Query psy993
Match_columns 164
No_of_seqs 112 out of 309
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 23:15:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy993.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/993hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02014 Reeler: Reeler domain 100.0 3.2E-41 7E-46 252.6 10.5 127 28-155 1-132 (132)
2 cd08544 Reeler Reeler, the N-t 100.0 5.5E-39 1.2E-43 241.0 17.4 130 28-161 1-134 (135)
3 KOG3539|consensus 98.3 1.5E-06 3.2E-11 76.8 6.6 68 87-158 34-102 (508)
4 cd08523 Reeler_cohesin_like Do 97.7 0.0018 3.9E-08 48.3 12.7 98 57-159 9-121 (124)
5 PF07705 CARDB: CARDB; InterP 87.8 6.4 0.00014 26.4 8.8 76 51-148 9-86 (101)
6 PF07703 A2M_N_2: Alpha-2-macr 80.8 9.8 0.00021 27.4 7.0 22 49-70 2-23 (136)
7 PF11714 Inhibitor_I53: Thromb 71.0 2.9 6.3E-05 28.2 1.6 23 1-23 1-23 (78)
8 PF02752 Arrestin_C: Arrestin 67.0 15 0.00032 25.9 4.8 37 48-84 7-45 (136)
9 PF07703 A2M_N_2: Alpha-2-macr 66.0 12 0.00026 27.0 4.2 33 46-79 95-127 (136)
10 PRK10626 hypothetical protein; 64.9 9.4 0.0002 31.6 3.8 37 28-66 23-66 (239)
11 PRK02710 plastocyanin; Provisi 61.7 14 0.0003 26.8 3.8 23 46-68 40-62 (119)
12 PF01835 A2M_N: MG2 domain; I 52.9 18 0.00039 24.7 3.1 24 50-83 4-27 (99)
13 COG2063 FlgH Flagellar basal b 51.7 42 0.00092 27.6 5.5 17 52-68 67-83 (230)
14 PRK12407 flgH flagellar basal 51.5 54 0.0012 26.7 6.1 19 50-68 58-76 (221)
15 PF00041 fn3: Fibronectin type 50.9 15 0.00033 23.3 2.3 19 121-139 12-30 (85)
16 COG5510 Predicted small secret 47.8 9.9 0.00021 23.3 0.9 25 1-33 2-26 (44)
17 PF13473 Cupredoxin_1: Cupredo 46.0 37 0.0008 23.5 3.9 34 47-81 29-62 (104)
18 PF00963 Cohesin: Cohesin doma 44.2 43 0.00094 24.4 4.2 35 49-83 2-37 (141)
19 PF11958 DUF3472: Domain of un 43.5 1.3E+02 0.0029 23.5 7.0 74 57-135 58-141 (184)
20 PF00339 Arrestin_N: Arrestin 39.6 68 0.0015 22.8 4.6 36 48-83 1-40 (149)
21 COG2373 Large extracellular al 38.1 1.3E+02 0.0028 31.6 7.6 23 48-70 753-775 (1621)
22 cd08759 Type_III_cohesin_like 37.5 57 0.0012 25.4 4.0 90 49-142 4-113 (160)
23 TIGR01451 B_ant_repeat conserv 36.5 69 0.0015 19.8 3.6 30 52-81 3-34 (53)
24 cd08547 Type_II_cohesin Type I 33.7 1E+02 0.0022 21.9 4.7 36 48-83 3-38 (132)
25 PF13199 Glyco_hydro_66: Glyco 33.1 40 0.00086 31.3 2.9 18 51-68 1-18 (559)
26 cd03445 Thioesterase_II_repeat 31.8 1.1E+02 0.0024 21.0 4.4 30 124-153 43-72 (94)
27 PRK00249 flgH flagellar basal 30.9 89 0.0019 25.4 4.3 19 50-68 57-75 (222)
28 PF07532 Big_4: Bacterial Ig-l 30.4 86 0.0019 19.5 3.4 32 113-145 21-56 (59)
29 COG4893 Uncharacterized protei 29.3 20 0.00044 26.3 0.3 19 24-46 26-44 (123)
30 PF11153 DUF2931: Protein of u 28.8 2.9E+02 0.0064 21.8 7.4 11 122-132 96-106 (216)
31 PRK12788 flgH flagellar basal 28.4 1.8E+02 0.0039 24.0 5.7 19 50-68 68-86 (234)
32 PF07172 GRP: Glycine rich pro 28.1 36 0.00077 24.1 1.3 8 3-10 5-12 (95)
33 PF01345 DUF11: Domain of unkn 27.9 1.2E+02 0.0026 19.5 3.9 30 52-81 32-63 (76)
34 PF08194 DIM: DIM protein; In 26.9 41 0.00089 19.7 1.2 10 1-10 1-10 (36)
35 KOG0668|consensus 26.8 41 0.00089 28.5 1.7 54 27-83 146-206 (338)
36 PF10807 DUF2541: Protein of u 25.8 1.3E+02 0.0028 22.7 4.0 77 81-159 20-103 (134)
37 PF08138 Sex_peptide: Sex pept 25.1 24 0.00052 22.6 0.0 19 1-19 1-19 (56)
38 PF10989 DUF2808: Protein of u 24.9 3E+02 0.0064 20.5 6.5 47 48-94 89-144 (146)
39 PRK12696 flgH flagellar basal 24.1 2.7E+02 0.0059 22.9 6.0 19 50-68 59-77 (236)
40 PF08612 Med20: TATA-binding r 23.7 1.3E+02 0.0027 24.2 4.0 34 50-84 129-164 (225)
41 PF02494 HYR: HYR domain; Int 23.2 2.2E+02 0.0048 18.5 4.9 49 103-155 7-57 (81)
42 PF04775 Bile_Hydr_Trans: Acyl 22.7 1.4E+02 0.003 21.8 3.7 60 45-106 2-72 (126)
43 PF09118 DUF1929: Domain of un 22.5 2.2E+02 0.0048 19.9 4.6 21 50-70 4-24 (98)
44 cd08546 cohesin_like Cohesin d 22.2 2.1E+02 0.0045 20.1 4.5 27 58-84 12-38 (135)
45 PF13956 Ibs_toxin: Toxin Ibs, 22.0 56 0.0012 16.3 1.0 6 1-6 2-7 (19)
46 CHL00084 rpl19 ribosomal prote 21.7 1.7E+02 0.0038 21.5 4.0 32 54-85 20-56 (117)
47 PF00386 C1q: C1q domain; Int 21.7 1.2E+02 0.0027 21.5 3.3 24 57-80 95-127 (127)
48 cd00600 Sm_like The eukaryotic 21.5 1.4E+02 0.003 18.4 3.1 22 60-83 6-27 (63)
49 cd02851 Galactose_oxidase_C_te 21.3 3.1E+02 0.0067 19.4 6.4 19 112-130 40-58 (101)
50 PRK15191 fimbrial protein BcfF 20.4 3.9E+02 0.0085 20.3 6.1 26 44-70 65-90 (172)
51 PRK12697 flgH flagellar basal 20.4 2.7E+02 0.0059 22.8 5.3 19 50-68 62-80 (226)
52 smart00060 FN3 Fibronectin typ 20.2 1.2E+02 0.0026 17.7 2.5 13 124-136 16-28 (83)
No 1
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=100.00 E-value=3.2e-41 Score=252.59 Aligned_cols=127 Identities=42% Similarity=0.777 Sum_probs=99.5
Q ss_pred ccCcCCCCC-CCCCCCCCCCCeEEEecCceeeCCCceEEEEeCCCCCceeEEEEEEeeCC--C--CceEEEeCCCCCcee
Q psy993 28 VCADMTPKH-PQTVPQDSESPYKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQARVGD--K--PVGQFTKSPSSKFYK 102 (164)
Q Consensus 28 aC~~m~P~H-~g~~pq~~~~py~i~~~~~~y~pG~~~~VtL~~~~~~~F~GFllqAr~~~--~--~vG~F~~~~~~~~~~ 102 (164)
