Query 034518
Match_columns 92
No_of_seqs 102 out of 107
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:43:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034518.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034518hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15249 GLTSCR1: Glioma tumor 17.1 52 0.0011 22.3 0.4 10 58-67 27-36 (109)
2 cd01102 Link_Domain The link d 14.1 74 0.0016 21.7 0.5 15 78-92 42-56 (92)
3 cd03518 Link_domain_HAPLN_modu 10.9 1.2E+02 0.0026 20.9 0.8 15 78-92 42-56 (95)
4 smart00445 LINK Link (Hyaluron 9.8 1.3E+02 0.0028 20.7 0.6 15 78-92 43-57 (94)
5 cd03519 Link_domain_HAPLN_modu 9.6 1.5E+02 0.0032 20.5 0.8 14 79-92 41-54 (91)
6 PF00023 Ank: Ankyrin repeat H 9.0 1.4E+02 0.003 15.3 0.4 11 62-72 3-13 (33)
7 cd03515 Link_domain_TSG_6_like 9.0 1.5E+02 0.0032 20.4 0.6 15 78-92 42-56 (93)
8 cd03520 Link_domain_CSPGs_modu 8.9 1.5E+02 0.0032 20.6 0.6 15 78-92 39-53 (96)
9 PF00193 Xlink: Extracellular 8.5 1.5E+02 0.0033 19.8 0.5 14 78-91 42-55 (92)
10 KOG0171 Mitochondrial inner me 7.7 1.6E+02 0.0035 22.7 0.4 13 79-91 133-145 (176)
No 1
>PF15249 GLTSCR1: Glioma tumor suppressor candidate region
Probab=17.14 E-value=52 Score=22.30 Aligned_cols=10 Identities=60% Similarity=1.182 Sum_probs=8.6
Q ss_pred hhhhccchhh
Q 034518 58 CVESMLPYHT 67 (92)
Q Consensus 58 cveSllPlHs 67 (92)
.++-|||||-
T Consensus 27 A~~RLLPYHv 36 (109)
T PF15249_consen 27 AVERLLPYHV 36 (109)
T ss_pred HHHHhcchhh
Confidence 4889999995
No 2
>cd01102 Link_Domain The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of
Probab=14.09 E-value=74 Score=21.71 Aligned_cols=15 Identities=33% Similarity=0.820 Sum_probs=12.3
Q ss_pred hccccccccccCCCC
Q 034518 78 LSISQCGYGWLPEGL 92 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg~ 92 (92)
.+.+...+|||++|.
T Consensus 42 ~G~~~C~~GWL~Dgs 56 (92)
T cd01102 42 DGFDVCTAGWLADGS 56 (92)
T ss_pred cchhhcCCccccCCe
Confidence 477888999999883
No 3
>cd03518 Link_domain_HAPLN_module_1 Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.
Probab=10.91 E-value=1.2e+02 Score=20.94 Aligned_cols=15 Identities=33% Similarity=0.913 Sum_probs=12.6
Q ss_pred hccccccccccCCCC
Q 034518 78 LSISQCGYGWLPEGL 92 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg~ 92 (92)
.+.|...+|||++|.
T Consensus 42 ~Gld~C~~GWL~Dgs 56 (95)
T cd03518 42 EGLDWCNAGWLSDGT 56 (95)
T ss_pred cCccccCcccccCCC
Confidence 678888999999883
No 4
>smart00445 LINK Link (Hyaluronan-binding).
Probab=9.79 E-value=1.3e+02 Score=20.65 Aligned_cols=15 Identities=33% Similarity=0.880 Sum_probs=12.2
Q ss_pred hccccccccccCCCC
Q 034518 78 LSISQCGYGWLPEGL 92 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg~ 92 (92)
.+.|...+|||++|.
T Consensus 43 ~Gld~C~~GWL~Dgs 57 (94)
T smart00445 43 DGFDTCDAGWLADGS 57 (94)
T ss_pred hchhhcCcccccCCe
Confidence 477888999999873
No 5
>cd03519 Link_domain_HAPLN_module_2 Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes.
Probab=9.56 E-value=1.5e+02 Score=20.48 Aligned_cols=14 Identities=36% Similarity=1.116 Sum_probs=12.0
Q ss_pred ccccccccccCCCC
Q 034518 79 SISQCGYGWLPEGL 92 (92)
Q Consensus 79 sv~s~~~~~Lsqg~ 92 (92)
+.|...+|||.+|.
