RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16208
(116 letters)
>gnl|CDD|237121 PRK12507, PRK12507, putative monovalent cation/H+ antiporter
subunit B; Reviewed.
Length = 332
Score = 30.8 bits (70), Expect = 0.13
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 21 GIDNVGGVFVVLIAGCGVSFLFSL 44
G D +G V+ IAG V L S
Sbjct: 154 GYDTLGETSVIFIAGIAVLLLLSR 177
>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel. This family
includes the four transmembrane regions of the
ionotropic glutamate receptors and NMDA receptors.
Length = 268
Score = 29.9 bits (68), Expect = 0.22
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 14 ETDNPELGIDNVGGVFVVLIAGC 36
+ +LG+++ G+F++L G
Sbjct: 246 AVSSSQLGLESFAGLFLILGIGL 268
>gnl|CDD|193227 pfam12751, Vac7, Vacuolar segregation subunit 7. Vac7 is localised
at the vacuole membrane, a location which is consistent
with its involvement in vacuole morphology and
inheritance. Vac7 has been shown to function as an
upstream regulator of the Fab1 lipid kinase pathway. The
Fab1 lipid kinase pathway is important for correct
regulation of membrane trafficking events.
Length = 386
Score = 29.4 bits (66), Expect = 0.38
Identities = 11/45 (24%), Positives = 27/45 (60%)
Query: 27 GVFVVLIAGCGVSFLFSLLEFLWNVRKVAVEEKLSPYEAFMLELK 71
+ ++L+ G +F+ +L + L +V+ +A++ L+ + ML+L
Sbjct: 308 SLLLLLVIGGATTFIVALTKPLLDVQVLAIQNVLASEQEIMLDLN 352
>gnl|CDD|132245 TIGR03201, dearomat_had, 6-hydroxycyclohex-1-ene-1-carbonyl-CoA
dehydrogenase. Members of this protein family are
6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase,
an enzyme in the anaerobic metabolism of aromatic
enzymes by way of benzoyl-CoA, as seen in Thauera
aromatica, Geobacter metallireducens, and Azoarcus sp.
The experimentally characterized form from T. aromatica
uses only NAD+, not NADP+. Note that Rhodopseudomonas
palustris uses a different pathway to perform a similar
degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA.
Length = 349
Score = 28.3 bits (63), Expect = 0.83
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 1 MFSVMDTLQKDEDETDNPELGIDNVGGVFVVLIAGCGV 38
M + K E PELG +V VV +AGCGV
Sbjct: 4 MTEPGKPMVKTRVEI--PELGAGDV----VVKVAGCGV 35
>gnl|CDD|169981 PRK09577, PRK09577, multidrug efflux protein; Reviewed.
Length = 1032
Score = 27.9 bits (62), Expect = 1.4
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 50 NVRKVAVEEKLSPYEA 65
NV ++ VEE LSPY+A
Sbjct: 414 NVERLMVEEGLSPYDA 429
>gnl|CDD|145042 pfam01686, Adeno_Penton_B, Adenovirus penton base protein. This
family consists of various adenovirus penton base
proteins, from both the Mastadenoviradae having
mammalian hosts and the Aviadenoviradae having avian
hosts. The penton base is a major structural protein
forming part of the penton which consists of a base and
a fibre, the pentons hold a morphologically prominent
position at the vertex capsomer in the adenovirus
particle. In mammalian adenovirus there is only one tail
on each base where as in avian adenovirus there are two.
Length = 454
Score = 27.7 bits (62), Expect = 1.5
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 30 VVLIAGCGVSFLFSLLEFLWNVRK 53
+VL+ GC V F +S L L +RK
Sbjct: 202 IVLLPGCAVDFTYSRLNNLLGIRK 225
>gnl|CDD|219985 pfam08713, DNA_alkylation, DNA alkylation repair enzyme.
Proteins in this family are predicted to be DNA
alkylation repair enzymes. The structure of a
hypothetical protein in this family shows it to adopt a
supercoiled alpha helical structure.
