Query psy13041
Match_columns 81
No_of_seqs 105 out of 1022
Neff 9.8
Searched_HMMs 46136
Date Fri Aug 16 17:58:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13041.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13041hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11838 ERAP1_C: ERAP1-like C 99.6 2.6E-15 5.5E-20 93.4 5.1 77 3-79 228-305 (324)
2 KOG1046|consensus 99.1 2.5E-10 5.5E-15 79.5 8.0 73 7-80 772-844 (882)
3 TIGR02412 pepN_strep_liv amino 98.7 8.1E-08 1.8E-12 66.9 6.7 74 4-78 728-803 (831)
4 PF10805 DUF2730: Protein of u 93.6 0.12 2.6E-06 27.9 3.0 43 30-75 1-43 (106)
5 COG0308 PepN Aminopeptidase N 90.4 0.55 1.2E-05 33.9 4.1 71 8-79 757-830 (859)
6 cd08330 CARD_ASC_NALP1 Caspase 89.6 0.78 1.7E-05 23.6 3.3 39 33-74 2-40 (82)
7 cd08329 CARD_BIRC2_BIRC3 Caspa 77.9 7.3 0.00016 20.5 3.9 40 32-74 9-48 (94)
8 PF00619 CARD: Caspase recruit 76.4 7.6 0.00016 19.5 3.7 40 31-74 1-41 (85)
9 PF06685 DUF1186: Protein of u 70.1 24 0.00052 22.1 5.9 65 13-80 134-198 (249)
10 PF15572 Imm26: Immunity prote 63.4 4.9 0.00011 21.5 1.2 18 24-41 67-84 (96)
11 PF03965 Penicillinase_R: Peni 62.8 22 0.00048 19.1 5.2 44 32-77 70-114 (115)
12 PF05596 Taeniidae_ag: Taeniid 60.1 7.1 0.00015 19.3 1.4 17 65-81 12-28 (64)
13 TIGR01565 homeo_ZF_HD homeobox 56.8 15 0.00032 17.7 2.2 18 63-80 7-24 (58)
14 COG3251 Uncharacterized protei 54.2 7.9 0.00017 19.4 1.0 22 21-42 39-60 (71)
15 PF04320 DUF469: Protein with 53.0 18 0.00039 19.5 2.3 29 52-80 58-86 (101)
16 KOG1756|consensus 50.2 39 0.00085 19.1 3.4 53 21-73 48-100 (131)
17 PF01371 Trp_repressor: Trp re 50.0 29 0.00064 18.1 2.8 17 59-75 22-38 (87)
18 cd08785 CARD_CARD9-like Caspas 48.8 39 0.00085 17.6 3.3 40 31-74 2-41 (86)
19 PF13475 DUF4116: Domain of un 47.4 27 0.00058 15.3 3.2 35 14-48 3-37 (49)
20 TIGR01321 TrpR trp operon repr 47.4 40 0.00087 17.9 3.0 38 36-75 7-44 (94)
21 TIGR02698 CopY_TcrY copper tra 46.5 51 0.0011 18.3 5.1 45 33-79 72-117 (130)
22 PF00046 Homeobox: Homeobox do 45.8 30 0.00066 15.7 2.3 17 64-80 7-23 (57)
23 PF09832 DUF2059: Uncharacteri 45.4 29 0.00062 16.5 2.2 16 63-78 16-31 (64)
24 cd08323 CARD_APAF1 Caspase act 44.3 47 0.001 17.2 3.3 37 34-74 3-39 (86)
25 PRK11702 hypothetical protein; 40.8 21 0.00046 19.5 1.4 29 52-80 65-93 (108)
26 TIGR03765 ICE_PFL_4695 integra 40.0 65 0.0014 17.6 3.6 39 29-77 35-73 (105)
27 PRK01381 Trp operon repressor; 37.6 68 0.0015 17.3 3.0 38 36-75 7-44 (99)
28 PF07443 HARP: HepA-related pr 37.6 14 0.0003 17.7 0.4 37 11-47 9-46 (55)
29 cd08163 MPP_Cdc1 Saccharomyces 37.5 69 0.0015 20.0 3.5 23 27-49 26-48 (257)
30 PF10384 Scm3: Centromere prot 36.0 42 0.0009 16.2 1.9 16 32-47 12-27 (58)
31 PF04691 ApoC-I: Apolipoprotei 35.5 60 0.0013 15.9 2.5 19 29-47 41-59 (61)
32 PF05106 Phage_holin_3: Phage 35.1 75 0.0016 16.9 3.0 22 22-43 3-24 (100)
33 PF00034 Cytochrom_C: Cytochro 33.2 56 0.0012 15.6 2.3 17 63-79 74-90 (91)
