RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy499
(122 letters)
>gnl|CDD|239875 cd04412, NDPk7B, Nucleoside diphosphate kinase 7 domain B (NDPk7B):
The nm23-H7 class of nucleoside diphosphate kinase
(NDPk7) consists of an N-terminal DM10 domain and two
functional catalytic NDPk modules, NDPk7A and NDPk7B.
The function of the DM10 domain, which also occurs in
multiple copies in other proteins, is unknown. NDPk7 is
predominantly expressed in testes, although appreciable
amount are also found in liver, heart, brain, ovary,
small intestine and spleen. The nm23-H7 gene is located
in or near the hereditary prostrate cancer
susceptibility locus. Nm23-H7 may be involved in the
development of colon and gastric carcinoma, the latter
possibly in a type-specific manner.
Length = 134
Score = 59.2 bits (144), Expect = 2e-12
Identities = 23/33 (69%), Positives = 28/33 (84%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDA 64
E AK+LRPNT+RA YG++ V+NAVH TDLPED
Sbjct: 94 EIAKQLRPNTLRARYGKDKVQNAVHCTDLPEDG 126
>gnl|CDD|197791 smart00562, NDK, Enzymes that catalyze nonsubstrate specific
conversions of nucleoside diphosphates to nucleoside
triphosphates. These enzymes play important roles in
bacterial growth, signal transduction and pathogenicity.
Length = 135
Score = 42.2 bits (100), Expect = 7e-06
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 33 TAKELRPNTIRAMYGRNSVENAVHVTDLPEDA 64
+E P TIR +G + NAVH +D PE A
Sbjct: 91 DPREAAPGTIRGDFGLDIGRNAVHGSDSPESA 122
>gnl|CDD|201162 pfam00334, NDK, Nucleoside diphosphate kinase.
Length = 135
Score = 41.7 bits (99), Expect = 8e-06
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
E P TIR + + NAVH +D PE A E
Sbjct: 93 AEAAPGTIRGDFAVSIGRNAVHGSDSPESAERE 125
>gnl|CDD|238335 cd00595, NDPk, Nucleoside diphosphate kinases (NDP kinases, NDPks):
NDP kinases, responsible for the synthesis of nucleoside
triphosphates (NTPs), are involved in numerous
regulatory processes associated with proliferation,
development, and differentiation. They are vital for
DNA/RNA synthesis, cell division, macromolecular
metabolism and growth. The enzymes generate NTPs or
their deoxy derivatives by terminal (gamma)
phosphotransfer from an NTP such as ATP or GTP to any
nucleoside diphosphate (NDP) or its deoxy derivative.
The sequence of NDPk has been highly conserved through
evolution. There is a single histidine residue conserved
in all known NDK isozymes, which is involved in the
catalytic mechanism. The first confirmed metastasis
suppressor gene was the NDP kinase protein encoded by
the nm23 gene. Unicellular organisms generally possess
only one gene encoding NDP kinase, while most
multicellular organisms possess not only an ortholog
that provides most of the NDP kinase enzymatic activity
but also multiple divergent paralogous genes. The human
genome codes for at least nine NDP kinases and can be
classified into two groups, Groups I and II, according
to their genomic architecture and distinct enzymatic
activity. Group I isoforms (A-D) are well-conserved,
catalytically active, and share 58-88% identity between
each other, while Group II are more divergent, with only
NDPk6 shown to be active. NDP kinases exist in two
different quaternary structures; all known eukaryotic
enzymes are hexamers, while some bacterial enzymes are
tetramers, as in Myxococcus. The hexamer can be viewed
as trimer of dimers, while tetramers are dimers of
dimers, with the dimerization interface conserved.
Length = 133
Score = 40.4 bits (95), Expect = 3e-05
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDA 64
E A+ L P ++RA +G + + NAVH +D E A
Sbjct: 93 EIARHLAPGSLRADFGTDVLRNAVHGSDSVESA 125
>gnl|CDD|215503 PLN02931, PLN02931, nucleoside diphosphate kinase family protein.
