RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10164
(887 letters)
>gnl|CDD|238585 cd01180, IPT_plexin_repeat1, First repeat of the IPT domain of
Plexins and Cell Surface Receptors (PCSR) . Plexins are
involved in the regulation of cell proliferation and of
cellular adhesion and repulsion receptors. In general,
there are three copies of the IPT domain present
preceeded by SEMA (semaphorin) and PSI (plexin,
semaphorin, integrin) domains.
Length = 94
Score = 56.9 bits (138), Expect = 5e-10
Identities = 31/91 (34%), Positives = 42/91 (46%), Gaps = 5/91 (5%)
Query: 5 PVVTGISPKEGPP--GTRVTIRGENLGKQPNDLIGLV-ICGCDC-LLSAEWKSPNKIIAR 60
PV+T P GP GTR+TI G NLG + ND+ V + G C E+ S KI+
Sbjct: 1 PVITEFFPLSGPLEGGTRLTICGSNLGLRKNDVRHGVRVGGVPCNPEPPEYSSSEKIVCT 60
Query: 61 SGP-GKGRGEIIVSTSLGGEGTCTIQFRGYH 90
+GP G V ++G T G+
Sbjct: 61 TGPAGNPVFNGPVEVTVGHGSFRTESSEGFS 91
>gnl|CDD|238337 cd00603, IPT_PCSR, IPT domain of Plexins and Cell Surface
Receptors (PCSR) and related proteins . This subgroup
contains IPT domains of plexins, receptors, like the
plasminogen-related growth factor receptors, the
hepatocyte growth factor-scatter factors, and the
macrophage-stimulating receptors and of fibrocystin.
Plexins are involved in the regulation of cell
proliferation and of cellular adhesion and repulsion
receptors. In general, there are three copies of the
IPT_PCSR domain present preceeded by SEMA (semaphorin)
and PSI (plexin, semaphorin, integrin) domains.
Length = 90
Score = 48.6 bits (116), Expect = 3e-07
Identities = 25/90 (27%), Positives = 39/90 (43%), Gaps = 7/90 (7%)
Query: 5 PVVTGISPKEGPP--GTRVTIRGENLGKQPNDLIGLVICGCDCLLSAEWKSPNKIIARSG 62
PV+T ISP GP GTR+TI G NLG + + + + G C + S +I+ R+
Sbjct: 1 PVITSISPSSGPLSGGTRLTITGSNLG-SGSPRVRVTVGGVPCKV--LNVSSTEIVCRTP 57
Query: 63 PG--KGRGEIIVSTSLGGEGTCTIQFRGYH 90
G G + V+ + +
Sbjct: 58 AAATPGEGPVEVTVDGANVSARVLSNTTFT 87
>gnl|CDD|238050 cd00102, IPT, Immunoglobulin-like fold, Plexins, Transcription
factors (IPT). IPTs are also known as Transcription
factor ImmunoGlobin (TIG) domains. They are present in
intracellular transcription factors, cell surface
receptors (such as plexins and scatter factor
receptors), as well as, cyclodextrin
glycosyltransferase and similar enzymes. Although they
are involved in DNA binding in transcription factors,
their function in other proteins is unknown. In these
transcription factors, IPTs form homo- or heterodimers
with the exception of the nuclear factor of activated
Tcells (NFAT) transcription factors which are mainly
monomers.
Length = 89
Score = 45.5 bits (108), Expect = 4e-06
Identities = 25/76 (32%), Positives = 31/76 (40%), Gaps = 5/76 (6%)
Query: 5 PVVTGISPKEGPP--GTRVTIRGENLGKQPNDLIGLVICGCDCLLSAEWKSPNKIIARSG 62
PV+T ISP GP GT VTI G N G N L G C + S I+ +
Sbjct: 1 PVITSISPSSGPVSGGTEVTITGSNFGSGSN-LRVTFGGGVPCSV--LSVSSTAIVCTTP 57
Query: 63 PGKGRGEIIVSTSLGG 78
P G V ++
Sbjct: 58 PYANPGPGPVEVTVDR 73
>gnl|CDD|216730 pfam01833, TIG, IPT/TIG domain. This family consists of a domain
that has an immunoglobulin like fold. These domains are
found in cell surface receptors such as Met and Ron as
well as in intracellular transcription factors where it
is involved in DNA binding. CAUTION: This family does
not currently recognise a significant number of
members.
Length = 84
Score = 44.4 bits (105), Expect = 8e-06
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 5 PVVTGISPKEGPP--GTRVTIRGENLGKQPNDLIGLVICGCDCLLSAEWKSPNKIIARSG 62
PV+T ISP GP GT +TI G N G D + G +C + S +I+ +
Sbjct: 1 PVITSISPATGPASGGTTITITGSNFGTDSEDTK-VTFGGTECTVIVSV-SSTQIVCTTP 58
Query: 63 PGK-GRGEIIVST 74
G G + V+
Sbjct: 59 AGAAGTVSVSVTV 71
>gnl|CDD|238584 cd01179, IPT_plexin_repeat2, Second repeat of the IPT domain of
Plexins and Cell Surface Receptors (PCSR) . Plexins are
involved in the regulation of cell proliferation and of
cellular adhesion and repulsion receptors. In general,
there are three copies of the IPT domain present
preceeded by SEMA (semaphorin) and PSI (plexin,
semaphorin, integrin) domains.
