RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 022012
(304 letters)
>gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated.
Length = 230
Score = 154 bits (391), Expect = 9e-46
Identities = 65/130 (50%), Positives = 83/130 (63%), Gaps = 1/130 (0%)
Query: 175 KKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKA 234
+K + + L +AI VK A A FDETV+ V L + PRK + VRG + LPHG K
Sbjct: 12 EKVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRGAVVLPHGTGKT 71
Query: 235 VRVAFFAEGADAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKIL 294
VRVA FA+G AEEA+AAGADIVGG +LIE+I G LD + +T M ++ K+ +IL
Sbjct: 72 VRVAVFAKGEKAEEAKAAGADIVGGEDLIEKIK-GGWLDFDVVIATPDMMGKVGKLGRIL 130
Query: 295 NQHGLMPNPK 304
GLMPNPK
Sbjct: 131 GPRGLMPNPK 140
>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 = 139 bits (352), Expect = 4e-40
Identities = 62/121 (51%), Positives = 79/121 (65%), Gaps = 1/121 (0%)
Query: 184 DLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEG 243
L +AI +K A A FDETVE +RL I PRK++ VRG++ LPHG K VRVA FA+G
Sbjct: 20 SLDEAIDLLKETATAKFDETVEVAIRLGIDPRKSDQQVRGSVVLPHGTGKTVRVAVFAKG 79
Query: 244 ADAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISKILNQHGLMPNP 303
A+EA+AAGAD VG +LIE+I G LD + +T M + K+ +IL GLMPNP
Sbjct: 80 EKAKEAKAAGADYVGSDDLIEKIK-KGWLDFDVVIATPDMMRVVGKLGRILGPRGLMPNP 138
Query: 304 K 304
K
Sbjct: 139 K 139
>gnl|CDD|223159 COG0081, RplA, Ribosomal protein L1 [Translation, ribosomal
structure and biogenesis].
Length = 228
Score = 131 bits (331), Expect = 6e-37
Identities = 62/135 (45%), Positives = 84/135 (62%)
Query: 170 IKPESKKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPH 229
+ S+K + + L +A+K +K +K FDETVE V L + PRK + VRG++ LP+
Sbjct: 8 YRAASEKVDRNKLYSLEEAVKLLKETSKRKFDETVEVAVNLKVDPRKPDQRVRGSVVLPN 67
Query: 230 GDKKAVRVAFFAEGADAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFK 289
G K VRVA FA+G AEEA+AAGAD VGG +LIE I + D + +T MP + K
Sbjct: 68 GTGKTVRVAVFADGEKAEEAKAAGADYVGGEDLIELIKNGRAKDFDVFIATPDMMPLVGK 127
Query: 290 ISKILNQHGLMPNPK 304
+ K+L GLMPNPK
Sbjct: 128 LGKVLGPRGLMPNPK 142
>gnl|CDD|177051 CHL00129, rpl1, ribosomal protein L1; Reviewed.
Length = 229
Score = 115 bits (289), Expect = 9e-31
Identities = 53/132 (40%), Positives = 75/132 (56%), Gaps = 1/132 (0%)
Query: 173 ESKKKESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDK 232
E + K + + +AI +K A A F ET EAH+ L I P+ + +R T+ LP G
Sbjct: 10 ELRSKIEKKLYSPEEAINLLKETATAKFIETAEAHISLNIDPKYADQQLRTTVTLPKGTG 69
Query: 233 KAVRVAFFAEGADAEEARAAGADIVGGLELIEEIASSGKLDVEKCFSTRQFMPRLFKISK 292
K +R+A EA+ AGADIVG +LIEEI + G LD + +T MP+L K+ +
Sbjct: 70 KTIRIAVLTNEEKITEAKNAGADIVGSDDLIEEI-TKGNLDFDLLIATPDMMPKLAKLGR 128
Query: 293 ILNQHGLMPNPK 304
+L GLMP+PK
Sbjct: 129 VLGPRGLMPSPK 140
>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 = 108 bits (271), Expect = 2e-28
Identities = 53/127 (41%), Positives = 73/127 (57%), Gaps = 7/127 (5%)
Query: 185 LMDAIKQVKANA--KATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAE 242
L +AIK +K + K FDETVE + L RK + +RGT+ LPHG K V+V FA+
Sbjct: 1 LEEAIKALKKTSVKKRKFDETVELQINLKKDDRKKDQRIRGTVILPHGLGKDVKVCVFAK 60
Query: 243 GADAEEARAAGADIVGGLELIEEI----ASSGKLDVEKCFSTRQFMPRLFKI-SKILNQH 297
A+EA+AAGAD+VGG +L ++I A D + + + M L K+ K+L
Sbjct: 61 DEQAKEAKAAGADVVGGEDLKKKIKNGEAKKLAKDFDLFLADPRIMMLLPKLLGKVLGPR 120
Query: 298 GLMPNPK 304
G MPNPK
Sbjct: 121 GKMPNPK 127
>gnl|CDD|216061 pfam00687, Ribosomal_L1, Ribosomal protein L1p/L10e family. This
family includes prokaryotic L1 and eukaryotic L10.
