RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4931
(186 letters)
>gnl|CDD|100103 cd00472, Ribosomal_L24e_L24, Ribosomal protein L24e/L24 is a
ribosomal protein found in eukaryotes (L24) and in
archaea (L24e, distinct from archaeal L24). L24e/L24 is
located on the surface of the large subunit, adjacent
to proteins L14 and L3, and near the translation factor
binding site. L24e/L24 appears to play a role in the
kinetics of peptide synthesis, and may be involved in
interactions between the large and small subunits,
either directly or through other factors. In mouse, a
deletion mutation in L24 has been identified as the
cause for the belly spot and tail (Bst) mutation that
results in disrupted pigmentation, somitogenesis and
retinal cell fate determination. L24 may be an
important protein in eukaryotic reproduction: in
shrimp, L24 expression is elevated in the ovary,
suggesting a role in oogenesis, and in Arabidopsis, L24
has been proposed to have a specific function in
gynoecium development. No protein with sequence or
structural homology to L24e/L24 has been identified in
bacteria, but a functionally equivalent protein may
exist. Bacterial L19 forms an interprotein beta sheet
with L14 that is similar to the L24e/L14 interprotein
beta sheet observed in the archaeal L24e structures.
Some eukaryotic L24 proteins were initially identified
as L30, and this alignment model contains several
sequences called L30.
Length = 54
Score = 105 bits (264), Expect = 1e-30
Identities = 35/54 (64%), Positives = 39/54 (72%)
Query: 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKA 54
M+ E C FC KIYPGHG +VRND K+FRFC SKC K F RK+NPRK WT A
Sbjct: 1 MKTEKCSFCGYKIYPGHGKMYVRNDGKVFRFCSSKCEKNFLRKRNPRKLKWTVA 54
>gnl|CDD|224986 COG2075, RPL24A, Ribosomal protein L24E [Translation, ribosomal
structure and biogenesis].
Length = 66
Score = 102 bits (255), Expect = 5e-29
Identities = 36/66 (54%), Positives = 45/66 (68%)
Query: 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRG 60
M++ C FC KI PG GI +VRND K+ RFC SKC KLFK +NPRK WTK YRK+
Sbjct: 1 MKVRVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEKLFKLGRNPRKLKWTKKYRKMHK 60
Query: 61 KDLAVD 66
K++ +
Sbjct: 61 KEIKEE 66
>gnl|CDD|110260 pfam01246, Ribosomal_L24e, Ribosomal protein L24e.
Length = 71
Score = 95.7 bits (238), Expect = 2e-26
Identities = 40/64 (62%), Positives = 44/64 (68%)
Query: 1 MRIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRG 60
M++E C F KIYPGHGI FVR D K+FRFC SKC K F K+NPRK AWTK YRK
Sbjct: 1 MKVELCSFSGYKIYPGHGIMFVRKDSKVFRFCSSKCEKNFHMKRNPRKLAWTKLYRKQHK 60
Query: 61 KDLA 64
K A
Sbjct: 61 KGEA 64
>gnl|CDD|179131 PRK00807, PRK00807, 50S ribosomal protein L24e; Validated.
Length = 52
Score = 67.7 bits (166), Expect = 8e-16
Identities = 25/52 (48%), Positives = 30/52 (57%)
Query: 3 IETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKA 54
TC FC +I PG G +V+ D I FC SKC K +K + PRK WTKA
Sbjct: 1 TRTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCEKNYKLGRVPRKLKWTKA 52
>gnl|CDD|214799 smart00746, TRASH, metallochaperone-like domain.
Length = 39
Score = 48.5 bits (116), Expect = 1e-08
Identities = 17/39 (43%), Positives = 21/39 (53%)
Query: 6 CYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKK 44
C FC IY V ND K++ FC SKC FK+K+
Sbjct: 1 CSFCGKDIYNPGTGIMVVNDGKVYYFCSSKCLSKFKKKR 39
>gnl|CDD|184885 PRK14891, PRK14891, 50S ribosomal protein L24e/unknown domain
fusion protein; Provisional.
