RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6263
(913 letters)
>gnl|CDD|227441 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 788 bits (2037), Expect = 0.0
Identities = 359/910 (39%), Positives = 517/910 (56%), Gaps = 57/910 (6%)
Query: 8 PDKDEKVTKGKGEKNPDEMSEEDKRLQEDLNMLVEKIKGSDKHLYLPALESMRDLIRTST 67
P+K K K ++ +++SEED L+ DL +LVE+I+ D L +L ++++I++ST
Sbjct: 20 PEKQTPNKKDKKKEEEEQLSEEDAMLKGDLELLVERIQDPDIDLQNNSLNMLKEVIKSST 79
Query: 68 TSMTSVPMPLKFLRNHYGALKEACEKMTDQKPKKLLCSIISVLAMSQDNV-EQECLKYCL 126
+SMT+VP PLKFLR +Y L E +K + K+ L I+S L M + + L Y L
Sbjct: 80 SSMTAVPKPLKFLRPNYLDLLEIYDKWLEGNKKRWLADILSALCMVYSENGKHKSLAYRL 139
Query: 127 MAKQKDVGDWGHEYVRQLEAEIAEEWAT-NKYEKP---QLLELIEDIIQFDMKHNAEIQA 182
D+ +WGHEYVR L EIAE N+ + P +L +I+ F +KHNAE A
Sbjct: 140 EGNIIDLKEWGHEYVRHLAGEIAEVKNDQNEMDAPSFADTRDLGLEIVPFFLKHNAEFDA 199
Query: 183 CDLLMEIDHLELLDKHMDVTNYPRVCLYLSNCALYVEEPERSVITNGVLNNYLKFKEYPR 242
DLL+E+ +E + +D NY RVCLYL +C + PE + L YLK + R
Sbjct: 200 IDLLVEVGGIEKVLDFVDTHNYNRVCLYLEDCVPLLPPPEDVALLETALKIYLKMGDLTR 259
Query: 243 ALTLALQLNDEPSVLKIFQLCEDPVVRKQLAYMAGRQQITIELPDEMPDKNDLQIIMTNS 302
A+ A++L +++ + EDP +KQ Y+ RQ + E DE + + I++N
Sbjct: 260 AVVGAIRLQKSKEIIEYVRAIEDPDYKKQCLYILARQNLYYEASDE-----EEKDILSNG 314
Query: 303 HINDHFHSLARELDIMEPKTPEEVYKTWLENIVLRPTYNLDVPVDSARHNLASTFVNAFV 362
+++DHF L +EL++ +PK PE++ K L+ + T L + SA NLA FVN +
Sbjct: 315 YLSDHFRYLGKELNLDKPKVPEDILKGHLKYD--KDTRQL-AGIGSANQNLAMGFVNDPI 371
Query: 363 NAGFSRDKLVSVEDGNKWMYKNKQHGMLSAAASLGLIYLWDVDGGLTPIDKYLYTSEDYI 422
N G+ D L+ ++D +W+YK K G++SA AS+G+I W+ D GL +DKYLY E Y
Sbjct: 372 NLGYENDSLIPLDD--EWIYKCKVPGLISAFASIGVIESWNSDKGLETLDKYLYADESYR 429
Query: 423 KAGALLALGIVNCGVRNECDPALALLSDYVLNDSITLRIGAVLGLGLAYAGTKRQEVVTL 482
KAGALL +G+ V E PALALLS+Y+ + S I A+LGLG A++GT+ +EV+ L
Sbjct: 430 KAGALLGIGLSGLRVFEERPPALALLSNYLQSSSSKHVIAAILGLGAAFSGTQAEEVLEL 489
Query: 483 LLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPVSELQDGHYSRFLP 542
L P++ S EVV FA++ ++VGT ++ S ILQT +E E + + RFL
Sbjct: 490 LQPIMFSTDSPIEVVFFASLTLGSVFVGTCNGDLTSLILQTFVERGKIESET-QWFRFLA 548
Query: 543 LALAITYLGKKDAIDTTLAALEVLPDPFRSMAKMMLKMCAYAGSGDVLVVQEFLHVCSEH 602
L LA + G+KD +D + + ++++K C Y G+GDVLV+Q LHV E
Sbjct: 549 LGLASLFYGRKDQVDDVEETIMAIEGALSKHEEILVKGCQYVGTGDVLVIQSLLHVKDE- 607
Query: 603 YTPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALG 662
T + K E + ++++A LG
Sbjct: 608 --FTGDTLKNEE--------------------------------------ALIESLALLG 627
Query: 663 VAVVALGEEIGSEMSTRIFGQLGRYGEPTVRRAVPLAIALCSMSNPALNVIDVLNKYSHD 722
A++A+GE+IGSEM R F YG +R +PLA + S SNP +NV D L + SHD
Sbjct: 628 CALIAMGEDIGSEMVLRHFSHSMHYGSSHIRSVLPLAYGILSPSNPQMNVFDTLERSSHD 687
Query: 723 LDEEVAHNAIFSMGLVGAGTNNARLATMLRQLAQYHVKNTGHLFMVRIAQGLTHMGKGTV 782