Length = 200
Score = 92.6 bits (231), Expect = 1e-22
Identities = 52/123 (42%), Positives = 68/123 (55%), Gaps = 7/123 (5%)
Query: 189 IKQVKANAKATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEG--ADA 246
+K +K AK FDETVE + L PRK + VRGT+ LPHG K V+V A+ A A
Sbjct: 1 VKALKKTAKRKFDETVELQINLKKDPRKKDQNVRGTVVLPHGLGKDVKVCVIAKDPEAKA 60
Query: 247 EEARAAGADIVGGLELIEEIASSGK----LDVEKCFSTRQFMPRLFKI-SKILNQHGLMP 301
+EA+ AGAD+VGG +L E+ D + + MP L K+ K+L G MP
Sbjct: 61 KEAKDAGADVVGGEDLKEKYKIKKGRKLAKDFDVFLADPDIMPLLPKLLGKVLGPRGKMP 120
Query: 302 NPK 304
NPK
Sbjct: 121 NPK 123
>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 = 62.5 bits (152), Expect = 3e-12
Identities = 32/85 (37%), Positives = 49/85 (57%), Gaps = 1/85 (1%)
Query: 221 VRGTMNLPHGDKKAVRVAFFAEGA-DAEEARAAGADIVGGLELIEEIASSGKLDVEKCFS 279
V+G + PH K ++A F +GA + EEAR AGAD VGG +LI++I + +
Sbjct: 39 VQGMFSFPHPFGKEPKIAVFTKGASEVEEAREAGADYVGGDDLIKKIEDGEIKPFDYLIA 98
Query: 280 TRQFMPRLFKISKILNQHGLMPNPK 304
+P L ++ ++L GLMP+PK
Sbjct: 99 HPDIVPELAQLRRLLGPKGLMPSPK 123
>gnl|CDD|235254 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed.
Length = 215
Score = 57.6 bits (140), Expect = 7e-10
Identities = 29/90 (32%), Positives = 47/90 (52%), Gaps = 2/90 (2%)
Query: 184 DLMDAIKQVKANAKAT-FDETVEAHVRLA-IPPRKTELIVRGTMNLPHGDKKAVRVAFFA 241
+ +A+K+ A F ++V+ V L I +K E + + LPHG K V++A A
Sbjct: 6 KIEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIA 65
Query: 242 EGADAEEARAAGADIVGGLELIEEIASSGK 271
+G A +A+ AGAD V E +EE+ +
Sbjct: 66 KGELALQAKEAGADYVITREELEELGGDKR 95
>gnl|CDD|217705 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family. Members
of this family are predicted integral membrane proteins
of unknown function. They are about 350 amino acids long
and contain about 6 transmembrane regions. They are
predicted to be permeases although there is no
verification of this.
Length = 354
Score = 40.3 bits (95), Expect = 7e-04
Identities = 16/76 (21%), Positives = 28/76 (36%)
Query: 138 DGERRRIQSEKKTLRFMRVPEQAQVSVPYPLLIKPESKKKESRPVLDLMDAIKQVKANAK 197
+G R + L + P + ++ E + +L IK++KA+
Sbjct: 204 NGTIYRFDKDGGELSILSFDRYEIDLSLTPQDLSSLTEDPEELSLSELYAYIKRLKASGL 263
Query: 198 ATFDETVEAHVRLAIP 213
E H RLA+P
Sbjct: 264 DVRKYRAELHRRLALP 279
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 34.7 bits (80), Expect = 0.032
Identities = 16/61 (26%), Positives = 28/61 (45%)
Query: 197 KATFDETVEAHVRLAIPPRKTELIVRGTMNLPHGDKKAVRVAFFAEGADAEEARAAGADI 256
K F ETVE + L + + G++ LP+ K ++V + +EA+ G D
Sbjct: 24 KRKFVETVELQIGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKLGLDF 83
Query: 257 V 257
+
Sbjct: 84 M 84
>gnl|CDD|237257 PRK12902, secA, preprotein translocase subunit SecA; Reviewed.
