Query psy9084
Match_columns 103
No_of_seqs 119 out of 444
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 18:27:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3586|consensus 100.0 3.8E-41 8.1E-46 268.4 9.1 99 4-103 97-252 (437)
2 cd00182 TBOX T-box DNA binding 100.0 9.6E-39 2.1E-43 235.5 9.5 97 4-103 19-167 (188)
3 smart00425 TBOX Domain first f 100.0 8.6E-37 1.9E-41 225.3 9.7 97 4-103 18-168 (190)
4 KOG3585|consensus 100.0 5.1E-33 1.1E-37 219.1 8.5 96 5-103 43-191 (328)
5 PF00907 T-box: T-box; InterP 100.0 1.2E-32 2.6E-37 200.3 8.1 96 5-102 18-165 (184)
6 PF04775 Bile_Hydr_Trans: Acyl 83.5 1.8 3.8E-05 29.8 3.5 30 21-50 5-34 (126)
7 PF00041 fn3: Fibronectin type 71.9 8.5 0.00019 22.6 3.8 24 21-44 56-79 (85)
8 cd00169 Chemokine Chemokine: s 65.4 2.9 6.2E-05 24.8 0.7 15 3-17 28-42 (59)
9 cd00273 Chemokine_CXC Chemokin 64.8 2.6 5.6E-05 25.5 0.4 15 3-17 32-46 (64)
10 PF09294 Interfer-bind: Interf 63.3 12 0.00027 23.7 3.4 21 22-42 68-88 (106)
11 smart00199 SCY Intercrine alph 62.2 3.1 6.7E-05 24.8 0.4 15 3-17 29-43 (59)
12 cd00272 Chemokine_CC Chemokine 60.7 4 8.6E-05 24.1 0.7 15 3-17 26-40 (57)
13 cd01119 Chemokine_CC_DCCL Chem 57.0 4.7 0.0001 24.3 0.6 15 3-17 30-44 (61)
14 smart00060 FN3 Fibronectin typ 55.4 21 0.00046 19.4 3.2 23 20-42 56-78 (83)
15 cd00063 FN3 Fibronectin type 3 45.8 33 0.00073 19.2 3.1 24 19-42 55-78 (93)
16 cd00271 Chemokine_C Chemokine_ 44.7 11 0.00023 23.8 0.8 16 2-17 32-47 (72)
17 PF00048 IL8: Small cytokines 44.3 10 0.00022 22.6 0.6 14 4-17 35-48 (64)
18 cd00274 Chemokine_CX3C Chemoki 29.7 26 0.00056 22.5 0.8 15 3-17 35-49 (76)
19 PF10179 DUF2369: Uncharacteri 28.3 63 0.0014 25.8 2.9 29 22-50 261-289 (300)
20 PF07569 Hira: TUP1-like enhan 25.3 40 0.00086 25.1 1.2 27 13-39 1-29 (219)
21 PF12503 CMV_1a_C: Cucumber mo 23.4 69 0.0015 21.1 1.9 26 7-32 30-61 (85)
22 PF15417 DUF4624: Domain of un 22.5 1.1E+02 0.0024 21.4 2.9 41 3-43 71-111 (132)
23 PF02257 RFX_DNA_binding: RFX 21.9 50 0.0011 21.5 1.0 22 15-36 55-76 (85)
No 1
>KOG3586|consensus
Probab=100.00 E-value=3.8e-41 Score=268.44 Aligned_cols=99 Identities=55% Similarity=0.860 Sum_probs=89.8
Q ss_pred CceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEccCCceeeeecc-----------------------------
Q psy9084 4 DEALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHR----------------------------- 54 (103)
Q Consensus 4 ~~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry~~~~----------------------------- 54 (103)
.||||+| |+||||||+++|+++||||.+.|.|+||++|+|++||||.+|+
T Consensus 97 GTEMIIT-KsGRRMFPTvrV~~~GldP~a~Y~vlmDvVPvD~KRYRYayH~S~WlvAGkADp~~p~R~yvHPDSP~sGe~ 175 (437)
T KOG3586|consen 97 GTEMIIT-KSGRRMFPTVRVKFSGLDPMADYYVLMDVVPVDSKRYRYAYHSSSWLVAGKADPAPPPRVYVHPDSPASGEQ 175 (437)
T ss_pred CceEEEe-cccccccceEEEEEecCCcccceEEEEeEEecccceeeeeecccceeeecCCCCCCCCceeeCCCCCCCHHH
Confidence 4789875 8999999999999999999999999999999999999999986
Q ss_pred ---ceeEeec----------------------CCeeEEEEcCCCCCCC---CCCCCeEEEEcCCceEEEcCCCCCCC
Q psy9084 55 ---QIGSLVS----------------------LPRFHVVLLSPESNSA---SATSPFKTFLFPETMFTAVTAYQNHR 103 (103)
Q Consensus 55 ---~~vsF~k----------------------qPrlhiv~~~~~~~~~---~~~~~~~tf~FpeT~FiAVTAYQN~~ 103 (103)
|+||||| |||+|||+.++..+.. ...+.++||+||||+|+|||||||++
T Consensus 176 wmkqiVSFdK~KLTNNelD~nGHIILNSMHkYQPRvHvV~~~~~~~s~~~~~~~e~~kTF~FpET~FtAVTAYQNq~ 252 (437)
T KOG3586|consen 176 WMKQIVSFDKLKLTNNELDDNGHIILNSMHKYQPRVHVVYLDPGNDSNKYVEKNEGFKTFVFPETVFTAVTAYQNQR 252 (437)
T ss_pred HHHhhhchheeeccccccccCCcEeeecccccCCceEEEEecCCCCccccccccccceeEeccceeEEEEeecccce
Confidence 8999999 9999999998754322 34578999999999999999999986
No 2
>cd00182 TBOX T-box DNA binding domain of the T-box family of transcriptional regulators. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors.
