Query 045131
Match_columns 107
No_of_seqs 103 out of 128
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 10:09:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01190 Pollen_Ole_e_I: Polle 99.7 9.2E-17 2E-21 108.4 8.1 57 1-58 24-87 (97)
2 PF09103 BRCA-2_OB1: BRCA2, ol 81.9 0.54 1.2E-05 33.3 0.5 60 26-91 41-116 (118)
3 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 79.5 3.3 7.1E-05 28.9 3.7 55 26-87 29-100 (100)
4 PF13715 DUF4480: Domain of un 75.6 2.7 5.8E-05 26.6 2.3 17 19-35 27-43 (88)
5 PF05738 Cna_B: Cna protein B- 74.2 8 0.00017 23.4 4.1 44 1-51 4-49 (70)
6 PF10670 DUF4198: Domain of un 73.8 6 0.00013 28.7 4.0 37 1-37 167-203 (215)
7 PF13620 CarboxypepD_reg: Carb 68.7 4.7 0.0001 24.9 2.2 18 18-35 29-47 (82)
8 PF01060 DUF290: Transthyretin 62.8 7.6 0.00017 25.0 2.4 19 17-35 29-47 (80)
9 PF08400 phage_tail_N: Prophag 62.5 11 0.00023 27.5 3.3 23 15-37 35-58 (134)
10 smart00557 IG_FLMN Filamin-typ 62.4 28 0.00061 22.6 5.1 30 3-34 46-75 (93)
11 PF00630 Filamin: Filamin/ABP2 62.1 25 0.00055 22.4 4.8 30 3-34 60-89 (101)
12 TIGR02513 type_III_yscB type I 60.9 8.8 0.00019 28.3 2.6 31 21-51 16-49 (139)
13 COG4850 Uncharacterized conser 58.0 34 0.00075 28.9 5.9 45 3-51 99-145 (373)
14 PRK13865 type IV secretion sys 54.7 6.2 0.00013 30.8 1.0 24 64-88 195-218 (229)
15 PF11974 MG1: Alpha-2-macroglo 51.4 23 0.00051 23.7 3.3 17 18-34 44-60 (97)
16 PF12565 DUF3747: Protein of u 51.2 26 0.00055 26.9 3.8 46 22-76 92-147 (181)
17 PF08884 Flagellin_D3: Flagell 49.0 34 0.00075 23.3 3.9 26 12-37 36-64 (90)
18 KOG1948 Metalloproteinase-rela 46.7 14 0.00029 35.0 2.0 29 2-32 923-951 (1165)
19 PRK13836 conjugal transfer pro 45.6 8.9 0.00019 29.2 0.6 26 63-89 186-211 (220)
20 PF10875 DUF2670: Protein of u 44.0 7.1 0.00015 28.6 -0.1 11 79-89 8-18 (139)
21 PRK13872 conjugal transfer pro 41.5 12 0.00025 28.7 0.7 26 63-89 192-217 (228)
22 TIGR02962 hdxy_isourate hydrox 40.9 81 0.0017 22.0 4.8 29 2-32 20-48 (112)
23 PF03983 SHD1: SLA1 homology d 33.6 22 0.00048 23.2 1.0 13 21-33 14-26 (70)
24 PRK13887 conjugal transfer pro 31.2 14 0.0003 28.7 -0.3 12 78-89 230-241 (250)
25 PF14686 fn3_3: Polysaccharide 31.1 29 0.00064 23.4 1.3 12 21-32 44-55 (95)
26 PHA02123 hypothetical protein 30.7 59 0.0013 23.6 2.8 57 20-82 40-110 (146)
27 PF13115 YtkA: YtkA-like 29.6 1.4E+02 0.0031 18.5 4.3 34 1-34 38-74 (86)
28 KOG0518 Actin-binding cytoskel 29.4 65 0.0014 30.9 3.5 31 2-34 800-830 (1113)
29 PF12249 AftA_C: Arabinofurano 29.3 18 0.0004 27.7 0.0 13 78-90 75-87 (178)
30 PF04335 VirB8: VirB8 protein; 28.6 18 0.00038 26.3 -0.2 26 63-88 176-203 (212)
31 cd03858 M14_CP_N-E_like Carbox 28.6 67 0.0015 26.1 3.2 15 20-34 325-339 (374)
32 PF14059 DUF4251: Domain of un 27.4 1.2E+02 0.0025 21.5 3.9 32 23-54 88-120 (138)
33 PF11224 DUF3023: Protein of u 26.4 59 0.0013 22.9 2.2 23 19-41 3-26 (130)
34 TIGR01646 vgr_GE Rhs element V 26.3 78 0.0017 26.4 3.3 28 20-47 362-395 (483)
35 TIGR03361 VI_Rhs_Vgr type VI s 25.1 90 0.0019 26.3 3.4 28 21-48 374-407 (513)
36 PF09904 HTH_43: Winged helix- 24.8 43 0.00093 23.0 1.2 19 14-32 51-69 (90)
37 PF07679 I-set: Immunoglobulin 24.0 85 0.0019 19.0 2.4 22 24-45 66-88 (90)
38 PF10709 DUF2511: Protein of u 23.0 84 0.0018 21.3 2.4 20 2-24 17-36 (87)
39 PF01835 A2M_N: MG2 domain; I 22.3 2.2E+02 0.0048 18.1 5.1 32 2-34 37-69 (99)
40 cd05717 Ig1_Necl-1-3_like Firs 22.0 2.1E+02 0.0046 17.8 4.3 30 39-69 65-94 (95)
41 PF10440 WIYLD: Ubiquitin-bind 20.9 39 0.00085 21.8 0.4 23 82-104 18-40 (65)
42 PF02369 Big_1: Bacterial Ig-l 20.8 81 0.0018 20.9 1.9 19 20-38 61-79 (100)
43 PF00576 Transthyretin: HIUase 20.4 1.6E+02 0.0036 20.4 3.5 28 2-30 20-47 (112)
44 COG2885 OmpA Outer membrane pr 20.3 63 0.0014 23.5 1.4 20 14-33 114-135 (190)
45 PF11589 DUF3244: Domain of un 20.2 2E+02 0.0043 19.1 3.8 34 2-36 49-82 (106)
46 PF04151 PPC: Bacterial pre-pe 20.1 81 0.0017 19.2 1.7 13 23-35 58-70 (70)
No 1
>PF01190 Pollen_Ole_e_I: Pollen proteins Ole e I like; InterPro: IPR006041 Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Ole e 1. A number of plant pollen proteins, whose biological function is not yet known, are structurally related []. These proteins are most probably secreted and consist of about 145 residues. There are six cysteines which are conserved in the sequence of these proteins. They seem to be involved in disulphide bonds.
