RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029509
(192 letters)
>gnl|CDD|235464 PRK05435, rpmA, 50S ribosomal protein L27; Validated.
Length = 82
Score = 170 bits (433), Expect = 1e-55
Identities = 57/81 (70%), Positives = 66/81 (81%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS +RLGVK FG Q K G IIVRQRGTKFHPG NVG GKDHT+F+
Sbjct: 2 AHKKGGGSTRNGRDSESKRLGVKRFGGQFVKAGNIIVRQRGTKFHPGVNVGRGKDHTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQISVY 136
L+DG+VKFE+ G +RK +SV
Sbjct: 62 LVDGVVKFERKGRNRKYVSVV 82
>gnl|CDD|223289 COG0211, RpmA, Ribosomal protein L27 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 155 bits (393), Expect = 2e-49
Identities = 58/82 (70%), Positives = 67/82 (81%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GST+NGRDS +RLGVK FG Q K G+IIVRQRGTKFHPG NVG GKDHT+F+
Sbjct: 2 AHKKGGGSTRNGRDSESKRLGVKKFGGQFVKAGSIIVRQRGTKFHPGVNVGRGKDHTLFA 61
Query: 116 LIDGLVKFEKFGPDRKQISVYP 137
L+DG+VKFE G +RK +SV P
Sbjct: 62 LVDGVVKFETKGKNRKYVSVVP 83
>gnl|CDD|201553 pfam01016, Ribosomal_L27, Ribosomal L27 protein.
Length = 80
Score = 153 bits (388), Expect = 7e-49
Identities = 59/80 (73%), Positives = 67/80 (83%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKG GSTKNGRDS G+RLGVK FG Q K G IIVRQRGTKFHPG+NVG+GKDHT+F+
Sbjct: 1 AHKKGGGSTKNGRDSNGKRLGVKKFGGQFVKAGNIIVRQRGTKFHPGENVGMGKDHTLFA 60
Query: 116 LIDGLVKFEKFGPDRKQISV 135
L+DG VKFEK +RK +SV
Sbjct: 61 LVDGYVKFEKKPKNRKYVSV 80
>gnl|CDD|214370 CHL00121, rpl27, ribosomal protein L27; Reviewed.
Length = 86
Score = 133 bits (336), Expect = 5e-41
Identities = 51/82 (62%), Positives = 61/82 (74%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
AHKKGAGSTKNGRDS +RLGVK FG + G I++RQRGTKF PG NVG GKD T+++
Sbjct: 2 AHKKGAGSTKNGRDSNAKRLGVKRFGGEKVSAGNILIRQRGTKFKPGLNVGCGKDFTLYA 61
Query: 116 LIDGLVKFEKFGPDRKQISVYP 137
LIDG VKF+K +K I+V
Sbjct: 62 LIDGFVKFKKKNKKQKSINVIN 83
>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 = 126 bits (318), Expect = 3e-38
Identities = 56/82 (68%), Positives = 64/82 (78%), Gaps = 1/82 (1%)
Query: 56 AHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFS 115
A KKG GSTKNGRDS +RLGVK G Q + G+IIVRQRGTKFHPG NVG+GKDHT+F+
Sbjct: 2 ATKKGVGSTKNGRDSEAKRLGVKRAGGQFVRAGSIIVRQRGTKFHPGNNVGMGKDHTLFA 61
Query: 116 LIDGLVKFEKFG-PDRKQISVY 136
L DG+VKFEK G RK +SV
Sbjct: 62 LSDGVVKFEKKGKRSRKFVSVV 83
>gnl|CDD|215565 PLN03083, PLN03083, E3 UFM1-protein ligase 1 homolog; Provisional.