Probab=100.00 E-value=9.6e-39 Score=235.49 Aligned_cols=97 Identities=43% Similarity=0.644 Sum_probs=87.2
Q ss_pred CceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEccCCceeeeecc-----------------------------
Q psy9084 4 DEALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHR----------------------------- 54 (103)
Q Consensus 4 ~~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry~~~~----------------------------- 54 (103)
.+|||+| |+||||||.++++|+||||++.|.|+||++++|++||||.+++
T Consensus 19 ~tEMIIT-k~GRrmFP~l~~~vsGLdp~~~Y~v~l~~~~~D~~Rykf~~~~W~~~g~~e~~~~~~~~~HPdsp~tG~~wM 97 (188)
T cd00182 19 GTEMIIT-KSGRRMFPTLKVKVSGLDPNALYSVLMDLVPVDDHRYKFSGGKWVVAGKAEPHLPPRVYVHPDSPATGAHWM 97 (188)
T ss_pred CcEEEEe-cCCcccccceEEEEeCCCcccceEEEEEEEEcCCcEEEecCCcEeEcCCCCCCCCCceEECCCCCcCHHHHh
Confidence 5789988 6899999999999999999999999999999999999998754
Q ss_pred -ceeEeec----------------------CCeeEEEEcCCCCCCCCCCCCeEEEEcCCceEEEcCCCCCCC
Q psy9084 55 -QIGSLVS----------------------LPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHR 103 (103)
Q Consensus 55 -~~vsF~k----------------------qPrlhiv~~~~~~~~~~~~~~~~tf~FpeT~FiAVTAYQN~~ 103 (103)
++|||+| ||||||+++++.... .....++|+||||+|||||||||++
T Consensus 98 ~~~isF~kvKlTN~~~~~~~~i~L~SmhKY~Prl~I~~~~~~~~~--~~~~~~~f~F~eT~FiAVTaYqN~~ 167 (188)
T cd00182 98 KQPVSFDKLKLTNNTLDNNGHIILNSMHKYQPRLHIVEVDDSSPF--SWRLVQTFSFPETEFIAVTAYQNQE 167 (188)
T ss_pred hCccccchhhcccCCCCCCCEEEEeccceEEeEEEEEEcCCCccc--cccccEEEECCCeEEEEEEeecCHh
Confidence 6899998 999999999765432 3567899999999999999999975
No 3
>smart00425 TBOX Domain first found in the mice T locus (Brachyury) protein.