Length = 212
Score = 26.4 bits (59), Expect = 3.0
Identities = 12/46 (26%), Positives = 17/46 (36%), Gaps = 3/46 (6%)
Query: 52 RKVAVEEKLSPYEAFMLELKFAIRCYGTSKPVRRKASTPSLKSNSL 97
+A EK + + + K G P RRK + K SL
Sbjct: 6 EALADPEKAAEMQRYF---KEGFPFLGVKTPERRKIAKDFRKELSL 48
>gnl|CDD|240312 PTZ00202, PTZ00202, tuzin; Provisional.
Length = 550
Score = 26.7 bits (59), Expect = 3.2
Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 14/64 (21%)
Query: 27 GVFVVLIAGCGVSFLFSLLEFLWNVRKVAVEEKLSPYEAFMLELKFAIRCYGTSKPVRRK 86
GV +A GV+ + F WN + +++ +LK A+ ++P+ +
Sbjct: 205 GVVSASVALLGVASV-----FGWNFKNYRTQQR-------SYQLKVAVSTL--TQPLNPR 250
Query: 87 ASTP 90
ST
Sbjct: 251 PSTL 254
>gnl|CDD|180638 PRK06602, PRK06602, NADH:ubiquinone oxidoreductase subunit A;
Validated.
Length = 121
Score = 25.6 bits (57), Expect = 4.2
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 28 VFVVLIAGCGVSFLFSLLEFLWNVRKVAVEEKLSPYEAFML-----ELKFAIRCY 77
+ LI G+ L + L R EK SPYE+ +KF +R Y
Sbjct: 11 FLIFLIVAIGLGILLLVAGKLLGPRAPD-REKNSPYESGFEAFGDARMKFDVRFY 64
>gnl|CDD|227652 COG5349, COG5349, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 126
Score = 25.8 bits (57), Expect = 4.3
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 28 VFVVLIAGCGVSFLFSLLEFLWN 50
FV+LI G V L +E N
Sbjct: 61 YFVILIVGHIVVGLALWVEVTLN 83
>gnl|CDD|143379 cd07874, STKc_JNK3, Catalytic domain of the Serine/Threonine
Kinase, c-Jun N-terminal Kinase 3. Serine/Threonine
Kinases (STKs), c-Jun N-terminal kinase 3 (JNK3)
subfamily, catalytic (c) domain. STKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
JNK3 subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. JNKs are mitogen-activated protein kinases
(MAPKs) that are involved in many stress-activated
responses including those during inflammation,
neurodegeneration, apoptosis, and persistent pain
sensitization, among others. Vetebrates harbor three
different JNK genes (Jnk1, Jnk2, and Jnk3). JNK3 is
expressed primarily in the brain, and to a lesser extent
in the heart and testis. Mice deficient in Jnk3 are
protected against kainic acid-induced seizures, stroke,
sciatic axotomy neural death, and neuronal death due to
NGF deprivation, oxidative stress, or exposure to
beta-amyloid peptide. This suggests that JNK3 may play
roles in the pathogenesis of these diseases.
Length = 355
Score = 26.2 bits (57), Expect = 4.7
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 3/59 (5%)
Query: 49 WNVRKVAVEEKLSPYEAFMLELKFAIRCYGTSKPVRRKASTPSLKSNSLANLDLFNNKM 107
WN KV +E+ +P FM +L+ +R Y ++P + P L +SL D +NK+
Sbjct: 227 WN--KV-IEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKL 282
>gnl|CDD|224040 COG1115, AlsT, Na+/alanine symporter [Amino acid transport and
metabolism].
