RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9958
(181 letters)
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 35.8 bits (83), Expect = 5e-04
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 48 KCPECKKAFRHKGNLLRHMTLH 69
KCP+C K+F K NL RH+ H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
Score = 28.9 bits (65), Expect = 0.14
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 12 CDHCDQTFRQKQLLKRHVN 30
C C ++F +K LKRH+
Sbjct: 2 CPDCGKSFSRKSNLKRHLR 20
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 33.2 bits (76), Expect = 0.004
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 47 HKCPECKKAFRHKGNLLRHMTLH 69
++CPEC K F+ K L HM H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 26.3 bits (58), Expect = 1.4
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 10 YLCDHCDQTFRQKQLLKRHV 29
Y C C + F+ K L+ H+
Sbjct: 1 YRCPECGKVFKSKSALREHM 20
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 35.2 bits (81), Expect = 0.005
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 11/59 (18%)
Query: 8 NPYLCDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHM 66
+PY+C C F LK+H+ E + CP C K FR+ + L H+
Sbjct: 72 SPYVCPLCLMPFSSSVSLKQHIRY-----------TEHSKVCPVCGKEFRNTDSTLDHV 119
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 34.6 bits (79), Expect = 0.026
Identities = 18/39 (46%), Positives = 24/39 (61%)
Query: 94 DGHKVEVIPDDEEEEEGEETEEEEEGGGEDDGHQYVVLE 132
DG E ++EEEEE EE EEEEE E++ + + LE
Sbjct: 859 DGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEEPLSLE 897
Score = 26.9 bits (59), Expect = 7.0
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 1/59 (1%)
Query: 95 GHKVEVIPDDEEEEEGEETEEEEEGGG-EDDGHQYVVLEVIQVQSEDGTQQNVAVVQSE 152
G E+ D+ E + E E E G E +G + +V+ E G Q+ A Q E
Sbjct: 786 GEDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGE 844
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 29.9 bits (67), Expect = 0.058
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 47 HKCPECKKAFRHKGNLLRHMTLH 69
KCP C K+F K L RH+ H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
Score = 29.5 bits (66), Expect = 0.088
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 10 YLCDHCDQTFRQKQLLKRHVNLYH 33
+ C C ++F K LKRH+ +H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 28.3 bits (64), Expect = 0.20
Identities = 8/24 (33%), Positives = 8/24 (33%)
Query: 46 THKCPECKKAFRHKGNLLRHMTLH 69
H C C K F L H H
Sbjct: 1 VHTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 31.6 bits (71), Expect = 0.25
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 5/60 (8%)
Query: 70 DPDSELIEQQVALKLGRQ----KKVHIIDGHKVEV-IPDDEEEEEGEETEEEEEGGGEDD 124
D D +I+++ A L + + +ID + DD+EE++ EE EEEEE G DD
Sbjct: 126 DLDMIIIKRRRARHLAEEDMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDD 185
Score = 31.2 bits (70), Expect = 0.38
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 100 VIPDDEEEEEGEETEEEEEGGGEDDGHQ 127
VI DD+E+E+ ++ +EE++ E++ +
Sbjct: 152 VIDDDDEDEDEDDDDEEDDEEEEEEEEE 179
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing
archaeal-type C2H2 Zn-finger [General function
prediction only].
Length = 65
Score = 29.2 bits (65), Expect = 0.27
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 12 CDHCDQTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHK 48
C C FR+++ RHVN H + PK K K
Sbjct: 20 CPRCGMVFRRRKDYIRHVNKAHGWLFGRGKPKGKRLK 56
Score = 25.0 bits (54), Expect = 8.4
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 48 KCPECKKAFRHKGNLLRHM 66
+CP C FR + + +RH+
Sbjct: 19 RCPRCGMVFRRRKDYIRHV 37
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 31.2 bits (70), Expect = 0.29
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 12/79 (15%)
Query: 1 MLIHIDQNPYLCD--HCDQTFRQKQLLKRHVNLYHNPHYVPPSP----------KEKTHK 48
ML D PY C C++ ++ + LK H+ H + +P K+K ++
Sbjct: 341 MLKVKDGKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYR 400
Query: 49 CPECKKAFRHKGNLLRHMT 67
C C K +++ L H
Sbjct: 401 CEVCDKRYKNLNGLKYHRK 419
>gnl|CDD|222792 PHA00435, PHA00435, capsid assembly protein.
