RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4716
(334 letters)
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 356 bits (916), Expect = e-120
Identities = 162/252 (64%), Positives = 204/252 (80%)
Query: 83 EDYVARMKENQKQIYYITGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYD 142
+DYV RMKE QK IYYITGE+K QV S F+ER+KK+G+EV+YMT+PIDEY +QQLK+++
Sbjct: 275 DDYVTRMKEGQKDIYYITGESKKQVEKSPFLERLKKKGYEVLYMTDPIDEYAMQQLKEFE 334
Query: 143 GKTLVSVTKEGLELPEDEEEKKKREEDKVKFENLCKVMKDILDKKVEKVIVSNRLVDSPC 202
GK LV+VTKEGL+L E EEEKKKREE K +FE LCK MKDIL KVEKV+VSNRLVDSPC
Sbjct: 335 GKKLVNVTKEGLKLEESEEEKKKREELKKEFEELCKWMKDILGDKVEKVVVSNRLVDSPC 394
Query: 203 CIVTSQYGWTANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKADADKNDK 262
+VTSQYGW+ANMERIMKAQALRD+S YM++KK LEINP H I++ LR++ +ADKNDK
Sbjct: 395 ALVTSQYGWSANMERIMKAQALRDSSMSAYMSSKKTLEINPRHPIIKELRKRVEADKNDK 454
Query: 263 AVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRMIKLGLGIEDEDEVATGDDVKAGDIPV 322
VKDL LL+ET+LL+SGF+LE+P+ A+RI+RMIKLGL I++++EV D+ +
Sbjct: 455 TVKDLARLLYETALLTSGFSLEDPKAFASRIYRMIKLGLSIDEDEEVEEEDEEAEVETTE 514
Query: 323 AEGEAEDASRME 334
E + S+ME
Sbjct: 515 PAEEDAEDSKME 526
Score = 42.1 bits (99), Expect = 3e-04
Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 48 RLLVEKEREKELSEDEEEEKKEE--EKEEDKTPKLEDEDYVARMKENQKQIYYITGETKD 105
L VEKE EKE+ ++EEEE+KEE E+EE T K E+ D +E +K+ + T +
Sbjct: 24 YLWVEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTE 83
>gnl|CDD|240341 PTZ00272, PTZ00272, heat shock protein 83 kDa (Hsp83); Provisional.
Length = 701
Score = 270 bits (691), Expect = 5e-85
Identities = 132/226 (58%), Positives = 179/226 (79%)
Query: 83 EDYVARMKENQKQIYYITGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYD 142
+DYV RMK QK IYYITG++K ++ S F+E+ ++RG EV++MTEPIDEYV+QQ+KD++
Sbjct: 450 KDYVTRMKAGQKSIYYITGDSKKKLETSPFIEQARRRGLEVLFMTEPIDEYVMQQVKDFE 509
Query: 143 GKTLVSVTKEGLELPEDEEEKKKREEDKVKFENLCKVMKDILDKKVEKVIVSNRLVDSPC 202
K +TKEG+ E EEEK++REE+K E LCK MK++L KVEKVIVS RL SPC
Sbjct: 510 DKKFACLTKEGVHFEESEEEKQQREEEKAACEKLCKTMKEVLGDKVEKVIVSERLSTSPC 569
Query: 203 CIVTSQYGWTANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKADADKNDK 262
+VTS++GW+A+ME+IM+ QALRD+S YM +KK +E+NP H I++ LR++ AD+NDK
Sbjct: 570 ILVTSEFGWSAHMEQIMRNQALRDSSMAQYMMSKKTMELNPRHPIIKELRRRVGADENDK 629
Query: 263 AVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRMIKLGLGIEDEDE 308
AVKDLV LLF+TSLL+SGF LE+P +A RI+RMIKLGL +++E+E
Sbjct: 630 AVKDLVFLLFDTSLLTSGFQLEDPTGYAERINRMIKLGLSLDEEEE 675
Score = 70.5 bits (172), Expect = 2e-13
Identities = 47/127 (37%), Positives = 66/127 (51%), Gaps = 39/127 (30%)
Query: 3 GFYSAYLVADKVTVTSKHNDDEQYIWESSAGGSFTIKPDNSQPLGR-------------- 48
GFYSAYLVAD+VTVTSK+N DE Y+WESSAGG+FTI + R
Sbjct: 122 GFYSAYLVADRVTVTSKNNSDESYVWESSAGGTFTITSTPESDMKRGTRITLHLKEDQME 181
Query: 49 -----------------------LLVEKEREKELSEDEEEE--KKEEEKEEDKTPKLEDE 83
L+VEK EKE+++++EE+ K +E+ EE K ++++
Sbjct: 182 YLEPRRLKELIKKHSEFIGYDIELMVEKTTEKEVTDEDEEDTKKADEDGEEPKVEEVKEG 241
Query: 84 DYVARMK 90
D + K
Sbjct: 242 DEGKKKK 248
>gnl|CDD|235366 PRK05218, PRK05218, heat shock protein 90; Provisional.
Length = 613
Score = 221 bits (567), Expect = 2e-67
Identities = 87/221 (39%), Positives = 138/221 (62%), Gaps = 11/221 (4%)
Query: 83 EDYVARMKENQKQIYYITGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYD 142
+YV RMKE QK+IYYITG++++ NS +E KK+G EV+ +T+PIDE+ + L+++D
Sbjct: 403 AEYVERMKEGQKKIYYITGDSREAAKNSPHLELFKKKGIEVLLLTDPIDEFWISYLEEFD 462
Query: 143 GKTLVSVTKEGLELP-EDEEEKKKREEDKVKFENLCKVMKDILDKKVEKVIVSNRLVDSP 201
GK SV + L+L EDEEEK+++EE + +F+ L + +K+ L KV+ V +S+RL DSP
Sbjct: 463 GKPFKSVARGDLDLGKEDEEEKEEKEEAEEEFKPLLERLKEALGDKVKDVRLSHRLTDSP 522
Query: 202 CCIVTSQYGWTANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKADADKND 261
C+V + + ME+++KA +K LEINP+H +V+ L +AD K
Sbjct: 523 ACLVADEGDMSTQMEKLLKAAG------QEVPESKPILEINPNHPLVKKLADEADEAK-- 574
Query: 262 KAVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRMIKLGLG 302
KDL LL++ +LL+ G +LE+P R++ ++ L
Sbjct: 575 --FKDLAELLYDQALLAEGGSLEDPAAFVKRLNELLLKLLA 613
Score = 55.1 bits (134), Expect = 2e-08
Identities = 19/40 (47%), Positives = 25/40 (62%), Gaps = 2/40 (5%)
Query: 3 GFYSAYLVADKVTVTSKH--NDDEQYIWESSAGGSFTIKP 40
GFYSA++VADKVTV ++ E WES G +TI+
Sbjct: 125 GFYSAFMVADKVTVITRSAGPAAEAVRWESDGEGEYTIEE 164
>gnl|CDD|223403 COG0326, HtpG, Molecular chaperone, HSP90 family [Posttranslational
modification, protein turnover, chaperones].
