RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7621
(247 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 162 bits (411), Expect = 4e-50
Identities = 75/144 (52%), Positives = 90/144 (62%), Gaps = 14/144 (9%)
Query: 117 MSVEKSFIVVYQKYTSTGGFVCIS---------FTG----FLYKMRAAYAHFPINCVTSE 163
+S + +I V + + CI TG F YKMR YAHFPIN ++
Sbjct: 47 LSKDGKYIKVEMWFGTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITD 106
Query: 164 NNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQ-KDELIIEGNDIENVSRSAALIQQSTTV 222
N +EIRNFLGEK +R VKM PGV V S+ KDE+I+ G D+E VSRSAALI QST V
Sbjct: 107 NGKTIEIRNFLGEKRVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLV 166
Query: 223 KNKDIRKFLDGLYVSEKTTVVTDA 246
+NKDIRKFLDG+YVSEK TV D
Sbjct: 167 RNKDIRKFLDGIYVSEKGTVDKDE 190
Score = 44.0 bits (104), Expect = 1e-05
Identities = 16/25 (64%), Positives = 19/25 (76%)
Query: 48 GTKKEIAAVRTVCSHISNMLKGVTK 72
GT +A +RTVCSHI NM+ GVTK
Sbjct: 61 GTPSHLACIRTVCSHIKNMMTGVTK 85
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 124 bits (313), Expect = 2e-35
Identities = 62/106 (58%), Positives = 75/106 (70%), Gaps = 5/106 (4%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSN---SKQKDEL 199
GF +K+R AYAHFPI+ S N L+EIRNFLGEK +RR +A VKV SK KDEL
Sbjct: 85 GFRFKVRFAYAHFPIS--VSVENQLVEIRNFLGEKRVRRQVVADTVKVYRTDPSKVKDEL 142
Query: 200 IIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEKTTVVTD 245
++EGND+E VSR AA++ Q VK KDIRKFLDG+YV KT V +
Sbjct: 143 VLEGNDLEQVSREAAVMHQLCLVKKKDIRKFLDGIYVQTKTNVEAE 188
Score = 30.7 bits (69), Expect = 0.51
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 31 LNKTYRWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
+NK R TF G+K + + T SH+ NM+ GVTK
Sbjct: 46 VNKKNR---TFTAVRWFGSKIPNSTINTALSHVRNMITGVTK 84
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 108 bits (273), Expect = 1e-29
Identities = 44/97 (45%), Positives = 63/97 (64%), Gaps = 4/97 (4%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIE 202
GF YK++ Y+HFP+ V + N + I NFLGEK RR K+ GVKV +++I+E
Sbjct: 84 GFEYKLKIVYSHFPMQ-VKVQGNEV-VIENFLGEKSPRRAKILGGVKVKVKG--EDVIVE 139
Query: 203 GNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEK 239
G D E+V ++AA I+Q+T +K D R F DG+Y+ EK
Sbjct: 140 GIDKEDVGQTAANIEQATKIKGFDRRVFQDGIYIVEK 176
Score = 42.9 bits (102), Expect = 3e-05
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
++ + KK A V T SHI NM+KGVT+
Sbjct: 54 IETEFARKKTKAMVGTFASHIKNMIKGVTE 83
>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 = 104 bits (261), Expect = 6e-28
Identities = 46/97 (47%), Positives = 63/97 (64%), Gaps = 4/97 (4%)
Query: 143 GFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIE 202
GF YKM+ Y+HFP+ V E N + I NFLGEK RR K+ GVKV +E+I+
Sbjct: 78 GFEYKMKVVYSHFPMQ-VKVEGNKV-VIENFLGEKAPRRAKIPGGVKVKVKG--EEVIVT 133
Query: 203 GNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEK 239
G D E+V ++AA I+Q+T +K +D R F DG+Y+ EK
Sbjct: 134 GIDKEDVGQTAANIEQATRIKGRDPRVFQDGIYIVEK 170