Length = 131
Score = 50.3 bits (120), Expect = 2e-08
Identities = 21/59 (35%), Positives = 28/59 (47%)
Query: 2 RIETCYFCSSKIYPGHGIQFVRNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYRKVRG 60
TC + +I PG G FVR D + F SKC K + + R WT+A R +G
Sbjct: 3 ETRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCEKNYDLGREARDLEWTEAGRAEKG 61
>gnl|CDD|140068 PTZ00033, PTZ00033, 60S ribosomal protein L24; Provisional.
Length = 125
Score = 49.6 bits (118), Expect = 3e-08
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 1 MRIETCYFCSSKIYPGHGIQFV----RNDCKIFRFCRSKCHKLFKRKKNPRKTAWTKAYR 56
MR C F ++PGHG ++V + + F R KC L+ RKKNPR WT+ YR
Sbjct: 1 MRTIACEFSHFAVHPGHGRRYVPFAFLSTKPVLTFLRPKCFALYMRKKNPRFLPWTRTYR 60
Query: 57 KVRGK 61
++ K
Sbjct: 61 RINRK 65
>gnl|CDD|183625 PRK12617, flgA, flagellar basal body P-ring biosynthesis protein
FlgA; Reviewed.
Length = 214
Score = 29.9 bits (67), Expect = 0.67
Identities = 18/60 (30%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 99 IKTKR-QNLYLAQRLRKAREVETARDIKAVQRDIA-----ILNDPTEAIKAKKKRMVEAG 152
+K +R Q++ + +R A E + DI +RD A +L DP A+ +R++ AG
Sbjct: 83 LKVRRNQDVLVLRRGITAGETISLADISIEKRDAARIVGAVLADPVAAVGKTARRILPAG 142
>gnl|CDD|233351 TIGR01304, IMP_DH_rel_2, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase. Most species with a
member of this family belong to the high GC
Gram-positive bacteria, and these also have the IMP
dehydrogenase described by TIGRFAMs equivalog model
TIGR01302 [Unknown function, General].
Length = 369
Score = 29.8 bits (67), Expect = 0.70
Identities = 9/33 (27%), Positives = 21/33 (63%)
Query: 109 AQRLRKAREVETARDIKAVQRDIAILNDPTEAI 141
++R R +++V+TA I A + ++ + P +A+
Sbjct: 23 SRRTRSSKDVDTAWQIDAYRFELPFIAHPMDAL 55
>gnl|CDD|216675 pfam01743, PolyA_pol, Poly A polymerase head domain. This family
includes nucleic acid independent RNA polymerases, such
as Poly(A) polymerase, which adds the poly (A) tail to
mRNA EC:2.7.7.19. This family also includes the tRNA
nucleotidyltransferase that adds the CCA to the 3' of
the tRNA EC:2.7.7.25. This family is part of the
nucleotidyltransferase superfamily.
Length = 126
Score = 28.8 bits (65), Expect = 0.93
Identities = 23/107 (21%), Positives = 36/107 (33%), Gaps = 19/107 (17%)
Query: 62 DLAVDPSFE-----FAKRRNVPLKYDREFWNKTVEAIKKVEHIKTKRQNLYLAQRLRKAR 116
D+A D E F R V L+ +EF V ++ + T R R +
Sbjct: 21 DIATDAGPEQVATLFRNRIIVHLESGKEFGTIHVLFGNQILEVATFRTESD-ESDFRNPK 79
Query: 117 EVETARDIK--AVQRDIAI-----------LNDPTEAIKAKKKRMVE 150
E ++ +RD I + DP IK K ++
Sbjct: 80 SEEFTGTLEEDLKRRDFTINALAYDPNDGEVIDPFGGIKDLKNGVIR 126
>gnl|CDD|227318 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
component [Inorganic ion transport and metabolism].