Length = 623
Score = 206 bits (527), Expect = 1e-61
Identities = 88/220 (40%), Positives = 133/220 (60%), Gaps = 11/220 (5%)
Query: 83 EDYVARMKENQKQIYYITGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYD 142
E+YV+RMKE QKQIYYITGE+ S +E K +G EV+ +T+ IDE+++ L +++
Sbjct: 413 EEYVSRMKEGQKQIYYITGESYQAAKGSPHLELFKAKGIEVLLLTDRIDEFMLTMLPEFE 472
Query: 143 GKTLVSVTKEGLELPEDEEE-KKKREEDKVKFENLCKVMKDILDKKVEKVIVSNRLVDSP 201
GK S+TK L+L EEE + EE+K +F+ L + +K+IL KV+ V +S+RL DSP
Sbjct: 473 GKPFKSITKGDLDLELLEEEDEADSEEEKKEFKPLLERVKEILGDKVKDVRLSHRLTDSP 532
Query: 202 CCIVTSQYGWTANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKADADKND 261
C+ T + MER++KAQ +KK LEINP+H +V+ L D +
Sbjct: 533 ACLTTDGADLSTQMERLLKAQGQEVP------ESKKILEINPNHPLVKKLASLED----E 582
Query: 262 KAVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRMIKLGL 301
+V DLV LL++ +LL+ G LE+P R++ ++ L
Sbjct: 583 ASVADLVELLYDQALLAEGGPLEDPAAFIERLNDLLSRLL 622
Score = 59.6 bits (145), Expect = 9e-10
Identities = 21/44 (47%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 3 GFYSAYLVADKVTVTSKHND-DEQYIWESSAGGSFTIKPDNSQP 45
GFYSA++VADKVTV ++ DE Y WES G +T++ + +P
Sbjct: 125 GFYSAFMVADKVTVITRSAGEDEAYHWESDGEGEYTVEDIDKEP 168
>gnl|CDD|185466 PTZ00130, PTZ00130, heat shock protein 90; Provisional.
Length = 814
Score = 127 bits (321), Expect = 1e-32
Identities = 77/248 (31%), Positives = 150/248 (60%), Gaps = 4/248 (1%)
Query: 83 EDYVARMKENQKQIYYITGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYD 142
+ Y+ MK +QK IYY +G++ + ++ ++ KK+ +V+++TE +DE VQ++++YD
Sbjct: 539 DTYIENMKPDQKFIYYASGDSYEYLSKIPQLQIFKKKNIDVVFLTESVDESCVQRVQEYD 598
Query: 143 GKTLVSVTKEGLELPEDEEEKKKREEDKVKFENLCKVMKDILDKKVEKVIVSNRLVDSPC 202
GK S+ K + E+EKKK E+ K ++ L V+ D L ++ KV +S RLVD+PC
Sbjct: 599 GKKFKSIQKGEITFELTEDEKKKEEKVKKMYKALIDVISDTLRNQIFKVEISRRLVDAPC 658
Query: 203 CIVTSQYGWTANMERIMKAQALRDTSTMGYMAAKKHLEINPDHSIVETLRQKADADKNDK 262
+V++++G + ME++MK + ++ + M+ +K LEINPDH I+ L +++ ++ D
Sbjct: 659 AVVSTEWGLSGQMEKLMKIN-VNNSDQIKAMSGQKILEINPDHPIMIDLLKRSVSNPKDS 717
Query: 263 AVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRMIKLGLGIEDEDEVATGDDVKAGDIPV 322
+ + + ++++++ L+SGF LE+ A ++ I LG+++ ++ DD+
Sbjct: 718 QLTESIKIIYQSAKLASGFDLEDTADLAQIVYDHINQKLGVDNNLKI---DDLDPAIFET 774
Query: 323 AEGEAEDA 330
+ E ED+
Sbjct: 775 KKIEQEDS 782
Score = 55.8 bits (134), Expect = 2e-08
Identities = 27/39 (69%), Positives = 32/39 (82%)
Query: 3 GFYSAYLVADKVTVTSKHNDDEQYIWESSAGGSFTIKPD 41
GFYSA+LVADKV V +K+N+DEQYIWES+A FTI D
Sbjct: 186 GFYSAFLVADKVIVYTKNNNDEQYIWESTADAKFTIYKD 224
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 35.8 bits (82), Expect = 0.037
Identities = 16/42 (38%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQ 93
E+EREKE E+E ++E E+E ++ K + +RM E Q
Sbjct: 599 EREREKE---KEKEREREREREAERAAKASSSSHESRMSEPQ 637
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 35.0 bits (80), Expect = 0.062
Identities = 15/27 (55%), Positives = 23/27 (85%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTP 78
E+E E+E E+EEEE++EEE+EE++ P
Sbjct: 867 EEEEEEEEEEEEEEEEEEEEEEENEEP 893
Score = 34.6 bits (79), Expect = 0.084
Identities = 21/48 (43%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYI 99
E+E E+E E+EEEE++EEE+EE+ L E R QKQ Y+
Sbjct: 866 EEEEEEEEEEEEEEEEEEEEEEEENEEPLSLEWPETR----QKQAIYL 909
Score = 34.2 bits (78), Expect = 0.12
Identities = 14/25 (56%), Positives = 22/25 (88%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDK 76
E+E E+E E+EEEE++EEE+EE++
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEE 889
Score = 32.3 bits (73), Expect = 0.41
Identities = 14/25 (56%), Positives = 22/25 (88%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDK 76
E+E E+E E+EEEE++EEE+EE++
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEE 888
Score = 32.3 bits (73), Expect = 0.45
Identities = 13/25 (52%), Positives = 22/25 (88%)
Query: 60 SEDEEEEKKEEEKEEDKTPKLEDED 84
SE+EEEE++EEE+EE++ + E+E+
Sbjct: 863 SEEEEEEEEEEEEEEEEEEEEEEEE 887
Score = 31.5 bits (71), Expect = 0.74
Identities = 13/29 (44%), Positives = 23/29 (79%)
Query: 56 EKELSEDEEEEKKEEEKEEDKTPKLEDED 84
+ E E+EEEE++EEE+EE++ + E+E+
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEEN 890
Score = 31.1 bits (70), Expect = 0.94
Identities = 14/29 (48%), Positives = 22/29 (75%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTPKLE 81
+E E+E E+EEEE++EEE+EE++ E
Sbjct: 864 EEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 28.4 bits (63), Expect = 7.2
Identities = 12/34 (35%), Positives = 23/34 (67%)
Query: 51 VEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
V+ + + EEEE++EEE+EE++ + E+E+
Sbjct: 852 VDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEE 885
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 33.1 bits (76), Expect = 0.23
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 29 ESSAGGSFTIKPDNSQPLGRLLVEKEREKELSEDEEE--EKKEEEKEEDKTPKLE 81
E G K D+ + L EKE ++ L E + KK+EEK++ + KLE
Sbjct: 536 EDKPDGPSVWKLDDKEE---LQREKEEKEALKEQKRLRKLKKQEEKKKKELEKLE 587
>gnl|CDD|218562 pfam05342, Peptidase_M26_N, M26 IgA1-specific Metallo-endopeptidase
N-terminal region. These peptidases, which cleave
mammalian IgA, are found in Gram-positive bacteria.