D V N IF+MGL+GAGT NARLA +LRQLA Y+ K + LF++RIAQGL +GKGT+
Sbjct: 688 GDLNVIINTIFAMGLIGAGTLNARLAQLLRQLASYYYKESKALFVLRIAQGLLSLGKGTM 747
Query: 783 SLSPFHTDRQILNPVALAGLLVVLTSFLDTKNIILGKSHYLLYCLVPAMYPRWLVTLDEN 842
++SP + D+ L P AGL + LD+ L SH L+Y L+ + P+ VTL E
Sbjct: 748 TISPLYFDKTTLMPKNTAGLFTTVFMLLDSSIFPLVSSHALMYFLLCQIRPQKYVTLSEK 807
Query: 843 QEPVSVSVRVGQAVDVIGKAGTPKTIAGVHTHTTPVLLAVGERAELATDDYVPLTPVMEG 902
EP+ V+VRVGQAV+ +G+AG PK I G THTTPVLL+ ERAEL TD+Y T +EG
Sbjct: 808 GEPIKVNVRVGQAVNTVGQAGRPKKITGWQTHTTPVLLSHKERAELDTDEYNVCTSYIEG 867
Query: 903 FVILRKKDKD 912
VIL+K
Sbjct: 868 VVILKKNPDY 877
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 78.1 bits (192), Expect = 1e-14
Identities = 103/504 (20%), Positives = 189/504 (37%), Gaps = 44/504 (8%)
Query: 119 QECLKYCLMAKQKDVGDWGHEYVRQLEAEIAEEW---ATNKYEKPQ-------LLELIED 168
Q+ ++Y L A + + D G Y + + E + + Y L ++E
Sbjct: 76 QQAIEYALRAGDRFLVDDGSFYYETIVYKSIEMYVHMMDSAYIGGDKDIIDRILDFVLEV 135
Query: 169 IIQFDMKHNAEIQACDLLMEIDHLELLDKHMDVTNYPRVCLYLSNCALYVEEPE--RSVI 226
I + + + E L++++K++ N + YL + A+ + E E R I
Sbjct: 136 IGAKCVDDSEIGYLLGIAAEGLRLDIIEKYLSDGNDCDIINYLLDLAITLVEEEGFRKEI 195
Query: 227 TNGVLNNYLKFKEYPRALTL---ALQLNDEPSVLKIFQLCEDPVVRKQLAYMAGRQQITI 283
+L K P + + LND + + A Q+
Sbjct: 196 L-RMLAEIGPGKPKPDYFYVIKAVVYLNDAEKAKALIEKLVKENDLLLYA------QVAF 248
Query: 284 ELPDEMPDKNDLQIIMTNSHINDHFHSLARELDIMEPKTPEEVYKTWLENIVLRPTYNLD 343
+L D + L+I++T + ++ + I+ + ++ +L L+
Sbjct: 249 DLEDSASQEI-LEILVTELVAQGYDQAV---MSILSGEFTKKYLGAFLLEKNNTDFKFLN 304
Query: 344 VPVDS-----ARHNLASTFVNAFVNAGFSRDKLVSVEDGNKWMYKNKQHGMLSAAASLGL 398
S +R + A + N+F+N G S D + W+ K +A ASLG+
Sbjct: 305 SSKSSLARKFSRFHYAVSLANSFMNLGTSNDSFY--RNNLDWLGKASNWAKFTATASLGV 362
Query: 399 IYLWDVDGGLTPIDKYL---YTSEDYIKAGALLALGIVNCGV-RNECDPALALLSDYVLN 454
I+L + + G + YL S + GAL ALG++ G R + + L D
Sbjct: 363 IHLGNSNPGYEILKPYLPSEVASSRQKEGGALYALGLIKAGFGREDTEYLLEYFLDTEDE 422
Query: 455 DSITLRIGAVLGLGLAYAGTKRQEVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYH 514
+ L G LG+GL G+ +E+ L +L + ++ + A L+ +GT
Sbjct: 423 LTPELAYGVCLGIGLINMGSANREIYEKLKELLKNDRAL--LGEAAVYGMGLLMLGTWSV 480
Query: 515 EVASAILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDPFRSMA 574
E + E Q R L + A+ G+++ D + L D
Sbjct: 481 EAIEDMRTY-----AGETQHERIKRGLGIGFALILYGRQEMADDYINELLYDKDSILRYN 535
Query: 575 KMMLKMCAYAGSGDVLVVQEFLHV 598
+ AY G+G++ VV LH
Sbjct: 536 GVFSLALAYVGTGNLGVVSTLLHY 559
Score = 36.1 bits (83), Expect = 0.10
Identities = 28/118 (23%), Positives = 51/118 (43%), Gaps = 3/118 (2%)
Query: 418 SEDYIKAGALLALGIVNCGVRNECDPALALLSDYVLNDSITLRIGAVLGLGLAYAGTKRQ 477
D ++ A++ALG V C R+ + LLS+ + + +R G + LG+A AGT +
Sbjct: 564 GNDDVRRAAVIALGFVCCDDRDLLVGTVELLSE---SHNFHVRAGVAVALGIACAGTGDK 620