Probab=100.00 E-value=8.6e-37 Score=225.30 Aligned_cols=97 Identities=46% Similarity=0.731 Sum_probs=85.7
Q ss_pred CceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEccCCceeeeecc-----------------------------
Q psy9084 4 DEALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHR----------------------------- 54 (103)
Q Consensus 4 ~~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry~~~~----------------------------- 54 (103)
.+|||+|+ +||||||.++++|+||||++.|.|+|+++++|++||||.+++
T Consensus 18 ~tEMIVTk-~GRrmFP~l~~~vsGLdp~~~Y~v~l~~~~~d~~rykf~~~~W~~~g~~e~~~~~~~~~Hpdsp~tG~~wM 96 (190)
T smart00425 18 GTEMIVTK-SGRRMFPTLKYKVSGLDPNALYSVLMDLVPVDDKRYKFNNGKWVVAGKAEPHMPSRVYVHPDSPATGAHWM 96 (190)
T ss_pred CcEEEEec-CCceeCCeeEEEEeCCCccCcEEEEEEEEEccCcEEEecCCcEEEcCCCCCCCCCceEECCCCccCHHHHh
Confidence 37898876 599999999999999999999999999999999999998764
Q ss_pred -ceeEeec------------------------CCeeEEEEcCCCCCCCCCCCCeEEEEcCCceEEEcCCCCCCC
Q psy9084 55 -QIGSLVS------------------------LPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHR 103 (103)
Q Consensus 55 -~~vsF~k------------------------qPrlhiv~~~~~~~~~~~~~~~~tf~FpeT~FiAVTAYQN~~ 103 (103)
++|+|+| ||||||+++++.... ....+++|+||||+|||||||||++
T Consensus 97 ~~~v~F~kvKlTN~~~~~~~~i~i~L~SmhkY~P~l~I~~~~~~~~~--~~~~~~~f~F~eT~FiaVTaYqN~~ 168 (190)
T smart00425 97 KQPVSFDKVKLTNNQSDKNGHLQIILNSMHKYQPRLHIVEVDDISKE--ILSQFKTFVFPETQFIAVTAYQNQK 168 (190)
T ss_pred hCcccccccceeccccccCCcEeeeeccCceEeeEEEEEEeCCcccc--cccceeEEECCceEEEEEeeecccc
Confidence 6788887 899999999764433 3466789999999999999999985
No 4
>KOG3585|consensus
Probab=99.98 E-value=5.1e-33 Score=219.09 Aligned_cols=96 Identities=36% Similarity=0.647 Sum_probs=84.5
Q ss_pred ceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEccCCceeeeecc------------------------------
Q psy9084 5 EALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHR------------------------------ 54 (103)
Q Consensus 5 ~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry~~~~------------------------------ 54 (103)
+||| +||+||||||.++|+|+||||++.|+|+|+++++|++||||.+++
T Consensus 43 ~Emi-itK~GRrmFP~l~~~VsGLdp~s~Y~i~l~~~~~D~~rykf~ng~W~p~gk~e~~~~~~~~~Hpd~p~TG~~WM~ 121 (328)
T KOG3585|consen 43 TEMI-VTKRGRRMFPALKFKVSGLDPNSLYSILLELVPIDDKRYKFNNGKWVPSGKAEPHVPSKVYVHPDGPATGAHWMS 121 (328)
T ss_pred cEEE-EecCCceeccccceeeccCCcccceEEEEEEEEccCceeeecCCeeccCCCCCCCCCceEEEecCCccchHHHhc
Confidence 4554 569999999999999999999999999999999999999999864
Q ss_pred ceeEeec-----------------------CCeeEEEEcCCCCCCCCCCCCeEEEEcCCceEEEcCCCCCCC
Q psy9084 55 QIGSLVS-----------------------LPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNHR 103 (103)
Q Consensus 55 ~~vsF~k-----------------------qPrlhiv~~~~~~~~~~~~~~~~tf~FpeT~FiAVTAYQN~~ 103 (103)
++|+|+| ||||||+++++. .......+++|.||||+|||||||||++
T Consensus 122 ~~V~F~kvKITN~~~~~~~~~i~l~SmHKY~P~l~i~~~~~~--~~~~~~~~~~~~F~eT~FIaVTaYQn~~ 191 (328)
T KOG3585|consen 122 EPVSFDKVKITNNKSDKKGKVIILNSMHKYQPVLHIVELDAS--LISPEISVQSFKFPETQFIAVTAYQNQE 191 (328)
T ss_pred CCcccceeEeeccccccCCceEeeecccceeeeEEEEEcccc--cCCCccceeEEEcccceeEEeeeeecce
Confidence 6789988 899999999722 1235688999999999999999999974
No 5
>PF00907 T-box: T-box; InterPro: IPR001699 Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis []. The T-box is defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family so far examined bind to the DNA consensus sequence TCACACCT. The T-box is a relatively large DNA-binding domain, generally comprising about a third of the entire protein (17-26 kDa). These genes were uncovered on the basis of similarity to the DNA binding domain [] of Mus musculus (Mouse) Brachyury (T) gene product, which similarity is the defining feature of the family. The Brachyury gene is named for its phenotype, which was identified 70 years ago as a mutant mouse strain with a short blunted tail. The gene, and its paralogues, have become a well-studied model for the family, and hence much of what is known about the T-box family is derived from the murine Brachyury gene. Consistent with its nuclear location, Brachyury protein has a sequence-specific DNA-binding activity and can act as a transcriptional regulator []. Homozygous mutants for the gene undergo extensive developmental anomalies, thus rendering the mutation lethal []. The postulated role of Brachyury is as a transcription factor, regulating the specification and differentiation of posterior mesoderm during gastrulation in a dose-dependent manner []. T-box proteins tend to be expressed in specific organs or cell types, especially during development, and they are generally required for the development of those tissues, for example, Brachyury is expressed in posterior mesoderm and in the developing notochord, and it is required for the formation of these cells in mice []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1H6F_B 4A04_A 1XBR_B 2X6V_B 2X6U_A.
