RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16349
(351 letters)
>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 = 56.4 bits (137), Expect = 2e-09
Identities = 49/224 (21%), Positives = 89/224 (39%), Gaps = 29/224 (12%)
Query: 99 QEALAAIRETHHPTMYNLPRAFIGATVEISTTTHQKKVKYMDPWTHIVEVEHSFDHGEDR 158
+EA+ A+++T R F TVE+ + K V + H G+D
Sbjct: 2 EEAIKALKKTSVKK-----RKFD-ETVELQINLKKDDRKKDQRIRGTVILPHGL--GKDV 53
Query: 159 SIIAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQF--VICNPKILADLMRI 216
+ F E A + + G +VG D K I+ G F + +P +M +
Sbjct: 54 KVCVFAKD-EQAKEAKAAGADVVGGEDLKKKIKNGEAKKLAKDFDLFLADP---RIMMLL 109
Query: 217 RGLL------KKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGYSDFHIGRL 270
LL + ++P K+ T+ DL + ++ +++ + K G +G++
Sbjct: 110 PKLLGKVLGPRGKMPNPKTGTVTEDLAKAIEEAKSSVEFRLDKG------GCIHVPVGKV 163
Query: 271 DMSQEQLEDNLKRILADISTMKPPSKPEDEDFITRILLWSEPSP 314
MS EQL +N++ ++ + P K I I L + P
Sbjct: 164 SMSPEQLVENIEAVINALVKKLPSKKG---QNIKSIYLKTTMGP 204
>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 = 51.9 bits (125), Expect = 8e-08
Identities = 36/146 (24%), Positives = 69/146 (47%), Gaps = 13/146 (8%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILAD 212
HG +++ +A ++ E A + + G VG D I+ I++G + F VI P ++
Sbjct: 65 HGTGKTVRVAVFAKGEKAKEAKAAGADYVGSDDLIEKIKKGWLD---FDVVIATPDMMRV 121
Query: 213 LMRIRGLLKKR--IPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDFHIGR 269
+ ++ +L R +P K+ T+ D+ K + G +++ K G IG+
Sbjct: 122 VGKLGRILGPRGLMPNPKTGTVTTDVAKAVKNAKKGQVEFRADK------AGNIHAPIGK 175
Query: 270 LDMSQEQLEDNLKRILADISTMKPPS 295
+ E+L++NL+ +L I KP
Sbjct: 176 VSFDSEKLKENLEALLDAIKKAKPSG 201
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 49.9 bits (120), Expect = 4e-07
Identities = 35/151 (23%), Positives = 60/151 (39%), Gaps = 24/151 (15%)
Query: 155 GEDRSIIAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILADLM 214
G+ + F E A + + G VG D I+ I+ G F I P D+M
Sbjct: 70 GKTVRVAVFA-DGEKAEEAKAAGADYVGGEDLIELIKNGRAK--DFDVFIATP----DMM 122
Query: 215 RIRGLL------KKRIPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDFH- 266
+ G L + +P K+ T+ D+ + L+ G +++ K H
Sbjct: 123 PLVGKLGKVLGPRGLMPNPKTGTVTDDVAKAVEELKKGTVEFRADKAGV--------IHV 174
Query: 267 -IGRLDMSQEQLEDNLKRILADISTMKPPSK 296
IG++ E+L +N++ +L I KP
Sbjct: 175 PIGKVSFDDEKLAENIEALLNAIVKAKPAGA 205
>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 = 48.7 bits (116), Expect = 4e-07
Identities = 31/150 (20%), Positives = 62/150 (41%), Gaps = 14/150 (9%)
Query: 99 QEALAAIRETHHPTMYNLPRAFIGATVEISTTTHQKKVKYMDPWTHIVEVEHSFDHGEDR 158
+A ++ +P+ + + + ++ V+ M H F
Sbjct: 4 IKAFVYLKTKSISMY--VPKQSVNLDIGLLMELGKESVQGM------FSFPHPFGKEPK- 54
Query: 159 SIIAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILADLMRIRG 218
I F + ++ G VG D IK IE G + F ++I +P I+ +L ++R
Sbjct: 55 -IAVFTKGASEVEEAREAGADYVGGDDLIKKIEDG--EIKPFDYLIAHPDIVPELAQLRR 111
Query: 219 LLKKR--IPTLKSQTLGVDLIGIAKRLQTG 246
LL + +P+ K T+G +L+ + + + G
Sbjct: 112 LLGPKGLMPSPKRGTVGDNLLSMIETFKKG 141
>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This
family includes prokaryotic L1 and eukaryotic L10.
