/114 (50%), Positives = 77/114 (67%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W V DAKGQVLGRLAS+VA ++ GK KPTY P+ D GD +V+NA+ I +TG+K + KVY
Sbjct: 1 WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60
Query: 78 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 131
Y HTGY G LK T R P +++AV MLP+NKL ++L+++ G+
Sbjct: 61 YRHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLPKNKLGRAALKRLKVYEGA 114
>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 = 149 bits (379), Expect = 8e-47
Identities = 60/118 (50%), Positives = 82/118 (69%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W V DA G+ LGRLAS+VA +++GK KPTY P+ D GD IV+NA+ + +TG+KL+ KVY
Sbjct: 13 WYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVY 72
Query: 78 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHPF 135
Y H+GY G LK RT +E + R P + AV MLP+N+L +KL+++ GSEHP
Sbjct: 73 YRHSGYPGGLKSRTFEEMIARKPERVLEHAVKGMLPKNRLGRKLFKKLKVYAGSEHPH 130
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 135 bits (343), Expect = 4e-41
Identities = 55/118 (46%), Positives = 77/118 (65%), Gaps = 1/118 (0%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W V DA+G+VLGRLAS+VA ++GK KPTY P+ D GD IV+NA+ + +TG+KL +K Y
Sbjct: 15 WYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKY 74
Query: 78 YWHTGYIGHLKERTLKEQME-RDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 134
Y H+GY G LK T + R P + +AV MLP+N L ++L+++ G HP
Sbjct: 75 YRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKRLKVYAGIPHP 132
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 121 bits (305), Expect = 2e-35
Identities = 53/117 (45%), Positives = 72/117 (61%)
Query: 18 WRVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVY 77
W + DAK Q LGRLA+++A++++GK+KP+Y P+ D GD IV+NA+ I VTG K K Y
Sbjct: 16 WYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTGNKTSQKFY 75
Query: 78 YWHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGSEHP 134
H+G G LK T +E R P I KAV MLP+ L KL+++ G HP
Sbjct: 76 VRHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLPKGPLGRKLFTKLKVYKGESHP 132
>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 = 44.0 bits (104), Expect = 4e-06
Identities = 32/124 (25%), Positives = 50/124 (40%), Gaps = 13/124 (10%)
Query: 19 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY 78
V D G +LGRLAS VA + +G+ +V+NA+ I ++G +NK+ Y
Sbjct: 1 TVIDGSGHILGRLASVVAKQLL------------NGEKVVVVNAEKIVISGNFYRNKLKY 48
Query: 79 WHTGYIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRD-RKLRIFPGSEHPFGD 137
L R P+ R+ V MLP R R+L+++ G
Sbjct: 49 KEFLRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDK 108
Query: 138 RPLE 141
+
Sbjct: 109 KKRV 112
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 36.0 bits (84), Expect = 0.004
Identities = 31/131 (23%), Positives = 55/131 (41%), Gaps = 26/131 (19%)
Query: 19 RVFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYY 78
V DA+GQ+LGRLAS VA + +G+ +++NA+ +TG + +V
Sbjct: 5 VVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGN--RERVIE 50
Query: 79 WHTGYIGHLKERTLKEQME------RDPTEAIRKAVLRMLPRNKLRDDRD--RKLRIFPG 130
Y + + R P ++ + MLP K R R+ ++L+++ G
Sbjct: 51 K---YKQRRERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPR-GREALKRLKVYVG 106
Query: 131 SEHPFGDRPLE 141
+ E
Sbjct: 107 VPKELEGKEFE 117
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 33.1 bits (76), Expect = 0.049
Identities = 34/127 (26%), Positives = 54/127 (42%), Gaps = 33/127 (25%)
Query: 20 VFDAKGQVLGRLASQVATVVQGKDKPTYAPNRDDGDMCIVLNAKDICVTGRKLKNKVYYW 79
V D KG +LGRLAS VA + G +V+ +D+ ++G +NKV Y
Sbjct: 7 VIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNKVKY- 53
Query: 80 HTGYIGHLKERTLKEQME----------RDPTEAIRKAVLRMLPRNKLRDDRD-RKLRIF 128
E L+++M R P++ + V MLP R ++L++F
Sbjct: 54 ---------EEFLRKRMNTNPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVF 104
Query: 129 PGSEHPF 135
G P+
Sbjct: 105 EGVPAPY 111
>gnl|CDD|216872 pfam02096, 60KD_IMP, 60Kd inner membrane protein.
Length = 193
Score = 29.0 bits (66), Expect = 1.1
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 148 RRVRELRPRVRRAMIREQKKAEMQQSNKDMRKNRKKE 184
+++EL+P ++ I+E+ K + Q+ ++M K K+
Sbjct: 30 AKMQELQPEIKE--IQEKYKDDPQKLQQEMMKLYKEH 64
>gnl|CDD|225914 COG3379, COG3379, Uncharacterized conserved protein [Function
unknown].
