RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16477
(172 letters)
>gnl|CDD|240267 PTZ00103, PTZ00103, 60S ribosomal protein L3; Provisional.
Length = 390
Score = 102 bits (256), Expect = 2e-26
Identities = 43/85 (50%), Positives = 59/85 (69%), Gaps = 6/85 (7%)
Query: 27 RQHITVCLKLAHTEDLYGAHMKLLKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPV 86
+++ +V +AHT+ L QKKAH+MEIQ+NGGSVA+K+ +A+ LE+ +PV
Sbjct: 151 KKYCSVIRVIAHTQ------PSKLPLGQKKAHVMEIQVNGGSVAEKVDFAKSLLEKEVPV 204
Query: 87 GQVFAQDEMIDCIGVTKGKGFKGFV 111
VF Q+EMID IGVTKG GF+G V
Sbjct: 205 DSVFQQNEMIDVIGVTKGHGFEGVV 229
Score = 45.1 bits (107), Expect = 5e-06
Identities = 20/30 (66%), Positives = 22/30 (73%)
Query: 127 SAKFGHGRFQTPADKLAFMGYLKKDRIREE 156
S+K GHGRFQT +K F G LKKDRIR E
Sbjct: 361 SSKIGHGRFQTKEEKAKFYGPLKKDRIRRE 390
>gnl|CDD|235260 PRK04231, rpl3p, 50S ribosomal protein L3P; Reviewed.
Length = 337
Score = 65.3 bits (160), Expect = 4e-13
Identities = 25/58 (43%), Positives = 42/58 (72%)
Query: 54 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGFV 111
+KK +MEI++ GGSV +++ +A++ L + I + VF + +++D I VTKGKGF+G V
Sbjct: 157 KKKPEIMEIRIGGGSVEERLEYAKELLGKEISISDVFKEGQLVDVIAVTKGKGFQGVV 214
>gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3.
Length = 199
Score = 63.9 bits (156), Expect = 5e-13
Identities = 25/59 (42%), Positives = 33/59 (55%), Gaps = 12/59 (20%)
Query: 55 KKAHLMEIQLNGGSVADKIAWARQHLE--QPIPVGQVFAQDEMIDCIGVTKGKGFKGFV 111
KAH+ME ++NGG + E Q I V VF + E +D GVTKGKGF+G +
Sbjct: 71 PKAHVMEFRVNGG----------EEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVM 119
>gnl|CDD|234286 TIGR03626, L3_arch, archaeal ribosomal protein L3. This model
describes exclusively the archaeal class of ribosomal
protein L3. A separate model (TIGR03625) describes the
bacterial/organelle form, and both belong to Pfam family
pfam00297. Eukaryotic proteins are excluded from this
model [Protein synthesis, Ribosomal proteins: synthesis
and modification].
Length = 330
Score = 59.7 bits (145), Expect = 4e-11
Identities = 26/57 (45%), Positives = 38/57 (66%)
Query: 55 KKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGFV 111
KK +MEI++ GGSV ++ +A L + I V VF + +++D I VTKGKGF+G V
Sbjct: 153 KKPEIMEIRIGGGSVEERFEYALSILGKEISVSDVFKEGQLVDVIAVTKGKGFQGVV 209
>gnl|CDD|223165 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal
structure and biogenesis].
Length = 218
Score = 57.6 bits (140), Expect = 1e-10
Identities = 22/56 (39%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 54 QKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKG 109
+ K HL E ++ GG VA+K ++ VF + E++D GVTKGKGF+G
Sbjct: 74 KPKRHLAEFRVGGGDVAEKFEVGQEIT------VDVFKEGELVDVTGVTKGKGFQG 123
>gnl|CDD|234564 PRK00001, rplC, 50S ribosomal protein L3; Validated.
Length = 210
Score = 30.5 bits (70), Expect = 0.28
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 5/31 (16%)
Query: 84 IPVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
VGQ +F + +D G +KGKGF G
Sbjct: 89 YEVGQEITVDIFEAGQKVDVTGTSKGKGFAG 119
>gnl|CDD|234285 TIGR03625, L3_bact, 50S ribosomal protein L3, bacterial. This
model describes bacterial (and mitochondrial and
chloroplast) class of ribosomal protein L3. A separate
model describes the archaeal form, where both belong to
Pfam family pfam00297. The name is phrased to meet the
needs of bacterial genome annotation. Organellar forms
typically will have transit peptides, N-terminal to the
region modeled here.
Length = 202
Score = 30.1 bits (69), Expect = 0.41
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 84 IPVGQ-----VFAQDEMIDCIGVTKGKGFKG 109
VG +F + +D G +KGKGF G
Sbjct: 88 YEVGDEITVDIFEAGQKVDVTGTSKGKGFAG 118
>gnl|CDD|220625 pfam10191, COG7, Golgi complex component 7 (COG7). COG7 is a
component of the conserved oligomeric Golgi complex
which is required for normal Golgi morphology and
localisation. Mutation in COG7 causes a congenital
disorder of glycosylation.