Length = 306
Score = 30.6 bits (69), Expect = 0.35
Identities = 26/84 (30%), Positives = 42/84 (50%), Gaps = 8/84 (9%)
Query: 101 IPDDEEEEEGEETEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSEDGTQQ--N 158
I +D EEEE EE EE+EE GE++ + E + E+ T+ + + + E+G Q
Sbjct: 75 ISEDGEEEEVEEGEEDEEEEGEEESEE---FEPLGDTPEELTEASEQLEEHEEGFQAMVE 131
Query: 159 VAV---VPASSLMGMGATINEHGE 179
AV + A ++ + A E G
Sbjct: 132 QAVERGLSAETITRIQAEYEEEGG 155
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 30.0 bits (68), Expect = 0.42
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 92 IIDGHKVEVIPDDEEEEEGEETEEEEEGGGEDDG 125
DG + E +P+++E++E + EE + E D
Sbjct: 7 SDDGEEDEELPEEDEDDESSDEEEVDLPDDEQDE 40
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 30.4 bits (69), Expect = 0.53
Identities = 16/37 (43%), Positives = 19/37 (51%)
Query: 82 LKLGRQKKVHIIDGHKVEVIPDDEEEEEGEETEEEEE 118
L GR V+ + E D+EEEEE EE EE E
Sbjct: 334 LPQGRCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEP 370
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 30.2 bits (69), Expect = 0.59
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 105 EEEEEGEETEEEEEGGGEDDG 125
EEEE EE EEEEE E++
Sbjct: 301 AEEEEEEEEEEEEEEPSEEEA 321
Score = 29.8 bits (68), Expect = 0.69
Identities = 12/47 (25%), Positives = 19/47 (40%)
Query: 75 LIEQQVALKLGRQKKVHIIDGHKVEVIPDDEEEEEGEETEEEEEGGG 121
+ + AL ++ + ++EEEEE EE EEE
Sbjct: 277 ALADKDALDEELKEVLSAQAQAAAAEEEEEEEEEEEEEEPSEEEAAA 323
Score = 27.9 bits (63), Expect = 2.8
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 99 EVIPDDEEEEEGEETEEEEEGGG 121
E ++EEEEE EE EEE G
Sbjct: 302 EEEEEEEEEEEEEEPSEEEAAAG 324
Score = 26.4 bits (59), Expect = 8.7
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 102 PDDEEEEEGEETEEEEEGGGE 122
++EEEEE EE E EE
Sbjct: 303 EEEEEEEEEEEEEPSEEEAAA 323
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The CAF-1
or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression in
addition to DNA-based checkpoints.
Length = 76
Score = 28.3 bits (64), Expect = 0.60
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 105 EEEEEGEETEEEEEGGGEDDG 125
EEEEEGE+ E E+E E+D
Sbjct: 49 EEEEEGEDLESEDEEDEEEDD 69
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 30.0 bits (68), Expect = 0.65
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 98 VEVIPDDEEEEEGEETEEEEEGGGEDDGHQYV---VLEVIQ 135
E ++EEEEE E EEEEE E + V V E I+
Sbjct: 303 PEPEEEEEEEEEVPEEEEEEEEEEERTFEEEVRATVAEAIR 343
>gnl|CDD|173534 PTZ00341, PTZ00341, Ring-infected erythrocyte surface antigen;
Provisional.
Length = 1136
Score = 30.1 bits (67), Expect = 0.68
Identities = 23/88 (26%), Positives = 40/88 (45%)
Query: 72 DSELIEQQVALKLGRQKKVHIIDGHKVEVIPDDEEEEEGEETEEEEEGGGEDDGHQYVVL 131
D+ ++ + L +QK + ++DG + E + D+EEE G+ EEE + H
Sbjct: 407 DALYTDEDLLFDLEKQKYMDMLDGSEDESVEDNEEEHSGDANEEELSVDEHVEEHNADDS 466
Query: 132 EVIQVQSEDGTQQNVAVVQSEDGTQQNV 159
Q E G Q+V + E ++V
Sbjct: 467 GEQQSDDESGEHQSVNEIVEEQSVNEHV 494
>gnl|CDD|217829 pfam03985, Paf1, Paf1. Members of this family are components of
the RNA polymerase II associated Paf1 complex. The Paf1
complex functions during the elongation phase of
transcription in conjunction with Spt4-Spt5 and
Spt16-Pob3i.