||.+|.|+| .+..||. ++||+|.++++.|+||+.|+|||+......|||||||||+.+ + ++|+|...+++...|
T Consensus 1 aC~~m~P~h~~~~~p~~-~~py~i~~~~~~y~pg~~~~Vtl~~~~~~~F~GFllqAr~~~~~~~~~vG~f~~~~~~~~~~ 79 (132)
T PF02014_consen 1 ACDDMTPRHGGPAQPQT-DSPYSISVSPSSYEPGQTYTVTLSSSGSSSFRGFLLQARDANNSSPAPVGTFQLPPDSDTTQ 79 (132)
T ss_dssp SSTTEE-CTTEEE--B--BTSEEEEET-SSB-TTBEEEEEEEETTTEEBSEEEEEEEETT--SSSBSSEEEES-TTTEEE
T ss_pred CccCccccCCCCCCCCC-CCCEEEEeCCCeEcCCCEEEEEEECCCCCceeEEEEEEEeCCCCCcccccccCcCCcccceE
Confidence 799999999 2345666 999999999999999999999996445589999999999987 2 599999997664579
Q ss_pred EeccCCCCCCeEEeeCCCCCceEEEEEeCCCCCCccEEEEEEEeecCcEEEEc
Q psy993 103 VINCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNESVNFVATVAKDGGEYWVG 155 (164)
Q Consensus 103 ~~~C~~~~~~aVTH~~~~~K~~v~~~W~AP~~~~G~V~F~aTvv~~~~~fwv~ 155 (164)
+++|+++.+++|||+++.+|.+++|+|+||.+..|+|+|||||||++++||++
T Consensus 80 ~~~C~~~~~~avTH~~~~~K~~v~~~W~AP~~~~g~V~fraTvv~~~~~~w~~ 132 (132)
T PF02014_consen 80 LLDCSGGDNNAVTHSNNSPKTSVTFTWTAPADFSGCVTFRATVVQSYDTFWVD 132 (132)
T ss_dssp ETTE----EEEEEESS-S-BSEEEEEEE--STTS-EEEEEEEEESSSCEEE-S
T ss_pred eecccccccceEEecCCCCccEEEEEEcCCCCCCceEEEEEEEEEeCcEEecC
Confidence 99998877799999999999999999999999999999999999999999986
No 2
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=100.00 E-value=5.5e-39 Score=241.02 Aligned_cols=130 Identities=38% Similarity=0.675 Sum_probs=117.4
Q ss_pred ccCcC--CCCCCCCCCCCCCCCeEEEecCceeeCCCceEEEEeCCCCCceeEEEEEEeeCC--CCceEEEeCCCCCceeE
Q psy993 28 VCADM--TPKHPQTVPQDSESPYKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQARVGD--KPVGQFTKSPSSKFYKV 103 (164)
Q Consensus 28 aC~~m--~P~H~g~~pq~~~~py~i~~~~~~y~pG~~~~VtL~~~~~~~F~GFllqAr~~~--~~vG~F~~~~~~~~~~~ 103 (164)
+|.+| .|.| +..++.. +||.|.++...|.||+.|+|||++.....|||||||||+.+ +++|+|...++ +.+|+
T Consensus 1 ~C~~~~~~p~h-~~~~~~~-~py~i~~~~~~y~pG~~~~Vtl~~~~~~~F~GF~lqAr~~~~~~~vG~f~~~~~-~~tk~ 77 (135)
T cd08544 1 ACVDMPPGPGH-GGDPQTT-SPYSITISGNSYVPGETYTVTLSGSSPSPFRGFLLQARDASSNEPVGTFQLPPD-SGTKL 77 (135)
T ss_pred CCcCCCCCCCC-CCCCCCC-CCEEEEeCCCEECCCCEEEEEEECCCCCceeEEEEEEEcCCCCcceEEEEeCCC-cccEE
Confidence 69999 8999 6666555 89999999889999999999999764468999999999985 79999999865 34799
Q ss_pred eccCCCCCCeEEeeCCCCCceEEEEEeCCCCCCccEEEEEEEeecCcEEEEccCCcce
Q psy993 104 INCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNESVNFVATVAKDGGEYWVGQQSEPV 161 (164)
Q Consensus 104 ~~C~~~~~~aVTH~~~~~K~~v~~~W~AP~~~~G~V~F~aTvv~~~~~fwv~~~S~~v 161 (164)
++|.+. +++|||+++.+|.+++|+|+||.+..|||+|||||||++++||+++.|+.|
T Consensus 78 ~~c~~~-~~avtH~~~~~k~~v~~~W~AP~~~~g~V~F~aTvv~~~~~~w~~~~s~~l 134 (135)
T cd08544 78 LTCCGS-DNAVTHSNNSKKTSVTFTWTAPSNGSGCVTFRATVVQSYDVFWVDVLSKTL 134 (135)
T ss_pred ecCCCC-CCcceeCCCCCCceeEEEEECCCCCCccEEEEEEEEEecCEEEeccccccc
Confidence 999877 599999999999999999999999999999999999999999999999876
No 3
>KOG3539|consensus
Probab=98.30 E-value=1.5e-06 Score=76.82 Aligned_cols=68 Identities=19% Similarity=0.422 Sum_probs=59.0
Q ss_pred CCceEEEeCCCCCceeE-eccCCCCCCeEEeeCCCCCceEEEEEeCCCCCCccEEEEEEEeecCcEEEEccCC
Q psy993 87 KPVGQFTKSPSSKFYKV-INCLGGSQNAATHIDAKAKSRVTLTWVAPEDLNESVNFVATVAKDGGEYWVGQQS 158 (164)
Q Consensus 87 ~~vG~F~~~~~~~~~~~-~~C~~~~~~aVTH~~~~~K~~v~~~W~AP~~~~G~V~F~aTvv~~~~~fwv~~~S 158 (164)
..+|.|+...++..+++ .+|. +.|.|.|..+|+++.+.|.||...+|||.|+|+|+++...|+..-..
T Consensus 34 ~~~g~w~v~~~~~~t~~sP~c~----~~V~~~~~~~kT~v~~~w~ape~~~Gci~l~A~v~e~r~~~~~dd~~ 102 (508)
T KOG3539|consen 34 QSLGPWQVGTDSGVTRFSPRCP----NSVENANDRPKTSVDVMWVAPESPSGCITLRARVMENRIAWFTDDGN 102 (508)
T ss_pred cccccceeccCccceeeCCCCc----cccccCCCCccccccceeecCCCCCcceEEeeeeccccceecccCCC
Confidence 35899998865555555 4997 68999999999999999999999999999999999999999987655
No 4
>cd08523 Reeler_cohesin_like Domains similar to the eukaryotic reeler domain and bacterial cohesins. This diverse family summarizes a set of distantly related domains, as revealed by structural similarity.
Probab=97.70 E-value=0.0018 Score=48.33 Aligned_cols=98 Identities=16% Similarity=0.041 Sum_probs=73.9
Q ss_pred eeCCCceEEEEeCCCC---CceeEEEEEEeeCC-----CCceEEEeCCCCC-ceeEe----ccCCCCCCeEEeeCCCCCc
Q psy993 57 VAPGGSISVVISSPPG---LSFKGFFVQARVGD-----KPVGQFTKSPSSK-FYKVI----NCLGGSQNAATHIDAKAKS 123 (164)
Q Consensus 57 y~pG~~~~VtL~~~~~---~~F~GFllqAr~~~-----~~vG~F~~~~~~~-~~~~~----~C~~~~~~aVTH~~~~~K~ 123 (164)
+.+|.-++|++.-++. ..+++|-|.+-.++ .++|++...|... ..+.. .|. .+||-+......
T Consensus 9 ~~~Gs~~~vtf~Vp~e~~~a~ttk~~v~lp~~~~~~~~~pv~~~~~~p~pgw~~~v~k~~~~~~----vsVTWtapgqf~ 84 (124)
T cd08523 9 VQVGTNLEVTLSIDEPVNFAPEIEFTVNLKSNSDLFEEFHATAHNIDPSCDHGTMIDKNDIMRR----VSVTWKAPSQEV 84 (124)
T ss_pred ccCCceEEEEEECCCCccCcceEEEEEEcCCCccccccceeeEEEeecCCCceEEEEecccCcc----eEEEEcCCCceE
Confidence 7899999999994433 67999999886541 5799998875532 23433 364 568888777777
Q ss_pred eEEEEEeCCCCCCccEEEEEEEeec--CcEEEEccCCc
Q psy993 124 RVTLTWVAPEDLNESVNFVATVAKD--GGEYWVGQQSE 159 (164)
Q Consensus 124 ~v~~~W~AP~~~~G~V~F~aTvv~~--~~~fwv~~~S~ 159 (164)
...|.|.||.+ .|+|.|.|+..++ .-++|.+..|.