Length = 768
Score = 29.4 bits (66), Expect = 1.2
Identities = 15/62 (24%), Positives = 28/62 (45%), Gaps = 4/62 (6%)
Query: 50 LKKRQKKAHLMEIQLNGGSVADKIAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKG 109
L++ L + L G V+D + + LE+ + V A+ + CI +T+G G
Sbjct: 370 LEESNLSIQLSAVPLEGAEVSDCV----RELEESVAKVFVLAEAAVERCIKITQGLALCG 425
Query: 110 FV 111
+
Sbjct: 426 LI 427
>gnl|CDD|235781 PRK06333, PRK06333, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 424
Score = 28.4 bits (64), Expect = 1.9
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 69 VADKIAWARQHLEQPIPVGQVF------AQDEMIDCIGVTKGKGFKGFVNSSLLFR 118
+ D+IA +LE P P + A+ +D ++ G GF G VN+S+LFR
Sbjct: 367 LRDQIAPPTLNLENPDPAAEGLDVVANKARPMDMD-YALSNGFGFGG-VNASILFR 420
>gnl|CDD|177551 PHA03175, PHA03175, UL43 envelope protein; Provisional.
Length = 413
Score = 28.0 bits (62), Expect = 2.6
Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 10/63 (15%)
Query: 83 PIPV-----GQVFAQDEMIDCIGVTKGKGFKGFVNSSLLFRDSKITSIISAKFGHGRFQT 137
P+ + G+V+ DC+ + GF GFV L + + + + G F +
Sbjct: 191 PLAIFIGEGGRVYCYAPSGDCLYLISRSGFHGFVQEGL-----RNFAPLREELGWTHFDS 245
Query: 138 PAD 140
D
Sbjct: 246 GGD 248
>gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
Length = 188
Score = 26.7 bits (60), Expect = 4.9
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 20 NGGSVADRQHI 30
NGGS AD QHI
Sbjct: 46 NGGSAADAQHI 56
>gnl|CDD|220393 pfam09772, Tmem26, Transmembrane protein 26. The function of this
family of transmembrane proteins has not, as yet, been
determined.
Length = 282
Score = 27.0 bits (60), Expect = 5.0
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 94 EMIDCIGVTKGKGFKGFVNSSLLFRDSKITSI 125
E I I KG+ +K F S L+ + I SI
Sbjct: 47 ETIYTIIFRKGREYKWFCPSVFLYLSAIIPSI 78
>gnl|CDD|150282 pfam09554, RE_HaeII, HaeII restriction endonuclease. This family
includes the HaeII (recognises and cleaves RGCGC^Y)
restriction endonuclease.
Length = 338
Score = 26.7 bits (59), Expect = 6.1
Identities = 19/88 (21%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 73 IAWARQHLEQPIPVGQVFAQDEMIDCIGVTKGKGFKGFVNSSLLFRD-------SKITSI 125
I +R HL +PI + ++ D + + ++ + ++ N S +RD ++++
Sbjct: 9 IKKSRVHLYKPIQIAEILYHDRVQKDLELSNLETYR---NRSKKWRDVICIRFLGRVST- 64
Query: 126 ISAKFGHGRFQ---TPADKLAFMGYLKK 150
SAKF F+ P + L+ +G +
Sbjct: 65 SSAKFQDNLFEENAMPPELLSILGEENR 92
>gnl|CDD|184204 PRK13645, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 289
Score = 26.5 bits (58), Expect = 8.3
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 90 FAQDEMIDCIGVTKGKG----FKGFVNSSLLFRDSKITSII 126
F++D ++D + T K FK N+SL F+ +K+T +I
Sbjct: 3 FSKDIILDNVSYTYAKKTPFEFKALNNTSLTFKKNKVTCVI 43
>gnl|CDD|132257 TIGR03213, 23dbph12diox, 2,3-dihydroxybiphenyl 1,2-dioxygenase.
Members of this protein family all have activity as
2,3-dihydroxybiphenyl 1,2-dioxygenase, the third enzyme
of a pathway for biphenyl degradation. Many of the
extradiol ring-cleaving dioxygenases, to which these
proteins belong, act on a range of related substrates.
Note that some members of this family may be found
operons for toluene or naphthalene degradation, where
other activities of the same enzyme may be more
significant; the trusted cutoff for this model is set
relatively high to exclude most such instances [Energy
metabolism, Other].
Length = 286
Score = 26.2 bits (58), Expect = 9.3
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 132 HGRF---QTPADKLAFMGYLKKD-----RIREEEKKASAASTAAGAA 170
R +D LA+ G+ D +++E+ +KA A T A AA
Sbjct: 46 AHRIAVHPGESDDLAYAGWEVADEAGLDQVKEKLEKAGVAVTVASAA 92
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
0.319 0.132 0.374
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,519,507
Number of extensions: 768800
Number of successful extensions: 657
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 29
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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 (21.8 bits)
S2: 55 (25.1 bits)