RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7634
(206 letters)
>gnl|CDD|201553 pfam01016, Ribosomal_L27, Ribosomal L27 protein.
Length = 80
Score = 54.8 bits (133), Expect = 2e-10
Identities = 32/79 (40%), Positives = 43/79 (54%), Gaps = 8/79 (10%)
Query: 26 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLNVGFG 84
A KK G ST+N R ++G R G +K G+ V+ G+I+ QR +HPG NVG G
Sbjct: 1 AHKKGGGSTKNG--RDSNGKRL--GVKKFGGQFVKAGNIIV---RQRGTKFHPGENVGMG 53
Query: 85 ARGTLFAMEKGKVKITVEK 103
TLFA+ G VK +
Sbjct: 54 KDHTLFALVDGYVKFEKKP 72
Score = 33.3 bits (77), Expect = 0.015
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 8/56 (14%)
Query: 152 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLN 206
A KK G ST+N R ++G R G +K G+ V+ G+I+ QR +HPG N
Sbjct: 1 AHKKGGGSTKNG--RDSNGKRL--GVKKFGGQFVKAGNII---VRQRGTKFHPGEN 49
>gnl|CDD|223289 COG0211, RpmA, Ribosomal protein L27 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 48.0 bits (115), Expect = 7e-08
Identities = 33/75 (44%), Positives = 41/75 (54%), Gaps = 8/75 (10%)
Query: 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLNVGF 83
A KK G STRN R + R G +K G+ V+ GSI+ QR +HPG+NVG
Sbjct: 1 MAHKKGGGSTRNG--RDSESKRL--GVKKFGGQFVKAGSIIV---RQRGTKFHPGVNVGR 53
Query: 84 GARGTLFAMEKGKVK 98
G TLFA+ G VK
Sbjct: 54 GKDHTLFALVDGVVK 68
Score = 28.7 bits (65), Expect = 0.66
Identities = 23/57 (40%), Positives = 30/57 (52%), Gaps = 8/57 (14%)
Query: 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLN 206
A KK G STRN R + R G +K G+ V+ GSI+ QR +HPG+N
Sbjct: 1 MAHKKGGGSTRNG--RDSESKRL--GVKKFGGQFVKAGSII---VRQRGTKFHPGVN 50
>gnl|CDD|232803 TIGR00062, L27, ribosomal protein L27. Eubacterial, chloroplast,
and mitochondrial. Mitochondrial members have an
additional C-terminal domain [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 83
Score = 47.0 bits (112), Expect = 2e-07
Identities = 30/75 (40%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 25 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLNVGF 83
A KK ST+N R + R G ++ G+ V GSI+ QR +HPG NVG
Sbjct: 1 MATKKGVGSTKNG--RDSEAKRL--GVKRAGGQFVRAGSIIV---RQRGTKFHPGNNVGM 53
Query: 84 GARGTLFAMEKGKVK 98
G TLFA+ G VK
Sbjct: 54 GKDHTLFALSDGVVK 68
Score = 27.4 bits (61), Expect = 1.9
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 151 NAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLN 206
A KK ST+N R + R G ++ G+ V GSI+ QR +HPG N
Sbjct: 1 MATKKGVGSTKNG--RDSEAKRL--GVKRAGGQFVRAGSII---VRQRGTKFHPGNN 50
>gnl|CDD|235464 PRK05435, rpmA, 50S ribosomal protein L27; Validated.
Length = 82
Score = 43.1 bits (103), Expect = 4e-06
Identities = 31/74 (41%), Positives = 41/74 (55%), Gaps = 8/74 (10%)
Query: 26 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLNVGFG 84
A KK G STRN R + R G ++ G+ V+ G+I+ QR +HPG+NVG G
Sbjct: 2 AHKKGGGSTRNG--RDSESKRL--GVKRFGGQFVKAGNIIV---RQRGTKFHPGVNVGRG 54
Query: 85 ARGTLFAMEKGKVK 98
TLFA+ G VK
Sbjct: 55 KDHTLFALVDGVVK 68
Score = 25.8 bits (58), Expect = 7.2
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 8/56 (14%)
Query: 152 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLN 206
A KK G STRN R + R G ++ G+ V+ G+I+ QR +HPG+N
Sbjct: 2 AHKKGGGSTRNG--RDSESKRL--GVKRFGGQFVKAGNII---VRQRGTKFHPGVN 50
>gnl|CDD|214370 CHL00121, rpl27, ribosomal protein L27; Reviewed.
Length = 86
Score = 38.1 bits (89), Expect = 3e-04
Identities = 30/74 (40%), Positives = 39/74 (52%), Gaps = 8/74 (10%)
Query: 26 AAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKGSILYISYVQR-LDYHPGLNVGFG 84
A KK ST+N R ++ R G ++ GE V G+IL QR + PGLNVG G
Sbjct: 2 AHKKGAGSTKNG--RDSNAKRL--GVKRFGGEKVSAGNILI---RQRGTKFKPGLNVGCG 54
Query: 85 ARGTLFAMEKGKVK 98
TL+A+ G VK
Sbjct: 55 KDFTLYALIDGFVK 68
>gnl|CDD|223238 COG0160, GabT, 4-aminobutyrate aminotransferase and related
aminotransferases [Amino acid transport and metabolism].