Query: 478 EVVTLLLPVLTDRKSTPEVVAFAAVAASLIYVGTGYHEVASAILQTLIELPVSELQDG 535
+L ++ D A AV L+ + I++ + V + + G
Sbjct: 621 VATDILEALMYDTNDFVRQSAMIAVGMILMQCNPELNPNVKRIIKKFNRVIVDKHESG 678
Score = 29.9 bits (67), Expect = 7.2
Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 5/102 (4%)
Query: 647 EKEKDLSSMQAVAALGVAVVALGEEIGSEMSTRIFGQLGRYGEPT----VRRAVPLAIAL 702
EK K+L AV +G + S + Y T ++R + + AL
Sbjct: 449 EKLKELLKNDRALLGEAAVYGMGLLMLGTWSVEAIEDMRTYAGETQHERIKRGLGIGFAL 508
Query: 703 CSMSNPALNVIDVLNKYSHDLDEEVAHNAIFSMGLVGAGTNN 744
+ D +N+ +D D + +N +FS+ L GT N
Sbjct: 509 ILYGRQEM-ADDYINELLYDKDSILRYNGVFSLALAYVGTGN 549
>gnl|CDD|216739 pfam01851, PC_rep, Proteasome/cyclosome repeat.
Length = 35
Score = 40.5 bits (96), Expect = 6e-05
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 462 GAVLGLGLAYAGTKRQEVVTLLLPVLTD 489
GA+L LGL +AG+ +E + LLLP L+D
Sbjct: 1 GAILALGLIHAGSGNEEALELLLPYLSD 28
Score = 36.3 bits (85), Expect = 0.002
Identities = 16/37 (43%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 425 GALLALGIVNCGVRNECDPALALLSDYVLNDSITLRI 461
GA+LALG+++ G NE AL LL Y+ + S +R
Sbjct: 1 GAILALGLIHAGSGNEE--ALELLLPYLSDTSNEVRA 35
Score = 33.6 bits (78), Expect = 0.017
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 730 NAIFSMGLVGAGTNNARLATMLRQLAQYHVKN 761
AI ++GL+ AG+ N +L
Sbjct: 1 GAILALGLIHAGSGNEEALELLLPYLSDTSNE 32
>gnl|CDD|204007 pfam08625, Utp13, Utp13 specific WD40 associated domain. Utp13 is
a component of the five protein Pwp2 complex that forms
part of a stable particle subunit independent of the U3
small nucleolar ribonucleoprotein that is essential for
the initial assembly steps of the 90S pre-ribosome. Pwp2
is capable of interacting directly with the 35 S
pre-rRNA 5' end.
Length = 138
Score = 36.0 bits (84), Expect = 0.024
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 231 LNNYLKFKEYPRALTLALQLNDEPSVLKIF-QLCEDP 266
L+N L+ +Y AL LAL L+ +L + + ED
Sbjct: 4 LSNLLREGDYSEALLLALTLDHPHRLLNVLKSVIEDE 40
>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 = 34.2 bits (79), Expect = 0.060
Identities = 16/51 (31%), Positives = 30/51 (58%)
Query: 612 EETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALG 662
EE AA A + + AAA +++E++++E+E++ S +A+A LG
Sbjct: 51 EEAIKKAAAAPVAAAAAAAAAAAAAEEEEEEEEEEEEEEEESEEEAMAGLG 101
Score = 30.8 bits (70), Expect = 1.00
Identities = 10/49 (20%), Positives = 26/49 (53%)
Query: 613 ETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAAL 661
+ +A A+A A + + +++E++++E+E + +M + AL
Sbjct: 55 KKAAAAPVAAAAAAAAAAAAAEEEEEEEEEEEEEEEESEEEAMAGLGAL 103
>gnl|CDD|215914 pfam00428, Ribosomal_60s, 60s Acidic ribosomal protein. This
family includes archaebacterial L12, eukaryotic P0, P1
and P2.
