RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7620
(189 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 250 bits (639), Expect = 1e-85
Identities = 110/190 (57%), Positives = 136/190 (71%), Gaps = 2/190 (1%)
Query: 1 MRQIVSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMV-NKRVLKVEKWF 59
M+ I S++ ++IP G+ VK+R VTV G G L R F+HL +DI + + + +KVE WF
Sbjct: 1 MKTIFSSEKIRIPEGVTVTVKSRKVTVTGKYGELTRSFRHLPVDIKLSKDGKYIKVEMWF 60
Query: 60 GTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEK 119
GT +A +RTVCSHI NM+ GVTK F YKMR YAHFPIN ++N +EIRNFLGEK
Sbjct: 61 GTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNFLGEK 120
Query: 120 YIRRVKMAPGVKVSNSKQ-KDELIIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYV 178
+R VKM PGV V S+ KDE+I+ G D+E VSRSAALI QST V+NKDIRKFLDG+YV
Sbjct: 121 RVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLVRNKDIRKFLDGIYV 180
Query: 179 SEKTTVVTDA 188
SEK TV D
Sbjct: 181 SEKGTVDKDE 190
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 182 bits (464), Expect = 5e-59
Identities = 98/189 (51%), Positives = 124/189 (65%), Gaps = 6/189 (3%)
Query: 3 QIVSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNK-RVLKVEKWFGT 61
+I S T+ IP + VK R VTVKG RGTL +D +HL +D + K R +WFG+
Sbjct: 2 KIKSQDTITIPEDVTVSVKDRIVTVKGKRGTLTKDLRHLQLDFRVNKKNRTFTAVRWFGS 61
Query: 62 KKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYI 121
K + + T SH+ NM+ GVTKGF +K+R AYAHFPI+ S N L+EIRNFLGEK +
Sbjct: 62 KIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPIS--VSVENQLVEIRNFLGEKRV 119
Query: 122 RRVKMAPGVKVSN---SKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYV 178
RR +A VKV SK KDEL++EGND+E VSR AA++ Q VK KDIRKFLDG+YV
Sbjct: 120 RRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMHQLCLVKKKDIRKFLDGIYV 179
Query: 179 SEKTTVVTD 187
KT V +
Sbjct: 180 QTKTNVEAE 188
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 167 bits (426), Expect = 2e-53
Identities = 76/173 (43%), Positives = 109/173 (63%), Gaps = 5/173 (2%)
Query: 9 TVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKEIAAV 68
++IP G+ ++ VTVKGP+G L RDF + + I + + +V +E F KK A V
Sbjct: 9 EIEIPEGVTVEIEGLVVTVKGPKGELTRDFWYPGVTISVEDGKV-VIETEFARKKTKAMV 67
Query: 69 RTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAP 128
T SHI NM+KGVT+GF YK++ Y+HFP+ V + N + I NFLGEK RR K+
Sbjct: 68 GTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQ-VKVQGNE-VVIENFLGEKSPRRAKILG 125
Query: 129 GVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEK 181
GVKV +++I+EG D E+V ++AA I+Q+T +K D R F DG+Y+ EK
Sbjct: 126 GVKVKVK--GEDVIVEGIDKEDVGQTAANIEQATKIKGFDRRVFQDGIYIVEK 176
>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 = 157 bits (400), Expect = 1e-49
Identities = 76/173 (43%), Positives = 111/173 (64%), Gaps = 5/173 (2%)
Query: 9 TVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKEIAAV 68
++IP G+ ++ VTVKGP+G + R+ + I+I + + +V+ +E F KK+ A V
Sbjct: 3 EIEIPEGVSVTIEGNIVTVKGPKGEVTRELWYPGIEISVEDGKVV-IETDFARKKDKAMV 61
Query: 69 RTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAP 128
T SHI NM+KGVT+GF YKM+ Y+HFP+ V E N + I NFLGEK RR K+
Sbjct: 62 GTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQ-VKVEGNK-VVIENFLGEKAPRRAKIPG 119
