RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10812
(723 letters)
>gnl|CDD|216025 pfam00617, RasGEF, RasGEF domain. Guanine nucleotide exchange
factor for Ras-like small GTPases.
Length = 185
Score = 227 bits (580), Expect = 3e-70
Identities = 77/187 (41%), Positives = 117/187 (62%), Gaps = 4/187 (2%)
Query: 262 LSALEIAEQMTYIDYHIFKSIRSEEFLGQAWLKSEKLTKAPHIVLFTQRFNTMSKLVANE 321
L LE+A Q+T I+ +F +I E L AW K + +P+I F RFN +S+ VA E
Sbjct: 3 LDPLELARQLTLIESELFSAIDPRELLDSAWGKKDS-KLSPNIEAFISRFNQLSRWVATE 61
Query: 322 ILNRSNLSQRVHVIEKWIAVADILKCLNNFNGVLTIISAMNNSSVFRLKKTWDKVSKTTK 381
IL+ +L +R VI+K+I +A + LNNFN ++ IIS +N+S + RLKKTW+ VSK K
Sbjct: 62 ILSEEDLKKRAKVIKKFIKIAQHCRELNNFNSLMAIISGLNSSPISRLKKTWELVSKKYK 121
Query: 382 QTYDELRQVVDAEENFHNFKSKLQHCDPPCIPYLGMYLTEFARLDEEYPTFTKEGETNLV 441
+ +EL +++ +NF N++ L+ +PPCIP+LG+YL + ++E P F G L+
Sbjct: 122 KLLEELEELMSPSKNFKNYREALKKANPPCIPFLGLYLKDLTFIEEGNPDFLDNG---LI 178
Query: 442 NFTKIRR 448
NF K R+
Sbjct: 179 NFEKRRK 185
Score = 57.9 bits (141), Expect = 1e-09
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 554 MVDAEEKFHNLKSKLQHCDPPCIPYLGMYLTELATLDEVYPTFTKEGETNLVYFTKIRR 612
++ + F N + L+ +PPCIP+LG+YL +L ++E P F G L+ F K R+
Sbjct: 130 LMSPSKNFKNYREALKKANPPCIPFLGLYLKDLTFIEEGNPDFLDNG---LINFEKRRK 185
>gnl|CDD|238087 cd00155, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases. Small GTP-binding proteins of the Ras
superfamily function as molecular switches in
fundamental events such as signal transduction,
cytoskeleton dynamics and intracellular trafficking.
Guanine-nucleotide-exchange factors (GEFs) positively
regulate these GTP-binding proteins in response to a
variety of signals. GEFs catalyze the dissociation of
GDP from the inactive GTP-binding proteins. GTP can then
bind and induce structural changes that allow
interaction with effectors.
Length = 237
Score = 215 bits (549), Expect = 4e-65
Identities = 84/232 (36%), Positives = 141/232 (60%), Gaps = 6/232 (2%)
Query: 259 IETLSALEIAEQMTYIDYHIFKSIRSEEFLGQAW-LKSEKLTKAPHIVLFTQRFNTMSKL 317
+L E+AEQ+T +D+ +F+ I E LG W K + + +P++ F +RFN +S
Sbjct: 1 FLSLDPKELAEQLTLLDFELFRKIEPFELLGSLWSKKDKNIHLSPNLERFIERFNNLSNW 60
Query: 318 VANEILNRSNLSQRVHVIEKWIAVADILKCLNNFNGVLTIISAMNNSSVFRLKKTWDKVS 377
VA+EIL +N +R ++ K+I VA + LNNFN ++ I+SA+++S + RLKKTW+ +S
Sbjct: 61 VASEILLCTNPKKRARLLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEVLS 120
Query: 378 KTTKQTYDELRQVVDAEENFHNFKSKLQHC--DPPCIPYLGMYLTEFARLDEEYPTFTKE 435
K+ ++EL ++VD NF N++ L+ +PPC+P+LG+YL + L E P F
Sbjct: 121 SKLKKLFEELEELVDPSRNFKNYRKLLKSVGPNPPCVPFLGVYLKDLTFLHEGNPDFL-- 178
Query: 436 GETNLVNFTKIRRMANTIRDITRYQNTPYKIEYNPKVANYILDTSWIIEDED 487
E NLVNF K R++A +R+I + Q+ Y++ + + ++ +I +ED
Sbjct: 179 -EGNLVNFEKRRKIAEILREIRQLQSNSYELNRDEDILAFLWKLLELILNED 229
Score = 49.2 bits (118), Expect = 2e-06
Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 555 VDAEEKFHNLKSKLQHC--DPPCIPYLGMYLTELATLDEVYPTFTKEGETNLVYFTKIRR 612
VD F N + L+ +PPC+P+LG+YL +L L E P F E NLV F K RR
Sbjct: 134 VDPSRNFKNYRKLLKSVGPNPPCVPFLGVYLKDLTFLHEGNPDFL---EGNLVNFEK-RR 189
Query: 613 RKLKPLQHQQQQQQQQQQQQMEDEV 637
+ + L+ +Q Q + ++++
Sbjct: 190 KIAEILREIRQLQSNSYELNRDEDI 214
>gnl|CDD|214539 smart00147, RasGEF, Guanine nucleotide exchange factor for Ras-like
small GTPases.
