RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2938
(113 letters)
>gnl|CDD|205076 pfam12796, Ank_2, Ankyrin repeats (3 copies).
Length = 91
Score = 41.1 bits (97), Expect = 6e-06
Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 72 GVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
G +VN D G T L+ A+ G E+V+ L E GAD+N
Sbjct: 51 GADVNAKDKDGNTALHLAARNGNLEIVKLLLEHGADIN 88
Score = 34.2 bits (79), Expect = 0.002
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 52 LIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
L ++ + + + ++ G +VN D T L+ A+ G E+V+ L E GADVN
Sbjct: 1 LHLAAKNGNLELVKLLLEKG-ADVNLGDT--DTALHLAARNGNLEIVKLLLEHGADVN 55
Score = 29.1 bits (66), Expect = 0.15
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 86 LNWASAFGTQEMVEFLCERGADVNKGK 112
L+ A+ G E+V+ L E+GADVN G
Sbjct: 1 LHLAAKNGNLELVKLLLEKGADVNLGD 27
>gnl|CDD|238125 cd00204, ANK, ankyrin repeats; ankyrin repeats mediate
protein-protein interactions in very diverse families of
proteins. The number of ANK repeats in a protein can
range from 2 to over 20 (ankyrins, for example). ANK
repeats may occur in combinations with other types of
domains. The structural repeat unit contains two
antiparallel helices and a beta-hairpin, repeats are
stacked in a superhelical arrangement; this alignment
contains 4 consecutive repeats.
Length = 126
Score = 40.1 bits (94), Expect = 2e-05
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 52 LIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVNK 110
L + + +++ + G +VN D+ G+T L+ A+ G E+V+ L E+GADVN
Sbjct: 11 LHLAASNGHLE-VVKLLLENGADVNAKDNDGRTPLHLAAKNGHLEIVKLLLEKGADVNA 68
Score = 37.0 bits (86), Expect = 4e-04
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 72 GVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
G +VN D G T L+ A+ G ++V+ L + GADVN
Sbjct: 63 GADVNARDKDGNTPLHLAARNGNLDVVKLLLKHGADVN 100
Score = 32.7 bits (75), Expect = 0.012
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 76 NFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
N D+ G+T L+ A++ G E+V+ L E GADVN
Sbjct: 1 NARDEDGRTPLHLAASNGHLEVVKLLLENGADVN 34
Score = 28.9 bits (65), Expect = 0.33
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 52 LIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFL 101
L R+ + D +++ + G +VN D G+T L+ A+ G E+V+ L
Sbjct: 77 LHLAARNGNLD-VVKLLLKHGADVNARDKDGRTPLHLAAKNGHLEVVKLL 125
>gnl|CDD|200936 pfam00023, Ank, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities. Repeats 13-24 are especially active,
with known sites of interaction for the Na/K ATPase,
Cl/HCO(3) anion exchanger, voltage-gated sodium channel,
clathrin heavy chain and L1 family cell adhesion
molecules. The ANK repeats are found to form a
contiguous spiral stack such that ion transporters like
the anion exchanger associate in a large central cavity
formed by the ANK repeat spiral, while clathrin and cell
adhesion molecules associate with specific regions
outside this cavity.
Length = 33
Score = 37.5 bits (88), Expect = 4e-05
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 82 GQTLLNWASAFGTQEMVEFLCERGADVN 109
G T L+ A+ G E+V+ L E GADVN
Sbjct: 2 GNTPLHLAARNGHLEVVKLLLEAGADVN 29
>gnl|CDD|205784 pfam13606, Ank_3, Ankyrin repeat. Ankyrins are multifunctional
adaptors that link specific proteins to the
membrane-associated, spectrin- actin cytoskeleton. This
repeat-domain is a 'membrane-binding' domain of up to 24
repeated units, and it mediates most of the protein's
binding activities.
Length = 30
Score = 36.5 bits (85), Expect = 9e-05
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 82 GQTLLNWASAFGTQEMVEFLCERGADVN 109
G T L+ A+ G E+V+ L E GAD+N
Sbjct: 2 GNTPLHLAARNGNLELVKLLLEHGADIN 29
>gnl|CDD|222980 PHA03095, PHA03095, ankyrin-like protein; Provisional.