Often found associated with pfam00746, they may be
attached to the cell wall.
Length = 252
Score = 32.3 bits (74), Expect = 0.26
Identities = 33/142 (23%), Positives = 57/142 (40%), Gaps = 24/142 (16%)
Query: 57 KELSEDEEEEKKEEEKEEDKTPKLE--DEDYVARMK-ENQKQIYYITGETKDQVANSSFV 113
+ E E E EE+ + K+E + V K EN +++ + + F+
Sbjct: 17 YDRGEGSETETLEEKPVQLDLKKVELKNISDVELYKVENGTYKQHVSLDEVPTDLSKYFL 76
Query: 114 ERVKKRGFEVIYMT-EPIDEYVVQQLKDYDGKTLVSVTKEGLELPEDEE----------- 161
+V F+ +Y+ I+E DGK + +T + +L ++ +
Sbjct: 77 -KVTSSDFKDVYLPVSSIEEVTK------DGKPVYKITAKAPDLVQEADNKYSDNYTFYL 129
Query: 162 EKKKREEDKV--KFENLCKVMK 181
EKKK EE V F+NL M
Sbjct: 130 EKKKPEEGNVYTSFKNLVDAMN 151
>gnl|CDD|221324 pfam11933, DUF3451, Domain of unknown function (DUF3451). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 199 to 238 amino acids in length. This domain
is found associated with pfam06512, pfam00520. This
domain has a conserved ADD sequence motif.
Length = 222
Score = 31.3 bits (71), Expect = 0.54
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 53 KEREKELSEDEEEEK--KEEEKEEDKTPKLEDEDYVARM 89
KER ++++EE EE + +K PK E D R
Sbjct: 12 KERRNRNDKNKKEEHSIGSEEGDSEKEPKSESADGRKRC 50
>gnl|CDD|232942 TIGR00366, TIGR00366, TIGR00366 family protein. [Hypothetical
proteins, Conserved].
Length = 438
Score = 31.3 bits (71), Expect = 0.68
Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTP--KLEDEDYVA 87
K + +L + E+EE+K+ +K+ED T KLE+ +A
Sbjct: 216 KSIDPKLLKKEKEEEKKLKKKEDATIAEKLENSRVLA 252
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 31.1 bits (71), Expect = 0.81
Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 2/59 (3%)
Query: 51 VEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYY--ITGETKDQV 107
+ E + + D+E+E+K+E KE +K +D + E +Q T D V
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPV 213
>gnl|CDD|237762 PRK14598, PRK14598, peptide deformylase; Provisional.
Length = 187
Score = 30.5 bits (69), Expect = 0.92
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 249 ETLRQKADADKN-DKAVKDLVNLLFETSLLSSGFTLEEPQV 288
E LRQKA K D +++L+ +FE+ +SG L PQV
Sbjct: 11 EVLRQKAKPLKGVDAEIEELIASMFESMYNASGIGLAAPQV 51
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 31.0 bits (71), Expect = 0.98
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 51 VEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQK 94
++KE E+EE+EKKEEEKEE++ E+++ K+ Q
Sbjct: 434 AFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKKKQA 477
Score = 30.3 bits (69), Expect = 1.5
Identities = 10/33 (30%), Positives = 22/33 (66%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
EK+RE+E E +++ ++KEE++ + E ++
Sbjct: 420 EKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKE 452
Score = 28.0 bits (63), Expect = 7.5
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 48 RLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQK 94
E+E++++ + +KKEEE+EE+K K E+++ E +K
Sbjct: 420 EKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEK 466
Score = 28.0 bits (63), Expect = 9.2
Identities = 12/47 (25%), Positives = 27/47 (57%)
Query: 48 RLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQK 94
+ E+++EK+ ++K+EEE+EE + + E E+ +E ++
Sbjct: 421 KKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKE 467
>gnl|CDD|162083 TIGR00878, purM, phosphoribosylaminoimidazole synthetase.
Alternate name: phosphoribosylformylglycinamidine
cyclo-ligase; AIRS; AIR synthase This enzyme is found as
a homodimeric monofunctional protein in prokaryotes and
as part of a larger, multifunctional protein, sometimes
with two copies of this enzyme in tandem, in eukaryotes
[Purines, pyrimidines, nucleosides, and nucleotides,
Purine ribonucleotide biosynthesis].