34 smart00151 SWIB SWI complex, B 33.1 31 0.00067 17.3 1.2 14 24-37 23-36 (77)
35 KOG2959|consensus 32.5 1.2E+02 0.0027 18.6 4.0 46 32-78 129-174 (238)
36 PF08671 SinI: Anti-repressor 32.0 25 0.00054 14.6 0.6 11 69-79 19-29 (30)
37 PF14778 ODR4-like: Olfactory 31.3 37 0.00081 22.3 1.7 28 29-56 43-70 (362)
38 COG5126 FRQ1 Ca2+-binding prot 31.3 1.1E+02 0.0025 17.9 3.9 62 8-76 37-101 (160)
39 PF10859 DUF2660: Protein of u 31.2 82 0.0018 16.2 2.8 22 26-47 43-64 (86)
40 PF13864 Enkurin: Calmodulin-b 31.0 87 0.0019 16.4 2.9 24 25-48 40-63 (98)
41 PF07818 HCNGP: HCNGP-like pro 30.9 91 0.002 16.5 3.9 42 34-77 13-54 (96)
42 PF08203 RNA_polI_A14: Yeast R 30.5 54 0.0012 16.8 1.8 16 66-81 58-73 (76)
43 PF00249 Myb_DNA-binding: Myb- 30.5 59 0.0013 14.3 2.5 26 11-46 7-32 (48)
44 PF02201 SWIB: SWIB/MDM2 domai 30.4 36 0.00077 17.0 1.2 13 25-37 24-36 (76)
45 PF11894 DUF3414: Protein of u 29.8 1.5E+02 0.0032 23.9 4.7 26 13-38 499-524 (1691)
46 cd04404 RhoGAP-p50rhoGAP RhoGA 29.4 60 0.0013 19.1 2.2 14 28-41 181-194 (195)
47 PF11637 UvsW: ATP-dependant D 29.1 71 0.0015 15.2 2.0 18 62-79 3-20 (54)
48 COG5448 Uncharacterized conser 28.8 68 0.0015 18.9 2.3 20 60-79 25-44 (184)
49 smart00389 HOX Homeodomain. DN 28.8 66 0.0014 14.3 2.2 16 64-79 7-22 (56)
50 PF08687 ASD2: Apx/Shroom doma 28.5 1.1E+02 0.0024 19.5 3.3 27 52-78 209-235 (264)
51 PF06240 COXG: Carbon monoxide 27.6 1E+02 0.0022 17.0 2.8 23 24-47 6-28 (140)
52 PF07349 DUF1478: Protein of u 27.3 36 0.00078 19.7 1.0 19 17-35 31-49 (162)
53 PF11256 DUF3055: Protein of u 27.1 69 0.0015 16.6 1.9 14 65-78 67-80 (81)
54 PF08513 LisH: LisH; InterPro 26.9 56 0.0012 12.8 1.4 8 29-36 6-13 (27)
55 cd00686 Terpene_cyclase_cis_tr 26.8 1.2E+02 0.0027 20.2 3.4 49 10-60 107-155 (357)
56 cd00086 homeodomain Homeodomai 26.7 75 0.0016 14.2 2.2 17 64-80 7-23 (59)
57 PRK00944 hypothetical protein; 26.5 22 0.00049 21.3 0.0 29 26-55 98-126 (195)
58 PF10755 DUF2585: Protein of u 26.0 22 0.00047 20.9 -0.1 27 26-53 69-95 (165)
59 PF05338 DUF717: Protein of un 25.9 74 0.0016 15.2 1.8 14 65-78 3-16 (55)
60 PLN02620 indole-3-acetic acid- 25.8 1.5E+02 0.0032 21.4 3.8 22 27-48 236-257 (612)
61 PF05595 DUF771: Domain of unk 25.8 78 0.0017 16.4 2.0 14 28-41 77-90 (91)
62 COG3543 Uncharacterized conser 25.5 70 0.0015 18.2 1.9 16 34-49 25-40 (135)
63 PF09499 RE_ApaLI: ApaLI-like 25.0 78 0.0017 19.0 2.1 30 8-37 159-189 (191)
64 PF05484 LRV_FeS: LRV protein 24.9 59 0.0013 15.7 1.3 14 67-80 38-51 (57)
65 TIGR01592 holin_SPP1 holin, SP 24.6 1.1E+02 0.0024 15.6 2.8 28 8-38 31-58 (75)
66 PHA02692 hypothetical protein; 24.6 47 0.001 16.7 1.0 6 71-76 19-24 (70)
67 PF15186 TEX13: Testis-express 24.5 89 0.0019 18.2 2.2 41 7-47 8-49 (152)
68 PF14680 FANCI_HD2: FANCI heli 24.4 86 0.0019 19.4 2.3 36 8-43 49-84 (234)
69 PHA02609 uvsW.1 hypothetical p 24.3 1.1E+02 0.0024 15.5 2.4 27 52-79 13-39 (76)