Length = 471
Score = 38.9 bits (91), Expect = 2e-04
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 17/86 (19%)
Query: 24 AALNQEGNIEYKAHTKTHKTFKTSNILQLIECIRSKDTDALIETIDSGGVEVNFMDDVGQ 83
AA + GN + T + K S +L L+ G+ +N + GQ
Sbjct: 216 AATDMLGNTPLHS-MATGSSCKRSLVLPLLI----------------AGISINARNRYGQ 258
Query: 84 TLLNWASAFGTQEMVEFLCERGADVN 109
T L++A+ F L GAD+N
Sbjct: 259 TPLHYAAVFNNPRACRRLIALGADIN 284
Score = 34.2 bits (79), Expect = 0.006
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 55 CIRSKDTDALIETIDSGGVEVNFMDDVGQTLLN-WASAFGTQE-MVEFLCERGADVNK 110
+ + T +I+ + G +VN D VG+T L+ + S F ++ L +GADVN
Sbjct: 90 YLYNATTLDVIKLLIKAGADVNAKDKVGRTPLHVYLSGFNINPKVIRLLLRKGADVNA 147
Score = 26.1 bits (58), Expect = 4.7
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 94 TQEMVEFLCERGADVNKG 111
T ++++ L + GADVN
Sbjct: 96 TLDVIKLLIKAGADVNAK 113
>gnl|CDD|165207 PHA02876, PHA02876, ankyrin repeat protein; Provisional.
Length = 682
Score = 36.6 bits (84), Expect = 0.001
Identities = 32/88 (36%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 32 IEYKAHTKTHKTFKT-----SNI----LQLIECIRSKDTDALIETIDSGGVEVNFMDDVG 82
+E +K T K SNI L L++ IR++D + + D+G VN +DD
Sbjct: 215 LECAVDSKNIDTIKAIIDNRSNINKNDLSLLKAIRNEDLETSLLLYDAG-FSVNSIDDCK 273
Query: 83 QTLLNWAS-AFGTQEMVEFLCERGADVN 109
T L+ AS A +V L ERGADVN
Sbjct: 274 NTPLHHASQAPSLSRLVPKLLERGADVN 301
Score = 35.0 bits (80), Expect = 0.004
Identities = 21/68 (30%), Positives = 35/68 (51%)
Query: 42 KTFKTSNILQLIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFL 101
K ++ ++LI+ +D + E + GG +VN D T +++A+ G +MV L
Sbjct: 138 KINESIEYMKLIKERIQQDELLIAEMLLEGGADVNAKDIYCITPIHYAAERGNAKMVNLL 197
Query: 102 CERGADVN 109
GADVN
Sbjct: 198 LSYGADVN 205
>gnl|CDD|165231 PHA02917, PHA02917, ankyrin-like protein; Provisional.
Length = 661
Score = 34.6 bits (79), Expect = 0.006
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 74 EVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
++N +D G+TLL+ A + Q +V L E G+DVN
Sbjct: 444 DINMIDKRGETLLHKAVRYNKQSLVSLLLESGSDVN 479
>gnl|CDD|206028 pfam13857, Ank_5, Ankyrin repeats (many copies).
Length = 56
Score = 31.6 bits (72), Expect = 0.013
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 64 LIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
L+E G +++N D G T L+ A+ +G E+V++L + G D+N
Sbjct: 1 LLEH---GPIDLNATDGNGNTPLHLAAKYGALELVQWLLKPGVDLN 43
>gnl|CDD|165205 PHA02874, PHA02874, ankyrin repeat protein; Provisional.
Length = 434
Score = 33.4 bits (76), Expect = 0.013
Identities = 19/46 (41%), Positives = 28/46 (60%)
Query: 64 LIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
+I+TI G++VN D +T L++A G E ++ L E GADVN
Sbjct: 106 MIKTILDCGIDVNIKDAELKTFLHYAIKKGDLESIKMLFEYGADVN 151
Score = 27.2 bits (60), Expect = 1.8
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 55 CIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
CI S D +A+ + I + G +N D T L A G ++VE + GAD+N
Sbjct: 8 CIYSGDIEAIEKIIKNKGNCINISVDETTTPLIDAIRSGDAKIVELFIKHGADIN 62
>gnl|CDD|222939 PHA02878, PHA02878, ankyrin repeat protein; Provisional.
