RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14782
(97 letters)
>gnl|CDD|185611 PTZ00428, PTZ00428, 60S ribosomal protein L4; Provisional.
Length = 381
Score = 157 bits (398), Expect = 2e-48
Identities = 62/92 (67%), Positives = 78/92 (84%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
MRNRR + RRGPLVVY D G+TKAFRNIPGV+L +V++LNLL+LAPGGHVGRF+IWT+S
Sbjct: 195 MRNRRYVMRRGPLVVYANDNGVTKAFRNIPGVDLCNVTRLNLLQLAPGGHVGRFIIWTKS 254
Query: 61 AFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
AFKKLD ++G++ + LKKGY+LP+P M N
Sbjct: 255 AFKKLDKIFGTYTEASALKKGYTLPRPLMTNA 286
>gnl|CDD|177779 PLN00185, PLN00185, 60S ribosomal protein L4-1; Provisional.
Length = 405
Score = 150 bits (381), Expect = 1e-45
Identities = 60/93 (64%), Positives = 76/93 (81%), Gaps = 1/93 (1%)
Query: 1 MRNRRRIQRRGPLVVYGKDRG-LTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTE 59
MRNRR + R+GPLVVYG + + KAFRNIPGVEL SV +LNLL+LAPGGH+GRFVIWT+
Sbjct: 200 MRNRRYVSRKGPLVVYGTEGAKIVKAFRNIPGVELCSVDRLNLLQLAPGGHLGRFVIWTK 259
Query: 60 SAFKKLDALYGSWKTKAPLKKGYSLPQPKMANT 92
SAF+KLD++YG+++ + KKGY LP+ KM N
Sbjct: 260 SAFEKLDSIYGTFEKPSEKKKGYVLPRAKMVNA 292
>gnl|CDD|235211 PRK04042, rpl4lp, 50S ribosomal protein L4P; Provisional.
Length = 254
Score = 89.9 bits (224), Expect = 1e-23
Identities = 31/70 (44%), Positives = 45/70 (64%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
MR RR + + L+V D + KA RN+PGV++++V LN+ LAPGGH GR +WTES
Sbjct: 185 MRGRRYKKPKSVLIVVSDDSPIVKAARNLPGVDVVTVDNLNVEHLAPGGHPGRLTVWTES 244
Query: 61 AFKKLDALYG 70
A ++L +
Sbjct: 245 AIEELRERFE 254
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P. One of the
primary rRNA binding proteins, this protein initially
binds near the 5'-end of the 23S rRNA. It is important
during the early stages of 50S assembly. It makes
multiple contacts with different domains of the 23S rRNA
in the assembled 50S subunit and ribosome.
Length = 251
Score = 88.0 bits (219), Expect = 7e-23
Identities = 34/66 (51%), Positives = 49/66 (74%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTES 60
MR RR + + L+V G D G++KA RN+PGV++++V+ LN+ LAPGGH GR +WTES
Sbjct: 184 MRGRRYKEPKSVLIVVGDDSGISKAARNLPGVDVVTVNNLNVEHLAPGGHPGRLTVWTES 243
Query: 61 AFKKLD 66
A +KL+
Sbjct: 244 AIEKLE 249
>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family. This
family includes Ribosomal L4/L1 from eukaryotes and
archaebacteria and L4 from eubacteria. L4 from yeast has
been shown to bind rRNA.
Length = 190
Score = 67.9 bits (167), Expect = 1e-15
Identities = 21/66 (31%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 3 NRRRIQRRGPLVVYG-KDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESA 61
++ + L+V KD L + RN+PGV++++V LN+ L P V+ T+SA
Sbjct: 128 KNLGLKNKKVLIVVDEKDENLYLSARNLPGVDVVTVDGLNVYDLLPADK----VVITKSA 183
Query: 62 FKKLDA 67
+KL+
Sbjct: 184 LEKLEE 189
>gnl|CDD|223166 COG0088, RplD, Ribosomal protein L4 [Translation, ribosomal
structure and biogenesis].
Length = 214
Score = 43.0 bits (102), Expect = 3e-06
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 11/58 (18%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWT 58
+ R + LVV G +P V+++ KL + KLAPG R +W
Sbjct: 168 LSARNLKNVKVVLVVGG-----------LPVVDVLRADKLVITKLAPGKIEERLTVWE 214
>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
Length = 205
Score = 35.1 bits (82), Expect = 0.002
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
+V D L + RN+P V+++ LN+ L V+ T++A KKL+
Sbjct: 152 IVTDEVDENLYLSARNLPNVDVLPAQGLNVYDLL----RADKVVLTKAAVKKLEERLA 205
>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
bacterial/organelle. Members of this protein family are
ribosomal protein L4. This model recognizes bacterial
and most organellar forms, but excludes homologs from
the eukaryotic cytoplasm and from archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 188
Score = 33.2 bits (77), Expect = 0.009
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKL 65
+V D L + RN+P V+++ + LN+ L V V+ TE+A +KL
Sbjct: 138 IVTDEVDENLYLSARNLPNVKVLPANGLNVYDLLRADKV---VL-TEAAVEKL 186
>gnl|CDD|214375 CHL00147, rpl4, ribosomal protein L4; Validated.