Length = 242
Score = 214 bits (546), Expect = 2e-64
Identities = 83/231 (35%), Positives = 133/231 (57%), Gaps = 5/231 (2%)
Query: 259 IETLSALEIAEQMTYIDYHIFKSIRSEEFLGQAWLKSEKLTKAPH-IVLFTQRFNTMSKL 317
+ L E+AEQ+T +D+ +F+ I E LG W K K + +P + F +RFN +S
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 318 VANEILNRSNLSQRVHVIEKWIAVADILKCLNNFNGVLTIISAMNNSSVFRLKKTWDKVS 377
VA EIL ++ R ++ K+I VA + LNNFN ++ I+SA+++S + RLKKTW+K+
Sbjct: 61 VATEILKQTTPKDRAELLSKFIQVAKHCRELNNFNSLMAIVSALSSSPISRLKKTWEKLP 120
Query: 378 KTTKQTYDELRQVVDAEENFHNFKSKLQHC-DPPCIPYLGMYLTEFARLDEEYPTFTKEG 436
K+ ++EL +++ E N+ N++ L C PPCIP+LG+ L + +DE P F +
Sbjct: 121 SKYKKLFEELEELLSPERNYKNYREALSSCNLPPCIPFLGVLLKDLTFIDEGNPDFLEN- 179
Query: 437 ETNLVNFTKIRRMANTIRDITRYQNTPYKIEYNPKVANYILDTSWIIEDED 487
LVNF K R++A +R+I + Q+ PY + N +L DE+
Sbjct: 180 --GLVNFEKRRQIAEILREIRQLQSQPYNLRPNRSDIQSLLQQLLDHLDEE 228
Score = 54.9 bits (133), Expect = 3e-08
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 198 IETLSALEIAEQMTYIDYHIFKSIRSEEFLGQAWLKSEKLTKAPH-IVLFTQRFNTVANK 256
+ L E+AEQ+T +D+ +F+ I E LG W K K + +P + F +RFN V+N
Sbjct: 1 LLLLDPKELAEQLTLLDFELFRKIDPSELLGSVWGKRSKKSPSPLNLEAFIRRFNEVSNW 60
Query: 257 ENIETLSA 264
E L
Sbjct: 61 VATEILKQ 68
Score = 51.1 bits (123), Expect = 6e-07
Identities = 27/74 (36%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 555 VDAEEKFHNLKSKLQHC-DPPCIPYLGMYLTELATLDEVYPTFTKEGETNLVYFTKIRRR 613
+ E + N + L C PPCIP+LG+ L +L +DE P F + G N F K RR+
Sbjct: 134 LSPERNYKNYREALSSCNLPPCIPFLGVLLKDLTFIDEGNPDFLENGLVN---FEK-RRQ 189
Query: 614 KLKPLQHQQQQQQQ 627
+ L+ +Q Q Q
Sbjct: 190 IAEILREIRQLQSQ 203
>gnl|CDD|100121 cd06224, REM, Guanine nucleotide exchange factor for Ras-like
GTPases; N-terminal domain (RasGef_N), also called REM
domain (Ras exchanger motif). This domain is common in
nucleotide exchange factors for Ras-like small GTPases
and is typically found immediately N-terminal to the
RasGef (Cdc25-like) domain. REM contacts the GTPase and
is assumed to participate in the catalytic activity of
the exchange factor. Proteins with the REM domain
include Sos1 and Sos2, which relay signals from
tyrosine-kinase mediated signalling to Ras, RasGRP1-4,
RasGRF1,2, CNrasGEF, and RAP-specific nucleotide
exchange factors, to name a few.
