RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11905
(317 letters)
>gnl|CDD|220824 pfam10607, CLTH, CTLH/CRA C-terminal to LisH motif domain. RanBPM
is a scaffolding protein and is important in regulating
cellular function in both the immune system and the
nervous system. This domain is at the C-terminus of the
proteins and is the binding domain for the CRA motif
(for CT11-RanBPM), which is comprised of approximately
100 amino acids at the C terminal of RanBPM. It was
found to be important for the interaction of RanBPM with
fragile X mental retardation protein (FMRP), but its
functional significance has yet to be determined. This
region contains CTLH and CRA domains annotated by SMART;
however, these may be a single domain, and it is
refereed to as a C-terminal to LisH motif.
Length = 144
Score = 129 bits (328), Expect = 2e-37
Identities = 56/147 (38%), Positives = 83/147 (56%), Gaps = 4/147 (2%)
Query: 62 TMENRIMIRDAIQNGRIQEATALVNELYPELLDNDRYIYFHLQQLHLLELIRENKIEEAL 121
+ R IR+++ NG ++EA NE PELL + + F L+ +ELIRE KI EAL
Sbjct: 1 VFKERNKIRESLLNGDLEEALEWCNENKPELLKINSNLEFELRLQQFIELIREGKILEAL 60
Query: 122 HFAQEQLSESGQSDPDILNELERTMALLAFGEP-MNSPFGDLLNQAHRQKVASQLNTAIL 180
+A+E L+ L E+++ M LLAF +P +SP+ LL+ + +K+A++ N AIL
Sbjct: 61 EYARENLAPFFNE--QHLKEIQKLMGLLAFPDPTDSSPYKSLLSPSRWEKLANEFNRAIL 118
Query: 181 KMEHHESTSPRLLNLLKIILWSQGELD 207
K+ S SP L LLK L + L
Sbjct: 119 KLLGLSSESP-LEILLKAGLSALKTLL 144
>gnl|CDD|214806 smart00757, CRA, CT11-RanBPM. protein-protein interaction domain
present in crown eukaryotes (plants, animals, fungi).
Length = 99
Score = 90.0 bits (224), Expect = 1e-22
Identities = 40/99 (40%), Positives = 61/99 (61%), Gaps = 1/99 (1%)
Query: 115 NKIEEALHFAQEQLSESGQSDPDILNELERTMALLAFGEPMN-SPFGDLLNQAHRQKVAS 173
KIEEAL +A+E L+ + L ELE+TMALLA+ +P SP+ +LL+ + R+K+A
Sbjct: 1 GKIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAE 60
Query: 174 QLNTAILKMEHHESTSPRLLNLLKIILWSQGELDKKKIE 212
+LN+AIL++ H +S+ L LL L + L +K
Sbjct: 61 ELNSAILELLHGKSSESPLEILLSAGLAALKTLLEKGGV 99
Score = 31.5 bits (72), Expect = 0.13
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 259 ALNTAILKMEHHESTSPRLLNLLKIILWSQGELDKKKIE 297
LN+AIL++ H +S+ L LL L + L +K
Sbjct: 61 ELNSAILELLHGKSSESPLEILLSAGLAALKTLLEKGGV 99
>gnl|CDD|128914 smart00668, CTLH, C-terminal to LisH motif. Alpha-helical motif of
unknown function.
Length = 58
Score = 59.9 bits (146), Expect = 5e-12
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 62 TMENRIMIRDAIQNGRIQEATALVNELYPELLDNDRYIYFHLQQLHLLELIRENKIEE 119
+ R IR+ I G EA ++ L P LL+ + + F L++ LEL+R+ K+EE
Sbjct: 1 EFDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKLEE 58
>gnl|CDD|128913 smart00667, LisH, Lissencephaly type-1-like homology motif.
Alpha-helical motif present in Lis1, treacle, Nopp140,
some katanin p60 subunits, muskelin, tonneau, LEUNIG
and numerous WD40 repeat-containing proteins. It is
suggested that LisH motifs contribute to the regulation
of microtubule dynamics, either by mediating
dimerisation, or else by binding cytoplasmic dynein
heavy chain or microtubules directly.