T Consensus 41 Gld~C~aGWL~Dgs 54 (91)
T cd03519 41 GLDRCDAGWLADGS 54 (91)
T ss_pred CCcccCcccCcCCC
Confidence 78888999999983
No 6
>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....
Probab=9.00 E-value=1.4e+02 Score=15.27 Aligned_cols=11 Identities=27% Similarity=0.344 Sum_probs=7.6
Q ss_pred ccchhhHHHHH
Q 034518 62 MLPYHTATASA 72 (92)
Q Consensus 62 llPlHsAvAsA 72 (92)
.-|||.|+-..
T Consensus 3 ~TpLh~A~~~~ 13 (33)
T PF00023_consen 3 NTPLHYAAQRG 13 (33)
T ss_dssp BBHHHHHHHTT
T ss_pred ccHHHHHHHHH
Confidence 45899887543
No 7
>cd03515 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accum
Probab=8.96 E-value=1.5e+02 Score=20.41 Aligned_cols=15 Identities=40% Similarity=0.979 Sum_probs=12.4
Q ss_pred hccccccccccCCCC
Q 034518 78 LSISQCGYGWLPEGL 92 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg~ 92 (92)
.+.|...+|||++|.
T Consensus 42 ~G~d~C~~GWL~Dgs 56 (93)
T cd03515 42 LGFHLCAAGWLAKGR 56 (93)
T ss_pred cCccccCcccccCCe
Confidence 578888999999873
No 8
>cd03520 Link_domain_CSPGs_modules_2_4 Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and
Probab=8.90 E-value=1.5e+02 Score=20.57 Aligned_cols=15 Identities=40% Similarity=1.013 Sum_probs=12.3
Q ss_pred hccccccccccCCCC
Q 034518 78 LSISQCGYGWLPEGL 92 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg~ 92 (92)
.+.+...+|||.+|.
T Consensus 39 ~Gld~C~~GWL~Dgs 53 (96)
T cd03520 39 QGLDQCDPGWLADGS 53 (96)
T ss_pred hccccccCccccccc
Confidence 577888999999873
No 9
>PF00193 Xlink: Extracellular link domain; InterPro: IPR000538 The link domain [] is a hyaluronan(HA)-binding region found in proteins of vertebrates that are involved in the assembly of extracellular matrix, cell adhesion, and migration. The structure has been shown [] to consist of two alpha helices and two antiparallel beta sheets arranged around a large hydrophobic core similar to that of C-type lectin. This domain contains four conserved cysteines involved in two disulphide bonds. The link domain has also been termed HABM [] (HA binding module) and PTR [] (proteoglycan tandem repeat). Proteins with such a domain include the proteoglycans aggrecan, brevican, neurocan and versican, which are expressed in the CNS; the cartilage link protein (LP), a proteoglycan that together with HA and aggrecan forms multimolecular aggregates; Tumour necrosis factor-inducible protein TSG-6, which may be involved in cell-cell and cell-matrix interactions during inflammation and tumourgenesis; and CD44 antigen, the main cell surface receptor for HA.; GO: 0005540 hyaluronic acid binding, 0007155 cell adhesion; PDB: 1O7B_T 2PF5_C 1O7C_T 2JCQ_A 2JCR_A 2JCP_A 1UUH_B 1POZ_A 2I83_A.
Probab=8.47 E-value=1.5e+02 Score=19.77 Aligned_cols=14 Identities=36% Similarity=1.025 Sum_probs=8.1
Q ss_pred hccccccccccCCC
Q 034518 78 LSISQCGYGWLPEG 91 (92)
Q Consensus 78 Lsv~s~~~~~Lsqg 91 (92)
.+.+...+|||.+|
T Consensus 42 ~G~~~C~~GWL~dg 55 (92)
T PF00193_consen 42 AGFETCRAGWLADG 55 (92)
T ss_dssp TT---SS-EEEGCC
T ss_pred hhhhHhHHHhhcCC
Confidence 47788889999887
No 10
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=7.71 E-value=1.6e+02 Score=22.70 Aligned_cols=13 Identities=46% Similarity=0.756 Sum_probs=8.1
Q ss_pred ccccccccccCCC
Q 034518 79 SISQCGYGWLPEG 91 (92)
Q Consensus 79 sv~s~~~~~Lsqg 91 (92)
|.|||+||-||.|
T Consensus 133 S~DSr~yGplP~g 145 (176)
T KOG0171|consen 133 SLDSRNYGPLPMG 145 (176)
T ss_pred cccccccCCCchh
Confidence 4566666666655
Done!