Length = 177
Score = 38.3 bits (89), Expect = 2e-04
Identities = 19/42 (45%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDA------FFE 67
AK PN+IRAM G +S +N VH +D PE A FF
Sbjct: 122 RKAKISHPNSIRAMCGLDSEKNCVHGSDSPESAEREISFFFG 163
>gnl|CDD|239879 cd04416, NDPk_TX, NDP kinase domain of thioredoxin
domain-containing proteins (TXNDC3 and TXNDC6): Txl-2
(TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of
Group II N-terminal thioredoxin domains followed by one
or three NDP kinase domains, respectively. Sptrx-2,
which has a tissue specific distribution in human
testis, has been considered as a member of the nm23
family (nm23-H8) and exhibits a high homology with sea
urchin IC1 (intermediate chain-1) protein, a component
of the sperm axonemal outer dynein arm complex. Txl-2 is
mainly represented in close association with
microtubules within tissues with cilia and flagella such
as seminiferous epithelium (spermatids) and lung airway
epithelium, suggesting possible role in control of
microtubule stability and maintenance.
Length = 132
Score = 37.6 bits (88), Expect = 3e-04
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDA 64
E AKE +P+++RA + R+ + NAVH + E+A
Sbjct: 92 EEAKEEKPDSLRAQFARDHLSNAVHGSSSAEEA 124
>gnl|CDD|239880 cd04418, NDPk5, Nucleoside diphosphate kinase homolog 5 (NDP kinase
homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced
apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is
almost exclusively found in testis, especially in the
flagella of spermatids and spermatozoa, in association
with axoneme microtubules, and may play a role in
spermatogenesis by increasing the ability of late-stage
spermatids to eliminate reactive oxygen species. It
belongs to the nm23 Group II genes and appears to differ
from the other human NDPks in that it lacks two
important catalytic site residues, and thus does not
appear to possess NDP kinase activity. NDPk5 confers
protection from cell death by Bax and alters the
cellular levels of several antioxidant enzymes,
including glutathione peroxidase 5 (Gpx5).
Length = 132
Score = 37.4 bits (87), Expect = 4e-04
Identities = 13/28 (46%), Positives = 20/28 (71%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTD 59
AKE P+++RA+YG + + NAVH +D
Sbjct: 91 LKAKETHPDSLRAIYGTDDLRNAVHGSD 118
>gnl|CDD|223183 COG0105, Ndk, Nucleoside diphosphate kinase [Nucleotide transport
and metabolism].
Length = 135
Score = 34.5 bits (80), Expect = 0.004
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 39 PNTIRAMYGRNSVENAVHVTDLPEDAFFEF 68
P TIR + + EN VH +D PE A E
Sbjct: 99 PGTIRGDFALSVGENVVHGSDSPESAEREI 128
>gnl|CDD|239876 cd04413, NDPk_I, Nucleoside diphosphate kinase Group I
(NDPk_I)-like: NDP kinase domains are present in a large
family of structurally and functionally conserved
proteins from bacteria to humans that generally catalyze
the transfer of gamma-phosphates of a nucleoside
triphosphate (NTP) donor onto a nucleoside diphosphate
(NDP) acceptor through a phosphohistidine intermediate.
The mammalian nm23/NDP kinase gene family can be divided
into two distinct groups. The group I genes encode
proteins that generally have highly homologous
counterparts in other organisms and possess the classic
enzymatic activity of a kinase. This group includes
vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its
counterparts in bacteria, archea and other eukaryotes.
NDP kinases exist in two different quaternary
structures; all known eukaryotic enzymes are hexamers,
while some bacterial enzymes are tetramers, as in
Myxococcus. They possess the NDP kinase active site
motif (NXXH[G/A]SD) and the nine residues that are most
essential for catalysis.