Length = 431
Score = 30.1 bits (68), Expect = 0.70
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 93 IDGHKVEVIPDDEEEEEGEETEEEEEGGGEDDGHQ 127
ID +V+ D+EEE+ +E EEEE E++G Q
Sbjct: 365 IDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQ 399
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 28.8 bits (65), Expect = 0.75
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDDG 125
EE++ EE EEEE+ E++
Sbjct: 74 AAAAEEKKEEEEEEEEKEESEEEA 97
Score = 26.8 bits (60), Expect = 2.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 102 PDDEEEEEGEETEEEEEGGG 121
++EEEEE +E EEE G
Sbjct: 81 KEEEEEEEEKEESEEEAAAG 100
Score = 26.8 bits (60), Expect = 2.9
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDD 124
EE+ EE EEEEE ++
Sbjct: 73 AAAAAEEKKEEEEEEEEKEESEE 95
Score = 26.8 bits (60), Expect = 3.0
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDD 124
EE +E EEEEE E +
Sbjct: 72 AAAAAAEEKKEEEEEEEEKEESE 94
Score = 26.5 bits (59), Expect = 4.1
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDDG 125
EE++E EE EEE+E E+
Sbjct: 75 AAAEEKKEEEEEEEEKEESEEEAA 98
Score = 26.1 bits (58), Expect = 5.2
Identities = 11/21 (52%), Positives = 11/21 (52%)
Query: 102 PDDEEEEEGEETEEEEEGGGE 122
EEEEE EE EE EE
Sbjct: 79 EKKEEEEEEEEKEESEEEAAA 99
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 26.6 bits (59), Expect = 0.85
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 1 MLIHIDQNPYLCDHCDQTFRQ 21
M H + PY C C ++F
Sbjct: 6 MRTHTGEKPYKCPVCGKSFSS 26
Score = 26.2 bits (58), Expect = 1.5
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 9/34 (26%)
Query: 25 LKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRH 58
L+RH+ + EK +KCP C K+F
Sbjct: 2 LRRHMRTHT---------GEKPYKCPVCGKSFSS 26
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 29.3 bits (66), Expect = 1.2
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 90 VHIIDGHKVEVIPDDEEEEEGEETEEEEEGGGE 122
+ I D + DDEEEE+ EE EEE+E G
Sbjct: 379 LEIEDANTER---DDEEEEDEEEEEEEDEDEGP 408
Score = 27.8 bits (62), Expect = 3.5
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 83 KLGRQKKVHIIDGHKVEVIPDDEEEEEGEETEEEEEGGGEDDG 125
K ++ +I+D I D E + EE E+EEE ED+
Sbjct: 363 KAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDED 405
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 29.0 bits (65), Expect = 1.3
Identities = 21/85 (24%), Positives = 29/85 (34%), Gaps = 8/85 (9%)
Query: 43 KEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGRQKKVHIIDGHKVEVIP 102
K F+ K L D D +L + +K + E
Sbjct: 122 INKKAGKKLALSKFKRKVGLFT-EEEEDIDEKL-------SMLEKKLKELEAEDVDEEDE 173
Query: 103 DDEEEEEGEETEEEEEGGGEDDGHQ 127
DEEEEE EE E+E+ +DD
Sbjct: 174 KDEEEEEEEEEEDEDFDDDDDDDDD 198
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.2 bits (65), Expect = 1.4
Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 12/77 (15%)
Query: 94 DGHKVEVIPDDEEEEEGEETEEEEEGGGED-----DGHQYVVLEVI----QVQSEDGTQQ 144
DG + V ++E E+G +++EE E G D H + + + E+ +
Sbjct: 4065 DGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDAKSTFASAEADEENTDKG 4124
Query: 145 NVA---VVQSEDGTQQN 158
V + EDG + N
Sbjct: 4125 IVGENEELGEEDGVRGN 4141
Score = 26.9 bits (59), Expect = 8.2
Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSED 153
+D++ +E E+ EE + G DD ++Q + + ++ED
Sbjct: 3945 LEDKDRQEKEDEEEMSDDVGIDD----------EIQPDIQENNSQPPPENED 3986
Score = 26.9 bits (59), Expect = 9.2
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 104 DEEEEEGEETEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSEDGTQQNV 159
DE +EE + E++E ED + L+ Q + +EDG ++NV
Sbjct: 4017 DENKEEAD-AEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENV 4071
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 27.7 bits (62), Expect = 1.4
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 97 KVEVIPDDEEEEEGEETEEEEEGGG 121
E ++EEEEE EE E EEE
Sbjct: 74 AAEEEEEEEEEEEEEEEESEEEAMA 98
Score = 27.7 bits (62), Expect = 1.7
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 102 PDDEEEEEGEETEEEEEGGG 121
++EEEEE EE EEE G
Sbjct: 80 EEEEEEEEEEEESEEEAMAG 99
Score = 26.2 bits (58), Expect = 5.0
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDD 124
EEE EE EEEEE E +
Sbjct: 71 AAAAAEEEEEEEEEEEEEEEESE 93
Score = 26.2 bits (58), Expect = 5.5
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 104 DEEEEEGEETEEEEEGGGE 122
+EEEEE EE EE EE
Sbjct: 80 EEEEEEEEEEEESEEEAMA 98
Score = 25.8 bits (57), Expect = 8.4
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDDG 125
EEEEE EE EEEEE E++
Sbjct: 73 AAAEEEEEEEEEEEEEEEESEEEA 96
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 29.0 bits (65), Expect = 1.4
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 101 IPDDEEEEEGEETEEEEEGGGED 123
+PD+EEEEE EE +EEEE +
Sbjct: 35 VPDEEEEEEKEEKKEEEEKTTDK 57
>gnl|CDD|216269 pfam01056, Myc_N, Myc amino-terminal region. The myc family
belongs to the basic helix-loop-helix leucine zipper
class of transcription factors, see pfam00010. Myc forms
a heterodimer with Max, and this complex regulates cell
growth through direct activation of genes involved in
cell replication. Mutations in the C-terminal 20
residues of this domain cause unique changes in the
induction of apoptosis, transformation, and G2 arrest.
Length = 329
Score = 28.4 bits (63), Expect = 2.0
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 102 PDDEEEEEGEETEEEEE 118
+E+EEE EE EEEEE
Sbjct: 227 ESEEDEEEEEEEEEEEE 243
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 28.8 bits (64), Expect = 2.0
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 99 EVIPDDEEEEEGEETEE--------EEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQ 150
E + DD E E+ E+ ++ EE+G GE +G + + + + +VQ
Sbjct: 201 EEMGDDTESEDEEDGDDDQPTENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQ 260
Query: 151 SED 153
S+
Sbjct: 261 SDQ 263
>gnl|CDD|234943 PRK01343, PRK01343, zinc-binding protein; Provisional.
