RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7622
(179 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 169 bits (431), Expect = 3e-54
Identities = 70/111 (63%), Positives = 82/111 (73%), Gaps = 1/111 (0%)
Query: 34 GTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEK 93
GT +A +RTVCSHI NM+ GVTK F YKMR YAHFPIN ++N +EIRNFLGEK
Sbjct: 61 GTPSHLACIRTVCSHIKNMMTGVTKKFQYKMRLVYAHFPINSNITDNGKTIEIRNFLGEK 120
Query: 94 YIRRVKMAPGVKVSNSKQ-KDELIIEGNDIENVSRSAALIQQSTTVKNKDI 143
+R VKM PGV V S+ KDE+I+ G D+E VSRSAALI QST V+NKDI
Sbjct: 121 RVRTVKMLPGVVVEKSESVKDEIIVTGADLELVSRSAALIHQSTLVRNKDI 171
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 132 bits (334), Expect = 1e-39
Identities = 51/114 (44%), Positives = 73/114 (64%), Gaps = 4/114 (3%)
Query: 29 VDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRN 88
++ + KK A V T SHI NM+KGVT+GF YK++ Y+HFP+ V + N + I N
Sbjct: 54 IETEFARKKTKAMVGTFASHIKNMIKGVTEGFEYKLKIVYSHFPMQ-VKVQGNE-VVIEN 111
Query: 89 FLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKD 142
FLGEK RR K+ GVKV +++I+EG D E+V ++AA I+Q+T +K D
Sbjct: 112 FLGEKSPRRAKILGGVKVKVK--GEDVIVEGIDKEDVGQTAANIEQATKIKGFD 163
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 128 bits (324), Expect = 5e-38
Identities = 67/130 (51%), Positives = 84/130 (64%), Gaps = 8/130 (6%)
Query: 17 LNKTYRWEETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCV 76
+NK R TF G+K + + T SH+ NM+ GVTKGF +K+R AYAHFPI+
Sbjct: 46 VNKKNR---TFTAVRWFGSKIPNSTINTALSHVRNMITGVTKGFRFKVRFAYAHFPIS-- 100
Query: 77 TSENNTLLEIRNFLGEKYIRRVKMAPGVKVSN---SKQKDELIIEGNDIENVSRSAALIQ 133
S N L+EIRNFLGEK +RR +A VKV SK KDEL++EGND+E VSR AA++
Sbjct: 101 VSVENQLVEIRNFLGEKRVRRQVVADTVKVYRTDPSKVKDELVLEGNDLEQVSREAAVMH 160
Query: 134 QSTTVKNKDI 143
Q VK KDI
Sbjct: 161 QLCLVKKKDI 170
>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 = 125 bits (315), Expect = 6e-37
Identities = 54/114 (47%), Positives = 74/114 (64%), Gaps = 4/114 (3%)
Query: 29 VDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRN 88
++ D KK+ A V T SHI NM+KGVT+GF YKM+ Y+HFP+ V E N + I N
Sbjct: 48 IETDFARKKDKAMVGTYRSHIKNMIKGVTEGFEYKMKVVYSHFPMQ-VKVEGNK-VVIEN 105
Query: 89 FLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKD 142
FLGEK RR K+ GVKV +E+I+ G D E+V ++AA I+Q+T +K +D
Sbjct: 106 FLGEKAPRRAKIPGGVKVKVK--GEEVIVTGIDKEDVGQTAANIEQATRIKGRD 157
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 99.5 bits (249), Expect = 7e-27
Identities = 31/114 (27%), Positives = 52/114 (45%), Gaps = 8/114 (7%)
Query: 29 VDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKMRAAYAHFPINCVTSENNTLLEIRN 88
V +G +K A TV + I+NM+KGVT+GF K+ + V +
Sbjct: 53 VRPVDGKRKR-ALHGTVRALINNMVKGVTEGFEKKLEIVGVGYRAQVVGG------NLEL 105
Query: 89 FLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNKD 142
FLG + +++ G+ V E+++EG D E V + AA I+ + +
Sbjct: 106 FLGYSHPVVIEIPEGITVEVPGP-TEIVVEGIDKELVGQVAANIRAARKPEPYK 158
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 60.3 bits (147), Expect = 8e-13
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 3/74 (4%)
Query: 71 FPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAA 130
P+ S + + LG K ++ PGV V ++ +I+ G D E V + AA
Sbjct: 1 IPVGVRVSIDGV--NLVLVLGPKGELTREIPPGVTVKV-EKITVIIVSGIDKEKVGQFAA 57
Query: 131 LIQQSTTVKNKDIH 144
LI
Sbjct: 58 LIGTYRAPIPNMGK 71
Score = 35.6 bits (83), Expect = 0.001
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 25 ETFDVDCDNGTKKE-----IAAVRTVCSHISNMLKGVTKG 59
E V +G KE A + T + I NM KGV+ G
Sbjct: 37 EKITVIIVSGIDKEKVGQFAALIGTYRAPIPNMGKGVSYG 76
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 33.5 bits (78), Expect = 0.031
Identities = 29/122 (23%), Positives = 47/122 (38%), Gaps = 43/122 (35%)
Query: 29 VDCDNGTKKEIAAVRTVCSHISNMLKGVTKGFLYKM-------RAA-----------YAH 70
V + +KK A T + I+NM+ GVT+GF K+ RA Y+H
Sbjct: 52 VTRPDDSKKARALHGTTRALINNMVVGVTEGFEKKLEIVGVGYRAQVKGKKLNLSLGYSH 111
Query: 71 FPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAA 130
P+ ++ G+ V K E++++G D + V + AA
Sbjct: 112 -PVE-----------------------YEIPEGITVEVPKPT-EIVVKGIDKQLVGQVAA 146
Query: 131 LI 132
I
Sbjct: 147 EI 148
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 32.4 bits (75), Expect = 0.065
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 44 TVCSHISNMLKGVTKGF 60
T + I+NM+ GV++GF
Sbjct: 66 TTRALINNMVIGVSEGF 82
>gnl|CDD|234891 PRK01033, PRK01033, imidazole glycerol phosphate synthase subunit
HisF; Provisional.