Length = 34
Score = 47.4 bits (114), Expect = 8e-08
Identities = 16/34 (47%), Positives = 26/34 (76%)
Query: 23 IQRSDMNKLIMNYLVTEGFKEAAEKFQQESGITP 56
I RS++N+LI+ YL+ G++E AE Q+ESG++
Sbjct: 1 ISRSELNRLILEYLLRNGYEETAETLQKESGLSL 34
>gnl|CDD|149534 pfam08513, LisH, LisH. The LisH (lis homology) domain mediates
protein dimerisation and tetramerisation. The LisH
domain is found in Sif2, a component of the Set3
complex which is responsible for repressing meiotic
genes. It has been shown that the LisH domain helps
mediate interaction with components of the Set3
complex.
Length = 27
Score = 43.8 bits (105), Expect = 1e-06
Identities = 14/27 (51%), Positives = 20/27 (74%)
Query: 26 SDMNKLIMNYLVTEGFKEAAEKFQQES 52
++N+LI +YLV G+KE AE F +ES
Sbjct: 1 EELNRLIYDYLVKSGYKETAEAFAKES 27
>gnl|CDD|220550 pfam10070, DUF2309, Uncharacterized protein conserved in bacteria
(DUF2309). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 783
Score = 34.5 bits (80), Expect = 0.067
Identities = 31/106 (29%), Positives = 45/106 (42%), Gaps = 17/106 (16%)
Query: 41 FKEAAEKFQQESGITPSLDLNTMENRIMIRDAIQNGRIQEA---TALVNELYPELLDNDR 97
F+EAA + + G + R R+A+ GRI EA AL L L D
Sbjct: 32 FEEAAARLARLFGARLYMP------RSDYREALAEGRIDEADLEAALAEALADSGLPAD- 84
Query: 98 YIYFHLQQLHLLELIRENKIEEALHFAQEQL-SESGQSDPDILNEL 142
L+ L L L++E+ + L + L S SG PD ++E
Sbjct: 85 -----LEAL-LAALLQEDAVPPRLPTLADLLDSLSGIDWPDEVDEQ 124
>gnl|CDD|233839 TIGR02384, RelB_DinJ, addiction module antitoxin, RelB/DinJ
family. Plasmids may be maintained stably in bacterial
populations through the action of addiction modules, in
which a toxin and antidote are encoded in a cassette on
the plasmid. In any daughter cell that lacks the
plasmid, the toxin persists and is lethal after the
antidote protein is depleted. Toxin/antitoxin pairs are
also found on main chromosomes, and likely represent
selfish DNA. Sequences in the seed for this alignment
all were found adjacent to toxin genes. The resulting
model appears to describe a narrower set of proteins
than pfam04221, although many in the scope of this
model are not obviously paired with toxin proteins.
Several toxin/antitoxin pairs may occur in a single
species [Cellular processes, Toxin production and
resistance, Mobile and extrachromosomal element
functions, Other].
Length = 84
Score = 30.7 bits (70), Expect = 0.18
Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 5/71 (7%)
Query: 28 MNKLIMNYLVTEGFKEAAEKFQQESGITPSLDLNTMENRIMIRDAIQNGRIQEATALVNE 87
M ++ + E K+ A +E G+TPS + R+ ++ I+ + L N+
Sbjct: 1 MATATISIRIDEELKKEAYAVFEELGLTPSTAI-----RMFLKQVIREQGLPFDLRLPND 55
Query: 88 LYPELLDNDRY 98
++ +
Sbjct: 56 ETLAAIEEIKE 66
>gnl|CDD|173924 cd02173, ECT, CTP:phosphoethanolamine cytidylyltransferase (ECT).
CTP:phosphoethanolamine cytidylyltransferase (ECT)
catalyzes the conversion of phosphoethanolamine to
CDP-ethanolamine as part of the CDP-ethanolamine
biosynthesis pathway. ECT expression in hepatocytes is
localized predominantly to areas of the cytoplasm that
are rich in rough endoplasmic reticulum. Several ECTs,
including yeast and human ECT, have large repetitive
sequences located within their N- and C-termini.