Length = 88
Score = 33.4 bits (77), Expect = 0.087
Identities = 12/32 (37%), Positives = 24/32 (75%)
Query: 620 AASATAGGSTESTPAAAANDKKEKKDKEKEKD 651
AA+A A + + AAAA ++K+++++E+E+D
Sbjct: 49 AAAAAAAAAAAAAAAAAAEEEKKEEEEEEEED 80
Score = 31.1 bits (71), Expect = 0.54
Identities = 10/37 (27%), Positives = 22/37 (59%)
Query: 616 ATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDL 652
+ AA+A A + + AA K+E++++E++ D+
Sbjct: 47 SAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEEDDDM 83
Score = 28.4 bits (64), Expect = 4.2
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 610 AKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKD 651
A + AA+A A + + AAA +KKE++++E+E D
Sbjct: 40 ANGSAKLSAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEEDD 81
Score = 28.4 bits (64), Expect = 4.7
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 609 SAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSS 654
+ KE + SA A + + AAAA E++ KE+E++
Sbjct: 34 NIKELIANGSAKLSAAAAAAAAAAAAAAAAAAAEEEKKEEEEEEEE 79
>gnl|CDD|235795 PRK06402, rpl12p, 50S ribosomal protein L12P; Reviewed.
Length = 106
Score = 32.6 bits (75), Expect = 0.20
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 612 EETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAA 660
EE AA A + + AAAA ++K+++++E+E+ S + AA
Sbjct: 51 EEAIKKAAAAPVAAAAAAAAAAAAAAAEEKKEEEEEEEEKEESEEEAAA 99
Score = 30.3 bits (69), Expect = 1.1
Identities = 11/52 (21%), Positives = 29/52 (55%)
Query: 610 AKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAAL 661
A ++ +A AA+A A + + A +++E++++++E + + + AL
Sbjct: 53 AIKKAAAAPVAAAAAAAAAAAAAAAEEKKEEEEEEEEKEESEEEAAAGLGAL 104
>gnl|CDD|219746 pfam08208, RNA_polI_A34, DNA-directed RNA polymerase I subunit
RPA34.5. This is a family of proteins conserved from
yeasts to human. Subunit A34.5 of RNA polymerase I is a
non-essential subunit which is thought to help Pol I
overcome topological constraints imposed on ribosomal
DNA during the process of transcription.
Length = 193
Score = 33.5 bits (77), Expect = 0.28
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 602 HYTPTTSSAK-EETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSS 654
+ PT A S G+ + + +T A +++EKK+K+K+K++
Sbjct: 112 RFFPTGYGAPDGPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKK 165
Score = 31.6 bits (72), Expect = 1.3
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 600 SEHYTPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKE-KKDKEKEKD 651
+ P+ ++ ETS T A E KKE KK+K+++KD
Sbjct: 120 APDGPPSELGSESETSEKETTAKVEKEAEVEEEEKKEKKKKKEVKKEKKEKKD 172
>gnl|CDD|182178 PRK09977, PRK09977, putative Mg(2+) transport ATPase; Provisional.
Length = 215
Score = 33.1 bits (76), Expect = 0.37
Identities = 12/58 (20%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 803 LVVLTSFLDTKNIILGKSHYLLYCLVPAMYPRWLVTLD-ENQEPVSVSVRVGQAVDVI 859
L+VL F ++ K ++L LV L + + VS++ + +V+
Sbjct: 127 LLVLEVFHQLTFRLMNKHYHLQLTLVNGNVVSMLDWFKQQKIKTDLVSLQENEDHEVV 184
>gnl|CDD|220046 pfam08863, YolD, YolD-like protein. Members of this family are
functionally uncharacterized. However it has been
predicted that thes proteins are functionally equivalent
to the UmuD subunit of polymerase V from gram-negative
bacteria.