70 PHA02819 hypothetical protein; 24.2 50 0.0011 16.6 1.0 6 66-71 17-22 (71)
71 KOG4519|consensus 24.1 1.1E+02 0.0025 20.5 2.9 52 29-81 250-301 (459)
72 PF11072 DUF2859: Protein of u 23.9 1.6E+02 0.0034 17.0 3.5 38 29-76 73-110 (142)
73 TIGR02217 chp_TIGR02217 conser 23.1 84 0.0018 19.3 2.0 18 62-79 51-68 (210)
74 PF02993 MCPVI: Minor capsid p 22.7 28 0.00062 21.7 0.0 41 37-77 31-71 (238)
75 COG3405 CelA Endoglucanase Y [ 22.7 1.2E+02 0.0027 20.0 2.8 30 11-40 58-87 (360)
76 COG1962 MtrH Tetrahydromethano 22.6 51 0.0011 21.1 1.1 26 21-46 227-252 (313)
77 CHL00088 apcB allophycocyanin 22.5 1E+02 0.0022 18.0 2.3 18 61-78 16-33 (161)
78 KOG0859|consensus 22.4 1.9E+02 0.0042 17.8 3.4 28 21-48 67-94 (217)
79 cd04386 RhoGAP_nadrin RhoGAP_n 22.2 91 0.002 18.5 2.1 15 27-41 184-198 (203)
80 cd08324 CARD_NOD1_CARD4 Caspas 22.1 1.4E+02 0.003 15.7 3.3 8 37-44 6-13 (85)
81 PHA03074 late transcription fa 22.1 1.2E+02 0.0027 18.7 2.6 30 51-80 51-80 (225)
82 PF02224 Cytidylate_kin: Cytid 22.1 1.3E+02 0.0029 17.5 2.6 26 8-33 30-55 (157)
83 PHA02650 hypothetical protein; 21.9 64 0.0014 16.7 1.2 6 66-71 17-22 (81)
84 PF10691 DUF2497: Protein of u 21.9 1.3E+02 0.0028 15.2 2.3 17 28-44 45-61 (73)
85 smart00315 RGS Regulator of G 21.8 1.2E+02 0.0026 15.6 2.4 18 19-36 4-21 (118)
86 PF04930 FUN14: FUN14 family; 21.7 1.2E+02 0.0025 16.0 2.3 14 33-46 42-55 (100)
87 PF07707 BACK: BTB And C-termi 21.6 1.2E+02 0.0027 15.2 2.4 22 22-43 12-33 (103)
88 PF11220 DUF3015: Protein of u 21.4 1.8E+02 0.0039 16.8 4.6 33 13-45 85-118 (144)
89 PF12123 Amidase02_C: N-acetyl 21.3 1E+02 0.0023 14.0 2.0 17 63-79 23-39 (45)
90 PF12108 SF3a60_bindingd: Spli 21.3 82 0.0018 12.8 1.7 6 70-75 17-22 (28)
91 PF05939 Phage_min_tail: Phage 21.2 1.1E+02 0.0023 16.5 2.0 17 64-80 50-66 (109)
92 COG3644 Uncharacterized protei 21.0 1.9E+02 0.0041 17.1 3.1 36 34-69 89-124 (194)
93 PF14658 EF-hand_9: EF-hand do 21.0 1.3E+02 0.0028 14.9 2.8 26 52-77 20-45 (66)
94 cd08327 CARD_RAIDD Caspase act 20.7 1.5E+02 0.0033 15.6 4.2 39 33-74 8-46 (94)
95 PF14228 MOR2-PAG1_mid: Cell m 20.6 1.3E+02 0.0029 23.3 3.0 28 10-37 681-708 (1120)
96 PF00615 RGS: Regulator of G p 20.6 90 0.002 15.9 1.7 18 19-36 4-21 (118)
97 PF14317 YcxB: YcxB-like prote 20.5 82 0.0018 14.1 1.4 15 62-77 48-62 (62)
98 PHA00440 host protein H-NS-int 20.4 1.4E+02 0.003 16.1 2.3 43 4-46 38-82 (98)
99 cd08332 CARD_CASP2 Caspase act 20.4 1.5E+02 0.0032 15.4 3.6 38 33-74 8-45 (90)
100 PF11004 Kdo_hydroxy: 3-deoxy- 20.1 36 0.00078 21.8 0.1 58 11-72 140-204 (281)
101 PHA02975 hypothetical protein; 20.1 70 0.0015 16.0 1.1 6 66-71 17-22 (69)
No 1