Probab=99.70 E-value=9.2e-17 Score=108.39 Aligned_cols=57 Identities=39% Similarity=0.753 Sum_probs=53.1
Q ss_pred CeEEEEeecCCCCceEEEEEEEcCCCeeEEEEecCC------Cc-ceeEEEEeeCCCccCccccc
Q 045131 1 ATVALECKESEGGEVVYSREVVSDQSGTYKIPIEGC------HA-KLCQVRLVKSPKPECSEIVA 58 (107)
Q Consensus 1 A~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~~d------h~-~~C~V~LvsSP~~~C~~~~~ 58 (107)
|+|+|+|++. .+.+.++.+++||++|+|+|+++++ |. +.|.|+|++||++.|+.+++
T Consensus 24 A~V~v~C~~~-~~~~~~~~~~~Td~~G~F~i~l~~~~~~~~~~~~~~C~v~l~~sp~~~C~~~~~ 87 (97)
T PF01190_consen 24 AKVSVECKDG-NGGVVFSAEAKTDENGYFSIELPSDPGSSSPHLSSSCRVKLVSSPDPSCNVPTN 87 (97)
T ss_pred CEEEEECCCC-CCCcEEEEEEEeCCCCEEEEEecCccccccCCCCCCcEEEEeCCCcCcCCCCcC
Confidence 7999999995 5559999999999999999999986 67 99999999999999999998
No 2
>PF09103 BRCA-2_OB1: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1; InterPro: IPR015187 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome []. ; GO: 0000724 double-strand break repair via homologous recombination; PDB: 1IYJ_D 1MIU_A.
Probab=81.90 E-value=0.54 Score=33.28 Aligned_cols=60 Identities=28% Similarity=0.470 Sum_probs=27.4
Q ss_pred CeeEEEEecCC--------------C-c-ceeEEEEeeCCCccCcccccCCCceeeEEeecCCCCCCCceeeecCCCccc
Q 045131 26 SGTYKIPIEGC--------------H-A-KLCQVRLVKSPKPECSEIVADGLSSARIDLTPSVGSDPELIRYANDLGFMK 89 (107)
Q Consensus 26 ~G~y~i~v~~d--------------h-~-~~C~V~LvsSP~~~C~~~~~~~r~~a~V~Lt~nnGi~s~~~R~aN~lgF~~ 89 (107)
+|||.|...-| + . .+|-+.|+.++++ |+..+. .+...+.| ..|++. ..|..-+|||.+
T Consensus 41 DGWY~Ika~lD~~L~~~l~~gki~vG~KL~v~GA~L~~~~~~-~~pLE~--~~~~~L~l-~~Nstr--~a~w~~kLG~~~ 114 (118)
T PF09103_consen 41 DGWYSIKAQLDPPLTRLLRKGKIRVGQKLRVCGAELLGSKEP-CSPLEA--PDSVMLKL-HANSTR--PARWDAKLGFQK 114 (118)
T ss_dssp -SS-EEEE---HHHHHHHHTT-S-TT-EEEESSBEEES--S----CCC----SS-EEE---CCCEE--EB-SSS-SEE-S
T ss_pred cCCEEEEEEeCHHHHHHHHhCCccCCccEEEECceecCCCCC-cCCCcC--CCceEEEE-EeeeEE--eccccccCCCCC
Confidence 59999986533 2 3 8899999987644 776653 22343444 445653 356666999998
Q ss_pred cC
Q 045131 90 KE 91 (107)
Q Consensus 90 ~~ 91 (107)
+.
T Consensus 115 ~~ 116 (118)
T PF09103_consen 115 DP 116 (118)
T ss_dssp --
T ss_pred CC
Confidence 74
No 3
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.
Probab=79.48 E-value=3.3 Score=28.87 Aligned_cols=55 Identities=27% Similarity=0.511 Sum_probs=37.8
Q ss_pred CeeEEEEecCC---------------Cc-ceeEEEEeeCCCccCcccccCCCceeeEEee-cCCCCCCCceeeecCCCc
Q 045131 26 SGTYKIPIEGC---------------HA-KLCQVRLVKSPKPECSEIVADGLSSARIDLT-PSVGSDPELIRYANDLGF 87 (107)
Q Consensus 26 ~G~y~i~v~~d---------------h~-~~C~V~LvsSP~~~C~~~~~~~r~~a~V~Lt-~nnGi~s~~~R~aN~lgF 87 (107)
+|||.|...-| +. -+|-+.|+.++++ |+..+. . ..|.|. +-|++. ..|..-+|||
T Consensus 29 DGWYsi~a~lD~~L~~~l~~gkl~vGqKL~i~GA~l~~~~~~-~sple~-~---~~~~L~l~~Nstr--~a~w~~~LGf 100 (100)
T cd04493 29 DGWYSIRAQLDPPLTNLVRKGKLRVGQKLRICGAELLGSANP-CSPLEA-P---DSVRLKINANSTR--RARWDARLGF 100 (100)
T ss_pred cCeEEEEEEeCHHHHHHHHcCCeecccEEEEECceeecCCCC-cCcccC-C---CcEEEEEEcccee--ccccccccCC
Confidence 59999986533 33 7899999999755 877765 2 345553 446653 3677778887
No 4
>PF13715 DUF4480: Domain of unknown function (DUF4480)
Probab=75.59 E-value=2.7 Score=26.63 Aligned_cols=17 Identities=24% Similarity=0.601 Sum_probs=14.1
Q ss_pred EEEEcCCCeeEEEEecC
Q 045131 19 REVVSDQSGTYKIPIEG 35 (107)
Q Consensus 19 ~e~~TD~~G~y~i~v~~ 35 (107)
....||++|.|.|.++.
T Consensus 27 ~~~~Td~~G~F~i~~~~ 43 (88)
T PF13715_consen 27 KGTVTDENGRFSIKLPE 43 (88)
T ss_pred ceEEECCCeEEEEEEcC
Confidence 34679999999999873
No 5
>PF05738 Cna_B: Cna protein B-type domain; InterPro: IPR008454 This entry represents a repeated B region domain found in the collagen-binding surface protein Cna in Staphylococcus aureus, as well as other related domains. The B region domain of Cna has a prealbumin-like beta-sandwich fold of seven strands in two sheets with a Greek key topology []. However, this domain does not mediate collagen binding, the IPR008456 from INTERPRO region carries out that function; instead it appears to form a stalk that presents the ligand binding domain away from the bacterial cell surface. Cna is a collagen-binding MSCRAMM (Microbial Surface Component Recognizing Adhesive Matrix Molecules), and is necessary and sufficient for S. aureus cells to adhere to cartilage.; PDB: 2X5P_A 3RKP_A 3KPT_A 1VLF_T 1TI2_F 1TI6_D 1TI4_J 1VLE_V 1VLD_X 3PF2_A ....
Probab=74.15 E-value=8 Score=23.45 Aligned_cols=44 Identities=27% Similarity=0.408 Sum_probs=25.2
Q ss_pred CeEEEEeecCCCCceEEEEEEEcCCCeeEEEEe--cCCCcceeEEEEeeCCCc
Q 045131 1 ATVALECKESEGGEVVYSREVVSDQSGTYKIPI--EGCHAKLCQVRLVKSPKP 51 (107)
Q Consensus 1 A~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v--~~dh~~~C~V~LvsSP~~ 51 (107)
|++.|.-.+ +......+.+||++|.|.+.- +|.. .++-+++|..