Length = 57
Score = 26.2 bits (58), Expect = 2.2
Identities = 7/16 (43%), Positives = 7/16 (43%)
Query: 39 PPSPKEKTHKCPECKK 54
P T CPEC K
Sbjct: 2 KVEPLRPTRPCPECGK 17
>gnl|CDD|173359 PTZ00064, PTZ00064, histone acetyltransferase; Provisional.
Length = 552
Score = 28.4 bits (63), Expect = 2.3
Identities = 14/48 (29%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 37 YVPPSPKEKT-----HKCPECKKAFRHKGNLLRHMT----LHDPDSEL 75
Y P P E H C C F + L+RH++ H P +E+
Sbjct: 266 YFSPLPDEYQNVDTLHFCEYCLDFFCFEDELIRHLSRCQLRHPPGNEI 313
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 28.1 bits (62), Expect = 2.3
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 103 DDEEEEEGEETEEEEEGGGEDDGHQ 127
D EEE EET EEE + DG++
Sbjct: 58 DSSEEEGEEETSNEEENNEDSDGNE 82
>gnl|CDD|225542 COG2995, PqiA, Uncharacterized paraquat-inducible protein A
[Function unknown].
Length = 418
Score = 28.5 bits (64), Expect = 2.4
Identities = 4/35 (11%), Positives = 6/35 (17%), Gaps = 3/35 (8%)
Query: 3 IHIDQNPYLCDHCDQTFRQKQ---LLKRHVNLYHN 34
+ C C + LY
Sbjct: 214 TGAREGLRSCLCCHYILPHDAEPRCPRCGSKLYVR 248
>gnl|CDD|215629 PLN03200, PLN03200, cellulose synthase-interactive protein;
Provisional.
Length = 2102
Score = 28.5 bits (64), Expect = 2.5
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 68 LHDPDSELIEQQVALKLGR--QKKVHIID--GHKVEVIPDDEEEEEG 110
+ D+ I Q AL LG + KVH++D GH + V ++ EG
Sbjct: 558 VRTADAATISQLTALLLGDLPESKVHVLDVLGHVLSVASLEDLVREG 604
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 27.0 bits (60), Expect = 2.7
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 105 EEEEEGEETEEEEEGGG 121
EEEE+ EE EEE +
Sbjct: 87 EEEEKEEEAEEESDDDM 103
Score = 25.8 bits (57), Expect = 6.9
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDD 124
E +E EE E+EEE E D
Sbjct: 78 EAAAEADEAEEEEKEEEAEEESD 100
Score = 25.8 bits (57), Expect = 7.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDDG 125
+ +E EE E+ EE EE +D
Sbjct: 81 AEADEAEEEEKEEEAEEESDDDML 104
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 27.9 bits (63), Expect = 2.7
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 103 DDEEEEEGEETEEEEEGG 120
DD++E+E E+ EEE + G
Sbjct: 57 DDDDEDEDEDDEEEADLG 74
Score = 26.8 bits (60), Expect = 5.6
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 103 DDEEEEEGEETEEEEEGGGED 123
DD+++E+ +E +EEE G D
Sbjct: 56 DDDDDEDEDEDDEEEADLGPD 76
>gnl|CDD|219038 pfam06459, RR_TM4-6, Ryanodine Receptor TM 4-6. This region covers
TM regions 4-6 of the ryanodine receptor 1 family.
Length = 217
Score = 27.7 bits (62), Expect = 2.7
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 96 HKVEVIPDDEEEEEGEETEEEEEGGGEDDGHQYVVLE 132
+KV P +EEEEEG + ++ E E+ +V+ E
Sbjct: 145 YKVSTSPAEEEEEEGSGSGDDGEEDEEEGIVYFVLQE 181
>gnl|CDD|222704 pfam14353, CpXC, CpXC protein. This presumed domain is
functionally uncharacterized. This domain is found in
bacteria and archaea, and is typically between 122 and
134 amino acids in length. It contains four conserved
cysteines forming two CpXC motifs.
Length = 128
Score = 27.3 bits (61), Expect = 3.1
Identities = 15/47 (31%), Positives = 17/47 (36%), Gaps = 6/47 (12%)
Query: 46 THKCPECKKAFRHKGNLLRH------MTLHDPDSELIEQQVALKLGR 86
T CP C FR L H M PD E+Q+AL
Sbjct: 38 TFTCPSCGHEFRLDYPFLYHDPEKKFMIYLVPDEAEREEQLALLEDL 84
>gnl|CDD|131020 TIGR01965, VCBS_repeat, VCBS repeat. This domain of about 100
residues is found multiple (up to 35) copies in long
proteins from several species of Vibrio, Colwellia,
Bradyrhizobium, and Shewanella (hence the name VCBS) and
in smaller copy numbers in proteins from several other
bacteria. The large protein size and repeat copy
numbers, species distribution, and suggested activities
of several member proteins suggests a role for this
domain in adhesion.
