RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029362
(194 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 248 bits (634), Expect = 9e-85
Identities = 109/194 (56%), Positives = 143/194 (73%), Gaps = 4/194 (2%)
Query: 1 MKTILSSETMDIPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKI 60
MKTI SSE + IP+GV V + ++ + V G G+L+R F+HL +D L D + +K+
Sbjct: 1 MKTIFSSEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKD----GKYIKV 56
Query: 61 DAWFGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIEIRNF 120
+ WFG+ A IRT SH+ N++TGVTK ++YKMR VYAHFPIN++I +N K IEIRNF
Sbjct: 57 EMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNF 116
Query: 121 LGEKKVRKVDMLDGVTVIRSDKVKDELVLDGNDIELVSRSAALINQKCHVKNKDIRKFLD 180
LGEK+VR V ML GV V +S+ VKDE+++ G D+ELVSRSAALI+Q V+NKDIRKFLD
Sbjct: 117 LGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLVRNKDIRKFLD 176
Query: 181 GIYVSEKSTILGEE 194
GIYVSEK T+ +E
Sbjct: 177 GIYVSEKGTVDKDE 190
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 197 bits (502), Expect = 1e-64
Identities = 102/193 (52%), Positives = 135/193 (69%), Gaps = 8/193 (4%)
Query: 4 ILSSETMDIPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAW 63
I S +T+ IP+ V V + +++ V+G RG L++D +HL LDF + R W
Sbjct: 3 IKSQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRV----NKKNRTFTAVRW 58
Query: 64 FGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIEIRNFLGE 123
FGS+ ++ I TALSHV N+ITGVTKG+R+K+RF YAHFPI+ S+ N +EIRNFLGE
Sbjct: 59 FGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPISVSVENQL--VEIRNFLGE 116
Query: 124 KKVRKVDMLDGVTVIRSD--KVKDELVLDGNDIELVSRSAALINQKCHVKNKDIRKFLDG 181
K+VR+ + D V V R+D KVKDELVL+GND+E VSR AA+++Q C VK KDIRKFLDG
Sbjct: 117 KRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCLVKKKDIRKFLDG 176
Query: 182 IYVSEKSTILGEE 194
IYV K+ + EE
Sbjct: 177 IYVQTKTNVEAEE 189
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 160 bits (408), Expect = 1e-50
Identities = 74/191 (38%), Positives = 114/191 (59%), Gaps = 13/191 (6%)
Query: 1 MKTILSSETMDIPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKI 60
M E ++IP+GV V+I V+ V+GP+G+L+RDF + + ++ E+ K+ I
Sbjct: 1 MVAAYIREEIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVT---ISVED---GKVVI 54
Query: 61 DAWFGSRKTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIEIRNF 120
+ F +KT A + T SH+ N+I GVT+G+ YK++ VY+HFP+ + N + I NF
Sbjct: 55 ETEFARKKTKAMVGTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQVKVQGNE--VVIENF 112
Query: 121 LGEKKVRKVDMLDGVTVIRSDKVK-DELVLDGNDIELVSRSAALINQKCHVKNKDIRKFL 179
LGEK R+ +L GV V KVK ++++++G D E V ++AA I Q +K D R F
Sbjct: 113 LGEKSPRRAKILGGVKV----KVKGEDVIVEGIDKEDVGQTAANIEQATKIKGFDRRVFQ 168
Query: 180 DGIYVSEKSTI 190
DGIY+ EK
Sbjct: 169 DGIYIVEKEVK 179
>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 = 147 bits (374), Expect = 2e-45
Identities = 68/181 (37%), Positives = 109/181 (60%), Gaps = 13/181 (7%)
Query: 8 ETMDIPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSR 67
E ++IP+GV V I ++ V+GP+G+++R+ + ++ ++ E+ K+ I+ F +
Sbjct: 2 EEIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIE---ISVEDG---KVVIETDFARK 55
Query: 68 KTSAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIEIRNFLGEKKVR 127
K A + T SH+ N+I GVT+G+ YKM+ VY+HFP+ + + I NFLGEK R
Sbjct: 56 KDKAMVGTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKV--EGNKVVIENFLGEKAPR 113
Query: 128 KVDMLDGVTVIRSDKVK-DELVLDGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSE 186
+ + GV V KVK +E+++ G D E V ++AA I Q +K +D R F DGIY+ E
Sbjct: 114 RAKIPGGVKV----KVKGEEVIVTGIDKEDVGQTAANIEQATRIKGRDPRVFQDGIYIVE 169
Query: 187 K 187
K
Sbjct: 170 K 170
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 128 bits (323), Expect = 1e-37
Identities = 46/177 (25%), Positives = 81/177 (45%), Gaps = 16/177 (9%)
Query: 12 IPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSA 71
IP GV V I +V+ V+GP+G+L+R+F +++ E + ++ A
Sbjct: 11 IPAGVTVSIEGQVVTVKGPKGELTREFHD-----NVVKVEVEDNILVVRPVDGKRKR--A 63
Query: 72 AIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIEIRNFLGEKKVRKVDM 131
T + + N++ GVT+G+ K+ V + +G N + FLG +++
Sbjct: 64 LHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQV-VGGN-----LELFLGYSHPVVIEI 117
Query: 132 LDGVTVIRSDKVKDELVLDGNDIELVSRSAALINQKCHVKNKDIRK-FLDGIYVSEK 187
+G+TV E+V++G D ELV + AA I + + DG Y+ K
Sbjct: 118 PEGITV--EVPGPTEIVVEGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYIRRK 172
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 57.2 bits (139), Expect = 2e-11
Identities = 17/80 (21%), Positives = 29/80 (36%), Gaps = 4/80 (5%)
Query: 102 FPINASIGNNNKAIEIRNFLGEKKVRKVDMLDGVTVIRSDKVKDELVLDGNDIELVSRSA 161