Length = 85
Score = 38.0 bits (89), Expect = 0.002
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 5 PVVTGISPKEGPP--GTRVTIRGENL--GKQPNDLIGLVICGCDCLLSAEWKSPNKIIAR 60
P +T +SP GP GTR+TI G++L G +G G C + S ++I+
Sbjct: 1 PSITSLSPSYGPQSGGTRLTITGKHLNAGSSVRVTVG----GQPCKIL--SVSSSQIVCL 54
Query: 61 SGPGKGRGEIIVSTSLGG 78
+ P GE V + G
Sbjct: 55 TPPSASPGEAPVKVLIDG 72
>gnl|CDD|214657 smart00429, IPT, ig-like, plexins, transcription factors.
Length = 90
Score = 34.3 bits (79), Expect = 0.035
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 4 PPVVTGISPKEGPP--GTRVTIRGENLG 29
PV+T ISP GP GT +T+ G+NL
Sbjct: 1 DPVITRISPTSGPVSGGTEITLCGKNLK 28
>gnl|CDD|217626 pfam03584, Herpes_ICP4_N, Herpesvirus ICP4-like protein N-terminal
region. The immediate-early protein ICP4 (infected-cell
polypeptide 4) is required for efficient transcription
of early and late viral genes and is thus essential for
productive infection. ICP4 is a large phosphoprotein
that binds DNA in a sequence specific manner as a
homodimer. ICP4 represses transcription from LAT, ICP4
and ORF-P that have high-affinity a ICP4 binding site
that spans the transcription initiation site. ICP4
proteins have two highly conserved regions, this family
contains the N-terminal region that contains sites for
DNA binding and homodimerisation.
Length = 175
Score = 31.9 bits (73), Expect = 0.74
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 9/79 (11%)
Query: 413 EPAPVFVPQPILCVEELTAIVSERFPDLWKLGQSYFSGELQGTVEPTNQLMFKKIILDVV 472
P PV+VP+ ++ A+V + + +L GT + N + K
Sbjct: 48 GPVPVYVPEMGDPAKQYEALVRLIYEPDRDAMAWLQNPKLSGTDQALNHICQKF----RG 103
Query: 473 ALSSKS--IRSSV---LPH 486
S I SV +PH
Sbjct: 104 GGRSHGSAITGSVAKPVPH 122
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 32.8 bits (75), Expect = 0.99
Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 6/62 (9%)
Query: 567 QYEFNPNKGAITQLPKQIELLLSDMV------QNIKTNVLSKDDKDNPLFNSDVAKHEFS 620
Y+ NKG + + K + + V + K ++ D N N ++ S
Sbjct: 54 VYKKITNKGDLYETRKIFYDYIKNGVKIKESQKGEKKRIVKLIDFRNISQNIFQFANQVS 113
Query: 621 IE 622
+
Sbjct: 114 FK 115
>gnl|CDD|237439 PRK13586, PRK13586,
1-(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase; Provisional.
Length = 232
Score = 30.9 bits (70), Expect = 2.5
Identities = 32/131 (24%), Positives = 56/131 (42%), Gaps = 20/131 (15%)
Query: 176 FDDLRVGLSFLKRKVESQKEGQLSFLKSNVSSVMEQMDTLFIFKEK-FEANVKEHGLDPT 234
FD ++VG R +E K L +V++++ T+ F V+E G +
Sbjct: 73 FDWIQVGGGI--RDIEKAKR----LLSLDVNALV--FSTIVFTNFNLFHDIVREIGSN-- 122
Query: 235 IKVEIAIKKSMTEATKLFQDVLAR--RERADKTRNALTVLQRYRFLFSLPLSISNNITKN 292
+V ++I T + VL R +E++ + + + + L + ISN T
Sbjct: 123 -RVLVSIDYDNT------KRVLIRGWKEKSMEVIDGIKKVNELELLGIIFTYISNEGTTK 175
Query: 293 DIDAVINDYAR 303
ID + DYAR
Sbjct: 176 GIDYNVKDYAR 186
>gnl|CDD|218088 pfam04437, RINT1_TIP1, RINT-1 / TIP-1 family. This family includes
RINT-1, a Rad50 interacting protein which participates
in radiation induced checkpoint control, as well as the
TIP-1 protein from yeast that seems to be involved in a
complex with Sec20p that is required for golgi
transport.
Length = 483
Score = 30.8 bits (70), Expect = 3.3
Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 7/99 (7%)
Query: 748 EWDTVIPPIDLKPYA--KEIIGNIITVHAELVRIVPSVISKVISGIVETVAEELSRLM-S 804
W ++ L+ + E++ + + + ++ + + I + L + S
Sbjct: 329 TWSSLSSTSALESLSPSAELVEALRYLRRRISKLERLLPLAIFLRIWRQLLLSLDTYIIS 388
Query: 805 CV---TKFSECGKQQAFIDMSSLKNTLSQYCTDSAKAYF 840
+ KFSE G Q DM +L S YC + +F
Sbjct: 389 SILMLNKFSEGGAAQFHFDMRNLFEVFSLYC-MRPENFF 426
>gnl|CDD|198065 smart00997, AdoHcyase_NAD, S-adenosyl-L-homocysteine hydrolase, NAD
binding domain.