Query: 129 GVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIRKFLDGLYVSEK 181
GVKV +E+I+ G D E+V ++AA I+Q+T +K +D R F DG+Y+ EK
Sbjct: 120 GVKVKVK--GEEVIVTGIDKEDVGQTAANIEQATRIKGRDPRVFQDGIYIVEK 170
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 130 bits (330), Expect = 7e-39
Identities = 46/178 (25%), Positives = 83/178 (46%), Gaps = 10/178 (5%)
Query: 5 VSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKE 64
+ + + IP G+ ++ + VTVKGP+G L R+F + + + + ++ K+
Sbjct: 4 IGKRPIVIPAGVTVSIEGQVVTVKGPKGELTREFHDNVVKVEVEDNILVVRPVDGKRKR- 62
Query: 65 IAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRV 124
A TV + I+NM+KGVT+GF K+ + V + FLG + +
Sbjct: 63 -ALHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGG------NLELFLGYSHPVVI 115
Query: 125 KMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKDIRK-FLDGLYVSEK 181
++ G+ V E+++EG D E V + AA I+ + + + DG Y+ K
Sbjct: 116 EIPEGITVEVPGP-TEIVVEGIDKELVGQVAANIRAARKPEPYKGKGIRYDGEYIRRK 172
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 60.7 bits (148), Expect = 8e-13
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 97 FPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAA 156
P+ S + + LG K ++ PGV V ++ +I+ G D E V + AA
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKV-EKITVIIVSGIDKEKVGQFAA 57
Query: 157 LIQQSTTVKNKDIRKFLDG 175
LI + G
Sbjct: 58 LIGTYRAPIPNMGKGVSYG 76
Score = 46.4 bits (111), Expect = 2e-07
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 9/68 (13%)
Query: 23 RTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKE-----IAAVRTVCSHISN 77
V V GP+G L R+ + + + + V G KE A + T + I N
Sbjct: 13 NLVLVLGPKGELTREIPP---GVTVKVE-KITVIIVSGIDKEKVGQFAALIGTYRAPIPN 68
Query: 78 MLKGVTKG 85
M KGV+ G
Sbjct: 69 MGKGVSYG 76
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 56.7 bits (138), Expect = 2e-10
Identities = 24/82 (29%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 5 VSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKE 64
+ + + IP G++ + VTVKGP+G L R + + + + L V + +K+
Sbjct: 3 IGKKPIAIPAGVEVTIDGNVVTVKGPKGELSRTLHPG-VTVKVEDG-QLTVSRPNDSKEA 60
Query: 65 IAAVRTVCSHISNMLKGVTKGF 86
A T + I+NM+ GV++GF
Sbjct: 61 RALHGTTRALINNMVIGVSEGF 82
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 55.5 bits (135), Expect = 6e-10
Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 2/82 (2%)
Query: 5 VSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAIDIHMVNKRVLKVEKWFGTKKE 64
+ + + IP G++ + VTVKGP+G L R + + + + + V + +KK
Sbjct: 4 IGKKPIAIPAGVEVTINGNVVTVKGPKGELSRTLNP-DVTVKVEDN-EITVTRPDDSKKA 61
Query: 65 IAAVRTVCSHISNMLKGVTKGF 86
A T + I+NM+ GVT+GF
Sbjct: 62 RALHGTTRALINNMVVGVTEGF 83
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 45.7 bits (109), Expect = 2e-06
Identities = 27/83 (32%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 10 VKIPRGLQCFVKARTVTVKGPRGTLKRDF-KHLAIDIHMVNKRVLKVEKWFGTKKEIAAV 68
+KIP + + + + VKGP+GTL R + I+I L V K +KK A
Sbjct: 9 IKIPDNVNVSIDDQIIKVKGPKGTLSRKIPDLITIEI---QDNSLFVSKKDESKKARALH 65
Query: 69 RTVCSHISNMLKGVTKGFLYKMR 91
+ I+NM+ GV++GF K+
Sbjct: 66 GLYRTLINNMVIGVSEGFEKKLE 88
>gnl|CDD|236326 PRK08655, PRK08655, prephenate dehydrogenase; Provisional.