Length = 122
Score = 47.0 bits (112), Expect = 2e-06
Identities = 23/65 (35%), Positives = 33/65 (50%)
Query: 94 DISPVEEVRNKRKESVLSTATTMRVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEIVCT 153
+I+P E + + S +RVLNVLR W+ + DF D+EL + EFL +V
Sbjct: 46 EIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYDFFDDEELLELLEEFLNRLVQE 105
Query: 154 PNLLP 158
LL
Sbjct: 106 GALLQ 110
Score = 46.3 bits (110), Expect = 4e-06
Identities = 22/65 (33%), Positives = 32/65 (49%)
Query: 659 DISPVEEVRNKRKESVLSTATTMRVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEIVCT 718
+I+P E + + S +RVLNVLR W+ + DF D+EL + EFL +V
Sbjct: 46 EIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYDFFDDEELLELLEEFLNRLVQE 105
Query: 719 PNLDF 723
L
Sbjct: 106 GALLQ 110
>gnl|CDD|214571 smart00229, RasGEFN, Guanine nucleotide exchange factor for
Ras-like GTPases; N-terminal motif. A subset of guanine
nucleotide exchange factor for Ras-like small GTPases
appear to possess this domain N-terminal to the RasGef
(Cdc25-like) domain. The recent crystal structureof Sos
shows that this domain is alpha-helical and plays a
"purely structural role" (Nature 394, 337-343).
Length = 127
Score = 41.6 bits (98), Expect = 2e-04
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 117 RVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEI 150
RVLN+LR W+ + +DF D +L LEFLE +
Sbjct: 74 RVLNILRTWVENYWEDFEDDPKLISFLLEFLELV 107
Score = 41.6 bits (98), Expect = 2e-04
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 682 RVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEI 715
RVLN+LR W+ + +DF D +L LEFLE +
Sbjct: 74 RVLNILRTWVENYWEDFEDDPKLISFLLEFLELV 107
>gnl|CDD|179798 PRK04239, PRK04239, hypothetical protein; Provisional.
Length = 110
Score = 37.6 bits (88), Expect = 0.003
Identities = 16/25 (64%), Positives = 20/25 (80%)
Query: 610 IRRRKLKPLQHQQQQQQQQQQQQME 634
IRRRKL+ LQ Q Q+QQQ Q++Q E
Sbjct: 6 IRRRKLEELQKQAQEQQQAQEEQEE 30
>gnl|CDD|216828 pfam01984, dsDNA_bind, Double-stranded DNA-binding domain. This
domain is believed to bind double-stranded DNA of 20
bases length.
Length = 105
Score = 36.4 bits (85), Expect = 0.007
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 5/35 (14%)
Query: 610 IRRRKLKPLQHQQ-----QQQQQQQQQQMEDEVSS 639
IRR +L LQ QQ QQQQ++QQQQ E + +
Sbjct: 1 IRRARLAELQQQQGGLEEQQQQEEQQQQEEAQKQA 35
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 37.7 bits (88), Expect = 0.019
Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 8/73 (10%)
Query: 617 PLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIATSASSNPRDISPVEEVRNKRKESVLS 676
Q Q Q + A +A + +PV + + KRKE+V+
Sbjct: 142 LQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAPVMD-KPKRKEAVI- 199
Query: 677 TATTMRVLNVLRH 689
V+NV H
Sbjct: 200 ------VMNVAAH 206
>gnl|CDD|216026 pfam00618, RasGEF_N, RasGEF N-terminal motif. A subset of guanine
nucleotide exchange factor for Ras-like small GTPases
appear to possess this motif/domain N-terminal to the
RasGef (Cdc25-like) domain.
Length = 94
Score = 34.3 bits (79), Expect = 0.029
Identities = 18/40 (45%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 111 STATTMRVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEI 150
+RVLNVLR WI + DF+ D EL L LEE
Sbjct: 59 YQEIRIRVLNVLRKWIENYNSDFVDDPEL----LSLLEEF 94
Score = 34.3 bits (79), Expect = 0.029
Identities = 18/40 (45%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 676 STATTMRVLNVLRHWISKHTQDFIQDKELRYMTLEFLEEI 715
+RVLNVLR WI + DF+ D EL L LEE
Sbjct: 59 YQEIRIRVLNVLRKWIENYNSDFVDDPEL----LSLLEEF 94
>gnl|CDD|217451 pfam03249, TSA, Type specific antigen. There are several antigenic
variants in Rickettsia tsutsugamushi, and a
type-specific antigen (TSA) of 56-kilodaltons located on
the rickettsial surface is responsible for the
variation. TSA proteins are probably integral membrane
proteins.