Probab=99.98 E-value=1.2e-32 Score=200.33 Aligned_cols=96 Identities=35% Similarity=0.593 Sum_probs=75.2
Q ss_pred ceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEccCCceeeeecc------------------------------
Q psy9084 5 EALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPVDDKRYRYAFHR------------------------------ 54 (103)
Q Consensus 5 ~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry~~~~------------------------------ 54 (103)
.|||+ |++||+|||.|+|+|+||+|++.|.|.|+++++|+++|||.+++
T Consensus 18 ~EMiv-t~~GR~~FP~l~y~vsGL~p~~~Y~i~l~~~~~d~~~~k~~~~~W~~~~~~~~~~~~~~~~h~~~~~~G~~WM~ 96 (184)
T PF00907_consen 18 NEMIV-TKNGRRMFPTLEYSVSGLDPDSLYSISLHFERVDNKRYKFSNGKWVPSGKAEPPMPPRVVIHPDGPQTGSEWMK 96 (184)
T ss_dssp -EEE--BTT-EE-SS-EEEEEESS-TTSEEEEEEEEEESCSEEEEEETTEEEEEEE---B-----EE-TT-SEEHHHHHH
T ss_pred CEEEE-eecccccccccEEEecCCCCCcceEEEEEEEEecCceeecccccccccccccccccceEEEEecCcCCHHHhCc
Confidence 57777 58999999999999999999999999999999999999998753
Q ss_pred ceeEeec----------------------CCeeEEEEcCCCCCCCCCCCCeEEEEcCCceEEEcCCCCCC
Q psy9084 55 QIGSLVS----------------------LPRFHVVLLSPESNSASATSPFKTFLFPETMFTAVTAYQNH 102 (103)
Q Consensus 55 ~~vsF~k----------------------qPrlhiv~~~~~~~~~~~~~~~~tf~FpeT~FiAVTAYQN~ 102 (103)
++|+|++ +|+|||+++++..... ......+|+||||+|||||||||+
T Consensus 97 ~~v~F~~vkitn~~~~~~~~I~L~s~hkY~Pvl~I~~~~~~~~~~-~~~~~~~f~f~~t~FIaVT~Yqn~ 165 (184)
T PF00907_consen 97 NGVSFDKVKITNNKEDKKGNIFLNSMHKYQPVLHIYEVNSNGSPS-PNQPVHEFSFPETEFIAVTAYQNE 165 (184)
T ss_dssp S-EEETT-EEESSTT-TST-EE--TTEEEEEEEEEEECTTTSCCC-SCSSEEEEE-GGG-EEEESS-SSH
T ss_pred ccEEeehhhhhCCCCCcccceEEccccEEEEEEEEEEcCCccccc-cccceEEeecCcCeEEeecccchh
Confidence 5788887 8999999997654321 246799999999999999999996
No 6
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=83.47 E-value=1.8 Score=29.81 Aligned_cols=30 Identities=17% Similarity=0.295 Sum_probs=20.0
Q ss_pred ceEEEeCCCCCCCeeEEEEEEEccCCceee
Q psy9084 21 FQVRLFNLDPDAEYMLMMDFVPVDDKRYRY 50 (103)
Q Consensus 21 l~~~vsGL~p~~~Y~v~v~~~~~d~~ryry 50 (103)
++++|+||.|.+.+.|.+.+.--....|+-
T Consensus 5 ~~I~v~GL~p~~~vtl~a~~~~~~g~~w~S 34 (126)
T PF04775_consen 5 VDIRVSGLPPGQEVTLRARLTDDNGVQWQS 34 (126)
T ss_dssp -EEEEES--TT-EEEEEEEEE-TTS-EEEE
T ss_pred eEEEEeCCCCCCEEEEEEEEEeCCCCEEEE
Confidence 689999999999999999998655556654
No 7
>PF00041 fn3: Fibronectin type III domain; InterPro: IPR003961 Fibronectins are multi-domain glycoproteins found in a soluble form in plasma, and in an insoluble form in loose connective tissue and basement membranes []. They contain multiple copies of 3 repeat regions (types I, II and III), which bind to a variety of substances including heparin, collagen, DNA, actin, fibrin and fibronectin receptors on cell surfaces. The wide variety of these substances means that fibronectins are involved in a number of important functions: e.g., wound healing; cell adhesion; blood coagulation; cell differentiation and migration; maintenance of the cellular cytoskeleton; and tumour metastasis []. The role of fibronectin in cell differentiation is demonstrated by the marked reduction in the expression of its gene when neoplastic transformation occurs. Cell attachment has been found to be mediated by the binding of the tetrapeptide RGDS to integrins on the cell surface [], although related sequences can also display cell adhesion activity. Plasma fibronectin occurs as a dimer of 2 different subunits, linked together by 2 disulphide bonds near the C terminus. The difference in the 2 chains occurs in the type III repeat region and is caused by alternative splicing of the mRNA from one gene []. The observation that, in a given protein, an