Length = 803
Score = 31.3 bits (71), Expect = 0.28
Identities = 29/153 (18%), Positives = 53/153 (34%), Gaps = 14/153 (9%)
Query: 20 SSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKI 79
SS ++S+ KG KS + +P E A KKG + K GRD +
Sbjct: 409 SSPAASNSDKGSKKKKGKSTSTKGGTAESIPDDEEDAPKKGKKNQKKGRDKSSKVPSDSK 468
Query: 80 FGDQVAKPGAIIVRQRGTKFHPGKNVGLGKDHTIFSLIDGLV-KFEKFGPDRKQISVYP- 137
G + + N + + + I V E+ G + +
Sbjct: 469 AGGKKESVKS-----------QEDNNNIPPEEWVMKKILEWVPDLEEDGTEDPGSILKHL 517
Query: 138 -REVQPENPNSYRARKREYFRLQREKKKARKEA 169
++P NS + R++ F E+++ +
Sbjct: 518 ADHLRPMLINSLKERRKALFTENAERRRRLLDN 550
>gnl|CDD|217966 pfam04209, HgmA, homogentisate 1,2-dioxygenase. Homogentisate
dioxygenase cleaves the aromatic ring during the
metabolic degradation of Phe and Tyr. Homogentisate
dioxygenase deficiency causes alkaptonuria. The
structure of homogentisate dioxygenase shows that the
enzyme forms a hexamer arrangement comprised of a dimer
of trimers. The active site iron ion is coordinated near
the interface between the trimers.
Length = 422
Score = 30.8 bits (70), Expect = 0.36
Identities = 23/94 (24%), Positives = 36/94 (38%), Gaps = 14/94 (14%)
Query: 15 KGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQR 74
K + S + F++G T+ + P S L I + K ++ G
Sbjct: 92 KPFPIPSKEPTDFVEGLHTIAG-----AGDPLSNHGLAIHVYSANKSMENKLFYNADGDF 146
Query: 75 LGV----KI-----FGDQVAKPGAIIVRQRGTKF 99
L V ++ FG + PG I V RGT+F
Sbjct: 147 LIVPQQGELDLYTEFGRLLVSPGEIAVIPRGTRF 180
>gnl|CDD|206751 cd01858, NGP_1, A novel nucleolar GTP-binding protein, circularly
permuted subfamily of the Ras GTPases. Autoantigen
NGP-1 (Nucleolar G-protein gene 1) has been shown to
localize in the nucleolus and nucleolar organizers in
all cell types analyzed, which is indicative of a
function in ribosomal assembly. NGP-1 and its homologs
show a circular permutation of the GTPase signature
motifs so that the C-terminal strands 5, 6, and 7
(strand 6 contains the G4 box with NKXD motif) are
relocated to the N terminus.
Length = 157
Score = 28.4 bits (64), Expect = 1.3
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 99 FHPGKNVGLGKDHTIFSLIDGLVKFEKFGPDRKQISV----YPREVQPENPNSYRARK 152
FH GK +LI+ L +F K D+KQISV YP + N+ R++K
Sbjct: 73 FHASITNPFGKG----ALINLLRQFAKLHSDKKQISVGFIGYPNVGKSSVINTLRSKK 126
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 28.5 bits (64), Expect = 2.1
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 169 AYLAQPQLVLASALDDAADGLP 190
AY P+LVL SA DAA G P
Sbjct: 242 AYEFNPELVLVSAGFDAARGDP 263
>gnl|CDD|173962 cd07978, TAF13, The TATA Binding Protein (TBP) Associated Factor 13
(TAF13) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 13 (TAF13) is one of several TAFs that bind TBP
and is involved in forming the Transcription Factor
IID (TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryotes. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs from various species were
originally named by their predicted molecular weight or
their electrophoretic mobility in polyacrylamide gels. A
new, unified nomenclature for the pol II TAFs has been
suggested to show the relationship between TAFs
orthologs and paralogs. Several hypotheses are proposed
for TAFs functions such as serving as activator-binding
sites, core-promoter recognition or a role in essential
catalytic activity. Each TAF, with the help of a
specific activator, is required only for expression of
subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and are
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF13 interacts with TAF11 and makes a
histone-like heterodimer similar to H3/H4-like proteins.