Length = 939
Score = 33.9 bits (78), Expect = 0.12
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 178 ESRPVLDLMDAIKQVKANAKATFDETVEAHVRLAIPPRKTEL 219
E R VL+ D +QV + T DE VEA+V +PP + +L
Sbjct: 759 ERRRVLEGRDLKEQVIGYGEKTMDEIVEAYVNPDLPPEEWDL 800
>gnl|CDD|236849 PRK11109, PRK11109, bifunctional PTS system fructose-specific
transporter subunit IIA/HPr protein; Provisional.
Length = 375
Score = 30.7 bits (70), Expect = 0.91
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 230 GDKKAVRVAFFAEGADAEEARAA-GADIVGGL 260
G KK R+ F A+G DAE+A A G I GL
Sbjct: 341 GVKKGHRLRFTAQGEDAEQALKAIGEAIAAGL 372
>gnl|CDD|222057 pfam13343, SBP_bac_6, Bacterial extracellular solute-binding
protein. This family includes bacterial extracellular
solute-binding proteins.
Length = 239
Score = 30.0 bits (68), Expect = 1.2
Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 144 IQSEKKTLRFMRVPEQAQVSVPYPLLIKPESKKKESRPVLDLM--DAIKQVKANAKATFD 201
+ +KK ++ + PE + P +L+K KK+ ++P +D + ++ + A A F
Sbjct: 153 LPRKKKNIKIV-WPEDGALVSPIFMLVKKGPKKELAKPFIDFLLSPEVQAILAKAGGKFP 211
Query: 202 ETVEAHV 208
V
Sbjct: 212 VNTNPAV 218
>gnl|CDD|205485 pfam13305, WHG, WHG domain. This presumed domain is around 80
amino acids in length. It is found to the C-terminus of
a DNA-binding helix-turn-helix domain. This domain may
be involved in binding to an as yet unknown ligand that
allows a transcriptional regulation response to that
molecule. The domain is named WHG after three conserved
residues near the C-terminus of the domain.
Length = 80
Score = 27.6 bits (62), Expect = 2.3
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 236 RVAFFAEGADAEEARAAGADIVGGLELIEEIASSGKLDVEK 276
R+ F A+ D E A +V EL+EE+ ++G L E
Sbjct: 19 RLMFGADLEDDPELDEAFELLV---ELLEELLAAGGLSPED 56
>gnl|CDD|221735 pfam12723, DUF3809, Protein of unknown function (DUF3809). This
family of proteins is functionally uncharacterized. This
family of proteins is found in Deinococci bacteria.
Proteins in this family are typically between 117 and
157 amino acids in length.
Length = 134
Score = 28.7 bits (64), Expect = 2.3
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 15/58 (25%)
Query: 95 GLTREDIR----YLKDVPTITPVSYP-----------SRVAPLPEAGEPASGEAEGEG 137
GL R+ + +VP + V P +R+ PLP GEPA E GE
Sbjct: 28 GLRRDAEGLRGELVVEVPLLGEVDLPFRSRLQPTAEGARLRPLPLTGEPAWVEVSGEA 85
>gnl|CDD|119339 cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase
superfamily. This superfamily contains a diverse set of
enzymes including enoyl-CoA hydratase, napthoate
synthase, methylmalonyl-CoA decarboxylase,
3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA
isomerase. Many of these play important roles in fatty
acid metabolism. In addition to a conserved structural
core and the formation of trimers (or dimers of
trimers), a common feature in this superfamily is the
stabilization of an enolate anion intermediate derived
from an acyl-CoA substrate. This is accomplished by two
conserved backbone NH groups in active sites that form
an oxyanion hole.