Length = 502
Score = 33.3 bits (76), Expect = 0.52
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 7/62 (11%)
Query: 588 TLDEVYPTFTKEGETNLVYFTKIRRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAF 647
L+E+ +F +G + +I+ + P Q QQQ Q QQQQ Q ++ AA A
Sbjct: 280 VLEELRESF--DGYIGNAFANQIQLNFVIPQQAQQQGQGQQQQAQ-----ATAQEAAAAA 332
Query: 648 AI 649
A+
Sbjct: 333 AV 334
>gnl|CDD|151935 pfam11498, Activator_LAG-3, Transcriptional activator LAG-3. The
C.elegans Notch pathway, involved in the control of
growth, differentiation and patterning in animal
development, relies on either of the receptors GLP-1 or
LIN-12. Both these receptors promote signalling by the
recruitment of LAG-3 to target promoters, where it then
acts as a transcriptional activator. LAG-3 works as a
ternary complex together with the DNA binding protein,
LAG-1.
Length = 476
Score = 32.2 bits (72), Expect = 1.0
Identities = 12/67 (17%), Positives = 24/67 (35%)
Query: 596 FTKEGETNLVYFTKIRRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIATSASS 655
F + + Y +++ +L+ QQQQ Q QQ + + I +
Sbjct: 393 FATQAHQHAAYLQQMQHMRLQEQIQHQQQQAQHHQQAQQQHQQPAQHGQMGYGIPNGYPA 452
Query: 656 NPRDISP 662
+ +P
Sbjct: 453 HMHGHAP 459
Score = 30.7 bits (68), Expect = 3.2
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 611 RRRKLKPLQHQQQQQQQQQQQQM 633
+R++ QHQQQQQQ+ QQQQM
Sbjct: 348 QRQQQIMHQHQQQQQQEHQQQQM 370
Score = 29.9 bits (66), Expect = 5.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 612 RRKLKPLQHQQQQQQQQQQQQM 633
+++ LQ QQQ Q QQ QM
Sbjct: 366 QQQQMLLQQQQQMHQLQQHHQM 387
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 32.2 bits (74), Expect = 1.1
Identities = 9/20 (45%), Positives = 9/20 (45%), Gaps = 2/20 (10%)
Query: 618 LQHQQQQQQQQQ--QQQMED 635
LQ Q Q Q QQ ME
Sbjct: 573 LQVTQGGQGGQSEMQQAMEG 592
Score = 32.2 bits (74), Expect = 1.3
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 619 QHQQQQQQQQQQQQMEDE 636
QQ QQ Q QQQ + +
Sbjct: 636 PGQQGQQGQGQQQGQQGQ 653
>gnl|CDD|219782 pfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25. Rpc25
is a strongly conserved subunit of RNA polymerase III
and has homology to Rpa43 in RNA polymerase I, Rpb7 in
RNA polymerase II and the archaeal RpoE subunit. Rpc25
is required for transcription initiation and is not
essential for the elongating properties of RNA
polymerase III.
Length = 121
Score = 30.4 bits (69), Expect = 1.2
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 121 VLRHWISKHTQDFIQDKELRYMTLEFLEEIVCTPNLL--PAEYKAATQ 166
+L I + + I+ ++L F ++I P+ L P+E+ Q
Sbjct: 6 ILTGKIKSSSAEGIK------VSLGFFDDIFIPPDNLPEPSEFDEEEQ 47
>gnl|CDD|225029 COG2118, COG2118, DNA-binding protein [General function prediction
only].
Length = 116
Score = 30.0 bits (68), Expect = 1.5
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 609 KIRRRKLKPLQHQQQQQQQQQQQQ 632
+IRRRKL LQ Q + ++Q++ Q+
Sbjct: 8 EIRRRKLAELQRQAKLEEQREAQE 31
>gnl|CDD|173487 PTZ00236, PTZ00236, mitochondrial import inner membrane translocase
subunit tim17; Provisional.