Length = 332
Score = 30.4 bits (69), Expect = 1.3
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 300 GLGIEDEDEVATGDDVKAGDIPVA 323
+G+ ++DE+ TG+ VK GD+ +
Sbjct: 154 AVGVVEKDEIITGEKVKPGDVLIG 177
>gnl|CDD|132750 cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan
nuclear receptors TR4 and TR2. The ligand binding
domain of the TR4 and TR2 (human testicular receptor 4
and 2): TR4 and TR2 are orphan nuclear receptors.
Several isoforms of TR4 and TR2 have been isolated in
various tissues. TR2 is abundantly expressed in the
androgen-sensitive prostate. TR4 transcripts are
expressed in many tissues, including central nervous
system, adrenal gland, spleen, thyroid gland, and
prostate. The expression of TR2 is negatively regulated
by androgen, retinoids, and radiation. The expression of
both mouse TR2 and TR4 is up-regulated by neurocytokine
ciliary neurotrophic factor (CNTF) in mouse. It has
shown that human TR2 binds to a wide spectrum of natural
hormone response elements (HREs) with distinct
affinities suggesting that TR2 may cross-talk with other
gene expression regulation systems. The genes responding
to TR2 or TR4 include genes that are regulated by
retinoic acid receptor, vitamin D receptor, peroxisome
proliferator-activated receptor. TR4/2 binds to HREs as
a dimer. Like other members of the nuclea r receptor
(NR) superfamily of ligand-activated transcription
factors, TR2-like receptors have a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and a C-terminal
ligand binding domain (LBD).
Length = 222
Score = 30.0 bits (68), Expect = 1.3
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 40 PDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKL 80
PD+ R +EK +EK L E + K ++E + KL
Sbjct: 143 PDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKL 183
>gnl|CDD|218223 pfam04712, Radial_spoke, Radial spokehead-like protein. This
family includes the radial spoke head proteins RSP4 and
RSP6 from Chlamydomonas reinhardtii, and several
eukaryotic homologues, including mammalian RSHL1, the
protein product of a familial ciliary dyskinesia
candidate gene.
Length = 481
Score = 30.4 bits (69), Expect = 1.4
Identities = 14/37 (37%), Positives = 24/37 (64%)
Query: 45 PLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLE 81
P GR +K+ E++E+E++EEE+EE + P+ E
Sbjct: 335 PQGRCTWVNPEQKDEEEEQEDEEEEEEEEEPEEPEPE 371
Score = 28.1 bits (63), Expect = 8.4
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKL 80
++E E+E E+EEEE++ EE E ++ P L
Sbjct: 348 DEEEEQEDEEEEEEEEEPEEPEPEEGPPL 376
>gnl|CDD|217049 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein. This
protein is covalently attached to the terminii of
replicating DNA in vivo.
Length = 548
Score = 30.0 bits (68), Expect = 1.7
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDE 83
E E+E E+EE ++EEE+EE++ E+E
Sbjct: 302 PPEPEEEEEEEEEVPEEEEEEEEEEERTFEEE 333
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 29.7 bits (67), Expect = 1.7
Identities = 12/41 (29%), Positives = 28/41 (68%)
Query: 45 PLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDY 85
+L + +++ KEL ++ +E+ E+++EE++ + EDED+
Sbjct: 149 IDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDF 189
Score = 27.8 bits (62), Expect = 7.6
Identities = 14/37 (37%), Positives = 26/37 (70%)
Query: 48 RLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
+L +K +E E + +EE++K+EE+EE++ + ED D
Sbjct: 154 SMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFD 190
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 30.0 bits (67), Expect = 2.1
Identities = 13/44 (29%), Positives = 28/44 (63%)
Query: 41 DNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
D S ++ + + +++ +D+EE+ +EEE+EE++ +DED
Sbjct: 144 DMSPRDNFVIDDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDED 187
>gnl|CDD|111553 pfam02667, SCFA_trans, Short chain fatty acid transporter. This
family consists of two sequences annotated as short
chain fatty acid transporters, however, there are no
references giving details of experimental
characterisation of this function.
Length = 453
Score = 29.8 bits (67), Expect = 2.2
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTP--KLEDEDYVA 87
K + +L + E+EE+K+ + ++D T KLE+ +A
Sbjct: 219 KSIDPKLLKKEKEEEKKLKSKKDATIAEKLENSRVLA 255
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.1 bits (67), Expect = 2.3
Identities = 28/142 (19%), Positives = 63/142 (44%), Gaps = 11/142 (7%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQVANSSF 112
K+ E+E EE K+ E+++ K + + + + + E +
Sbjct: 1653 KKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKKAAEALK---KEAEEAKKAEELKK 1709
Query: 113 VERVKKRGFEVIYMTEPIDEYVVQQLKDYDGKTLVSVTKEGLELPEDEEEKKK----REE 168
E +K+ E + E ++ ++ K K K+ E +DEEEKKK ++E
Sbjct: 1710 KEAEEKKKAEELKKAEEENKIKAEEAK----KEAEEDKKKAEEAKKDEEEKKKIAHLKKE 1765
Query: 169 DKVKFENLCKVMKDILDKKVEK 190
++ K E + K + ++++++++
Sbjct: 1766 EEKKAEEIRKEKEAVIEEELDE 1787
Score = 29.3 bits (65), Expect = 3.7
Identities = 32/139 (23%), Positives = 51/139 (36%), Gaps = 9/139 (6%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQVANSS 111
E ++ E + EE KK+ + + K + + A+ + E K + A
Sbjct: 1313 EAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKK 1372
Query: 112 FVERVKKRGFEVIYMTEPIDEYVVQQLKDYDGKTLVSVTKEGLELPEDEEEKKKREEDKV 171
E KK+ E + + K + K K+ EL + KKK +E K
Sbjct: 1373 -KEEAKKKADAAKKKAEEKKKADEAKKKAEEDK------KKADELKKAAAAKKKADEAKK 1425
Query: 172 KFENLCKVMKDILDKKVEK 190
K E K D KK E+
Sbjct: 1426 KAEEKKKA--DEAKKKAEE 1442
Score = 28.2 bits (62), Expect = 8.0
Identities = 26/132 (19%), Positives = 48/132 (36%), Gaps = 8/132 (6%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQVANSSF 112
K++ +E + E K E E D+ E++ A K+ + + K +
Sbjct: 1335 KKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKK--ADAAKKKAEEKKK 1392
Query: 113 VERVKKRGFEVIYMTEPIDEYVVQQLKDYDGKTLVSVTKEGLELPEDEEEK------KKR 166
+ KK+ E + + + + K + K K+ E + EE KK+
Sbjct: 1393 ADEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKK 1452
Query: 167 EEDKVKFENLCK 178
E+ K E K
Sbjct: 1453 AEEAKKAEEAKK 1464
>gnl|CDD|165442 PHA03171, PHA03171, UL37 tegument protein; Provisional.
