RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10344
(189 letters)
>gnl|CDD|153327 cd07643, I-BAR_IMD_MIM, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Missing In
Metastasis. The IMD domain, also called
Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a
dimerization and lipid-binding module that bends
membranes and induces membrane protrusions. Members of
this subfamily include missing in metastasis (MIM) or
metastasis suppressor 1 (MTSS1), metastasis suppressor
1-like (MTSSL) or ABBA (Actin-Bundling protein with
BAIAP2 homology), and similar proteins. They contain an
N-terminal IMD and a WASP homology 2 (WH2) actin-binding
motif at the C-terminus. MIM was originally identified
as a missing transcript from metastatic bladder and
prostate cancer cells. It is a scaffold protein that
functions in a signaling pathway between the PDGF
receptor, Src kinases, and actin assembly. It may also
function as a cofactor of the Sonic hedgehog (Shh)
transcriptional pathway and may participate in tumor
development and progression via this pathway. ABBA
regulates actin and plasma membrane dynamics to promote
the extension of radial glia, which is important in
neuronal migration, axon guidance and neurogenesis. The
IMD domain of MIM binds and bundles actin filaments,
binds membranes, and interacts with the small GTPase
Rac.
Length = 231
Score = 156 bits (396), Expect = 3e-48
Identities = 64/111 (57%), Positives = 85/111 (76%), Gaps = 1/111 (0%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRA 62
K+YKKAR E+KK+S+DT+RLQKK RKG L A+Q+VN++ +LEE EKKA+R
Sbjct: 122 KEYKKARQEIKKKSSDTIRLQKKA-RKGKGDLQPQLDSAMQDVNDKYLLLEETEKKAVRN 180
Query: 63 ALIEERSRYCVFVTFLKPVVDEEVAMLSELSHLQEVMVQLEKHTSDPYSLP 113
ALIEER R+C FV+FLKPV+DEE++ML E++HLQ +M L T+DP+ LP
Sbjct: 181 ALIEERGRFCTFVSFLKPVLDEEISMLGEVTHLQTIMEDLASLTADPHKLP 231
>gnl|CDD|149453 pfam08397, IMD, IRSp53/MIM homology domain. The N-terminal
predicted helical stretch of the insulin receptor
tyrosine kinase substrate p53 (IRSp53) is an
evolutionary conserved F-actin bundling domain involved
in filopodium formation. The domain has been named IMD
after the IRSp53 and missing in metastasis (MIM)
proteins in which it occurs. Filopodium-inducing IMD
activity is regulated by Cdc42 and Rac1 and is
SH3-independent.
Length = 218
Score = 90.2 bits (224), Expect = 1e-22
Identities = 42/108 (38%), Positives = 68/108 (62%), Gaps = 2/108 (1%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRA 62
+YKK R EL+K+ +D +LQ+K +KG L++AL++VN+++ LEE EK+ +R
Sbjct: 109 TEYKKKRDELEKKQSDLKKLQRKS-QKGKNDSKYQLKEALEDVNDKQLELEEFEKQGVRE 167
Query: 63 ALIEERSRYCVFVTFLKPVVDEEVAMLSE-LSHLQEVMVQLEKHTSDP 109
AL+EE+ R+C V PV +EE+A E ++ LQ + ++ TSD
Sbjct: 168 ALLEEKRRFCFLVDKHCPVSNEELAFHGEAITLLQTKLPDWQELTSDA 215
>gnl|CDD|153289 cd07605, I-BAR_IMD, Inverse (I)-BAR, also known as the IRSp53/MIM
homology Domain (IMD), a dimerization module that binds
and bends membranes. Inverse (I)-BAR (or IMD) is a
member of the Bin/Amphiphysin/Rvs (BAR) domain family.