Length = 200
Score = 39.9 bits (94), Expect = 8e-04
Identities = 29/145 (20%), Positives = 62/145 (42%), Gaps = 12/145 (8%)
Query: 155 GEDRSIIAFCSQ-HETAAQLQDMGVALVGDSDTIK--GIERGLVTMPTFQFVICNPKILA 211
G+D + A + +D G +VG D + I++G F + +P I+
Sbjct: 44 GKDVKVCVIAKDPEAKAKEAKDAGADVVGGEDLKEKYKIKKGRKLAKDFDVFLADPDIMP 103
Query: 212 DLMRI--RGL-LKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGYSDFHIG 268
L ++ + L + ++P K+ T+ D+ + ++G K G +G
Sbjct: 104 LLPKLLGKVLGPRGKMPNPKT-TVTPDVAKAIEEAKSGTVEFRKDK-----GGCIHVKVG 157
Query: 269 RLDMSQEQLEDNLKRILADISTMKP 293
++ MS E+L +N++ ++ + P
Sbjct: 158 KVSMSPEELVENIEAVINALVKKLP 182
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed.
Length = 229
Score = 35.0 bits (81), Expect = 0.040
Identities = 40/148 (27%), Positives = 65/148 (43%), Gaps = 19/148 (12%)
Query: 154 HGEDRSI-IAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKI--- 209
G ++I IA + E + ++ G +VG D I+ I +G + F +I P +
Sbjct: 66 KGTGKTIRIAVLTNEEKITEAKNAGADIVGSDDLIEEITKGNLD---FDLLIATPDMMPK 122
Query: 210 LADLMRI---RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQEQDFGYSDFH 266
LA L R+ RGL+ P+ KS T+ DL + G K + D G
Sbjct: 123 LAKLGRVLGPRGLM----PSPKSGTVTTDLASAINEFKKG-KLEYRADKT----GIVHVL 173
Query: 267 IGRLDMSQEQLEDNLKRILADISTMKPP 294
G+ + ++E L +NL+ I I +P
Sbjct: 174 FGKSNFTEEDLLENLQAIYESIEQNRPS 201
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 34.0 bits (79), Expect = 0.081
Identities = 36/148 (24%), Positives = 68/148 (45%), Gaps = 21/148 (14%)
Query: 155 GEDRSIIAFCSQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILADLM 214
G+ + F + E A + + G +VG D I+ I+ G + F VI P ++ +
Sbjct: 69 GKTVRVAVFA-KGEKAEEAKAAGADIVGGEDLIEKIKGGWLD---FDVVIATPDMMGKVG 124
Query: 215 RI------RGLLKKRIPTLKSQTLGVDLIGIAKRLQTG-IKYSMKKDPQEQDFGYSDFHI 267
++ RGL+ P K+ T+ +D+ K + G +++ + K G I
Sbjct: 125 KLGRILGPRGLM----PNPKTGTVTMDVAKAVKEAKAGKVEFRVDK------AGIIHAPI 174
Query: 268 GRLDMSQEQLEDNLKRILADISTMKPPS 295
G++ E+L++NLK ++ I KP +
Sbjct: 175 GKVSFDAEKLKENLKALIDAIKKAKPAT 202
>gnl|CDD|216436 pfam01329, Pterin_4a, Pterin 4 alpha carbinolamine dehydratase.
Pterin 4 alpha carbinolamine dehydratase is also known
as DCoH (dimerisation cofactor of hepatocyte nuclear
factor 1-alpha).
Length = 96
Score = 29.4 bits (67), Expect = 0.72
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 15/59 (25%)
Query: 82 EDDIYLQKDYKLRIFQFQEALAAI--------RETHHPTMYNLPRAFIGATVEISTTTH 132
D L + +K + F+EALA + E HHP + N+ V ++ TTH
Sbjct: 24 VDGDALTRTFKFK--DFKEALAFVNAVAELAEAEGHHPDLTNVYN-----RVTVTLTTH 75
>gnl|CDD|217953 pfam04190, DUF410, Protein of unknown function (DUF410). This
family of proteins is from Caenorhabditis elegans and
has no known function. The protein has some GO
references indicating that the protein has a positive
regulation of growth rate and is involved in nematode
larval development.
Length = 251
Score = 30.9 bits (70), Expect = 0.92
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 279 DNLKRILADISTMKPPSKPEDEDFITRILLWSEPSPEKF 317
+ R+ I+ + P S+PE + + R + WS PS K+
Sbjct: 50 SKVARLAELINELDP-SEPERKKCVDRAIKWSTPSEGKY 87
>gnl|CDD|213321 cd05974, MACS_like_1, Uncharacterized subfamily of medium-chain
acyl-CoA synthetase (MACS). MACS catalyzes the two-step
activation of medium chain fatty acids (containing 4-12
carbons). The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. MACS
enzymes are localized to mitochondria.
