RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12586
(309 letters)
>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein. The
Ligand-gated Ion Channel (LIC) Family of
Neurotransmitter Receptors TC 1.A.9)Members of the LIC
family of ionotropic neurotransmitter receptors are
found only in vertebrate and invertebrate animals. They
exhibit receptor specificity for (1)acetylcholine, (2)
serotonin, (3) glycine, (4) glutamate and (5)
g-aminobutyric acid (GABA). All of these receptor
channels are probably hetero- orhomopentameric. The best
characterized are the nicotinic acetyl-choline receptors
which are pentameric channels of a2bgd subunit
composition. All subunits arehomologous. The three
dimensional structures of the protein complex in both
the open and closed configurations have been solved at
0.9 nm resolution.The channel protein complexes of the
LIC family preferentially transport cations or anions
depending on the channel (e.g., the acetylcholine
receptors are cationselective while glycine receptors
are anion selective) [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 459
Score = 109 bits (273), Expect = 7e-27
Identities = 39/120 (32%), Positives = 64/120 (53%), Gaps = 5/120 (4%)
Query: 62 KEREEGDTTNYQVNGEFDLLSYSSVKNVVNYSCCVEPYPDITYYISLRRRPMFYVFNLIL 121
+ + D + + EF+LL + YP +T+ LRRRP++Y+ L +
Sbjct: 191 QGAVQVDDSLFISLPEFELLGVYGTRYC-TSETNTGEYPCLTFSFVLRRRPLYYLLQLYI 249
Query: 122 PCILINCIALLVFYVPSE-SGEKVTLGISALLSMTVFLMTIRETLPPTEN---ISEYVLV 177
P ILI ++ + F++P++ SG +V+LGI+ LL+MT F +RE+LP I Y V
Sbjct: 250 PSILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSGVRESLPAVSYVKAIDVYFAV 309
>gnl|CDD|201987 pfam01813, ATP-synt_D, ATP synthase subunit D. This is a family of
subunit D form various ATP synthases including V-type H+
transporting and Na+ dependent. Subunit D is suggested
to be an integral part of the catalytic sector of the
V-ATPase.
Length = 191
Score = 98.4 bits (246), Expect = 7e-25
Identities = 37/59 (62%), Positives = 47/59 (79%)
Query: 216 LASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQ 274
LA LET+ + L + IR+T +RVNALE VVIPRL T+ YI+ EL+E EREEF+RLKKI+
Sbjct: 133 LAELETALRLLAEEIRKTQRRVNALEKVVIPRLEETIKYIRMELEEREREEFFRLKKIK 191
>gnl|CDD|224312 COG1394, NtpD, Archaeal/vacuolar-type H+-ATPase subunit D [Energy
production and conversion].
Length = 211
Score = 87.3 bits (217), Expect = 2e-20
Identities = 41/72 (56%), Positives = 55/72 (76%), Gaps = 4/72 (5%)
Query: 216 LASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQD 275
LA LET+ + L + IR+T +RVNALEYV+IPRL T+ YI+S+L+E ERE+F RLKKI+
Sbjct: 143 LAELETTLRLLLEEIRKTKRRVNALEYVIIPRLENTIKYIESKLEEREREDFVRLKKIKK 202
Query: 276 KKREALERRTRE 287
KK E +T+E
Sbjct: 203 KK----EAKTKE 210
>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
transmembrane region. This family includes the four
transmembrane helices that form the ion channel.
Length = 228
Score = 82.7 bits (205), Expect = 1e-18
Identities = 31/51 (60%), Positives = 45/51 (88%), Gaps = 1/51 (1%)
Query: 119 LILPCILINCIALLVFYVPSESG-EKVTLGISALLSMTVFLMTIRETLPPT 168
LI+PC+LI+ ++ LVF++P+++G EKVTLGI+ LL+MTVFL+ IRE+LP T
Sbjct: 1 LIIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRESLPKT 51
>gnl|CDD|129409 TIGR00309, V_ATPase_subD, H(+)-transporting ATP synthase, vacuolar
type, subunit D. Although this ATPase can run
backwards, using a proton gradient to synthesize ATP,
the primary biological role is to acidify some
compartment, such as yeast vacuole (a lysosomal homolog)
or the interior of a prokaryote [Transport and binding
proteins, Cations and iron carrying compounds].
Length = 209
Score = 81.0 bits (200), Expect = 3e-18
Identities = 34/62 (54%), Positives = 44/62 (70%)
Query: 216 LASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQD 275
LA +ET+ + L + I T +RVNALE+V+IPRL T+ YI LDEM+RE F RLKKI+
Sbjct: 145 LAEIETTIRLLAEEIEITKRRVNALEHVIIPRLKNTIKYINMRLDEMDRENFVRLKKIKS 204
Query: 276 KK 277
K
Sbjct: 205 SK 206
>gnl|CDD|178991 PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed.
Length = 204
Score = 80.3 bits (199), Expect = 5e-18
Identities = 35/60 (58%), Positives = 44/60 (73%)
Query: 216 LASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQD 275
LA +E + + L I +T +RVNALEYV+IPRL T+ YIK +LDEMERE F RLKKI+
Sbjct: 145 LAEVEKTIQLLADEIEKTKRRVNALEYVIIPRLEETIKYIKMKLDEMERENFVRLKKIKS 204
>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel ligand
binding domain. This family is the extracellular ligand
binding domain of these ion channels. This domain forms
a pentameric arrangement in the known structure.
Length = 215
Score = 53.0 bits (128), Expect = 3e-08
Identities = 21/60 (35%), Positives = 32/60 (53%)
Query: 53 LFLLQLDLLKEREEGDTTNYQVNGEFDLLSYSSVKNVVNYSCCVEPYPDITYYISLRRRP 112
L EE D +++ NGE+D++ + +N Y C E YPD+T+Y LRR+P
Sbjct: 156 LRWKDDTPPILDEEIDLSDFTENGEWDIVDVPAKRNEYPYGCYSELYPDVTFYFVLRRKP 215
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 35.5 bits (82), Expect = 0.034
Identities = 25/98 (25%), Positives = 51/98 (52%), Gaps = 4/98 (4%)
Query: 201 RAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELD 260
R + +E T E+ R + E K L + + + + + L+ + L R ++ ++SEL+
Sbjct: 402 RPREKEGTEEEERREITVYEKRIKKLEETVERLEEENSELKRELE-ELKREIEKLESELE 460
Query: 261 EMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
RE R K +D++ A +RR +E+ L+E+++
Sbjct: 461 RFRRE--VRDKVRKDREIRARDRRIER-LEKELEEKKK 495
>gnl|CDD|216295 pfam01093, Clusterin, Clusterin.
