RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16800
(221 letters)
>gnl|CDD|200956 pfam00046, Homeobox, Homeobox domain.
Length = 57
Score = 94.5 bits (236), Expect = 1e-25
Identities = 31/54 (57%), Positives = 37/54 (68%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
RT FT +QL ELEKEF N+Y + R E+A L L E QVK+WFQNRR K K+
Sbjct: 4 RTTFTPEQLEELEKEFEKNRYPSAEEREELAKKLGLTERQVKVWFQNRRAKWKR 57
>gnl|CDD|197696 smart00389, HOX, Homeodomain. DNA-binding factors that are
involved in the transcriptional regulation of key
developmental processes.
Length = 57
Score = 87.3 bits (217), Expect = 5e-23
Identities = 32/53 (60%), Positives = 38/53 (71%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQK 191
RT+FT +QL ELEKEF N Y +R R E+A L L+E QVK+WFQNRR K K
Sbjct: 5 RTSFTPEQLEELEKEFQKNPYPSREEREELAKKLGLSERQVKVWFQNRRAKWK 57
>gnl|CDD|238039 cd00086, homeodomain, Homeodomain; DNA binding domains involved in
the transcriptional regulation of key eukaryotic
developmental processes; may bind to DNA as monomers or
as homo- and/or heterodimers, in a sequence-specific
manner.
Length = 59
Score = 86.5 bits (215), Expect = 1e-22
Identities = 33/55 (60%), Positives = 37/55 (67%)
Query: 139 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKKR 193
RT FT +QL ELEKEF N Y +R R E+A L L E QVKIWFQNRR K K+
Sbjct: 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58
>gnl|CDD|227863 COG5576, COG5576, Homeodomain-containing transcription factor
[Transcription].
Length = 156
Score = 44.7 bits (106), Expect = 5e-06
Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 137 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQKK 192
S R T++QL LE+EF N Y + RI+++ +L + V+IWFQN+R K+KK
Sbjct: 53 SKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKK 108
>gnl|CDD|219055 pfam06484, Ten_N, Teneurin Intracellular Region. This family is
found in the intracellular N-terminal region of the
Teneurin family of proteins. These proteins are
'pair-rule' genes and are involved in tissue patterning,
specifically probably neural patterning. The
intracellular domain is cleaved in response to
homophilic interaction of the extracellular domain, and
translocates to the nucleus. Here it probably carries
out to some transcriptional regulatory activity. The
length of this region and the conservation suggests that
there may be two structural domains here (personal obs:C
Yeats).
Length = 370
Score = 32.3 bits (73), Expect = 0.18
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 102 HPHPTSPSTDYTTPLTALKYPPP--AALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKY 159
+ P S+ ++P+ L PPP AA LL +S Q ++ E EF N +
Sbjct: 158 NGPPLHCSSASSSPVEQLPSPPPSPAANECQGRLLGSSAA---QAAQDSDSEDEFGPNSF 214
Query: 160 LTRA 163
L +
Sbjct: 215 LVKT 218
>gnl|CDD|182698 PRK10750, PRK10750, potassium transporter; Provisional.
Length = 483
Score = 31.0 bits (70), Expect = 0.51
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 181 IWFQNRRMKQKKRIKEGILIGVGEGSLMGAQGSSP 215
+W+ NR+ K + + +EG LI V +++G+ G+ P
Sbjct: 53 LWWPNRKEKGELKSREGFLIVVLFWTVLGSVGALP 87
>gnl|CDD|220535 pfam10037, MRP-S27, Mitochondrial 28S ribosomal protein S27.
Members of this family of small ribosomal proteins
possess one of three conserved blocks of sequence found
in proteins that stimulate the dissociation of guanine
nucleotides from G-proteins, leaving open the
possibility that MRP-S27 might be a functional partner
of GTP-binding ribosomal proteins.