T Consensus 4 a~f~L~~~~---~~~~~~~~~~Td~~G~~~f~~L~~G~Y----~l~E~~aP~G 49 (70)
T PF05738_consen 4 ATFELYDED---GNEVIEVTVTTDENGKYTFKNLPPGTY----TLKETKAPDG 49 (70)
T ss_dssp EEEEEEETT---SEEEEEEEEEGGTTSEEEEEEEESEEE----EEEEEETTTT
T ss_pred eEEEEEECC---CCEEEEEEEEECCCCEEEEeecCCeEE----EEEEEECCCC
Confidence 345554433 444443478999999999872 2332 4444555543
No 6
>PF10670 DUF4198: Domain of unknown function (DUF4198)
Probab=73.83 E-value=6 Score=28.66 Aligned_cols=37 Identities=11% Similarity=-0.034 Sum_probs=24.6
Q ss_pred CeEEEEeecCCCCceEEEEEEEcCCCeeEEEEecCCC
Q 045131 1 ATVALECKESEGGEVVYSREVVSDQSGTYKIPIEGCH 37 (107)
Q Consensus 1 A~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~~dh 37 (107)
|.|.+.-.+..........+.+||++|.+.|.++...
T Consensus 167 a~V~~~~~~~~~~~~~~~~~~~TD~~G~~~~~~~~~G 203 (215)
T PF10670_consen 167 AEVEAFSPGGWYDVEHEAKTLKTDANGRATFTLPRPG 203 (215)
T ss_pred EEEEEEECCCccccccceEEEEECCCCEEEEecCCCE
Confidence 3566666653222222377889999999999987653
No 7
>PF13620 CarboxypepD_reg: Carboxypeptidase regulatory-like domain; PDB: 3MN8_D 3P0D_I 3KCP_A 2B59_B 1UWY_A 1H8L_A 1QMU_A 2NSM_A.
Probab=68.67 E-value=4.7 Score=24.93 Aligned_cols=18 Identities=11% Similarity=0.313 Sum_probs=12.3
Q ss_pred EEEEEcCCCeeEEEE-ecC
Q 045131 18 SREVVSDQSGTYKIP-IEG 35 (107)
Q Consensus 18 ~~e~~TD~~G~y~i~-v~~ 35 (107)
.....||++|.|.|. ++.
T Consensus 29 ~~~~~Td~~G~f~~~~l~~ 47 (82)
T PF13620_consen 29 VYTTTTDSDGRFSFEGLPP 47 (82)
T ss_dssp CCEEE--TTSEEEEEEE-S
T ss_pred EEEEEECCCceEEEEccCC
Confidence 466899999999998 664
No 8
>PF01060 DUF290: Transthyretin-like family; InterPro: IPR001534 This new apparently nematode-specific protein family has been called family 2 []. The proteins show weak similarity to transthyretin (formerly called prealbumin) which transports thyroid hormones. The specific function of this protein is unknown.; GO: 0005615 extracellular space
Probab=62.83 E-value=7.6 Score=25.03 Aligned_cols=19 Identities=16% Similarity=0.310 Sum_probs=14.9
Q ss_pred EEEEEEcCCCeeEEEEecC
Q 045131 17 YSREVVSDQSGTYKIPIEG 35 (107)
Q Consensus 17 ~~~e~~TD~~G~y~i~v~~ 35 (107)
.-.+.+||++|.|.|.=..
T Consensus 29 ll~~~~Td~~G~F~l~G~~ 47 (80)
T PF01060_consen 29 LLDETKTDSDGNFELSGST 47 (80)
T ss_pred eeEEEEECCCceEEEEEEc
Confidence 3457899999999998543
No 9
>PF08400 phage_tail_N: Prophage tail fibre N-terminal; InterPro: IPR013609 This entry represents the N terminus of phage 933W tail fibre protein. The characteristics of the protein distribution suggest prophage matches.
Probab=62.53 E-value=11 Score=27.55 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=18.6
Q ss_pred eEEEEEEEcCCCeeEEEEec-CCC
Q 045131 15 VVYSREVVSDQSGTYKIPIE-GCH 37 (107)
Q Consensus 15 v~~~~e~~TD~~G~y~i~v~-~dh 37 (107)
+.+.....||++|.|.|++. |.+
T Consensus 35 ~~t~as~~t~~~G~Ys~~~epG~Y 58 (134)
T PF08400_consen 35 VGTVASVVTGEAGEYSFDVEPGVY 58 (134)
T ss_pred EEEEEEEEcCCCceEEEEecCCeE
Confidence 35677889999999999987 554
No 10
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=62.42 E-value=28 Score=22.59 Aligned_cols=30 Identities=23% Similarity=0.586 Sum_probs=18.2
Q ss_pred EEEEeecCCCCceEEEEEEEcCCCeeEEEEec
Q 045131 3 VALECKESEGGEVVYSREVVSDQSGTYKIPIE 34 (107)
Q Consensus 3 V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~ 34 (107)
+.++.++...| +|.+.-+-.+.|.|.|.|.
T Consensus 46 ~~~~v~d~~dG--ty~v~y~P~~~G~~~i~V~ 75 (93)
T smart00557 46 VPVEVKDNGDG--TYTVSYTPTEPGDYTVTVK 75 (93)
T ss_pred eEeEEEeCCCC--EEEEEEEeCCCEeEEEEEE
Confidence 34445554444 5666666777777777655
No 11
>PF00630 Filamin: Filamin/ABP280 repeat; InterPro: IPR017868 The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715 from INTERPRO), their rods fall into three families. The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280) is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich []. The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a beta-sandwich, formed by two beta-sheets arranged in an immunoglobulin-like fold [, ]. Because conserved residues that form the core of the repeats are preserved in filamin, the repeat structure should be common to the members of the gelation factor/filamin family. The head to tail homodimerisation is crucial to the function of the ABP120 and ABP280 proteins. This interaction involves a small portion at the distal end of the rod domains. For the gelation factor it has been shown that the carboxy-terminal repeat 6 dimerises through a double edge-to-edge extension of the beta-sheet and that repeat 5 contributes to dimerisation to some extent [, , ].; PDB: 2DI9_A 2EEC_A 2DIC_A 2EEA_A 2DMC_A 2EE9_A 2D7O_A 2D7N_A 2K7P_A 2NQC_A ....
Probab=62.10 E-value=25 Score=22.40 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=17.9
Q ss_pred EEEEeecCCCCceEEEEEEEcCCCeeEEEEec
Q 045131 3 VALECKESEGGEVVYSREVVSDQSGTYKIPIE 34 (107)
Q Consensus 3 V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~ 34 (107)
+.++..+.+.| +|.+.-+--..|.|+|.|.
T Consensus 60 ~~~~v~~~~~G--~y~v~y~p~~~G~y~i~V~ 89 (101)
T PF00630_consen 60 VPVEVIDNGDG--TYTVSYTPTEPGKYKISVK 89 (101)
T ss_dssp EEEEEEEESSS--EEEEEEEESSSEEEEEEEE
T ss_pred cceEEEECCCC--EEEEEEEeCccEeEEEEEE
Confidence 34444554444 6666666667777777665
No 12
>TIGR02513 type_III_yscB type III secretion system chaperone, YscB family. Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. YscB acts, along with SycN (TIGR02503), as a chaperone for YopN, a key part of a complex that regulates type III secretion so it responds to contact with the eukaryotic target cell.