Length = 434
Score = 32.8 bits (75), Expect = 0.20
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 258 ELDEMEREEFYR-LKKIQDKKREALERRTREQIERHLKEEEEH 299
E E E + L+K + +K EAL+ E +E L+EEEE
Sbjct: 33 ERTEEEHKNLMSTLEKTKKEKEEALKL-ANE-VEEKLEEEEEV 73
>gnl|CDD|221432 pfam12128, DUF3584, Protein of unknown function (DUF3584). This
protein is found in bacteria and eukaryotes. Proteins in
this family are typically between 943 to 1234 amino
acids in length. This family contains a P-loop motif
suggesting it is a nucleotide binding protein. It may be
involved in replication.
Length = 1198
Score = 32.7 bits (75), Expect = 0.30
Identities = 25/107 (23%), Positives = 43/107 (40%), Gaps = 5/107 (4%)
Query: 201 RAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELD 260
+ LP L +E L + ++ L+ + +L R L+ L
Sbjct: 347 LQADLD-QLPSIRSELEEVEARLDALTGKHQDVQRKYERLKQKIKEQLERDLEKNNERLA 405
Query: 261 EMEREEFYRLKKIQDKKREALERRTREQIE---RHLKEEEEHLKHPI 304
+ REE R K ++ +ALE + R+Q+E EEE L+ +
Sbjct: 406 AI-REEKDRQKAAIEEDLQALESQLRQQLEAGKLEFNEEEYELELRL 451
>gnl|CDD|192537 pfam10329, DUF2417, Region of unknown function (DUF2417). This is
a region of a family of proteins conserved in fungi some
of whose members also have the Abhydrolase_1, pfam00561,
domain in their sequence. The function of this region is
not known.
Length = 227
Score = 31.5 bits (72), Expect = 0.41
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 110 RRPMFYVFNLILPCILINCIALLVFYVPSESGEKVTLGISALLSMTVFLMTI 161
R F +L L I N I L F VPS E+V + A+L + ++ +
Sbjct: 65 RGSGFLDLDLTLLAIGANLITLWFFSVPS-KLERVLGYVLAVLLLIDLIIIL 115
>gnl|CDD|218896 pfam06098, Radial_spoke_3, Radial spoke protein 3. This family
consists of several radial spoke protein 3 (RSP3)
sequences. Eukaryotic cilia and flagella present in
diverse types of cells perform motile, sensory, and
developmental functions in organisms from protists to
humans. They are centred by precisely organised,
microtubule-based structures, the axonemes. The axoneme
consists of two central singlet microtubules, called the
central pair, and nine outer doublet microtubules. These
structures are well-conserved during evolution. The
outer doublet microtubules, each composed of A and B
sub-fibres, are connected to each other by nexin links,
while the central pair is held at the centre of the
axoneme by radial spokes. The radial spokes are T-shaped
structures extending from the A-tubule of each outer
doublet microtubule to the centre of the axoneme. Radial
spoke protein 3 (RSP3), is present at the proximal end
of the spoke stalk and helps in anchoring the radial
spoke to the outer doublet. It is thought that radial
spokes regulate the activity of inner arm dynein through
protein phosphorylation and dephosphorylation.
Length = 288
Score = 31.6 bits (72), Expect = 0.51
Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 15/65 (23%)
Query: 250 RTLDYIKSELDEMEREEFYRLKKIQDK-------------KREALERRTREQIERHLKEE 296
+TL+ ++ L+ +E EE L++ Q + + E ERR RE+ ER K++
Sbjct: 139 KTLE--QALLEVLEEEELAELRQQQRQFEQRRNAELAETQRLEEAERRRREEKERRKKQD 196
Query: 297 EEHLK 301
+E +
Sbjct: 197 KERKQ 201
>gnl|CDD|220368 pfam09730, BicD, Microtubule-associated protein Bicaudal-D. BicD
proteins consist of three coiled-coiled domains and are
involved in dynein-mediated minus end-directed transport
from the Golgi apparatus to the endoplasmic reticulum
(ER). For full functioning they bind with GSK-3beta
pfam05350 to maintain the anchoring of microtubules to
the centromere. It appears that amino-acid residues
437-617 of BicD and the kinase activity of GSK-3 are
necessary for the formation of a complex between BicD
and GSK-3beta in intact cells.
Length = 711
Score = 31.3 bits (71), Expect = 0.66
Identities = 31/116 (26%), Positives = 55/116 (47%), Gaps = 24/116 (20%)
Query: 191 DELLPTRYRGRAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEY----VVIP 246
DE+ ++R Q+++ LE + +L K + + R + +E+ I
Sbjct: 83 DEIKEYKFREARLLQDYS---------ELEEENISLQKQV--SVLRQSQVEFEGLKHEIR 131
Query: 247 RLARTLDYIKSELDEMEREEFYRLKKIQDKK-REALE--RRTREQIERHLKEEEEH 299
RL + + S+L+E RLK+I +K+ EALE + REQ + L++E H
Sbjct: 132 RLEEETELLNSQLEEAA-----RLKEIAEKQLEEALETLKTEREQ-KNALRKELSH 181
>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 = 30.4 bits (69), Expect = 0.85
Identities = 19/46 (41%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 256 KSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
E E ER+E L++ ++KK+E ER+ RE+ R KE+EE+ K
Sbjct: 34 LEEKREGERKEEEELEEEREKKKEEEERKEREEQAR--KEQEEYEK 77
Score = 28.1 bits (63), Expect = 4.4
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 258 ELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLKHP 303
E +E EREE R K + ++ E E E+ KEEEE +
Sbjct: 22 EAEEEEREE--RKKLEEKREGERKEEEELEEEREKKKEEEERKERE 65
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.0 bits (71), Expect = 0.92
Identities = 11/53 (20%), Positives = 32/53 (60%), Gaps = 5/53 (9%)
Query: 255 IKSELDEMEREEFYRLKKIQDK---KREALERRTR--EQIERHLKEEEEHLKH 302
+++EL+ +E L++++ + + E L+R+ ++ E +L+++E+ L +
Sbjct: 63 LRAELERELKERRNELQRLERRLLQREETLDRKMESLDKKEENLEKKEKELSN 115
Score = 29.5 bits (67), Expect = 2.5
Identities = 22/87 (25%), Positives = 42/87 (48%), Gaps = 10/87 (11%)
Query: 225 TLNKVIRQTNQRVNALEYV--VIPRLARTLDYIKSELDEMEREEFYRLKKI----QDKKR 278
TL++ + +++ LE + + LD + EL+E+ E+ L++I Q++ +
Sbjct: 91 TLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERISGLTQEEAK 150
Query: 279 EAL----ERRTREQIERHLKEEEEHLK 301
E L E R + + +KE EE K
Sbjct: 151 EILLEEVEEEARHEAAKLIKEIEEEAK 177
>gnl|CDD|227862 COG5575, ORC2, Origin recognition complex, subunit 2 [DNA
replication, recombination, and repair].