T Consensus 85 ~f~vs~~~~P~-~~~v~~~A~Qty~dg~vv~w~~~g~~ 121 (124)
T cd08523 85 RAKVSLRAEPK-AEHVYLSASSEKGDHRIAGTQDEGSG 121 (124)
T ss_pred EEEEEeecCCC-CCEEEEEEEEEEeCCEEEEEEecCCc
Confidence 99999999996 8999999997555 34889987663
No 5
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=87.77 E-value=6.4 Score=26.43 Aligned_cols=76 Identities=17% Similarity=0.322 Sum_probs=44.4
Q ss_pred EecCceeeCCCceEEEEe--CCCCCceeEEEEEEeeCCCCceEEEeCCCCCceeEeccCCCCCCeEEeeCCCCCceEEEE
Q psy993 51 VLKKKSVAPGGSISVVIS--SPPGLSFKGFFVQARVGDKPVGQFTKSPSSKFYKVINCLGGSQNAATHIDAKAKSRVTLT 128 (164)
Q Consensus 51 ~~~~~~y~pG~~~~VtL~--~~~~~~F~GFllqAr~~~~~vG~F~~~~~~~~~~~~~C~~~~~~aVTH~~~~~K~~v~~~ 128 (164)
...+....+|+.++|++. ..+...-.+|.++-...+..+++... .--.......++|.
T Consensus 9 ~~~~~~~~~g~~~~i~~~V~N~G~~~~~~~~v~~~~~~~~~~~~~i--------------------~~L~~g~~~~v~~~ 68 (101)
T PF07705_consen 9 TVSPSNVVPGEPVTITVTVKNNGTADAENVTVRLYLDGNSVSTVTI--------------------PSLAPGESETVTFT 68 (101)
T ss_dssp EEC-SEEETTSEEEEEEEEEE-SSS-BEEEEEEEEETTEEEEEEEE--------------------SEB-TTEEEEEEEE
T ss_pred eeCCCcccCCCEEEEEEEEEECCCCCCCCEEEEEEECCceeccEEE--------------------CCcCCCcEEEEEEE
Confidence 456788899999877776 33334467777776554433333322 11122334479999
Q ss_pred EeCCCCCCccEEEEEEEeec
Q psy993 129 WVAPEDLNESVNFVATVAKD 148 (164)
Q Consensus 129 W~AP~~~~G~V~F~aTvv~~ 148 (164)
|+++ ..|...+++.+=.+
T Consensus 69 ~~~~--~~G~~~i~~~iD~~ 86 (101)
T PF07705_consen 69 WTPP--SPGSYTIRVVIDPD 86 (101)
T ss_dssp EE-S--S-CEEEEEEEESTT
T ss_pred EEeC--CCCeEEEEEEEeeC
Confidence 9999 47889988887443
No 6
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=80.83 E-value=9.8 Score=27.42 Aligned_cols=22 Identities=36% Similarity=0.588 Sum_probs=17.7
Q ss_pred EEEecCceeeCCCceEEEEeCC
Q psy993 49 KIVLKKKSVAPGGSISVVISSP 70 (164)
Q Consensus 49 ~i~~~~~~y~pG~~~~VtL~~~ 70 (164)
+|..+++.|++|+.+++++..+
T Consensus 2 ~i~~~~~~~~~Ge~~~v~v~~~ 23 (136)
T PF07703_consen 2 QISTDKDSYKPGETAKVTVQSP 23 (136)
T ss_dssp EEEE-SSSB-TTSEEEEEEEEE
T ss_pred EEEcCCCCcCCCCEEEEEEEcC
Confidence 5778899999999999999965
No 7
>PF11714 Inhibitor_I53: Thrombin inhibitor Madanin ; InterPro: IPR021716 Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva [].
Probab=70.97 E-value=2.9 Score=28.20 Aligned_cols=23 Identities=30% Similarity=0.495 Sum_probs=19.6
Q ss_pred ChhHHHHHHHHHHhhcceecCCC
Q psy993 1 MNQFLLLCVSAVAISSVHAFSSG 23 (164)
Q Consensus 1 m~~~~~~~~~~~~~~~~~a~p~G 23 (164)
|.-|.++++++.+.+.+.|||--
T Consensus 1 MKhFaiLilavVaSAvVMAyPe~ 23 (78)
T PF11714_consen 1 MKHFAILILAVVASAVVMAYPER 23 (78)
T ss_pred CchHHHHHHHHHHHHHHHhcccc
Confidence 78888888888889999999854
No 8
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=66.98 E-value=15 Score=25.90 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=24.8
Q ss_pred eEEEecCceeeCCCceEEEEe--CCCCCceeEEEEEEee
Q psy993 48 YKIVLKKKSVAPGGSISVVIS--SPPGLSFKGFFVQARV 84 (164)
Q Consensus 48 y~i~~~~~~y~pG~~~~VtL~--~~~~~~F~GFllqAr~ 84 (164)
|++.+++..|.|||.+.|++. .......+++.+.-.+
T Consensus 7 ~~~~i~~~~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~ 45 (136)
T PF02752_consen 7 LSISIPRTAYVPGETIPVNVEIDNQSKKKIKKIKVSLVE 45 (136)
T ss_dssp EEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEE
T ss_pred EEEEECCCEECCCCEEEEEEEEEECCCCEEEEEEEEEEE
Confidence 677888999999999887776 4445677777766543
No 9
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=65.97 E-value=12 Score=26.96 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=24.2
Q ss_pred CCeEEEecCceeeCCCceEEEEeCCCCCceeEEE
Q psy993 46 SPYKIVLKKKSVAPGGSISVVISSPPGLSFKGFF 79 (164)
Q Consensus 46 ~py~i~~~~~~y~pG~~~~VtL~~~~~~~F~GFl 79 (164)
..-+|..+++.|+||+.++++|+.+. ..+-|+.
T Consensus 95 ~~v~l~~~~~~~~Pg~~~~~~i~~~~-~s~v~l~ 127 (136)
T PF07703_consen 95 LKVELTASPDEYKPGEEVTLRIKAPP-NSLVGLS 127 (136)
T ss_dssp SSEEEEESSSSBTTTSEEEEEEEEST-TEEEEEE
T ss_pred ceEEEEEecceeCCCCEEEEEEEeCC-CCEEEEE
Confidence 44677777899999999999999531 3455544
No 10
>PRK10626 hypothetical protein; Provisional
Probab=64.94 E-value=9.4 Score=31.61 Aligned_cols=37 Identities=22% Similarity=0.400 Sum_probs=23.7
Q ss_pred ccCcCCCCCCCC--CCCC-----CCCCeEEEecCceeeCCCceEEE
Q psy993 28 VCADMTPKHPQT--VPQD-----SESPYKIVLKKKSVAPGGSISVV 66 (164)
Q Consensus 28 aC~~m~P~H~g~--~pq~-----~~~py~i~~~~~~y~pG~~~~Vt 66 (164)
.|. ..|.+ .. .|+. ....|.|..+.+-|.-|+.+.++
T Consensus 23 qC~-V~l~~-DV~Itpq~v~V~~~sg~l~I~~dg~L~inGk~v~L~ 66 (239)
T PRK10626 23 QCS-VTPQD-DVIISPQTVQVVGASGNLVISPDGNVMRNGKQLSLN 66 (239)
T ss_pred CCC-CCCCC-CeEEcCCeEEEEecCCceEEcCCCCEEECCEEecCC
Confidence 798 66655 32 2331 24458888887788888876554
No 11
>PRK02710 plastocyanin; Provisional
Probab=61.74 E-value=14 Score=26.80 Aligned_cols=23 Identities=9% Similarity=0.108 Sum_probs=15.7
Q ss_pred CCeEEEecCceeeCCCceEEEEe
Q psy993 46 SPYKIVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 46 ~py~i~~~~~~y~pG~~~~VtL~ 68 (164)
..|....+.-++.+|++|+++..
T Consensus 40 ~~~~F~P~~i~v~~Gd~V~~~N~ 62 (119)
T PRK02710 40 GMLAFEPSTLTIKAGDTVKWVNN 62 (119)
T ss_pred CeeEEeCCEEEEcCCCEEEEEEC
Confidence 45666666567788998776644
No 12
>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=52.92 E-value=18 Score=24.70 Aligned_cols=24 Identities=17% Similarity=0.373 Sum_probs=17.1
Q ss_pred EEecCceeeCCCceEEEEeCCCCCceeEEEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVISSPPGLSFKGFFVQAR 83 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~~~~~~~F~GFllqAr 83 (164)
|..|+.-|+|||+|. |++++..+.