Length = 452
Score = 26.0 bits (58), Expect = 5.1
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 12/57 (21%)
Query: 26 GGVFVVLIAGCGVSFLFSL-----------LEFLWNVRKVAVEEK-LSPYEAFMLEL 70
G + L+ G G+ F L + L+ RK + +S ++A M L
Sbjct: 17 GYPLIYLLLGTGLYFTIRLGFVQFRHLKEMFKLLFGSRKGKAGKGGVSSFQALMTSL 73
>gnl|CDD|223036 PHA03295, PHA03295, envelope glycoprotein H; Provisional.
Length = 714
Score = 25.8 bits (57), Expect = 6.0
Identities = 20/67 (29%), Positives = 25/67 (37%), Gaps = 7/67 (10%)
Query: 40 FLFSLLEFLWNVRK---VAVEEKLSPYEAFMLELKFAIRCYGTSKPVRRKASTPSLKSN- 95
FL+ LL F + V V L A +L F RC+ S P P +
Sbjct: 317 FLYGLLLFSASTTNTGPVPVLRALDRQSALLLAGDFLNRCFDVSPPGNT---YPKYPTAL 373
Query: 96 SLANLDL 102
LA DL
Sbjct: 374 QLARSDL 380
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase
subunit beta/beta'; Reviewed.
Length = 2890
Score = 26.0 bits (57), Expect = 6.5
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 81 KPVRRKASTPSLKSNSLANLDLFNNKM 107
K ++ K +T S +SL DL N+KM
Sbjct: 485 KTIKDKLTTMSGAFDSLMPHDLVNSKM 511
>gnl|CDD|223908 COG0838, NuoA, NADH:ubiquinone oxidoreductase subunit 3 (chain A)
[Energy production and conversion].
Length = 123
Score = 25.3 bits (56), Expect = 6.7
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 28 VFVVLIAGCGVSFLFSLLEFLWNVRKVAVEEKLSPYEAFMLE-----LKFAIRCYG 78
+ V L+ G + FL LL + EKLSPYE L+F+++ Y
Sbjct: 15 LVVALLLGVLMLFLSKLLG-----PRRPNPEKLSPYECGNPPFGGARLRFSVQYYL 65
>gnl|CDD|226684 COG4231, COG4231, Indolepyruvate ferredoxin oxidoreductase, alpha
and beta subunits [Energy production and conversion].
Length = 640
Score = 25.8 bits (57), Expect = 6.8
Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 10/68 (14%)
Query: 18 PELGIDNVGGVFVVLIAGCGVSF-LFSLLEFLWNVRKVAVEEKLSPYEAFMLELKFAIRC 76
+LG+D +L G + FL + +V V E+ P+ +E +
Sbjct: 267 EDLGLD-----DELLKLGTPYPLPEQLIENFLKGLERVLVVEEGEPF----IEEQVKALL 317
Query: 77 YGTSKPVR 84
Y PV
Sbjct: 318 YDAGLPVE 325
>gnl|CDD|143375 cd07870, STKc_PFTAIRE2, Catalytic domain of the Serine/Threonine
Kinase, PFTAIRE-2 kinase. Serine/Threonine Kinases
(STKs), PFTAIRE-2 subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The PFTAIRE-2 subfamily is part of a larger superfamily
that includes the catalytic domains of other protein
STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. PFTAIRE-2 shares sequence
similarity with Cyclin-Dependent Kinases (CDKs), which
belong to a large family of STKs that are regulated by
their cognate cyclins. Together, CDKs and cyclins are
involved in the control of cell-cycle progression,
transcription, and neuronal function. PFTAIRE-2 is also
referred to as ALS2CR7 (amyotrophic lateral sclerosis 2
(juvenile) chromosome region candidate 7). It may be
associated with amyotrophic lateral sclerosis 2 (ALS2),
an autosomal recessive form of juvenile ALS. The
function of PFTAIRE-2 is not yet known.