individual repeat of one of the 3 types (e.g., the first FnIII repeat) shows much less similarity to its subsequent tandem repeats within that protein than to its equivalent repeat between fibronectins from other species, has suggested that the repeating structure of fibronectin arose at an early stage of evolution. It also seems to suggest that the structure is subject to high selective pressure []. The fibronectin type III repeat region is an approximately 100 amino acid domain, different tandem repeats of which contain binding sites for DNA, heparin and the cell surface []. The superfamily of sequences believed to contain FnIII repeats represents 45 different families, the majority of which are involved in cell surface binding in some manner, or are receptor protein tyrosine kinases, or cytokine receptors.; GO: 0005515 protein binding; PDB: 1UEM_A 1TDQ_A 1X5I_A 2IC2_B 2IBG_C 2IBB_A 3R8Q_A 2FNB_A 1FNH_A 2EDB_A ....
Probab=71.91 E-value=8.5 Score=22.60 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=20.3
Q ss_pred ceEEEeCCCCCCCeeEEEEEEEcc
Q psy9084 21 FQVRLFNLDPDAEYMLMMDFVPVD 44 (103)
Q Consensus 21 l~~~vsGL~p~~~Y~v~v~~~~~d 44 (103)
..+.+.||+|...|.+.|..+..+
T Consensus 56 ~~~~i~~L~p~t~Y~~~v~a~~~~ 79 (85)
T PF00041_consen 56 TSYTITGLQPGTTYEFRVRAVNSD 79 (85)
T ss_dssp SEEEEESCCTTSEEEEEEEEEETT
T ss_pred eeeeeccCCCCCEEEEEEEEEeCC
Confidence 379999999999999999876543
No 8
>cd00169 Chemokine Chemokine: small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 subfamilies based on the arrangement of the two N-terminal cysteines; some members can bind multiple receptors and many chemokine receptors can bind more than one chemokine; this redundancy allows precise control in stimulating the immune system and in contributing to the homeostasis of a cell; when expressed inappropriately, chemokines play a role in autoimmune diseases, vascular irregularities, graft rejection, neoplasia, and allergies; exist as monomers, dimers and multimers, but are believed to function as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine_CXC (cd00273), Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for chemokine subgroups.
Probab=65.43 E-value=2.9 Score=24.83 Aligned_cols=15 Identities=13% Similarity=-0.121 Sum_probs=13.0
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
+..|+|.+|++||++
T Consensus 28 ~~~aIIf~tk~g~~i 42 (59)
T cd00169 28 SIPAVIFTTKKGRKV 42 (59)
T ss_pred CCceEEEEEcCCCEE
Confidence 578999999999874
No 9
>cd00273 Chemokine_CXC Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif which may be a general requirement for binding to CXC chemokine receptors; those with the ELR motif are chemotatic for neutrophils and have been shown to be angiogenic, while those without the motif act on T and B cells, and are typically angiostatic; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups.
Probab=64.83 E-value=2.6 Score=25.53 Aligned_cols=15 Identities=13% Similarity=0.207 Sum_probs=12.9
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
|..|+|.+||+||++
T Consensus 32 ~~~~VI~~tk~g~~i 46 (64)
T cd00273 32 PNTEIIATLKNGRKV 46 (64)
T ss_pred CCceEEEEEecCCEE
Confidence 578999999999874
No 10
>PF09294 Interfer-bind: Interferon-alpha/beta receptor, fibronectin type III; InterPro: IPR015373 Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha []. ; PDB: 1A21_A 3LQM_B 3ELA_T 1AHW_C 2A2Q_T 1TFH_B 1FAK_T 1WSS_T 1W2K_T 2FIR_T ....
Probab=63.32 E-value=12 Score=23.70 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=16.5
Q ss_pred eEEEeCCCCCCCeeEEEEEEE
Q psy9084 22 QVRLFNLDPDAEYMLMMDFVP 42 (103)
Q Consensus 22 ~~~vsGL~p~~~Y~v~v~~~~ 42 (103)
.+.+.+|+|+..|++.+....