T Consensus 4 i~TDr~iYrPGetV~----------~~~~~~~~~ 27 (99)
T PF01835_consen 4 IQTDRPIYRPGETVH----------FRAIVRDLD 27 (99)
T ss_dssp EEESSSEE-TTSEEE----------EEEEEEEEC
T ss_pred EECCccCcCCCCEEE----------EEEEEeccc
Confidence 567889999999994 666655555
No 13
>COG2063 FlgH Flagellar basal body L-ring protein [Cell motility and secretion]
Probab=51.69 E-value=42 Score=27.63 Aligned_cols=17 Identities=18% Similarity=0.413 Sum_probs=14.7
Q ss_pred ecCceeeCCCceEEEEe
Q psy993 52 LKKKSVAPGGSISVVIS 68 (164)
Q Consensus 52 ~~~~~y~pG~~~~VtL~ 68 (164)
-|+..++.|+.+||+|+
T Consensus 67 ~D~RA~~vGDilTV~i~ 83 (230)
T COG2063 67 EDRRASNVGDILTIVIQ 83 (230)
T ss_pred cccccccCCCEEEEEEE
Confidence 35677889999999998
No 14
>PRK12407 flgH flagellar basal body L-ring protein; Reviewed
Probab=51.54 E-value=54 Score=26.74 Aligned_cols=19 Identities=11% Similarity=0.448 Sum_probs=16.3
Q ss_pred EEecCceeeCCCceEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~ 68 (164)
+.-|...++.|+.++|.|.
T Consensus 58 Lf~D~rA~~VGDiiTV~i~ 76 (221)
T PRK12407 58 LLQDRRAYRVGDILTVILD 76 (221)
T ss_pred ccccccccCCCCEEEEEEE
Confidence 5566788899999999998
No 15
>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=50.92 E-value=15 Score=23.34 Aligned_cols=19 Identities=26% Similarity=0.601 Sum_probs=14.3
Q ss_pred CCceEEEEEeCCCCCCccE
Q psy993 121 AKSRVTLTWVAPEDLNESV 139 (164)
Q Consensus 121 ~K~~v~~~W~AP~~~~G~V 139 (164)
.++.+.+.|++|....+++
T Consensus 12 ~~~sv~v~W~~~~~~~~~~ 30 (85)
T PF00041_consen 12 SPTSVTVSWKPPSSGNGPI 30 (85)
T ss_dssp CSSEEEEEEEESSSTSSSE
T ss_pred CCCEEEEEEECCCCCCCCe
Confidence 6678999999997445544
No 16
>COG5510 Predicted small secreted protein [Function unknown]
Probab=47.83 E-value=9.9 Score=23.27 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=14.3
Q ss_pred ChhHHHHHHHHHHhhcceecCCCCccCccCcCC
Q psy993 1 MNQFLLLCVSAVAISSVHAFSSGAPEGVCADMT 33 (164)
Q Consensus 1 m~~~~~~~~~~~~~~~~~a~p~GaP~~aC~~m~ 33 (164)
|..+++++++++++... ..+|++|.
T Consensus 2 mk~t~l~i~~vll~s~l--------laaCNT~r 26 (44)
T COG5510 2 MKKTILLIALVLLASTL--------LAACNTMR 26 (44)
T ss_pred chHHHHHHHHHHHHHHH--------HHHhhhhh
Confidence 56666665555554443 34787774
No 17
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=46.00 E-value=37 Score=23.54 Aligned_cols=34 Identities=9% Similarity=0.261 Sum_probs=19.8
Q ss_pred CeEEEecCceeeCCCceEEEEeCCCCCceeEEEEE
Q psy993 47 PYKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQ 81 (164)
Q Consensus 47 py~i~~~~~~y~pG~~~~VtL~~~~~~~F~GFllq 81 (164)
.+.+.++.-+..+|++++|++.+.+... ..|.+.
T Consensus 29 ~~~f~P~~i~v~~G~~v~l~~~N~~~~~-h~~~i~ 62 (104)
T PF13473_consen 29 DFGFSPSTITVKAGQPVTLTFTNNDSRP-HEFVIP 62 (104)
T ss_dssp -EEEES-EEEEETTCEEEEEEEE-SSS--EEEEEG
T ss_pred CCeEecCEEEEcCCCeEEEEEEECCCCc-EEEEEC
Confidence 4556666566778999999998543232 444443
No 18
>PF00963 Cohesin: Cohesin domain; InterPro: IPR002102 Cohesin domains interact with a complementary domain, termed the dockerin domain (see IPR002105 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non-hydrolytic protein which organises the hydrolytic enzymes in a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose-binding domain and nine cohesin domains which are responsible for integrating the individual enzymatic subunits into the complex.; GO: 0030246 carbohydrate binding, 0000272 polysaccharide catabolic process; PDB: 2BM3_A 3P0D_I 3KCP_A 2B59_A 3L8Q_B 3FNK_C 3GHP_B 2CCL_A 1ANU_A 1OHZ_A ....
Probab=44.21 E-value=43 Score=24.43 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=24.9
Q ss_pred EEEecCceeeCCCceEEEEe-CCCCCceeEEEEEEe
Q psy993 49 KIVLKKKSVAPGGSISVVIS-SPPGLSFKGFFVQAR 83 (164)
Q Consensus 49 ~i~~~~~~y~pG~~~~VtL~-~~~~~~F~GFllqAr 83 (164)
+|.++..+.++|++++|+|. ......+.|+.++-.
T Consensus 2 ~l~~~~~~a~~G~tv~V~V~v~~~~~~i~~~~~~l~ 37 (141)
T PF00963_consen 2 TLSVDSVSAKPGETVTVPVNVSNVSNSIAGMQFTLS 37 (141)
T ss_dssp EEEESECEE-TTSEEEEEEEEESCTTTEEEEEEEEE
T ss_pred EEEeCCceECCCCEEEEEEEEEcCCCcEEEEEEEEE
Confidence 46777778899999999998 332223888887766
No 19
>PF11958 DUF3472: Domain of unknown function (DUF3472); InterPro: IPR021862 This presumed domain is functionally uncharacterised. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Probab=43.46 E-value=1.3e+02 Score=23.47 Aligned_cols=74 Identities=11% Similarity=0.294 Sum_probs=46.0
Q ss_pred eeCCCceEEEEeCC----CCCceeEEEEEEeeCC-CCceEEEeCCCCCcee-----EeccCCCCCCeEEeeCCCCCceEE
Q psy993 57 VAPGGSISVVISSP----PGLSFKGFFVQARVGD-KPVGQFTKSPSSKFYK-----VINCLGGSQNAATHIDAKAKSRVT 126 (164)
Q Consensus 57 y~pG~~~~VtL~~~----~~~~F~GFllqAr~~~-~~vG~F~~~~~~~~~~-----~~~C~~~~~~aVTH~~~~~K~~v~ 126 (164)
-+.|..|+.+|+.. ....|+|++.-....+ ..||+|..+......+ ++.=. .-.+.+..++....
T Consensus 58 W~~g~~Y~f~v~~~~~~~g~t~~~~~v~d~~t~~~~~Igs~~~p~~~~~l~~~~s~FvE~f-----~~~~g~~~r~~~~~ 132 (184)
T PF11958_consen 58 WKAGHTYRFLVENTPDGDGGTWYTGYVTDPTTGKWTLIGSIKRPKTNGYLKGSYSGFVEYF-----SPENGNCSRKPYYG 132 (184)
T ss_pred cccCCEEEEEEEEeecCCCCcEEEEEEEECCCCcEEEEEEEEEcCccccccccceEeEeec-----CCCcCcccccceee
Confidence 45789999999843 3678999988877555 6799999874432111 11110 01223333455677
Q ss_pred EEEeCCCCC
Q psy993 127 LTWVAPEDL 135 (164)
Q Consensus 127 ~~W~AP~~~ 135 (164)
..|..|...