Length = 291
Score = 25.7 bits (56), Expect = 6.8
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 19 ELGIDNVGGVFVVLIAG----CGVSFLFSLLEFLWNVRKVAVEE 58
L I G +F+ ++ G GVS +F LE +W V V E+
Sbjct: 184 ALDIWGAGCIFIEMLQGQPAFPGVSDVFEQLEKIWTVLGVPTED 227
>gnl|CDD|132881 cd07064, AlkD_like_1, A new structural DNA glycosylase containing
HEAT-like repeats. This domain represents a new and
uncharacterized structural superfamily of DNA
glycosylases that form an alpha-alpha superhelix fold
that are not belong to the identified five structural
DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg
and helix-hairpin-helix). DNA glycosylases removing
alkylated base residues have been identified in all
organisms investigated and may be universally present in
nature. DNA glycosylases catalyze the first step in Base
Excision Repair (BER) pathway by cleaving damaged DNA
bases within double strand DNA to produce an abasic
site. The resulting abasic site is further processed by
AP endonuclease, phosphodiesterase, DNA polymerases, and
DNA ligase functions to restore the DNA to an undamaged
state. All glycosylase examined to date utilize a
similar strategy for binding DNA and base flipping
despite their structural diversity. The known structures
for members of this family, AlkC and AlkD from Bacillus
cereus, are distant homologues and are composed of six
variant HEAT (Huntington/Elongation/ A subunit/Target of
rapamycin) repeats. HEAT motifs are ~45-amino acid
sequences that form antiparallel alpha-helices, which
are packed by a conserved hyrophobic interface and are
tandemly repeated to form superhelical alpha-structures.
AlkD and AlkC are specific for removal of
3-methyladenine (3mA) and 7-methylguanine (7mG) from the
DNA by base excision repair. Homologues of AlkC and AlkD
were also identified in other organisms.
Length = 208
Score = 25.6 bits (57), Expect = 7.2
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 76 CYGTSKPVRRKASTPSLKSNSLANLD 101
YG P RR S P LK + L + +
Sbjct: 20 FYGIKTPERRALSKPFLKESKLPDKE 45
>gnl|CDD|212147 cd11540, NTP-PPase_u3, Nucleoside Triphosphate
Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain
found in a group of uncharacterized proteins from
bacteria and archaea. This family corresponds to a
group of uncharacterized hypothetical proteins from
bacteria and archaea, showing a high sequence
similarity to the dimeric 2-deoxyuridine
5'-triphosphate nucleotidohydrolase (dUTP
pyrophosphatase or dUTPase) and NTP-PPase MazG
proteins. However, unlike typical tandem-domain MazG
proteins, members in this family consist of a single
MazG-like domain that contains a well conserved
divalent ion-binding motif EXX[E/D].
Length = 76
Score = 24.5 bits (54), Expect = 7.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 16 DNPELGIDNVGGVFVVLIAGC 36
+ E D++G V VVLI C
Sbjct: 42 NKQEEIKDSIGDVLVVLIILC 62
>gnl|CDD|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit. This model
recognizes specificially the D subunit of NADH
dehydrogenase I complex. It excludes the related chain
of NAD(P)H-quinone oxidoreductases from chloroplast and
Synechocystis, where the quinone may be plastoquinone
rather than ubiquinone. This subunit often appears as a
C/D fusion [Energy metabolism, Electron transport].
Length = 386
Score = 25.8 bits (57), Expect = 7.4
Identities = 15/39 (38%), Positives = 18/39 (46%)
Query: 53 KVAVEEKLSPYEAFMLELKFAIRCYGTSKPVRRKASTPS 91
+V E P E+ EL F I G +KP R K PS
Sbjct: 313 RVPAGEVYVPIESPKGELGFYIISDGGTKPYRLKIRAPS 351
>gnl|CDD|216181 pfam00902, TatC, Sec-independent protein translocase protein
(TatC). The bacterial Tat system has a remarkable
ability to transport folded proteins even enzyme
complexes across the cytoplasmic membrane. It is
structurally and mechanistically similar to the Delta
pH-driven thylakoidal protein import pathway. A
functional Tat system or Delta pH-dependent pathway
requires three integral membrane proteins: TatA/Tha4,
TatB/Hcf106 and TatC/cpTatC. The TatC protein is
essential for the function of both pathways. It might
be involved in twin-arginine signal peptide
recognition, protein translocation and proton
translocation. Sequence analysis predicts that TatC
contains six transmembrane helices (TMHs), and
experimental data confirmed that N- and C-termini of
TatC or cpTatC are exposed to the cytoplasmic or
stromal face of the membrane. The cytoplasmic
N-terminus and the first cytoplasmic loop region of the
Escherichia coli TatC protein are essential for protein
export. At least two TatC molecules co-exist within
each Tat translocon.