Length = 535
Score = 30.8 bits (69), Expect = 1.1
Identities = 13/39 (33%), Positives = 16/39 (41%)
Query: 260 DEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
+ K K R A RR R +IERHL E +
Sbjct: 63 PRTPGHRIIKAKGAYTKDRSAKRRRGRIEIERHLLGEFD 101
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 30.6 bits (70), Expect = 1.1
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 13/68 (19%)
Query: 233 TNQRVNALEYVVI----------PRLARTLDYIKSELDEMEREEFYRLKKIQDKKREALE 282
T Q + L+ I RL + ++ IK EL+E + F + K+ + +R LE
Sbjct: 231 TGQVIGELDRFTIYPASHYVTPRERLEQAIESIKEELEE-RLKFFEKNNKLLEAQR--LE 287
Query: 283 RRTREQIE 290
+RT +E
Sbjct: 288 QRTEYDLE 295
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 30.4 bits (69), Expect = 1.2
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 248 LARTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLKH 302
LA+ + ++++EL+E +R KK + + + E R EQ+ER LKE E K
Sbjct: 228 LAQEIAHLRNELEEAQRSLESLEKKFRSEGGDLFEER--EQLERQLKEIEAARKA 280
Score = 28.1 bits (63), Expect = 7.0
Identities = 22/99 (22%), Positives = 44/99 (44%), Gaps = 7/99 (7%)
Query: 208 TLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMERE-- 265
T+P + + LE + N++ R + L + L ++ ++ LDE ++
Sbjct: 416 TIPSEEQIAQLLEELGEAQNELFRSEAEIEELLR--QLETLKEAIEALRKTLDEKTKQKI 473
Query: 266 ---EFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
E R I DK ++ L+ + +ER L++ EE +
Sbjct: 474 NAFELERAITIADKAKKTLKEFREKLLERKLQQLEEEIT 512
>gnl|CDD|214415 MTH00065, ND6, NADH dehydrogenase subunit 6; Provisional.
Length = 172
Score = 29.8 bits (68), Expect = 1.3
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 18/75 (24%)
Query: 97 EPYPD------ITYYISLRRRPMFYVFNLILPCILINCIALLVFYVPSESGEKVTL---- 146
EPYP+ + Y+ +FY+ LI+ IL C L F + E +
Sbjct: 76 EPYPEAWGSWSVLVYV------LFYLLLLIVGYILFGCNFSLEFLFTNYDTEFSVVGYDW 129
Query: 147 -GISALLSM-TVFLM 159
G+ + S FLM
Sbjct: 130 GGVGLMYSSGGWFLM 144
>gnl|CDD|220555 pfam10079, DUF2317, Uncharacterized protein conserved in bacteria
(DUF2317). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 541
Score = 30.2 bits (69), Expect = 1.3
Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 243 VVIPRLARTL--DYIKSELDEMER--EEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
+++PRL+ TL ++ +LD++ E+ + L ++ K + LE + +I+ +E +
Sbjct: 374 ILLPRLSATLIEPKVEKKLDKLGLSIEDVF-LHGLELLKEKVLEEKANSEIDIDFEEAKA 432
Query: 299 HLKH 302
L+
Sbjct: 433 ELEA 436
>gnl|CDD|220719 pfam10368, YkyA, Putative cell-wall binding lipoprotein. YkyA is a
family of proteins containing a lipoprotein signal and a
hydrolase domain. It is similar to cell wall binding
proteins and might also be recognisable by a host immune
defence system. It is thus likely to belong to pathways
important for pathogenicity.
Length = 205
Score = 29.6 bits (67), Expect = 1.4
Identities = 22/103 (21%), Positives = 47/103 (45%), Gaps = 6/103 (5%)
Query: 202 AQSQEFTLPEQVRPLASLET-SHKTLNKVIRQT---NQRVNALEYVVIPRLARTLDYIKS 257
A QE E+ + L LE + +++I+ N+ + L + + + +K
Sbjct: 28 AAEQEKPFEEEQKKLEELEKKEQELYDQIIQLGKDDNEAIKKLSDQALANVDKREKLLKK 87
Query: 258 ELDEMER--EEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
E + +E+ EEF KK +K + ++ +Q+ + +KE +
Sbjct: 88 EKESIEKSEEEFKSAKKYIEKIEDKKLKKKAKQLVKVMKERYK 130
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 30.2 bits (68), Expect = 1.5
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 5/44 (11%)
Query: 255 IKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
I+ +DE E+F +++K+RE LE+ +E+ ER + EE+
Sbjct: 237 IEGGMDEHSFEDFL----LEEKRRE-LEKLAKEEAERERQAEEQ 275
>gnl|CDD|218152 pfam04568, IATP, Mitochondrial ATPase inhibitor, IATP. ATP
synthase inhibitor prevents the enzyme from switching to
ATP hydrolysis during collapse of the electrochemical
gradient, for example during oxygen deprivation ATP
synthase inhibitor forms a one to one complex with the
F1 ATPase, possibly by binding at the alpha-beta
interface. It is thought to inhibit ATP synthesis by
preventing the release of ATP. The minimum inhibitory
region for bovine inhibitor is from residues 39 to 72.
The inhibitor has two oligomeric states, dimer (the
active state) and tetramer. At low pH, the inhibitor
forms a dimer via antiparallel coiled coil interactions
between the C terminal regions of two monomers. At high
pH, the inhibitor forms tetramers and higher oligomers
by coiled coil interactions involving the N terminus and
inhibitory region, thus preventing the inhibitory
activity.
Length = 90
Score = 28.1 bits (63), Expect = 1.5
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 5/42 (11%)
Query: 261 EMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLKH 302
E +EE Y + K++E L +E++E H KE EE KH
Sbjct: 52 EAAQEEEY----FRQKEKEQL-AALKEKLEEHKKEIEELEKH 88
>gnl|CDD|153101 cd01042, DMQH, Demethoxyubiquinone hydroxylase, ferritin-like
diiron-binding domain. Demethoxyubiquinone hydroxylases
(DMQH) are members of the ferritin-like,
diiron-carboxylate family which are present in
eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the
Coq7 family). DMQH participates in one of the last steps
of ubiquinone biosysnthesis and is responsible for DMQ
hydroxylation, resulting in the formation of
hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a
mitochondrial inner membrane protein and Coq7 is a
proposed interfacial integral membrane protein.
Mutations in the Caenorhabditis elegans gene clk-1
affect biological timing and extend longevity. The
conserved residues of a diiron center are present in
this domain.