Length = 417
Score = 30.1 bits (68), Expect = 0.89
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 143 TNKQLTELEKEFHFNKYLTRARRIEIAS--VLQLNETQVKIW-FQNRRMKQKKR 193
+L L K L+ R+ L+L E + ++W F+NR++ Q+K+
Sbjct: 346 WRSKLQALAK-VESRSLLSVEERLPTIEKEDLELYEQRQQLWFFENRKLWQRKK 398
>gnl|CDD|163257 TIGR03425, urea_degr_2, urea carboxylase-associated protein 2. A
number of bacteria degrade urea as a nitrogen source by
the urea carboxylase/allophanate hydrolase pathway,
which uses biotin and consumes ATP, rather than my means
of the nickel-dependent enzyme urease. This model
represents one of a pair of homologous, tandem
uncharacterized genes found together with the urea
carboxylase and allophanate hydrolase genes.
Length = 233
Score = 29.2 bits (66), Expect = 1.4
Identities = 14/27 (51%), Positives = 15/27 (55%), Gaps = 3/27 (11%)
Query: 103 PHPTSPSTDYT-TP--LTALKYPPPAA 126
PHP P DY P LTA + PP AA
Sbjct: 184 PHPLDPRPDYQPKPVRLTAWRAPPVAA 210
>gnl|CDD|233280 TIGR01128, holA, DNA polymerase III, delta subunit. DNA polymerase
III delta (holA) and delta prime (holB) subunits are
distinct proteins encoded by separate genes. The delta
prime subunit (holB) exhibits sequence homology to the
tau and gamma subunits (dnaX), but the delta subunit
(holA) does not demonstrate this same homology with
dnaX. The delta, delta prime, gamma, chi and psi
subunits form the gamma complex subassembly of DNA
polymerase III holoenzyme, which couples ATP to assemble
the ring-shaped beta subunit around DNA forming a DNA
sliding clamp [DNA metabolism, DNA replication,
recombination, and repair].
Length = 302
Score = 28.8 bits (65), Expect = 1.9
Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 3/86 (3%)
Query: 131 QSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQVKIWFQNRRMKQ 190
+ L N + +L+K K+L + EI E ++ W Q R K
Sbjct: 68 EEYLANPPPDTLLLIEAPKLDKRKKLTKWLKALKNAEIVECKTPKEQELPRWIQARLKKL 127
Query: 191 KKRIKE---GILIGVGEGSLMGAQGS 213
RI +L + EG+L+
Sbjct: 128 GLRIDPDAVQLLAELVEGNLLAIAQE 153
>gnl|CDD|200497 cd11236, Sema_plexin_like, The Sema domain, a protein interacting
module, of Plexins and MET-like receptor tyrosine
kinases. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestor of semaphorins. Ligand binding activates signal
transduction pathways controlling axon guidance in the
nervous system and other developmental processes
including cell migration and morphogenesis, immune
function, and tumor progression. Plexins are divided
into four types (A-D) according to sequence similarity.
In vertebrates, type A Plexins serve as the co-receptors
for neuropilins to mediate the signalling of class 3
semaphorins except Sema3E, which signals through Plexin
D1. Plexins serve as direct receptors for several other
members of the semaphorin family: class 6 semaphorins
signal through type A plexins and class 4 semaphorins
through type B. Plexin C1 serves as the receptor of
Sema7A and plays regulation roles in both immune and
nervous systems. This family also includes the Met and
RON receptor tyrosine kinases. The Sema domain is
located at the N-terminus and contains four disulfide
bonds formed by eight conserved cysteine residues. It
serves as a ligand-recognition and -binding module.
Length = 401
Score = 28.8 bits (65), Expect = 2.2
Identities = 12/52 (23%), Positives = 18/52 (34%), Gaps = 3/52 (5%)
Query: 68 CVFSLSSLRDLFPVKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTAL 119
CVFS+ + F +G +P S + TS + T T
Sbjct: 292 CVFSMKDIEAAFNDNCPLG---GGVPITTSAVLSDSLLTSVAVTTTRNHTVA 340
>gnl|CDD|221116 pfam11457, DUF3021, Protein of unknown function (DUF3021). This is
a bacterial family of uncharacterized proteins.