T Consensus 68 ~~~l~~L~p~t~YCv~V~~~~ 88 (106)
T PF09294_consen 68 SVTLSDLKPGTNYCVSVQAFS 88 (106)
T ss_dssp EEEEES--TTSEEEEEEEEEE
T ss_pred EEEEeCCCCCCCEEEEEEEEe
Confidence 468999999999999999944
No 11
>smart00199 SCY Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). Family of cytokines involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response.
Probab=62.17 E-value=3.1 Score=24.78 Aligned_cols=15 Identities=20% Similarity=0.133 Sum_probs=12.5
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
+..|+|.+|++||++
T Consensus 29 ~~~avIf~tk~g~~~ 43 (59)
T smart00199 29 PKPAVIFTTKKGRKV 43 (59)
T ss_pred CCccEEEEEeCCCEE
Confidence 567999999999853
No 12
>cd00272 Chemokine_CC Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_C
Probab=60.73 E-value=4 Score=24.14 Aligned_cols=15 Identities=13% Similarity=-0.084 Sum_probs=12.7
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
+..|+|.+|++||++
T Consensus 26 ~~~aVIf~tk~g~~i 40 (57)
T cd00272 26 SKPAVIFKTKRGREV 40 (57)
T ss_pred CCcEEEEEeCCCCEE
Confidence 467999999999874
No 13
>cd01119 Chemokine_CC_DCCL Chemokine_CC_DCCL: subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic progenitor proliferation by blocking progression through the cell cycle; DCCL subgroup contains Exodus-1 (also known as CCL20, MIP-3alpha, LARC, ST38 (mouse)), Exodus-2 (also known as CCL21, SLC, 6-Ckine, TCA4, CKbeta9), and Exodus-3 (also known as CCL-19, ELC, MIP-3beta, CKbeta11). Exodus-3 was shown to inhibit the growth of human breast cancer cells in vivo in a mouse model; Exodus-1, -2, and -3 were all shown to significantly inhibit chronic myelogenous leukemia progenitor cell proliferation; Exodus-2 and -3 show potent immunotherapeutic activity toward solid tumors; chemotatic for T cells, B cells, dendritic cells, macrophage progenitor cells, and NK cells; exist as monomers and dimers, but are believed to be funct
Probab=57.02 E-value=4.7 Score=24.29 Aligned_cols=15 Identities=13% Similarity=-0.028 Sum_probs=12.7
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
|..|+|.+|++||+.
T Consensus 30 ~~~aVIf~tk~g~~i 44 (61)
T cd01119 30 DIPAIIFHTRRGRKV 44 (61)
T ss_pred CCCEEEEEEcCCCEE
Confidence 578999999999874
No 14
>smart00060 FN3 Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.
Probab=55.44 E-value=21 Score=19.39 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=19.3
Q ss_pred cceEEEeCCCCCCCeeEEEEEEE
Q psy9084 20 TFQVRLFNLDPDAEYMLMMDFVP 42 (103)
Q Consensus 20 ~l~~~vsGL~p~~~Y~v~v~~~~ 42 (103)
..++.+.||.|...|.+.|....
T Consensus 56 ~~~~~i~~L~~~~~Y~v~v~a~~ 78 (83)
T smart00060 56 STSYTLTGLKPGTEYEFRVRAVN 78 (83)
T ss_pred ccEEEEeCcCCCCEEEEEEEEEc
Confidence 46788999999999999887665
No 15
>cd00063 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
Probab=45.78 E-value=33 Score=19.25 Aligned_cols=24 Identities=25% Similarity=0.324 Sum_probs=19.1
Q ss_pred ccceEEEeCCCCCCCeeEEEEEEE
Q psy9084 19 PTFQVRLFNLDPDAEYMLMMDFVP 42 (103)
Q Consensus 19 P~l~~~vsGL~p~~~Y~v~v~~~~ 42 (103)
...++.+.||.|...|.+.|....
T Consensus 55 ~~~~~~i~~l~p~~~Y~~~v~a~~ 78 (93)
T cd00063 55 SETSYTLTGLKPGTEYEFRVRAVN 78 (93)
T ss_pred cccEEEEccccCCCEEEEEEEEEC
Confidence 346788999999999998876554
No 16
>cd00271 Chemokine_C Chemokine_C, C or lymphotactin subgroup, 1 of 4 subgroup designations of chemokines based on the arrangement of two N-terminal, conserved cysteine residues. Most of the known chemokines (cd00169) belong to either the CC (cd00272) or CXC (cd00273) subclass. The two other subclasses each have a single known member: fractalkine for the CX3C (cd00274) class and lymphotactin for the C (cd00271) class. Chemokine_Cs differ structurally since they contain only one of the two disulfide bridges that are conserved in all other chemokines and they possess a unique C-terminal extension, which is required for biological activity and thought to play a role in receptor binding. Lymphotactin, a mediator of mucosal immunity, has been found to chemoattract neutrophils and B cells through the XCR1 receptor and thought to be a factor in acute allograft rejection and inflammatory bowel disease.