P+ + + + LG K ++ GVTV + +++ G D E V + A
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKV--EKITVIIVSGIDKEKVGQFA 56
Query: 162 ALINQKCHVKNKDIRKFLDG 181
ALI + G
Sbjct: 57 ALIGTYRAPIPNMGKGVSYG 76
Score = 37.9 bits (89), Expect = 2e-04
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 15/85 (17%)
Query: 12 IPDGVKVKINAKVIE-VEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRK-- 68
IP GV+V I+ + V GP+G+L+R+ K+ + G K
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPP---------GVTVKVEKITVIIVSGIDKEK 51
Query: 69 ---TSAAIRTALSHVGNLITGVTKG 90
+A I T + + N+ GV+ G
Sbjct: 52 VGQFAALIGTYRAPIPNMGKGVSYG 76
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 51.7 bits (125), Expect = 1e-08
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 12 IPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTSA 71
IP GV+V I+ V+ 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 = 50.1 bits (121), Expect = 6e-08
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 11 DIPDGVKVKINAKVIEVEGPRGKLSRDFKHLNLDFHLMTDEETGKRKLKIDAWFGSRKTS 70
IP GV+V IN V+ 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|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 37.6 bits (88), Expect = 0.002
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 15/89 (16%)
Query: 12 IPDGVKVKINAKVIEVEGPRGKLSRDF-KHLNLDFHLMTDEETGKRKLKIDAWFGSRKTS 70
IPD V V I+ ++I+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|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 = 29.2 bits (66), Expect = 1.4
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 129 VDMLDGVTVIRS--------DKVKDELVLDGNDIELVS 158
D+ + TV+R+ D LVLDG +++L+S
Sbjct: 16 FDLHEEETVVRARLTVRRNPDGNGAPLVLDGEELKLLS 53
>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 = 28.8 bits (65), Expect = 2.2
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 135 VTVIRSDKVKDELVLDGNDIELVS 158
+ V+R+ LVLDG D++LVS
Sbjct: 29 LQVVRNGGSGAPLVLDGEDLKLVS 52
>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 = 28.1 bits (63), Expect = 3.2
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 3/43 (6%)
Query: 96 RFVYAHFPINASIGNNNKAIEIRNFLGEKKVRKVDMLDGVTVI 138
Y H PI A I +E F E + + V+
Sbjct: 251 LLTYGHLPIVAGIILTAVGLE---FSLEHPLGHAVERTALAVL 290
>gnl|CDD|131576 TIGR02524, dot_icm_DotB, Dot/Icm secretion system ATPase DotB.
Members of this protein family are the DotB component of
Dot/Icm secretion systems, as found in obligate
intracellular pathogens Legionella pneumophila and
Coxiella burnetii. While this system resembles type IV
secretion systems and has been called a form of type IV,
the liturature now seems to favor calling this the
Dot/Icm system. This family is most closely related to
TraJ proteins of plasmid transfer, rather than to
proteins of other type IV secretion systems.
Length = 358
Score = 27.7 bits (61), Expect = 3.8
Identities = 33/123 (26%), Positives = 54/123 (43%), Gaps = 7/123 (5%)
Query: 70 SAAIRTALSHVGNLITGVTKGYRYKMRFVYAHFPINASIGNNNKAIE-IRNFLGEKKVRK 128
SAA+ AL+ T + G +R + FP IG IE IR + +K V
Sbjct: 228 SAALEAALTGHPVYTTLHSSGVAETIRRLVGSFPAEERIGRTIDIIETIRLCIWQKLVPS 287
Query: 129 VDMLDGVTVIRSDKVKDE----LVLDGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYV 184
VD + +R V DE ++LDG+ E+ + + L+ + + D +G +
Sbjct: 288 VD--EKRVALREFLVFDEEIRDILLDGDPEEITAATRKLVAEHGQLMQVDAEAKFEGGII 345
Query: 185 SEK 187
SE+
Sbjct: 346 SER 348
>gnl|CDD|226742 COG4292, COG4292, Predicted membrane protein [Function unknown].
Length = 387
Score = 27.0 bits (60), Expect = 6.6
Identities = 5/21 (23%), Positives = 7/21 (33%)
Query: 96 RFVYAHFPINASIGNNNKAIE 116
Y H PI I ++
Sbjct: 274 LLTYGHLPIVIGIIVLAAGLD 294
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 26.9 bits (60), Expect = 8.5
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 7/40 (17%)
Query: 152 NDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSEKSTIL 191
N I+LVS+ AL N ++I++F+ G ++E + I+
Sbjct: 142 NKIDLVSKEKALENY------EEIKEFVKG-TIAENAPII 174
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 26.6 bits (59), Expect = 9.5
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 140 SDKVKDELVLDGNDIELVSRSAALINQKCHVKNKDIRKF 178
++ +K LDG + + S + ++ K ++K KD+R+F
Sbjct: 120 NNDIKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQF 158
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
0.318 0.136 0.379
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,673,060
Number of extensions: 906920
Number of successful extensions: 857
Number of sequences better than 10.0: 1
Number of HSP's gapped: 834
Number of HSP's successfully gapped: 34
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
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 (21.7 bits)
S2: 56 (25.3 bits)