RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13296
(101 letters)
>gnl|CDD|150420 pfam09744, Jnk-SapK_ap_N, JNK_SAPK-associated protein-1. This is
the N-terminal 200 residues of a set of proteins
conserved from yeasts to humans. Most of the proteins in
this entry have an RhoGEF pfam00621 domain at their
C-terminal end.
Length = 158
Score = 89.8 bits (223), Expect = 2e-24
Identities = 55/78 (70%), Positives = 65/78 (83%)
Query: 23 VQSLAGSIYQEFEKMITKYDEDVVKDLMPLVVNVLESLDLAFTENQEHEVELELLREDNE 82
V LA SIYQEFE++I Y E+VVK+LMPLV+ VLE+LD +ENQE EVELELLREDNE
Sbjct: 1 VYDLANSIYQEFERLIDNYGEEVVKNLMPLVIRVLENLDSLASENQELEVELELLREDNE 60
Query: 83 QLVTQYEREKQLRKAADQ 100
+L TQYEREK+LRK A+Q
Sbjct: 61 RLSTQYEREKELRKQAEQ 78
>gnl|CDD|234342 TIGR03752, conj_TIGR03752, integrating conjugative element protein,
PFL_4705 family. Members of this protein family are
found occasionally on plasmids such as the Pseudomonas
putida toluene catabolic TOL plasmid pWWO_p085. Usually,
however, they are found on the bacterial main chromosome
in regions flanked by markers of conjugative transfer
and/or transposition [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 472
Score = 29.6 bits (67), Expect = 0.19
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 66 ENQEHEVELELLREDNEQLVTQYEREKQLRKAADQI 101
E +E L L +NE L + ER ++ ++ DQ
Sbjct: 67 EVKELRKRLAKLISENEALKAENERLQKREQSIDQQ 102
>gnl|CDD|233067 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 524
Score = 29.0 bits (65), Expect = 0.39
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 69 EHEVELELLREDNEQLVT-QYEREKQLRKAADQ 100
E E E+E+L+ DN + Q + K+LR DQ
Sbjct: 437 EEEDEVEVLKVDNSSVREEQIAKLKKLRAERDQ 469
>gnl|CDD|177669 PLN00035, PLN00035, histone H4; Provisional.
Length = 103
Score = 26.7 bits (59), Expect = 1.2
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 23 VQSLAGSIYQEFEKMITKYDEDVVKD 48
V+ ++G IY+E ++ + E+V++D
Sbjct: 44 VKRISGLIYEETRGVLKIFLENVIRD 69
>gnl|CDD|238352 cd00652, TBP_TLF, TATA box binding protein (TBP): Present in
archaea and eukaryotes, TBPs are transcription factors
that recognize promoters and initiate transcription. TBP
has been shown to be an essential component of three
different transcription initiation complexes: SL1, TFIID
and TFIIIB, directing transcription by RNA polymerases
I, II and III, respectively. TBP binds directly to the
TATA box promoter element, where it nucleates polymerase
assembly, thus defining the transcription start site.
TBP's binding in the minor groove induces a dramatic DNA
bending while its own structure barely changes. The
conserved core domain of TBP, which binds to the TATA
box, has a bipartite structure, with intramolecular
symmetry generating a saddle-shaped structure that sits
astride the DNA. New members of the TBP family, called
TBP-like proteins (TBLP, TLF, TLP) or TBP-related
factors (TRF1, TRF2,TRP), are similar to the core domain
of TBPs, with identical or chemically similar amino
acids at many equivalent positions, suggesting similar
structure. However, TLFs contain distinct, conserved
amino acids at several positions that distinguish them
from TBP.
Length = 174
Score = 26.7 bits (60), Expect = 1.9
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 36 KMITKYDEDVVKDLMPLVVNVLESLDLAFTENQEHEVELELLREDNEQLVTQYERE 91
+++ K V K V N++ S DL F + LE L + + YE E
Sbjct: 78 RILQKLGFPVEKFPEFKVQNIVASCDLGF------PIRLEELALKHPE-NASYEPE 126
>gnl|CDD|224202 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and
metabolism].
Length = 533
Score = 26.8 bits (60), Expect = 2.0
Identities = 17/65 (26%), Positives = 29/65 (44%), Gaps = 16/65 (24%)
Query: 40 KYDEDVVKDLMPLVVNVLESLDLAFTENQEHEVELELLREDNE---QLVTQYER----EK 92
+ ED +++L L LE+L LA + L+ D E +LV + +R E+
Sbjct: 435 AFSEDGLEELDALFALTLENLRLAIS---------VLVTGDLELARRLVERKKRVRRLER 485
Query: 93 QLRKA 97
+ K
Sbjct: 486 RSSKR 490
>gnl|CDD|106506 PRK13560, PRK13560, hypothetical protein; Provisional.