Probab=44.72 E-value=11 Score=23.76 Aligned_cols=16 Identities=13% Similarity=-0.035 Sum_probs=13.4
Q ss_pred CCCceeeecccCCcCC
Q psy9084 2 GPDEALCGWPWISRRM 17 (103)
Q Consensus 2 ~~~~~~~~~t~~GRrm 17 (103)
+|..|+|.+|+.||+.
T Consensus 32 ~~~~AVIF~Tkkgr~i 47 (72)
T cd00271 32 GSVRAVIFITKRGLKI 47 (72)
T ss_pred CCCCeEEEEecCCCEE
Confidence 4678999999999874
No 17
>PF00048 IL8: Small cytokines (intecrine/chemokine), interleukin-8 like; InterPro: IPR001811 Many low-molecular weight factors secreted by cells including fibroblasts, macrophages and endothelial cells, in response to a variety of stimuli such as growth factors, interferons, viral transformation and bacterial products, are structurally related [, , ]. Most members of this family of proteins seem to have mitogenic, chemotactic or inflammatory activities. These small cytokines are also called intercrines or chemokines. They are cationic proteins of 70 to 100 amino acid residues that share four conserved cysteine residues involved in two disulphide bonds, as shown in the following schematic representation: +------------------------------------+ | | xxxxxxxxxxxxxxxxxxxxxxCxCxxxxxxxxxxxxxxxxxxxxxxxCxxxxxxxxxxxxCxxxxx | | +-------------------------+ 'C': conserved cysteine involved in a disulphide bond. Chemokines can be sorted into main groups based on the spacing of the two amino-terminal cysteines. In the first group (see IPR001089 from INTERPRO), the two cysteines are separated by a single residue (C-x-C), while in the second group (see IPR000827 from INTERPRO), they are adjacent (C-C).; GO: 0008009 chemokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 3HP3_B 2K01_A 2KEE_A 2K04_C 2J7Z_A 1QG7_A 2KED_A 2NWG_B 2KEC_A 1VMC_A ....
Probab=44.33 E-value=10 Score=22.62 Aligned_cols=14 Identities=14% Similarity=-0.111 Sum_probs=11.7
Q ss_pred CceeeecccCCcCC
Q psy9084 4 DEALCGWPWISRRM 17 (103)
Q Consensus 4 ~~~~~~~t~~GRrm 17 (103)
..|+|.+|+.||+.
T Consensus 35 ~~avI~~~k~g~~~ 48 (64)
T PF00048_consen 35 RPAVIFTTKKGREV 48 (64)
T ss_dssp SCEEEEEETTSEEE
T ss_pred CceEEEEecCCCcE
Confidence 57999999999863
No 18
>cd00274 Chemokine_CX3C Chemokine_CX3C: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteines; differ structurally from the other subgroups in that they are attached to a membrane-spanning domain via a mucin-like stalk and can be proteolytically cleaved to a freely diffusible form; chemotatic for T cells, monocytes, and natural killer cells; function as monomers and are found only in vertebrates and a few viruses; currently only fractalkine (sometimes called neurotactin) has been identified as a member of this subfamily; the primary source of fractalkine is neurons, and they exhibit cell adhesion and chemoattractive properties in the central nervous system. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_CC (cd00272), and Chemokine_C (cd00271) for the additional chemokine subgroups.
Probab=29.72 E-value=26 Score=22.51 Aligned_cols=15 Identities=13% Similarity=-0.103 Sum_probs=12.6
Q ss_pred CCceeeecccCCcCC
Q psy9084 3 PDEALCGWPWISRRM 17 (103)
Q Consensus 3 ~~~~~~~~t~~GRrm 17 (103)
|..|+|.+|+.||++
T Consensus 35 ~~~AVIF~Tkkgr~i 49 (76)
T cd00274 35 GKRAIILETRQHRLF 49 (76)
T ss_pred CCCeEEEEECCCCEE
Confidence 567999999999964
No 19
>PF10179 DUF2369: Uncharacterised conserved protein (DUF2369); InterPro: IPR019326 This is a proline-rich region of a group of proteins found from plants to fungi. The function is largely unknown, although the entry contains Fibronectin type-III domain-containing protein C4orf31, which promotes matrix assembly and cell adhesiveness.