The dimer may be structurally and functionally similar
to the spt3 protein within the SAGA histone
acetyltransferase complex.
Length = 92
Score = 26.7 bits (60), Expect = 2.8
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 150 ARKREYFRLQREKKKARK 167
AR RE ++ E KKARK
Sbjct: 72 ARLRELLSMKDELKKARK 89
>gnl|CDD|238356 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. Topo
I enzymes are divided into: topo type IA (bacterial)
and type IB (eukaryotic). Topo I relaxes superhelical
tension in duplex DNA by creating a single-strand nick,
the broken strand can then rotate around the unbroken
strand to remove DNA supercoils and, the nick is
religated, liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 215
Score = 28.0 bits (63), Expect = 3.0
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 154 EYFRLQREKKKAR-KEAYLAQ 173
+YF ++EKKKA KE A
Sbjct: 92 QYFEEEKEKKKAMSKEEKKAI 112
>gnl|CDD|216176 pfam00890, FAD_binding_2, FAD binding domain. This family includes
members that bind FAD. This family includes the
flavoprotein subunits from succinate and fumarate
dehydrogenase, aspartate oxidase and the alpha subunit
of adenylylsulphate reductase.
Length = 401
Score = 27.3 bits (61), Expect = 5.3
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 72 GQRLGVKIFGDQVAKPGAIIVRQRGTKF 99
G RLG + + + G I+V G +F
Sbjct: 256 GIRLGSGLLIEALRGEGGILVNDDGRRF 283
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 26.5 bits (59), Expect = 5.8
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 148 YRA-RKREYFRLQREKKKARKE 168
YRA R+REY RL+ +K +KE
Sbjct: 41 YRALRRREYERLELMDEKWKKE 62
>gnl|CDD|218404 pfam05056, DUF674, Protein of unknown function (DUF674). This
family is found in Arabidopsis thaliana and contains
several uncharacterized proteins.
Length = 462
Score = 27.5 bits (61), Expect = 5.8
Identities = 22/98 (22%), Positives = 39/98 (39%), Gaps = 8/98 (8%)
Query: 10 LIGSFKGLSLSSSSSSSFLK-GDFTVCPK---SVTVSLPPTSPL-PLTIESAHKKGAGST 64
L SFK LS ++ SS + C K +T PP + ++ + G T
Sbjct: 324 LFRSFKDLSGDEATESSKCALPHYYNCQKQLLGITTQQPPVYYRYVYSNCISYLRDYGLT 383
Query: 65 KNGRDSRGQRLGV---KIFGDQVAKPGAIIVRQRGTKF 99
++ + + + + K G + + +RGTKF
Sbjct: 384 EDSEKDKLKPVILIDPKSEGSGTSASESGGFVKRGTKF 421
>gnl|CDD|227277 COG4941, COG4941, Predicted RNA polymerase sigma factor containing
a TPR repeat domain [Transcription].
Length = 415
Score = 27.0 bits (60), Expect = 6.3
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 7/59 (11%)
Query: 135 VYPREVQPENPNSY---RARKREYFRLQREKKKARKEAYLA----QPQLVLASALDDAA 186
+PR P NP ++ R R R++R ++ L ++ A ALDD
Sbjct: 46 RWPRAGPPRNPAAWLIAVGRNRAIDRVRRRARRDAAPPELLLSDEDEEMEEAEALDDEH 104
>gnl|CDD|165099 PHA02732, PHA02732, hypothetical protein; Provisional.