Length = 471
Score = 29.0 bits (65), Expect = 1.8
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 3/74 (4%)
Query: 75 KVYYWHTGYIG---HLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRDDRDRKLRIFPGS 131
K YYW GY +L+ R + + + + + + L + + D + R++
Sbjct: 311 KAYYWGGGYSRIYINLEGREPRGIVGKKEFDKVIDELTINLEKIEGPDGEEVIFRVYYPE 370
Query: 132 EHPFGDRPLEPYVM 145
E GDR P +M
Sbjct: 371 ELYPGDRGAGPDLM 384
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 28.3 bits (64), Expect = 1.8
Identities = 12/33 (36%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 157 VRRAMIREQKKAEMQQSNKDMRKNRKKEVEAEV 189
+R+A+ EQ K+E++Q K + + K+E+E V
Sbjct: 112 MRKALQAEQGKSELEQEIKKL-EEEKEELEKRV 143
>gnl|CDD|148609 pfam07100, ASRT, Anabaena sensory rhodopsin transducer. The family
of bacterial Anabaena sensory rhodopsin transducers are
likely to bind sugars or related metabolites. The entire
protein is comprised of a single globular domain with an
eight-stranded beta-sandwich fold. There are a few
characteristics which define this beta-sandwich fold as
being distinct from other so-named folds, and these are:
1) a well conserved tryptophan, usually following a
polar residue, present at the start of the first strand;
this tryptophan appears to be central to a hydrophobic
interaction required to hold the two beta-sheets of the
sandwich together, and 2) a nearly absolutely conserved
asparagine located at the end of the second beta-strand,
that hydrogen bonds with the backbone carbonyls of the
residues 2 and 4 positions downstream from it, thereby
stabilising the characteristic tight turn between
strands 2 and 3 of the structure.
Length = 120
Score = 27.6 bits (62), Expect = 2.3
Identities = 16/40 (40%), Positives = 20/40 (50%), Gaps = 11/40 (27%)
Query: 120 DRDRKLRI--FPGSEHPFGDR-PLEPY--VMPPRRVRELR 154
D D L+I + F DR P+ PY +P RR R LR
Sbjct: 38 DEDAHLKITVY------FEDRDPVGPYEVTVPARRTRHLR 71
>gnl|CDD|218715 pfam05719, GPP34, Golgi phosphoprotein 3 (GPP34). This family
consists of several eukaryotic GPP34 like proteins.
GPP34 localises to the Golgi complex and is conserved
from yeast to humans. The cytosolic-ally exposed
location of GPP34 predict a role for a novel coat
protein in Golgi trafficking.
Length = 205
Score = 28.0 bits (63), Expect = 2.6
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 88 KERTLKEQMERDPTEAIRKAVL-RMLPRNKLRDDRDRKLRIFPGSEHPFGDRPLEPYVMP 146
+ R++K+ +ER +R+ V ++ R LR ++ R L +FP + +P D
Sbjct: 73 RPRSVKDWLERLSGRGLRERVAAGLVARGILRREKRRFLGLFPTTRYPLVD--------- 123
Query: 147 PRRVRELRPRVRRA 160
P LR R+R A
Sbjct: 124 PAAEAALRARLRAA 137
>gnl|CDD|220884 pfam10826, DUF2551, Protein of unknown function (DUF2551). This
Archaeal family of proteins has no known function.
Length = 83
Score = 26.5 bits (59), Expect = 3.3
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 92 LKEQMERDPTEAIRKAVLRMLPRNK 116
LK+ + RD IR+AVLR+ + K
Sbjct: 1 LKKYLSRDKN-GIRRAVLRLFLKVK 24
>gnl|CDD|227127 COG4789, EscV, Type III secretory pathway, component EscV
[Intracellular trafficking and secretion].
Length = 689
Score = 27.3 bits (61), Expect = 5.6
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 83 YIGHLKERTLKEQMERDPTEAIRKAVLRMLPRNKLRD 119
+IG + R L +QMER ++ + K V R +P ++ +
Sbjct: 496 FIGIQETRYLLDQMERKYSDLV-KEVQRQIPLQRIAE 531
>gnl|CDD|206172 pfam14002, YniB, YniB-like protein. The YniB-like protein family
includes the E. coli YniB protein, which is functionally
uncharacterized. This family of proteins is found in
bacteria. Proteins in this family are approximately 180
amino acids in length. This family of proteins are
integral membrane proteins.
Length = 166
Score = 26.5 bits (59), Expect = 7.0
Identities = 6/33 (18%), Positives = 17/33 (51%)
Query: 148 RRVRELRPRVRRAMIREQKKAEMQQSNKDMRKN 180
R+V+ +R + +I E+ K ++ + + +
Sbjct: 99 RQVKFIREGIEDQLILEKAKGVEGRTREQLEEK 131
>gnl|CDD|153361 cd07677, F-BAR_FCHSD2, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH and double SH3
domains 2 (FCHSD2). F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. FCH and double SH3 domains 2 (FCHSD2)
contains an N-terminal F-BAR domain and two SH3 domains
at the C-terminus. It has been characterized only in
silico, and its biological function is still unknown.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 260
Score = 27.0 bits (59), Expect = 7.2
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 146 PPRRVRELRPRVRRAMIREQKK--AEMQQSNKDMRKNRKKEVEAEVTA 191
P R VR + + + + + K AE+Q++ KD+ K +KK E E A
Sbjct: 100 PARTVRLYKEQQLKRCVDQLTKIQAELQETVKDLAKGKKKYFETEQMA 147
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
0.321 0.136 0.402
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,050,519
Number of extensions: 959354
Number of successful extensions: 1338
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1325
Number of HSP's successfully gapped: 59
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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: 56 (25.3 bits)