Length = 195
Score = 28.3 bits (64), Expect = 4.1
Identities = 17/69 (24%), Positives = 25/69 (36%), Gaps = 15/69 (21%)
Query: 207 HVRLAIPPRKTELIVRGTMNLPH--GDKKAVRVAFFAEGADAEEARAAGADIVGGLELIE 264
V+L + P GT LP G +A + AEEA G L++
Sbjct: 130 EVKLGLVP-----GGGGTQRLPRLVGPARARELLLTGRRISAEEALELG--------LVD 176
Query: 265 EIASSGKLD 273
E+ +L
Sbjct: 177 EVVPDEELL 185
>gnl|CDD|133454 cd05312, NAD_bind_1_malic_enz, NAD(P) binding domain of malic
enzyme (ME), subgroup 1. Malic enzyme (ME), a member of
the amino acid dehydrogenase (DH)-like domain family,
catalyzes the oxidative decarboxylation of L-malate to
pyruvate in the presence of cations (typically Mg++ or
Mn++) with the concomitant reduction of cofactor NAD+ or
NADP+. ME has been found in all organisms, and plays
important roles in diverse metabolic pathways such as
photosynthesis and lipogenesis. This enzyme generally
forms homotetramers. The conversion of malate to
pyruvate by ME typically involves oxidation of malate to
produce oxaloacetate, followed by decarboxylation of
oxaloacetate to produce pyruvate and CO2. This
subfamily consists of eukaryotic and bacterial ME.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DH, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 279
Score = 28.3 bits (64), Expect = 5.1
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 171 KPESKKKESRPVLDLMDAIKQVKANA-------KATFDETV 204
KP ++K E + L++ +K VK F E V
Sbjct: 83 KPFARKDEEKEGKSLLEVVKAVKPTVLIGLSGVGGAFTEEV 123
>gnl|CDD|168165 PRK05671, PRK05671, aspartate-semialdehyde dehydrogenase; Reviewed.
Length = 336
Score = 27.8 bits (62), Expect = 7.1
Identities = 18/40 (45%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 231 DKKAVRVAFFAEGAD-----AEEARAAGA---DIVGGLEL 262
D V++AFFA GA AE+ARAAG D+ G L
Sbjct: 63 DFSQVQLAFFAAGAAVSRSFAEKARAAGCSVIDLSGALPS 102
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 28.1 bits (63), Expect = 7.6
Identities = 8/36 (22%), Positives = 14/36 (38%), Gaps = 1/36 (2%)
Query: 72 QQQQNELQSDNPPHDFQAEEARTGLTREDIRYLKDV 107
QQ ++ P F+ + R L E Y+ +
Sbjct: 124 QQLGPLPEAGQPQEQFEVTQERDALQAEK-AYINAL 158
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 28.0 bits (62), Expect = 7.6
Identities = 18/118 (15%), Positives = 34/118 (28%), Gaps = 2/118 (1%)
Query: 21 ASPSVTFQRTLCSSTAVQDDDESQNPPKQPIPVVSYASKPKDESNAPIENAQQQQNELQS 80
P + V D+ +++ + ++ S A IE Q Q+
Sbjct: 324 NQPDDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTPAVEETSEADIEREQPGDLAGQA 383
Query: 81 DNPPHDFQAEEARTGLTREDIRYLKDVPTITPVSYPSRVAPLPEAGEPASGEAEGEGD 138
+ + + T P + AP+P+ +P G GD
Sbjct: 384 PAAHQVDAEAASAAPEEPAALA--SEAHDETEPEVPEKAAPIPDPAKPDELAVAGPGD 439
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 27.8 bits (63), Expect = 9.4
Identities = 25/111 (22%), Positives = 33/111 (29%), Gaps = 37/111 (33%)
Query: 196 AKATFDETVEAHVRLAIPPRKTELI-----VRGTMNLPHGDKKAVRV--------AFFAE 242
A DE EA ELI +R MN+P K + + A
Sbjct: 708 ADEAIDEAAEAEFEWLK-----ELITAIRNIRAEMNIPPSKKLPLLLKGADAEDRARLEA 762
Query: 243 GAD-----------------AEEARAAGADIVGGLELIEEIASSGKLDVEK 276
E A + +VGG EL + G +DVE
Sbjct: 763 NEAYIKRLARLESLEILADDEEAPEGAASAVVGGAELFLPLE--GLIDVEA 811
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 0.364
Gapped
Lambda K H
0.267 0.0659 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,538,802
Number of extensions: 1498312
Number of successful extensions: 1485
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1477
Number of HSP's successfully gapped: 50
Length of query: 304
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 208
Effective length of database: 6,679,618
Effective search space: 1389360544
Effective search space used: 1389360544
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)