RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 019646
(337 letters)
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed.
Length = 229
Score = 348 bits (896), Expect = e-121
Identities = 134/216 (62%), Positives = 170/216 (78%), Gaps = 1/216 (0%)
Query: 114 ISTKPKKGKAALPLKRDRMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVK 173
I K + A+ L ++ ++ KF ETAEAH LNIDPKY DQQLR TV+LPKGTGK+++
Sbjct: 15 IEKKLYSPEEAINLLKE-TATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTGKTIR 73
Query: 174 VAVLAQGEKFNEAKNAGADLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPR 233
+AVL EK EAKNAGAD+VG DDLIE+I G ++FD LIA+PDMM K+A LG++LGPR
Sbjct: 74 IAVLTNEEKITEAKNAGADIVGSDDLIEEITKGNLDFDLLIATPDMMPKLAKLGRVLGPR 133
Query: 234 GLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVK 293
GLMP+PK+GTVTT++ AI EFKKGK+EYRADKTGIVH+ FGK++F+E+DLL N A +
Sbjct: 134 GLMPSPKSGTVTTDLASAINEFKKGKLEYRADKTGIVHVLFGKSNFTEEDLLENLQAIYE 193
Query: 294 SIEANKPKGAKGVYWKSAYICSSMGPSIRLNIKEML 329
SIE N+P G KG YWKS YICS+MGPSI+++I +
Sbjct: 194 SIEQNRPSGVKGKYWKSFYICSTMGPSIQIDISLLR 229
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 332 bits (854), Expect = e-115
Identities = 105/199 (52%), Positives = 141/199 (70%)
Query: 132 MSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGA 191
++ KF ET + L +DP+ DQQ+R V LP GTGK+V+VAV A+GEK EAK AGA
Sbjct: 32 TATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKTVRVAVFAKGEKAEEAKAAGA 91
Query: 192 DLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQA 251
D+VGG+DLIE+IKGG+++FD +IA+PDMM KV LG+ILGPRGLMPNPK GTVT ++ +A
Sbjct: 92 DIVGGEDLIEKIKGGWLDFDVVIATPDMMGKVGKLGRILGPRGLMPNPKTGTVTMDVAKA 151
Query: 252 IEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSA 311
++E K GKVE+R DK GI+H P GK F + L N A + +I+ KP AKG Y KS
Sbjct: 152 VKEAKAGKVEFRVDKAGIIHAPIGKVSFDAEKLKENLKALIDAIKKAKPATAKGTYIKSV 211
Query: 312 YICSSMGPSIRLNIKEMLD 330
+ S+MGP ++++ +
Sbjct: 212 SLSSTMGPGVKVDPSSLAA 230
>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 = 307 bits (788), Expect = e-105
Identities = 107/196 (54%), Positives = 142/196 (72%)
Query: 132 MSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGA 191
++ KF ET E RL IDP+ +DQQ+R +V LP GTGK+V+VAV A+GEK EAK AGA
Sbjct: 31 TATAKFDETVEVAIRLGIDPRKSDQQVRGSVVLPHGTGKTVRVAVFAKGEKAKEAKAAGA 90
Query: 192 DLVGGDDLIEQIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQA 251
D VG DDLIE+IK G+++FD +IA+PDMM V LG+ILGPRGLMPNPK GTVTT++ +A
Sbjct: 91 DYVGSDDLIEKIKKGWLDFDVVIATPDMMRVVGKLGRILGPRGLMPNPKTGTVTTDVAKA 150
Query: 252 IEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSA 311
++ KKG+VE+RADK G +H P GK F + L N A + +I+ KP GAKG Y K+
Sbjct: 151 VKNAKKGQVEFRADKAGNIHAPIGKVSFDSEKLKENLEALLDAIKKAKPSGAKGQYIKNI 210
Query: 312 YICSSMGPSIRLNIKE 327
+ S+MGP I++++
Sbjct: 211 ALSSTMGPGIKVDLNS 226
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 275 bits (705), Expect = 1e-92
Identities = 106/194 (54%), Positives = 137/194 (70%), Gaps = 1/194 (0%)
Query: 133 SSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEAKNAGAD 192
S KF ET E L +DP+ DQ++R +V LP GTGK+V+VAV A GEK EAK AGAD
