RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8838
(319 letters)
>gnl|CDD|191968 pfam08213, DUF1713, Mitochondrial domain of unknown function
(DUF1713). This domain is found at the C terminal end
of mitochondrial proteins of unknown function.
Length = 34
Score = 42.7 bits (101), Expect = 3e-06
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 192 HAIVMIIRRRRKMKKHKLKKLRIRMKFEWAKIRQ 225
A ++ +RRRKMKKHK KKLR R + K+ +
Sbjct: 1 QADSVLRKRRRKMKKHKYKKLRKRTRALRRKLDK 34
>gnl|CDD|215038 PLN00040, PLN00040, Protein MAK16 homolog; Provisional.
Length = 233
Score = 31.7 bits (72), Expect = 0.43
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 196 MIIRRRRKMKKHKLKKLRIRMKFEWAKIRQRREMKKEKAFQLEMS 240
+IR R+ K + K + K K +RRE K +KA QLE S
Sbjct: 118 YLIRMRKLALKTREKIVTTPRKLL--KRERRRESKAQKAAQLEKS 160
>gnl|CDD|233621 TIGR01891, amidohydrolases, amidohydrolase. This model represents
a subfamily of amidohydrolases which are a subset of
those sequences detected by pfam01546. Included within
this group are hydrolases of hippurate
(N-benzylglycine), indoleacetic acid (IAA) N-conjugates
of amino acids, N-acetyl-L-amino acids and
aminobenzoylglutamate. These hydrolases are of the
carboxypeptidase-type, most likely utilizing a zinc ion
in the active site [Protein fate, Degradation of
proteins, peptides, and glycopeptides].
Length = 363
Score = 30.4 bits (69), Expect = 1.2
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 12/56 (21%)
Query: 39 PVWALIADNDSTAIEEHFGQKFNSQ-RGLMDGFSQCQLMAVSLCGHSLIMELVFLT 93
PV AL AD D+ I+E + S G+M CGH L ++ T
Sbjct: 57 PVVALRADMDALPIQEQTDLPYKSTNPGVMHA-----------CGHDLHTAILLGT 101
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.9 bits (69), Expect = 1.2
Identities = 28/104 (26%), Positives = 49/104 (47%), Gaps = 5/104 (4%)
Query: 201 RRKMKKHKLKKLRIRMKFEWAKIRQRREMKK--EKAFQLEMSTKVKEGERFSAEQYVENK 258
++K + K K ++ E KI+ E KK E + E + K +E E+ +AE +
Sbjct: 1639 KKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALKKEA 1698
Query: 259 LQLLHAEQLAESWKNVPESFIKEWTERKERHRNEKQAKESRKKA 302
+ AE+L K E K +K N+ +A+E++K+A
Sbjct: 1699 EEAKKAEELK---KKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739
Score = 29.0 bits (64), Expect = 4.2
Identities = 29/117 (24%), Positives = 47/117 (40%), Gaps = 3/117 (2%)
Query: 186 SQAPEKHAIVMIIRRRRKMKKHKLKKLRIRMKFEWAKIRQRREMKKEKAFQLEMSTKVKE 245
+ A K R + KL + +MK E AK + ++K E+ + E K E
Sbjct: 1577 NMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVE 1636
Query: 246 GERFSAEQYVENKLQLLHAEQLAESWKNVPESFIKEWTERKERHRNEKQAKESRKKA 302
+ + + +L AE E K K+ E K++ K+A+E KKA
Sbjct: 1637 QLKKKEAEEKKKAEELKKAE---EENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKA 1690
Score = 28.6 bits (63), Expect = 6.3
Identities = 20/100 (20%), Positives = 45/100 (45%), Gaps = 2/100 (2%)
Query: 201 RRKMKKHKLKKLRIRMKFEWAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVENKLQ 260
++K ++ K + + E A +K +A + + K+ + +A++ E K +
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD--AAKKKAEEKKK 1392
Query: 261 LLHAEQLAESWKNVPESFIKEWTERKERHRNEKQAKESRK 300
A++ AE K + K +K+ +K+A+E +K
Sbjct: 1393 ADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKK 1432
>gnl|CDD|239471 cd03376, TPP_PFOR_porB_like, Thiamine pyrophosphate (TPP family),
PFOR porB-like subfamily, TPP-binding module; composed
of proteins similar to the beta subunit (porB) of the
Helicobacter pylori four-subunit pyruvate ferredoxin
oxidoreductase (PFOR), which are also found in archaea
and some hyperthermophilic bacteria. PFOR catalyzes the
oxidative decarboxylation of pyruvate to form
acetyl-CoA, a crucial step in many metabolic pathways.