Length = 164
Score = 30.8 bits (70), Expect = 1.5
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 611 RRRKLKPLQHQQQQQQQQQQQQMED 635
RR+ P Q QQQQ+ ++Q + ED
Sbjct: 135 RRQMRTPRQQFQQQQEMEKQLEEED 159
Score = 29.2 bits (66), Expect = 4.1
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 613 RKLKPLQHQQQQQQQQQQQQMEDE 636
R+ QQ QQQQ+ ++Q+E+E
Sbjct: 135 RRQMRTPRQQFQQQQEMEKQLEEE 158
>gnl|CDD|236544 PRK09506, mrcB, bifunctional glycosyl transferase/transpeptidase;
Reviewed.
Length = 830
Score = 30.9 bits (70), Expect = 2.8
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 616 KPLQHQQQQQQQQQQQQMEDEV 637
+P Q QQQ QQQ +Q+ D V
Sbjct: 799 QPSQPQQQPQQQPAEQKDSDGV 820
>gnl|CDD|222647 pfam14282, FlxA, FlxA-like protein. This family includes FlxA from
E. coli. The expression of FlxA is regulated by the FliA
sigma factor, a transcription factor specific for class
3 flagellar operons. However FlxA is not required for
flagellar function or formation.
Length = 106
Score = 28.9 bits (65), Expect = 2.8
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 619 QHQQQQ---QQQQQQQQMEDEVSSTST 642
Q QQQQ QQQQQ +ED S TS
Sbjct: 69 QLQQQQSEEAQQQQQSSIEDSPSQTSA 95
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 30.7 bits (69), Expect = 3.0
Identities = 9/59 (15%), Positives = 19/59 (32%)
Query: 605 VYFTKIRRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIATSASSNPRDISPV 663
+ K+R + + QQQQQQ + + +A + + +
Sbjct: 340 LKQMKLRNMRGQQQTQQQQQQQGGNHPAAHQQQMNQQVGQGGQMVALGYLNIQGNQGGL 398
>gnl|CDD|233867 TIGR02436, TIGR02436, four helix bundle protein. This family
describes a protein of unknown function whose structure
is a bundle of four long alpha helices. Some of the
first members of this family were found encoded in the
(atypically large) intervening sequence (IVS) of
Leptospira 23S RNA, a region often present in the rRNA
gene and removed during rRNA processing without
re-ligation. However, this location is not conserved,
and naming this protein as a 23S RNA protein is both
confusing and inaccurate.
Length = 108
Score = 29.0 bits (66), Expect = 3.0
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 249 RFNTVANKENIETLSALEIAEQMTYIDYHIFKSIRSE 285
RF ++A ET + LE+A+ + YID ++ + E
Sbjct: 56 RFLSIALGSAAETETQLELAKDLGYIDEEEYEELLEE 92
>gnl|CDD|236545 PRK09510, tolA, cell envelope integrity inner membrane protein
TolA; Provisional.
Length = 387
Score = 29.8 bits (67), Expect = 5.4
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 609 KIRRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIA 650
++ ++ K + +Q +Q+Q E+ + + AA A A A
Sbjct: 110 RLAAQEQKKQAEEAAKQAALKQKQAEEAAAKAAAAAKAKAEA 151
>gnl|CDD|132086 TIGR03042, PS_II_psbQ_bact, photosystem II protein PsbQ. This
protein through the member sll1638 from Synechocystis
sp. PCC 6803, was shown to be part of the cyanobacteria
photosystem II. It is homologous to (but quite diverged
from) the chloroplast PsbQ protein, called
oxygen-evolving enhancer protein 3 (OEE3). We designate
this cyanobacteria protein PsbQ by homology [Energy
metabolism, Photosynthesis].
Length = 142
Score = 28.5 bits (64), Expect = 6.1
Identities = 28/122 (22%), Positives = 50/122 (40%), Gaps = 25/122 (20%)
Query: 59 RKSQRSLLLIFSTRSSTSTAATAFAIATS--ASSNPRDISPVEEVRNKRK-ESVLSTATT 115
+S SLLL+ F ++ S A++ P SP + + +R+ E + +
Sbjct: 1 LRSLASLLLV---------LLLTFLVSCSGPAAAVPPTYSPAQLAQIQRQAEGIEAAKDR 51
Query: 116 MRVLNVL---RHWISKHTQDFIQD--KELRYMTLEFLEEIVCTPNLLPAEYKAATQLTRM 170
+ L L W+ T++ I E+R + +L +LLP + K A L +
Sbjct: 52 LPELASLVAKEDWV--FTRNLIHGPMGEVR-REMTYL-----NQSLLPKDQKEALALAKE 103
Query: 171 LT 172
L
Sbjct: 104 LK 105
>gnl|CDD|113452 pfam04684, BAF1_ABF1, BAF1 / ABF1 chromatin reorganising factor.
