RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029415
(194 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 248 bits (634), Expect = 9e-85
Identities = 111/194 (57%), Positives = 148/194 (76%), Gaps = 4/194 (2%)
Query: 1 MKTILSSETMEIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKI 60
MKTI SSE + IPEGV V + ++ + V G G+L+R+F+HL +D L DG + +K+
Sbjct: 1 MKTIFSSEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKDG----KYIKV 56
Query: 61 DAWFGSRKTSAAIRTALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADKSIEIRNF 120
+ WFG+ A IRT SH++N++TGVTK ++YKMR VYAHFPIN++I + K+IEIRNF
Sbjct: 57 EMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNF 116
Query: 121 LGEKKVRRVEMLDGVTVLRSDKVKDELILDGNDIELVSRSAALINQKCHVKNKDIRKFLD 180
LGEK+VR V+ML GV V +S+ VKDE+I+ G D+ELVSRSAALI+Q V+NKDIRKFLD
Sbjct: 117 LGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLVRNKDIRKFLD 176
Query: 181 GIYVSEKGTIVGED 194
GIYVSEKGT+ ++
Sbjct: 177 GIYVSEKGTVDKDE 190
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 200 bits (509), Expect = 6e-66
Identities = 102/193 (52%), Positives = 136/193 (70%), Gaps = 8/193 (4%)
Query: 4 ILSSETMEIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKIDAW 63
I S +T+ IPE V V + +I+ V+G RG L+++ +HL LDF + R W
Sbjct: 3 IKSQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRV----NKKNRTFTAVRW 58
Query: 64 FGSRKTSAAIRTALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADKSIEIRNFLGE 123
FGS+ ++ I TALSHV+N+ITGVTKG+R+K+RF YAHFPI+ S+ N + +EIRNFLGE
Sbjct: 59 FGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPISVSVEN--QLVEIRNFLGE 116
Query: 124 KKVRRVEMLDGVTVLRSD--KVKDELILDGNDIELVSRSAALINQKCHVKNKDIRKFLDG 181
K+VRR + D V V R+D KVKDEL+L+GND+E VSR AA+++Q C VK KDIRKFLDG
Sbjct: 117 KRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCLVKKKDIRKFLDG 176
Query: 182 IYVSEKGTIVGED 194
IYV K + E+
Sbjct: 177 IYVQTKTNVEAEE 189
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 165 bits (419), Expect = 4e-52
Identities = 76/192 (39%), Positives = 114/192 (59%), Gaps = 13/192 (6%)
Query: 1 MKTILSSETMEIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKI 60
M E +EIPEGV V+I ++ V+GP+G+L+R+F + + + DG K+ I
Sbjct: 1 MVAAYIREEIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVTISV-EDG-----KVVI 54
Query: 61 DAWFGSRKTSAAIRTALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADKSIEIRNF 120
+ F +KT A + T SH++N+I GVT+G+ YK++ VY+HFP+ + + I NF
Sbjct: 55 ETEFARKKTKAMVGTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQVKV--QGNEVVIENF 112
Query: 121 LGEKKVRRVEMLDGVTVLRSDKVK-DELILDGNDIELVSRSAALINQKCHVKNKDIRKFL 179
LGEK RR ++L GV V KVK +++I++G D E V ++AA I Q +K D R F
Sbjct: 113 LGEKSPRRAKILGGVKV----KVKGEDVIVEGIDKEDVGQTAANIEQATKIKGFDRRVFQ 168
Query: 180 DGIYVSEKGTIV 191
DGIY+ EK
Sbjct: 169 DGIYIVEKEVKG 180
>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 = 153 bits (388), Expect = 1e-47
Identities = 72/181 (39%), Positives = 107/181 (59%), Gaps = 13/181 (7%)
Query: 8 ETMEIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKIDAWFGSR 67
E +EIPEGV V I I+ V+GP+G+++R + ++ + K+ I+ F +
Sbjct: 2 EEIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIEISVEDG------KVVIETDFARK 55
Query: 68 KTSAAIRTALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADKSIEIRNFLGEKKVR 127
K A + T SH++N+I GVT+G+ YKM+ VY+HFP+ + + I NFLGEK R
Sbjct: 56 KDKAMVGTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQVKV--EGNKVVIENFLGEKAPR 113
Query: 128 RVEMLDGVTVLRSDKVK-DELILDGNDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSE 186
R ++ GV V KVK +E+I+ 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 = 127 bits (321), Expect = 2e-37