Length = 477
Score = 33.3 bits (76), Expect = 0.017
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 38 TKTHKTFKTSNILQLIECIRSKDTDALIET-----IDSGGVEVNFMD-DVGQTLLNWASA 91
T +K +T +++ I K D +IE + S G ++N D G T L++A+
Sbjct: 122 TNRYKNIQTIDLVY----IDKKSKDDIIEAEITKLLLSYGADINMKDRHKGNTALHYATE 177
Query: 92 FGTQEMVEFLCERGADVN 109
Q + E L GA+VN
Sbjct: 178 NKDQRLTELLLSYGANVN 195
Score = 25.6 bits (56), Expect = 6.6
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 57 RSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQ-EMVEFLCERGADVN 109
L+E G + D G T L+ + + ++++ L E G DVN
Sbjct: 213 NKPIVHILLEN----GASTDARDKCGNTPLHISVGYCKDYDILKLLLEHGVDVN 262
>gnl|CDD|223738 COG0666, Arp, FOG: Ankyrin repeat [General function prediction
only].
Length = 235
Score = 32.9 bits (74), Expect = 0.020
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 47 SNILQLIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQ-----EMVEFL 101
+ + SK D +++ + + G +VN D G T L+ A+ G E+ + L
Sbjct: 71 LDGRLPLHSAASKGDDKIVKLLLASGADVNAKDADGDTPLHLAALNGNPPEGNIEVAKLL 130
Query: 102 CERGAD 107
E GAD
Sbjct: 131 LEAGAD 136
Score = 32.9 bits (74), Expect = 0.022
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 79 DDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
D+ G T L+WA+ G ++VE L E GAD N
Sbjct: 144 DEDGNTPLHWAALNGDADIVELLLEAGADPN 174
Score = 31.7 bits (71), Expect = 0.052
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 1/62 (1%)
Query: 52 LIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVNKG 111
L + D D + +++G + N + G T L+ A+ G E+V+ L ++G ++
Sbjct: 151 LHWAALNGDADIVELLLEAGA-DPNSRNSYGVTALDPAAKNGRIELVKLLLDKGLHLSLL 209
Query: 112 KL 113
K
Sbjct: 210 KF 211
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 32.2 bits (73), Expect = 0.043
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 70 SGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADV 108
+GG + N D G+T L+ A A G ++V L E GAD
Sbjct: 103 TGGADPNCRDYDGRTPLHIACANGHVQVVRVLLEFGADP 141
>gnl|CDD|197603 smart00248, ANK, ankyrin repeats. Ankyrin repeats are about 33
amino acids long and occur in at least four consecutive
copies. They are involved in protein-protein
interactions. The core of the repeat seems to be an
helix-loop-helix structure.
Length = 30
Score = 29.1 bits (66), Expect = 0.062
Identities = 12/29 (41%), Positives = 20/29 (68%)
Query: 82 GQTLLNWASAFGTQEMVEFLCERGADVNK 110
G+T L+ A+ G E+V+ L ++GAD+N
Sbjct: 2 GRTPLHLAAENGNLEVVKLLLDKGADINA 30
>gnl|CDD|215625 PLN03192, PLN03192, Voltage-dependent potassium channel;
Provisional.
Length = 823
Score = 31.4 bits (71), Expect = 0.082
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 52 LIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVNKG 111
L + D A+ E + G + V+ D G T L A A +MV L GADV+K
Sbjct: 626 LCTAAKRNDLTAMKELLKQG-LNVDSEDHQGATALQVAMAEDHVDMVRLLIMNGADVDKA 684
Query: 112 KL 113
Sbjct: 685 NT 686
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 30.2 bits (69), Expect = 0.16
Identities = 16/65 (24%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 23 QAALNQEGNIEYKAHTKTHKTFKTSN---ILQLIECIRSKDTDALIETID---SGGVE-V 75
Q GNI Y+ ++ + +++L+E I +KDT ++ +D GV+
Sbjct: 221 QLISFGNGNITYE---DVNELLGLVDDEKLIELLEAILNKDTAEALKILDEILESGVDPE 277
Query: 76 NFMDD 80
F++D
Sbjct: 278 KFLED 282
>gnl|CDD|173966 cd08047, TAF7, TATA Binding Protein (TBP) Associated Factor 7
(TAF7) 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 7 (TAF7) is one of several TAFs that bind TBP
and are 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
preinitiation complex. TFIID complex is composed of the
TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF 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. TAF7 is
involved in the regulation of the transition from PIC
assembly to initiation and elongation. 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.