Length = 99
Score = 26.5 bits (59), Expect = 3.4
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 130 VLEVIQVQSEDGTQQNVAV 148
+ + V S DGT Q V +
Sbjct: 57 LTDTFTVTSADGTSQTVTI 75
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 28.0 bits (62), Expect = 3.5
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 103 DDEEEEEGEETEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSEDGTQQNVAVV 162
++EEEEE EE +E EE GED+ + E ++ + + + DG +
Sbjct: 449 EEEEEEEEEEEQESEEEEGEDEEEE----EEVEADNGSEEEMEGSSEGDGDGEEPEEDAE 504
Query: 163 PASSLMGMGATINE 176
+S M + ++E
Sbjct: 505 RRNSEMAGISRMSE 518
>gnl|CDD|234869 PRK00942, PRK00942, acetylglutamate kinase; Provisional.
Length = 283
Score = 27.8 bits (63), Expect = 3.5
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 16/53 (30%)
Query: 57 RHKGNLLRHMTLHDPDSELIEQQV--------------ALKLGRQKKVHIIDG 95
KG L+ +T + + ELIE V A + G + VHIIDG
Sbjct: 210 DDKGQLISELTASEAE-ELIEDGVITGGMIPKVEAALDAARGGV-RSVHIIDG 260
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 27.3 bits (61), Expect = 3.5
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 90 VHIIDGHKV---EVIPDDEEEEEGEETEEEEEGGGEDD 124
VHI H V E DD+EE+E EE +EE++ E +
Sbjct: 99 VHISGQHLVASEEDESDDDEEDEEEEDDEEDDDEDESE 136
>gnl|CDD|215056 PLN00104, PLN00104, MYST -like histone acetyltransferase;
Provisional.
Length = 450
Score = 27.8 bits (62), Expect = 3.6
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 10 YLCDHCDQTFRQKQLLKRHV---NLYHNP 35
Y C+ C + ++K+ L+RH+ +L H P
Sbjct: 199 YFCEFCLKFMKRKEQLQRHMKKCDLKHPP 227
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 26.4 bits (59), Expect = 3.7
Identities = 9/23 (39%), Positives = 10/23 (43%)
Query: 102 PDDEEEEEGEETEEEEEGGGEDD 124
EE +EEEE EDD
Sbjct: 59 AAAAAAAAEEEKKEEEEEEEEDD 81
Score = 26.0 bits (58), Expect = 4.7
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 105 EEEEEGEETEEEEEGGG 121
++EEE EE E+++ G G
Sbjct: 70 KKEEEEEEEEDDDMGFG 86
Score = 25.3 bits (56), Expect = 8.5
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 105 EEEEEGEETEEEEEGGG 121
EE++E EE EEE++ G
Sbjct: 68 EEKKEEEEEEEEDDDMG 84
Score = 25.3 bits (56), Expect = 9.3
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 102 PDDEEEEEGEETEEEEEGGG 121
++E++EE EE EE+++ G
Sbjct: 66 AEEEKKEEEEEEEEDDDMGF 85
>gnl|CDD|234004 TIGR02772, Ku_bact, Ku protein, prokaryotic. Members of this
protein family are Ku proteins of non-homologous end
joining (NHEJ) DNA repair in bacteria and in at least
one member of the archaea (Archaeoglobus fulgidus). Most
members are encoded by a gene adjacent to the gene for
the DNA ligase that completes the repair. The NHEJ
system is broadly but rather sparsely distributed, being
present in about one fifth of the first 250 completed
prokarytotic genomes. A few species (e.g. Archaeoglobus
fulgidus and Bradyrhizobium japonicum) have multiple
copies that appear to represent recent paralogous family
expansion [DNA metabolism, DNA replication,
recombination, and repair].
Length = 258
Score = 27.6 bits (62), Expect = 3.9
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 90 VHIIDGHKVEVIPDDEEEEEGEETEEEEEGGG-EDDGHQYVVLE 132
+H DG++V E G+E E EE G E D +YV++E
Sbjct: 34 LHREDGNRVRYQKVCSET--GKEVEREEIVKGYEYDKGKYVIIE 75
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and
recognises the first three GAG bases of the consensus
in a manner similar to that seen in other classical
zinc finger-DNA complexes. The second basic region
forms a helix that interacts in the major groove
recognising the last G of the consensus, while the
first basic region wraps around the DNA in the minor
groove and recognises the A in the fourth position of
the consensus sequence.
Length = 54
Score = 25.7 bits (56), Expect = 4.0
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 41 SPKEKTHKCPECKKAFRHKGNLLRHMTL 68
S E+ CP C+ R NL RH+ L
Sbjct: 19 SQSEQPATCPICQAVIRQSRNLRRHLEL 46
Score = 24.9 bits (54), Expect = 5.9
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 7 QNPYLCDHCDQTFRQKQLLKRHVNLYH 33
+ P C C RQ + L+RH+ L H
Sbjct: 22 EQPATCPICQAVIRQSRNLRRHLELRH 48
>gnl|CDD|216966 pfam02301, HORMA, HORMA domain. The HORMA (for Hop1p, Rev7p and
MAD2) domain has been suggested to recognise chromatin
states that result from DNA adducts, double stranded
breaks or non-attachment to the spindle and acts as an
adaptor that recruits other proteins. MAD2 is a spindle
checkpoint protein which prevents progression of the
cell cycle upon detection of a defect in mitotic spindle
integrity.