>PF11838 ERAP1_C: ERAP1-like C-terminal domain; InterPro: IPR024571 This entry represents the uncharacterised C-terminal domain of zinc metallopeptidases belonging to MEROPS peptidase family M1 (aminopeptidase N, clan MA), with a single member characterised in Streptomyces lividans: aminopeptidase G []. The rest of the members of this family are identified as aminopeptidase N of the actinomycete-type. The spectrum of activity may differ somewhat from the aminopeptidase N clade of Escherichia coli and most other proteobacteria, which are well separated phylogenetically within the M1 family. ; PDB: 3MDJ_A 2YD0_A 3QNF_C 3RJO_A 1Z5H_A 3Q7J_A 1Z1W_A 3SE6_B.
Probab=99.58 E-value=2.6e-15 Score=93.43 Aligned_cols=77 Identities=39% Similarity=0.708 Sum_probs=65.0
Q ss_pred CCCCccccchHHHHHHHhh-cCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhhc
Q psy13041 3 KDEKNIRSQDYFTVIVMVA-GNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 3 l~~~~v~~qd~~~~~~~~~-~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~~ 79 (81)
++++.++.||+..++.+++ .||.|+..+|+|+++||+.|.+++++++..+.+++..+++.+||+++++++++||+.+
T Consensus 228 l~~~~v~~~d~~~~~~~~~~~~~~~~~~~~~~~~~n~~~i~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~~~f~~~~ 305 (324)
T PF11838_consen 228 LSNDKVRSQDIRYVLAGLASSNPVGRDLAWEFFKENWDAIIKKFGTNSSALSRVIKSFAGNFSTEEQLDELEEFFEDK 305 (324)
T ss_dssp HCTSTS-TTTHHHHHHHHH-CSTTCHHHHHHHHHHCHHHHHCHC-TTSHCCHHHHHCCCTT--SHHHHHHHHHHHHHH
T ss_pred cCCcccccHHHHHHHHHHhcCChhhHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHhccCCCHHHHHHHHHHHhhC
Confidence 4554599999999999998 9999999999999999999999999865568889988888999999999999999543
No 2
>KOG1046|consensus
Probab=99.15 E-value=2.5e-10 Score=79.50 Aligned_cols=73 Identities=37% Similarity=0.731 Sum_probs=68.5
Q ss_pred ccccchHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhhcC
Q psy13041 7 NIRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 7 ~v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~~~ 80 (81)
.++.||....+.+++.|+.|...+|+|+.+||+.+.++++ +...+.+++..++..+.+..+++++++|++..+
T Consensus 772 ~v~~qd~~~~~~~~~~~~~g~~~a~~~~~~n~~~l~~~~~-~~~~~~~li~~~~~~~~~~~~~~~~~~f~~~~~ 844 (882)
T KOG1046|consen 772 NVRDQDVLTLLQGISGNPRGVELAWKFLQDNWKELLNRYG-NNFELSRLISFITEPFATEEKLDEVEKFFADIP 844 (882)
T ss_pred cccchhHHHHHHHHhcCcccHHHHHHHHHHHHHHHHHhcC-CcHHHHHHHHHHHhccCCHHHHHHHHHHHhcCC
Confidence 4999999999999999999999999999999999999999 667899999999999999999999999998653
No 3
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=98.68 E-value=8.1e-08 Score=66.92 Aligned_cols=74 Identities=8% Similarity=0.021 Sum_probs=59.3
Q ss_pred CCCccccchHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhc--ccCCHHHHHHHHHHHhh
Q psy13041 4 DEKNIRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCG--KFTTQERLDEVSEKSLK 78 (81)
Q Consensus 4 ~~~~v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~--~~~t~~~~~~~~~f~~~ 78 (81)
+++.++.||+..++.+++ ++.++..+|+|+++||+.|.++++..+..+.+.+...+. .+|+.+.++++++||++
T Consensus 728 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 803 (831)
T TIGR02412 728 TTDALPNSKQRAIIEGFW-QPEQALLLAAYAERYFANLADIWKRRGPAIAQAISRGLFPATAVNYDTLATADKWLRS 803 (831)