Length = 162
Score = 29.5 bits (67), Expect = 0.27
Identities = 10/53 (18%), Positives = 21/53 (39%), Gaps = 13/53 (24%)
Query: 30 GNIEYKA-------HTKTHKT------FKTSNILQLIECIRSKDTDALIETID 69
+Y A ++HKT +KT++I Q++ D++ +
Sbjct: 46 NGQKYPAKLVDLPTIIESHKTLDKKNLYKTADISQMLIVYEPDDSEKEAKEAK 98
>gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
Length = 326
Score = 29.5 bits (67), Expect = 0.31
Identities = 7/24 (29%), Positives = 12/24 (50%)
Query: 46 TSNILQLIECIRSKDTDALIETID 69
T N LQL + + +T + +D
Sbjct: 200 TQNSLQLADALLQGNTGKALALLD 223
>gnl|CDD|222277 pfam13637, Ank_4, Ankyrin repeats (many copies).
Length = 54
Score = 27.6 bits (62), Expect = 0.36
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 84 TLLNWASAFGTQEMVEFLCERGADVNK 110
T L+ A+ G E+V++L E+G D+N+
Sbjct: 3 TALHKAAISGRLELVKYLLEKGVDINR 29
Score = 26.0 bits (58), Expect = 1.2
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 52 LIECIRSKDTDA---LIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVEFL 101
L + S + L+E GV++N D+ G T L+ A+ G E+++ L
Sbjct: 5 LHKAAISGRLELVKYLLEK----GVDINRTDEDGNTALHIAAENGNLEVLKLL 53
>gnl|CDD|143462 cd07144, ALDH_ALD2-YMR170C, Saccharomyces cerevisiae aldehyde
dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent
Saccharomyces cerevisiae aldehyde dehydrogenase 2
(YMR170c, ALD5, EC=1.2.1.5) and other similar sequences,
are present in this CD.
Length = 484
Score = 29.3 bits (66), Expect = 0.40
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 47 SNILQLIECIRSKDTDALIETIDSGG-VEVNFMDDVGQTL 85
+ L+E +++D A IE +DSG N + D+ + +
Sbjct: 75 DKLADLVE--KNRDLLAAIEALDSGKPYHSNALGDLDEII 112
>gnl|CDD|165157 PHA02795, PHA02795, ankyrin-like protein; Provisional.
Length = 437
Score = 28.4 bits (63), Expect = 0.78
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 74 EVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
++N +D G+TLL A G ++V +L E GA+VN
Sbjct: 213 DINQLDAGGRTLLYRAIYAGYIDLVSWLLENGANVN 248
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 28.2 bits (63), Expect = 0.80
Identities = 15/74 (20%), Positives = 28/74 (37%), Gaps = 7/74 (9%)
Query: 40 THKTFKTSNILQLIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVE 99
+ N+ L E +AL I G++V + +G + G++ M++
Sbjct: 101 IPRMLGLENLPGLTE---LLAGEALEPVIQHDGIKVLSILPLGPVPVIPRGLLGSKAMLQ 157
Query: 100 FLCERGADVNKGKL 113
L DV G+
Sbjct: 158 LL----EDVLWGEY 167
>gnl|CDD|143505 cd06836, PLPDE_III_ODC_DapDC_like_1, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Uncharacterized Proteins with
similarity to Ornithine and Diaminopimelate
Decarboxylases. This subfamily contains uncharacterized
proteins with similarity to ornithine decarboxylase
(ODC) and diaminopimelate decarboxylase (DapDC). ODC and
DapDC are fold type III PLP-dependent enzymes that
contain an N-terminal PLP-binding TIM-barrel domain and
a C-terminal beta-sandwich domain, similar to bacterial
alanine racemases. They exist as homodimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. ODC participates in the formation of
putrescine by catalyzing the decarboxylation of
ornithine, the first step in polyamine biosynthesis.