Probab=60.86 E-value=8.8 Score=28.33 Aligned_cols=31 Identities=19% Similarity=0.392 Sum_probs=22.1
Q ss_pred EEcCCCeeEEEEecCCCc---ceeEEEEeeCCCc
Q 045131 21 VVSDQSGTYKIPIEGCHA---KLCQVRLVKSPKP 51 (107)
Q Consensus 21 ~~TD~~G~y~i~v~~dh~---~~C~V~LvsSP~~ 51 (107)
.+-|++|.|.|+|++.-- +-=.-.|.+||.+
T Consensus 16 FVAd~qG~Yhl~iD~~~l~l~q~~sellletpL~ 49 (139)
T TIGR02513 16 FVADRQGVYHLTIDQHLVMLAQHGSELVLETPLD 49 (139)
T ss_pred cccCCCCceEEEEcCcEEEeeccCceEEEecccc
Confidence 358999999999998742 2334456777764
No 13
>COG4850 Uncharacterized conserved protein [Function unknown]
Probab=58.03 E-value=34 Score=28.90 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=33.2
Q ss_pred EEEEeecCCCCceEEEEEEEcCCCeeEEEEecCCCc--ceeEEEEeeCCCc
Q 045131 3 VALECKESEGGEVVYSREVVSDQSGTYKIPIEGCHA--KLCQVRLVKSPKP 51 (107)
Q Consensus 3 V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~~dh~--~~C~V~LvsSP~~ 51 (107)
|.|.|... .++ ++-+.||.+|+|-|...-+|. ..=+.+.+.++..
T Consensus 99 vpV~~T~~-~~~---tv~~~Td~~Gyf~i~~~~~~~~~~g~~av~lq~eg~ 145 (373)
T COG4850 99 VPVYVTLK-NGA---TVNVATDDEGYFIIHAVIPFPPTKGNHAVRLQSEGE 145 (373)
T ss_pred ceEEEecC-CCc---eEEeEecCCCceEEEEecccCCCCCceeEEeecCCC
Confidence 66777773 333 334589999999999888886 6667778888764
No 14
>PRK13865 type IV secretion system protein VirB8; Provisional
Probab=54.66 E-value=6.2 Score=30.79 Aligned_cols=24 Identities=17% Similarity=0.210 Sum_probs=14.8
Q ss_pred eeEEeecCCCCCCCceeeecCCCcc
Q 045131 64 ARIDLTPSVGSDPELIRYANDLGFM 88 (107)
Q Consensus 64 a~V~Lt~nnGi~s~~~R~aN~lgF~ 88 (107)
|.|......-+.. ..|..|||||.
T Consensus 195 ATv~y~~~~~~~e-~~R~~NPLGF~ 218 (229)
T PRK13865 195 ATVRYEKVTSLPG-RLRLTNPGGLI 218 (229)
T ss_pred EEEEEccCCCCCH-HHHhcCCCCcE
Confidence 4444442222444 57999999996
No 15
>PF11974 MG1: Alpha-2-macroglobulin MG1 domain; InterPro: IPR021868 This is the N-terminal MG1 domain from alpha-2-macroglobulin [].
Probab=51.40 E-value=23 Score=23.72 Aligned_cols=17 Identities=12% Similarity=-0.003 Sum_probs=14.7
Q ss_pred EEEEEcCCCeeEEEEec
Q 045131 18 SREVVSDQSGTYKIPIE 34 (107)
Q Consensus 18 ~~e~~TD~~G~y~i~v~ 34 (107)
-.+++||++|...+...
T Consensus 44 l~~g~TD~~G~a~~~~~ 60 (97)
T PF11974_consen 44 LASGKTDADGFASFDST 60 (97)
T ss_pred eeeeeeCCCceEEecCC
Confidence 36889999999999877
No 16
>PF12565 DUF3747: Protein of unknown function (DUF3747); InterPro: IPR022222 This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif.
Probab=51.22 E-value=26 Score=26.93 Aligned_cols=46 Identities=24% Similarity=0.386 Sum_probs=28.6
Q ss_pred EcCCCeeEEEEecCCC---------c-ceeEEEEeeCCCccCcccccCCCceeeEEeecCCCCCC
Q 045131 22 VSDQSGTYKIPIEGCH---------A-KLCQVRLVKSPKPECSEIVADGLSSARIDLTPSVGSDP 76 (107)
Q Consensus 22 ~TD~~G~y~i~v~~dh---------~-~~C~V~LvsSP~~~C~~~~~~~r~~a~V~Lt~nnGi~s 76 (107)
.||+|| |.|-+.|+. . ..=++.|+..|.. .+....|++-|-.|+++
T Consensus 92 ~tDSNG-YSlR~~G~Dlg~~YrLrlv~~~~el~L~a~~~~--------~~~~p~ivigrt~g~~~ 147 (181)
T PF12565_consen 92 YTDSNG-YSLRIGGQDLGLRYRLRLVQRNGELVLVATPRR--------DPSAPEIVIGRTGGIAN 147 (181)
T ss_pred ccCCCC-cEEEECCeecCceEEEEEEEECCEEEEEecCCC--------CCCcceEEEEecCCCcC
Confidence 489998 677777642 1 3346677765532 12234577878888865
No 17
>PF08884 Flagellin_D3: Flagellin D3 domain; InterPro: IPR014981 This domain is found in the central portion bacterial flagellin FliC, it contains a structural motif called a beta-folium fold []. Although no specific function is assigned its deletion leads to a reduction in filament stability []. ; PDB: 1IO1_A 1UCU_A 3A5X_A.
Probab=49.03 E-value=34 Score=23.27 Aligned_cols=26 Identities=12% Similarity=0.277 Sum_probs=15.1
Q ss_pred CCceEEEEEEE--cCCCeeEEEEecC-CC
Q 045131 12 GGEVVYSREVV--SDQSGTYKIPIEG-CH 37 (107)
Q Consensus 12 ~~~v~~~~e~~--TD~~G~y~i~v~~-dh 37 (107)
+|+.--.+++. +.++|+|.+.|+. +.
T Consensus 36 ~gkYYv~V~g~~~~~knG~Yev~Vd~~~G 64 (90)
T PF08884_consen 36 SGKYYVEVTGTTATAKNGYYEVTVDDTDG 64 (90)
T ss_dssp T--EEEEEEEET-SS--EEEEEEE-TTT-
T ss_pred CCCeEEEEEeeccCCCCccEEEEEecCCC
Confidence 45555556666 8999999999998 54
No 18
>KOG1948 consensus Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones]
Probab=46.73 E-value=14 Score=35.02 Aligned_cols=29 Identities=34% Similarity=0.588 Sum_probs=22.4
Q ss_pred eEEEEeecCCCCceEEEEEEEcCCCeeEEEE
Q 045131 2 TVALECKESEGGEVVYSREVVSDQSGTYKIP 32 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~ 32 (107)
-|.+|-+.- +- --|.-|++||++|.|+|.