Archaea, anaerobic bacteria and eukaryotes that lack
mitochondria (and therefore pyruvate dehydrogenase) use
PFOR to oxidatively decarboxylate pyruvate, with
ferredoxin or flavodoxin as the electron acceptor. The
36-kDa porB subunit contains the binding sites for the
cofactors, TPP and a divalent metal cation, which are
required for activity.
Length = 235
Score = 28.7 bits (65), Expect = 3.2
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 126 GMDKSYSLPPLASTSTSVVLDNPVFNKNVKIDIPLM 161
G+ +S S P A T+T+ V K K D+PL+
Sbjct: 124 GIQRSGSTPYGAWTTTTPVGKVSFGKKQPKKDLPLI 159
>gnl|CDD|226673 COG4220, COG4220, Phage DNA packaging protein, Nu1 subunit of
terminase [DNA replication, recombination, and repair].
Length = 174
Score = 28.6 bits (64), Expect = 3.3
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 219 EWAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVENKLQLLHAEQLAESWKNVPESF 278
E + R+R + + +A E+ GE + L + A ++A ++P S
Sbjct: 72 ELREARERHRLTRAQADAQELKNARDSGEVVETA-FCTFVLSRI-AREIASILDSIPLSV 129
Query: 279 IKEWTERKERH 289
+ + E RH
Sbjct: 130 QRRFPELTNRH 140
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 29.1 bits (66), Expect = 3.5
Identities = 17/62 (27%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 219 EWAKIRQR-REMKKEK---AFQLEMSTKV--KEGERFSAEQYVENKLQLLHAEQLAESWK 272
E ++++ RE + FQLE ++ + GE E+ E + +L ++E+LAE+ +
Sbjct: 172 ELEDLQEKERERAQRADLLQFQLEELEELNLQPGED---EELEEERKRLSNSEKLAEAIQ 228
Query: 273 NV 274
N
Sbjct: 229 NA 230
>gnl|CDD|176050 cd08405, C2B_Synaptotagmin-7, C2 domain second repeat present in
Synaptotagmin 7. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 7, a member of
class 2 synaptotagmins, is located in presynaptic plasma
membranes in neurons, dense-core vesicles in endocrine
cells, and lysosomes in fibroblasts. It has been shown
to play a role in regulation of Ca2+-dependent lysosomal
exocytosis in fibroblasts and may also function as a
vesicular Ca2+-sensor. It is distinguished from the
other synaptotagmins by having over 12 splice forms.
Previously all synaptotagmins were thought to be calcium
sensors in the regulation of neurotransmitter release
and hormone secretion, but it has been shown that not
all of them bind calcium. Of the 17 identified
synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10).
The function of the two C2 domains that bind calcium
are: regulating the fusion step of synaptic vesicle
exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that can
adopt 2 structural arrangements: Type I and Type II,
distinguished by a circular permutation involving their
N- and C-terminal beta strands. Many C2 domains are
Ca2+-dependent membrane-targeting modules that bind a
wide variety of substances including bind phospholipids,
inositol polyphosphates, and intracellular proteins.
Most C2 domain proteins are either signal transduction
enzymes that contain a single C2 domain, such as protein
kinase C, or membrane trafficking proteins which contain
at least two C2 domains, such as synaptotagmin 1.
However, there are a few exceptions to this including
RIM isoforms and some splice variants of piccolo/aczonin
and intersectin which only have a single C2 domain. C2
domains with a calcium binding region have negatively
charged residues, primarily aspartates, that serve as
ligands for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 28.2 bits (63), Expect = 3.7
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 147 NPVFNKNVKIDIPL-----MPFYIEKIDKLNERNNSIIEDPVIP---SQAPEKHAIVMII 198
NPVFN++ +IPL I +DK N +I + KH M+
Sbjct: 64 NPVFNESFIFNIPLERLRETTLIITVMDKDRLSRNDLIGKIYLGWKSGGLELKHWKDMLS 123
Query: 199 RRRRKMKK-HKLK 210
+ R+ + + H+LK
Sbjct: 124 KPRQPVAQWHRLK 136
>gnl|CDD|225606 COG3064, TolA, Membrane protein involved in colicin uptake [Cell
envelope biogenesis, outer membrane].