Length = 92
Score = 31.0 bits (71), Expect = 0.49
Identities = 18/86 (20%), Positives = 33/86 (38%), Gaps = 15/86 (17%)
Query: 139 EYVRQLEAEIAEEWATNKYEKP----QLLELIEDIIQFDMKHNAEIQAC--------DLL 186
E+ L I E+ NK EKP LE I +++ ++ EI
Sbjct: 3 EHFESLREYIKEQ---NKVEKPELDEDQLEEINELLSQALESEQEILITYYEDGYIETYY 59
Query: 187 MEIDHLELLDKHMDVTNYPRVCLYLS 212
I ++ L+K + +T+ + +
Sbjct: 60 GTIHKIDPLNKTLKITDAFNNTIKIK 85
>gnl|CDD|235665 PRK05996, motB, flagellar motor protein MotB; Validated.
Length = 423
Score = 33.5 bits (77), Expect = 0.58
Identities = 13/61 (21%), Positives = 20/61 (32%)
Query: 604 TPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALGV 663
A E A A G + AA + +++ + L + A A GV
Sbjct: 229 QAQPKKAATEEELIADAKKAATGEPAANAAKAAKPEPMPDDQQKEAEQLQAAIAQAIGGV 288
Query: 664 A 664
A
Sbjct: 289 A 289
>gnl|CDD|165706 PLN00138, PLN00138, large subunit ribosomal protein LP2;
Provisional.
Length = 113
Score = 31.2 bits (70), Expect = 0.79
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 615 SATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSM 655
S G A +A A + A AA KKE+K +EKE+ M
Sbjct: 67 SGGGVAVAAAAAPAAGGAAAPAAEAKKEEKVEEKEESDDDM 107
>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 = 30.4 bits (69), Expect = 1.3
Identities = 10/38 (26%), Positives = 20/38 (52%)
Query: 615 SATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDL 652
G A +A A + + A +KKE++++E + D+
Sbjct: 61 GGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEESDDDM 98
Score = 29.2 bits (66), Expect = 2.6
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 614 TSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKD 651
G AA A A + + A A K+EKK++E+E+
Sbjct: 59 GGGGGGAAPAAAAAAAAAAAAEAK--KEEKKEEEEEES 94
Score = 28.8 bits (65), Expect = 3.9
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 614 TSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKD 651
++ G A + + AAAA KKE+K +E+E++
Sbjct: 56 SNVGGGGGGAAPAAAAAAAAAAAAEAKKEEKKEEEEEE 93
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 30.3 bits (68), Expect = 1.4
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 618 GTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSM 655
G A+A A + +T A A KKE+K +E+E++ +
Sbjct: 69 GGVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDL 106
>gnl|CDD|218976 pfam06292, DUF1041, Domain of Unknown Function (DUF1041). This
family consists of several eukaryotic domains of unknown
function. Members of this family are often found in
tandem repeats and co-occur with pfam00168, pfam00130
and pfam00169 domains.
Length = 104
Score = 29.3 bits (66), Expect = 2.6
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 5/70 (7%)
Query: 116 NVEQECLKYCLMAKQKDVGDWGHE-YVRQ----LEAEIAEEWATNKYEKPQLLELIEDII 170
NV ++CLK C + + + Y RQ + A +L+EL +I
Sbjct: 2 NVVRKCLKACALVTYTRLFNNCKILYNRQIQEDTGRDDQPPPAKRLEFWIRLIELCVSVI 61
Query: 171 QFDMKHNAEI 180
Q D +H +
Sbjct: 62 QEDKEHYTPV 71
>gnl|CDD|234207 TIGR03434, ADOP, Acidobacterial duplicated orphan permease.
Members of this protein family are found, so far, only
in three species of Acidobacteria, namely Acidobacteria
bacterium Ellin345, Acidobacterium capsulatum ATCC
51196, and Solibacter usitatus Ellin6076, where they
form large paralogous families. Each protein contains
two copies of a domain called the efflux ABC transporter
permease protein (pfam02687). However, unlike other
members of that family (including LolC, FtsX, and MacB),
genes for these proteins are essentially never found
fused or adjacent to ABC transporter ATP-binding protein
(pfam00005) genes. We name this family ADOP, for
Acidobacterial Duplicated Orphan Permease, to reflect
the restricted lineage, internal duplication, lack of
associated ATP-binding cassette proteins, and permease
homology. The function is unknown.
Length = 803
Score = 31.3 bits (72), Expect = 2.6
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 11/56 (19%)
Query: 461 IGAVLGLGLAYAGTKRQEVVTLLLPVLTDRKSTPE----VVAFAAVAASLIYVGTG 512
G LGL LAY G + ++ LLP R + V+ FA + + TG
Sbjct: 331 AGGALGLLLAYWGLR---LLLALLPASLPRLAEISLDGRVLLFALALS----LLTG 379
>gnl|CDD|223086 COG0007, CysG, Uroporphyrinogen-III methylase [Coenzyme
metabolism].