ABF1 is a sequence-specific DNA binding protein involved
in transcription activation, gene silencing and
initiation of DNA replication. ABF1 is known to remodel
chromatin, and it is proposed that it mediates its
effects on transcription and gene expression by
modifying local chromatin architecture. These functions
require a conserved stretch of 20 amino acids in the
C-terminal region of ABF1 (amino acids 639 to 662 S.
cerevisiae). The N-terminal two thirds of the protein
are necessary for DNA binding, and the N-terminus (amino
acids 9 to 91 in S. cerevisiae) is thought to contain a
novel zinc-finger motif which may stabilise the protein
structure.
Length = 508
Score = 29.7 bits (66), Expect = 6.7
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 619 QHQQQQQQQQQQQQMEDEVSS 639
HQ QQQ Q Q+Q + V +
Sbjct: 321 HHQHQQQDLQHQEQHQQHVDN 341
>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 = 29.3 bits (66), Expect = 6.9
Identities = 13/62 (20%), Positives = 29/62 (46%)
Query: 611 RRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIATSASSNPRDISPVEEVRNKR 670
R++L ++++ +Q+ QQ + AA + + + S S+ P EE + +
Sbjct: 125 LRQRLAKEKYEEWCRQKAQQAAKQRTPKHKKEAAESASSSLSGSAKPERNVSQEEAKKRL 184
Query: 671 KE 672
+E
Sbjct: 185 QE 186
>gnl|CDD|187823 cd09692, Cas5_I-B, CRISPR/Cas system-associated RAMP superfamily
protein Cas5. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas5 is a RAMP superfamily protein; Subunit of the
Cascade complex.
Length = 189
Score = 29.0 bits (65), Expect = 6.9
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 557 AEEKFHNLKSKLQHCDPPCIPYLGMYLTELATLDEVYPTFTKEGETNLV 605
+EKF LK+KL+ + IPYLG +A +D V E + V
Sbjct: 114 DDEKFEELKNKLEALESIFIPYLGKSE-FIANIDYVGKFENTELADDTV 161
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 27.6 bits (62), Expect = 7.0
Identities = 8/43 (18%), Positives = 18/43 (41%)
Query: 609 KIRRRKLKPLQHQQQQQQQQQQQQMEDEVSSTSTAATAFAIAT 651
K + R+ + QQ + +Q+Q ++E + S +
Sbjct: 44 KAKAREADKARKQQLKAKQRQAANDDEEDTIESVTQSQSNKLP 86
>gnl|CDD|222639 pfam14271, DUF4359, Domain of unknown function (DUF4359). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 130 amino acids in length.
There are two completely conserved residues (P and S)
that may be functionally important.
Length = 107
Score = 27.7 bits (62), Expect = 7.1
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 12/88 (13%)
Query: 158 PAEYK--AATQLTRMLTKEECTKHET--NLQDLL--APPQVANKENIETLSAL-EIAEQM 210
+Y+ A QLT L E C + + LQ L+ P V ++ L + +Q
Sbjct: 11 KEDYEEYAGEQLTEYLKDELCQEKKLPMFLQLLISACPTLVDSQR-----PQLQALIDQF 65
Query: 211 TYIDYHIFKSIRSEEFLGQAWLKSEKLT 238
T + SI + E GQ L S K
Sbjct: 66 TRRQNYGLFSIYTTELEGQDPLPSYKFE 93
>gnl|CDD|213932 TIGR04319, SerAla_Lrha_rpt, surface protein repeat Ser-Ala-175.
This serine and alanine-rich surface protein repeat,
about 175 amino acids long, occurs up to nine times in
surface proteins of some Lactobacillus strains,
particularly in Lactobacillus rhamnosus. Members
proteins have the N-terminal variant signal sequence
described by TIGR03715 and C-terminal LPXTG signals for
surface attachment by sortase.