Length = 499
Score = 29.6 bits (66), Expect = 2.3
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 47 GRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
G E++ ++E + E EE+ EEE+ E P++ D
Sbjct: 83 GEEAEEEDNDRECPDTEAEEEDEEEEIEAPDPEVNPLD 120
>gnl|CDD|223957 COG1026, COG1026, Predicted Zn-dependent peptidases,
insulinase-like [General function prediction only].
Length = 978
Score = 29.6 bits (67), Expect = 2.8
Identities = 23/143 (16%), Positives = 52/143 (36%), Gaps = 25/143 (17%)
Query: 24 EQYIWESSAGGSFTIKPDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDE 83
+Y ++ + + P EL E + EK+E E + ++ +L DE
Sbjct: 441 RKYFLDNPHYVTVIVLPS---------------PELEE--KLEKEERELLQKRSSELTDE 483
Query: 84 DYVARMKENQKQIYYITGETKDQVANSSFV-----ERVKKRGFEVIYMTEPIDEYVVQQL 138
D + ++ ++ K++ + D + + + V + TE +E V
Sbjct: 484 D-LEKIIKDSKKLKERQ-DQPDSEEDLATLPTLKLGDVPDPIEKTSLETEVSNEAKVLHH 541
Query: 139 KDYDGK-TLVSVTKEGLELPEDE 160
+ T + + + LP +
Sbjct: 542 DLFTNGITYLRLYFDLDMLPSEL 564
>gnl|CDD|220077 pfam08938, DUF1916, Domain of unknown function (DUF1916). This
domain is found in various eukaryotic HBS1-like
proteins.
Length = 148
Score = 28.6 bits (64), Expect = 2.8
Identities = 18/68 (26%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 56 EKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQVANSSFVER 115
E+E ++ E+E + + E P+L++ D AR+ ++ + G++ V++ + VE
Sbjct: 57 EEEDEDEYEDENERRDSESVSNPQLDELDQ-ARLYSCLDEMREVLGDS---VSDRTLVEA 112
Query: 116 VKKRGFEV 123
V K F+V
Sbjct: 113 VLKHDFDV 120
>gnl|CDD|218561 pfam05340, DUF740, Protein of unknown function (DUF740). This
family consists of several uncharacterized plant
proteins of unknown function.
Length = 565
Score = 29.6 bits (66), Expect = 2.8
Identities = 22/74 (29%), Positives = 42/74 (56%), Gaps = 5/74 (6%)
Query: 20 HNDDEQYIWESSAGGSFTIKPDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKE--EDKT 77
H+DDE+ + S A I P+ +P+ LV +E E+ E++EE ++E + ++K+
Sbjct: 110 HDDDEENLPSSIAPPE--IDPEPRKPIVPDLVLEEEEEVEMEEDEEYYEKEPGKVVDEKS 167
Query: 78 PKLEDEDYVARMKE 91
+ E+E+ MK+
Sbjct: 168 EEEEEEELKT-MKD 180
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 29.4 bits (66), Expect = 3.0
Identities = 12/33 (36%), Positives = 24/33 (72%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
K +E++L ++E E+K++E+ +EDK + +DE
Sbjct: 400 AKAKEEKLKQEENEKKQKEQADEDKEKRQKDER 432
>gnl|CDD|227391 COG5058, LAG1, Protein transporter of the TRAM (translocating
chain-associating membrane) superfamily, longevity
assurance factor [Intracellular trafficking and
secretion].
Length = 395
Score = 29.4 bits (66), Expect = 3.0
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 48 RLLVEKEREKELSEDEEEEKKEEEKEEDKT 77
R++ E E + E S+DE EE+ + E EDK
Sbjct: 365 RVIWEGELKDERSDDESEEESDLESSEDKN 394
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 29.3 bits (66), Expect = 3.5
Identities = 29/108 (26%), Positives = 46/108 (42%), Gaps = 15/108 (13%)
Query: 25 QYIWESSAGGSFTIKPDNSQ-----PLGRLLVE---KEREKELSEDEEEEKKEEEKEEDK 76
Q +WE+ +T + Q L +E ER+ E EDEEEE++E+E E
Sbjct: 350 QALWETLNKQKWTKAKETEQDYILDAFSALEIEDANTERDDEEEEDEEEEEEEDEDEGPS 409
Query: 77 TPKLEDEDY----VARMKENQKQIYYITGETKDQVANSSFVERVKKRG 120
+DE++ V E+ + K+ + S+V R K G
Sbjct: 410 KEHSDDEEFEEDDVESKYEDSDGNSSLAVGYKN---DRSYVVRGDKIG 454
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 28.5 bits (64), Expect = 3.7
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 53 KEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
KE EKE + E++E K + ++ED+ + E+E+
Sbjct: 66 KEEEKEAANSEDKEDKGDAEKEDEESEEENEE 97
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 28.9 bits (65), Expect = 4.1
Identities = 16/59 (27%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 31 SAGGSFTIKPD-----NSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
GG F +K + + L+EK E+E +D E + E+E++ED+ + +D++
Sbjct: 258 KKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDE 316
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 29.1 bits (66), Expect = 4.2
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 3 GFYSAYLVADKVTVTSKHNDDEQYI-WESSAGGSFTIKPDNSQP 45
G S +LVAD++ V S+ D + W A G+++++ ++
Sbjct: 110 GLLSCFLVADEIVVVSRSAKDGPAVEWRGKADGTYSVRKLETER 153
>gnl|CDD|217126 pfam02589, DUF162, Uncharacterized ACR, YkgG family COG1556.