T Consensus 133 ~~f~~~~~~ 141 (184)
T PF11958_consen 133 NQFSRPKSG 141 (184)
T ss_pred eeEcCcCCC
Confidence 888888876
No 20
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=39.55 E-value=68 Score=22.84 Aligned_cols=36 Identities=31% Similarity=0.438 Sum_probs=24.2
Q ss_pred eEEEec--CceeeCCCceE--EEEeCCCCCceeEEEEEEe
Q psy993 48 YKIVLK--KKSVAPGGSIS--VVISSPPGLSFKGFFVQAR 83 (164)
Q Consensus 48 y~i~~~--~~~y~pG~~~~--VtL~~~~~~~F~GFllqAr 83 (164)
|.|..+ +..|.+|+.|+ |.|........+++-|+.+
T Consensus 1 ~~I~ld~~~~~y~~Ge~I~G~V~l~~~~~~~i~~i~v~l~ 40 (149)
T PF00339_consen 1 FEIELDNPKPVYFPGEVISGKVVLELSKPIKIKSIKVRLK 40 (149)
T ss_dssp EEEEES-SEEEEESS--EEEEEEECTTT-TTTSEEEEEEE
T ss_pred CEEEECCCCCEECCCCEEEEEEEEEECCccceeEEEEEEE
Confidence 567777 67899999995 6666444467888887766
No 21
>COG2373 Large extracellular alpha-helical protein [General function prediction only]
Probab=38.11 E-value=1.3e+02 Score=31.63 Aligned_cols=23 Identities=30% Similarity=0.632 Sum_probs=20.7
Q ss_pred eEEEecCceeeCCCceEEEEeCC
Q psy993 48 YKIVLKKKSVAPGGSISVVISSP 70 (164)
Q Consensus 48 y~i~~~~~~y~pG~~~~VtL~~~ 70 (164)
-+|..++..|++|++.+++|+.+
T Consensus 753 l~i~ldK~~Y~~Gdtakl~I~~p 775 (1621)
T COG2373 753 LKLKLDKPEYQPGDTAKLLITTP 775 (1621)
T ss_pred eEEecCccccCCCceEEEEeccC
Confidence 56778999999999999999977
No 22
>cd08759 Type_III_cohesin_like Cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents type III cohesins and closely related domains.
Probab=37.50 E-value=57 Score=25.37 Aligned_cols=90 Identities=17% Similarity=0.134 Sum_probs=46.9
Q ss_pred EEEecCceeeCCCceEEEEeCCCCCcee--EEEEEEeeCC-CCce----E-----EEeCCCCCceeEeccCCCCCCeEEe
Q psy993 49 KIVLKKKSVAPGGSISVVISSPPGLSFK--GFFVQARVGD-KPVG----Q-----FTKSPSSKFYKVINCLGGSQNAATH 116 (164)
Q Consensus 49 ~i~~~~~~y~pG~~~~VtL~~~~~~~F~--GFllqAr~~~-~~vG----~-----F~~~~~~~~~~~~~C~~~~~~aVTH 116 (164)
.|..++.+|.+|++++|.|.+......- ||.|.--... +-|| . +.+... .+. .=.+.....+++
T Consensus 4 ~l~~~k~~~~aGetvti~vkg~~l~~VnA~~~~l~yD~~~le~V~~e~~~~~~~~Menls~---~r~-h~~g~~~ly~~f 79 (160)
T cd08759 4 SLVPSKTTVKAGETITIDLYGQGLKNVNALGAHIPFDNSKLELVKDEDGATSTAGMENLSK---EKT-HDDGTADVYLFF 79 (160)
T ss_pred EEeccccccCCCCEEEEEEEecccceeeeeeeEEecChHHcEEEcccccchhhhhheecce---eee-cCCCcceEEEEE
Confidence 3566778899999999999965333333 3333322110 1111 1 111100 011 111111246777
Q ss_pred eCCCCCce-------EEEEEeCCCCC-CccEEEE
Q psy993 117 IDAKAKSR-------VTLTWVAPEDL-NESVNFV 142 (164)
Q Consensus 117 ~~~~~K~~-------v~~~W~AP~~~-~G~V~F~ 142 (164)
+|...|.. .+|+=+||.+. ..+|.|.
T Consensus 80 aN~G~~~~~~Gd~~L~ti~lkAk~~~~~~~i~l~ 113 (160)
T cd08759 80 ANEGDKDLLNGDGVLATFTLKAKEDGDKYDIELA 113 (160)
T ss_pred EeccCccccCCCceEEEEEEEecccCcccceEEe
Confidence 77766663 57888888752 4567665
No 23
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=36.45 E-value=69 Score=19.79 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=18.4
Q ss_pred ecCceeeCCCceEEEEe--CCCCCceeEEEEE
Q psy993 52 LKKKSVAPGGSISVVIS--SPPGLSFKGFFVQ 81 (164)
Q Consensus 52 ~~~~~y~pG~~~~VtL~--~~~~~~F~GFllq 81 (164)
+++....+|+.++.||. +.....-.+..|+
T Consensus 3 ~d~~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~ 34 (53)
T TIGR01451 3 VDKTVATIGDTITYTITVTNNGNVPATNVVVT 34 (53)
T ss_pred cCccccCCCCEEEEEEEEEECCCCceEeEEEE
Confidence 46678899999766555 4433445554443
No 24
>cd08547 Type_II_cohesin Type II cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type II cohesins; their interactions with dockerin mediate attachment of the cellulosome complex to the bacterial cell wall.
Probab=33.68 E-value=1e+02 Score=21.90 Aligned_cols=36 Identities=11% Similarity=0.233 Sum_probs=26.7
Q ss_pred eEEEecCceeeCCCceEEEEeCCCCCceeEEEEEEe
Q psy993 48 YKIVLKKKSVAPGGSISVVISSPPGLSFKGFFVQAR 83 (164)
Q Consensus 48 y~i~~~~~~y~pG~~~~VtL~~~~~~~F~GFllqAr 83 (164)
+.+..++....+|+.++|+|.......+.++.++..
T Consensus 3 ~sl~~~~~~v~~G~~~~v~v~~~~~~~~~~~~~~l~ 38 (132)
T cd08547 3 VSLSAPSTTVKVGETFTVTVKVNNATNLAGYQFTLS 38 (132)
T ss_pred EEEeCCCcccCCCCEEEEEEEEeccCceEEEEEEEE
Confidence 345555555899999999998444458999988877
No 25
>PF13199 Glyco_hydro_66: Glycosyl hydrolase family 66; PDB: 3VMO_A 3VMN_A 3VMP_A.
Probab=33.09 E-value=40 Score=31.29 Aligned_cols=18 Identities=22% Similarity=0.397 Sum_probs=12.1
Q ss_pred EecCceeeCCCceEEEEe
Q psy993 51 VLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 51 ~~~~~~y~pG~~~~VtL~ 68 (164)
+.++..|.||++|+++++
T Consensus 1 ~tDKA~Y~PGe~V~l~~~ 18 (559)
T PF13199_consen 1 TTDKARYRPGEKVTLTAS 18 (559)
T ss_dssp EES-SSB-TTS-EEEE-E
T ss_pred CCCcceeCCCCeEEEEEE
Confidence 357889999999999988
No 26
>cd03445 Thioesterase_II_repeat2 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene.
Probab=31.81 E-value=1.1e+02 Score=20.95 Aligned_cols=30 Identities=13% Similarity=0.382 Sum_probs=26.8
Q ss_pred eEEEEEeCCCCCCccEEEEEEEeecCcEEE
Q psy993 124 RVTLTWVAPEDLNESVNFVATVAKDGGEYW 153 (164)
Q Consensus 124 ~v~~~W~AP~~~~G~V~F~aTvv~~~~~fw 153 (164)
+++..+..|....++|.+++.+++++..|-
T Consensus 43 s~~~~Fl~p~~~~~pv~~~v~~lr~GRs~~ 72 (94)
T cd03445 43 SLHSYFLRPGDPDQPIEYEVERLRDGRSFA 72 (94)
T ss_pred EEEEEecCCCCCCCCEEEEEEEEECCCcEE
Confidence 889999999988899999999999888764
No 27
>PRK00249 flgH flagellar basal body L-ring protein; Reviewed
Probab=30.90 E-value=89 Score=25.43 Aligned_cols=19 Identities=16% Similarity=0.399 Sum_probs=16.4
Q ss_pred EEecCceeeCCCceEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~ 68 (164)
+.-|...++.|+.+||.|.
T Consensus 57 lf~D~rA~~VGDivTV~i~ 75 (222)
T PRK00249 57 LFKDRRARNVGDILTVVLQ 75 (222)
T ss_pred cccccccccCCCeEEEEEE
Confidence 5566788899999999998
No 28
>PF07532 Big_4: Bacterial Ig-like domain (group 4); InterPro: IPR011081 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.