It is a dimerization and lipid-binding module that bends
membranes and induces membrane protrusions in the
opposite direction compared to classical BAR and F-BAR
domains, which produce membrane invaginations. IMD
domains are found in Insulin Receptor tyrosine kinase
Substrate p53 (IRSp53), Missing in Metastasis (MIM), and
Brain-specific Angiogenesis Inhibitor 1-Associated
Protein 2-like (BAIAP2L) proteins. These are
multi-domain proteins that act as scaffolding proteins
and transducers of a variety of signaling pathways that
link membrane dynamics and the underlying actin
cytoskeleton. Most members contain an N-terminal IMD, an
SH3 domain, and a WASP homology 2 (WH2) actin-binding
motif at the C-terminus, exccept for MIM which does not
carry an SH3 domain. Some members contain additional
domains and motifs. The IMD domain binds and bundles
actin filaments, binds membranes and produces membrane
protrusions, and interacts with the small GTPase Rac.
Length = 223
Score = 68.2 bits (167), Expect = 2e-14
Identities = 33/97 (34%), Positives = 51/97 (52%), Gaps = 1/97 (1%)
Query: 2 LKKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALR 61
K+YK+ R +L K ++ +LQKK + G L +AL+E+N+++ LE + LR
Sbjct: 118 KKEYKQKREDLDKARSELKKLQKKSQKSGTGKYQEKLDQALEELNDKQKELEAFVSQGLR 177
Query: 62 AALIEERSRYCVFVTFLKPVVDEEVAM-LSELSHLQE 97
AL+EER RYC V V E+A ++ L
Sbjct: 178 DALLEERRRYCFLVDKHCSVAKHEIAYHAKAMTLLST 214
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 37.2 bits (87), Expect = 0.002
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 17/74 (22%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAIL---------E 53
KK KKA+ E +K Q+K RKG + +L++A +E KA
Sbjct: 15 KKAKKAKKEKRK--------QRKQARKGADDGDDELKQAAEEAKAEKAERDRELNRQRQA 66
Query: 54 EAEKKALRAALIEE 67
EAE+KA+ A + +
Sbjct: 67 EAEQKAIVAQIKQL 80
>gnl|CDD|217803 pfam03938, OmpH, Outer membrane protein (OmpH-like). This family
includes outer membrane proteins such as OmpH among
others. Skp (OmpH) has been characterized as a
molecular chaperone that interacts with unfolded
proteins as they emerge in the periplasm from the Sec
translocation machinery.
Length = 157
Score = 31.5 bits (72), Expect = 0.15
Identities = 17/69 (24%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRA 62
K A+ +L+K LQ ++ +K +LQK Q++ ++ A L E +KA +
Sbjct: 31 PAGKAAQKQLEKEFKK---LQAELQKK-----EKELQKEEQKLQKQAATLSEEARKAKQQ 82
Query: 63 ALIEERSRY 71
L +++
Sbjct: 83 ELQQKQQEL 91
>gnl|CDD|224178 COG1258, COG1258, Predicted pseudouridylate synthase [Translation,
ribosomal structure and biogenesis].
Length = 398
Score = 31.9 bits (73), Expect = 0.15
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 29 KGVVGRNADLQKALQEVNERKAI----LEEAEKKALRAALIEERSR--YCVFVTFLKPVV 82
K RN DL + +E+N + LE ++ + ER R Y V +PV
Sbjct: 236 KEPRRRNVDLDELEEEINRGGKVEVFDLEFVGREEVEEIKETERHRKVYRALVYSDRPVS 295
Query: 83 DEEV 86
DE++
Sbjct: 296 DEKL 299
>gnl|CDD|173275 PRK14814, PRK14814, NADH dehydrogenase subunit B; Provisional.
Length = 186
Score = 30.4 bits (68), Expect = 0.38
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 20 LRLQKKVGRKGVVGRNADLQKALQEVNERKAIL 52
++LQ K+ +G+ R ++ + +QE+NER L
Sbjct: 151 VKLQTKLKTQGLEARRQEVMQKIQELNERNKPL 183
>gnl|CDD|214922 smart00935, OmpH, Outer membrane protein (OmpH-like). This
family includes outer membrane proteins such as OmpH
among others. Skp (OmpH) has been characterized as a
molecular chaperone that interacts with unfolded
proteins as they emerge in the periplasm from the Sec
translocation machinery.