Length = 152
Score = 30.3 bits (69), Expect = 0.63
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 95 NDRYIY-------FHLQQLHLLELIRE--NKIEEALHFAQEQLSESGQSDPDILNELERT 145
D+ +Y FH+ + LE RE + + +H Q G + P I+N ER
Sbjct: 1 GDKVVYVDGAFDLFHIGHIEFLEKARELGDYLIVGVHDDQTVNEYKGSNYP-IMNLHERV 59
Query: 146 MALLA 150
+++LA
Sbjct: 60 LSVLA 64
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 30.9 bits (70), Expect = 0.94
Identities = 11/60 (18%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 71 DAIQNGRIQEATALVNELYPELLDNDRYIYFHLQQLHLLELIRENKIEEALHFAQEQLSE 130
+AI NG ++ +++++Y D + I ++ L+E + + + + + QL
Sbjct: 252 NAIFNGDVKRVFTVLDDVYYSGKDYEVLIQQAIED--LVEDLERERANDIIQVS-RQLLN 308
>gnl|CDD|183918 PRK13252, PRK13252, betaine aldehyde dehydrogenase; Provisional.
Length = 488
Score = 29.8 bits (68), Expect = 2.1
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 142 LERTMALLAFGEPM--NSPFGDLLNQAHRQKVAS 173
LER + G+PM + FG L++ AHR KV
Sbjct: 305 LERVERIRI-GDPMDPATNFGPLVSFAHRDKVLG 337
>gnl|CDD|132044 TIGR02999, Sig-70_X6, RNA polymerase sigma factor, TIGR02999
family. This group of sigma factors are members of the
sigma-70 family (TIGR02937) and are found in a variety
of species including Rhodopirellula baltica which
encodes a paralogous group of five.
Length = 183
Score = 28.8 bits (65), Expect = 2.7
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 59 DLNTMENRIMIRDAIQNGRIQEATALVNELYPELLDND 96
+L + R + R+ +G+ + TALV+E Y L D D
Sbjct: 29 ELRRIARRQLRRER--SGQTLQTTALVHEAYLRLSDQD 64
>gnl|CDD|237905 PRK15083, PRK15083, PTS system mannitol-specific transporter
subunit IICBA; Provisional.
Length = 639
Score = 29.3 bits (66), Expect = 3.5
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 15/79 (18%)
Query: 77 RIQEA--TALVNELYPELLDNDRYIYFHLQQLHLLELIREN--------KIEEALHFAQE 126
R+ A E + L + F +L +L EN EEA+ FA E
Sbjct: 465 RLVAAQRHTENEEKVKDSLKDS----FEDSSANLFKLGAENIFLGLKAATKEEAIRFAGE 520
Query: 127 QLSESGQSDPDILNE-LER 144
QL + G +P+ ++ L+R
Sbjct: 521 QLVKGGYVEPEYVDAMLDR 539
>gnl|CDD|214755 smart00638, LPD_N, Lipoprotein N-terminal Domain.
Length = 574
Score = 28.8 bits (65), Expect = 4.8
Identities = 15/97 (15%), Positives = 32/97 (32%), Gaps = 2/97 (2%)
Query: 16 NKLETIHIQRS-DMNKLIMNYLVTEGFKEAAEKFQQESGITPSLDLNTMENRIMIRDAIQ 74
I + ++ ++N G AEK + + +L + N I+ +
Sbjct: 150 KAELQIQVTKTKNLNNCQQREAYHFGLAAYAEKCPECTNRMGNLKSTSSVNYIIKNGKLG 209
Query: 75 NGRIQEATALVNELY-PELLDNDRYIYFHLQQLHLLE 110
I+ + P + + + I Q+L L
Sbjct: 210 VLIIEAVVTEEKVVVSPNIYNGQKAIVESRQKLTLKS 246
>gnl|CDD|225394 COG2838, Icd, Monomeric isocitrate dehydrogenase [Energy production
and conversion].
Length = 744
Score = 28.2 bits (63), Expect = 6.4
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 5/74 (6%)
Query: 31 LIMNYLVTEGFKEAAEKFQQ---ESGITPSLDLNTMENRIMIRDAIQNGRIQEATALVNE 87
+I + V +K+ K G+ + L+ + ++I A Q I+ V
Sbjct: 267 IIFGHAVKVFYKDVFAKHGDLFDALGVNVNNGLSDLYSKIESLPASQRAEIEADIHAVYA 326
Query: 88 LYPEL--LDNDRYI 99
P+L +D+D+ I
Sbjct: 327 HRPDLAMVDSDKGI 340
>gnl|CDD|237080 PRK12370, PRK12370, invasion protein regulator; Provisional.