Length = 212
Score = 25.5 bits (57), Expect = 7.5
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 28 VFVVLIAGCGVSFLFS--LLEFL-WNVRKVAVEEK----LSPYEAFMLELKFAI 74
+ I G + + FS ++ FL + SP EAF LK ++
Sbjct: 14 SLIAFILGFIICYFFSEEIILFLLAPLLNALPPNSKLIYTSPTEAFFTYLKLSL 67
>gnl|CDD|233445 TIGR01511, ATPase-IB1_Cu, copper-(or silver)-translocating P-type
ATPase. This model describes the P-type ATPase
primarily responsible for translocating copper ions
accross biological membranes. These transporters are
found in prokaryotes and eukaryotes. This model
encompasses those species which pump copper ions out of
cells or organelles (efflux pumps such as CopA of
Escherichia coli ) as well as those which pump the ion
into cells or organelles either for the purpose of
supporting life in extremely low-copper environments
(for example CopA of Enterococcus hirae ) or for the
specific delivery of copper to a biological complex for
which it is a necessary component (for example FixI of
Bradyrhizobium japonicum, or CtaA and PacS of
Synechocystis). The substrate specificity of these
transporters may, to a varying degree, include silver
ions (for example, CopA from Archaeoglobus fulgidus).
Copper transporters from this family are well known as
the genes which are mutated in two human disorders of
copper metabolism, Wilson's and Menkes' diseases. The
sequences contributing to the seed of this model are
all experimentally characterized. The copper P-type
ATPases have been characterized as Type IB based on a
phylogenetic analysis which combines the
copper-translocating ATPases with the
cadmium-translocating species. This model and that
describing the cadmium-ATPases (TIGR01512) are well
separated, and thus we further type the copper-ATPases
as IB1 (and the cadmium-ATPases as IB2). Several
sequences which have not been characterized
experimentally fall just below the cutoffs for both of
these models. A sequence from Enterococcus faecalis
scores very high against this model, but yet is
annotated as an "H+/K+ exchanging ATPase". BLAST of
this sequence does not hit anything else annotated in
this way. This error may come from the characterization
paper published in 1987. Accession GP|7415611 from
Saccharomyces cerevisiae appears to be mis-annotated as
a cadmium resistance protein. Accession
OMNI|NTL01HS00542 from Halobacterium which scores above
trusted for this model is annotated as
"molybdenum-binding protein" although no evidence can
be found for this classification [Cellular processes,
Detoxification, Transport and binding proteins, Cations
and iron carrying compounds].
Length = 572
Score = 25.7 bits (57), Expect = 7.6
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 31 VLIA-GCGVSFLFSLLEFLWNV 51
LIA G V++ +SL+ L N
Sbjct: 22 TLIALGTTVAYGYSLVALLANQ 43
>gnl|CDD|183831 PRK12933, secD, preprotein translocase subunit SecD; Reviewed.
Length = 604
Score = 25.4 bits (56), Expect = 8.5
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 12 EDETDNPELGIDNVGGVFVVLIAGCGVSFLF 42
E+ T P LG +N+ F L G G++ LF
Sbjct: 426 EERTIGPSLGAENIENGFAALALGMGITLLF 456
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 0.135 0.390
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,802,505
Number of extensions: 507706
Number of successful extensions: 543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 42
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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 (24.2 bits)