T Consensus 923 gVaieA~sd-n~-~~y~eeattdenG~yRiR 951 (1165)
T KOG1948|consen 923 GVAIEALSD-NC-DLYQEEATTDENGTYRIR 951 (1165)
T ss_pred CeEEEEecC-CC-CccccccccccCCcEEEe
Confidence 366776663 22 678899999999999986
No 19
>PRK13836 conjugal transfer protein TrbF; Provisional
Probab=45.58 E-value=8.9 Score=29.20 Aligned_cols=26 Identities=15% Similarity=0.087 Sum_probs=16.5
Q ss_pred eeeEEeecCCCCCCCceeeecCCCccc
Q 045131 63 SARIDLTPSVGSDPELIRYANDLGFMK 89 (107)
Q Consensus 63 ~a~V~Lt~nnGi~s~~~R~aN~lgF~~ 89 (107)
++-++++.+.=... ..|..|||||.=
T Consensus 186 ~~i~ti~~~~p~te-~~~~~NPLGf~V 211 (220)
T PRK13836 186 RGIATVTLTPPQDE-ATIRLNPIGLYL 211 (220)
T ss_pred EEEEEEEEcCCCCH-HHHHhCCCeEEE
Confidence 34455554322344 689999999963
No 20
>PF10875 DUF2670: Protein of unknown function (DUF2670); InterPro: IPR022714 This bacterial family of proteins has no known function and appears to be restricted to Rickettsiaceae.
Probab=43.98 E-value=7.1 Score=28.57 Aligned_cols=11 Identities=36% Similarity=0.594 Sum_probs=9.0
Q ss_pred eeeecCCCccc
Q 045131 79 IRYANDLGFMK 89 (107)
Q Consensus 79 ~R~aN~lgF~~ 89 (107)
+-+||||||+-
T Consensus 8 lIaaNPMg~fl 18 (139)
T PF10875_consen 8 LIAANPMGFFL 18 (139)
T ss_pred HHhhCCchhhH
Confidence 45799999985
No 21
>PRK13872 conjugal transfer protein TrbF; Provisional
Probab=41.46 E-value=12 Score=28.66 Aligned_cols=26 Identities=19% Similarity=0.121 Sum_probs=17.1
Q ss_pred eeeEEeecCCCCCCCceeeecCCCccc
Q 045131 63 SARIDLTPSVGSDPELIRYANDLGFMK 89 (107)
Q Consensus 63 ~a~V~Lt~nnGi~s~~~R~aN~lgF~~ 89 (107)
.|.|......-... ..|..|||||.=
T Consensus 192 ~atvt~~~~~p~~e-~~~~~NPLGf~V 217 (228)
T PRK13872 192 TAILTIVIQPPRDA-ERLRKNPLGIYV 217 (228)
T ss_pred EEEEEEEEcCCCCH-HHHhhCCCeEEE
Confidence 45565543333444 689999999963
No 22
>TIGR02962 hdxy_isourate hydroxyisourate hydrolase. Members of this family, hydroxyisourate hydrolase, represent a distinct clade of transthyretin-related proteins. Bacterial members typically are encoded next to ureidoglycolate hydrolase and often near either xanthine dehydrogenase or xanthine/uracil permease genes and have been demonstrated to have hydroxyisourate hydrolase activity. In eukaryotes, a clade separate from the transthyretins (a family of thyroid-hormone binding proteins) has also been shown to have HIU hydrolase activity in urate catabolizing organisms. Transthyretin, then, would appear to be the recently diverged paralog of the more ancient HIUH family.
Probab=40.94 E-value=81 Score=22.01 Aligned_cols=29 Identities=17% Similarity=0.015 Sum_probs=20.8
Q ss_pred eEEEEeecCCCCceEEEEEEEcCCCeeEEEE
Q 045131 2 TVALECKESEGGEVVYSREVVSDQSGTYKIP 32 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~ 32 (107)
.|+|...+ + +.-+.-.+++||++|..+-.
T Consensus 20 ~V~L~~~~-~-~~~~~i~~~~Tn~DGR~~~~ 48 (112)
T TIGR02962 20 PVTLYRLD-G-SGWTPLAEGVTNADGRCPDL 48 (112)
T ss_pred EEEEEEec-C-CCeEEEEEEEECCCCCCcCc
Confidence 68888765 2 33466679999999988743
No 23
>PF03983 SHD1: SLA1 homology domain 1, SHD1 ; InterPro: IPR007131 The SLA1 homology domain is found in the cytoskeleton assembly control protein SLA1, which is responsible for the correct formation of the actin cytoskeleton.; GO: 0008092 cytoskeletal protein binding, 0030674 protein binding, bridging, 0042802 identical protein binding, 0043130 ubiquitin binding; PDB: 2HBP_A.
Probab=33.59 E-value=22 Score=23.23 Aligned_cols=13 Identities=23% Similarity=0.601 Sum_probs=8.9
Q ss_pred EEcCCCeeEEEEe
Q 045131 21 VVSDQSGTYKIPI 33 (107)
Q Consensus 21 ~~TD~~G~y~i~v 33 (107)
-.||.+|.|+|+-
T Consensus 14 tWtD~tG~f~VeA 26 (70)
T PF03983_consen 14 TWTDRTGKFKVEA 26 (70)
T ss_dssp EEEBSSS--EEEE
T ss_pred EEEeCCCCEEEEE
Confidence 4799999999873
No 24
>PRK13887 conjugal transfer protein TrbF; Provisional
Probab=31.22 E-value=14 Score=28.74 Aligned_cols=12 Identities=8% Similarity=-0.227 Sum_probs=10.4
Q ss_pred ceeeecCCCccc
Q 045131 78 LIRYANDLGFMK 89 (107)
Q Consensus 78 ~~R~aN~lgF~~ 89 (107)
..|..|||||.=
T Consensus 230 ~~r~~NPLGf~V 241 (250)
T PRK13887 230 EQLRNNPHSIYV 241 (250)
T ss_pred HHHhhCCCeEEE
Confidence 689999999963
No 25
>PF14686 fn3_3: Polysaccharide lyase family 4, domain II; PDB: 1NKG_A 2XHN_B 3NJX_A 3NJV_A.
Probab=31.09 E-value=29 Score=23.36 Aligned_cols=12 Identities=33% Similarity=0.800 Sum_probs=6.9
Q ss_pred EEcCCCeeEEEE
Q 045131 21 VVSDQSGTYKIP 32 (107)
Q Consensus 21 ~~TD~~G~y~i~ 32 (107)
+.||++|.|.|+
T Consensus 44 t~td~~G~Fti~ 55 (95)
T PF14686_consen 44 TRTDSDGNFTIP 55 (95)
T ss_dssp EE--TTSEEE--
T ss_pred EEeCCCCcEEeC
Confidence 468999999998
No 26
>PHA02123 hypothetical protein
Probab=30.73 E-value=59 Score=23.63 Aligned_cols=57 Identities=18% Similarity=0.287 Sum_probs=34.4
Q ss_pred EEEcCCCeeEEEEec--CC----Cc-ceeE-------EEEeeCCCccCcccccCCCceeeEEeecCCCCCCCceeee
Q 045131 20 EVVSDQSGTYKIPIE--GC----HA-KLCQ-------VRLVKSPKPECSEIVADGLSSARIDLTPSVGSDPELIRYA 82 (107)
Q Consensus 20 e~~TD~~G~y~i~v~--~d----h~-~~C~-------V~LvsSP~~~C~~~~~~~r~~a~V~Lt~nnGi~s~~~R~a 82 (107)
..-||++|.|.-.+. -| .+ +.|. .+|+.|...+=++.+. ..|-.| .-|||.+ ++.|.