Length = 162
Score = 29.7 bits (68), Expect = 3.6
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 321 FEVESNINDLRNMLRKKLKIMPQ----TLQEQKTLI-----RNLVNLDAG 361
F+VE ++ L + +K ++ PQ TL + K + R LVNL A
Sbjct: 112 FDVEIDVAALEELAVEKREVRPQVDEYTLPDGKRIYLLAEGR-LVNLAAA 160
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription].
Length = 151
Score = 29.2 bits (66), Expect = 5.0
Identities = 12/64 (18%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 277 FLFSLPLSISNNITKNDIDAVINDYARAMNLFGKTDVALFKKVLFE-VESNINDLRNMLR 335
L+ +S +++ DI I + L + + + + L + V N +L ++
Sbjct: 20 ALYQW--ELSGSVSAEDILEDIEEEFVENELDIELADSEYFRSLVKGVLENQEELDELIS 77
Query: 336 KKLK 339
LK
Sbjct: 78 PHLK 81
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 30.0 bits (68), Expect = 5.9
Identities = 25/119 (21%), Positives = 43/119 (36%), Gaps = 10/119 (8%)
Query: 532 QIVSKLLFDLKLHTLLCLVKHCGSQIKELKHKENWQYEFNPNKGAITQLPKQIELLLSDM 591
L D+ L L+ L + K L E Q + N I + Q + + ++
Sbjct: 18 LKARGLSVDIDLEKLIALDDE---RKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEI 74
Query: 592 VQNIKTNVLSKDDKDNPLFNSDVAKHEFSIEVNKLLSAVVNLLDELSSSSSDQEDNMPV 650
+ +K + K L A E+ L ++ N+ E D+EDN+ V
Sbjct: 75 KKELK------ELK-EELTELSAALKALEAELQDKLLSIPNIPHESVPVGKDEEDNLEV 126
>gnl|CDD|133949 PHA01399, PHA01399, membrane protein P6.
Length = 242
Score = 29.6 bits (66), Expect = 6.3
Identities = 14/52 (26%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 763 KEIIGNIITVHAELVRIVPSVISKVISGIVETVAEELSRLMSCVTK-FSECG 813
K+ I ++ ++V+ V I K I IV+ + + +S ++ ++K FS+ G
Sbjct: 8 KKAIKKVVDAVVKVVKAVVDAIVKAIKAIVKIIKKIVSVILDFISKIFSKIG 59
>gnl|CDD|224814 COG1902, NemA, NADH:flavin oxidoreductases, Old Yellow Enzyme
family [Energy production and conversion].
Length = 363
Score = 29.9 bits (68), Expect = 7.1
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 289 ITKNDIDAVINDYARA 304
+T+ +I+ VI D+ARA
Sbjct: 139 LTEEEIEEVIEDFARA 154
>gnl|CDD|217752 pfam03833, PolC_DP2, DNA polymerase II large subunit DP2.
Length = 852
Score = 29.7 bits (67), Expect = 7.7
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 207 SVMEQMDTLFIFKEKFEANVKEHGLDPTIKVEIAIKKSMTE 247
+ +++D + E +E GLDPT KVEI + K M E
Sbjct: 6 KLEDEVDRAYEIAEA----ARERGLDPTDKVEIPLAKDMAE 42
>gnl|CDD|217433 pfam03223, V-ATPase_C, V-ATPase subunit C.
Length = 371
Score = 29.5 bits (67), Expect = 7.8
Identities = 30/126 (23%), Positives = 53/126 (42%), Gaps = 12/126 (9%)
Query: 653 LIGSPLVYSDKQLNGTFYEERLLLT--LSNCQYICFFIFPR-----LDDLFIQNG-LPTI 704
L+ P++ +D Q N ++E LL++ SN + F P LD L + L +
Sbjct: 3 LVSLPVLKTDSQANQI-WKELLLVSSLGSNLSNVSKFNIPDLKVGTLDSLVTLSDELGKL 61
Query: 705 KESLELSTENLV-ILENKLIENYIEIKSDPLVGTIEPSMYLGHFEWDTVIPPIDLKPYAK 763
+E + + IL L + ++ S V + YL F+WD+ P K
Sbjct: 62 DTQVEGVLKKIERILRELLEDQGGKLSSTLRVNDVSLDQYLTRFQWDSAKYPTKQS--LK 119
Query: 764 EIIGNI 769
E++ +
Sbjct: 120 ELVDLL 125
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 0.135 0.387
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 44,779,320
Number of extensions: 4470384
Number of successful extensions: 3899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3892
Number of HSP's successfully gapped: 33
Length of query: 887
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 781
Effective length of database: 6,236,078
Effective search space: 4870376918
Effective search space used: 4870376918
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)