T ss_pred CCCCCCHHHHHHHHhhcC-CCCcHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhcCCcccCCHHHHHHHHHHHHh
Confidence 333389999999999987 569999999999999999999998632455545444343 89999999999999963
No 4
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=93.57 E-value=0.12 Score=27.90 Aligned_cols=43 Identities=23% Similarity=0.631 Sum_probs=29.0
Q ss_pred HHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHH
Q psy13041 30 AWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEK 75 (81)
Q Consensus 30 ~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f 75 (81)
.|+|+++||..|...++. ...-+..-+.+.+++.++++++++-
T Consensus 1 ~~~~~~~~w~ii~a~~~~---~~~~~~~~l~~~~a~~~~~~~l~~~ 43 (106)
T PF10805_consen 1 MWEFIKKNWGIIWAVFGI---AGGIFWLWLRRTYAKREDIEKLEER 43 (106)
T ss_pred ChHHHHhCcHHHHHHHHH---HHHHHHHHHHHhhccHHHHHHHHHH
Confidence 489999999998877753 2222333345568888888888443
No 5
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=90.41 E-value=0.55 Score=33.95 Aligned_cols=71 Identities=21% Similarity=0.196 Sum_probs=55.3
Q ss_pred cccchHHHHHHHhhcCCchHHHHHHHHHHhHH---HHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhhc
Q psy13041 8 IRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWD---YLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 8 v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~---~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~~ 79 (81)
+..|++.........++.+++..|.|...||+ .+....+++......++.. ...+.....++++++|++..
T Consensus 757 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~-~~~~~~~~~~~~i~~~~~~~ 830 (859)
T COG0308 757 VLEQDIGLMIHAAFEAPNPNEARWLYGTFAFENPALLHALDGSGYRFLGVIVLE-LNIFNPQLALRKIEEFLELK 830 (859)
T ss_pred hHHHHHHHHhhhhhhCCcchhhHHHHHHHhhhchhhhhhhccccccccceEEEE-eeccchhhHHHHHHHHhhhh
Confidence 78889988888888999999999999999997 6777777654334444433 45788888899999998754
No 6
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=89.57 E-value=0.78 Score=23.58 Aligned_cols=39 Identities=23% Similarity=0.349 Sum_probs=25.5
Q ss_pred HHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 33 YVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 33 f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
|+..|+..+.++...-...+..++ ....-|+++.+++++
T Consensus 2 fv~~~r~~Li~~v~~v~~ilD~L~---~~~Vit~e~~~~I~a 40 (82)
T cd08330 2 FVDQHREALIARVTNVDPILDKLH---GKKVITQEQYSEVRA 40 (82)
T ss_pred hHHHHHHHHHHHHhhHHHHHHHHH---HCCCCCHHHHHHHHc
Confidence 788999999888864222344444 235667777777664
No 7
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=77.89 E-value=7.3 Score=20.53 Aligned_cols=40 Identities=13% Similarity=0.284 Sum_probs=27.7
Q ss_pred HHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 32 DYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 32 ~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
.+++.|+..+.+++......+..++ ..+.-|+++.++++.