Length = 553
Score = 28.3 bits (63), Expect = 6.7
Identities = 17/74 (22%), Positives = 30/74 (40%), Gaps = 5/74 (6%)
Query: 75 NGRIQEATALVNELYPELLDNDRYIYFHLQQLHLLELIRENKIEEALHFAQEQLSESGQS 134
G+++EA +NE LD R L I++A+ E S+ Q
Sbjct: 385 AGQLEEALQTINECLK--LDPTR---AAAGITKLWITYYHTGIDDAIRLGDELRSQHLQD 439
Query: 135 DPDILNELERTMAL 148
+P +L+ ++L
Sbjct: 440 NPILLSMQVMFLSL 453
>gnl|CDD|216899 pfam02142, MGS, MGS-like domain. This domain composes the whole
protein of methylglyoxal synthetase and the domain is
also found in Carbamoyl phosphate synthetase (CPS)
where it forms a regulatory domain that binds to the
allosteric effector ornithine. This family also
includes inosicase. The known structures in this family
show a common phosphate binding site.
Length = 92
Score = 26.3 bits (59), Expect = 7.3
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 7/48 (14%)
Query: 47 KFQQESGITPSLDLNT----MENRIMIRDAIQNGRIQEATALVNELYP 90
KF +E+GI + T R+ I D I+NG I ++N LYP
Sbjct: 24 KFLKEAGIPTEVVNKTGEGRPGGRVQIGDLIKNGEID---LVINTLYP 68
>gnl|CDD|235536 PRK05627, PRK05627, bifunctional riboflavin kinase/FMN
adenylyltransferase; Reviewed.
Length = 305
Score = 27.8 bits (63), Expect = 7.8
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 42 KEAAEKFQQESGITPSLDLNTMENRI---MIRDAIQNGRIQEATAL 84
KEA ++F E I P + + R+ IR A+ G ++ A L
Sbjct: 138 KEAGKEFGFEVTIVPEVKEDGE--RVSSTAIRQALAEGDLELANKL 181
>gnl|CDD|212571 cd11698, DHR2_DOCK9, Dock Homology Region 2, a GEF domain, of
Class D Dedicator of Cytokinesis 9. Dock9, also called
Zizimin1, is an atypical guanine nucleotide exchange
factor (GEF) that lacks the conventional Dbl homology
(DH) domain. As a GEF, it activates the small GTPase
Cdc42 by exchanging bound GDP for free GTP. It plays
important roles in spine formation and dendritic
growth. DOCK proteins are divided into four classes
(A-D) based on sequence similarity and domain
architecture; class D includes Dock9, 10 and 11. All
DOCKs contain two homology domains: the DHR-1 (Dock
homology region-1), also called CZH1 (CED-5, Dock180,
and MBC-zizimin homology 1), and DHR-2 (also called
CZH2 or Docker). The DHR-1 domain binds
phosphatidylinositol-3,4,5-triphosphate. This alignment
model represents the DHR-2 domain of Dock9, which
contains the catalytic GEF activity for Cdc42. Class D
DOCKs also contain a Pleckstrin homology (PH) domain at
the N-terminus.
Length = 415
Score = 27.7 bits (61), Expect = 8.1
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 14/59 (23%)
Query: 12 KTWLNKLETIHIQRSDMNK----------LIMNYLVTEG-FKEAAEKFQQESGITPSLD 59
KTWL+ + IH++ D+++ L+ YL +G F++ F+ ITP++D
Sbjct: 4 KTWLDSMARIHVKNGDLSEAAMCYVHVAALVAEYLTRKGMFRQGCTAFRV---ITPNID 59
>gnl|CDD|177949 PLN02315, PLN02315, aldehyde dehydrogenase family 7 member.
Length = 508
Score = 27.9 bits (62), Expect = 9.2
Identities = 14/38 (36%), Positives = 24/38 (63%)
Query: 231 LSFTQSSYLLSLVSSTCNAATGRYSIKVALNTAILKME 268
+SFT SS + +V T NA G+ ++++ N AI+ M+
Sbjct: 240 VSFTGSSKVGLMVQQTVNARFGKCLLELSGNNAIIVMD 277
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
0.316 0.130 0.364
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,623,031
Number of extensions: 1483097
Number of successful extensions: 1564
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1557
Number of HSP's successfully gapped: 50
Length of query: 317
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 220
Effective length of database: 6,635,264
Effective search space: 1459758080
Effective search space used: 1459758080
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 (21.6 bits)
S2: 59 (26.5 bits)