Sbjct: 34 SKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPNGTGKTVRVAVFADGEKAEEAKAAGAD 93
Query: 193 LVGGDDLIEQIKGG-FMEFDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQA 251
VGG+DLIE IK G +FD IA+PDMM V LGK+LGPRGLMPNPK GTVT ++ +A
Sbjct: 94 YVGGEDLIELIKNGRAKDFDVFIATPDMMPLVGKLGKVLGPRGLMPNPKTGTVTDDVAKA 153
Query: 252 IEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGAKGVYWKSA 311
+EE KKG VE+RADK G++H+P GK F ++ L N A + +I KP GAKG Y KS
Sbjct: 154 VEELKKGTVEFRADKAGVIHVPIGKVSFDDEKLAENIEALLNAIVKAKPAGAKGQYIKSV 213
Query: 312 YICSSMGPSIRLNI 325
Y+ ++MGP +++++
Sbjct: 214 YVSTTMGPGVKVDL 227
>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 = 227 bits (582), Expect = 3e-74
Identities = 92/203 (45%), Positives = 123/203 (60%), Gaps = 8/203 (3%)
Query: 127 LKRDRMSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNEA 186
LK+ + KF ET E L D + DQ++R TV LP G GK VKV V A+ E+ EA
Sbjct: 8 LKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAKDEQAKEA 67
Query: 187 KNAGADLVGGDDLIEQIKGG-----FMEFDKLIASP-DMMVKVASLGKILGPRGLMPNPK 240
K AGAD+VGG+DL ++IK G +FD +A P MM+ LGK+LGPRG MPNPK
Sbjct: 68 KAAGADVVGGEDLKKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPRGKMPNPK 127
Query: 241 AGTVTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKP 300
GTVT ++ +AIEE K VE+R DK G +H+P GK S + L+ N A + ++ P
Sbjct: 128 TGTVTEDLAKAIEEAKS-SVEFRLDKGGCIHVPVGKVSMSPEQLVENIEAVINALVKKLP 186
Query: 301 KGAKGVYWKSAYICSSMGPSIRL 323
KG KS Y+ ++MGPS+ +
Sbjct: 187 S-KKGQNIKSIYLKTTMGPSLPI 208
>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This
family includes prokaryotic L1 and eukaryotic L10.
Length = 200
Score = 207 bits (528), Expect = 2e-66
Identities = 91/197 (46%), Positives = 121/197 (61%), Gaps = 11/197 (5%)
Query: 132 MSSTKFTETAEAHFRLNIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGE--KFNEAKNA 189
+ KF ET E L DP+ DQ +R TV LP G GK VKV V+A+ K EAK+A
Sbjct: 7 TAKRKFDETVELQINLKKDPRKKDQNVRGTVVLPHGLGKDVKVCVIAKDPEAKAKEAKDA 66
Query: 190 GADLVGGDDLIE--QIKGG---FMEFDKLIASPDMMVKVAS-LGKILGPRGLMPNPKAGT 243
GAD+VGG+DL E +IK G +FD +A PD+M + LGK+LGPRG MPNPK T
Sbjct: 67 GADVVGGEDLKEKYKIKKGRKLAKDFDVFLADPDIMPLLPKLLGKVLGPRGKMPNPKT-T 125
Query: 244 VTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVKSIEANKPKGA 303
VT ++ +AIEE K G VE+R DK G +H+ GK S ++L+ N A + ++ PKG
Sbjct: 126 VTPDVAKAIEEAKSGTVEFRKDKGGCIHVKVGKVSMSPEELVENIEAVINALVKKLPKGW 185
Query: 304 KGVYWKSAYICSSMGPS 320
+ KS Y+ ++MGPS
Sbjct: 186 Q--NIKSVYLKTTMGPS 200
>gnl|CDD|235254 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
Length = 215
Score = 119 bits (300), Expect = 3e-32
Identities = 70/210 (33%), Positives = 103/210 (49%), Gaps = 18/210 (8%)
Query: 122 KAALPLKRDRMSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQG 180
K AL R FT++ + L +ID K + ++ V LP G GK VK+AV+A+G
Sbjct: 12 KEALEEAPKR----NFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAKG 67
Query: 181 EKFNEAKNAGADLVGGDDLIEQIKGGFMEFDKL-------IASPDMMVKVA-SLGKILGP 232
E +AK AGAD V + +E++ G KL IA D+M + LG +LGP
Sbjct: 68 ELALQAKEAGADYVITREELEELGGDKRAAKKLANEYDFFIAEADLMPLIGRYLGPVLGP 127
Query: 233 RGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAV 292
