RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029052
(200 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 213 bits (544), Expect = 5e-71
Identities = 91/170 (53%), Positives = 122/170 (71%), Gaps = 4/170 (2%)
Query: 1 MKTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKI 60
MKTI SSE + IP+GV + + ++ + V G G+L+R F+HL +D L D + +K+
Sbjct: 1 MKTIFSSEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKD----GKYIKV 56
Query: 61 DAWFGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNF 120
+ WFG+ A IRT SH+ N++TGVTK ++YKMR VYAHFPIN++I + K+IEIRNF
Sbjct: 57 EMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNF 116
Query: 121 LGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSAALINQVGLC 170
LGEK+VR V ML GV V +SE VKDE+I+ G D+ELVSRSAALI+Q L
Sbjct: 117 LGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLV 166
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 166 bits (422), Expect = 1e-52
Identities = 83/168 (49%), Positives = 117/168 (69%), Gaps = 8/168 (4%)
Query: 4 ILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAW 63
I S +T+ IP+ V + + +I+ V+G RG L++D +HL LDF + R W
Sbjct: 3 IKSQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRV----NKKNRTFTAVRW 58
Query: 64 FGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGE 123
FGS+ ++ I TALSHV N+ITGVTKG+R+K+RF YAHFPI+ S+ N +EIRNFLGE
Sbjct: 59 FGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPISVSVENQL--VEIRNFLGE 116
Query: 124 KKVRKVDMLDGVTVVRSE--KVKDELILDGNDIELVSRSAALINQVGL 169
K+VR+ + D V V R++ KVKDEL+L+GND+E VSR AA+++Q+ L
Sbjct: 117 KRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCL 164
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 139 bits (352), Expect = 6e-42
Identities = 62/167 (37%), Positives = 101/167 (60%), Gaps = 13/167 (7%)
Query: 1 MKTILSSETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKI 60
M E ++IP+GV ++I ++ V+GP+G+L+RDF + + ++ E+ K+ I
Sbjct: 1 MVAAYIREEIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVT---ISVED---GKVVI 54
Query: 61 DAWFGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNF 120
+ F +KT A + T SH+ N+I GVT+G+ YK++ VY+HFP+ + + I NF
Sbjct: 55 ETEFARKKTKAMVGTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQVKV--QGNEVVIENF 112
Query: 121 LGEKKVRKVDMLDGVTVVRSEKVK-DELILDGNDIELVSRSAALINQ 166
LGEK R+ +L GV V KVK +++I++G D E V ++AA I Q
Sbjct: 113 LGEKSPRRAKILGGVKV----KVKGEDVIVEGIDKEDVGQTAANIEQ 155
>gnl|CDD|234296 TIGR03653, arch_L6P, archaeal ribosomal protein L6P. Members of
this protein family are the archaeal ribosomal protein
L6P. The top-scoring proteins not selected by this model
are eukaryotic cytosolic ribosomal protein L9. Bacterial
ribosomal protein L6 scores lower and is described by a
distinct model [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 170
Score = 128 bits (324), Expect = 5e-38
Identities = 59/160 (36%), Positives = 96/160 (60%), Gaps = 13/160 (8%)
Query: 8 ETMDIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSR 67
E ++IP+GV + I I+ V+GP+G+++R+ + ++ ++ E+ K+ I+ F +
Sbjct: 2 EEIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIE---ISVEDG---KVVIETDFARK 55
Query: 68 KTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVR 127
K A + T SH+ N+I GVT+G+ YKM+ VY+HFP+ + + I NFLGEK R