DapDC participates in the last step of lysine
biosynthesis, the conversion of
meso-2,6-diaminoheptanedioate to L-lysine. Proteins in
this subfamily may function as PLP-dependent
decarboxylases. Homodimer formation and the presence of
the PLP cofactor may be required for catalytic activity.
Length = 379
Score = 28.1 bits (63), Expect = 0.81
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 49 ILQLIECIRSKDTDALIETID-SGGVEVNFMDD 80
++ L E I + I ID GG+ VNF +
Sbjct: 192 VVDLAEEINRRVGRRQITRIDIGGGLPVNFESE 224
>gnl|CDD|218418 pfam05076, SUFU, Suppressor of fused protein (SUFU). SUFU,
encoding the human orthologue of Drosophila suppressor
of fused, appears to have a conserved role in the
repression of Hedgehog signaling. SUFU exerts its
repressor role by physically interacting with GLI
proteins in both the cytoplasm and the nucleus. SUFU has
been found to be a tumour-suppressor gene that
predisposes individuals to medulloblastoma by modulating
the SHH signaling pathway. Genomic contextual analysis
of bacterial SUFU versions revealed that they are
immunity proteins against diverse nuclease toxins in
polymorphic toxin systems.
Length = 168
Score = 27.3 bits (61), Expect = 1.3
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 48 NILQLI-------ECIRSKDTDALIETIDSGGVEV 75
N LQL+ E + +AL+E ++ GG+++
Sbjct: 129 NFLQLVPITEEELEFAKENGAEALLELLEEGGIDI 163
>gnl|CDD|222948 PHA02941, PHA02941, hypothetical protein; Provisional.
Length = 356
Score = 27.6 bits (61), Expect = 1.3
Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 13/47 (27%)
Query: 16 RYQPSHCQAALNQEGNIEYKAHTKTHKTFKTSN-ILQLIECIRSKDT 61
++C LN+E NI K S ILQL E I+SK T
Sbjct: 222 PEGVAYCVLPLNKEANI------------KASEFILQLYEMIKSKIT 256
>gnl|CDD|176661 cd07237, BphC1-RGP6_C_like, C-terminal domain of
2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC, EC
1.13.11.39) 1 from Rhodococcus globerulus P6
(BphC1-RGP6) and similar proteins. This subfamily
contains the C-terminal, catalytic, domain of
BphC1-RGP6 and similar proteins. BphC catalyzes the
extradiol ring cleavage reaction of
2,3-dihydroxybiphenyl, the third step in the
polychlorinated biphenyls (PCBs) degradation pathway
(bph pathway). This subfamily of BphCs belongs to the
type I extradiol dioxygenase family, which require a
metal in the active site in its catalytic mechanism.
Polychlorinated biphenyl degrading bacteria demonstrate
a multiplicity of BphCs. For example, three types of
BphC enzymes have been found in Rhodococcus globerulus
(BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I
extradiol dioxygenases. BphC1-RGP6 has an internal
duplication, it is a two-domain dioxygenase which forms
octamers, and has Fe(II) at the catalytic site. Its
C-terminal repeat is represented in this subfamily.
BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases,
they belong to a different subfamily of the
ED_TypeI_classII_C (C-terminal domain of type I, class
II extradiol dioxygenases) family.
Length = 154
Score = 26.8 bits (60), Expect = 1.9
Identities = 6/14 (42%), Positives = 9/14 (64%)
Query: 72 GVEVNFMDDVGQTL 85
+EV +DDVG+
Sbjct: 78 MLEVTSLDDVGRAY 91
>gnl|CDD|222984 PHA03100, PHA03100, ankyrin repeat protein; Provisional.
Length = 422
Score = 27.3 bits (61), Expect = 1.9
Identities = 15/48 (31%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 64 LIETIDSGGVEVNFMDDVGQTLLNWASA--FGTQEMVEFLCERGADVN 109
+++ + G VN D+ G T L +A + + +VE+L + GA+VN
Sbjct: 88 IVKLLLEYGANVNAPDNNGITPLLYAISKKSNSYSIVEYLLDNGANVN 135
Score = 25.4 bits (56), Expect = 8.7
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 72 GVEVNFMDDVGQTLLNWASAFGTQEMVEFLCERGADVN 109
GV +N D G T L++A E V++L + GA+ N
Sbjct: 182 GVPINIKDVYGFTPLHYAVYNNNPEFVKYLLDLGANPN 219
>gnl|CDD|129641 TIGR00550, nadA, quinolinate synthetase complex, A subunit. This
protein, termed NadA, plays a role in the synthesis of
pyridine, a precursor to NAD. The quinolinate synthetase
complex consists of A protein (this protein) and B
protein. B protein converts L-aspartate to
iminoaspartate, an unstable reaction product which in
the absence of A protein is spontaneously hydrolyzed to
form oxaloacetate. The A protein, NadA, converts
iminoaspartate to quinolate [Biosynthesis of cofactors,
prosthetic groups, and carriers, Pyridine nucleotides].