Score = 40.0 bits (94), Expect = 3e-04
Identities = 15/30 (50%), Positives = 20/30 (66%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
++ D KK+ A V T SHI NM+KGVT+
Sbjct: 48 IETDFARKKDKAMVGTYRSHIKNMIKGVTE 77
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 83.4 bits (207), Expect = 7e-20
Identities = 22/99 (22%), Positives = 39/99 (39%), Gaps = 8/99 (8%)
Query: 142 TGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELII 201
GF K+ + V + FLG + +++ G+ V E+++
Sbjct: 81 EGFEKKLEIVGVGYRAQVVGGN------LELFLGYSHPVVIEIPEGITVEVPGP-TEIVV 133
Query: 202 EGNDIENVSRSAALIQQSTTVKNKDIRK-FLDGLYVSEK 239
EG D E V + AA I+ + + + DG Y+ K
Sbjct: 134 EGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYIRRK 172
Score = 32.1 bits (74), Expect = 0.13
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
V +G +K A TV + I+NM+KGVT+
Sbjct: 53 VRPVDGKRKR-ALHGTVRALINNMVKGVTE 81
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 68.0 bits (167), Expect = 4e-15
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 155 FPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAA 214
P+ S + + LG K ++ PGV V ++ +I+ G D E V + AA
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKV-EKITVIIVSGIDKEKVGQFAA 57
Query: 215 LIQQSTTVKNKDIRKFLDG 233
LI + G
Sbjct: 58 LIGTYRAPIPNMGKGVSYG 76
Score = 33.7 bits (78), Expect = 0.010
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 39 ETFDVDCDNGTKKE-----IAAVRTVCSHISNMLKGVTK 72
E V +G KE A + T + I NM KGV+
Sbjct: 37 EKITVIIVSGIDKEKVGQFAALIGTYRAPIPNMGKGVSY 75
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 30.2 bits (68), Expect = 1.1
Identities = 29/97 (29%), Positives = 38/97 (39%), Gaps = 26/97 (26%)
Query: 175 GEKYIRRVKMAPGVKVSNSKQKDELI-----------IEGNDIE-----------NVSRS 212
+ R+K APG KV N + ELI ++ +E VS+
Sbjct: 558 ADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYAGVEVAKKGKAKQGYEVSQG 617
Query: 213 AAL--IQQSTTVKNKDIRKFL--DGLYVSEKTTVVTD 245
L I + T NKDI + DG YV T VV D
Sbjct: 618 GTLLWIPEETHEINKDISLLMVEDGQYVEAGTEVVKD 654
>gnl|CDD|234460 TIGR04084, rSAM_AF0577, putative peptide-modifying radical SAM
enzyme, AF0577 family. This radical SAM family contains
a C-terminal region motif CXXCX5CX3C that is found in
PqqE and other radical SAM enzymes that act on peptide
substrates. Members of this family are found primarily
in the Archaea, but also several eukaryotes (Trichomonas
vaginalis G3, Entamoeba dispar SAW760, Giardia
intestinalis ATCC 50581, etc.). The function is unknown.
Length = 347
Score = 29.7 bits (67), Expect = 1.5
Identities = 22/62 (35%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 19 DLNPGGGGGCLYLNKTYRW-EETFDVDCDNGTKKEIAAVRTVCSHI----SNMLKGVTKV 73
+ GG CLY K W EE F + KE +RTV I S + KGV K+
Sbjct: 276 EYRRYCGGRCLYAIKERYWGEEGFKAVDE--VTKEY--LRTVLEIIPEIESLVDKGVIKL 331
Query: 74 KD 75
D
Sbjct: 332 SD 333
>gnl|CDD|236619 PRK09737, PRK09737, EcoKI restriction-modification system protein
HsdS; Provisional.