Probab=30.40 E-value=86 Score=19.50 Aligned_cols=32 Identities=22% Similarity=0.305 Sum_probs=20.9
Q ss_pred eEEeeCCCCCceEEEEEeCCCC----CCccEEEEEEE
Q psy993 113 AATHIDAKAKSRVTLTWVAPED----LNESVNFVATV 145 (164)
Q Consensus 113 aVTH~~~~~K~~v~~~W~AP~~----~~G~V~F~aTv 145 (164)
.|+..+.+.+ .+.++|.+.+. ..|.+.|.+++
T Consensus 21 ~v~~~dGs~~-~~~V~W~~~~~~~~~~~G~y~v~G~v 56 (59)
T PF07532_consen 21 TVTYSDGSTE-EVPVTWDPIDPYDYNKPGTYTVTGTV 56 (59)
T ss_pred EEEECCCCEE-EEEeEeCCCChhhccCCEEEEEEEEE
Confidence 4455554443 59999996422 24889998886
No 29
>COG4893 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.29 E-value=20 Score=26.34 Aligned_cols=19 Identities=37% Similarity=0.891 Sum_probs=14.7
Q ss_pred CccCccCcCCCCCCCCCCCCCCC
Q psy993 24 APEGVCADMTPKHPQTVPQDSES 46 (164)
Q Consensus 24 aP~~aC~~m~P~H~g~~pq~~~~ 46 (164)
-|.++|-+|.|.| ||+.++
T Consensus 26 N~LaaCvd~r~~~----p~~~~n 44 (123)
T COG4893 26 NPLAACVDIRPVH----PQEMDN 44 (123)
T ss_pred ChHHHHHhccccC----CcccCc
Confidence 3688999999999 565554
No 30
>PF11153 DUF2931: Protein of unknown function (DUF2931); InterPro: IPR021326 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently, there is no known function.
Probab=28.75 E-value=2.9e+02 Score=21.77 Aligned_cols=11 Identities=9% Similarity=0.380 Sum_probs=6.6
Q ss_pred CceEEEEEeCC
Q psy993 122 KSRVTLTWVAP 132 (164)
Q Consensus 122 K~~v~~~W~AP 132 (164)
-..+.|.|.+=
T Consensus 96 P~~i~i~W~S~ 106 (216)
T PF11153_consen 96 PDSIYICWDSY 106 (216)
T ss_pred CCEEEEEEEEc
Confidence 33677777653
No 31
>PRK12788 flgH flagellar basal body L-ring protein; Reviewed
Probab=28.43 E-value=1.8e+02 Score=23.98 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=15.9
Q ss_pred EEecCceeeCCCceEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~ 68 (164)
+.-|+...+.|+.+||.|.
T Consensus 68 Lf~D~RA~~VGDIlTV~I~ 86 (234)
T PRK12788 68 LYRDPRASRTGDLLTVTIS 86 (234)
T ss_pred cccccccccCCCeEEEEEE
Confidence 4556777889999999998
No 32
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=28.10 E-value=36 Score=24.08 Aligned_cols=8 Identities=50% Similarity=0.688 Sum_probs=3.3
Q ss_pred hHHHHHHH
Q psy993 3 QFLLLCVS 10 (164)
Q Consensus 3 ~~~~~~~~ 10 (164)
.||||.|+
T Consensus 5 ~~llL~l~ 12 (95)
T PF07172_consen 5 AFLLLGLL 12 (95)
T ss_pred HHHHHHHH
Confidence 34444333
No 33
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=27.89 E-value=1.2e+02 Score=19.54 Aligned_cols=30 Identities=13% Similarity=0.301 Sum_probs=19.4
Q ss_pred ecCceeeCCCceEEEEe--CCCCCceeEEEEE
Q psy993 52 LKKKSVAPGGSISVVIS--SPPGLSFKGFFVQ 81 (164)
Q Consensus 52 ~~~~~y~pG~~~~VtL~--~~~~~~F~GFllq 81 (164)
.++..+.+|+.++.+|. ......-.+..|+
T Consensus 32 ~~~~~~~~Gd~v~ytitvtN~G~~~a~nv~v~ 63 (76)
T PF01345_consen 32 VNPSTANPGDTVTYTITVTNTGPAPATNVVVT 63 (76)
T ss_pred cCCCcccCCCEEEEEEEEEECCCCeeEeEEEE
Confidence 45788999999776665 4444455554443
No 34
>PF08194 DIM: DIM protein; InterPro: IPR013172 Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila []. This entry includes DIMs 1 to 4 and DIM23.
Probab=26.92 E-value=41 Score=19.72 Aligned_cols=10 Identities=20% Similarity=0.089 Sum_probs=5.3
Q ss_pred ChhHHHHHHH
Q psy993 1 MNQFLLLCVS 10 (164)
Q Consensus 1 m~~~~~~~~~ 10 (164)
|.++.+++++
T Consensus 1 Mk~l~~a~~l 10 (36)
T PF08194_consen 1 MKCLSLAFAL 10 (36)
T ss_pred CceeHHHHHH
Confidence 6766554333
No 35
>KOG0668|consensus
Probab=26.85 E-value=41 Score=28.46 Aligned_cols=54 Identities=22% Similarity=0.303 Sum_probs=35.5
Q ss_pred CccCcCCCCCCCCCCCCCC---CCeEEE-ec---CceeeCCCceEEEEeCCCCCceeEEEEEEe
Q psy993 27 GVCADMTPKHPQTVPQDSE---SPYKIV-LK---KKSVAPGGSISVVISSPPGLSFKGFFVQAR 83 (164)
Q Consensus 27 ~aC~~m~P~H~g~~pq~~~---~py~i~-~~---~~~y~pG~~~~VtL~~~~~~~F~GFllqAr 83 (164)
+-|.+|---|....|++-. .-=++. ++ .+.|-||+.|+|.+.+. .|||=-|-.-
T Consensus 146 dyCHS~GImHRDVKPhNvmIdh~~rkLrlIDWGLAEFYHp~~eYnVRVASR---yfKGPELLVd 206 (338)
T KOG0668|consen 146 DYCHSMGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASR---YFKGPELLVD 206 (338)
T ss_pred hHHHhcCcccccCCcceeeechhhceeeeeecchHhhcCCCceeeeeeehh---hcCCchheee
Confidence 4699998888666666411 111121 12 47799999999999874 7998655543
No 36
>PF10807 DUF2541: Protein of unknown function (DUF2541); InterPro: IPR020240 This entry represents proteins found in the Gammaproteobacteria that have no known function.
Probab=25.81 E-value=1.3e+02 Score=22.67 Aligned_cols=77 Identities=18% Similarity=0.253 Sum_probs=47.8
Q ss_pred EEeeCC-CCceEEEeCCCCCc---eeEeccCCCCCCeEEee-CC--CCCceEEEEEeCCCCCCccEEEEEEEeecCcEEE
Q psy993 81 QARVGD-KPVGQFTKSPSSKF---YKVINCLGGSQNAATHI-DA--KAKSRVTLTWVAPEDLNESVNFVATVAKDGGEYW 153 (164)
Q Consensus 81 qAr~~~-~~vG~F~~~~~~~~---~~~~~C~~~~~~aVTH~-~~--~~K~~v~~~W~AP~~~~G~V~F~aTvv~~~~~fw 153 (164)
+|+..| ...|.-..+.+++. .+...|.... ++-=+ .. -.-+-+++..++-...+-.+.|...+=++..+=|
T Consensus 20 ~A~A~d~~~LG~t~m~~ne~~~~~l~lpvCR~vk--rIql~AdRgDi~L~~a~v~Fk~~~g~s~~l~~~~~ikeg~tT~W 97 (134)
T PF10807_consen 20 QAQANDHKTLGRTIMPRNETNDLTLKLPVCRRVK--RIQLKADRGDIQLSGATVYFKNANGESQTLNFPRSIKEGQTTDW 97 (134)
T ss_pred hhccCceEEEEEEEeeccCCCCceeeccceeeee--eEEEeeccCCeEeeeeEEEEEeccccceEEcccccccCCCccCc
Confidence 444444 45676666544332 2566887543 22222 11 1223456777777666778888888888888999
Q ss_pred EccCCc
Q psy993 154 VGQQSE 159 (164)
Q Consensus 154 v~~~S~ 159 (164)
.+++|+
T Consensus 98 i~i~sd 103 (134)
T PF10807_consen 98 ININSD 103 (134)
T ss_pred EEecCC
Confidence 998865
No 37
>PF08138 Sex_peptide: Sex peptide (SP) family; InterPro: IPR012608 This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The male seminal fluid proteins are referred to as accessory gland proteins (Acps). The SP is one of the most interesting Acps and plays an important role in reproduction [].; GO: 0005179 hormone activity, 0046008 regulation of female receptivity, post-mating, 0005576 extracellular region; PDB: 2LAQ_A.