Length = 140
Score = 29.9 bits (68), Expect = 0.41
Identities = 13/67 (19%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 5 YKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRAAL 64
K A+ +L+K Q ++ + +LQK +++ + A L EA ++ L
Sbjct: 16 GKAAQKQLEKEFKK---RQAELEKL-----EKELQKLKEKLQKDAATLSEAAREKKEKEL 67
Query: 65 IEERSRY 71
++ +
Sbjct: 68 QKKVQEF 74
>gnl|CDD|235185 PRK03980, PRK03980, flap endonuclease-1; Provisional.
Length = 292
Score = 30.2 bits (69), Expect = 0.60
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 44 EVNERKAILEEAEKK---ALRAALIEERSRYCVFVTFLKP 80
E+ ER+ + EEAE+K A +EE +Y + L
Sbjct: 43 EIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTD 82
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 30.4 bits (68), Expect = 0.72
Identities = 18/77 (23%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 105 HTSDPYSLPPASEQVMADMKGSDTTWLLPSPTSSPGSLGSRKSSMCSISSINSSSSGSSK 164
+++ Y+ P S + S+T + P ++ P S ++ S + ++++ S+K
Sbjct: 419 NSNPGYNNAPNSNTPYNNPPNSNTPYSNPPNSNPPYSNLPYSNTPYSNAPLSNAPPSSAK 478
Query: 165 SHHSPSHN-YWNRSIHQ 180
HHS H Y +R+ +Q
Sbjct: 479 DHHSAYHAAYQHRAANQ 495
>gnl|CDD|215364 PLN02678, PLN02678, seryl-tRNA synthetase.
Length = 448
Score = 29.7 bits (67), Expect = 0.91
Identities = 14/62 (22%), Positives = 32/62 (51%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRA 62
K++++ + EL + +L K+V + + +A A + +++ +EAE + +A
Sbjct: 40 KEWRQRQFELDSLRKEFNKLNKEVAKLKIAKEDATELIAETKELKKEITEKEAEVQEAKA 99
Query: 63 AL 64
AL
Sbjct: 100 AL 101
>gnl|CDD|218712 pfam05710, Coiled, Coiled coil. This region is found in a group of
Dictyostelium discoideum proteins. It is likely to form
a coiled-coil. Some of the proteins are regulated by
cyclic AMP and are expressed late in development.
Length = 90
Score = 28.3 bits (63), Expect = 0.92
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 147 SSMCSISSINSSSSGSSKSHHSPSHNYWNRSI 178
+S+ SI + SSS S S S S + + SI
Sbjct: 5 ASISSIGNSKSSSKSSISSFGSSSLSMGSNSI 36
>gnl|CDD|220506 pfam09989, DUF2229, CoA enzyme activase uncharacterized domain
(DUF2229). Members of this family include various
bacterial hypothetical proteins, as well as CoA enzyme
activases. The exact function of this domain has not, as
yet, been defined.
Length = 218
Score = 28.7 bits (65), Expect = 1.4
Identities = 10/36 (27%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 2 LKKYKKARSELKKRSTDTLRLQKKVGRKGVV--GRN 35
L++ + + +L+K+ + L ++ G+KG+V GR
Sbjct: 154 LEEQEAFKKDLRKKGEEALAYLEEEGKKGIVLLGRP 189
>gnl|CDD|219186 pfam06810, Phage_GP20, Phage minor structural protein GP20. This
family consists of several phage minor structural
protein GP20 sequences of around 180 residues in
length. The function of this family is unknown.
Length = 156
Score = 28.5 bits (64), Expect = 1.4
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 6 KKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNER-KAILEEAEKK 58
+ +LK R L+KK V N +LQK ++++ ++ K EE E K
Sbjct: 30 DSLKKQLKNRDKQIEDLKKK------VKDNEELQKKIEKLKQQNKTAKEEYEAK 77
>gnl|CDD|133138 cd05471, pepsin_like, Pepsin-like aspartic proteases, bilobal
enzymes that cleave bonds in peptides at acidic pH.