Length = 1467
Score = 27.4 bits (60), Expect = 7.0
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 9/45 (20%)
Query: 3 TASMSASLIGSFKGLSLSSSSSSSFLKGDFTVCPKSVTVSLPPTS 47
MS + +FK L S++SS P + T PP S
Sbjct: 1210 IIGMSGTNTFTFKAAQLQLSAASS---------PPAATTPTPPPS 1245
>gnl|CDD|239052 cd02137, Nitroreductase_1, Nitroreductase-like family 1. A
subfamily of the nitroreductase family containing
uncharacterized proteins that are similar to
nitroreductase. Nitroreductase catalyzes the reduction
of nitroaromatic compounds such as nitrotoluenes,
nitrofurans and nitroimidazoles. This process requires
NAD(P)H as electron donor in an obligatory two-electron
transfer and uses FMN as cofactor. The enzyme is
typically a homodimer. Members of this family are also
called NADH dehydrogenase, oxygen-insensitive NAD(P)H
nitrogenase or dihydropteridine reductase.
Length = 148
Score = 26.4 bits (59), Expect = 7.0
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 145 PNSYRARKREYFRLQREKKKAR-KEAYLAQPQLVLASAL 182
P+S+ + + ++ +KKA+ EA + QPQ+ ASA+
Sbjct: 35 PSSFNLQPWRFVVVRDPEKKAKLAEAAMNQPQVTTASAV 73
>gnl|CDD|164583 MTH00005, ATP6, ATP synthase F0 subunit 6; Provisional.
Length = 231
Score = 26.6 bits (59), Expect = 7.9
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 4 ASMSA-----SLIGSFKGLSLSSSSSSSFL 28
A+MSA SLIG + +L SS SS+ L
Sbjct: 167 ANMSAGHIVLSLIGIYAASALFSSISSTIL 196
>gnl|CDD|223033 PHA03291, PHA03291, envelope glycoprotein I; Provisional.
Length = 401
Score = 26.8 bits (59), Expect = 8.0
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 2/57 (3%)
Query: 36 PKSVTVSLPPTSPLPLTIESAHKKGAGSTKNGRDSRGQRLGVKIFGDQVAKPGAIIV 92
P++ T +P P T A +T SR + +I Q+A P +II
Sbjct: 245 PQAGTTPEAEGTPAPPTPGGGEAPPANATPAPEASRYELTVTQII--QIAIPASIIA 299
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 26.6 bits (59), Expect = 8.3
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 36 PKSVTVSLPPTSPLPLTIESAHKKGA 61
++V +LPPT P+PL I+ H A
Sbjct: 6 RETVKSALPPTKPIPLNID--HLPEA 29
>gnl|CDD|182786 PRK10860, PRK10860, tRNA-specific adenosine deaminase; Provisional.
Length = 172
Score = 26.3 bits (58), Expect = 8.3
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 155 YFRLQREKKKARKEAYLAQP 174
+FR++R++ KA K+A +
Sbjct: 153 FFRMRRQEIKALKKAQRSTD 172
>gnl|CDD|233352 TIGR01310, L7, 60S ribosomal protein L7, eukaryotic. This model
describes the eukaryotic 60S (cytosolic) ribosomal
protein L7 and paralogs that may or may not also be L7.
Human, Drosophila, and Arabidopsis all have both a
typical L7 and an L7-related paralog. This family is
designated subfamily rather than equivalog to reflect
these uncharacterized paralogs. Members of this family
average ~ 250 residues in length, somewhat longer than
the archaeal L30P/L7E homolog (~ 155 residues) and much
longer than the related bacterial/organellar form (~ 60
residues).
Length = 235
Score = 26.6 bits (59), Expect = 9.3
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 146 NSYRARKREYFRLQREKKKARKEAYLAQPQLV 177
YR +RE RL+R KK K A+ +LV
Sbjct: 44 KEYRKAEREIIRLKRLAKKPGKFYVPAEHKLV 75
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
0.315 0.132 0.376
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,586,467
Number of extensions: 894150
Number of successful extensions: 723
Number of sequences better than 10.0: 1
Number of HSP's gapped: 723
Number of HSP's successfully gapped: 35
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
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: 42 (22.0 bits)
S2: 56 (25.3 bits)