Length = 244
Score = 30.7 bits (70), Expect = 3.1
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 486 VLTDRKSTPEVVAFAAVAASLIYVG--TGYHEVA-SAILQTLIEL 527
VL DR EV+A A A IYVG G H I L+EL
Sbjct: 33 VLYDRLVPEEVLALARRDAERIYVGKRPGGHSKPQDEINALLVEL 77
>gnl|CDD|100108 cd04411, Ribosomal_P1_P2_L12p, Ribosomal protein P1, P2, and L12p.
Ribosomal proteins P1 and P2 are the eukaryotic proteins
that are functionally equivalent to bacterial L7/L12.
L12p is the archaeal homolog. Unlike other ribosomal
proteins, the archaeal L12p and eukaryotic P1 and P2 do
not share sequence similarity with their bacterial
counterparts. They are part of the ribosomal stalk
(called the L7/L12 stalk in bacteria), along with 28S
rRNA and the proteins L11 and P0 in eukaryotes (23S
rRNA, L11, and L10e in archaea). In bacterial ribosomes,
L7/L12 homodimers bind the extended C-terminal helix of
L10 to anchor the L7/L12 molecules to the ribosome.
Eukaryotic P1/P2 heterodimers and archaeal L12p
homodimers are believed to bind the L10 equivalent
proteins, eukaryotic P0 and archaeal L10e, in a similar
fashion. P1 and P2 (L12p, L7/L12) are the only proteins
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 two copies each of P1
and P2 (two heterodimers). Bacteria may have four or six
copies (two or three homodimers), depending on the
species. As in bacteria, the stalk is crucial for
binding of initiation, elongation, and release factors
in eukaryotes and archaea.
Length = 105
Score = 29.2 bits (65), Expect = 3.6
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 608 SSAKEETSATGTAASA-TAGGSTESTPAAAANDKKEKKDKEKEKDL 652
S KE S+ AA+A A + + PA A + KE++++E+++D
Sbjct: 55 SKGKELMSSQAAAAAAPAATAAATAEPAEKAEEAKEEEEEEEDEDF 100
>gnl|CDD|172341 PRK13808, PRK13808, adenylate kinase; Provisional.
Length = 333
Score = 30.2 bits (68), Expect = 4.6
Identities = 11/46 (23%), Positives = 17/46 (36%)
Query: 605 PTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEK 650
+ + + A TA SA T + A A +K K+ K
Sbjct: 220 KSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAK 265
>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 = 28.6 bits (64), Expect = 4.6
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 613 ETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALG 662
+ +A AA+A A + + A ++EKK KE+EK+ +A+A LG
Sbjct: 55 KKAAVAAAAAAPAAAAAAAAEEKAEEKEEEKK-KEEEKEEEEEEALAGLG 103
>gnl|CDD|237019 PRK11907, PRK11907, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 814
Score = 30.6 bits (69), Expect = 4.7
Identities = 13/38 (34%), Positives = 15/38 (39%)
Query: 601 EHYTPTTSSAKEETSATGTAASATAGGSTESTPAAAAN 638
E TP S A EE T T +AT S+ A
Sbjct: 43 EQTTPVESDATEEADNTETPVAATTAAEAPSSSETAET 80
>gnl|CDD|221203 pfam11748, DUF3306, Protein of unknown function (DUF3306). This
family of proteobacterial species proteins has no known
function.
Length = 115
Score = 28.8 bits (65), Expect = 4.8
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 690 PTVRRAVPLAIALCSM-SNPALNVIDVLNKYSHD 722
++RA AL + NP NV+D L+ Y+ D
Sbjct: 79 EALKRA-----ALRKLFRNPEFNVMDGLDDYADD 107
>gnl|CDD|184900 PRK14907, rplD, 50S ribosomal protein L4; Provisional.
Length = 295
Score = 30.3 bits (68), Expect = 5.0
Identities = 12/61 (19%), Positives = 18/61 (29%)
Query: 605 PTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALGVA 664
TTS +T T S A + KK K + S++ +
Sbjct: 23 ATTSKETAKTKKTAKTTSTKAAKKAAKVKKTKSVKTTTKKVTVKFEKTESVKKESVAKKT 82
Query: 665 V 665
V
Sbjct: 83 V 83
>gnl|CDD|106976 PHA00667, PHA00667, hypothetical protein.