Pepsin-like aspartic proteases are found in mammals,
plants, fungi and bacteria. These well known and
extensively characterized enzymes include pepsins,
chymosin, renin, cathepsins, and fungal aspartic
proteases. Several have long been known to be medically
(renin, cathepsin D and E, pepsin) or commercially
(chymosin) important. Structurally, aspartic proteases
are bilobal enzymes, each lobe contributing a catalytic
Aspartate residue, with an extended active site cleft
localized between the two lobes of the molecule. The N-
and C-terminal domains, although structurally related by
a 2-fold axis, have only limited sequence homology
except the vicinity of the active site. This suggests
that the enzymes evolved by an ancient duplication
event. Most members of the pepsin family specifically
cleave bonds in peptides that are at least six residues
in length, with hydrophobic residues in both the P1 and
P1' positions. The active site is located at the groove
formed by the two lobes, with an extended loop
projecting over the cleft to form an 11-residue flap,
which encloses substrates and inhibitors in the active
site. Specificity is determined by nearest-neighbor
hydrophobic residues surrounding the catalytic
aspartates, and by three residues in the flap.The
enzymes are mostly secreted from cells as inactive
proenzymes that activate autocatalytically at acidic pH.
This family of aspartate proteases is classified by
MEROPS as the peptidase family A1 (pepsin A, clan AA).
Length = 283
Score = 28.9 bits (65), Expect = 1.5
Identities = 13/53 (24%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 113 PPASEQVMADMKGSDTTWLLPSPTSSPGSLGSRKSSMCSISSINSSSSGSSKS 165
PP V+ D GS W+ S +S + S S +G + S
Sbjct: 10 PPQKFSVIFDT-GSSLLWVPSSNCTSCSCQKHPRFKYDSSKSSTYKDTGCTFS 61
>gnl|CDD|215288 PLN02525, PLN02525, phosphatidic acid phosphatase family protein.
Length = 352
Score = 28.6 bits (64), Expect = 2.0
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 129 TWLLPSPTSSPGSLGSRKSSMCSISSINSSSSGSSKSHHSPSHNYWNR 176
WLLP ++ LG S + S+ S SG S Y +
Sbjct: 267 KWLLPVVCNA---LGIPIRSTSYVPSLKGSVSGKKSDEPKQSVGYLQK 311
>gnl|CDD|224495 COG1579, COG1579, Zn-ribbon protein, possibly nucleic acid-binding
[General function prediction only].
Length = 239
Score = 27.7 bits (62), Expect = 3.5
Identities = 24/106 (22%), Positives = 46/106 (43%), Gaps = 8/106 (7%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALRA 62
K KKA++EL+ + L+ ++ + + + + L+ +QE+ ER EE
Sbjct: 31 KALKKAKAELEALNKALEALEIEL--EDLENQVSQLESEIQEIRERIKRAEEKLSAVKDE 88
Query: 63 ALIEERSRYCVFVTFLKPVVDEEVAMLSELSHLQEVMVQLEKHTSD 108
E + + K + ++ EL+ L E + +LEK D
Sbjct: 89 ---RELRALNIEIQIAK---ERINSLEDELAELMEEIEKLEKEIED 128
>gnl|CDD|224003 COG1077, MreB, Actin-like ATPase involved in cell morphogenesis
[Cell division and chromosome partitioning].
Length = 342
Score = 28.0 bits (63), Expect = 3.6
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 47 ERKAILEEAEKKALR-AALIEE 67
ER+AI E AE R LIEE
Sbjct: 116 ERRAIKEAAESAGAREVYLIEE 137
>gnl|CDD|119241 pfam10721, DUF2514, Protein of unknown function (DUF2514). This
family is conserved in bacteria and some viruses. The
function is not known.