Length = 289
Score = 28.7 bits (64), Expect = 1.4
Identities = 20/77 (25%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 108 LAQRLRKA-REVETARD--IKAVQRDIAILNDPTEAIKAKKKRMVEAGIVEEIHESENEA 164
L + L+K EVET RD K V++ + ++N E ++ +K+R+ G +++ + A
Sbjct: 162 LERELQKRLLEVETLRDQVDKMVEQQVRVINSQLERLRLEKRRLQLNGQLDDEFQQHYVA 221
Query: 165 EENMEVDTHWETNEDKL 181
E++ E+ + +L
Sbjct: 222 EKS-ELQKRLAQLQTEL 237
>gnl|CDD|222613 pfam14235, DUF4337, Domain of unknown function (DUF4337). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 187 and 201 amino
acids in length. There is a single completely conserved
residue Q that may be functionally important.
Length = 158
Score = 27.5 bits (62), Expect = 2.8
Identities = 13/76 (17%), Positives = 28/76 (36%), Gaps = 7/76 (9%)
Query: 100 KTKRQNLYLAQRLRKAREVETARDIKAVQRDIAILNDPTEAIKAKKKRMVEAGIVEEIHE 159
K+ +Q+L E+E A +Q IA +++ K + + E
Sbjct: 47 KSIKQHLAELAA--DLLELEAAAPRAELQAKIARYKKEKARYRSEAKE-----LEAKAKE 99
Query: 160 SENEAEENMEVDTHWE 175
+E E++ + +
Sbjct: 100 AEAESDHALHQHHRFA 115
>gnl|CDD|197352 cd10044, Reelin_repeat_8_subrepeat_1, N-terminal subrepeat of
tandem repeat unit 8 of reelin and related proteins.
Reelin is an extracellular glycoprotein involved in
neuronal development, specifically in the brain cortex.
It contains 8 tandemly repeated units, each of which is
composed of two highly similar subrepeats and a central
EGF domain. This model characterizes the N-terminal
subrepeat, which directly contacts the C-terminal
subrepeat and the EGF domain in a compact arrangement.
Consecutive reelin repeat units are packed together to
form an overall rod-like molecular structure. Reelin
repeats 5 and 6 are reported to interact with neuronal
receptors, the apolipoprotein E receptor 2 (ApoER2) and
the very-low-density lipoprotein receptor (VLDLR),
triggering a signaling cascade upon binding and
subsequent tyrosine phosphorylation of the cytoplasmic
disabled-1 (Dab1).
Length = 176
Score = 27.5 bits (61), Expect = 3.5
Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 13 IYPGHGIQFVRN-DCKIFRFCRSKCHKLFKRKKNPRKTAWT 52
+ PG+ IQF C C + + +PR W
Sbjct: 60 VQPGYMIQFKIVVGCGSVSSCGDLHPVMLEYTTDPRSDHWQ 100
>gnl|CDD|236322 PRK08649, PRK08649, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 368
Score = 27.1 bits (61), Expect = 6.2
Identities = 10/31 (32%), Positives = 17/31 (54%)
Query: 111 RLRKAREVETARDIKAVQRDIAILNDPTEAI 141
R R +V T+ I A + +I I+ P +A+
Sbjct: 28 RTRDPEDVSTSWQIDAYRFEIPIIASPMDAV 58
>gnl|CDD|201501 pfam00912, Transgly, Transglycosylase. The penicillin-binding
proteins are bifunctional proteins consisting of
transglycosylase and transpeptidase in the N- and
C-terminus respectively. The transglycosylase domain
catalyzes the polymerisation of murein glycan chains.
Length = 177
Score = 26.8 bits (60), Expect = 6.3
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 75 RNVPLKYDREFWNKTVEAI--KKVEHIKTKRQ--NLYLAQ 110
+N+ L +R K EAI ++E +K + LYL
Sbjct: 74 KNLFLTTERTLSRKLREAILALRLERRYSKDEILELYLNT 113
>gnl|CDD|221313 pfam11917, DUF3435, Protein of unknown function (DUF3435). This
family of proteins are functionally uncharacterized.
This protein is found in eukaryotes. Proteins in this
family are typically between 435 to 791 amino acids in
length. This family is related to pfam00589 suggesting
it may be an integrase enzyme.