Length = 158
Score = 29.6 bits (65), Expect = 5.0
Identities = 11/57 (19%), Positives = 19/57 (33%), Gaps = 3/57 (5%)
Query: 607 TSSAKEETSA---TGTAASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAA 660
TS+ ++ +A +A PAA EKK + ++ A
Sbjct: 11 TSALRDLIAAIKAGVPTTAAQVAAVAAEAPAAQQEASTEKKPRATSAKTTAATAPTP 67
>gnl|CDD|220712 pfam10355, Ytp1, Protein of unknown function (Ytp1). This is a
family of proteins found in fungi. The region appears to
contain regions similar to mitochondrial electron
transport proteins. The C-terminal domain is hydrophobic
and negatively charged. There are consensus sites for
both N-linked glycosylation and cAMP-dependent protein
kinase phosphorylation.
Length = 272
Score = 29.5 bits (67), Expect = 6.9
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 461 IGAVLGLGLAYAGTKRQ-EVVTLLL----PVLTDRKSTPEVVAFAAVAASLIYVGTGYHE 515
I G L AG R E + LLL L R T + F +A L+++G+ +
Sbjct: 175 IHKQWGYLLMGAGLFRIIEYLFLLLDPPSSSLPSRPPTEYLTPFCLIAGGLVFMGSTEEQ 234
Query: 516 VASAI 520
V +
Sbjct: 235 VQALE 239
>gnl|CDD|99806 cd06210, MMO_FAD_NAD_binding, Methane monooxygenase (MMO) reductase
of methanotrophs catalyzes the NADH-dependent
hydroxylation of methane to methanol. This
multicomponent enzyme mediates electron transfer via a
hydroxylase (MMOH), a coupling protein, and a reductase
which is comprised of an N-terminal [2Fe-2S] ferredoxin
domain, an FAD binding subdomain, and an NADH binding
subdomain. Oxygenases oxidize hydrocarbons using
dioxygen as the oxidant. Dioxygenases add both atom of
oxygen to the substrate, while mono-oxygenases add one
atom to the substrate and one atom to water.
Length = 236
Score = 29.2 bits (66), Expect = 8.4
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 736 GLVGAGTNNARLATMLRQLAQYHVKNTGHLF 766
V GT A L +MLR++A++ LF
Sbjct: 112 WFVAGGTGLAPLLSMLRRMAEWGEPQEARLF 142
>gnl|CDD|211927 TIGR04204, MAST_ArtA_sort, MAST domain. This model describes a
domain (or in most cases the full length) of archaeal
surface proteins that are putative targets for
C-terminal processing by archaeosortase A (TIGR04125).
Most members of this family belong to proteins encoded
by tandem genes in the genus Methanosarcina. The
putative processing signal, PGF-CTERM (TIGR04126),
included within the domain definition, takes a variant
form, with consensus motif PAF instead of PGF. We
suggest the name MAST domain: Methanosarcina
Archaeosortase-Sorted Tandem gene family domain.
Length = 182
Score = 29.0 bits (65), Expect = 8.5
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 7/57 (12%)
Query: 585 GSGDVLVVQEF----LHVCSEHY---TPTTSSAKEETSATGTAASATAGGSTESTPA 634
+ + LV EF + +EHY TPT+ + E T ++ S S PA
Sbjct: 107 ETDEPLVPGEFTIAYPIISNEHYEGETPTSEEPETENQPTSKKPASENSSSPASAPA 163
>gnl|CDD|237803 PRK14724, PRK14724, DNA topoisomerase III; Provisional.
Length = 987
Score = 29.9 bits (67), Expect = 8.5
Identities = 29/122 (23%), Positives = 43/122 (35%), Gaps = 13/122 (10%)
Query: 566 LPDPFRSMA-----KMMLKMCAYAGSGDVLVVQEFLHVCSEHYTPTTSSAKEETSATGTA 620
L D F SM K L AG V EF S+ + P ++A + +A+
Sbjct: 817 LLDKFVSMRTRRAFKAFLAWDKEAGK----VNFEFEPRESK-FPPRKTAAAKAGAASAAF 871
Query: 621 ASATAGGSTESTPAAAANDKKEKKDKEKEKDLSSMQAVAALGVAV---VALGEEIGSEMS 677
A + + AAA K K ++ + A + AL IG+E
Sbjct: 872 GGTVAVKAAKPAKKAAAKKVAAKTAAAKTPRKAAKKKAAPPAAGLKPSAALAAVIGAEPV 931
Query: 678 TR 679
R
Sbjct: 932 AR 933
>gnl|CDD|213371 cd12837, EcCorA-like_u1, uncharacterized subgroup of the
Escherichia coli Mg2+ transporter CorA_like subfamily.