Length = 215
Score = 28.4 bits (64), Expect = 0.46
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 13 LVVYGKDRGLTKAFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDALYG 70
++V K L + RN+ VELIS LN+ L +I T+ A K ++ +Y
Sbjct: 161 IIVPEKTENLYLSTRNLKNVELISADTLNIKSLLKAKQ----IIITKEALKIIEEVYN 214
>gnl|CDD|218319 pfam04900, Fcf1, Fcf1. Fcf1 is a nucleolar protein involved in
pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2
leads to a decrease in synthesis of the 18S rRNA and
results in a deficit in 40S ribosomal subunits.
Length = 101
Score = 27.6 bits (62), Expect = 0.51
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 5 RRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSK 39
R+ + +V +DR L + R IPGV +I +++
Sbjct: 59 DRVGKHNCYIVATQDRELRRRLRKIPGVPIIYINR 93
>gnl|CDD|222716 pfam14374, Ribos_L4_asso_C, 60S ribosomal protein L4 C-terminal
domain. This family is found at the very C-terminal of
60 ribosomal L4 proteins.
Length = 80
Score = 27.2 bits (61), Expect = 0.54
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 80 KGYSLPQPKMANT 92
KGY+LP+PKMAN
Sbjct: 1 KGYNLPRPKMANA 13
>gnl|CDD|199892 cd07184, E_set_Isoamylase_like_N, N-terminal Early set domain
associated with the catalytic domain of isoamylase-like
(also called glycogen 6-glucanohydrolase) proteins. E
or "early" set domains are associated with the
catalytic domain of isoamylase-like proteins at the
N-terminal end. Isoamylase is one of the
starch-debranching enzymes that catalyze the hydrolysis
of alpha-1,6-glucosidic linkages specific in
alpha-glucans such as amylopectin or glycogen.
Isoamylase contains a bound calcium ion, but this is
not in the same position as the conserved calcium ion
that has been reported in other alpha-amylase family
enzymes. The N-terminal domain of isoamylase may be
related to the immunoglobulin and/or fibronectin type
III superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase. This domain is also a member of the
CBM48 (Carbohydrate Binding Module 48) family whose
members include pullulanase, maltooligosyl trehalose
synthase, starch branching enzyme, glycogen branching
enzyme, glycogen debranching enzyme, and the beta
subunit of AMP-activated protein kinase.
Length = 86
Score = 26.4 bits (59), Expect = 1.1
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 4/33 (12%)
Query: 51 VGRFVIWTESA--FKKLDALYGSWKTKAPLKKG 81
VG F W A KKL G++ L G
Sbjct: 19 VGDFNDWDPQATPMKKLKN--GTFSATLDLPAG 49
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 27.3 bits (60), Expect = 1.5
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 12 PLVVYGKDRGLTKAFRN 28
P YG +GL++AFRN
Sbjct: 1008 PPGGYGGRKGLSRAFRN 1024
>gnl|CDD|184735 PRK14547, rplD, 50S ribosomal protein L4; Provisional.
Length = 298
Score = 26.5 bits (58), Expect = 2.3
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 9 RRGPLVVYGKDRGLTK-AFRNIPGVELISVSKLNLLKLAPGGHVGRFVIWTESAFKKLDA 67
+R LVV + + + + RN+ V ++ +LN + +V++T+SA +
Sbjct: 150 QRALLVVAERSDAVERLSVRNLARVHVLGADQLNTYDVL----NVDWVVFTQSALEAFVG 205
Query: 68 LYGSWKTKA 76
W + A
Sbjct: 206 AKSRWGSAA 214
>gnl|CDD|238660 cd01364, KISc_BimC_Eg5, Kinesin motor domain, BimC/Eg5 spindle pole
proteins, participate in spindle assembly and chromosome
segregation during cell division. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Kinesins are
microtubule-dependent molecular motors that play
important roles in intracellular transport and in cell
division. In most kinesins, the motor domain is found at
the N-terminus (N-type), N-type kinesins are (+)
end-directed motors, i.e. they transport cargo towards
the (+) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and move
along the microtubule at a speed of about 6400 Angstroms
per second. To achieve that, kinesin head groups work in
pairs. Upon replacing ADP with ATP, a kinesin motor
domain increases its affinity for microtubule binding
and locks in place. Also, the neck linker binds to the
motor domain, which repositions the other head domain
through the coiled-coil domain close to a second tubulin
dimer, about 80 Angstroms along the microtubule.