Identities = 49/182 (26%), Positives = 80/182 (43%), Gaps = 16/182 (8%)
Query: 12 IPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKIDAWFGSRKTSA 71
IP GV V I +++ V+GP+G+L+R F + + E L + G RK A
Sbjct: 11 IPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKV----EVEDNI--LVVRPVDGKRKR-A 63
Query: 72 AIRTALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADKSIEIRNFLGEKKVRRVEM 131
T + + N++ GVT+G+ K+ V + N + FLG +E+
Sbjct: 64 LHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGGN------LELFLGYSHPVVIEI 117
Query: 132 LDGVTVLRSDKVKDELILDGNDIELVSRSAALINQKCHVKNKDIRK-FLDGIYVSEKGTI 190
+G+TV E++++G D ELV + AA I + + DG Y+ K
Sbjct: 118 PEGITV--EVPGPTEIVVEGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYIRRKEGK 175
Query: 191 VG 192
G
Sbjct: 176 TG 177
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 57.2 bits (139), Expect = 2e-11
Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 4/80 (5%)
Query: 102 FPINASIANADKSIEIRNFLGEKKVRRVEMLDGVTVLRSDKVKDELILDGNDIELVSRSA 161
P+ ++ + LG K E+ GVTV + +I+ G D E V + A
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKV--EKITVIIVSGIDKEKVGQFA 56
Query: 162 ALINQKCHVKNKDIRKFLDG 181
ALI + G
Sbjct: 57 ALIGTYRAPIPNMGKGVSYG 76
Score = 38.7 bits (91), Expect = 1e-04
Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 17/86 (19%)
Query: 12 IPEGVKVKINAKIIE-VEGPRGKLSRNFKH-LNLDFHLMTDGETGKRKLKIDAWFGSRK- 68
IP GV+V I+ + V GP+G+L+R + + K+ + G K
Sbjct: 1 IPVGVRVSIDGVNLVLVLGPKGELTREIPPGVTVKV----------EKITVIIVSGIDKE 50
Query: 69 ----TSAAIRTALSHVQNLITGVTKG 90
+A I T + + N+ GV+ G
Sbjct: 51 KVGQFAALIGTYRAPIPNMGKGVSYG 76
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 52.8 bits (128), Expect = 6e-09
Identities = 23/81 (28%), Positives = 43/81 (53%), Gaps = 7/81 (8%)
Query: 11 EIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKIDAWFGSRKTS 70
IP GV+V I+ ++ V+GP+G+LSR + + DG+ L + S++
Sbjct: 9 AIPAGVEVTIDGNVVTVKGPKGELSRTLHP-GVTVKV-EDGQ-----LTVSRPNDSKEAR 61
Query: 71 AAIRTALSHVQNLITGVTKGY 91
A T + + N++ GV++G+
Sbjct: 62 ALHGTTRALINNMVIGVSEGF 82
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 50.8 bits (123), Expect = 3e-08
Identities = 25/82 (30%), Positives = 42/82 (51%), Gaps = 9/82 (10%)
Query: 11 EIPEGVKVKINAKIIEVEGPRGKLSRNFKHL-NLDFHLMTDGETGKRKLKIDAWFGSRKT 69
IP GV+V IN ++ V+GP+G+LSR + + D E + + S+K
Sbjct: 10 AIPAGVEVTINGNVVTVKGPKGELSRTLNPDVTVK---VEDNE-----ITVTRPDDSKKA 61
Query: 70 SAAIRTALSHVQNLITGVTKGY 91
A T + + N++ GVT+G+
Sbjct: 62 RALHGTTRALINNMVVGVTEGF 83
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 36.4 bits (85), Expect = 0.003
Identities = 26/89 (29%), Positives = 44/89 (49%), Gaps = 15/89 (16%)
Query: 12 IPEGVKVKINAKIIEVEGPRGKLSRNF-KHLNLDFHLMTDGETGKRKLKIDAWFGSRKTS 70
IP+ V V I+ +II+V+GP+G LSR + + E L + S+K
Sbjct: 11 IPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITI--------EIQDNSLFVSKKDESKKAR 62
Query: 71 A---AIRTALSHVQNLITGVTKGYRYKMR 96
A RT ++ N++ GV++G+ K+
Sbjct: 63 ALHGLYRTLIN---NMVIGVSEGFEKKLE 88
>gnl|CDD|213552 TIGR00691, spoT_relA, (p)ppGpp synthetase, RelA/SpoT family. The
functions of E. coli RelA and SpoT differ somewhat. RelA
(EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP
(or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also
act as a secondary ppGpp synthetase. The two proteins
are strongly similar. In many species, a single homolog
to SpoT and RelA appears reponsible for both ppGpp
synthesis and ppGpp degradation. (p)ppGpp is a
regulatory metabolite of the stringent response, but
appears also to be involved in antibiotic biosynthesis
in some species [Cellular processes, Adaptations to
atypical conditions].