Length = 186
Score = 27.3 bits (61), Expect = 4.1
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 57 RHKGNLLRHMTLHDPDSELIEQQV--ALKLGRQKKVHIIDGHKVEVIPDDEEEEEGEETE 114
R K NL ++ + +E+ V AL + + + V VI DD++ E+ E E
Sbjct: 35 RKKYNLPVLVSEDPQLIDYLEKGVFDAL---EKGYLKKL----VLVIYDDKDPEKNEVLE 87
Query: 115 E 115
Sbjct: 88 R 88
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 27.9 bits (62), Expect = 4.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 103 DDEEEEEGEETEEEEEGGGEDD 124
D++E E E++E E E GED
Sbjct: 661 DEDECEAIEDSESESESDGEDG 682
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 27.6 bits (62), Expect = 4.1
Identities = 17/98 (17%), Positives = 33/98 (33%), Gaps = 28/98 (28%)
Query: 82 LKLGRQKKVHIIDGHK------------VEVIPDDEEEEEG----------EETEEEEEG 119
L+L V++ID H+ V + D + EEE + EE+++
Sbjct: 70 LQLDEDVIVYVIDSHRPWNLDNVFGSDQVVIFDDGDIEEELQDEPRYDDAYRDLEEDDDD 129
Query: 120 GGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSEDGTQQ 157
E D E + + + + +D +
Sbjct: 130 DEESDE------EDEESSKSEDDEDDDDDDDDDDIATR 161
>gnl|CDD|222450 pfam13909, zf-H2C2_5, C2H2-type zinc-finger domain.
Length = 24
Score = 24.9 bits (55), Expect = 4.2
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 10 YLCDHCDQTFRQKQLLKRHVNLYHN 34
Y C HC + K+ L+RH+ L+H
Sbjct: 1 YKCSHCPYSSTPKK-LERHLKLHHG 24
>gnl|CDD|177826 PLN02169, PLN02169, fatty acid (omega-1)-hydroxylase/midchain
alkane hydroxylase.
Length = 500
Score = 27.7 bits (61), Expect = 4.2
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 80 VALKLGRQKKVHIIDGHKVEVIP 102
VAL++ + +I+GHK+E IP
Sbjct: 460 VALEIIKNYDFKVIEGHKIEAIP 482
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 25.1 bits (55), Expect = 4.4
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 10 YLCDHCDQTFRQKQLLKRHVNLYHN 34
Y C C FR+K+ + H+ H
Sbjct: 2 YQCLRCGGIFRKKKEVIEHLLSVHK 26
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 27.7 bits (62), Expect = 4.5
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 7/82 (8%)
Query: 52 CKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGRQKKVHIIDGHKV-EVIPDDEEEEEG 110
KA+ L + +L E + + R K +I G+ + E + +EEE
Sbjct: 350 AYKAYLAYKPKLEKVE-----RKLPELGIWKDVER-IKALVIRGYPLAEALSKVKEEERP 403
Query: 111 EETEEEEEGGGEDDGHQYVVLE 132
E E EE + ++
Sbjct: 404 REKEGTEEEERREITVYEKRIK 425
>gnl|CDD|220661 pfam10263, SprT-like, SprT-like family. This family represents a
domain found in eukaryotes and prokaryotes. The domain
contains a characteristic motif of the zinc
metallopeptidases. This family includes the bacterial
SprT protein.
Length = 153
Score = 27.0 bits (60), Expect = 4.9
Identities = 6/48 (12%), Positives = 13/48 (27%), Gaps = 5/48 (10%)
Query: 22 KQLLKRHVNLYHNPHYVPPSPKEKT---HKCPECKKAFRHKGNLLRHM 66
H + + ++C C + + K + RH
Sbjct: 94 GGAGPLEPTTTH--RFDIEVVSGRKRYIYRCGSCGQLYPRKRRIRRHK 139
>gnl|CDD|226111 COG3583, COG3583, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 309
Score = 27.1 bits (60), Expect = 5.3
Identities = 20/88 (22%), Positives = 30/88 (34%), Gaps = 14/88 (15%)
Query: 103 DDEEEEEGEETEEEEEGGGEDDGHQYVVLE---------VIQVQSEDGTQQNVAVVQSED 153
+D +G+E +E G + VV E V +V E+ VAV
Sbjct: 227 EDPSMNKGKEKVVQEGQPGTKEVTFEVVTENGKETSREVVKEVVVEEAKDAVVAV----- 281
Query: 154 GTQQNVAVVPASSLMGMGATINEHGETG 181
GT+ SS +T + T
Sbjct: 282 GTKGVAKNSRGSSASSSKSTGSSASNTS 309
>gnl|CDD|129586 TIGR00495, crvDNA_42K, 42K curved DNA binding protein. Proteins
identified by This model have been identified in a
number of species as a nuclear (but not nucleolar)
protein with a cell cycle dependence. Various names
given to members of this family have included cell cycle
protein p38-2G4, DNA-binding protein GBP16, and
proliferation-associated protein 1. This protein is
closely related to methionine aminopeptidase, a
cobolt-binding protein [Unknown function, General].