Length = 387
Score = 28.8 bits (64), Expect = 4.6
Identities = 22/106 (20%), Positives = 45/106 (42%), Gaps = 3/106 (2%)
Query: 200 RRRKMKKHKLKKL-RIRMKFEWAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVENK 258
R ++++K +LK + + E K Q + ++E+ + + + K+ E A+ E
Sbjct: 102 RLKQLEKERLKAQEQQKQAEEAEKQAQLEQKQQEEQARKAAAEQKKKAEAAKAKAAAEAA 161
Query: 259 LQLLHAE--QLAESWKNVPESFIKEWTERKERHRNEKQAKESRKKA 302
AE + AE E + + + E +AK + +KA
Sbjct: 162 KLKAAAEAKKKAEEAAKAAEEAKAKAEAAAAKKKAEAEAKAAAEKA 207
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 28.1 bits (63), Expect = 5.0
Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 6/84 (7%)
Query: 201 RRKMKKHKLKKLRIRMKFEWAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVENKLQ 260
+K K + K+ R + + + RE +K+ + E K +E E+ E + +
Sbjct: 5 AKKRAKLEEKQARRQQR---EAEEEEREERKKLEEKREGERKEEEELEEEREKKKEEEER 61
Query: 261 LLHAEQLA---ESWKNVPESFIKE 281
EQ E ++ + SF+ E
Sbjct: 62 KEREEQARKEQEEYEKLKSSFVVE 85
>gnl|CDD|215333 PLN02618, PLN02618, tryptophan synthase, beta chain.
Length = 410
Score = 28.2 bits (63), Expect = 5.7
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 227 REMKKEKAFQLEMSTKVKEGERFSAEQYVENKLQLLHAEQLAESWKNV----PESFIK 280
+ + FQ E++ +K+ YV + L AE+L E +K PE ++K
Sbjct: 43 NALATDPEFQEELAGILKD--------YVGRETPLYFAERLTEHYKRADGEGPEIYLK 92
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The family
functions as a highly conserved exonuclease that is
required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing and
export.
Length = 134
Score = 27.3 bits (61), Expect = 6.0
Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 200 RRRKMKKHKLKKLRIRMKFEWAKIRQRREMKKE-KAFQLEMSTKVKEGERFSAE 252
+RK ++ K + + K +I +R+ +++E K + + KE + E
Sbjct: 28 HKRKQQRRKKAQEEAKEKEREERIEERKRIREERKQELEKQLKERKEALKLLEE 81
>gnl|CDD|216842 pfam02009, Rifin_STEVOR, Rifin/stevor family. Several multicopy
gene families have been described in Plasmodium
falciparum, including the stevor family of subtelomeric
open reading frames and the rif interspersed repetitive
elements. Both families contain three predicted
transmembrane segments. It has been proposed that stevor
and rif are members of a larger superfamily that code
for variant surface antigens.
Length = 290
Score = 28.1 bits (63), Expect = 6.9
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 7/27 (25%)
Query: 193 AIVMII------RRRRKM-KKHKLKKL 212
+++II RR++KM KK + KL
Sbjct: 261 LVMLIIYLILRYRRKKKMKKKLQYIKL 287
>gnl|CDD|118092 pfam09556, RE_HaeIII, HaeIII restriction endonuclease. This family
includes the HaeIII (recognises and cleaves GG^CC)
restriction endonuclease.
Length = 300
Score = 27.9 bits (62), Expect = 6.9
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 151 NKNVKIDIPLMPFYIEKIDKLNERNNSII 179
NK +I +PL+ +I +I++LNE N I
Sbjct: 165 NKEERIYVPLLKAFIREIERLNENNKGKI 193
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 27.8 bits (62), Expect = 7.1
Identities = 16/107 (14%), Positives = 45/107 (42%), Gaps = 13/107 (12%)
Query: 200 RRRKMKKHKLKKLRIRMKFE---WAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVE 256
R ++ ++ +L++ + K+E K +Q + + K + E + S+
Sbjct: 116 REKEREEAELRQRLAKEKYEEWCRQKAQQAAKQRTPKHKK-EAAESA------SSSLSGS 168
Query: 257 NKLQLLHAEQLAESWKNVPESFIKEWTERKERHRNEKQAKESRKKAL 303
K + E K + + + +++++ R E++ K+ +K+
Sbjct: 169 AKPE---RNVSQEEAKKRLQEWELKKLKQQQQKREEERRKQRKKQQE 212
>gnl|CDD|206039 pfam13868, Trichoplein, Tumour suppressor, Mitostatin. Trichoplein
or mitostatin, was first defined as a meiosis-specific
nuclear structural protein. It has since been linked
with mitochondrial movement. It is associated with the
mitochondrial outer membrane, and over-expression leads
to reduction in mitochondrial motility whereas lack of
it enhances mitochondrial movement. The activity appears
to be mediated through binding the mitochondria to the
actin intermediate filaments (IFs).