Length = 447
Score = 31.8 bits (73), Expect = 0.25
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 14/71 (19%)
Query: 38 PIRKNSGFRF-PKGFRKQEGEVVEKGSILYIS-YVQRLDYHPGLNVGFGARGTLFAMEKG 95
PI+ G PKGF K ++ + IL I+ VQ GFG G +FA E
Sbjct: 230 PIQGEGGIIVPPKGFLKALRKLCREHGILLIADEVQ---------TGFGRTGKMFAFEHF 280
Query: 96 KVK---ITVEK 103
V+ +T+ K
Sbjct: 281 GVEPDIVTLAK 291
>gnl|CDD|234144 TIGR03197, MnmC_Cterm, tRNA U-34 5-methylaminomethyl-2-thiouridine
biosynthesis protein MnmC, C-terminal domain. In
Escherichia coli, the protein previously designated YfcK
is now identified as the bifunctional enzyme MnmC. It
acts, following the action of the heterotetramer of GidA
and MnmE, in the modification of U-34 of certain tRNA to
5-methylaminomethyl-2-thiouridine (mnm5s2U). In other
bacterial, the corresponding proteins are usually but
always found as a single polypeptide chain, but
occasionally as the product of tandem genes. This model
represents the C-terminal region of the multifunctional
protein [Protein synthesis, tRNA and rRNA base
modification].
Length = 381
Score = 29.5 bits (67), Expect = 1.2
Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 2/25 (8%)
Query: 69 YVQRLDYHPGL--NVGFGARGTLFA 91
+ Y+PGL G G+RG A
Sbjct: 324 IAEPAPYYPGLYVLGGLGSRGLTSA 348
>gnl|CDD|236032 PRK07495, PRK07495, 4-aminobutyrate aminotransferase; Provisional.
Length = 425
Score = 28.2 bits (63), Expect = 3.6
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 11/63 (17%)
Query: 37 KPIRKNSGF-RFPKGFRKQEGEVVEKGSILYIS-YVQRLDYHPGLNVGFGARGTLFAMEK 94
+P++ GF P F K E+ ++ IL I+ VQ GF G LFAME
Sbjct: 205 EPVQGEGGFYPAPAAFMKALRELCDQHGILLIADEVQ---------TGFARTGKLFAMEH 255
Query: 95 GKV 97
+V
Sbjct: 256 HEV 258
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 28.0 bits (63), Expect = 3.8
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 135 EEQHSRFRLVDEPRVRNAAKKTGTSTRNKPIRKNSGFRFPKGFRKQEGEVVEKG 188
E S F LVD+ R R A+ T R + ++ R +G + + G +
Sbjct: 71 AEDESSFSLVDD-RSRLKARTTKHGKRKRRGKQTRTQRRGQGPQGKRGMTSRRA 123
>gnl|CDD|179736 PRK04073, rocD, ornithine--oxo-acid transaminase; Provisional.
Length = 396
Score = 27.4 bits (61), Expect = 5.4
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 9/62 (14%)
Query: 38 PIRKNSGFRFP-KGFRKQEGEVVEKGSILYISYVQRLDYHPGLNVGFGARGTLFAMEKGK 96
PI+ +G P +GF K E+ ++ ++L+I+ + G G G LFA +
Sbjct: 194 PIQGEAGINIPPEGFLKAARELCKEENVLFIA--------DEIQTGLGRTGKLFACDWDN 245
Query: 97 VK 98
V
Sbjct: 246 VT 247
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 27.3 bits (61), Expect = 5.5
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 102 EKCNLNWKH-TWVIANYSGQEGLPIYKKHI 130
EK + +H + Y +GL I +KHI
Sbjct: 252 EKLDAILRHLQLLADYYGESKGLRIARKHI 281
>gnl|CDD|235656 PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate
transaminase; Provisional.
Length = 423
Score = 27.1 bits (61), Expect = 6.6
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 81 VGFGARGTLFAMEKGKVK---ITVEK 103
GFG GTLFA E+ V + + K
Sbjct: 244 TGFGRTGTLFACEQAGVSPDIMCLSK 269
>gnl|CDD|233000 TIGR00508, bioA, adenosylmethionine-8-amino-7-oxononanoate
transaminase. All members of the seed alignment have
been demonstrated experimentally to act as EC 2.6.1.62,
an enzyme in the biotin biosynthetic pathway. Alternate
names include 7,8-diaminopelargonic acid
aminotransferase, DAPA aminotransferase, and
adenosylmethionine-8-amino-7-oxononanoate
aminotransferase. The gene symbol is bioA in E. coli and
BIO3 in S. cerevisiae [Biosynthesis of cofactors,
prosthetic groups, and carriers, Biotin].
Length = 417
Score = 26.7 bits (60), Expect = 9.2
Identities = 9/18 (50%), Positives = 9/18 (50%)
Query: 81 VGFGARGTLFAMEKGKVK 98
GFG G LFA E V
Sbjct: 240 TGFGRTGKLFACEHAGVT 257
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
0.318 0.135 0.402
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: 10,353,121
Number of extensions: 939183
Number of successful extensions: 783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 773
Number of HSP's successfully gapped: 23
Length of query: 206
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 114
Effective length of database: 6,857,034
Effective search space: 781701876
Effective search space used: 781701876
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: 57 (25.7 bits)