Probab=28.27 E-value=63 Score=25.76 Aligned_cols=29 Identities=14% Similarity=0.257 Sum_probs=22.7
Q ss_pred eEEEeCCCCCCCeeEEEEEEEccCCceee
Q psy9084 22 QVRLFNLDPDAEYMLMMDFVPVDDKRYRY 50 (103)
Q Consensus 22 ~~~vsGL~p~~~Y~v~v~~~~~d~~ryry 50 (103)
--+|+||+|...|.+-+-+......-.+|
T Consensus 261 tetI~~L~PG~~Yl~dV~~~~~~G~sl~Y 289 (300)
T PF10179_consen 261 TETIKGLKPGTTYLFDVYVNGPSGQSLPY 289 (300)
T ss_pred eeecccCCCCcEEEEEEEEecCCCceeec
Confidence 34799999999998888887766555555
No 20
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.32 E-value=40 Score=25.08 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=19.1
Q ss_pred CCcCCCccceE--EEeCCCCCCCeeEEEE
Q psy9084 13 ISRRMFPTFQV--RLFNLDPDAEYMLMMD 39 (103)
Q Consensus 13 ~GRrmFP~l~~--~vsGL~p~~~Y~v~v~ 39 (103)
+|||++|.+.. .+.=|+....|.+.+.
T Consensus 1 sGrrl~P~i~Lgs~~~~l~~~~~~Ll~iT 29 (219)
T PF07569_consen 1 SGRRLLPPIVLGSPVSFLECNGSYLLAIT 29 (219)
T ss_pred CCccccCcEecCCceEEEEeCCCEEEEEe
Confidence 69999998654 3444788889955544
No 21
>PF12503 CMV_1a_C: Cucumber mosaic virus 1a protein C terminal ; InterPro: IPR022184 This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with PF01443 from PFAM, PF01660 from PFAM. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the (Cucumber mosaic virus. The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. ; GO: 0008168 methyltransferase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=23.42 E-value=69 Score=21.07 Aligned_cols=26 Identities=23% Similarity=0.176 Sum_probs=17.2
Q ss_pred eeec-ccCCcCCCcc-----ceEEEeCCCCCC
Q psy9084 7 LCGW-PWISRRMFPT-----FQVRLFNLDPDA 32 (103)
Q Consensus 7 ~~~~-t~~GRrmFP~-----l~~~vsGL~p~~ 32 (103)
|+|+ -.+||.|+|. +-|+=+||-|+.
T Consensus 30 lVNvHf~~GrWm~P~~~~Y~VGyNe~GLGpK~ 61 (85)
T PF12503_consen 30 LVNVHFPNGRWMYPEGYEYMVGYNESGLGPKF 61 (85)
T ss_pred cEEEEecCCceecCCCeEEEeeecCCCCCcCc
Confidence 4444 3579999995 445557777754
No 22
>PF15417 DUF4624: Domain of unknown function (DUF4624)
Probab=22.51 E-value=1.1e+02 Score=21.44 Aligned_cols=41 Identities=27% Similarity=0.408 Sum_probs=33.9
Q ss_pred CCceeeecccCCcCCCccceEEEeCCCCCCCeeEEEEEEEc
Q psy9084 3 PDEALCGWPWISRRMFPTFQVRLFNLDPDAEYMLMMDFVPV 43 (103)
Q Consensus 3 ~~~~~~~~t~~GRrmFP~l~~~vsGL~p~~~Y~v~v~~~~~ 43 (103)
.||-|-.-|..|.-+--.+.++++.|.....|.+.+.=..+
T Consensus 71 ~devLWsn~~~~~V~~dt~tisL~nlqk~kEY~V~ftGtkI 111 (132)
T PF15417_consen 71 TDEVLWSNTWNGKVSGDTFTISLNNLQKEKEYVVCFTGTKI 111 (132)
T ss_pred ccceeeccccccccccceEEEEhhhcccCceEEEEEeccEe
Confidence 35667777889999999999999999999999987654443
No 23
>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.
Probab=21.90 E-value=50 Score=21.52 Aligned_cols=22 Identities=23% Similarity=0.573 Sum_probs=16.2
Q ss_pred cCCCccceEEEeCCCCCCCeeE
Q psy9084 15 RRMFPTFQVRLFNLDPDAEYML 36 (103)
Q Consensus 15 RrmFP~l~~~vsGL~p~~~Y~v 36 (103)
|..||.++.+-.|.--+++|..
T Consensus 55 r~vFP~l~~RRLG~RG~SkYhY 76 (85)
T PF02257_consen 55 RQVFPNLKTRRLGTRGQSKYHY 76 (85)
T ss_dssp HHHSTT-EEEEESSTT--EEEE
T ss_pred HHHcCCCcccccccCCCcceEE
Confidence 3469999999999999999974
Done!