T Consensus 40 ~eftdeng~yesals~scd~~~~~~~d~clgiifnsdyw~id~ar~d~~il~~--servmi---s~~givq-nv~yi 110 (146)
T PHA02123 40 QEFTDENGTYESALSASCDREVREQYDNCLGIVFNSDYWLIDGARDDKNILVG--TERVMI---SLNGIVQ-NVDYI 110 (146)
T ss_pred hhhhcCCCcEeehhcccccHHHHhhcCceEEEEecCceEEEecccCCCceeec--ceEEEE---EecceEe-eeEEE
Confidence 446999999984433 22 12 5664 5677777777666665 223333 3478877 66664
No 27
>PF13115 YtkA: YtkA-like
Probab=29.64 E-value=1.4e+02 Score=18.55 Aligned_cols=34 Identities=21% Similarity=0.308 Sum_probs=17.8
Q ss_pred CeEEEEeecCC--C-CceEEEEEEEcCCCeeEEEEec
Q 045131 1 ATVALECKESE--G-GEVVYSREVVSDQSGTYKIPIE 34 (107)
Q Consensus 1 A~V~leCk~~~--~-~~v~~~~e~~TD~~G~y~i~v~ 34 (107)
|.|.|+...-. . .......+....+.|.|.+++.
T Consensus 38 a~V~~~~~m~~~~g~~~~~~~~~~~~~~~G~Y~~~~~ 74 (86)
T PF13115_consen 38 ADVQFEIWMPDMEGMEPMTSKVELEETGPGVYEAEVT 74 (86)
T ss_pred CEEEEEEEeCCCCCCCCCceeeeeecCCCCeEEEEee
Confidence 45666665532 1 1224445555566777776654
No 28
>KOG0518 consensus Actin-binding cytoskeleton protein, filamin [Cytoskeleton]
Probab=29.36 E-value=65 Score=30.91 Aligned_cols=31 Identities=29% Similarity=0.478 Sum_probs=25.6
Q ss_pred eEEEEeecCCCCceEEEEEEEcCCCeeEEEEec
Q 045131 2 TVALECKESEGGEVVYSREVVSDQSGTYKIPIE 34 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~ 34 (107)
||-|.|.++..| ++.+..+-++.|.|.|.++
T Consensus 800 kvd~~~~d~~dG--t~kV~ytPtepG~Y~I~i~ 830 (1113)
T KOG0518|consen 800 KVDLNVEDREDG--TCKVSYTPTEPGTYIINIK 830 (1113)
T ss_pred ccccceeecCCC--eEEEEEeCCCCceEEEEEE
Confidence 688999998777 5666666899999999876
No 29
>PF12249 AftA_C: Arabinofuranosyltransferase A C terminal; InterPro: IPR020959 The arabinofuranosyltransferase enzyme AftA is involved in cell wall arabinan biosynthesis in bacteria []. It catalyses the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. As this enzyme is important for cell growth and is found in some important pathogens, such as Mycobacterium tuberculosis, it represents a potential target for the devlopment of new antibacterial drugs. This entry represents the C-terminal domain of AftA.; GO: 0016757 transferase activity, transferring glycosyl groups, 0044038 cell wall macromolecule biosynthetic process, 0005886 plasma membrane, 0016021 integral to membrane
Probab=29.32 E-value=18 Score=27.69 Aligned_cols=13 Identities=31% Similarity=0.378 Sum_probs=10.1
Q ss_pred ceeeecCCCcccc
Q 045131 78 LIRYANDLGFMKK 90 (107)
Q Consensus 78 ~~R~aN~lgF~~~ 90 (107)
.-+||||||=+.+
T Consensus 75 TsHYANPLaeF~~ 87 (178)
T PF12249_consen 75 TSHYANPLAEFDE 87 (178)
T ss_pred chhhcCchhhHHH
Confidence 4589999996654
No 30
>PF04335 VirB8: VirB8 protein; InterPro: IPR007430 VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself []. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer []. ; GO: 0016020 membrane; PDB: 2CC3_B 2BHM_C.
Probab=28.60 E-value=18 Score=26.33 Aligned_cols=26 Identities=27% Similarity=0.217 Sum_probs=13.3
Q ss_pred eeeEEeecC--CCCCCCceeeecCCCcc
Q 045131 63 SARIDLTPS--VGSDPELIRYANDLGFM 88 (107)
Q Consensus 63 ~a~V~Lt~n--nGi~s~~~R~aN~lgF~ 88 (107)
++.|..... +-..+...|..|||||.
T Consensus 176 ~~~v~~~~~~~~~~~~~~~~~~NPlGf~ 203 (212)
T PF04335_consen 176 RATVTYEYRPINPPMTEEDRLINPLGFY 203 (212)
T ss_dssp EEEEEEEE--EGCGS-HHHHTT-TT-EE
T ss_pred EEEEEEEecCCCCCCCHHHHhhCCCceE
Confidence 455555321 23223368999999996
No 31
>cd03858 M14_CP_N-E_like Carboxypeptidase (CP) N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes eight members, of which five (CPN, CPE, CPM, CPD, CPZ) are considered enzymatically active, while the other three are non-active (CPX1, PCX2, ACLP/AEBP1) and lack the critical active site and substrate-binding residues considered necessary for CP activity. These non-active members may function as binding proteins or display catalytic activity towards other substrates. Unlike the A/B CP subfamily, enzymes belonging to the N/E subfamily are not produced as inactive precursors that require proteolysis to produce the active form; rather, they rely on their substrate specificity and subcellular compartmentalization to prevent inappr
Probab=28.59 E-value=67 Score=26.12 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=12.5
Q ss_pred EEEcCCCeeEEEEec
Q 045131 20 EVVSDQSGTYKIPIE 34 (107)
Q Consensus 20 e~~TD~~G~y~i~v~ 34 (107)
...||.+|.|.+.++
T Consensus 325 ~~~Td~~G~f~~~l~ 339 (374)
T cd03858 325 DVTTAEDGDYWRLLL 339 (374)
T ss_pred eeEECCCceEEEecC
Confidence 467999999998775
No 32
>PF14059 DUF4251: Domain of unknown function (DUF4251); PDB: 3FYF_B.