Probab=25.06 E-value=24 Score=22.56 Aligned_cols=19 Identities=11% Similarity=0.221 Sum_probs=0.0
Q ss_pred ChhHHHHHHHHHHhhccee
Q psy993 1 MNQFLLLCVSAVAISSVHA 19 (164)
Q Consensus 1 m~~~~~~~~~~~~~~~~~a 19 (164)
|+.-++++++++++..+.+
T Consensus 1 Mk~p~~llllvlllGla~s 19 (56)
T PF08138_consen 1 MKTPIFLLLLVLLLGLAQS 19 (56)
T ss_dssp -------------------
T ss_pred CcchHHHHHHHHHHHHHhc
Confidence 5555556666666666655
No 38
>PF10989 DUF2808: Protein of unknown function (DUF2808); InterPro: IPR021256 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=24.85 E-value=3e+02 Score=20.50 Aligned_cols=47 Identities=28% Similarity=0.437 Sum_probs=27.6
Q ss_pred eEEEec-CceeeCCCceEEEEeC---CCCCceeEEEEEEeeCC-CC----ceEEEe
Q psy993 48 YKIVLK-KKSVAPGGSISVVISS---PPGLSFKGFFVQARVGD-KP----VGQFTK 94 (164)
Q Consensus 48 y~i~~~-~~~y~pG~~~~VtL~~---~~~~~F~GFllqAr~~~-~~----vG~F~~ 94 (164)
-.|++. .+-+.||++|+|.|++ +....--=|-+.|...+ ++ +|+|.+
T Consensus 89 ~~i~I~f~~PV~pG~tv~V~l~~v~NP~~~G~Y~f~v~a~p~G~~p~~~ylG~~rl 144 (146)
T PF10989_consen 89 RTITITFDEPVPPGTTVTVVLSPVRNPRSGGTYQFNVTAFPPGDNPIGQYLGTWRL 144 (146)
T ss_pred CEEEEEeCCCCCCCCEEEEEEEeeeCCCCCCeEEEEEEEECCCCCcccceeeEEEE
Confidence 344443 2557899999999973 32222333666677654 33 666654
No 39
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=24.12 E-value=2.7e+02 Score=22.88 Aligned_cols=19 Identities=16% Similarity=0.218 Sum_probs=16.2
Q ss_pred EEecCceeeCCCceEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~ 68 (164)
+.-|+...+.|+.+||.|.
T Consensus 59 Lf~D~RA~~VGDivTV~i~ 77 (236)
T PRK12696 59 LFADSRARRVGDIVLVKIV 77 (236)
T ss_pred cccccccccCCCEEEEEEE
Confidence 5557788899999999998
No 40
>PF08612 Med20: TATA-binding related factor (TRF) of subunit 20 of Mediator complex; InterPro: IPR013921 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Proteins in this entry are subunit Med20 of the Mediator complex, and is found in the non-essential part of the head []. and related to the TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the pre-initiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2HZS_C 3RJ1_M 2HZM_G.
Probab=23.68 E-value=1.3e+02 Score=24.22 Aligned_cols=34 Identities=24% Similarity=0.405 Sum_probs=22.2
Q ss_pred EEecCce-eeCCCceEEEEe-CCCCCceeEEEEEEee
Q psy993 50 IVLKKKS-VAPGGSISVVIS-SPPGLSFKGFFVQARV 84 (164)
Q Consensus 50 i~~~~~~-y~pG~~~~VtL~-~~~~~~F~GFllqAr~ 84 (164)
+.++... |+-|+ .+|.+. -..+..|||++|+.+-
T Consensus 129 ~kie~~~~YelgD-f~VRvg~v~~~~~~rGilvEVEy 164 (225)
T PF08612_consen 129 IKIEGGGTYELGD-FTVRVGNVFQGQSFRGILVEVEY 164 (225)
T ss_dssp EEEESEEEEEETT-EEEEEEEEEETTEEEEEEEEEEE
T ss_pred EEEeeeeEEEECC-EEEEEEEEEECCCCcEEEEEEEE
Confidence 4444333 88877 556665 2223479999999996
No 41
>PF02494 HYR: HYR domain; InterPro: IPR003410 This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion. In the Sushi repeat-containing protein (SrpX), this domain is found between two sushi repeats.
Probab=23.21 E-value=2.2e+02 Score=18.52 Aligned_cols=49 Identities=22% Similarity=0.379 Sum_probs=27.9
Q ss_pred EeccCCCCCCeEEeeCCCCCceEEEEEeCCCC--CCccEEEEEEEeecCcEEEEc
Q psy993 103 VINCLGGSQNAATHIDAKAKSRVTLTWVAPED--LNESVNFVATVAKDGGEYWVG 155 (164)
Q Consensus 103 ~~~C~~~~~~aVTH~~~~~K~~v~~~W~AP~~--~~G~V~F~aTvv~~~~~fwv~ 155 (164)
.+.|+. + ++..-...+....+.|..|.. ..|.+.....--...+.|-++
T Consensus 7 ~i~CP~---~-i~~~~~~~~~~~~v~w~~p~~~Dn~~~~~~~~~~~~~g~~f~~G 57 (81)
T PF02494_consen 7 VITCPD---D-ITVTVEPGQSTASVSWTEPTATDNSGSIVSITCNHPPGDLFPVG 57 (81)
T ss_pred EEECCC---C-cEEEecCCCceEEEEecCCEEEecCCceEeeeccCCCCceEeec
Confidence 449983 3 555555555577899998874 235333322333445566665
No 42
>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=22.74 E-value=1.4e+02 Score=21.82 Aligned_cols=60 Identities=12% Similarity=0.279 Sum_probs=29.9
Q ss_pred CCCeEEEecCceeeCCCceEEEEe--CCCCCceeEEEEEEeeCC--------C-CceEEEeCCCCCceeEecc
Q psy993 45 ESPYKIVLKKKSVAPGGSISVVIS--SPPGLSFKGFFVQARVGD--------K-PVGQFTKSPSSKFYKVINC 106 (164)
Q Consensus 45 ~~py~i~~~~~~y~pG~~~~VtL~--~~~~~~F~GFllqAr~~~--------~-~vG~F~~~~~~~~~~~~~C 106 (164)
+.|+.|.++ ...|++.|+|++. ...+..|+.+-.-.-+.+ . .-|++.....-.....+..
T Consensus 2 De~~~I~v~--GL~p~~~vtl~a~~~~~~g~~w~S~A~f~Ad~~G~VDl~~~~p~~GsY~gvdpMGLfWSm~p 72 (126)
T PF04775_consen 2 DEPVDIRVS--GLPPGQEVTLRARLTDDNGVQWQSYATFRADENGIVDLSRDAPLGGSYTGVDPMGLFWSMKP 72 (126)
T ss_dssp TS--EEEEE--S--TT-EEEEEEEEE-TTS-EEEEEEEEE--TTS-EETTTS-EEEESSEES-TTHHHHT-EE
T ss_pred CCCeEEEEe--CCCCCCEEEEEEEEEeCCCCEEEEEEEEEcCCCCeEEeccCCCCCcEEcCcccccceEEccc
Confidence 457888887 5789999999998 333456776655444432 1 2677777643333333433
No 43
>PF09118 DUF1929: Domain of unknown function (DUF1929); InterPro: IPR015202 This domain adopts a secondary structure consisting of a bundle of seven, mostly antiparallel, beta-strands surrounding a hydrophobic core. The 7 strands are arranged in 2 sheets, in a Greek-key topology. Their precise function, has not, as yet, been defined, though they are mostly found in sugar-utilising enzymes, such as galactose oxidase []. ; PDB: 2JKX_A 2EIC_A 1K3I_A 1GOH_A 2EIB_A 2WQ8_A 2VZ1_A 1GOF_A 2VZ3_A 1GOG_A ....