Length = 130
Score = 34.0 bits (79), Expect = 0.005
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 39 PNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
P TIR + + N VH +D E A E
Sbjct: 97 PGTIRGDFALSIGRNIVHGSDSVESAERE 125
>gnl|CDD|239878 cd04415, NDPk7A, Nucleoside diphosphate kinase 7 domain A (NDPk7A):
The nm23-H7 class of nucleoside diphosphate kinase
(NDPk7) consists of an N-terminal DM10 domain and two
functional catalytic NDPk modules, NDPk7A and NDPk7B.
The function of the DM10 domain, which also occurs in
multiple copies in other proteins, is unknown. NDPk7 is
predominantly expressed in testes, although appreciable
amount are also found in liver, heart, brain, ovary,
small intestine and spleen. The nm23-H7 gene is located
in or near the hereditary prostrate cancer
susceptibility locus. Nm23-H7 may be involved in the
development of colon and gastric carcinoma, the latter
possibly in a type-specific manner.
Length = 131
Score = 31.6 bits (72), Expect = 0.041
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 33 TAKELRPNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
A+ PN+IRA++G + NA H +D A E
Sbjct: 92 VARSDAPNSIRALFGTDGTRNAAHGSDSVASAARE 126
>gnl|CDD|173008 PRK14542, PRK14542, nucleoside diphosphate kinase; Provisional.
Length = 137
Score = 31.2 bits (70), Expect = 0.076
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 35 KELRPNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
KE TIRA+Y + NAVH +D +A E
Sbjct: 94 KEAAAGTIRALYAESKEANAVHGSDSDANAALE 126
>gnl|CDD|179085 PRK00668, ndk, mulitfunctional nucleoside diphosphate
kinase/apyrimidinic endonuclease/3'-; Validated.
Length = 134
Score = 30.5 bits (70), Expect = 0.100
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 39 PNTIRAMYGRNSVENAVHVTDLPEDAFFE 67
P TIR + + EN VH +D PE A E
Sbjct: 98 PGTIRGDFALSIGENVVHGSDSPESAARE 126
>gnl|CDD|239877 cd04414, NDPk6, Nucleoside diphosphate kinase 6 (NDP kinase 6,
NDPk6, NM23-H6; NME6; Inhibitor of p53-induced
apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding
NDPk6 is expressed mainly in mitochondria, but also
found at a lower level in most tissues. NDPk6 has all
nine residues considered crucial for enzyme structure
and activity, and has been found to have NDP kinase
activity. It may play a role in cell growth and cell
cycle progression. The nm23-H6 gene locus has been
implicated in a variety of malignant tumors.
Length = 135
Score = 29.7 bits (67), Expect = 0.24
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 39 PNTIRAMYGRNSVENAVHVTDLPEDAFFEFG 69
P++IR +YG NA H +D P A E
Sbjct: 101 PDSIRGLYGLTDTRNATHGSDSPASAQREIA 131
>gnl|CDD|184734 PRK14545, PRK14545, nucleoside diphosphate kinase; Provisional.
Length = 139
Score = 27.9 bits (62), Expect = 0.83
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 41 TIRAMYGRNSVENAVHVTDLPEDAFFE 67
TIR Y ++ ENAVH +D E+A E
Sbjct: 102 TIRKKYAKSIGENAVHGSDSDENAQIE 128
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 26.3 bits (58), Expect = 4.7
Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 32 ETAKELRPNTIRAMYGRNSVENAVHVTDLPEDAFFEFGKQCK 73
E ++ PN + M R + N V T+ P++ F KQ
Sbjct: 596 EDLRKGVPNILFQMLLRGA--NGVGYTNYPDNVVKYFVKQAA 635
>gnl|CDD|173007 PRK14541, PRK14541, nucleoside diphosphate kinase; Provisional.