Length = 165
Score = 29.4 bits (67), Expect = 1.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 284 RTREQIERHLKEEEEHLK 301
R I+ L EE++HL
Sbjct: 30 AVRPLIKEMLDEEKDHLA 47
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 30.0 bits (68), Expect = 1.6
Identities = 21/91 (23%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 211 EQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRL 270
E+ + L + ++ + + + + LE + + L+ +K E++E+E+E
Sbjct: 197 EKEKELEEVLREINEISSELPELREELEKLE-----KEVKELEELKEEIEELEKELESLE 251
Query: 271 KKIQDKKREALERRTREQIERHLKEEEEHLK 301
+K E R E+IE LK+E E L+
Sbjct: 252 GSK--RKLEEKIRELEERIEE-LKKEIEELE 279
Score = 28.9 bits (65), Expect = 4.0
Identities = 27/89 (30%), Positives = 47/89 (52%), Gaps = 6/89 (6%)
Query: 212 QVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLK 271
Q+ L E ++K L +VI++ +R+ LE + RT + I+ + E E+E L+
Sbjct: 153 QILGLDDYENAYKNLGEVIKEIKRRIERLEKF----IKRTEN-IEELIKEKEKELEEVLR 207
Query: 272 KIQDKKREALE-RRTREQIERHLKEEEEH 299
+I + E E R E++E+ +KE EE
Sbjct: 208 EINEISSELPELREELEKLEKEVKELEEL 236
>gnl|CDD|190882 pfam04144, SCAMP, SCAMP family. In vertebrates, secretory carrier
membrane proteins (SCAMPs) 1-3 constitute a family of
putative membrane-trafficking proteins composed of
cytoplasmic N-terminal sequences with NPF repeats, four
central transmembrane regions (TMRs), and a cytoplasmic
tail. SCAMPs probably function in endocytosis by
recruiting EH-domain proteins to the N-terminal NPF
repeats but may have additional functions mediated by
their other sequences.
Length = 177
Score = 29.1 bits (66), Expect = 1.9
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 94 CCVEP--YPDITYYI--SLRR--RPMFYVFNLILPCILINCIALLVFYVPSESGEKVTLG 147
C V+P Y DI+ I +R ++Y++ ++ + N IA L ++ G G
Sbjct: 12 CPVKPCFYHDISEEIPVEYQRLVYFLYYLWLGLVLTLFYNIIACLALFIGGGGG--TDFG 69
Query: 148 ISAL 151
+S L
Sbjct: 70 LSIL 73
>gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase.
Ribonucleotide reductase (RNR) catalyzes the reductive
synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in strict or facultative anaerobic bacteria,
bacteriophage, and archaea, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Many
organisms have more than one class of RNR present in
their genomes. All three RNRs have a ten-stranded
alpha-beta barrel domain that is structurally similar to
the domain of PFL (pyruvate formate lyase). The class
III enzyme from phage T4 consists of two subunits, this
model covers the larger subunit which contains the
active and allosteric sites.
Length = 555
Score = 29.6 bits (67), Expect = 2.1
Identities = 20/97 (20%), Positives = 40/97 (41%), Gaps = 15/97 (15%)
Query: 205 QEFTLPEQVRPL---ASLETSHKTLNKVIRQTNQRVNALEYVVI--PRLARTLDYIKSEL 259
+P VR + L+ + + + + V I PR+A ++
Sbjct: 252 NSDNVPGDVRAMGCRLFLDKNELKRGGGLEGSGDGTGNIGVVTINLPRIA-----YEARG 306
Query: 260 DEMEREEFY-RLKKIQDKKREALERRTREQIERHLKE 295
DE E+F+ L + + ++ALE R R++++ L
Sbjct: 307 DE---EKFFELLDEYLELAKDALEIR-RKRLKEALAR 339
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.7 bits (67), Expect = 2.2
Identities = 22/81 (27%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 224 KTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELD--EMEREEFYRLKKIQDKKREAL 281
+ L +VI++ ++ LE +L+ L+ I+ L+ E E +E +L++IQ+++ E
Sbjct: 174 ELLKEVIKEAKAKIEELEG----QLSELLEDIEDLLEALEEELKELKKLEEIQEEQEEEE 229
Query: 282 ERRTREQIERHLKEEEEHLKH 302
+ E +E L E EE +
Sbjct: 230 LEQEIEALEERLAELEEEKER 250
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 2.4
Identities = 22/103 (21%), Positives = 46/103 (44%), Gaps = 6/103 (5%)
Query: 201 RAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVI--PRLARTLDYIKSE 258
+ +++E E+ + +E K + ++ + A E I A+ + K +
Sbjct: 1619 KIKAEELKKAEEEK--KKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKK 1676
Query: 259 LDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
+E ++ E K + K+EA E + E++++ KE EE K
Sbjct: 1677 AEEAKKAEEDEKKAAEALKKEAEEAKKAEELKK--KEAEEKKK 1717
Score = 27.8 bits (61), Expect = 8.9
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 249 ARTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEH 299
A+ + K + +E+++ E + K Q KK+EA E++ E+++ K EEE+
Sbjct: 1612 AKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAEELK---KAEEEN 1659
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 29.2 bits (66), Expect = 2.8
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 247 RLARTLDYIKSELDEMEREEFYRLKK-IQDKKREALE---RRTREQIERHLKEE 296
L L+ ++ L++ R EF R K+ ++ K E L R E E+ LK E
Sbjct: 208 ELLARLESKEAALEKQLRLEFEREKEELRKKYEEKLRQELERQAEAHEQKLKNE 261
Score = 28.8 bits (65), Expect = 3.9
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 252 LDYIKSELDEMEREEFYRLKKIQDKKRE----ALERRTREQIERHLKEEEEHLKH 302
LD + +L E++ EE L++ +KRE LE ++E E+ L+
Sbjct: 172 LDQLSKKLAELKAEEEEELERALKEKREELLSKLEEELLARLESKEAALEKQLRL 226
>gnl|CDD|222665 pfam14303, NAM-associated, No apical meristem-associated C-terminal
domain. This domain is found in a number of different
types of plant proteins including NAM-like proteins.
Length = 147
Score = 28.5 bits (64), Expect = 2.9
Identities = 11/43 (25%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 256 KSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
++E ++ + E F + +K+R LE +++ E L +EE+
Sbjct: 83 EAEKEKEKEERFMKALAEAEKERAELE---KKKAEAKLMKEEK 122
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 29.3 bits (65), Expect = 3.1
Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 224 KTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSEL------DEMEREEFYRLKK--IQD 275
K L++V+++ QR+N L IP + D ++ EL + + YR KK I++
Sbjct: 38 KKLDEVVKRIVQRINELYDGKIPHIENIQDIVELELMRAGLFEVAKAYILYRKKKAEIRE 97
Query: 276 KKREALERRTREQIER 291
+K+ L ++ ++I++
Sbjct: 98 EKKRILNKKELDEIDK 113
>gnl|CDD|218511 pfam05227, CHASE3, CHASE3 domain. CHASE3 is an extracellular
sensory domain, which is present in various classes of
transmembrane receptors that are parts of signal
transduction pathways in bacteria. Specifically, CHASE3
domains are found in histidine kinases, adenylate
cyclases, methyl-accepting chemotaxis proteins and
predicted diguanylate cyclases/phosphodiesterases.