Length = 389
Score = 27.2 bits (60), Expect = 5.4
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 84 LGRQKKVHIIDGHKVEV-IPDDEEEEEGEETEEEE 117
L Q K H+IDG KV + P D ++++ + E EE
Sbjct: 187 LSHQLKQHVIDGEKVIISNPSDSQKKDHDTAEFEE 221
>gnl|CDD|220135 pfam09184, PPP4R2, PPP4R2. PPP4R2 (protein phosphatase 4 core
regulatory subunit R2) is the regulatory subunit of the
histone H2A phosphatase complex. It has been shown to
confer resistance to the anticancer drug cisplatin in
yeast, and may confer resistance in higher eukaryotes.
Length = 285
Score = 27.1 bits (60), Expect = 5.4
Identities = 18/32 (56%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 93 IDGHKVEVIPDDEEEEEGEETEEEEEGGGEDD 124
DG VE E+EEE EETEEEEE ED+
Sbjct: 255 QDGDYVEEKELKEDEEE-EETEEEEEEEDEDE 285
>gnl|CDD|215642 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 27.1 bits (60), Expect = 5.5
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 32 YHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHM---TLHDPDSELIEQQVA 81
Y++P+ P + K + C C K R K +LLRH+ + P I V
Sbjct: 34 YYSPYPEPYASCTKLYICEYCLKYMRKKKSLLRHLAKCDIRQPPGGGIYGAVT 86
Score = 26.7 bits (59), Expect = 6.3
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 10 YLCDHCDQTFRQKQLLKRHVNLYHNPHYVPP 40
Y+C++C + R+K+ L RH L PP
Sbjct: 49 YICEYCLKYMRKKKSLLRH--LAKCDIRQPP 77
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 26.3 bits (58), Expect = 5.5
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 97 KVEVIPDDEEEEEGEETEEEEEGGG 121
K E +++++EE +E EEEE G
Sbjct: 77 KAEEKEEEKKKEEEKEEEEEEALAG 101
>gnl|CDD|235302 PRK04456, PRK04456, acetyl-CoA decarbonylase/synthase complex
subunit beta; Reviewed.
Length = 463
Score = 27.3 bits (61), Expect = 5.6
Identities = 15/25 (60%), Positives = 16/25 (64%)
Query: 98 VEVIPDDEEEEEGEETEEEEEGGGE 122
VE +EEEEE EE EEEEE E
Sbjct: 399 VERWAAEEEEEEEEEEEEEEEPVAE 423
>gnl|CDD|222800 PHA00458, PHA00458, single-stranded DNA-binding protein.
Length = 233
Score = 27.1 bits (60), Expect = 5.8
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 102 PDDEEEEEGEETEEEEEGGGED 123
P DEEE + ++ EE EE D
Sbjct: 211 PQDEEEWDEDDEEESEEDEDGD 232
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 26.9 bits (60), Expect = 6.0
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 94 DGHKVEVIPDDEEEEEGEETEEEEEGGGEDD 124
D +E + + EEEE E+ E E E+D
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEED 305
>gnl|CDD|148682 pfam07222, PBP_sp32, Proacrosin binding protein sp32. This family
consists of several mammalian specific proacrosin
binding protein sp32 sequences. sp32 is a sperm specific
protein which is known to bind with with 55- and 53-kDa
proacrosins and the 49-kDa acrosin intermediate. The
exact function of sp32 is unclear, it is thought however
that the binding of sp32 to proacrosin may be involved
in packaging the acrosin zymogen into the acrosomal
matrix.
Length = 243
Score = 26.9 bits (59), Expect = 6.6
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 83 KLGRQKKVHIIDGHKVEVIPDDEEEEEGEETEE--EEEGGGEDD 124
+ K + HK E EE+EE E EE +EEG G DD
Sbjct: 200 EQLLSKLQEYLQEHKTEEKQPQEEQEEEEVEEEAKQEEGQGTDD 243
>gnl|CDD|224356 COG1439, COG1439, Predicted nucleic acid-binding protein, consists
of a PIN domain and a Zn-ribbon module [General function
prediction only].
Length = 177
Score = 26.6 bits (59), Expect = 6.9
Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 4/62 (6%)
Query: 99 EVIPDDEEEEEGEETEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSEDGTQQN 158
P E +E E + G+ +EV+ + E G + VA+ ++D + QN
Sbjct: 59 VAEPSTEYVKE---VREAAKKTGDLGNLSPTDIEVLALALELGEEVQVALA-TDDYSVQN 114
Query: 159 VA 160
VA
Sbjct: 115 VA 116
>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740). This
family consists of several uncharacterized plant
proteins of unknown function.