Length = 807
Score = 26.6 bits (58), Expect = 2.9
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 1 MELDQETVYGTHDDSHIVMSEKVQSLAGSIYQEF 34
M L E +Y + D + I + ++SL + F
Sbjct: 653 MALAHEKLYQSEDLADIDFLDYIESLTAHLKNSF 686
>gnl|CDD|129911 TIGR00831, a_cpa1, Na+/H+ antiporter, bacterial form. The
Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC
2.A.36) The CPA1 family is a large family of proteins
derived from Gram-positive and Gram-negative bacteria,
blue green bacteria, yeast, plants and animals.
Transporters from eukaryotes have been functionally
characterized, and all of these catalyze Na+:H+
exchange. Their primary physiological functions may be
in (1) cytoplasmic pH regulation, extruding the H+
generated during metabolism, and (2) salt tolerance (in
plants), due to Na+ uptake into vacuoles. This model is
specific for the bacterial members of this family
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 525
Score = 26.4 bits (58), Expect = 3.1
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 16 HIVMSEKVQSLAGSIYQEFEKMITKY-DEDVVKDLMPLVVNVLESL-DLAFTENQEHEVE 73
+SE + +E E++I +Y K + V L + +A E +
Sbjct: 406 RKFVSEHSE-------RELEEIIARYIAARSAKFALMKAVEQLRIVEPVARELLPELDAR 458
Query: 74 LELLREDNEQLVTQYEREKQLRKAA 98
+E LR D E+ + EK LR+ A
Sbjct: 459 IEELRADGEEKIRSGMGEKNLRRRA 483
>gnl|CDD|185397 PTZ00015, PTZ00015, histone H4; Provisional.
Length = 102
Score = 25.5 bits (56), Expect = 3.7
Identities = 9/28 (32%), Positives = 18/28 (64%)
Query: 23 VQSLAGSIYQEFEKMITKYDEDVVKDLM 50
V+ ++G IY+E ++ + E+VV+D
Sbjct: 45 VKRISGDIYEEVRGVLKAFLENVVRDST 72
>gnl|CDD|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon;
Provisional.
Length = 257
Score = 25.4 bits (56), Expect = 5.2
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 28 GSIYQEFEKMITKYDEDVVKDLMPLVVNVLESLDLAFTENQEHEVEL 74
Y EK +++ +D+ DL +L++L L EN+E+ + L
Sbjct: 17 SLSYGMLEKSLSRLLKDIDIDL-----ELLKALGLPLVENKENLITL 58
>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the
lysosomal accumulation of unestrified cholesterol. It is
an integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis
[Transport and binding proteins, Other].
Length = 1204
Score = 25.6 bits (56), Expect = 5.5
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 55 NVLESLDLAFTENQEHEVELELLREDNEQLVT 86
NV LD++F+ E +E EL RE ++T
Sbjct: 545 NVQAKLDISFS--SERSIEDELKRESTADVIT 574
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 25.3 bits (56), Expect = 7.1
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 41 YDEDVVKDLMPL--VVNVLESLDLAFTENQEHEVELELLREDNEQLVTQYEREKQLRKAA 98
D ++ + L L + E L L FT + E E +EL+ + VT +E+ +
Sbjct: 83 VDPELYRSLKSLLELDGDEEELCLTFTVSGEGEGTIELIPNGSNIPVTNENKEEYVNLYV 142
Query: 99 DQI 101
D
Sbjct: 143 DYR 145
>gnl|CDD|223944 COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy
production and conversion].
Length = 472
Score = 24.9 bits (55), Expect = 9.0
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 85 VTQYEREKQLRKAADQI 101
++ ER LR+ AD +
Sbjct: 55 LSAEERAAILRRIADLL 71
>gnl|CDD|204414 pfam10211, Ax_dynein_light, Axonemal dynein light chain. Axonemal
dynein light chain proteins play a dynamic role in
flagellar and cilia motility. Eukaryotic cilia and
flagella are complex organelles consisting of a core
structure, the axoneme, which is composed of nine
microtubule doublets forming a cylinder that surrounds a
pair of central singlet microtubules. This
ultra-structural arrangement seems to be one of the most
stable micro-tubular assemblies known and is responsible
for the flagellar and ciliary movement of a large number
of organisms ranging from protozoan to mammals. This
light chain interacts directly with the N-terminal half
of the heavy chains.
Length = 189
Score = 24.5 bits (54), Expect = 9.8
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 66 ENQEHEVELELLREDNEQLVTQYERE 91
E + H E+ L++ N+QL +Q E+
Sbjct: 164 EEKRHADEIAFLKKQNQQLKSQLEQI 189
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
0.311 0.129 0.336
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,991,401
Number of extensions: 428446
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 100
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.3 bits)