Environmental factors that are recognised by CHASE3
domains are not known at this time.
Length = 138
Score = 28.0 bits (63), Expect = 3.3
Identities = 22/84 (26%), Positives = 28/84 (33%), Gaps = 17/84 (20%)
Query: 210 PEQVRPLASLETSHKT----LNKVI--RQTNQRVNALEYVVIPRLARTLDYIKSELDEME 263
PEQ L LE L + I R+ AL V +D I++ + EM
Sbjct: 66 PEQQERLDRLEALIDQRLEELEETIALRREGGLDAALALVRSGEGKALMDEIRALIAEMI 125
Query: 264 REEFYRLKKIQDKKREALERRTRE 287
EE R L R E
Sbjct: 126 AEE-----------RRLLAERNAE 138
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 28.8 bits (64), Expect = 3.5
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 257 SELDEMEREEFYRLKKI----QDKKREALERRTREQIERH-LKEEEE 298
EL+E++++ R K + Q +K+E +R++RE+ E+ LKEE E
Sbjct: 214 LELEELKKKREERRKVLEEEEQRRKQEEADRKSREEEEKRRLKEEIE 260
>gnl|CDD|222253 pfam13597, NRDD, Anaerobic ribonucleoside-triphosphate reductase.
Length = 542
Score = 28.7 bits (65), Expect = 4.1
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 263 EREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLKH 302
+ E F L + KR+ +E + K+ L +
Sbjct: 297 DEEFFEELDRYDLAKRKLIEELIAAGLLPFYKQYLWRLDN 336
>gnl|CDD|148679 pfam07218, RAP1, Rhoptry-associated protein 1 (RAP-1). This family
consists of several rhoptry-associated protein 1 (RAP-1)
sequences which appear to be specific to Plasmodium
falciparum.
Length = 790
Score = 28.9 bits (64), Expect = 4.2
Identities = 28/109 (25%), Positives = 52/109 (47%), Gaps = 15/109 (13%)
Query: 200 GRAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSEL 259
G + E P L LE + +TN + AL++ + +L +D +K++
Sbjct: 187 GIVGADEEAPPAPKNTLTPLEELY--------ETNVNLFALKHP-LEKLEEEIDILKNDG 237
Query: 260 DEMEREEFYRL----KKIQDKKREALERRTREQIERHLK--EEEEHLKH 302
D++ EE + L ++ ++ K+EALE+ E E K EE + ++H
Sbjct: 238 DKVAEEEEFELDEEHEEAEEDKKEALEKIGAEGDEEKFKFDEEIKFIEH 286
>gnl|CDD|179382 PRK02195, PRK02195, V-type ATP synthase subunit D; Provisional.
Length = 201
Score = 28.4 bits (64), Expect = 4.2
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 226 LNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLK----KIQDKKR 278
L + +R+T QRVN E V+IP + IK L + E R K KI+ +K
Sbjct: 145 LEEELRKTTQRVNLFEKVLIPETKANIKKIKIFLGDQETAAVVRQKIAKKKIEKRKE 201
>gnl|CDD|234017 TIGR02794, tolA_full, TolA protein. TolA couples the inner
membrane complex of itself with TolQ and TolR to the
outer membrane complex of TolB and OprL (also called
Pal). Most of the length of the protein consists of
low-complexity sequence that may differ in both length
and composition from one species to another,
complicating efforts to discriminate TolA (the most
divergent gene in the tol-pal system) from paralogs such
as TonB. Selection of members of the seed alignment and
criteria for setting scoring cutoffs are based largely
conserved operon struction. //The Tol-Pal complex is
required for maintaining outer membrane integrity. Also
involved in transport (uptake) of colicins and
filamentous DNA, and implicated in pathogenesis.
Transport is energized by the proton motive force. TolA
is an inner membrane protein that interacts with
periplasmic TolB and with outer membrane porins ompC,
phoE and lamB [Transport and binding proteins, Other,
Cellular processes, Pathogenesis].
Length = 346
Score = 28.6 bits (64), Expect = 4.2
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 255 IKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
I+ + ++E R KK++ + EA ++R EQ KE E+
Sbjct: 55 IQQQKKPAAKKEQERQKKLEQQAEEAEKQRAAEQ--ARQKELEQRAA 99
>gnl|CDD|153281 cd07597, BAR_SNX8, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 8. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX8 and the yeast counterpart Mvp1p
are involved in sorting and delivery of late-Golgi
proteins, such as carboxypeptidase Y, to vacuoles. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 246
Score = 28.4 bits (64), Expect = 4.4
Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 226 LNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQ--DKKREALER 283
+ + A E V+ +L LD + S D ER E L IQ K+ E ++
Sbjct: 100 FQLLSDLSEDEARAEEDGVLEKLKLQLDLLVSLRDLFERHEKLSLNNIQRLLKRIELNKK 159
Query: 284 R 284
+
Sbjct: 160 K 160
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 28.7 bits (65), Expect = 4.6
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 13/60 (21%)
Query: 247 RLARTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTRE--------QIERHLKEEEE 298
RL + LD ++ E+D ++ E K+I+ K +E +E+ RE I++ L E+++
Sbjct: 193 RLEKLLDLLEKEIDLLQLE-----KRIRKKVKEQMEKSQREYYLREQLKAIQKELGEDDD 247
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 28.5 bits (64), Expect = 5.1
Identities = 19/103 (18%), Positives = 37/103 (35%), Gaps = 21/103 (20%)
Query: 214 RPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEM---------ER 264
P A L + V R+ + P A +D +K+ L ++ E+
Sbjct: 131 PPPALLVSPEDAQRSV------RLAIYYGALNPARAERIDALKATLKQLAAVRAEIAAEQ 184
Query: 265 EEFYRLKKIQDKKREALER------RTREQIERHLKEEEEHLK 301
E L Q ++ L + +T Q+ L +++ L+
Sbjct: 185 AELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELSADQKKLE 227
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 28.6 bits (64), Expect = 5.1
Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 9/104 (8%)
Query: 209 LPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREE-- 266
L E L LE L + +R QR ++ R A L +++ D++ R+
Sbjct: 232 LDEYRDELERLEA----LERALRNFLQRYRRYARTMLRRRATRLRSAQTQYDQLSRDLGR 287
Query: 267 -FYRLKKIQDKKREALERRTREQIERH-LKEEEEHLK-HPIFQK 307
L+ ++++RE R + E L+ E L+ P +Q
Sbjct: 288 ARDELETAREEERELDARTEALEREADALRTRLEALQGSPAYQD 331
>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 = 5.1
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 4/52 (7%)
Query: 250 RTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
R K +E + +E R ++I+++KR ER+ +++E+ LKE +E LK
Sbjct: 30 RKQQRRKKAQEEAKEKE--REERIEERKRIREERK--QELEKQLKERKEALK 77
>gnl|CDD|238383 cd00751, thiolase, Thiolase are ubiquitous enzymes that catalyze
the reversible thiolytic cleavage of 3-ketoacyl-CoA into
acyl-CoA and acetyl-CoA, a 2-step reaction involving a
covalent intermediate formed with a catalytic cysteine.