Length = 418
Score = 26.9 bits (60), Expect = 7.0
Identities = 10/42 (23%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 91 EAIKKVEHIKTKRQNLYLAQRLRKAREVETARDIKAVQRDIA 132
E I+K +H+K + LY ++ KA+ ++ +R++
Sbjct: 292 ELIRKRDHLKKEIIALY--GQVAKAKGTPLYERLEKRRREVR 331
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 27.1 bits (60), Expect = 7.6
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 6/45 (13%)
Query: 113 RKAREVETARDIKAVQRDIAILNDPTEAIKAKKKRMVEAGIVEEI 157
+KAR V AR + A RD+ +L+DP A+ A V +VEE
Sbjct: 787 QKAR-VSLARAVYA-NRDVYLLDDPLSALDAH----VGERVVEEC 825
>gnl|CDD|116863 pfam08279, HTH_11, HTH domain. This family includes
helix-turn-helix domains in a wide variety of proteins.
Length = 55
Score = 24.7 bits (55), Expect = 7.8
Identities = 11/50 (22%), Positives = 24/50 (48%), Gaps = 8/50 (16%)
Query: 106 LYLAQRLRKAREVETARDI--------KAVQRDIAILNDPTEAIKAKKKR 147
L + + L +ARE + +++ + ++RDI L I+++ R
Sbjct: 3 LQILELLLQAREPISGQELAEKLGVSRRTIRRDIKALEALGVPIESEPGR 52
>gnl|CDD|199864 cd06240, M14-like_1_3, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 274
Score = 26.5 bits (59), Expect = 7.9
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 83 REFWNKTV---EAIKKVEHIKTKRQNLYLAQRLRKAREVETARDIKAV 127
RE + E + K++H K + L + L + + + A + KA+
Sbjct: 12 REQIMAAISSPENLAKLDHYKAILRKLADPRGLSEEQARKLAAEGKAI 59
>gnl|CDD|183583 PRK12544, PRK12544, RNA polymerase sigma factor; Provisional.
Length = 206
Score = 26.3 bits (58), Expect = 8.4
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 132 AILNDPTEAIKAKKKRMVEAGIVEEIHESENEAEENMEVDTHWETNE 178
AIL + + +KKR V A + E E + EE + HW+ +E
Sbjct: 75 AILKNKIIDLLRQKKRHVSASSLLRDEEEEEDFEELFDESGHWQKDE 121
>gnl|CDD|233423 TIGR01464, hemE, uroporphyrinogen decarboxylase. This model
represents uroporphyrinogen decarboxylase (HemE), which
converts uroporphyrinogen III to coproporphyrinogen III.
This step takes the pathway toward protoporphyrin IX, a
common precursor of both heme and chlorophyll, rather
than toward precorrin 2 and its products [Biosynthesis
of cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 338
Score = 26.5 bits (59), Expect = 9.3
Identities = 13/32 (40%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 123 DIKAVQ--RDIAILNDPTEAIKAKKKRMVEAG 152
D A+Q D A+L P EA++ K +R++EA
Sbjct: 275 DGVAIQGNLDPAVLYAPEEALEEKVERILEAF 306
>gnl|CDD|215286 PLN02523, PLN02523, galacturonosyltransferase.
Length = 559
Score = 26.8 bits (59), Expect = 9.4
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 91 EAIKKVEHIKTKRQNLYLAQRLRKAREVETAR-DIKAVQRDIAILN 135
E K V H+ T R NL + + K R++ A ++KAV+ D LN
Sbjct: 274 EPWKHVFHVVTDRMNLAAMKVMFKMRDLNGAHVEVKAVE-DYKFLN 318
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
0.320 0.133 0.398
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,449,613
Number of extensions: 873733
Number of successful extensions: 1153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1131
Number of HSP's successfully gapped: 71
Length of query: 186
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 95
Effective length of database: 6,901,388
Effective search space: 655631860
Effective search space used: 655631860
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: 56 (25.4 bits)