Length = 683
Score = 28.9 bits (65), Expect = 2.1
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 6/67 (8%)
Query: 116 EIRNFLGEKKVRRVEMLDGVTVLRSDKVKDELILDGNDIELVSRSAAL--INQKCHVKNK 173
I++ + E+KV R L+ +++ L G + EL RS L I QK K +
Sbjct: 172 NIKSLVNEQKVNRENKLEKF----KSELEKRLEDSGIEAELEGRSKHLYSIYQKMTRKGQ 227
Query: 174 DIRKFLD 180
+ + D
Sbjct: 228 NFDEIHD 234
>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 = 2.4
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 135 VTVLRSDKVKDELILDGNDIELVS 158
+ V+R+ L+LDG D++LVS
Sbjct: 29 LQVVRNGGSGAPLVLDGEDLKLVS 52
>gnl|CDD|238445 cd00873, KU80, Ku-core domain, Ku80 subfamily; Ku80 is a subunit of
the Ku protein, which plays a key role in multiple
nuclear processes such as DNA repair, chromosome
maintenance, transcription regulation, and V(D)J
recombination. The mechanism underlying the regulation
of all the diverse functions of Ku is still unclear,
although it seems that Ku is a multifunctional protein
that works in nuclei. In mammalian cells, the Ku
heterodimer recruits the catalytic subunit of
DNA-dependent protein kinase (DNA-PK), which is
dependent on its association with the Ku70/80
heterodimer bound to DNA for its protein kinase
activity.
Length = 300
Score = 27.6 bits (62), Expect = 4.5
Identities = 15/70 (21%), Positives = 26/70 (37%), Gaps = 11/70 (15%)
Query: 87 VTKGYRYKMRFVYAHFPINASIANA-----DKSIEIRNFLGEKKVRRVEMLDGVTVL--R 139
+ KGYRY V P++ A K ++I F+ V R ++ + + +
Sbjct: 70 LIKGYRYGRDIV----PLSEEDEEATKLSTSKGLDILGFIKASNVPRYYLMGESSYVVPQ 125
Query: 140 SDKVKDELIL 149
D L
Sbjct: 126 QDDEAAALAF 135
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 27.5 bits (62), Expect = 4.8
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 2 KTILSSETMEIPEGVKVKINAKIIEVEGPRGKLSRNFKHLNLDFHLMTDGETGKRKLKID 61
KT+L+S+ E + + E R +L RN + +D M + K LKI
Sbjct: 286 KTLLASKFAE--AACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEE----KGLLKII 339
Query: 62 AWFGSRKTSAAIRTALSHVQNLI 84
+R S + L ++ I
Sbjct: 340 C---ARPESYGLEDHLIIIKREI 359
>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 = 7.4
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 7/40 (17%)
Query: 152 NDIELVSRSAALINQKCHVKNKDIRKFLDGIYVSEKGTIV 191
N I+LVS+ AL N ++I++F+ G ++E I+
Sbjct: 142 NKIDLVSKEKALENY------EEIKEFVKG-TIAENAPII 174
>gnl|CDD|233197 TIGR00937, 2A51, chromate transporter, chromate ion transporter
(CHR) family. Members of this family probably act as
chromate transporters, and are found in Pseudomonas
aeruginosa, Alcaligenes eutrophus, Vibrio cholerae,
Bacillus subtilis, cyanobacteria and archaea. The
protein reduces chromate accumulation and is essential
for chromate resistance. Cutoffs for this model have now
been lowered, compared to a previous version, giving the
model a scope more similar to that of pfam02417. Members
of the original, more narrowly defined family score
above 500.00 bits [Transport and binding proteins,
Anions].
Length = 368
Score = 27.0 bits (60), Expect = 7.6
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 169 HVKNKDIRKFLDGIYVSEKGTIVG 192
KN IR FLDG+ G +V
Sbjct: 300 LGKNPIIRAFLDGVNAGVVGLLVA 323
>gnl|CDD|172919 PRK14443, PRK14443, acylphosphatase; Provisional.
Length = 93
Score = 25.8 bits (56), Expect = 8.1
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 75 TALSHVQNLITGVTKGYRYKMRFVYAHFPINASIANADK-SIEIRNFLGEKKVRR 128
TA+ V + GV G+RY + V + I+ ++ N D S+EI E+ + +
Sbjct: 5 TAILRVTGFVQGV--GFRYTTKHVAYKYDISGTVKNLDDGSVEIHAIAEEENLNK 57
>gnl|CDD|236540 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
Reviewed.
Length = 247
Score = 26.6 bits (59), Expect = 8.5
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 140 SDKVKDELILDGNDIELVSRSAALINQKCHVKNKDIRKF 178
++ +K LDG + + S + ++ K ++K KD+R+F
Sbjct: 120 NNDIKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQF 158
>gnl|CDD|240362 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 26.9 bits (60), Expect = 8.8
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 7/40 (17%)
Query: 142 KVKDELILDGNDIELVSRSAALINQKCHVKNKDIRKFLDG 181
K+K +IL N I+LV + A ++IR F+ G
Sbjct: 170 KLKHIIILQ-NKIDLVKEAQAQDQY------EEIRNFVKG 202
>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 = 26.6 bits (59), Expect = 9.0
Identities = 6/14 (42%), Positives = 6/14 (42%)
Query: 96 RFVYAHFPINASIA 109
Y H PI A I
Sbjct: 251 LLTYGHLPIVAGII 264
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 0.378
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,690,473
Number of extensions: 907319
Number of successful extensions: 824
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 43
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 (25.4 bits)