Length = 258
Score = 28.4 bits (64), Expect = 2.1
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 73 INCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELII 117
I C+ ++ L++ F +YI A V++ N K+ DELI+
Sbjct: 7 IPCLLLKDGGLVKTVKFKDPRYIGDPINA--VRIFNEKEVDELIV 49
>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 = 28.2 bits (63), Expect = 2.4
Identities = 22/70 (31%), Positives = 27/70 (38%), Gaps = 7/70 (10%)
Query: 1 MCIR-NLNPGGGGGCLYLNKTYRW-EETFDVDCDNGTKKEIAAVRTVCSHISNMLKGVTK 58
C+ GG CLY K W EE F + KE +RTV I + V K
Sbjct: 271 ECLSCEYRRYCGGRCLYAIKERYWGEEGFKAVDE--VTKEY--LRTVLEIIPEIESLVDK 326
Query: 59 GFLYKMRAAY 68
G K+ Y
Sbjct: 327 GV-IKLSDLY 335
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 27.9 bits (62), Expect = 3.8
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 9/47 (19%)
Query: 103 GVKVSNSKQKDE---------LIIEGNDIENVSRSAALIQQSTTVKN 140
V NS +E L+I GN I++V++ L + S TV
Sbjct: 489 NVSSDNSSASNEYSYNMSEQLLVIGGNPIKDVTKEENLAEWSKTVST 535
>gnl|CDD|177062 CHL00140, rpl6, ribosomal protein L6; Validated.
Length = 178
Score = 26.8 bits (60), Expect = 4.8
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 44 TVCSHISNMLKGVTKGFLYKMR 65
+ I+NM+ GV++GF K+
Sbjct: 67 LYRTLINNMVIGVSEGFEKKLE 88
>gnl|CDD|218666 pfam05633, DUF793, Protein of unknown function (DUF793). This
family consists of several plant proteins of unknown
function.
Length = 389
Score = 27.5 bits (61), Expect = 4.8
Identities = 18/75 (24%), Positives = 27/75 (36%), Gaps = 10/75 (13%)
Query: 82 TLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIENVSRSAALIQQSTTVKNK 141
T L+ R LGE +RR K K +L I D ++ S + + ++
Sbjct: 140 TALKQRRPLGEGQVRRAK----------KALTDLAIGMLDEKDSGGSGGGHRNRSFGRSW 189
Query: 142 DIHLNPGGGGGGCLY 156
H G GG
Sbjct: 190 SFHHRSIGSSGGGTG 204
>gnl|CDD|173391 PTZ00098, PTZ00098, phosphoethanolamine N-methyltransferase;
Provisional.
Length = 263
Score = 26.5 bits (58), Expect = 8.2
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 10/47 (21%)
Query: 123 ENVSRSAALIQQSTTVKNKDIHLNP--------GGGGGGCLYLNKTY 161
E+ S + +TT DI LN G GGGC Y+N+ Y
Sbjct: 30 EDYISSGGIE--ATTKILSDIELNENSKVLDIGSGLGGGCKYINEKY 74
>gnl|CDD|147812 pfam05858, BIV_Env, Bovine immunodeficiency virus surface protein
(SU). The bovine lentivirus also known as the bovine
immunodeficiency-like virus (BIV) has conserved and
hypervariable regions in the surface envelope gene. This
family corresponds to the SU surface protein.
Length = 548
Score = 26.6 bits (58), Expect = 8.4
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 6/71 (8%)
Query: 82 TLLEIRNFLGEKYIRRVKMAPGVKVSNSKQKDELIIEGNDIEN------VSRSAALIQQS 135
L + R LG+ + R + G SN +Q L + N + S L Q +
Sbjct: 448 QLNKSREDLGKNFNRPLSCVGGDLSSNCEQHTTLCGYNTNCLNFGNRAFSTNSLILCQHN 507
Query: 136 TTVKNKDIHLN 146
+T L+
Sbjct: 508 STQNKTFYSLS 518
>gnl|CDD|219396 pfam07388, A-2_8-polyST, Alpha-2,8-polysialyltransferase (POLYST).
This family contains the bacterial enzyme
alpha-2,8-polysialyltransferase (EC:2.4.99.-)
(approximately 500 residues long). This catalyzes the
polycondensation of alpha-2,8-linked sialic acid
required for the synthesis of polysialic acid (PSA).
Length = 414
Score = 26.4 bits (58), Expect = 10.0
Identities = 17/72 (23%), Positives = 25/72 (34%), Gaps = 12/72 (16%)
Query: 58 KGFLYKMRAAYAHFPINCVTSENNTLLEIRNFLGEKYIRRVKMAPGVKVSNS--KQKDEL 115
KG+ K + FP +I F +KY R G+ S + +
Sbjct: 184 KGYPDKFDILHVTFP--------EYAKKI--FNAKKYFRFFAHIGGISSSTRIANLQHKY 233
Query: 116 IIEGNDIENVSR 127
I ND VS+
Sbjct: 234 RISRNDYIFVSQ 245
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 0.420
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,883,327
Number of extensions: 777138
Number of successful extensions: 601
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 24
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
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 (25.5 bits)