Probab=27.36 E-value=1.2e+02 Score=21.53 Aligned_cols=32 Identities=16% Similarity=0.266 Sum_probs=18.3
Q ss_pred cCCCeeEEEEecCCCc-ceeEEEEeeCCCccCc
Q 045131 23 SDQSGTYKIPIEGCHA-KLCQVRLVKSPKPECS 54 (107)
Q Consensus 23 TD~~G~y~i~v~~dh~-~~C~V~LvsSP~~~C~ 54 (107)
+|+.|...|...-.+. +...+.|-=.|...|+
T Consensus 88 ~~kKg~~~i~f~~~~~~~~~~~~i~i~~ng~a~ 120 (138)
T PF14059_consen 88 TDKKGNWRISFSVRGKEDSYTFTITIFPNGSAS 120 (138)
T ss_dssp E-TT--EEEEEEEE-SS-EEEEEEEE-TTSEEE
T ss_pred eccCCCEEEEEEECCCceEEEEEEEEecCCEEE
Confidence 7999998888776666 7788888655544443
No 33
>PF11224 DUF3023: Protein of unknown function (DUF3023); InterPro: IPR021387 This bacterial family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=26.44 E-value=59 Score=22.90 Aligned_cols=23 Identities=22% Similarity=0.249 Sum_probs=18.9
Q ss_pred EEEEcCCCeeEEEEecCCCc-cee
Q 045131 19 REVVSDQSGTYKIPIEGCHA-KLC 41 (107)
Q Consensus 19 ~e~~TD~~G~y~i~v~~dh~-~~C 41 (107)
--|.||.+|.-.|.+..+|. +.|
T Consensus 3 CIG~T~~~g~L~V~i~~~~~~~~~ 26 (130)
T PF11224_consen 3 CIGNTDNNGKLNVHINKDHPKNLL 26 (130)
T ss_pred EEeeeCCCCcEEEEECCCCcCCcc
Confidence 35789999999999999886 444
No 34
>TIGR01646 vgr_GE Rhs element Vgr protein. This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E.
Probab=26.32 E-value=78 Score=26.44 Aligned_cols=28 Identities=18% Similarity=0.399 Sum_probs=22.2
Q ss_pred EEEcCCCeeEEEEecCCC-----c-ceeEEEEee
Q 045131 20 EVVSDQSGTYKIPIEGCH-----A-KLCQVRLVK 47 (107)
Q Consensus 20 e~~TD~~G~y~i~v~~dh-----~-~~C~V~Lvs 47 (107)
|..||+.|.|+|.++-|. . ..|++++.+
T Consensus 362 ~~~~d~~GRvkV~f~wd~~~~~~~~~S~W~Rvaq 395 (483)
T TIGR01646 362 EIHTDKYGRIRVHFHWDRYGQSNDYSSCWIRVAQ 395 (483)
T ss_pred eeccCCCCcEEEEeecCCCCCCCCCCceEEEEec
Confidence 445999999999988543 2 689999877
No 35
>TIGR03361 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus.
Probab=25.11 E-value=90 Score=26.30 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=22.7
Q ss_pred EEcCCCeeEEEEecCC----C-c-ceeEEEEeeC
Q 045131 21 VVSDQSGTYKIPIEGC----H-A-KLCQVRLVKS 48 (107)
Q Consensus 21 ~~TD~~G~y~i~v~~d----h-~-~~C~V~LvsS 48 (107)
..||+.|.|+|.++-| . + ..|+|++.+.
T Consensus 374 i~~D~~GRvkV~f~wd~~~~~~~~~S~wvRvaqp 407 (513)
T TIGR03361 374 IYTDEYGRVKVQFHWDRYGKRDEKSSCWVRVAQP 407 (513)
T ss_pred EeECCCCCEEEEecccCCCCCCCCCceEEEeccc
Confidence 4599999999999854 2 4 8899999874
No 36
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=24.84 E-value=43 Score=23.01 Aligned_cols=19 Identities=21% Similarity=0.496 Sum_probs=11.9
Q ss_pred ceEEEEEEEcCCCeeEEEE
Q 045131 14 EVVYSREVVSDQSGTYKIP 32 (107)
Q Consensus 14 ~v~~~~e~~TD~~G~y~i~ 32 (107)
++.|..+|.....|+|+|.
T Consensus 51 ~~~Fvq~G~R~~~GyY~i~ 69 (90)
T PF09904_consen 51 ECEFVQDGERNNAGYYRIS 69 (90)
T ss_dssp EEEEE--TTS-S--EEEEE
T ss_pred EEEEEecCccCCCCcEEee
Confidence 5677888999999999997
No 37
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=23.99 E-value=85 Score=18.98 Aligned_cols=22 Identities=23% Similarity=0.391 Sum_probs=13.0
Q ss_pred CCCeeEEEEecCCCc-ceeEEEE
Q 045131 24 DQSGTYKIPIEGCHA-KLCQVRL 45 (107)
Q Consensus 24 D~~G~y~i~v~~dh~-~~C~V~L 45 (107)
+..|.|+..+...+. ..|.+.|
T Consensus 66 ~D~G~Y~C~~~n~~g~~~~~~~l 88 (90)
T PF07679_consen 66 EDAGTYTCVASNSSGEATASVNL 88 (90)
T ss_dssp GGSEEEEEEEEETTEEEEEEEEE
T ss_pred hhCEEEEEEEEECCCEEEEEEEE
Confidence 455666666666655 5555544
No 38
>PF10709 DUF2511: Protein of unknown function (DUF2511); InterPro: IPR019648 This entry is represented by Bacteriophage PsP3, Gp28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.03 E-value=84 Score=21.31 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=14.3
Q ss_pred eEEEEeecCCCCceEEEEEEEcC
Q 045131 2 TVALECKESEGGEVVYSREVVSD 24 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD 24 (107)
.|.|+|+. +...|.+...|+
T Consensus 17 ev~l~C~~---~~alfv~n~~tl 36 (87)
T PF10709_consen 17 EVMLECRP---GNALFVINPSTL 36 (87)
T ss_pred eEEEEEcC---CCEEEEEcCCCC
Confidence 58999987 566688665553
No 39
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=22.29 E-value=2.2e+02 Score=18.09 Aligned_cols=32 Identities=19% Similarity=0.444 Sum_probs=24.1
Q ss_pred eEEEEeecCCCCceEEEEEE-EcCCCeeEEEEec
Q 045131 2 TVALECKESEGGEVVYSREV-VSDQSGTYKIPIE 34 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~-~TD~~G~y~i~v~ 34 (107)
.|.|+=+| -.|+..+.... .++..|.|...+.