Length = 310
Score = 27.0 bits (60), Expect = 2.3
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 32 IEYKAHTKTHKTFKTSNILQLIECIRSKDTDALI 65
+ H H+ F T ++ +L + K DA I
Sbjct: 169 WPEQGHCSVHEKFTTEDLERL----KEKYPDAEI 198
>gnl|CDD|199917 cd11295, Mago_nashi, Mago nashi proteins, integral members of the
exon junction complex. Members of this family, which
was originally identified in Drosophila and called mago
nashi, are integral members of the exon junction complex
(EJC). The EJC is a multiprotein complex that is
deposited on spliced mRNAs after intron removal at a
conserved position upstream of the exon-exon junction,
and transported to the cytoplasm where it has been shown
to influence translation, surveillance, and localization
of the spliced mRNA. It consists of four core proteins
(eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP
and is supposed to be a binding platform for more
peripherally and transiently associated factors along
mRNA travel. Mago and Y14 form a stable heterodimer that
stabilizes the complex by inhibiting eIF4AIII's ATPase
activity. In humans, but not Drosophila, EJC is involved
in nonsense-mediated mRNA decay (NMD) via binding to
Upf3b, a central NMD effector. EJC is stripped off the
mRNA during the first round of translation and then the
complex components are transported back into the nucleus
and recycled. The Mago-Y14 heterodimer has been shown to
interact with the cytoplasmic protein PYM, an EJC
disassembly factor, and specifically binds to the
karyopherin nuclear receptor importin 13.
Length = 143
Score = 26.1 bits (58), Expect = 3.2
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 28 QEGNIEYKAHTKTHKTFKTSNILQLIECIRSKDTDAL 64
QE I H +F TS I L++ +SKD + L
Sbjct: 83 QELEIVMG---DEHISFTTSKIGSLVDVQQSKDPEGL 116
>gnl|CDD|177834 PLN02178, PLN02178, cinnamyl-alcohol dehydrogenase.
Length = 375
Score = 26.5 bits (58), Expect = 3.6
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 48 NILQLIECIRSKDTDALIETIDSGGVEVNFMDDVGQTLLNWASAFGTQEMVE 99
I+ IE I+ D ++ ++ + V F+ DV +LL +SA E V+
Sbjct: 315 KIVSDIELIKMSDINSAMDRLAKSDVRYRFVIDVANSLLPESSAEILTEHVD 366
>gnl|CDD|143491 cd06817, PLPDE_III_DSD, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase.
This subfamily is composed of chicken D-serine
dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic
proteins. Chicken DSD catalyzes the dehydration of
D-serine to aminoacrylate, which is rapidly hydrolyzed
to pyruvate and ammonia. It is a fold type III
PLP-dependent enzyme with similarity to bacterial
alanine racemase (AR), which contains an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain. AR exists as dimers with active
sites that lie at the interface between the TIM barrel
domain of one subunit and the beta-sandwich domain of
the other subunit. Experimental data suggest that
chicken DSD also exists as dimers. Sequence comparison
and biochemical experiments show that chicken DSD is
distinct from the ubiquitous bacterial DSDs coded by
dsdA gene, mammalian L-serine dehydratases (LSD) and
mammalian serine racemase (SerRac), which are fold type
II PLP-dependent enzymes.
Length = 389
Score = 26.5 bits (59), Expect = 3.7
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 20 SHCQAALN--QEGNIEYKAHTKTHKT 43
+C+ L + ++++ H KTHKT
Sbjct: 18 RNCERMLQRAKALGVKFRPHVKTHKT 43
>gnl|CDD|240293 PTZ00149, PTZ00149, hypoxanthine phosphoribosyltransferase;
Provisional.