Length = 185
Score = 28.4 bits (64), Expect = 4.4
Identities = 17/81 (20%), Positives = 31/81 (38%), Gaps = 17/81 (20%)
Query: 112 FVERVKKRGFEVIYMTEPID--EYVVQQLKDYDGKTLVSVT---------------KEGL 154
F E ++ G EV + E +++ L + T +E L
Sbjct: 4 FKENLEANGAEVHRAKTAEEANEIILELLPEGGVVIEGGETDLGELGLAPALHSGREEVL 63
Query: 155 ELPEDEEEKKKREEDKVKFEN 175
+L E + ++ REE + KF +
Sbjct: 64 DLFEPKLTREAREELREKFLD 84
>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family. Isy1 protein is
important in the optimisation of splicing.
Length = 253
Score = 28.4 bits (64), Expect = 4.4
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 2/69 (2%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYV-ARMKENQKQIYYITGETKDQVANS 110
E EREKEL E EE KE + E+ + + E E+ + + ++ + + ++ T+++V
Sbjct: 181 EAEREKELIEKLVEEWKEIQDEDLQAEEDEREEDIYIPLDDDAEFVAHVPVPTQEEV-EE 239
Query: 111 SFVERVKKR 119
+E+ K+
Sbjct: 240 WLLEKRKRE 248
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 28.9 bits (65), Expect = 4.5
Identities = 38/150 (25%), Positives = 76/150 (50%), Gaps = 10/150 (6%)
Query: 40 PDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYI 99
P+ + L +L E + +EL E+ EE +KE E E KLE +++E +++I +
Sbjct: 217 PELREELEKLEKEVKELEELKEEIEELEKELESLEGSKRKLE-----EKIRELEERIEEL 271
Query: 100 TGETKDQVANSSFVERVKKRGFEVIYMTEPIDEYVVQQLKDYDGKTLVSVTKEGLELPED 159
E ++ ++ +K++ E I ++E +EY+ + + + +S +E E+
Sbjct: 272 KKEIEELEEKVKELKELKEKAEEYIKLSEFYEEYLD---ELREIEKRLSRLEE--EINGI 326
Query: 160 EEEKKKREEDKVKFENLCKVMKDILDKKVE 189
EE K+ EE + + E L K +K++ + E
Sbjct: 327 EERIKELEEKEERLEELKKKLKELEKRLEE 356
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 28.9 bits (65), Expect = 4.7
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 56 EKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQV 107
EK L E+ EEE+ +EE E + E R+K K+ + + +
Sbjct: 520 EKLLIEEAEEEEIDEEAEILDKAQQEATMVAERIKALIKEGFKVYDKKTGTY 571
>gnl|CDD|179712 PRK04019, rplP0, acidic ribosomal protein P0; Validated.
Length = 330
Score = 28.7 bits (65), Expect = 5.0
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 56 EKELSEDEEEEKKEEEKEED 75
+E E+EEEE++EE EE+
Sbjct: 301 AEEEEEEEEEEEEEEPSEEE 320
>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 156 to 174 amino acids in length. This domain is
found associated with pfam07780, pfam01728.
Length = 154
Score = 28.0 bits (63), Expect = 5.0
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 46 LGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQK 94
LG EKE E+E E E EE EEE+ ++ K + + +EN++
Sbjct: 94 LGLDKKEKEEEEE-EEVEVEELDEEEQIDELLEKELAKLKREKRRENER 141
>gnl|CDD|107385 cd06390, PBP1_iGluR_AMPA_GluR1, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the GluR1 subunit of the AMPA receptor.
N-terminal leucine/isoleucine/valine-binding protein
(LIVBP)-like domain of the GluR1 subunit of the AMPA
(alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic
acid) receptor. The AMPA receptor is a member of the
glutamate-receptor ion channels (iGluRs) which are the
major mediators of excitatory synaptic transmission in
the central nervous system. AMPA receptors are composed
of four types of subunits (GluR1, GluR2, GluR3, and
GluR4) which combine to form a tetramer and play an
important role in mediating the rapid excitatory
synaptic current. Furthermore, this N-terminal domain of
the iGluRs has homology with LIVBP, a bacterial
periplasmic binding protein, as well as with the
structurally related glutamate-binding domain of the
G-protein-coupled metabotropic receptors (mGluRs).
Length = 364
Score = 28.8 bits (64), Expect = 5.0
Identities = 15/76 (19%), Positives = 37/76 (48%), Gaps = 16/76 (21%)
Query: 86 VARMKENQKQIYYITGETKDQVANSSFVE----RVKK-----RGFEVIYMTEPIDEYVVQ 136
+ ++++N +YI +AN F++ + ++ GF+++ T+ ++Q
Sbjct: 191 IIKLEKNGIGYHYI-------LANLGFMDIDLTKFRESGANVTGFQLVNYTDTTVSRIMQ 243
Query: 137 QLKDYDGKTLVSVTKE 152
Q K++D + L V +
Sbjct: 244 QWKNFDARDLPRVDWK 259
>gnl|CDD|100110 cd05832, Ribosomal_L12p, Ribosomal protein L12p. This subfamily
includes archaeal L12p, the protein that is functionally
equivalent to L7/L12 in bacteria and the P1 and P2
proteins in eukaryotes. L12p is homologous to P1 and P2
but is not homologous to bacterial L7/L12. It is located
in the L12 stalk, with proteins L10, L11, and 23S rRNA.
L12p is the only protein in the ribosome to occur as
multimers, always appearing as sets of dimers. Recent
data indicate that most archaeal species contain six
copies of L12p (three homodimers), while eukaryotes have
four copies (two heterodimers), and bacteria may have
four or six copies (two or three homodimers), depending
on the species. The organization of proteins within the
stalk has been characterized primarily in bacteria,
where L7/L12 forms either two or three homodimers and
each homodimer binds to the extended C-terminal helix of
L10. L7/L12 is attached to the ribosome through L10 and
is the only ribosomal protein that does not directly
interact with rRNA. Archaeal L12p is believed to
function in a similar fashion. However, hybrid ribosomes
containing the large subunit from E. coli with an
archaeal stalk are able to bind archaeal and eukaryotic
elongation factors but not bacterial elongation factors.
In several mesophilic and thermophilic archaeal species,
the binding of 23S rRNA to protein L11 and to the
L10/L12p pentameric complex was found to be
temperature-dependent and cooperative.