Length = 162
Score = 27.4 bits (61), Expect = 3.7
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 31 VVGRNADLQKALQEVNERKAILEEAEKKALRAALIEERSR 70
GR+ + Q+ +R A AE A AA EE+ R
Sbjct: 20 AHGRSWEDAGWQQKWADRDAADALAEVIAETAARAEEQRR 59
>gnl|CDD|220662 pfam10265, DUF2217, Uncharacterized conserved protein (DUF2217).
This is a family of conserved proteins of from 500 - 600
residues found from worms to humans. Its function is not
known.
Length = 515
Score = 27.4 bits (61), Expect = 4.6
Identities = 18/59 (30%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 104 KHTSDPYSLPPASEQVMADMKGSDTTWLLPSPTSSPGSLGSRKSSMCSISSINSSSSGS 162
+ S + K +DT S SS S S+ S+S NSSSSGS
Sbjct: 54 RPLSRKIGKCSSRRVRSPSSKPNDTLSGASSKLSSKHS--GSSHSLASVSDRNSSSSGS 110
>gnl|CDD|234306 TIGR03674, fen_arch, flap structure-specific endonuclease.
Endonuclease that cleaves the 5'-overhanging flap
structure that is generated by displacement synthesis
when DNA polymerase encounters the 5'-end of a
downstream Okazaki fragment. Has 5'-endo-/exonuclease
and 5'-pseudo-Y-endonuclease activities. Cleaves the
junction between single and double-stranded regions of
flap DNA.
Length = 338
Score = 27.2 bits (61), Expect = 4.9
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 44 EVNERKAILEEAEKK---ALRAALIEERSRYCVFVTFLKP-VVDEEVAMLS 90
+ ER+ I EEAE+K AL +EE +Y + L +V+ +L
Sbjct: 90 TLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLD 140
>gnl|CDD|214963 smart00996, AdoHcyase, S-adenosyl-L-homocysteine hydrolase.
Length = 426
Score = 27.5 bits (62), Expect = 5.0
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 63 ALIE---ERSRYCVFVTFLKPVVDEEVAMLSELSHLQEVMVQLEKHTSD 108
A IE + +Y V L +DE+VA L HL+++ +L K T +
Sbjct: 363 AQIELFTKPGKYKNGVYVLPKKLDEKVARL----HLEKLGAKLTKLTKE 407
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 26.1 bits (58), Expect = 5.2
Identities = 6/31 (19%), Positives = 16/31 (51%)
Query: 36 ADLQKALQEVNERKAILEEAEKKALRAALIE 66
+L+ ++++ + +AE+ A A + E
Sbjct: 1 EELEALIEKLEKEIEAARKAERAAALAEIRE 31
>gnl|CDD|153329 cd07645, I-BAR_IMD_BAIAP2L1, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Brain-specific
Angiogenesis Inhibitor 1-Associated Protein 2-Like 1.
The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs
(I-BAR) domain, is a dimerization and lipid-binding
module that bends membranes and induces membrane
protrusions. BAIAP2L1 (Brain-specific Angiogenesis
Inhibitor 1-Associated Protein 2-Like 1) is also known
as IRTKS (Insulin Receptor Tyrosine Kinase Substrate).
It is widely expressed, serves as a substrate for the
insulin receptor, and binds the small GTPase Rac. It
plays a role in regulating the actin cytoskeleton and
colocalizes with F-actin, cortactin, VASP, and vinculin.
BAIAP2L1 expression leads to the formation of short
actin bundles, distinct from filopodia-like protrusions
induced by the expression of the related protein IRSp53.
It contains an N-terminal IMD, an SH3 domain, and a WASP
homology 2 (WH2) actin-binding motif at the C-terminus.
The IMD domain of BAIAP2L1 binds and bundles actin
filaments, and binds the small GTPase Rac.