Length = 437
Score = 29.6 bits (67), Expect = 1.0
Identities = 18/84 (21%), Positives = 33/84 (39%), Gaps = 22/84 (26%)
Query: 41 LAIDIHMVNKRVLKVEKWFGTKKEIAAVRTVCSHISNMLK-GVTKGFLYKMRAAYAHF-- 97
L I M N ++ ++ + F + C +S ++K G + F+ +M+ A HF
Sbjct: 223 LYASIQMNNPQIPEIHETFIKE---------CEELSELVKNGDREEFVERMKEAAKHFGD 273
Query: 98 ----------PINCVTSENNTLLE 111
I + E LL+
Sbjct: 274 TERALGRSDKAIYALNQEFEKLLK 297
>gnl|CDD|107353 cd06358, PBP1_NHase, Type I periplasmic-binding protein of the
nitrile hydratase (NHase) system that selectively
converts nitriles to corresponding amides. This group
includes the type I periplasmic-binding protein of the
nitrile hydratase (NHase) system that selectively
converts nitriles to corresponding amides, which are
subsequently converted by amidases to yield free
carboxylic acids and ammonia. NHases from bacteria and
fungi have been purified and characterized. In
Rhodococcus sp., the nitrile hydratase operon consists
of six genes encoding NHase regulator 2, NHase regulator
1, amidase, NHase alpha subunit, NHase beta subunit, and
NHase activator. The operon produces a constitutive
hydratase that has a broad substrate spectrum: aliphatic
and aromatic nitriles, mononitriles and dinitriles,
hydroxynitriles and amino-nitriles, and a constitutive
amidase of equally low substrate specificity. NHases are
metalloenzymes containing either cobalt or iron, and
therefore can be classified into two subgroups: ferric
NHases and cobalt NHases.
Length = 333
Score = 28.8 bits (65), Expect = 1.6
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 22 ARTVTVKGPRGTLKRDFKHLAIDIH 46
V+ GPRGT+ +H ++
Sbjct: 305 LEDVSYDGPRGTVTMRGRHARQPVY 329
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 28.7 bits (64), Expect = 2.0
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 129 GVKVSNSKQKDE---------LIIEGNDIENVSRSAALIQQSTTVKN 166
V NS +E L+I GN I++V++ L + S TV
Sbjct: 489 NVSSDNSSASNEYSYNMSEQLLVIGGNPIKDVTKEENLAEWSKTVST 535
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.0 bits (63), Expect = 2.9
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 99 INCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELII 143
I C+ ++ L++ F +YI A V++ N K+ DELI+
Sbjct: 7 IPCLLLKDGGLVKTVKFKDPRYIGDPINA--VRIFNEKEVDELIV 49
>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 = 28.3 bits (63), Expect = 3.1
Identities = 29/97 (29%), Positives = 38/97 (39%), Gaps = 26/97 (26%)
Query: 117 GEKYIRRVKMAPGVKVSNSKQKDELI-----------IEGNDIE-----------NVSRS 154
+ R+K APG KV N + ELI ++ +E VS+
Sbjct: 558 ADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYAGVEVAKKGKAKQGYEVSQG 617
Query: 155 AAL--IQQSTTVKNKDIRKFL--DGLYVSEKTTVVTD 187
L I + T NKDI + DG YV T VV D
Sbjct: 618 GTLLWIPEETHEINKDISLLMVEDGQYVEAGTEVVKD 654
>gnl|CDD|226242 COG3719, Rna, Ribonuclease I [Translation, ribosomal structure and
biogenesis].
Length = 249
Score = 27.4 bits (61), Expect = 3.7
Identities = 8/67 (11%), Positives = 23/67 (34%), Gaps = 3/67 (4%)
Query: 1 MRQIVSNQTVKIPRGLQCFVKARTVTVKGPRGTLKRDFKHLAID-IHMVNKRVLKVEKWF 59
R++ + +K+P + +T++ + L D + + + E
Sbjct: 158 TRRL--FEELKLPPVRKLLADGKTLSRDEIEQAFDKANGGLKGDAVRVSCQGNYLTELRI 215
Query: 60 GTKKEIA 66
K++
Sbjct: 216 CLDKDLQ 222
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
0.320 0.133 0.374
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,077,497
Number of extensions: 817164
Number of successful extensions: 604
Number of sequences better than 10.0: 1
Number of HSP's gapped: 585
Number of HSP's successfully gapped: 27
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
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 (25.4 bits)