Probab=22.46 E-value=2.2e+02 Score=19.88 Aligned_cols=21 Identities=19% Similarity=0.418 Sum_probs=13.0
Q ss_pred EEecCceeeCCCceEEEEeCC
Q psy993 50 IVLKKKSVAPGGSISVVISSP 70 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~~~ 70 (164)
|...+.....|++++|++...
T Consensus 4 i~~~p~~i~yg~~~tv~~~~~ 24 (98)
T PF09118_consen 4 ITSAPTTIKYGQTFTVTVTVP 24 (98)
T ss_dssp EEES-SEEETT-EEEEEE--S
T ss_pred cccCCCeEecCCEEEEEEECC
Confidence 444667888999999888754
No 44
>cd08546 cohesin_like Cohesin domain, interaction parter of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. Cohesin modules are phylogenetically distributed into three groups: type I cohesin-dockerin interactions mediate assembly of a range of dockerin-borne enzymes to the complex, while type-II interactions mediate attachment of the cellulosome complex to the bacterial cell wall. Recently discovered type-III cohesins, such as found in the anchoring scaffoldin ScaE, appears to contribute to increased stability of the elaborate cellulosome complex. While the p
Probab=22.19 E-value=2.1e+02 Score=20.10 Aligned_cols=27 Identities=7% Similarity=0.000 Sum_probs=21.1
Q ss_pred eCCCceEEEEeCCCCCceeEEEEEEee
Q psy993 58 APGGSISVVISSPPGLSFKGFFVQARV 84 (164)
Q Consensus 58 ~pG~~~~VtL~~~~~~~F~GFllqAr~ 84 (164)
.+|+.++|+|.......+.++.++-.=
T Consensus 12 ~~G~~~~v~v~~~~~~~~~~~~~~l~y 38 (135)
T cd08546 12 KVGETVTVTVKVNNVPNVAAADFTLSY 38 (135)
T ss_pred cCCCEEEEEEEEecCCCeEEEEEEEEE
Confidence 899999999984333478899888773
No 45
>PF13956 Ibs_toxin: Toxin Ibs, type I toxin-antitoxin system
Probab=21.97 E-value=56 Score=16.29 Aligned_cols=6 Identities=17% Similarity=0.512 Sum_probs=2.6
Q ss_pred ChhHHH
Q psy993 1 MNQFLL 6 (164)
Q Consensus 1 m~~~~~ 6 (164)
|.+.+.
T Consensus 2 Mk~vII 7 (19)
T PF13956_consen 2 MKLVII 7 (19)
T ss_pred ceehHH
Confidence 444444
No 46
>CHL00084 rpl19 ribosomal protein L19
Probab=21.71 E-value=1.7e+02 Score=21.49 Aligned_cols=32 Identities=9% Similarity=0.166 Sum_probs=23.7
Q ss_pred CceeeCCCceEEEEe---CC--CCCceeEEEEEEeeC
Q psy993 54 KKSVAPGGSISVVIS---SP--PGLSFKGFFVQARVG 85 (164)
Q Consensus 54 ~~~y~pG~~~~VtL~---~~--~~~~F~GFllqAr~~ 85 (164)
...+.+|++++|++. |. .-+.|.|..|.-+..
T Consensus 20 ~p~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~ 56 (117)
T CHL00084 20 LPKIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNS 56 (117)
T ss_pred CCccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCC
Confidence 346889999999984 22 234799999997753
No 47
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=21.67 E-value=1.2e+02 Score=21.46 Aligned_cols=24 Identities=29% Similarity=0.580 Sum_probs=15.1
Q ss_pred eeCCCceEEEEeC-------C--CCCceeEEEE
Q psy993 57 VAPGGSISVVISS-------P--PGLSFKGFFV 80 (164)
Q Consensus 57 y~pG~~~~VtL~~-------~--~~~~F~GFll 80 (164)
.+.||.|.|.+.. . ....|-||||
T Consensus 95 L~~GD~V~v~~~~~~~~~~~~~~~~stFsGfLl 127 (127)
T PF00386_consen 95 LNKGDTVWVRLDSGNGIYSSGSNPYSTFSGFLL 127 (127)
T ss_dssp E-TT-EEEEEEEEEEEEEBBTTSBTEEEEEEEE
T ss_pred eCCCCEEEEEEecCceEEeCCCCCCEEEEEEEC
Confidence 6678888887762 1 2467888886
No 48
>cd00600 Sm_like The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=21.47 E-value=1.4e+02 Score=18.39 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=15.5
Q ss_pred CCceEEEEeCCCCCceeEEEEEEe
Q psy993 60 GGSISVVISSPPGLSFKGFFVQAR 83 (164)
Q Consensus 60 G~~~~VtL~~~~~~~F~GFllqAr 83 (164)
|.+++|.|... ..|.|.+...-
T Consensus 6 g~~V~V~l~~g--~~~~G~L~~~D 27 (63)
T cd00600 6 GKTVRVELKDG--RVLEGVLVAFD 27 (63)
T ss_pred CCEEEEEECCC--cEEEEEEEEEC
Confidence 67788888854 56888766544
No 49
>cd02851 Galactose_oxidase_C_term Galactose oxidase C-terminus domain. Galactose oxidase is an extracellular monomeric enzyme which catalyses the stereospecific oxidation of a broad range of primary alcohol substrates and possesses a unique mononuclear copper site essential for catalysing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active center necessary for the reaction was found to be situated at a tyrosine residue. The C-terminus of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=21.32 E-value=3.1e+02 Score=19.45 Aligned_cols=19 Identities=32% Similarity=0.413 Sum_probs=12.7
Q ss_pred CeEEeeCCCCCceEEEEEe
Q psy993 112 NAATHIDAKAKSRVTLTWV 130 (164)
Q Consensus 112 ~aVTH~~~~~K~~v~~~W~ 130 (164)
.++||+.+...+.+.+.=+
T Consensus 40 ~~~THs~~~~QR~v~L~~~ 58 (101)
T cd02851 40 GSATHTVNTDQRRIPLTLF 58 (101)
T ss_pred ccccccccCCccEEEeeeE
Confidence 4778887777776655433
No 50
>PRK15191 fimbrial protein BcfF; Provisional
Probab=20.42 E-value=3.9e+02 Score=20.26 Aligned_cols=26 Identities=19% Similarity=0.346 Sum_probs=14.6
Q ss_pred CCCCeEEEecCceeeCCCceEEEEeCC
Q psy993 44 SESPYKIVLKKKSVAPGGSISVVISSP 70 (164)
Q Consensus 44 ~~~py~i~~~~~~y~pG~~~~VtL~~~ 70 (164)
..-||.|.... .-...+.++|+..+.
T Consensus 65 ~~~~F~I~L~~-C~~~~~~v~v~F~G~ 90 (172)
T PRK15191 65 AWQPFAIDLQN-CGSTASGVTVSFSGA 90 (172)
T ss_pred CCCCeEEEEeC-CCCCCCeEEEEEeCC
Confidence 34689888741 101124677877754
No 51
>PRK12697 flgH flagellar basal body L-ring protein; Reviewed
Probab=20.35 E-value=2.7e+02 Score=22.79 Aligned_cols=19 Identities=16% Similarity=0.385 Sum_probs=16.5
Q ss_pred EEecCceeeCCCceEEEEe
Q psy993 50 IVLKKKSVAPGGSISVVIS 68 (164)
Q Consensus 50 i~~~~~~y~pG~~~~VtL~ 68 (164)
+.-|...++.|+.+||.|.
T Consensus 62 Lf~D~RA~~VGDiiTV~i~ 80 (226)
T PRK12697 62 LFEDQRPRNVGDILTIVIA 80 (226)
T ss_pred cccccccccCCCEEEEEEE
Confidence 5667788899999999998
No 52
>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=20.17 E-value=1.2e+02 Score=17.69 Aligned_cols=13 Identities=46% Similarity=0.820 Sum_probs=10.1
Q ss_pred eEEEEEeCCCCCC
Q psy993 124 RVTLTWVAPEDLN 136 (164)
Q Consensus 124 ~v~~~W~AP~~~~ 136 (164)
.+.+.|.+|....
T Consensus 16 ~~~v~W~~~~~~~ 28 (83)
T smart00060 16 SVTLSWEPPPDDG 28 (83)
T ss_pred EEEEEECCCCCCC
Confidence 8899999876543
Done!