RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7547
(138 letters)
>gnl|CDD|240234 PTZ00027, PTZ00027, 60S ribosomal protein L6; Provisional.
Length = 190
Score = 60.9 bits (148), Expect = 2e-12
Identities = 22/38 (57%), Positives = 28/38 (73%)
Query: 3 NKRVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDF 40
+ + +KVE WFGT +A +RTVCSHI NM+ GVTK F
Sbjct: 50 DGKYIKVEMWFGTPSHLACIRTVCSHIKNMMTGVTKKF 87
>gnl|CDD|235496 PRK05518, rpl6p, 50S ribosomal protein L6P; Reviewed.
Length = 180
Score = 46.0 bits (110), Expect = 6e-07
Identities = 17/34 (50%), Positives = 20/34 (58%)
Query: 8 KVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
+E F KK A V T SHI NM+KGVT+ F
Sbjct: 53 VIETEFARKKTKAMVGTFASHIKNMIKGVTEGFE 86
>gnl|CDD|140206 PTZ00179, PTZ00179, 60S ribosomal protein L9; Provisional.
Length = 189
Score = 44.5 bits (105), Expect = 3e-06
Identities = 20/48 (41%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 2 VNK--RVLKVEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFTIFTNRC 47
VNK R +WFG+K + + T SH+ NM+ GVTK F F R
Sbjct: 46 VNKKNRTFTAVRWFGSKIPNSTINTALSHVRNMITGVTKGFR-FKVRF 92
>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 = 43.0 bits (102), Expect = 6e-06
Identities = 17/33 (51%), Positives = 21/33 (63%)
Query: 9 VEKWFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
+E F KK+ A V T SHI NM+KGVT+ F
Sbjct: 48 IETDFARKKDKAMVGTYRSHIKNMIKGVTEGFE 80
>gnl|CDD|215872 pfam00347, Ribosomal_L6, Ribosomal protein L6.
Length = 76
Score = 36.4 bits (85), Expect = 4e-04
Identities = 12/38 (31%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 6 VLKVEKWFGTKKE-----IAAVRTVCSHISNMLKGVTK 38
+ V G KE A + T + I NM KGV+
Sbjct: 38 KITVIIVSGIDKEKVGQFAALIGTYRAPIPNMGKGVSY 75
>gnl|CDD|223175 COG0097, RplF, Ribosomal protein L6P/L9E [Translation, ribosomal
structure and biogenesis].
Length = 178
Score = 34.8 bits (81), Expect = 0.005
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 10/49 (20%)
Query: 2 VNKRVLKVEK---------WFGTKKEIAAVRTVCSHISNMLKGVTKDFT 41
+ V+KVE G +K A TV + I+NM+KGVT+ F
Sbjct: 37 FHDNVVKVEVEDNILVVRPVDGKRKR-ALHGTVRALINNMVKGVTEGFE 84
>gnl|CDD|213843 TIGR03654, L6_bact, ribosomal protein L6, bacterial type.
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 175
Score = 29.7 bits (68), Expect = 0.31
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 24 TVCSHISNMLKGVTKDFT 41
T + I+NM+ GV++ F
Sbjct: 66 TTRALINNMVIGVSEGFE 83
>gnl|CDD|235495 PRK05498, rplF, 50S ribosomal protein L6; Validated.
Length = 178
Score = 29.3 bits (67), Expect = 0.49
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 24 TVCSHISNMLKGVTKDFT 41
T + I+NM+ GVT+ F
Sbjct: 67 TTRALINNMVVGVTEGFE 84
>gnl|CDD|183035 PRK11199, tyrA, bifunctional chorismate mutase/prephenate
dehydrogenase; Provisional.
Length = 374
Score = 28.3 bits (64), Expect = 1.5
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 4/27 (14%)
Query: 104 MRNTVISTNGSGFKTSSLTKPHINRKI 130
MR + S N GFKT P + R +
Sbjct: 79 MRESYSSENDKGFKT---LNPDL-RPV 101
>gnl|CDD|225107 COG2197, CitB, Response regulator containing a CheY-like receiver
domain and an HTH DNA-binding domain [Signal
transduction mechanisms / Transcription].
Length = 211
Score = 27.3 bits (61), Expect = 2.5
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 5/23 (21%)
Query: 17 KEIA-----AVRTVCSHISNMLK 34
KEIA + +TV +H+SN+L+
Sbjct: 167 KEIAEELNLSEKTVKTHVSNILR 189
>gnl|CDD|215965 pfam00516, GP120, Envelope glycoprotein GP120. The entry of HIV
requires interaction of viral GP120 with CD4 and a
chemokine receptor on the cell surface.