They are found in prokaryotes and eukaryotes (cytosol,
microbodies and mitochondria). There are 2 functional
different classes: thiolase-I (3-ketoacyl-CoA thiolase)
and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I
can cleave longer fatty acid molecules and plays an
important role in the beta-oxidative degradation of
fatty acids. Thiolase-II has a high substrate
specificity. Although it can cleave acetoacyl-CoA, its
main function is the synthesis of acetoacyl-CoA from two
molecules of acetyl-CoA, which gives it importance in
several biosynthetic pathways.
Length = 386
Score = 28.2 bits (64), Expect = 5.3
Identities = 10/32 (31%), Positives = 13/32 (40%)
Query: 190 ADELLPTRYRGRAQSQEFTLPEQVRPLASLET 221
DE++P GR E RP +LE
Sbjct: 191 KDEIVPVEVPGRKGPVVVDRDEGPRPDTTLEK 222
>gnl|CDD|221250 pfam11831, Myb_Cef, pre-mRNA splicing factor component. This
family is a region of the Myb-Related Cdc5p/Cef1
proteins, in fungi, and is part of the pre-mRNA splicing
factor complex.
Length = 363
Score = 28.5 bits (64), Expect = 5.4
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 253 DYIKSELDEMEREEFYRLKKIQDKKREALERRTREQI 289
+ E D +R+ K+ ++ +E E R R Q+
Sbjct: 160 MEEELEEDAADRD---ARKRAAEEAKEQEELRRRSQV 193
>gnl|CDD|173502 PTZ00266, PTZ00266, NIMA-related protein kinase; Provisional.
Length = 1021
Score = 28.5 bits (63), Expect = 5.5
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 261 EMEREEFYRLKKIQDKKREALERRTREQIERHLKEEE 297
EM+ E R+++++ ++RE LER E+IER E E
Sbjct: 451 EMKILEKKRIERLEREERERLERERMERIERERLERE 487
Score = 28.5 bits (63), Expect = 6.2
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 6/42 (14%)
Query: 256 KSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEE 297
K ++ +EREE RL+ RE +ER RE++ER E E
Sbjct: 457 KKRIERLEREERERLE------RERMERIERERLERERLERE 492
>gnl|CDD|218678 pfam05656, DUF805, Protein of unknown function (DUF805). This
family consists of several bacterial proteins of unknown
function.
Length = 112
Score = 26.9 bits (60), Expect = 5.8
Identities = 11/56 (19%), Positives = 23/56 (41%), Gaps = 5/56 (8%)
Query: 108 LRRRP--MFYVFNLILPCILINCIALLVFYVPSESGEKVTLGISALLSMTVFLMTI 161
R F +FN++ I + + L S S + L+S+ +F+ ++
Sbjct: 9 ASRSEYWWFVLFNIL---ITLVLLILAALLSGSSSLLSGGGLLLGLISLAIFIPSL 61
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 28.2 bits (64), Expect = 6.3
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 224 KTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQDKKREALER 283
L K+ ++ Q+ L+ R L+ + EL++ + +E + ++ +KK E LE
Sbjct: 82 NELQKLEKRLLQKEENLD-----RKLELLEKREEELEK-KEKELEQKQQELEKKEEELEE 135
Query: 284 RTREQIER 291
EQ++
Sbjct: 136 LIEEQLQE 143
Score = 27.4 bits (62), Expect = 9.6
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 10/87 (11%)
Query: 225 TLNKVIRQTNQRVNALEYVV--IPRLARTLDYIKSELDEMEREEFYRLKKI------QDK 276
L++ + +R LE + + + L+ + EL+E+ E+ L++I + K
Sbjct: 97 NLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELERISGLTAEEAK 156
Query: 277 KR--EALERRTREQIERHLKEEEEHLK 301
+ E +E R + +KE EE K
Sbjct: 157 EILLEKVEEEARHEAAVLIKEIEEEAK 183
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 28.4 bits (63), Expect = 6.4
Identities = 19/110 (17%), Positives = 42/110 (38%), Gaps = 4/110 (3%)
Query: 201 RAQSQEFTLPEQVRPLASLETSHKTLNKVIRQTNQRVNALEYVVIPRLARTLDYIKSELD 260
R+ +F L + + L S L+ + +Q + + L+ + R L +++EL
Sbjct: 20 RSDLPKF-LSQPLEGSHHLGVSTSALSSLQKQVEESMTLLQRAELIRSKSKLIQLENELM 78
Query: 261 EMEREEFYRLKKIQDKKREALERRTRE---QIERHLKEEEEHLKHPIFQK 307
+ E E +++ K E RE +E ++ + +
Sbjct: 79 QKELEHKRAQIELERKASTLAENYERELDRNLELEVRLKALEELEKKAEN 128
>gnl|CDD|218684 pfam05672, MAP7, MAP7 (E-MAP-115) family. The organisation of
microtubules varies with the cell type and is presumably
controlled by tissue-specific microtubule-associated
proteins (MAPs). The 115-kDa epithelial MAP
(E-MAP-115/MAP7) has been identified as a
microtubule-stabilising protein predominantly expressed
in cell lines of epithelial origin. The binding of this
microtubule associated protein is nucleotide
independent.
Length = 171
Score = 27.4 bits (60), Expect = 6.7
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 247 RLARTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
R AR + E + E+EE RL++ + K+R A ER RE+ R +EE K
Sbjct: 33 RQAR-EQREQEEQERREQEEQDRLEREELKRRAAEERLRREEEARRQEEERAREK 86
Score = 27.4 bits (60), Expect = 7.9
Identities = 15/39 (38%), Positives = 27/39 (69%), Gaps = 2/39 (5%)
Query: 263 EREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
+ EE RL + +K+R+A E+R +E+ ER +EE++ L+
Sbjct: 20 DAEEATRL--LAEKRRQAREQREQEEQERREQEEQDRLE 56
>gnl|CDD|240579 cd12931, eNOPS_SF, NOPS domain, including C-terminal helical
extension region, in the p54nrb/PSF/PSP1 family. All
members in this family contain a DBHS domain (for
Drosophila behavior, human splicing), which comprises
two conserved RNA recognition motifs (RRM1 and RRM2),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a charged
protein-protein interaction NOPS (NONA and PSP1) domain
with a long helical C-terminal extension. The NOPS
domain specifically binds to RRM2 domain of the partner
DBHS protein via a substantial interaction surface. Its
highly conserved C-terminal residues are critical for
functional DBHS dimerization while the highly conserved
C-terminal helical extension, forming a right-handed
antiparallel heterodimeric coiled-coil, is essential for
localization of these proteins to subnuclear bodies. PSF
has an additional large N-terminal domain that
differentiates it from other family members. The
p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and
DNA-binding protein (p54nrb), polypyrimidine
tract-binding protein (PTB)-associated-splicing factor
(PSF) and paraspeckle protein 1 (PSP1), which are
ubiquitously expressed and are well conserved in
vertebrates. p54nrb, also termed NONO or NMT55, is a
multi-functional protein involved in numerous nuclear
processes including transcriptional regulation,
splicing, DNA unwinding, nuclear retention of
hyperedited double-stranded RNA, viral RNA processing,
control of cell proliferation, and circadian rhythm
maintenance. PSF, also termed POMp100, is also a
multi-functional protein that binds RNA, single-stranded
DNA (ssDNA), double-stranded DNA (dsDNA) and many
factors, and mediates diverse activities in the cell.