Length = 433
Score = 30.4 bits (69), Expect = 1.5
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 8/47 (17%)
Query: 83 DDIYLQKDYKLRIFQFQEAL--------AAIRETHHPTMYNLPRAFI 121
DD++ DY++ F+ + AL AA+ + P +P+A+I
Sbjct: 331 DDVFKSSDYRISPFEVESALLEHPAVAEAAVVPSPDPIRLAVPKAYI 377
>gnl|CDD|235254 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
Length = 215
Score = 29.1 bits (66), Expect = 2.6
Identities = 32/153 (20%), Positives = 54/153 (35%), Gaps = 40/153 (26%)
Query: 155 GEDRSIIAFCSQHETAAQLQDMGVALV----------GDSDTIKGIERGLVTMPTFQFVI 204
G++ I E A Q ++ G V GD K + + F I
Sbjct: 56 GKEVKIAVIAKG-ELALQAKEAGADYVITREELEELGGDKRAAKKLAN------EYDFFI 108
Query: 205 CNPKILADLMRI-------RGLLKKRIPTLKSQTLGVDLIGIAKRLQTGIKYSMKKDPQE 257
++ + R RG + +P D+ + +RL+ ++ K P
Sbjct: 109 AEADLMPLIGRYLGPVLGPRGKMPTPLPP------NADIKPLVERLKNTVRIRTKDQPT- 161
Query: 258 QDFGYSDFH--IGRLDMSQEQLEDNLKRILADI 288
FH +G DMS E+L +N+ +L I
Sbjct: 162 -------FHVRVGTEDMSPEELAENIDAVLNRI 187
>gnl|CDD|235041 PRK02472, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 447
Score = 29.4 bits (67), Expect = 3.1
Identities = 13/61 (21%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 165 SQHETAAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILADLMRIRGLLKKRI 224
S++ A +L + G+ ++ S ++ ++ F ++ NP I + L+K I
Sbjct: 40 SENPEAQELLEEGIKVICGSHPLELLDED------FDLMVKNPGIPYTNPMVEKALEKGI 93
Query: 225 P 225
P
Sbjct: 94 P 94
>gnl|CDD|217903 pfam04112, Mak10, Mak10 subunit, NatC N(alpha)-terminal
acetyltransferase. NatC N(alpha)-terminal
acetyltransferases contains Mak10p, Mak31p and Mak3p
subunits. All three subunits are associated with each
other to form the active complex.
Length = 167
Score = 27.3 bits (61), Expect = 7.9
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 318 KLDLSGLIEKPKAKELDTGEEIDDEPKEMAAQKV 351
K+D SG+IE + + D E D + + +V
Sbjct: 26 KMD-SGMIELTEEEPFDLEEAYDTGLRPLDLPEV 58
>gnl|CDD|237660 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 27.9 bits (62), Expect = 9.4
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 13/54 (24%)
Query: 102 LAAIRETHHPTM--------YNL----PRAFIGATVEISTTTHQKKVKYMDPWT 143
L I E HP + YNL P A +G VE+ T + KVK ++ T
Sbjct: 262 LVVIEEEPHPELIRDENDLIYNLLLSVPTAALGGAVEVPTIDGKAKVK-IEAGT 314
>gnl|CDD|163534 TIGR03822, AblA_like_2, lysine-2,3-aminomutase-related protein.
Members of this protein form a distinctive clade,
homologous to lysine-2,3-aminomutase (of Bacillus,
Clostridium, and methanogenic archaea) and likely
similar in function. Members of this family are found in
Rhodopseudomonas, Caulobacter crescentus,
Bradyrhizobium, etc.
Length = 321
Score = 27.8 bits (62), Expect = 9.8
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 13/46 (28%)
Query: 170 AAQLQDMGVALVGDSDTIKGIERGLVTMPTFQFVICNPKILADLMR 215
A+L D G+ +V S ++G+ +P+ LA LMR
Sbjct: 220 CARLIDAGIPMVSQSVLLRGVND-------------DPETLAALMR 252
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 0.134 0.381
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,390,567
Number of extensions: 1820874
Number of successful extensions: 1651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1644
Number of HSP's successfully gapped: 21
Length of query: 351
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 253
Effective length of database: 6,590,910
Effective search space: 1667500230
Effective search space used: 1667500230
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: 59 (26.5 bits)