Length = 226
Score = 27.2 bits (60), Expect = 5.4
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 2 LKKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKALR 61
L +K++++LKK +R +K GR+ + L+ V R++ +++ R
Sbjct: 125 LDSLEKSQADLKK-----IR-RKSQGRRNASKYEHKENEYLETVTSRQSDIQKFIADGCR 178
Query: 62 AALIEERSRYCVFV 75
AL+EE+ R+C V
Sbjct: 179 EALLEEKRRFCFLV 192
>gnl|CDD|220413 pfam09805, Nop25, Nucleolar protein 12 (25kDa). Members of this
family of proteins are part of the yeast nuclear pore
complex-associated pre-60S ribosomal subunit. The
family functions as a highly conserved exonuclease that
is required for the 5'-end maturation of 5.8S and 25S
rRNAs, demonstrating that 5'-end processing also has a
redundant pathway. Nop25 binds late pre-60S ribosomes,
accompanying them from the nucleolus to the nuclear
periphery; and there is evidence for both physical and
functional links between late 60S subunit processing
and export.
Length = 134
Score = 26.5 bits (59), Expect = 5.6
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 6 KKARSELKKRSTDTLRLQKKVGRKGV-VGRNADLQKALQEVNERKAILEEAE 56
KKA+ E K++ R ++ RK + R +L+K L+E E +LEE
Sbjct: 36 KKAQEEAKEK----EREERIEERKRIREERKQELEKQLKERKEALKLLEEEN 83
>gnl|CDD|152006 pfam11570, E2R135, Coiled-coil receptor-binding R-domain of
colicin E2. E2 is a DNase which utilises the outer
membrane receptor BtuB to bind to and enter the cell.
This family of proteins is E2R135 (residues 321-443)
which is the part of E2 which is responsible for
binding to BtuB in a coiled coil formation.
Length = 134
Score = 26.3 bits (57), Expect = 6.3
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 12/56 (21%)
Query: 3 KKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKK 58
+ Y++AR+EL + + D R Q++ KA+Q N RK+ L+ A K
Sbjct: 8 RNYERARAELNQANEDVARNQERQA------------KAVQVYNSRKSELDAANKT 51
>gnl|CDD|225907 COG3372, COG3372, Predicted nuclease of restriction
endonuclease-like fold [General function prediction
only].
Length = 396
Score = 26.9 bits (60), Expect = 6.4
Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 15/107 (14%)
Query: 3 KKYKKARSE---LKKRST-------DTLRLQKKVGRKGVVGRNADLQKALQEVNERKAIL 52
K K R L++ D +++ + +G + Q+ LQE + ++
Sbjct: 58 AKDKLVRGLAKILERECEFEVVSALDPREVRRFLFERGPALSEEERQRVLQEAADHFSVS 117
Query: 53 EEAEKKALRAALIEERSRYCVFVTFLKPVVDEEVAMLSELSHLQEVM 99
E + AL A L EE+ + V F + + + LS LQ ++
Sbjct: 118 PEEIEDALYADLEEEK----ILVEFPDITPEWLLRRYN-LSLLQTLL 159
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 27.3 bits (60), Expect = 6.6
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 134 SPTSSPGSLGSRKSSMCSISSINSSSSGSSKSHHSPSHNYWNRSIH 179
S SS + S SS SI S S S S HSP N+S H
Sbjct: 128 SSISSSLTNISFFSSPTSIY---SCLSNSLSSKHSPKVIKENQSTH 170
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 25.6 bits (57), Expect = 6.9
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 36 ADLQKALQEVNERKAILEEAEKKALRA--ALIEERSRY 71
A LQ L ++ L EAE K L++ IEER+R
Sbjct: 27 AALQAELAKLKAENEEL-EAEVKDLKSDPDYIEERARS 63
>gnl|CDD|221247 pfam11825, Nuc_recep-AF1, Nuclear/hormone receptor activator site
AF-1. Nuclear receptors (NRs) are a family of
ligand-inducible transcription factors, and, like other
transcription factors, they contain a distinct DNA
binding domain that allows for target gene recognition
and several activation domains that possess the ability
to activate transcription. One of these activation
domains is at the N-terminal, although there are two
distinct motifs within this domain, between residues
20-36 and between 74 and the end of this domain, which
are the binding regions. One of the co-activators is
TIF1beta, which appears to bind at the first motif.