Length = 140
Score = 26.1 bits (57), Expect = 4.8
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 41 TIRAMYGRNSVENAVHVTDLPEDAFFEFG 69
T+R +Y + EN VH +D E+A E G
Sbjct: 100 TVRKLYADSKGENIVHGSDSAENAAIEAG 128
>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 721
Score = 26.2 bits (58), Expect = 5.1
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 18 PSYKGNSFSFIFYQETAKELRPNTI 42
P+YK + ++ +Y+ A E+ P I
Sbjct: 620 PAYKIDQDNYAYYERGAYEVGPKPI 644
>gnl|CDD|220307 pfam09601, DUF2459, Protein of unknown function (DUF2459). This
conserved hypothetical protein of unknown function is
found in several Proteobacteria. Its function is
unknown and its genome context is not well-conserved.
It is found amid urease genes in at least one species.
Length = 172
Score = 25.7 bits (57), Expect = 5.3
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 29 FYQETA--KELRP-NTIRAMYGRNSVENAVHVTDLPEDA 64
FY T +L P +RA+ G SV + V + P
Sbjct: 51 FYLSTPTWADLTPGTVLRALTGDASVLHVVVLGRPPAPG 89
>gnl|CDD|184733 PRK14540, PRK14540, nucleoside diphosphate kinase; Provisional.
Length = 134
Score = 25.6 bits (56), Expect = 6.3
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 36 ELRPNTIRAMYGRNSVENAVHVTDLPEDA 64
E P TIR +G + N +H +D E A
Sbjct: 96 EAEPGTIRGDFGLYTPANIIHASDSKESA 124
>gnl|CDD|216901 pfam02145, Rap_GAP, Rap/ran-GAP.
Length = 187
Score = 25.6 bits (57), Expect = 7.0
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 22 GNSFSFIFYQETAKELRPNTIR 43
GN I + E+ PNTI+
Sbjct: 80 GNDIVNIIFNESGLPFNPNTIK 101
>gnl|CDD|115473 pfam06817, RVT_thumb, Reverse transcriptase thumb domain. This
domain is known as the thumb domain. It is composed of
a four helix bundle.
Length = 70
Score = 24.5 bits (54), Expect = 7.0
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 1/20 (5%)
Query: 72 CKLLKITLKLTEKRPLWTFE 91
CKLL+ LTE P T E
Sbjct: 43 CKLLRGAKALTEVVP-LTEE 61
>gnl|CDD|178473 PLN02885, PLN02885, nicotinate phosphoribosyltransferase.
Length = 545
Score = 25.8 bits (57), Expect = 8.0
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 12/71 (16%)
Query: 62 EDAFFEFGKQ--CKLLKITLKLTE------KRPLWTFESPIG--QVLSLSLTCLQN-PMK 110
EDAFF++ + C +++ + E + PL E P+ Q+L + L N
Sbjct: 86 EDAFFDYLRGLDCSDVEV-YAIPEGSVVFPRVPLMRIEGPLAVVQLLETTFLTLVNYASL 144
Query: 111 IVPNGNRARLI 121
+ N R RL+
Sbjct: 145 VATNAARHRLV 155
>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain.
RNase R is a processive 3' to 5' exoribonuclease, which
is a homolog of RNase II. RNase R degrades RNA with
secondary structure having a 3' overhang of at least 7
nucleotides. RNase R and PNPase play an important role
in the degradation of RNA with extensive secondary
structure, such as rRNA, tRNA, and certain mRNA which
contains repetitive extragenic palindromic sequences.
The C-terminal S1 domain binds ssRNA.
Length = 83
Score = 24.7 bits (55), Expect = 8.8
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 51 VENAVHVTDLPEDAFFEF 68
VE VHV+ L +D ++EF
Sbjct: 26 VEGLVHVSTLGDD-YYEF 42
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
0.320 0.137 0.412
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,154,881
Number of extensions: 508558
Number of successful extensions: 424
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 32
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.0 bits)