Length = 241
Score = 25.9 bits (57), Expect = 4.8
Identities = 13/62 (20%), Positives = 24/62 (38%)
Query: 16 RYQPSHCQAALNQEGNIEYKAHTKTHKTFKTSNILQLIECIRSKDTDALIETIDSGGVEV 75
Y + QE + K++ T K + + C++ K + + ID+G V
Sbjct: 108 NYSSTESPKPPYQEHYVRVKSYCNDESTGKLEIVSDDLSCLKDKHVLIVEDIIDTGNTLV 167
Query: 76 NF 77
F
Sbjct: 168 KF 169
>gnl|CDD|215531 PLN02981, PLN02981, glucosamine:fructose-6-phosphate
aminotransferase.
Length = 680
Score = 26.3 bits (58), Expect = 5.1
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 26 LNQEGNIEYKAHTKTHKTFKTSNILQLIECIRSKDTDALIE 66
+ + + + T + F T N + E + D A++E
Sbjct: 212 VKELPEEKNSSAVFTSEGFLTKNRDKPKEFFLASDASAVVE 252
>gnl|CDD|143494 cd06820, PLPDE_III_LS_D-TA_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Low Specificity D-Threonine
Aldolase-like. This subfamily is composed of
uncharacterized bacterial proteins with similarity to
low specificity D-threonine aldolase (D-TA), which is a
fold type III PLP-dependent enzyme that catalyzes the
interconversion between D-threonine/D-allo-threonine
and glycine plus acetaldehyde. Both PLP and divalent
cations (eg. Mn2+) are required for catalytic activity.
Low specificity D-TAs show similarity to bacterial
alanine racemase (AR), which contains an N-terminal
PLP-binding TIM-barrel domain and a C-terminal
beta-sandwich domain. AR exists as homodimers with
active sites that lie at the interface between the TIM
barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Based on its similarity to
AR, it is possible that low specificity D-TAs also form
dimers in solution. Experimental data show that the
monomeric form of low specificity D-TAs exhibit full
catalytic activity.
Length = 353
Score = 25.7 bits (57), Expect = 5.8
Identities = 8/21 (38%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 23 QAALNQEGNIEYKAHTKTHKT 43
QA + G + + H KTHK+
Sbjct: 21 QAYADAHG-LSLRPHIKTHKS 40
>gnl|CDD|205645 pfam13467, RHH_4, Ribbon-helix-helix domain. This short
bacterial protein contains a ribbon-helix-helix domain
that is likely to be DNA-binding.
Length = 65
Score = 24.4 bits (54), Expect = 5.9
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 48 NILQLIECIRSKDTDALIETIDSGGVEVNF 77
+IL+ I ALI ID+ E N
Sbjct: 24 DILEEIAEREGLTVAALIAEIDARR-EGNL 52
>gnl|CDD|236670 PRK10307, PRK10307, putative glycosyl transferase; Provisional.
Length = 412
Score = 25.7 bits (57), Expect = 7.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 94 TQEMVEFLCERGADV 108
T EM E+L RG +V
Sbjct: 21 TGEMAEWLAARGHEV 35
>gnl|CDD|236617 PRK09723, PRK09723, putative fimbrial-like adhesin protein;
Provisional.
Length = 421
Score = 25.5 bits (56), Expect = 7.3
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 5/24 (20%)
Query: 18 QPSHCQAALNQEGNI-----EYKA 36
QP H QA L Q+GNI E+KA
Sbjct: 389 QPLHFQATLKQDGNIAIEPGEFKA 412
>gnl|CDD|165195 PHA02859, PHA02859, ankyrin repeat protein; Provisional.
Length = 209
Score = 25.2 bits (55), Expect = 9.2
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 96 EMVEFLCERGADVN 109
E+++FL E GADVN
Sbjct: 67 EILKFLIENGADVN 80
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
0.316 0.130 0.375
Gapped
Lambda K H
0.267 0.0786 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,258,377
Number of extensions: 415045
Number of successful extensions: 481
Number of sequences better than 10.0: 1
Number of HSP's gapped: 480
Number of HSP's successfully gapped: 63
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (21.6 bits)
S2: 53 (24.1 bits)