RG MP P +I +E K V R H+ G D S ++L N A +
Sbjct: 128 RGKMPTPLPPNA--DIKPLVERLKN-TVRIRTKDQPTFHVRVGTEDMSPEELAENIDAVL 184
Query: 293 KSIEANKPKGAKGVYWKSAYICSSMGPSIR 322
IE+ KG + + KS Y+ ++MGP+++
Sbjct: 185 NRIESKLEKGRQNI--KSVYVKTTMGPAVK 212
>gnl|CDD|233298 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial. This
model represents the mitochondrial homolog of bacterial
ribosomal protein L1. Unlike chloroplast L1, this form
was not sufficiently similar to bacterial forms to
include in a single bacterial/organellar L1 model
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 141
Score = 96.4 bits (240), Expect = 2e-24
Identities = 53/119 (44%), Positives = 76/119 (63%), Gaps = 6/119 (5%)
Query: 146 RLNIDPKYNDQ----QLRATVSLPKGTGKSVKVAVLAQGE-KFNEAKNAGADLVGGDDLI 200
+N+D + ++ S P GK K+AV +G + EA+ AGAD VGGDDLI
Sbjct: 23 SVNLDIGLLMELGKESVQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGGDDLI 82
Query: 201 EQIKGGFME-FDKLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKG 258
++I+ G ++ FD LIA PD++ ++A L ++LGP+GLMP+PK GTV N+ IE FKKG
Sbjct: 83 KKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMPSPKRGTVGDNLLSMIETFKKG 141
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 60.9 bits (148), Expect = 7e-11
Identities = 52/210 (24%), Positives = 94/210 (44%), Gaps = 24/210 (11%)
Query: 127 LKRDRMSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQGEKFNE 185
L+ KF ET E L + D + D++ +V LP ++KV VL +E
Sbjct: 17 LEGSEEKKRKFVETVELQIGLKDYDTQ-KDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDE 75
Query: 186 AKNAGADLVGGDDLIE------QIKGGFMEFDKLIASPDMMVKVASLGKILGPRGLMPNP 239
AK G D + + L + +K ++D +AS ++ ++ ++LGP GL
Sbjct: 76 AKKLGLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSLLPQIP---RLLGP-GL---N 128
Query: 240 KAG------TVTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAVK 293
KAG T +I I E K V+++ K + + G + +E+ L N + ++
Sbjct: 129 KAGKFPTLITHNDDIEDKINELKS-SVKFQLKKVLCLGVAVGNVEMTEEQLRQNIVLSIN 187
Query: 294 SIEANKPKGAKGVYWKSAYICSSMGPSIRL 323
+ + K + + K+ +I S+MG R+
Sbjct: 188 FLVSLLKKNWQNI--KTLHIKSTMGKPQRI 215
>gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional.
Length = 214
Score = 34.3 bits (78), Expect = 0.058
Identities = 44/211 (20%), Positives = 95/211 (45%), Gaps = 20/211 (9%)
Query: 122 KAALPLKRDRMSSTKFTETAEAHFRL-NIDPKYNDQQLRATVSLPKGTGKSVKVAVLAQG 180
+A L + ++R KF E+ + L N DP+ D++ ++ LP + V +L
Sbjct: 14 QAVLKVDKER----KFKESIDLQVNLKNYDPQ-KDKRFSGSLKLPNVCRPRMTVCLLCDL 68
Query: 181 EKFNEAKNAGADLVGGDDLIEQ------IKGGFMEFDKLIASPDMMVKVASLGKILGPR- 233
+ AK G + ++L + +K ++D + S + + ++ +++GP
Sbjct: 69 VHEDIAKKEGVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESI---IKTVPRLVGPHM 125
Query: 234 -GLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADKTGIVHIPFGKADFSEDDLLINFLAAV 292
+ P + + ++P + E + V+++ K + G + +E+ L N + A+
Sbjct: 126 HRMGKFPTVCSPSESLPDKVVELRS-TVKFQLKKVLCLGTCVGHVEMTEEQLRQNVVMAI 184
Query: 293 KSIEANKPKGAKGVYWKSAYICSSMGPSIRL 323
+ + K + + KSAYI S+MG R+
Sbjct: 185 NFLVSLLKKNWQNL--KSAYIKSTMGKPQRI 213
>gnl|CDD|236914 PRK11466, PRK11466, hybrid sensory histidine kinase TorS;
Provisional.