T Consensus 37 ~~~v~i~d-p~g~~v~~~~~~~~~~~G~~~~~~~ 69 (99)
T PF01835_consen 37 PVTVTIKD-PSGNEVFRWSVNTTNENGIFSGSFQ 69 (99)
T ss_dssp EEEEEEEE-TTSEEEEEEEEEETTCTTEEEEEEE
T ss_pred ceEEEEEC-CCCCEEEEEEeeeeCCCCEEEEEEE
Confidence 35566667 47888888888 8899998887654
No 40
>cd05717 Ig1_Necl-1-3_like First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-3 (also known as cell adhesion molecules CADM3, CADM1, and CADM2 respectively). Ig1_Necl-1-3_like: N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and Necl-3 (CADM2). At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the form
Probab=22.04 E-value=2.1e+02 Score=17.84 Aligned_cols=30 Identities=20% Similarity=0.318 Sum_probs=15.2
Q ss_pred ceeEEEEeeCCCccCcccccCCCceeeEEee
Q 045131 39 KLCQVRLVKSPKPECSEIVADGLSSARIDLT 69 (107)
Q Consensus 39 ~~C~V~LvsSP~~~C~~~~~~~r~~a~V~Lt 69 (107)
.|=.|.+-.|..=.|...+. ....+.+.||
T Consensus 65 ~I~~v~~~DsG~Y~C~~~~~-~~~~~~~~~~ 94 (95)
T cd05717 65 SISNVSLSDEGRYTCSLYTM-PVQTAKATVT 94 (95)
T ss_pred EEccCCcccCEEEEEEEecC-CCceEEEEEE
Confidence 44444444555556665554 3335555554
No 41
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=20.90 E-value=39 Score=21.80 Aligned_cols=23 Identities=30% Similarity=0.374 Sum_probs=20.5
Q ss_pred ecCCCccccCCchhHHHHHHHhc
Q 045131 82 ANDLGFMKKESLPECAKVLEEMF 104 (107)
Q Consensus 82 aN~lgF~~~~pl~~C~~~lk~~~ 104 (107)
-.+|||-++...|.=.++|+.||
T Consensus 18 m~~lG~~~~~v~~vl~~LL~lY~ 40 (65)
T PF10440_consen 18 MRQLGFSKKQVRPVLKNLLKLYD 40 (65)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHc
Confidence 34899999999999999999987
No 42
>PF02369 Big_1: Bacterial Ig-like domain (group 1); InterPro: IPR003344 Proteins that contain this domain are found in a variety of bacterial and phage surface proteins such as intimins. Intimin is a bacterial cell-adhesion molecule that mediates the intimate bacterial host-cell interaction. It contains three domains; two immunoglobulin-like domains and a C-type lectin-like module implying that carbohydrate recognition may be important in intimin-mediated cell adhesion [].; PDB: 1CWV_A 4E9L_A 1F02_I 1F00_I.
Probab=20.76 E-value=81 Score=20.90 Aligned_cols=19 Identities=16% Similarity=0.358 Sum_probs=12.9
Q ss_pred EEEcCCCeeEEEEecCCCc
Q 045131 20 EVVSDQSGTYKIPIEGCHA 38 (107)
Q Consensus 20 e~~TD~~G~y~i~v~~dh~ 38 (107)
...||++|.+.+.+.....
T Consensus 61 ~~~Td~~G~a~~tltst~a 79 (100)
T PF02369_consen 61 SATTDSNGIATVTLTSTKA 79 (100)
T ss_dssp -EEE-TTSEEEEEEE-SS-
T ss_pred ccEECCCEEEEEEEEecCc
Confidence 4789999999998876643
No 43
>PF00576 Transthyretin: HIUase/Transthyretin family; InterPro: IPR023416 This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyse the conversion of 5-hydroxyisourate (HIU) to OHCU [, ]. HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage [, ]. HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence. Transthyretin (formerly prealbumin) is one of 3 thyroid hormone-binding proteins found in the blood of vertebrates []. It is produced in the liver and circulates in the bloodstream, where it binds retinol and thyroxine (T4) []. It differs from the other 2 hormone-binding proteins (T4-binding globulin and albumin) in 3 distinct ways: (1) the gene is expressed at a high rate in the brain choroid plexus; (2) it is enriched in cerebrospinal fluid; and (3) no genetically caused absence has been observed, suggesting an essential role in brain function, distinct from that played in the bloodstream []. The protein consists of around 130 amino acids, which assemble as a homotetramer that contains an internal channel in which T4 is bound. Within this complex, T4 appears to be transported across the blood-brain barrier, where, in the choroid plexus, the hormone stimulates further synthesis of transthyretin. The protein then diffuses back into the bloodstream, where it binds T4 for transport back to the brain [].; PDB: 1TFP_B 1KGJ_D 1IE4_C 1GKE_C 1KGI_D 2H0J_B 2H0E_B 2H0F_B 1ZD6_A 3DGD_D ....
Probab=20.35 E-value=1.6e+02 Score=20.44 Aligned_cols=28 Identities=29% Similarity=0.296 Sum_probs=19.6
Q ss_pred eEEEEeecCCCCceEEEEEEEcCCCeeEE
Q 045131 2 TVALECKESEGGEVVYSREVVSDQSGTYK 30 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD~~G~y~ 30 (107)
.|+|.=.+ ..+.-+.-.+++||++|..+
T Consensus 20 ~V~L~~~~-~~~~~~~l~~~~Td~DGR~~ 47 (112)
T PF00576_consen 20 PVTLYRLD-SDGSWTLLAEGVTDADGRIK 47 (112)
T ss_dssp EEEEEEEE-TTSCEEEEEEEEBETTSEES
T ss_pred EEEEEEec-CCCCcEEEEEEEECCCCccc
Confidence 35555444 25667788899999998763
No 44
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=20.29 E-value=63 Score=23.51 Aligned_cols=20 Identities=20% Similarity=0.245 Sum_probs=15.2
Q ss_pred ceEEEEEEEcCCCee--EEEEe
Q 045131 14 EVVYSREVVSDQSGT--YKIPI 33 (107)
Q Consensus 14 ~v~~~~e~~TD~~G~--y~i~v 33 (107)
.....+||.||+.|. |++.+
T Consensus 114 ~~~i~V~GHTD~~Gs~~yN~~L 135 (190)
T COG2885 114 ITRILVEGHTDSTGSDEYNQAL 135 (190)
T ss_pred CcEEEEEecCCCCCCHHHhHHH
Confidence 567889999999996 44443
No 45
>PF11589 DUF3244: Domain of unknown function (DUF3244); InterPro: IPR021638 This family of proteins with unknown function appear to be restricted to Bacteroidetes. The protein may have an immunoglobulin-like beta-sandwich fold however this cannot be confirmed. ; PDB: 3D33_B 3SD2_A.
Probab=20.25 E-value=2e+02 Score=19.14 Aligned_cols=34 Identities=29% Similarity=0.503 Sum_probs=20.9
Q ss_pred eEEEEeecCCCCceEEEEEEEcCCCeeEEEEecCC
Q 045131 2 TVALECKESEGGEVVYSREVVSDQSGTYKIPIEGC 36 (107)
Q Consensus 2 ~V~leCk~~~~~~v~~~~e~~TD~~G~y~i~v~~d 36 (107)
.|.+.=+| .+|++.|+....+.....+.|.+++.
T Consensus 49 ~vtI~I~d-~~G~vVy~~~~~~~~~~~~~I~L~~~ 82 (106)
T PF11589_consen 49 DVTITIKD-STGNVVYSETVSNSAGQSITIDLNGL 82 (106)
T ss_dssp EEEEEEEE-TT--EEEEEEESCGGTTEEEEE-TTS
T ss_pred CEEEEEEe-CCCCEEEEEEccCCCCcEEEEEeCCC
Confidence 45666677 67888888777666665666666543
No 46
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=20.07 E-value=81 Score=19.16 Aligned_cols=13 Identities=38% Similarity=0.672 Sum_probs=10.2
Q ss_pred cCCCeeEEEEecC
Q 045131 23 SDQSGTYKIPIEG 35 (107)
Q Consensus 23 TD~~G~y~i~v~~ 35 (107)
.-+.|+|.|.|.+
T Consensus 58 ~~~~GtYyi~V~~ 70 (70)
T PF04151_consen 58 APAAGTYYIRVYG 70 (70)
T ss_dssp ESSSEEEEEEEE-
T ss_pred cCCCEEEEEEEEC
Confidence 3789999999864
Done!