RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 034832
(82 letters)
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 72.5 bits (179), Expect = 2e-17
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
D +H +GKVS E L+EN+ A ++A+ AKPA K T Y+ S + STMGP
Sbjct: 165 DKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGT-----YIKSVSLSSTMGP 219
Query: 62 SFPVSIQSLS 71
V SL+
Sbjct: 220 GVKVDPSSLA 229
>gnl|CDD|211630 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast.
This model describes bacterial (and chloroplast)
ribosomal protein L1. The apparent mitochondrial L1 is
sufficiently diverged to be the subject of a separate
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 227
Score = 69.2 bits (170), Expect = 4e-16
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
D N+H +GKVS E L+EN+ A ++A+ AKP+G K Y+ + + STMGP
Sbjct: 164 DKAGNIHAPIGKVSFDSEKLKENLEALLDAIKKAKPSGAK-----GQYIKNIALSSTMGP 218
Query: 62 SFPVSIQSL 70
V + SL
Sbjct: 219 GIKVDLNSL 227
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 57.2 bits (139), Expect = 1e-11
Identities = 27/65 (41%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
D +HV +GKVS +E L EN+ A +NA++ AKPAG K Y+ S ++ +TMG
Sbjct: 166 ADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQ-----YIKSVYVSTTMG 220
Query: 61 PSFPV 65
P V
Sbjct: 221 PGVKV 225
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed.
Length = 229
Score = 56.9 bits (138), Expect = 1e-11
Identities = 28/70 (40%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
D T VHV GK + EE L EN+ A ++ +P+G+K Y SF++CSTMGP
Sbjct: 165 DKTGIVHVLFGKSNFTEEDLLENLQAIYESIEQNRPSGVK-----GKYWKSFYICSTMGP 219
Query: 62 SFPVSIQSLS 71
S + I L
Sbjct: 220 SIQIDISLLR 229
>gnl|CDD|238235 cd00403, Ribosomal_L1, Ribosomal protein L1. The L1 protein,
located near the E-site of the ribosome, forms part of
the L1 stalk along with 23S rRNA. In bacteria and
archaea, L1 functions both as a ribosomal protein that
binds rRNA, and as a translation repressor that binds
its own mRNA. Like several other large ribosomal
subunit proteins, L1 displays RNA chaperone activity.
L1 is one of the largest ribosomal proteins. It is
composed of two domains that cycle between open and
closed conformations via a hinge motion. The RNA-binding
site of L1 is highly conserved, with both mRNA and rRNA
binding the same binding site.
Length = 208
Score = 56.0 bits (136), Expect = 2e-11
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 1 MDNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMG 60
+D +HV +GKVS+ E L EN+ A +NAL+ P+ + + S ++ +TMG
Sbjct: 150 LDKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLPSKKGQ------NIKSIYLKTTMG 203
Query: 61 PSFPV 65
PS P+
Sbjct: 204 PSLPI 208
>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This
family includes prokaryotic L1 and eukaryotic L10.
Length = 200
Score = 47.2 bits (113), Expect = 5e-08
Identities = 24/61 (39%), Positives = 34/61 (55%), Gaps = 7/61 (11%)
Query: 2 DNTSNVHVGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVNSFHMCSTMGP 61
D +HV +GKVS+ E L EN+ A +NAL +KK K + S ++ +TMGP
Sbjct: 147 DKGGCIHVKVGKVSMSPEELVENIEAVINAL-------VKKLPKGWQNIKSVYLKTTMGP 199
Query: 62 S 62
S
Sbjct: 200 S 200
>gnl|CDD|112335 pfam03512, Glyco_hydro_52, Glycosyl hydrolase family 52.
Length = 428
Score = 27.5 bits (61), Expect = 0.60
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 29 VNALLLAKPAGLKKTSKFA------GYVNSFHMCSTMGPSFPVSIQSLSR-ALDQYNKVA 81
ALL+ PAG KKT +FA G V + S + +I+ + AL Q+N++
Sbjct: 215 TGALLMDVPAGEKKTYRFAVCFYRGGVVTAGMDTSYYYTRYFANIEEVGEYALAQFNRLL 274
>gnl|CDD|215460 PLN02855, PLN02855, Bifunctional selenocysteine lyase/cysteine
desulfurase.
Length = 424
Score = 27.8 bits (62), Expect = 0.60
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 5 SNVHVGLGKVSLKE----ELLRENVGAFVNA 31
SNVH G+ +S K EL R+ V AF+NA
Sbjct: 61 SNVHRGIHALSAKATDAYELARKKVAAFINA 91
>gnl|CDD|220191 pfam09344, Cas_CT1975, CT1975-like protein. CRISPR is a term for
Clustered, Regularly Interspaced Short Palidromic
Repeats. A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family is represented
by CT1975 of Chlorobium tepidum.
Length = 353
Score = 27.7 bits (62), Expect = 0.65
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 18 EELLRENVGAFVNALLLAKPAGLKKTSKFAGY 49
EEL E V A A + P+G K+ S FA
Sbjct: 234 EELALEAVEALTEAFVTVSPSG-KQNS-FAPR 263
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 25.9 bits (57), Expect = 2.1
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 11/57 (19%)
Query: 9 VGLGKVSLKEELLRENVGAFVNALLLAKPAGLKKTSKFAGYVN--SFHMCSTMGPSF 63
V +G V + EE LR+N+ +N L+ + LKK + N + H+ STMG
Sbjct: 166 VAVGNVEMTEEQLRQNIVLSINFLV----SLLKK-----NWQNIKTLHIKSTMGKPQ 213
>gnl|CDD|177251 MTH00208, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 628
Score = 24.9 bits (55), Expect = 5.3
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 49 YVNSFHMCSTMGPSFPVSIQSLSRALDQ 76
+VN H SF S+ +R LD+
Sbjct: 551 FVNISHSIIISF-SFFTSLFGSTRTLDR 577
>gnl|CDD|237006 PRK11867, PRK11867, 2-oxoglutarate ferredoxin oxidoreductase
subunit beta; Reviewed.
Length = 286
Score = 24.4 bits (54), Expect = 8.9
Identities = 10/47 (21%), Positives = 18/47 (38%), Gaps = 12/47 (25%)
Query: 26 GAFVNALLLAKPA-GLKK-----------TSKFAGYVNSFHMCSTMG 60
G+ + AL A GL + + GY+N++ + G
Sbjct: 26 GSILAALQRALAELGLDPENVAVVSGIGCSGRLPGYINTYGFHTIHG 72
>gnl|CDD|213531 TIGR00447, pth, peptidyl-tRNA hydrolase. The natural substrate
for this enzyme may be peptidyl-tRNAs that drop off the
ribosome during protein synthesis. Peptidyl-tRNA
hydrolase is a bacterial protein; YHR189W from
Saccharomyces cerevisiae appears to be orthologous and
likely has the same function [Protein synthesis,
Other].
Length = 188
Score = 24.2 bits (53), Expect = 9.2
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 9 VGLGKVSLKEELLRENVGAFVNALLLAK-PAGLKKTSKFAGYVNSF 53
VGLG K R N G +V LL ++ L+ KF GY
Sbjct: 5 VGLGNPGKKYAGTRHNAGFWVLDLLASRLGLSLRTEKKFFGYTERG 50
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
0.317 0.130 0.367
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,886,107
Number of extensions: 293831
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 13
Length of query: 82
Length of database: 10,937,602
Length adjustment: 51
Effective length of query: 31
Effective length of database: 8,675,548
Effective search space: 268941988
Effective search space used: 268941988
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: 53 (24.2 bits)