Sbjct: 56 KDKAMVGTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKV--EGNKVVIENFLGEKAPR 113
Query: 128 KVDMLDGVTVVRSEKVK-DELILDGNDIELVSRSAALINQ 166
+ + GV V KVK +E+I+ G D E V ++AA I Q
Sbjct: 114 RAKIPGGVKV----KVKGEEVIVTGIDKEDVGQTAANIEQ 149
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 116 bits (292), Expect = 6e-33
Identities = 39/156 (25%), Positives = 73/156 (46%), Gaps = 15/156 (9%)
Query: 12 IPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSA 71
IP GV + I +++ V+GP+G+L+R+F +++ E + ++ A
Sbjct: 11 IPAGVTVSIEGQVVTVKGPKGELTREFHD-----NVVKVEVEDNILVVRPVDGKRKR--A 63
Query: 72 AIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDM 131
T + + N++ GVT+G+ K+ V + GN + FLG +++
Sbjct: 64 LHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGGN------LELFLGYSHPVVIEI 117
Query: 132 LDGVTVVRSEKVKDELILDGNDIELVSRSAALINQV 167
+G+TV E++++G D ELV + AA I
Sbjct: 118 PEGITV--EVPGPTEIVVEGIDKELVGQVAANIRAA 151
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 50.5 bits (122), Expect = 4e-08
Identities = 21/80 (26%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 12 IPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSA 71
IP GV++ I+ ++ V+GP+G+LSR +T + +L + S++ A
Sbjct: 10 IPAGVEVTIDGNVVTVKGPKGELSRTLH------PGVTVKVEDG-QLTVSRPNDSKEARA 62
Query: 72 AIRTALSHVGNLITGVTKGY 91
T + + N++ GV++G+
Sbjct: 63 LHGTTRALINNMVIGVSEGF 82
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 49.3 bits (119), Expect = 1e-07
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 11 DIPDGVKIKINAKIIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTS 70
IP GV++ IN ++ V+GP+G+LSR +T + ++ + S+K
Sbjct: 10 AIPAGVEVTINGNVVTVKGPKGELSRTLN------PDVTVKVEDN-EITVTRPDDSKKAR 62
Query: 71 AAIRTALSHVGNLITGVTKGY 91
A T + + N++ GVT+G+
Sbjct: 63 ALHGTTRALINNMVVGVTEGF 83
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 46.8 bits (112), Expect = 1e-07
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 4/66 (6%)
Query: 102 FPINASIGNANKSIEIRNFLGEKKVRKVDMLDGVTVVRSEKVKDELILDGNDIELVSRSA 161
P+ + + LG K ++ GVTV + +I+ G D E V + A
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKVEK--ITVIIVSGIDKEKVGQFA 56
Query: 162 ALINQV 167
ALI
Sbjct: 57 ALIGTY 62
Score = 40.3 bits (95), Expect = 4e-05
Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 17/86 (19%)
Query: 12 IPDGVKIKINAKIIE-VEGPRGKLSRDFKH-LNLDFHLMTDEETGKRKLKIDAWFGSRK- 68
IP GV++ I+ + V GP+G+L+R+ + + K+ + G K
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKV----------EKITVIIVSGIDKE 50
Query: 69 ----TSAAIRTALSHVGNLITGVTKG 90
+A I T + + N+ GV+ G
Sbjct: 51 KVGQFAALIGTYRAPIPNMGKGVSYG 76
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 39.1 bits (92), Expect = 4e-04
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 15/89 (16%)
Query: 12 IPDGVKIKINAKIIEVEGPRGKLSRDF-KHLNLDFHLMTDEETGKRKLKIDAWFGSRKTS 70
IPD V + I+ +II+V+GP+G LSR + + E L + S+K
Sbjct: 11 IPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITI--------EIQDNSLFVSKKDESKKAR 62
Query: 71 A---AIRTALSHVGNLITGVTKGYRYKMR 96
A RT ++ N++ GV++G+ K+
Sbjct: 63 ALHGLYRTLIN---NMVIGVSEGFEKKLE 88
>gnl|CDD|189007 cd09600, M1_APN_1, Peptidase M1 family containing Aminopeptidase N.
This family contains aminopeptidase N (APN; CD13;
Alanyl aminopeptidase; EC 3.4.11.2), a Type II integral
membrane protease belonging to the M1 gluzincin family.