Meanwhile, ATP hydrolysis takes place, and when the
second head domain binds to the microtubule, the first
domain again replaces ADP with ATP, triggering a
conformational change that pulls the first domain
forward.
Length = 352
Score = 26.5 bits (59), Expect = 2.6
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 28 NIPGVELISVSKLNLLKLAPGGHVGR 53
I G EL+ + KLNL+ LA ++GR
Sbjct: 233 TISGEELVKIGKLNLVDLAGSENIGR 258
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 26.0 bits (57), Expect = 3.1
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 7 IQRRGPLVVYGKD---RGLTKAFRNIPGVELISVSKLNL 42
+ + GP VY D AF+NIP V+L KL +
Sbjct: 84 LSKEGPCTVYSSDLKSENGEVAFKNIPIVKLAEGQKLEI 122
>gnl|CDD|188336 TIGR03535, DapD_actino,
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase. This enzyme is part of the
diaminopimelate pathway of lysine biosynthesis. This
model represents a clade of the enzyme specific to
Actinobacteria. Alternate name: tetrahydrodipicolinate
N-succinyltransferase.
Length = 319
Score = 25.9 bits (57), Expect = 4.1
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 4 RRRIQRRGPLVVYGKDR 20
R R++ RGP+ VY D+
Sbjct: 125 RARLRARGPVTVYSVDK 141
>gnl|CDD|189036 cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-processing protein
Fcf1- and Utp23-like homologs found in eukaryotes except
fungi. PIN domain homologs of Fcf1/Utp24
(FAF1-copurifying factor 1/U three-associated protein
24) and Utp23, essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly, are
included in this subfamily. Fcf1 is a component of the
small subunit (SSU) processome and an essential
nucleolar protein required for processing of the 18S
pre-rRNA at sites A0-A2. These PIN (PilT N terminus)
domains are homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but apparently lack the H3TH domain or
extensive arch/clamp region seen in the latter. PIN
domains typically contain three or four conserved acidic
residues (putative metal-binding, active site residues).
The Fcf1-Utp23 homolog PIN domain subfamily has three of
these conserved acidic residues rather than the four
seen in the Fcf1 PIN domain subfamily.
Length = 147
Score = 25.2 bits (56), Expect = 4.8
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 19 DRGLTKAFRNIPGVELI 35
D+ L + R IPGV L+
Sbjct: 121 DKELREKLRKIPGVPLL 137
>gnl|CDD|215204 PLN02356, PLN02356, phosphateglycerate kinase.
Length = 423
Score = 25.0 bits (54), Expect = 7.9
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 7/58 (12%)
Query: 1 MRNRRRIQRRGPLVVYGKDRGLTKAFRNIPGVELISVSKLNLLK-------LAPGGHV 51
+ N R+ + + PL GL A N P + + S+S+ + L PGG V
Sbjct: 26 LCNSRKRKTKKPLSKKKPRNGLIDAIGNTPLIRINSLSEATGCEILGKCEFLNPGGSV 83
>gnl|CDD|240510 cd06086, KOW_Spt5_6, KOW domain of Spt5, repeat 6. Spt5, an
eukaryotic ortholog of NusG, contains multiple KOW
motifs at its C-terminus. Spt5 is involved in
transcription elongation and termination. KOW domain is
known as an RNA-binding motif that is shared so far
among some families of ribosomal proteins, the
essential bacterial transcriptional elongation factor
NusG, the eukaryotic chromatin elongation factor Spt5,
the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5
domains play critical roles in recruitment of multiple
other eukaryotic transcription elongation and RNA
biogenesis factors and additionally are involved in the
binding of the eukaryotic Spt5 proteins to RNA
polymerases.
Length = 58
Score = 23.6 bits (52), Expect = 8.1
Identities = 12/43 (27%), Positives = 21/43 (48%), Gaps = 1/43 (2%)
Query: 14 VVYGKDRGLTKAFRNIPGVELISVSKLNL-LKLAPGGHVGRFV 55
V+ G+DRG T +I G + I + +K+ P + + V
Sbjct: 16 VIKGEDRGSTGELISIDGADGIVKMDSDGDIKILPMNFLAKLV 58
>gnl|CDD|237735 PRK14503, PRK14503, mannosyl-3-phosphoglycerate synthase;
Provisional.
Length = 393
Score = 25.1 bits (55), Expect = 8.4
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 6 RIQRRGPLVVYGKDRGLTKAFRNIP 30
R+ +R ++V+ KD GL +A +
Sbjct: 106 RLTQRPIIIVHQKDPGLAEALKEAG 130
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
0.321 0.138 0.415
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,936,274
Number of extensions: 394913
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 28
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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 (21.9 bits)
S2: 53 (24.1 bits)