Length = 565
Score = 26.9 bits (59), Expect = 7.3
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 100 VIPDDEEEEEGE-ETEEEEEGGGEDDG 125
++PD EEE E E EE+EE ++ G
Sbjct: 134 IVPDLVLEEEEEVEMEEDEEYYEKEPG 160
>gnl|CDD|215224 PLN02400, PLN02400, cellulose synthase.
Length = 1085
Score = 26.9 bits (59), Expect = 8.1
Identities = 18/68 (26%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 43 KEKTHKCPECKKAF-RHKGNLLRHMTLHDPDSELIEQQVALKLGRQKKVHIIDGHKVEVI 101
K+ T CP+CK + RHKG+ + D + +E + G K H G +E+
Sbjct: 75 KDGTQCCPQCKTRYRRHKGSPRVEGDEDEDDVDDLENEFNYAQGNGKARHQWQGEDIELS 134
Query: 102 PDDEEEEE 109
E +
Sbjct: 135 SSSRHESQ 142
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 26.7 bits (59), Expect = 8.3
Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 5/60 (8%)
Query: 99 EVIPDDEEEEEGEE-----TEEEEEGGGEDDGHQYVVLEVIQVQSEDGTQQNVAVVQSED 153
+ I +D +EE+G++ E+ E G E +G + + +G + + ++ +
Sbjct: 225 DGIEEDADEEDGDDDQPDNNEDSEAGREESEGSDESEEDEAEATDGEGEEGEMDAAEASE 284
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 24.6 bits (53), Expect = 8.4
Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 47 HKCPECKKAFRHKGNLLRHMTLHDPDSELIEQQVALKLGRQKKVHIIDGHKVEVIPDDE 105
++CP C + + + +++ H+ H+ + LKL K++ + G +E+ ++E
Sbjct: 6 YECPICGEIYIKRKSMITHLRKHNTN---------LKLSNCKRISLRTGEYIEIKAEEE 55
>gnl|CDD|205505 pfam13325, MCRS_N, N-terminal region of micro-spherule protein.
This domain is found in plants and higher eukaryotes,
and is the N-terminal region of micro-spherule proteins
which repress the transactivation activities of Nrf1
(p45 nuclear factor-erythroid 2 (p45 NF-E2)-related
factor 1). In conjunction with DIPA the full-length
protein acts as a transcription repressor. The exact
function of the region is not known.
Length = 199
Score = 26.2 bits (58), Expect = 8.8
Identities = 17/73 (23%), Positives = 25/73 (34%), Gaps = 13/73 (17%)
Query: 17 QTFRQKQLLKRHVNLYHNPHYVPPSPKEKTHKCPECKKAFRHKGNLLRHMTLHDPDSELI 76
Q +Q LL VPP K +F + L L +P E +
Sbjct: 123 QLMKQYGLLPDQS--------VPPLEKGDQQT-----LSFSDAEDELNDADLTEPRDEAL 169
Query: 77 EQQVALKLGRQKK 89
E ++ L R K+
Sbjct: 170 EHELELADRRNKR 182
>gnl|CDD|215789 pfam00208, ELFV_dehydrog, Glutamate/Leucine/Phenylalanine/Valine
dehydrogenase.
Length = 237
Score = 26.3 bits (59), Expect = 8.9
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 67 TLHDPDSELIEQQVALKLGRQKKVHIIDGHKVEVIPDDE 105
++DP+ IE+ + LK +V G E I +E
Sbjct: 67 YIYDPNGIDIEELLELKEEGGGRVVEYAGSGAEYISGEE 105
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 26.5 bits (59), Expect = 9.0
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 99 EVIPDDEEEEEGEETEEEEEGGGEDDGH 126
E DD+ EEE E+ + +E E+D
Sbjct: 335 EEDDDDDLEEEEEDVDLSDEEEDEEDED 362
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 26.4 bits (58), Expect = 9.1
Identities = 14/22 (63%), Positives = 16/22 (72%)
Query: 103 DDEEEEEGEETEEEEEGGGEDD 124
D+ EEE EE+EEEEE EDD
Sbjct: 11 DESGEEEEEESEEEEETDSEDD 32
>gnl|CDD|239980 cd04607, CBS_pair_NTP_transferase_assoc, This cd contains two
tandem repeats of the cystathionine beta-synthase (CBS
pair) domain associated with the NTP (Nucleotidyl
transferase) domain downstream. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown.
Length = 113
Score = 25.6 bits (57), Expect = 9.6
Identities = 13/49 (26%), Positives = 29/49 (59%), Gaps = 5/49 (10%)
Query: 62 LLRHMTLHDPDSELIEQQ-VALKLG--RQKKVHIIDGHKVEVIP--DDE 105
LL+ ++L DP SE++ + + K+G R++ + ++ + +P D+E
Sbjct: 50 LLKGLSLDDPVSEVMNRNPITAKVGSSREEILALMRERSIRHLPILDEE 98
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
0.312 0.132 0.387
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,208,365
Number of extensions: 859856
Number of successful extensions: 2765
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2240
Number of HSP's successfully gapped: 248
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (25.5 bits)