Length = 106
Score = 27.1 bits (60), Expect = 5.0
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 54 EREKELSEDEEEEKKEEEKEEDKTPKLE 81
E++ E EEE+KKEEEKEE++ L
Sbjct: 73 AAEEKAEEKEEEKKKEEEKEEEEEEALA 100
>gnl|CDD|148630 pfam07133, Merozoite_SPAM, Merozoite surface protein (SPAM). This
family consists of several Plasmodium falciparum SPAM
(secreted polymorphic antigen associated with
merozoites) proteins. Variation among SPAM alleles is
the result of deletions and amino acid substitutions in
non-repetitive sequences within and flanking the alanine
heptad-repeat domain. Heptad repeats in which the a and
d position contain hydrophobic residues generate
amphipathic alpha-helices which give rise to helical
bundles or coiled-coil structures in proteins. SPAM is
an example of a P. falciparum antigen in which a
repetitive sequence has features characteristic of a
well-defined structural element.
Length = 164
Score = 27.5 bits (61), Expect = 6.1
Identities = 19/59 (32%), Positives = 33/59 (55%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQIYYITGETKDQVANS 110
E+E E+E+ E E+ E +EE E+++ + ++ED V +K I I T+D A +
Sbjct: 55 EEEDEEEIEEPEDIEDEEEIVEDEEEEEEDEEDNVDLKDIEKKNINDIFNSTQDDNAQN 113
>gnl|CDD|182075 PRK09786, PRK09786, endodeoxyribonuclease RUS; Reviewed.
Length = 120
Score = 27.1 bits (60), Expect = 6.6
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 8/45 (17%)
Query: 252 RQKADADKNDKAVKDLVNLLFETSLLSSGFTLEEPQVHAARIHRM 296
R++ D D KA D +L +GF L++ QV R+ +M
Sbjct: 66 RRRRDLDNLQKAAFD--------ALTKAGFWLDDAQVVDYRVVKM 102
>gnl|CDD|234311 TIGR03685, L12P_arch, 50S ribosomal protein L12P. This model
represents the L12P protein of the large (50S) subunit
of the archaeal ribosome.
Length = 105
Score = 26.9 bits (60), Expect = 6.7
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 52 EKEREKELSEDEEEEKKEEEKEED 75
E+E E+EEEE++EEE EE+
Sbjct: 72 AAAAEEEEEEEEEEEEEEEESEEE 95
>gnl|CDD|100109 cd05831, Ribosomal_P1, Ribosomal protein P1. This subfamily
represents the eukaryotic large ribosomal protein P1.
Eukaryotic P1 and P2 are functionally equivalent to the
bacterial protein L7/L12, but are not homologous to
L7/L12. P1 is located in the L12 stalk, with proteins
P2, P0, L11, and 28S rRNA. P1 and P2 are the only
proteins in the ribosome to occur as multimers, always
appearing as sets of heterodimers. Recent data indicate
that eukaryotes have four copies (two heterodimers),
while most archaeal species contain six copies of L12p
(three homodimers) and bacteria may have four or six
copies (two or three homodimers), depending on the
species. Experiments using S. cerevisiae P1 and P2
indicate that P1 proteins are positioned more
internally with limited reactivity in the C-terminal
domains, while P2 proteins seem to be more externally
located and are more likely to interact with other
cellular components. In lower eukaryotes, P1 and P2 are
further subdivided into P1A, P1B, P2A, and P2B, which
form P1A/P2B and P1B/P2A heterodimers. Some plant
species have a third P-protein, called P3, which is not
homologous to P1 and P2. In humans, P1 and P2 are
strongly autoimmunogenic. They play a significant role
in the etiology and pathogenesis of systemic lupus
erythema (SLE). In addition, the ribosome-inactivating
protein trichosanthin (TCS) interacts with human P0,
P1, and P2, with its primary binding site located in
the C-terminal region of P2. TCS inactivates the
ribosome by depurinating a specific adenine in the
sarcin-ricin loop of 28S rRNA.
Length = 103
Score = 26.9 bits (60), Expect = 6.7
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 6/24 (25%)
Query: 61 EDEEEEKKEEEKEEDKTPKLEDED 84
E ++EEKKEEE+EE D+D
Sbjct: 80 EAKKEEKKEEEEEE------SDDD 97
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 28.4 bits (63), Expect = 7.1
Identities = 15/47 (31%), Positives = 27/47 (57%), Gaps = 3/47 (6%)
Query: 41 DNSQPLGRLLVEKEREKELSE---DEEEEKKEEEKEEDKTPKLEDED 84
D+ Q R++ E R EL+E D+ E + EE+ ++D+ + E E+
Sbjct: 181 DDQQAFARVVREMLRSMELAEEMGDDTESEDEEDGDDDQPTENEQEE 227
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 28.3 bits (63), Expect = 7.2
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 52 EKEREKELSEDEEEEKKEEEKEEDKTPKLEDE 83
E+E E++ SE+EE E +EEE+E + E+E
Sbjct: 454 EEEEEEQESEEEEGEDEEEEEEVEADNGSEEE 485
Score = 28.3 bits (63), Expect = 7.5
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 28 WESSAGGSFTIKPDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDED 84
SS G + E+E E+E E+EE+E +EEE E+++ + + D
Sbjct: 423 KASSTSGESPSMASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEAD 479
>gnl|CDD|235229 PRK04156, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 567
Score = 28.3 bits (64), Expect = 7.4
Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 54 EREKELSE------DEEEEKKEEEKEEDKTPKLEDEDYVARMKEN 92
E+ + L E +EEEEKKEE+K P E V R N
Sbjct: 65 EQRERLEELAPELLEEEEEKKEEKKGLPPLPNAEKGKVVMRFAPN 109
>gnl|CDD|233566 TIGR01771, L-LDH-NAD, L-lactate dehydrogenase. This model
represents the NAD-dependent L-lactate dehydrogenases
from bacteria and eukaryotes. This enzyme function as as
the final step in anaerobic glycolysis. Although lactate
dehydrogenases have in some cases been mistaken for
malate dehydrogenases due to the similarity of these two
substrates and the apparent ease with which evolution
can toggle these activities, critical residues have been
identified which can discriminate between the two
activities. At the time of the creation of this model no
hits above the trusted cutoff contained critical
residues typical of malate dehydrogenases [Energy
metabolism, Anaerobic, Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 299
Score = 27.9 bits (63), Expect = 7.9
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 15/61 (24%)
Query: 92 NQKQIYYITGETKDQVAN------SSFVERVKKRGFEVIYM--TEPID--EYVVQQLKDY 141
QK GET+ ++ S V V K GF+ I++ T P+D YV +L +
Sbjct: 75 PQKP-----GETRLELVGRNVRIMKSIVPEVVKSGFDGIFLVATNPVDILTYVAWKLSGF 129
Query: 142 D 142
Sbjct: 130 P 130
>gnl|CDD|201301 pfam00554, RHD, Rel homology domain (RHD). Proteins containing the
Rel homology domain (RHD) are eukaryotic transcription
factors. The RHD is composed of two structural domains.