Length = 106
Score = 25.9 bits (57), Expect = 7.2
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 2/50 (4%)
Query: 113 PPASEQVMADMKGSDTTWLLPSPTSSPGSLGSRKSSMCSISSINSSSSGS 162
P M+ + LL SP +L S + + S S+ SSS GS
Sbjct: 5 PSTGRGSMSAPDLHPS--LLGSPMGPMSTLSSPINGLGSPYSVISSSMGS 52
>gnl|CDD|153330 cd07646, I-BAR_IMD_IRSp53, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Insulin Receptor
tyrosine kinase Substrate p53. The IMD domain, also
called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a
dimerization and lipid-binding module that bends
membranes and induces membrane protrusions. IRSp53
(Insulin Receptor tyrosine kinase Substrate p53) is also
known as BAIAP2 (Brain-specific Angiogenesis Inhibitor
1-Associated Protein 2). It is a scaffolding protein
that takes part in many signaling pathways including
Cdc42-induced filopodia formation, Rac-mediated
lamellipodia extension, and spine morphogenesis. IRSp53
exists as multiple splicing variants that differ mainly
at the C-termini. One variant (T-form) is expressed
exclusively in human breast cancer cells. The gene
encoding IRSp53 is a putative susceptibility gene for
Gilles de la Tourette syndrome. IRSp53 contains an
N-terminal IMD, a CRIB (Cdc42 and Rac interactive
binding motif), an SH3 domain, and a WASP homology 2
(WH2) actin-binding motif at the C-terminus. Its IMD
domain binds and bundles actin filaments, binds
membranes, and interacts with the small GTPase Rac.
Length = 232
Score = 26.4 bits (58), Expect = 8.4
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 8/78 (10%)
Query: 6 KKARSELKKRSTDTLRLQ---KKVGRKGVVGRNADL--QKALQEV---NERKAILEEAEK 57
KK ++E + + + Q KK+ +K +N K LQ + + ++ LE
Sbjct: 117 KKYQTEHRSKGESLEKCQAELKKLRKKSQGSKNPQKYSDKELQYIEAISNKQGELENYVS 176
Query: 58 KALRAALIEERSRYCVFV 75
+ AL EER RYC V
Sbjct: 177 DGYKTALTEERRRYCFLV 194
>gnl|CDD|225381 COG2825, HlpA, Outer membrane protein [Cell envelope biogenesis,
outer membrane].
Length = 170
Score = 26.2 bits (58), Expect = 8.8
Identities = 14/70 (20%), Positives = 30/70 (42%)
Query: 1 MLKKYKKARSELKKRSTDTLRLQKKVGRKGVVGRNADLQKALQEVNERKAILEEAEKKAL 60
+ ++KK + EL+K + + K+ G + +D KA E+ + K + +K+
Sbjct: 49 LESEFKKRQKELQKMQKELKAKEAKLQDDGKMEALSDRAKAEAEIKKEKLVNAFNKKQQE 108
Query: 61 RAALIEERSR 70
+ R
Sbjct: 109 YEKDLNRREA 118
>gnl|CDD|232924 TIGR00334, 5S_RNA_mat_M5, ribonuclease M5. This family of
orthologous proteins shows a weak but significant
similarity to the central region of the DnaG-type DNA
primase. The region of similarity is termed the Toprim
(topoisomerase-primase) domain and is also shared by
RecR, OLD family nucleases, and type IA and II
topoisomerases [Transcription, RNA processing].
Length = 174
Score = 25.9 bits (57), Expect = 9.7
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 35 NADLQKALQEVNERKAILEEAEKKALRAAL 64
N + K L + N++K +EEA +A+ AAL
Sbjct: 76 NCFIPKHLAKPNKKKIGVEEASVEAIIAAL 105
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
0.310 0.123 0.340
Gapped
Lambda K H
0.267 0.0810 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,233,951
Number of extensions: 835483
Number of successful extensions: 1182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1153
Number of HSP's successfully gapped: 103
Length of query: 189
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 98
Effective length of database: 6,901,388
Effective search space: 676336024
Effective search space used: 676336024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 56 (25.2 bits)