It includes bacterial-type alanyl aminopeptidases as
well as PfA-M1 aminopeptidase (Plasmodium
falciparum-type). APN consists of a small N-terminal
cytoplasmic domain, a single transmembrane domain and a
large extracellular ectodomain that contains the active
site. It preferentially cleaves neutral amino acids from
the N-terminus of oligopeptides and, in higher
eukaryotes, is present in a variety of human tissues and
cell types (leukocyte, fibroblast, endothelial and
epithelial cells). APN expression is dysregulated in
inflammatory diseases such as chronic pain, rheumatoid
arthritis, multiple sclerosis, systemic sclerosis,
systemic lupus erythematosus,
polymyositis/dermatomyosytis and pulmonary sarcoidosis,
and is enhanced in tumor cells such as melanoma, renal,
prostate, pancreas, colon, gastric and thyroid cancers.
It is predominantly expressed on stem cells and on cells
of the granulocytic and monocytic lineages at distinct
stages of differentiation, thus considered a marker of
differentiation. Thus, APN inhibition may lead to the
development of anti-cancer and anti-inflammatory drugs.
APNs are also present in many pathogenic bacteria and
represent potential drug targets, Some APNs have been
used commercially, such as one from Lactococcus lactis
used in the food industry. APN also serves as a receptor
for coronaviruses, although the virus receptor
interaction site seems to be distinct from the enzymatic
site and aminopeptidase activity is not necessary for
viral infection. APNs have also been extensively studied
as putative Cry toxin receptors. Cry1 proteins are
pore-forming toxins that bind to the midgut epithelial
cell membrane of susceptible insect larvae, causing
extensive damage. Several different toxins, including
Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have
been shown to bind to APNs; however, a direct role of
APN in cytotoxicity has been yet to be firmly
established.
Length = 861
Score = 30.7 bits (70), Expect = 0.48
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 135 VTVVRSEKVKDELILDGNDIELVS 158
+ VVR+ L+LDG D++LVS
Sbjct: 29 LQVVRNGGSGAPLVLDGEDLKLVS 52
>gnl|CDD|233858 TIGR02414, pepN_proteo, aminopeptidase N, Escherichia coli type.
The M1 family of zinc metallopeptidases contains a
number of distinct, well-separated clades of proteins
with aminopeptidase activity. Several are designated
aminopeptidase N, EC 3.4.11.2, after the Escherichia
coli enzyme, suggesting a similar activity profile (see
SP|P04825 for a description of catalytic activity). This
family consists of all aminopeptidases closely related
to E. coli PepN and presumed to have similar (not
identical) function. Nearly all are found in
Proteobacteria, but members are found also in
Cyanobacteria, plants, and apicomplexan parasites. This
family differs greatly in sequence from the family of
aminopeptidases typified by Streptomyces lividans PepN
(TIGR02412), from the membrane bound aminopeptidase N
family in animals, etc [Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 863
Score = 28.4 bits (64), Expect = 3.0
Identities = 11/38 (28%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 129 VDMLDGVTVVRS--------EKVKDELILDGNDIELVS 158
D+ + TVVR+ + L+LDG +++L+S
Sbjct: 16 FDLHEEETVVRARLTVRRNPDGNGAPLVLDGEELKLLS 53
>gnl|CDD|145918 pfam03025, Papilloma_E5, Papillomavirus E5. The E5 protein from
papillomaviruses is about 80 amino acids long. The
proteins are contain three regions that are predicted to
be transmembrane alpha helices. The function of this
protein is unknown.
Length = 72
Score = 26.5 bits (59), Expect = 3.1
Identities = 8/14 (57%), Positives = 11/14 (78%), Gaps = 1/14 (7%)
Query: 170 CVCLCVCVRNLPVL 183
CVCLC+C +P+L
Sbjct: 10 CVCLCLC-CLVPLL 22
>gnl|CDD|102357 PRK06395, PRK06395, phosphoribosylamine--glycine ligase;
Provisional.