Length = 914
Score = 34.1 bits (78), Expect = 0.12
Identities = 20/44 (45%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 173 KVAVLAQGEKFNEAKNAGADLVGGDDLIEQIKGGFME--FDKLI 214
++A LAQG+ N A +AGA G DLIEQ + E D+LI
Sbjct: 150 EIARLAQGQANNAATSAGATQAGIYDLIEQDQRQAAESALDRLI 193
>gnl|CDD|220262 pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2
(CRISPR_cse2). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family of proteins,
represented by CT1973 from Chlorobaculum tepidum, is
encoded by genes found in the CRISPR/Cas subtype Ecoli
regions of many bacteria (most of which are mesophiles),
and not in Archaea. It is designated Cse2.
Length = 143
Score = 28.5 bits (64), Expect = 3.1
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 121 GKAALPLKRDRMSSTKFTETAEAHFRLNID-PKYND--QQLRATVSLPKGTGKSVKVAVL 177
G+A L++D S + +E FR + ++ ++LR V L +G G V A L
Sbjct: 65 GRALARLRQDGDKS----DVSERRFRQLLRADTPDELLRRLRRLVRLLRGDGVPVDYADL 120
Query: 178 AQ 179
A+
Sbjct: 121 AR 122
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 28.8 bits (65), Expect = 5.8
Identities = 13/55 (23%), Positives = 23/55 (41%)
Query: 212 KLIASPDMMVKVASLGKILGPRGLMPNPKAGTVTTNIPQAIEEFKKGKVEYRADK 266
++I P +M+ V L I PRG+ I + + + K +Y+ D
Sbjct: 39 RIILPPLVMIAVTVLISIFQPRGIFIIASIAMSLVTIIFSTTTYFREKKKYKKDV 93
>gnl|CDD|235583 PRK05731, PRK05731, thiamine monophosphate kinase; Provisional.
Length = 318
Score = 27.9 bits (63), Expect = 7.6
Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 25/88 (28%)
Query: 150 DPKYNDQQLRATVSL--PKGTGKSVKVAVLAQGEKFNEAKNAGADLVGGDDLIEQIKGGF 207
P ++L PK ++ + LA G F A GA+L+GGD
Sbjct: 80 RPAA------FLLALALPKDLDEAW-LEALADG-LFELADRYGAELIGGD---------- 121
Query: 208 MEFDKLIASPDMMVKVASLGKILGPRGL 235
PD+ + V ++G + G R L
Sbjct: 122 -----TTRGPDLSISVTAIGDVPGGRAL 144
>gnl|CDD|236398 PRK09185, PRK09185, 3-oxoacyl-(acyl carrier protein) synthase I;
Reviewed.
Length = 392
Score = 27.9 bits (63), Expect = 8.3
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 72 GLPGHMLAAASAVEA 86
GL GH L AA AVEA
Sbjct: 316 GLTGHTLGAAGAVEA 330
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 27.7 bits (62), Expect = 9.8
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 249 PQAIEEFKKGKVEYRADKTGIVHIP-FGKADFSEDDLLINFLAAVKSIE-ANKP 300
+ I+ KK + R + G+V P GK+ LIN L K + +N+P
Sbjct: 117 EEKIKRLKKKGLLKRKIRVGVVGYPNVGKST------LINRLLGKKVAKTSNRP 164
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
0.313 0.130 0.372
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,851,277
Number of extensions: 1610050
Number of successful extensions: 1066
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1050
Number of HSP's successfully gapped: 25
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 59 (26.7 bits)