PSP1, also termed PSPC1, is a novel nucleolar factor
that accumulates within a new nucleoplasmic compartment,
termed paraspeckles, and diffusely distributes in the
nucleoplasm. The cellular function of PSP1 remains
unknown currently. The family also includes some
p54nrb/PSF/PSP1 homologs from invertebrate species. For
instance, the Drosophila melanogaster gene
no-ontransient A (nonA) encoding puff-specific protein
Bj6 (also termed NONA) and Chironomus tentans hrp65 gene
encoding protein Hrp65. D. melanogaster NONA is involved
in eye development and behavior and may play a role in
circadian rhythm maintenance, similar to vertebrate
p54nrb. C. tentans Hrp65 is a component of nuclear
fibers associated with ribonucleoprotein particles in
transit from the gene to the nuclear pore.
Length = 90
Score = 26.4 bits (59), Expect = 6.9
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 276 KKREALERRTREQIERHLKEEEEHLKH 302
K LE++ REQ+E+ LKE E L+
Sbjct: 54 KALYELEKQQREQLEKELKEAREKLEA 80
Score = 26.1 bits (58), Expect = 9.9
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 241 EYVVIPRLAR--TLDYIKS----ELDEMEREEFYRLKKIQDKKREALERRTREQIERHLK 294
E V PR A + +Y L E+E+++ +L+K + RE LE ++E
Sbjct: 32 EREVGPRFAPPGSFEYEFGQRWKALYELEKQQREQLEKELKEAREKLE----AEMEAARY 87
Query: 295 EEE 297
E +
Sbjct: 88 EHQ 90
>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 = 28.0 bits (63), Expect = 6.9
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 258 ELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
E +E+E+E + + + + R LE++ E+ ER E EE L+
Sbjct: 270 EDEELEQENAEKRRMKRLEHRRELEQQIEEKEERRAAEREEELE 313
>gnl|CDD|235131 PRK03562, PRK03562, glutathione-regulated potassium-efflux system
protein KefC; Provisional.
Length = 621
Score = 28.0 bits (63), Expect = 7.0
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 265 EEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
EE + KKR A+ ++T + + E+ EHL
Sbjct: 557 EEMAPHENDT-KKRAAVAKQTSAMLSEIITEDREHLS 592
>gnl|CDD|239285 cd02987, Phd_like_Phd, Phosducin (Phd)-like family, Phd subfamily;
Phd is a cytosolic regulator of G protein functions. It
specifically binds G protein betagamma (Gbg)-subunits
with high affinity, resulting in the solubilization of
Gbg from the plasma membrane. This impedes the formation
of a functional G protein trimer (G protein
alphabetagamma), thereby inhibiting G protein-mediated
signal transduction. Phd also inhibits the GTPase
activity of G protein alpha. Phd can be phosphorylated
by protein kinase A and G protein-coupled receptor
kinase 2, leading to its inactivation. Phd was
originally isolated from the retina, where it is highly
expressed and has been implicated to play an important
role in light adaptation. It is also found in the pineal
gland, liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain.
Length = 175
Score = 27.3 bits (61), Expect = 7.1
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 6/59 (10%)
Query: 247 RLARTLDYIKSELDEME--REEF---YRLKKIQDKKREALERRTREQIERHLKEEEEHL 300
R + L + E D+ + +EEF YR +++Q+ + R ++ L E+ L
Sbjct: 17 RKFKQLKESEQEDDDDDEDKEEFLQQYREQRMQEMHAKLPFGRRFGKV-YELDSGEQFL 74
>gnl|CDD|204935 pfam12474, PKK, Polo kinase kinase. This domain family is found in
eukaryotes, and is approximately 140 amino acids in
length. The family is found in association with
pfam00069. Polo-like kinase 1 (Plx1) is essential during
mitosis for the activation of Cdc25C, for spindle
assembly, and for cyclin B degradation. This family is
Polo kinase kinase (PKK) which phosphorylates Polo
kinase and Polo-like kinase to activate them. PKK is a
serine/threonine kinase.
Length = 142
Score = 26.9 bits (60), Expect = 7.8
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 261 EMEREEFYRLKKIQDKKREALERRTREQIERHLKEEEEHLK 301
+ER + L K +K+ E LER+ + IE+ + + + L+
Sbjct: 14 FLERTQ---LLKRHEKELEQLERQQKRTIEKLEQRQTQELR 51
>gnl|CDD|224477 COG1561, COG1561, Uncharacterized stress-induced protein [Function
unknown].
Length = 290
Score = 27.6 bits (62), Expect = 8.0
Identities = 19/78 (24%), Positives = 36/78 (46%), Gaps = 5/78 (6%)
Query: 230 IRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKIQDKKREALERRTREQI 289
I + + + ALE +++ L LD +L EM E LK ++ +A+E E++
Sbjct: 119 IEEEEEDLEALEALILAALEEALD----DLIEMREREGAALKADLLQRLDAIEELV-EKV 173
Query: 290 ERHLKEEEEHLKHPIFQK 307
E + E E + + +
Sbjct: 174 ESLMPEILEWYRERLVAR 191
>gnl|CDD|222677 pfam14319, Zn_Tnp_IS91, Transposase zinc-binding domain. This
domain is likely to be a zinc-binding domain. It is
found at the N-terminus of transposases belonging to the
IS91 family.