This is the N-terminal domain that is similar to that
found in P53. The C-terminal domain has an
immunoglobulin-like fold (See pfam01833) that binds to
DNA.
Length = 169
Score = 27.3 bits (61), Expect = 8.2
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 8/64 (12%)
Query: 233 MAAKKHLEINPDHSIVETLRQKADADKNDKAVKDLVNLLFETSLLSS--GFTLEEPQVHA 290
+ + L I+P + E LRQ D D N +V L F+ L + FT P V +
Sbjct: 110 LKERIELNIDPFNVGFEALRQIKDMDLN------VVRLCFQAFLPDTRGNFTTPLPPVVS 163
Query: 291 ARIH 294
I+
Sbjct: 164 NPIY 167
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 28.0 bits (63), Expect = 8.5
Identities = 14/71 (19%), Positives = 28/71 (39%), Gaps = 5/71 (7%)
Query: 36 FTIKPDNSQPLGRLLVEKEREKELSEDEEEEKKEEEKEEDKTPKLEDEDYVARMKENQKQ 95
FT K + E + E E + + + K+E+E ++ P L E+ KE+ +
Sbjct: 222 FTKKLKETSETEEREEETDVEIETTSETKGTKQEQEGSTEEDPSLFSEE-----KEDPDK 276
Query: 96 IYYITGETKDQ 106
+ +
Sbjct: 277 TEDLDKLEILK 287
>gnl|CDD|235439 PRK05385, PRK05385, phosphoribosylaminoimidazole synthetase;
Provisional.
Length = 327
Score = 27.7 bits (63), Expect = 8.6
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 301 LGIEDEDEVATGDDVKAGDI 320
+G+ ++D++ G VK GD+
Sbjct: 155 VGVVEKDKIIDGSKVKEGDV 174
>gnl|CDD|216413 pfam01287, eIF-5a, Eukaryotic elongation factor 5A hypusine,
DNA-binding OB fold. eIF5A, previously thought to be an
initiation factor, has been shown to be required for
peptide chain elongation in yeast.
Length = 69
Score = 25.6 bits (57), Expect = 8.7
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 9/53 (16%)
Query: 116 VKKRGFEVIYMTEPIDEYVVQQLKDYDGKTLVSVTKEGLELPEDEEEKKKREE 168
VK+ +++I ++ D ++ L D DG+T KE L+LP+ E ++ +E+
Sbjct: 2 VKRTEYQLIDISG--DGFL--SLMDEDGET-----KEDLKLPDGELGEEIKEK 45
>gnl|CDD|119440 cd06578, HemD, Uroporphyrinogen-III synthase (HemD) catalyzes the
asymmetrical cyclization of tetrapyrrole (linear) to
uroporphyrinogen-III, the fourth step in the
biosynthesis of heme. This ubiquitous enzyme is present
in eukaryotes, bacteria and archaea. Mutations in the
human uroporphyrinogen-III synthase gene cause
congenital erythropoietic porphyria, a recessive inborn
error of metabolism also known as Gunther disease.
Length = 239
Score = 27.7 bits (62), Expect = 9.0
Identities = 12/61 (19%), Positives = 25/61 (40%), Gaps = 10/61 (16%)
Query: 103 TKDQVANSSFVERVKKRGFEVIYM----TEPID----EYVVQQLKDYDGKTLVSVTKEGL 154
T+ + ++ G EV+ + EP+D + + L +YD L+ + +
Sbjct: 4 TRPRPQADELAALLEALGAEVLELPLIEIEPLDDAELDAALADLDEYDW--LIFTSPNAV 61
Query: 155 E 155
E
Sbjct: 62 E 62
>gnl|CDD|219523 pfam07697, 7TMR-HDED, 7TM-HD extracellular. This entry represents
the extracellular domain of the 7TM-HD (7TM Receptors
with HD hydrolase).
Length = 218
Score = 27.3 bits (61), Expect = 9.8
Identities = 22/148 (14%), Positives = 52/148 (35%), Gaps = 9/148 (6%)
Query: 61 EDEEEEKKEEEKEEDKTPKL--EDEDYVARMKENQKQIYYITGETKDQVANSSFVERVKK 118
DEE +++ ++ + P + D + ++E ++ E K + +R+K
Sbjct: 20 VDEEATEEKRKEAAESVPPVYDIDPEVTQNLEEEINSLFDEIREVKASAEKAEKADRLKS 79
Query: 119 RGFEVIYMTEP-IDEYVVQQLKDYDG--KTLVSVTKEGLE--LPEDEEEKKKREEDKVKF 173
+++ + +D + + L + E + K E K++
Sbjct: 80 LNLSTFQLSDEQWSTLLNADDEDLKLLEDAIRTALDRILSQGIREGLLIEAKEEAAKLQL 139
Query: 174 E--NLCKVMKDILDKKVEKVIVSNRLVD 199
E NL ++ + +I N D
Sbjct: 140 ESLNLSPPLRLAAKLLLSSLIKPNLFYD 167
>gnl|CDD|237837 PRK14861, tatA, twin arginine translocase protein A; Provisional.
Length = 61
Score = 25.3 bits (56), Expect = 10.0
Identities = 15/35 (42%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 40 PDNSQPLGRLLVE-KEREKELSEDEEEEKKEEEKE 73
P+ + LG+ L E K+ KEL++D+ +EKK++EK
Sbjct: 27 PELGKALGKTLREFKKATKELTDDDFQEKKKKEKM 61
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
0.309 0.129 0.350
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,126,802
Number of extensions: 1703776
Number of successful extensions: 6108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4848
Number of HSP's successfully gapped: 508
Length of query: 334
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 237
Effective length of database: 6,635,264
Effective search space: 1572557568
Effective search space used: 1572557568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 59 (26.6 bits)