A uncharacterized subgroup of the Escherichia coli
CorA-Salmonella typhimurium ZntB_like family
(EcCorA_ZntB-like) family of the MIT superfamily of
essential membrane proteins involved in transporting
divalent cations (uptake or efflux) across membranes.
The EcCorA_ZntB-like family includes the Mg2+
transporters Escherichia coli and Salmonella typhimurium
CorAs, which can also transport Co2+, and Ni2+.
Structures of the intracellular domain of
EcCorA_ZntB-like family members, Vibrio parahaemolyticus
and Salmonella typhimurium ZntB, form funnel-shaped
homopentamers, the tip of the funnel is formed from two
C-terminal transmembrane (TM) helices from each monomer,
and the large opening of the funnel from the N-terminal
cytoplasmic domains. The GMN signature motif of the MIT
superfamily occurs just after TM1, mutation within this
motif is known to abolish Mg2+ transport through
Salmonella typhimurium CorA. Natural variants such as
GVN and GIN, such as occur in some ZntB family proteins,
may be associated with the transport of different
divalent cations, such as zinc and cadmium. The
functional diversity of MIT transporters may also be due
to minor structural differences regulating gating,
substrate selection, and transport.
Length = 298
Score = 29.4 bits (67), Expect = 8.7
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 714 DVLNKYSHDLDEEVAHNAIFSMGLVGAGTNNARLATMLRQLAQYH 758
DVL + DLD ++ IF + L ++LR++ +
Sbjct: 120 DVLERVGADLDR-LSRR-IFRSSAKRRRRASRDLRSVLRRIGRAG 162
>gnl|CDD|113514 pfam04747, DUF612, Protein of unknown function, DUF612. This
family includes several uncharacterized proteins from
Caenorhabditis elegans.
Length = 517
Score = 29.6 bits (65), Expect = 8.8
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 611 KEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKEK 650
K E+ A+ E+TP A+ N KK KKDK+K +
Sbjct: 265 KSESENVPAASETPVEPVVETTPPASENQKKNKKDKKKSE 304
>gnl|CDD|178232 PLN02625, PLN02625, uroporphyrin-III C-methyltransferase.
Length = 263
Score = 29.2 bits (66), Expect = 8.9
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 486 VLTDRKSTPEVVAFAAVAASLIYVG--TGYHE 515
VL DR +P+++ A L+YVG GYH
Sbjct: 44 VLYDRLVSPDILDLVPPGAELLYVGKRGGYHS 75
>gnl|CDD|217349 pfam03065, Glyco_hydro_57, Glycosyl hydrolase family 57. This
family includes alpha-amylase (EC:3.2.1.1),
4--glucanotransferase (EC:2.4.1.-) and amylopullulanase
enzymes.
Length = 312
Score = 29.3 bits (66), Expect = 9.9
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 1/66 (1%)
Query: 510 GTGYHEVASAILQTLIELPVSELQDGHYSRFLPLALAITYLGKKDAIDTTLAALEVLPDP 569
+HE S IL+ L +LP EL+ + ++ I G K I +A+ D
Sbjct: 234 WGEHHENESGILEFLYQLPE-ELEKNGLIETVTVSEFIKKFGPKGIIYLPIASTLSGADI 292
Query: 570 FRSMAK 575
++
Sbjct: 293 EGDLSA 298
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 29.5 bits (66), Expect = 10.0
Identities = 29/76 (38%), Positives = 33/76 (43%), Gaps = 18/76 (23%)
Query: 590 LVVQEFLHVCSEHYTPTTSSAKEETSATGTAASATAGGSTESTPAAAANDKKEKKDKEKE 649
L+VQ F S+H P + A E G+AA ATA S EST AA D
Sbjct: 1116 LLVQFF----SDH-APRIARAVSEAINAGSAAVATA--SPESTVDAAVRAHGVLAD---- 1164
Query: 650 KDLSSMQAVAALGVAV 665
AVAAL AV
Sbjct: 1165 -------AVAALSPAV 1173
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
0.317 0.133 0.382
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 46,851,315
Number of extensions: 4736751
Number of successful extensions: 5196
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5111
Number of HSP's successfully gapped: 76
Length of query: 913
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 807
Effective length of database: 6,236,078
Effective search space: 5032514946
Effective search space used: 5032514946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (28.4 bits)