Length = 134
Score = 28.0 bits (63), Expect = 2.5
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 188 MKQKKRIKEGILIGVGEGSLM 208
MK K++ LIG+G GS++
Sbjct: 1 MKLIKKLINSGLIGIGIGSII 21
>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 = 28.5 bits (64), Expect = 2.9
Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 10/72 (13%)
Query: 1 MDEKEERQRRGSRSR---------KDDENKGGVGGEV-GKVGEEMKEKEEERLPGEGREG 50
KE + R R+R +DE++ + E +EE E
Sbjct: 347 PSTKESKMRDKRRARLDPIDFEEVDEDEDEEEEQRSDEHEEEEGEDSEEEGSQSREDGSS 406
Query: 51 EERDFSARDVKT 62
E D ++
Sbjct: 407 ESSSDVGSDSES 418
>gnl|CDD|224777 COG1864, NUC1, DNA/RNA endonuclease G, NUC1 [Nucleotide transport
and metabolism].
Length = 281
Score = 27.8 bits (62), Expect = 4.0
Identities = 14/104 (13%), Positives = 31/104 (29%), Gaps = 17/104 (16%)
Query: 98 PLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFN 157
L P P + + H N + + L HF+
Sbjct: 20 FLAYLPVQYPPLPK-----------LSSRIGVHLPTYNPNIAAPTKDGLPNYLLVYNHFS 68
Query: 158 KYLTRARRIEIASVLQLNETQVKI------WFQNRRMKQKKRIK 195
R+ ++ + ++ + +K +F + R+ +K R
Sbjct: 69 VVYNRSTKLPNWVAVNIDGSSLKKIKRRDKFFPDTRIPEKYRAT 112
>gnl|CDD|184256 PRK13700, PRK13700, conjugal transfer protein TraD; Provisional.
Length = 732
Score = 28.0 bits (62), Expect = 4.1
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 8 QRRGSRSRKDDENKGGVGGEVGKVGEEMKEKEEERL-----PGEGREGEERDFSARD 59
Q+ S D ++ GV G + +E+K K EE + PG GE D +A +
Sbjct: 638 QQPVSPVINDKKSDAGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYE 694
>gnl|CDD|181661 PRK09124, PRK09124, pyruvate dehydrogenase; Provisional.
Length = 574
Score = 27.6 bits (62), Expect = 6.1
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 3/57 (5%)
Query: 83 GEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGR 139
GV V +P +++ + P P + + + P L + +LLN S
Sbjct: 150 LNRGVAVVVLPGDVA---LKPAPERATPHWYHAPQPVVTPAEEELRKLAALLNGSSN 203
>gnl|CDD|221266 pfam11851, DUF3371, Domain of unknown function (DUF3371). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 125 to 142 amino acids in length.
Length = 131
Score = 26.6 bits (59), Expect = 6.8
Identities = 15/87 (17%), Positives = 26/87 (29%), Gaps = 22/87 (25%)
Query: 81 VKGEIGVTKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPPAALSQHQSLLNNSGRT 140
+K E + Q P +L P P P+T L N G
Sbjct: 26 IKQEPQLEDNQCPQDLYPHSSQPDLPPPTT----------------------LDLNDGTI 63
Query: 141 NFTNKQLTELEKEFHFNKYLTRARRIE 167
F++ F ++ L +++
Sbjct: 64 TFSDPLSHFTGSPFSYSSPLKEESKLD 90
>gnl|CDD|233277 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. This model
describes the P-type ATPase responsible for
translocating calcium ions across the endoplasmic
reticulum membrane of eukaryotes , and is of particular
importance in the sarcoplasmic reticulum of skeletal and
cardiac muscle in vertebrates. These pumps transfer Ca2+
from the cytoplasm to the lumen of the endoplasmic
reticulum. In humans and mice, at least, there are
multiple isoforms of the SERCA pump with overlapping but
not redundant functions. Defects in SERCA isoforms are
associated with diseases in humans. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1 the latter of which is
modelled by TIGR01522 [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 917
Score = 27.1 bits (60), Expect = 9.5
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 23 GVGGEVGKVGEEMKEKEEERLPGEGREGEERDFSARDVKTIGIFFCVF 70
G+ E+GK+ +EM+ E+E P + + E F K IG C+
Sbjct: 171 GMSTEIGKIRDEMRAAEQEDTPLQKKLDE---FGELLSKVIG-LICIL 214
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
0.313 0.134 0.379
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,385,645
Number of extensions: 1071391
Number of successful extensions: 872
Number of sequences better than 10.0: 1
Number of HSP's gapped: 863
Number of HSP's successfully gapped: 44
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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 (21.9 bits)
S2: 57 (25.7 bits)