Length = 461
Score = 29.1 bits (65), Expect = 2.2
Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 9/105 (8%)
Query: 110 LLALVLCMSVEKSFIVVYQKYTSTGGFVCISFTGFLYKMRAAYAHFPINCVTSENNTLLE 169
L L CM + KY + IS G + A P N V + L+
Sbjct: 56 LTTLPYCMDAPEDV----SKYQLQDRDIVISSAGSIGFSFLAQNPLPSNVVFASFAIRLK 111
Query: 170 IRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAA 214
N+ E +++ ++ S+ + + L+ GN ++N++ +
Sbjct: 112 PVNYFSEYFLKHF-----LESSDYRNQLSLMSAGNAVQNINAQSL 151
>gnl|CDD|240150 cd05023, S-100A11, S-100A11: S-100A11 domain found in proteins
similar to S100A11. S100A11 is a member of the S-100
domain family within EF-hand Ca2+-binding proteins
superfamily. Note that the S-100 hierarchy, to which
this S-100A11 group belongs, contains only S-100 EF-hand
domains, other EF-hands have been modeled separately.
S100 proteins exhibit unique patterns of tissue- and
cell type-specific expression and have been implicated
in the Ca2+-dependent regulation of diverse
physiological processes, including cell cycle
regulation, differentiation, growth, and metabolic
control . S100 proteins have also been associated with a
variety of pathological events, including neoplastic
transformation and neurodegenerative diseases such as
Alzheimer's, usually via over expression of the protein.
S100A11 is expressed in smooth muscle and other tissues
and involves in calcium-dependent membrane aggregation,
which is important for cell vesiculation . As is the
case for many other S100 proteins, S100A11 is homodimer,
which is able to form a heterodimer with S100B through
subunit exchange. Ca2+ binding to S100A11 results in a
conformational change in the protein, exposing a
hydrophobic surface that interacts with target proteins.
In addition to binding to annexin A1 and A6 S100A11
also interacts with actin and transglutaminase.
Length = 89
Score = 27.4 bits (61), Expect = 2.4
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 116 CMSVEKSFIVVYQKYTSTGGFVC-ISFTGFLYKMRAAYAHF 155
C+ +S I V+QKY G +S T FL M A F
Sbjct: 7 CI---ESLIAVFQKYAGKDGDSYQLSKTEFLSFMNTELASF 44
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.8 bits (65), Expect = 2.6
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 157 INCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELII 201
I C+ ++ L++ F +YI A V++ N K+ DELI+
Sbjct: 7 IPCLLLKDGGLVKTVKFKDPRYIGDPINA--VRIFNEKEVDELIV 49
>gnl|CDD|224608 COG1694, MazG, Predicted pyrophosphatase [General function
prediction only].
Length = 102
Score = 27.3 bits (61), Expect = 2.9
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 105 LAQVFLLALVLCMSVEKSFIVVYQKYTS 132
LA V LA +L + +E + V +K
Sbjct: 63 LADVLFLANLLDIDLEFALEEVVRKIAE 90
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 28.3 bits (63), Expect = 4.2
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 187 GVKVSNSKQKDE---------LIIEGNDIENVSRSAALIQQSTTVKN 224
V NS +E L+I GN I++V++ L + S TV
Sbjct: 489 NVSSDNSSASNEYSYNMSEQLLVIGGNPIKDVTKEENLAEWSKTVST 535
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 26.6 bits (60), Expect = 8.8
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 58 TVCSHISNMLKGVTK 72
T + I+NM+ GV++
Sbjct: 66 TTRALINNMVIGVSE 80
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 26.6 bits (60), Expect = 9.6
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 43 VDCDNGTKKEIAAVRTVCSHISNMLKGVTK 72
V + +KK A T + I+NM+ GVT+
Sbjct: 52 VTRPDDSKKARALHGTTRALINNMVVGVTE 81
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
0.322 0.136 0.406
Gapped
Lambda K H
0.267 0.0759 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,072,999
Number of extensions: 1096694
Number of successful extensions: 843
Number of sequences better than 10.0: 1
Number of HSP's gapped: 833
Number of HSP's successfully gapped: 27
Length of query: 247
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 153
Effective length of database: 6,768,326
Effective search space: 1035553878
Effective search space used: 1035553878
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: 58 (26.1 bits)