Length = 111
Score = 26.4 bits (59), Expect = 8.2
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 4/27 (14%)
Query: 191 DELLPTRYRGRAQSQEFTLPEQVRPLA 217
ELLP Y FTLP ++R LA
Sbjct: 80 AELLPVPYF---HVV-FTLPHELRALA 102
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 27.3 bits (61), Expect = 8.2
Identities = 17/78 (21%), Positives = 33/78 (42%), Gaps = 9/78 (11%)
Query: 226 LNKVIRQTNQRVNALEYVVIP---RLARTLDYIKSELDEMEREEFYRLKKIQD--KKREA 280
LN I+ +R+N+LE + + + I+ + +ER E K + + + E
Sbjct: 94 LNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLE----KNLAEAEARLEE 149
Query: 281 LERRTREQIERHLKEEEE 298
RE+ + + EE
Sbjct: 150 EVAEIREEGQELSSKREE 167
>gnl|CDD|191634 pfam06886, TPX2, Targeting protein for Xklp2 (TPX2). This family
represents a conserved region approximately 60 residues
long within the eukaryotic targeting protein for Xklp2
(TPX2). Xklp2 is a kinesin-like protein localised on
centrosomes throughout the cell cycle and on spindle
pole microtubules during metaphase. In Xenopus, it has
been shown that Xklp2 protein is required for centrosome
separation and maintenance of spindle bi-polarity. TPX2
is a microtubule-associated protein that mediates the
binding of the C-terminal domain of Xklp2 to
microtubules. It is phosphorylated during mitosis in a
microtubule-dependent way.
Length = 57
Score = 25.4 bits (56), Expect = 8.4
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 263 EREEFYRLKKIQDKKREALERRTREQIERHLKEEEE 298
+R EF KK+++K E +E+ E KEEEE
Sbjct: 9 KRAEFD--KKLEEK--EKALEAEKEEAEARQKEEEE 40
>gnl|CDD|100078 cd05709, S2P-M50, Site-2 protease (S2P) class of zinc
metalloproteases (MEROPS family M50) cleaves
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. Members of this family use
proteolytic activity within the membrane to transfer
information across membranes to integrate gene
expression with physiologic stresses occurring in
another cellular compartment. The domain core structure
appears to contain at least three transmembrane helices
with a catalytic zinc atom coordinated by three
conserved residues contained within the consensus
sequence HExxH, together with a conserved aspartate
residue. The S2P/M50 family of RIP proteases is widely
distributed; in eukaryotic cells, they regulate such
processes as sterol and lipid metabolism, and
endoplasmic reticulum (ER) stress responses. In
sterol-depleted mammalian cells, a two-step proteolytic
process releases the N-terminal domains of sterol
regulatory element-binding proteins (SREBPs) from
membranes of the ER. These domains translocate into the
nucleus, where they activate genes of cholesterol and
fatty acid biosynthesis. It is the second proteolytic
step that is carried out by the SREBP Site-2 protease
(S2P) which is present in this CD superfamily.
Prokaryotic S2P/M50 homologs have been shown to regulate
stress responses, sporulation, cell division, and cell
differentiation. In Escherichia coli, the S2P homolog
RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses, and in Bacillus
subtilis, the S2P homolog SpoIVFB is involved in the
pro-sigmaK pathway of spore formation. Some of the
subfamilies within this hierarchy contain one or two PDZ
domain insertions, with putative regulatory roles, such
as the inhibition of substrate cleavage as seen by the
RseP PDZ domain.
Length = 180
Score = 27.2 bits (61), Expect = 8.4
Identities = 14/69 (20%), Positives = 27/69 (39%), Gaps = 6/69 (8%)
Query: 96 VEPYPDITYYISLRRRPMFYV------FNLILPCILINCIALLVFYVPSESGEKVTLGIS 149
+P + R V NL+L +L+ + LL P+ G+ + G++
Sbjct: 58 AKPVGENPRAFKKPRWQRLLVALAGPLANLLLALLLLLLLLLLGGLPPAPVGQAASSGLA 117
Query: 150 ALLSMTVFL 158
LL+ +
Sbjct: 118 NLLAFLALI 126
>gnl|CDD|221739 pfam12730, ABC2_membrane_4, ABC-2 family transporter protein. This
family is related to the ABC-2 membrane transporter
family pfam01061.
Length = 230
Score = 27.3 bits (61), Expect = 9.1
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 108 LRRRPMFYVFNLILPCILINCIALLVFYVPSESGEKVTLGISALLSMTVFLMTI 161
L+R +F + LILP +L LL +L +S+ ++ + +
Sbjct: 7 LKRTKIFLIL-LILPLLLALLALLLFGVNGDTGLSPGSLLLSSFSFLSALFLPL 59
>gnl|CDD|223419 COG0342, SecD, Preprotein translocase subunit SecD [Intracellular
trafficking and secretion].
Length = 506
Score = 27.7 bits (62), Expect = 9.2
Identities = 20/105 (19%), Positives = 32/105 (30%), Gaps = 2/105 (1%)
Query: 169 ENISEYVLVSSDHFRVKYIIVADELLPTRYRGRAQSQEFTLPEQVRPLASLETSHKTLNK 228
E +S + + + A EL R R + L + E + +
Sbjct: 77 EGVSYSGVRVEGNGITVPLRDAAELDKARKLLRLLHRGVVLFLALTEAELDEIRKDAVQQ 136
Query: 229 VIRQTNQRVNALEYVVIPRLARTLDYIKSELDEMEREEFYRLKKI 273
I RVN L + D I EL ++ R K +
Sbjct: 137 NITILRNRVNELGVAEPVIQRQGADRIVVELPGVQDTA--RAKDL 179
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 27.6 bits (62), Expect = 9.5
Identities = 12/69 (17%), Positives = 32/69 (46%), Gaps = 4/69 (5%)
Query: 216 LASLETSHKTLNKVIRQTNQR----VNALEYVVIPRLARTLDYIKSELDEMEREEFYRLK 271
L LE + + K++++ ++ + + + +L T + + EL+E+E E +
Sbjct: 343 LKELEEELEKIKKLLKKLPKKARGQLPPEKREQLEKLLETKEKLSEELEELEEELKELKE 402
Query: 272 KIQDKKREA 280
+++ E
Sbjct: 403 ELESLYSEG 411
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 27.3 bits (61), Expect = 9.9
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 255 IKSELDEMEREEFYRLKKIQDKKREALERRTREQI---ERHLKEEEEHLKH 302
K+E E E+E +K +++ EA ER +E + ++ E E L
Sbjct: 211 AKAEAAEAEQELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAEREKLLA 261
>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 = 27.4 bits (61), Expect = 9.9
Identities = 11/43 (25%), Positives = 24/43 (55%)
Query: 255 IKSELDEMEREEFYRLKKIQDKKREALERRTREQIERHLKEEE 297
K L E E ++ + ++ ++++R ++ +E+ ER K EE
Sbjct: 180 AKKRLQEWELKKLKQQQQKREEERRKQRKKQQEEEERKQKAEE 222
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
0.321 0.137 0.394
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: 16,178,179
Number of extensions: 1603009
Number of successful extensions: 2661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2594
Number of HSP's successfully gapped: 199
Length of query: 309
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 212
Effective length of database: 6,635,264
Effective search space: 1406675968
Effective search space used: 1406675968
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: 59 (26.6 bits)