Length = 175
Score = 28.7 bits (64), Expect = 7.2
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 1/85 (1%)
Query: 6 VVGPLAAVKLYAGRRSIGCCEGESAARQATPRAS-FQQDSPQHSSKAGVVITSFRKSQRS 64
G L A YA + S S A +A AS ++ Q SS A + ++ +
Sbjct: 82 AAGNLDAASSYANQASKAASNASSLADKANSAASKALSEALQASSAAAIASSAASSAATL 141
Query: 65 LLLIFSTRSSTSTAATAFAIATSAS 89
+ S + S A+ A A+SAS
Sbjct: 142 AGSLASANDAKSDASAASDAASSAS 166
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 29.3 bits (66), Expect = 7.8
Identities = 10/26 (38%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 612 RRKLKPLQHQQQQ---QQQQQQQQME 634
+ +L+ Q QQ+ +QQ QQQ++E
Sbjct: 186 KAELEEKQSQQKTLLYEQQAQQQKLE 211
>gnl|CDD|236910 PRK11433, PRK11433, aldehyde oxidoreductase 2Fe-2S subunit;
Provisional.
Length = 217
Score = 28.6 bits (64), Expect = 8.9
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 6/65 (9%)
Query: 63 RSLLLIFSTRSSTSTAATAFAIATSASSNPRD---ISPVE-EVRNKRKESVLSTATTMRV 118
R LL S ++ + AA + ++ ISPV +V K ++ + T TT+
Sbjct: 14 RRDLLKVSAATAATAAAYPHSTLAASVPAATPAPEISPVTLKVNGKTEQLEVDTRTTL-- 71
Query: 119 LNVLR 123
L+ LR
Sbjct: 72 LDALR 76
>gnl|CDD|131641 TIGR02592, cas_Cas5h, CRISPR-associated protein Cas5, subtype
I-B/HMARI. This is a CRISPR-associated protein unique
to the hmari subtype of cas genes and CRISPR repeat,
which is the only subtype present in Haloarcula
marismortui ATCC 43049. The hmari type, though uncommon,
is also found in the Aquificae, Thermotogae, Firmicutes,
and Dictyoglomi [Mobile and extrachromosomal element
functions, Other].
Length = 241
Score = 28.7 bits (64), Expect = 9.2
Identities = 21/118 (17%), Positives = 38/118 (32%), Gaps = 26/118 (22%)
Query: 393 AEENFHNFKSKLQHCDPPCIPYLGMYLTEF-ARLD--EEYPTFTKEGETNLVNFTKIRR- 448
+E K +L++ PYLG ++E A + E E L + +
Sbjct: 114 DDEVPKELKDRLENFKFIYTPYLG--VSEHIANITYVGYL-----EAEEKLDDTNSVDSI 166
Query: 449 MANTIRDITRYQNTPYKIEYNPKVANYILDTSWIIEDEDMANTIRDITQYQNTPYKIE 506
+ N + +I I+ K ++ IR+ + PY E
Sbjct: 167 VPNDVYEIQLESKNFNDIKEIIKK---------------SSSKIREFKYEEMLPYAFE 209
>gnl|CDD|215106 PLN00212, PLN00212, glutelin; Provisional.
Length = 493
Score = 29.0 bits (65), Expect = 9.4
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 615 LKPLQHQQQQQQQQQQQQMEDEV 637
L+P QQQ+Q QQQQQ++ +V
Sbjct: 266 LQPTLTQQQEQAQQQQQRLYQQV 288
>gnl|CDD|221896 pfam13016, Gliadin, Cys-rich Gliadin N-terminal. This is a
cysteine-rich N-terminal region of gliadin and avenin
plant proteins. The exact function is not known.
Length = 77
Score = 27.0 bits (60), Expect = 9.6
Identities = 7/15 (46%), Positives = 8/15 (53%)
Query: 619 QHQQQQQQQQQQQQM 633
Q QQ Q QQQ+
Sbjct: 1 QQQQPLIQPSLQQQL 15
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 0.129 0.370
Gapped
Lambda K H
0.267 0.0717 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 35,831,800
Number of extensions: 3448677
Number of successful extensions: 5458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5183
Number of HSP's successfully gapped: 85
Length of query: 723
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 619
Effective length of database: 6,324,786
Effective search space: 3915042534
Effective search space used: 3915042534
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: 63 (28.1 bits)