Length = 493
Score = 27.4 bits (61), Expect = 3.2
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 9/48 (18%)
Query: 74 PPGYDM--CQSLCYNGTINVHRCTNI-AHDCTSMRNTVIST----NGS 114
P G+ + C +NG +C+N+ CT V+ST NGS
Sbjct: 203 PAGFAILKCNDKKFNGF--GPKCSNVSTVQCTHGIRPVVSTQLLLNGS 248
>gnl|CDD|143632 cd07430, GH15_N, Glycoside hydrolase family 15, N-terminal domain.
Members of this family are N-terminal domains uniquely
found in bacterial and archaeal glucoamylases and
glucodextranases. Glucoamylase (glucan
1,4-alpha-glucosidase; 4-alpha-D-glucan glucohydrolase;
amyloglucosidase; exo-1,4-alpha-glucosidase;
gamma-amylase; lysosomal alpha-glucosidase; EC 3.2.1.3)
hydrolyzes beta-1,4-glucosidic linkages of starch,
glycogen and malto-oligosaccharides, releasing
beta-D-glucose from the non-reducing end.
Glucodextranase (glucan 1,6-alpha-glucosidase;
exo-1,6-alpha-glucosidase; EC 3.2.1.70) uses an
inverting reaction mechanism to hydrolyze
alpha-1,6-glucosidic linkages of dextran and related
oligosaccharides, releasing beta-D-glucose from the
non-reducing end. These N-terminal domains adopt a
structure consisting of antiparallel beta-strands,
divided into two beta-sheets, with one sheet wrapped by
an extended polypeptide, which appears to stabilize the
domain. The function of these domains in the enzymes is
as yet unknown. However, it is suggested that domain N
of bacterial GA is involved in folding and/or the
thermostability of the A domain that forms an
(alpha/alpha)6-barrel structure.
Length = 260
Score = 26.4 bits (59), Expect = 4.5
Identities = 9/40 (22%), Positives = 15/40 (37%)
Query: 88 TINVHRCTNIAHDCTSMRNTVISTNGSGFKTSSLTKPHIN 127
+ T+ D MR + +G G + L PH+
Sbjct: 97 RLEKEIFTDPDRDVLLMRVRFEALDGGGLRLYVLLAPHLG 136
>gnl|CDD|223973 COG1043, LpxA, Acyl-[acyl carrier protein].
Length = 260
Score = 26.0 bits (58), Expect = 6.3
Identities = 7/24 (29%), Positives = 11/24 (45%), Gaps = 4/24 (16%)
Query: 89 INVHRCTNIAHDCTSMRNTVISTN 112
H +AHDC N +++ N
Sbjct: 117 AYAH----VAHDCVIGNNCILANN 136
>gnl|CDD|109261 pfam00196, GerE, Bacterial regulatory proteins, luxR family.
Length = 58
Score = 24.4 bits (54), Expect = 7.0
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 5/25 (20%)
Query: 15 TKKEIAAV-----RTVCSHISNMLK 34
+ KEIA + +TV H SN+++
Sbjct: 20 SNKEIADILGISEKTVKVHRSNIMR 44
>gnl|CDD|220204 pfam09362, DUF1996, Domain of unknown function (DUF1996). This
family of proteins are functionally uncharacterized.
Length = 228
Score = 25.7 bits (57), Expect = 9.6
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 52 CYSCAGGNCSYKMTSSYPSIICPPG 76
+ C GG T+++P+ CP G
Sbjct: 114 SFRCLGGENRGPDTNAFPTEPCPGG 138
>gnl|CDD|237198 PRK12771, PRK12771, putative glutamate synthase (NADPH) small
subunit; Provisional.
Length = 564
Score = 25.6 bits (57), Expect = 9.8
Identities = 7/12 (58%), Positives = 8/12 (66%), Gaps = 2/12 (16%)
Query: 49 SRRCYSCAGGNC 60
+ RC SC GNC
Sbjct: 503 AARCLSC--GNC 512
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 0.132 0.421
Gapped
Lambda K H
0.267 0.0624 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,326,005
Number of extensions: 489473
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 344
Number of HSP's successfully gapped: 28
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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: 54 (24.8 bits)