Length = 435
Score = 27.9 bits (62), Expect = 3.6
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 2 KTILSSETMDIPDGVK-IKINAKIIEVEG 29
K I+ + MD P+GVK I+INA+ + EG
Sbjct: 270 KGIMYGQFMDTPNGVKVIEINARFADPEG 298
>gnl|CDD|213285 cd05918, A_NRPS_SidN3_like, The adenylation (A) domain of
siderophore-synthesizing nonribosomal peptide
synthetases (NRPS). The adenylation (A) domain of NRPS
recognizes a specific amino acid or hydroxy acid and
activates it as an (amino) acyl adenylate by hydrolysis
of ATP. The activated acyl moiety then forms a thioester
to the enzyme-bound cofactor phosphopantetheine of a
peptidyl carrier protein domain. This family of
siderophore-synthesizing NRPS includes the third
adenylation domain of SidN from the endophytic fungus
Neotyphodium lolii, ferrichrome siderophore synthetase,
HC-toxin synthetase, and enniatin synthase. NRPSs are
large multifunctional enzymes which synthesize many
therapeutically useful peptides. These natural products
include antibiotics, immunosuppressants, plant and
animal toxins, and enzyme inhibitors. NRPS has a
distinct modular structure in which each module is
responsible for the recognition, activation, and in some
cases, modification of a single amino acid residue of
the final peptide product. The modules can be subdivided
into domains that catalyze specific biochemical
reactions.
Length = 447
Score = 27.6 bits (62), Expect = 5.4
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 9/57 (15%)
Query: 147 LILDGNDIELVSRSAALINQVG-LCV---CLCVCVRNLPVLTARSFILTEMPCEEQG 199
+LD + LV I VG LC+ + N P LTA FI G
Sbjct: 270 WVLDPDLEPLV-----PIGAVGELCIGGPGVARGYLNRPELTAEKFIPDPFWLNNPG 321
>gnl|CDD|219169 pfam06772, LtrA, Bacterial low temperature requirement A protein
(LtrA). This family consists of several bacteria
specific low temperature requirement A (LtrA) protein
sequences which have been found to be essential for
growth at low temperatures in Listeria monocytogenes.
Length = 354
Score = 27.3 bits (61), Expect = 6.4
Identities = 9/37 (24%), Positives = 11/37 (29%), Gaps = 3/37 (8%)
Query: 96 RFVYAHFPINASIGNANKSIEIRNFLGEKKVRKVDML 132
Y H PI A I +E F E +
Sbjct: 251 LLTYGHLPIVAGIILTAVGLE---FSLEHPLGHAVER 284
>gnl|CDD|217478 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
specificity factor, Rap94.
Length = 796
Score = 27.4 bits (61), Expect = 6.7
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 92 RYKMRFVYAHFPINASIGNANKSIEIRNFLGEKKV 126
+Y +R++Y + I I++FL K V
Sbjct: 207 KYNLRYIY-----LYKVDGLTIPIVIKDFLDVKYV 236
>gnl|CDD|176883 cd08874, START_STARD9-like, C-terminal START domain of mammalian
STARD9, and related domains; lipid binding. This
subfamily includes the steroidogenic acute regulatory
protein (StAR)-related lipid transfer (START) domains of
mammalian STARD9 (also known as KIAA1300), and related
domains. The START domain family belongs to the SRPBCC
(START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. Some members of this subfamily have N-terminal
kinesin motor domains. STARD9 interacts with
supervillin, a protein important for efficient
cytokinesis, perhaps playing a role in coordinating
microtubule motors with actin and myosin II functions at
membranes. The human gene encoding STARD9 lies within a
target region for LGMD2A, an autosomal recessive form of
limb-girdle muscular dystrophy.
Length = 205
Score = 26.8 bits (59), Expect = 6.9
Identities = 6/25 (24%), Positives = 10/25 (40%)
Query: 170 CVCLCVCVRNLPVLTARSFILTEMP 194
C+ + L V+ +S MP
Sbjct: 112 CLQVEAKEGELSVVACQSVYDKSMP 136
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 0.137 0.397
Gapped
Lambda K H
0.267 0.0638 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,875,180
Number of extensions: 916047
Number of successful extensions: 801
Number of sequences better than 10.0: 1
Number of HSP's gapped: 780
Number of HSP's successfully gapped: 29
Length of query: 200
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 108
Effective length of database: 6,857,034
Effective search space: 740559672
Effective search space used: 740559672
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 (21.9 bits)
S2: 56 (25.5 bits)