Length = 349
Score = 27.6 bits (62), Expect = 8.7
Identities = 20/106 (18%), Positives = 46/106 (43%), Gaps = 2/106 (1%)
Query: 199 RRRRKMKKHKLKKLRIRMKFEWAKIRQRREMKKEKAFQLEMSTKVKEGERFSAEQYVENK 258
+ R+K K+ K+ R + + + A+ Q E ++ + + E ER +Q + +
Sbjct: 216 KERQKEKEEAEKRRRQKQELQRAREEQIEEKEERLQEERAE--EEAERERMLEKQAEDEE 273
Query: 259 LQLLHAEQLAESWKNVPESFIKEWTERKERHRNEKQAKESRKKALH 304
L+ +AE+ ++ E++ER E++ + + L
Sbjct: 274 LEQENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELEEGERLR 319
>gnl|CDD|168292 PRK05906, PRK05906, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 454
Score = 27.8 bits (62), Expect = 9.3
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 49 STAIEEHFGQKFNSQRGLMDGFS--QCQLMAVSLCGHSLIMELVFLTISQSALGLTVLK 105
A E F ++ +SQ+ L FS Q A+ CGH EL FL I++ GL K
Sbjct: 112 EDAPEGFFPEEVSSQQELEHTFSRLDEQEGAILFCGHQANWELPFLYITKRYPGLAFAK 170
>gnl|CDD|216960 pfam02283, CobU, Cobinamide kinase / cobinamide phosphate
guanyltransferase. This family is composed of a group
of bifunctional cobalamin biosynthesis enzymes which
display cobinamide kinase and cobinamide phosphate
guanyltransferase activity. The crystal structure of the
enzyme reveals the molecule to be a trimer with a
propeller-like shape.
Length = 165
Score = 27.0 bits (61), Expect = 9.5
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 6/36 (16%)
Query: 263 HAEQLAESWKNVP------ESFIKEWTERKERHRNE 292
AE+LA + ++F E ER RHR
Sbjct: 14 FAERLALASGGPVVYIATAQAFDDEMAERIARHRAR 49
>gnl|CDD|227545 COG5220, TFB3, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH, subunit TFB3 [Cell division and chromosome
partitioning / Transcription / DNA replication,
recombination, and repair].
Length = 314
Score = 27.7 bits (61), Expect = 9.6
Identities = 23/95 (24%), Positives = 45/95 (47%), Gaps = 9/95 (9%)
Query: 149 VFNKNVKIDIPLMPFYIEKIDKLNERNNSIIEDPVIPSQAPEKHAIVMIIRRRRKMKKHK 208
VF ID+ L ++K +++N+ +SI+ + P PE VM +++ ++K
Sbjct: 117 VFELLELIDVSLTEEKVKKYEEMNQ--DSILNNLERP--TPE----VMPGKQKNVLQKRM 168
Query: 209 LKKLRIRMKFEWAKIRQRRE-MKKEKAFQLEMSTK 242
K R + + R +E KKE +L +++
Sbjct: 169 KLKKRQLERQIEEEERMNKEWTKKEIGNRLGTASE 203
>gnl|CDD|226727 COG4277, COG4277, Predicted DNA-binding protein with the
Helix-hairpin-helix motif [General function prediction
only].
Length = 404
Score = 27.5 bits (61), Expect = 9.9
Identities = 18/69 (26%), Positives = 30/69 (43%), Gaps = 13/69 (18%)
Query: 184 IPSQAPEKHAIVMIIRRRRKMKKHKLKKLRIRMK----------FEWAKIRQR---REMK 230
+P + +++ RRR ++ LKKL + +K F+ K+ R R
Sbjct: 335 VPGIGVKSARRIVMTRRRTRLTLEDLKKLGVVLKRAKPFITLDGFQGGKLEWRKDLRAAL 394
Query: 231 KEKAFQLEM 239
EKA QL +
Sbjct: 395 SEKAEQLSL 403
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
0.318 0.131 0.375
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,057,529
Number of extensions: 1533591
Number of successful extensions: 1863
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1813
Number of HSP's successfully gapped: 104
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)