T Consensus 9 ~~L~~~R~~Lv~~l~~v~~ilD~Ll---~~~Vlt~ee~e~I~~ 48 (94)
T cd08329 9 SLIRKNRMALFQHLTSVLPILDSLL---SANVITEQEYDVIKQ 48 (94)
T ss_pred HHHHHhHHHHHHHHhhhHHHHHHHH---HcCCCCHHHHHHHHc
Confidence 6789999999999862222455555 345777788777764
No 8
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=76.39 E-value=7.6 Score=19.45 Aligned_cols=40 Identities=18% Similarity=0.406 Sum_probs=26.9
Q ss_pred HHHHHHhHHHHHHHhC-CCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 31 WDYVKKNWDYLLKRFG-LNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 31 ~~f~~~n~~~i~~~~~-~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
|+.+..|+..+.+.+. .. ..+..++ ...+-|.++.+++..
T Consensus 1 ~~~L~~~r~~Lv~~l~~~~-~ild~L~---~~~vlt~~e~e~I~~ 41 (85)
T PF00619_consen 1 QELLRKNRQELVEDLDDLD-DILDHLL---SRGVLTEEEYEEIRS 41 (85)
T ss_dssp HHHHHHTHHHHHHHSSHHH-HHHHHHH---HTTSSSHHHHHHHHT
T ss_pred CHHHHHhHHHHHHHhCcHH-HHHHHHH---HCCCCCHHHHHHHHc
Confidence 6778889999888887 32 2344443 346777788777765
No 9
>PF06685 DUF1186: Protein of unknown function (DUF1186); InterPro: IPR010602 This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown.
Probab=70.13 E-value=24 Score=22.11 Aligned_cols=65 Identities=18% Similarity=0.373 Sum_probs=44.8
Q ss_pred HHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhhcC
Q psy13041 13 YFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 13 ~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~~~ 80 (81)
+..+...+..+|..|+.+.+|+.+=++...++-+ ++..+.+|..+. -++-.+-+.++++-|+.+.
T Consensus 134 ~~aL~~l~~~~~~~Re~vi~~f~~ll~~~l~~~~--~~~~~~Lv~~~~-dL~~~EL~~~I~~~f~~~l 198 (249)
T PF06685_consen 134 ISALAFLVHEGPISREEVIQYFRELLNYFLERNP--SFLWGSLVADIC-DLYPEELLPEIRKAFEDGL 198 (249)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHhccCc--hHHHHHHHHHHH-hcCHHHhHHHHHHHHHcCC
Confidence 3333444568889999999998887766444433 245677776654 6777888888988887664
No 10
>PF15572 Imm26: Immunity protein 26
Probab=63.39 E-value=4.9 Score=21.48 Aligned_cols=18 Identities=17% Similarity=0.586 Sum_probs=13.3
Q ss_pred CchHHHHHHHHHHhHHHH
Q psy13041 24 PKGLPVAWDYVKKNWDYL 41 (81)
Q Consensus 24 ~~~~~~~~~f~~~n~~~i 41 (81)
..++.+.-+|+++||++.
T Consensus 67 ~~~~aiSt~Wli~NW~kw 84 (96)
T PF15572_consen 67 KEGRAISTEWLIENWEKW 84 (96)
T ss_pred cccccccHHHHHHHHHHh
Confidence 344466679999999874
No 11
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=62.76 E-value=22 Score=19.06 Aligned_cols=44 Identities=14% Similarity=0.226 Sum_probs=27.3
Q ss_pred HHHHHhHHHHHHHhCCCchhhhchHHHhhcc-cCCHHHHHHHHHHHh
Q psy13041 32 DYVKKNWDYLLKRFGLNHRVFGRIIPSVCGK-FTTQERLDEVSEKSL 77 (81)
Q Consensus 32 ~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~-~~t~~~~~~~~~f~~ 77 (81)
+|...-...+..++-++ ....++..+... -.|+++++++++.++
T Consensus 70 e~~~~~~~~~l~~~~~g--s~~~l~~~l~~~~~ls~~el~~L~~li~ 114 (115)
T PF03965_consen 70 EYLAQELRQFLDRLFDG--SIPQLVAALVESEELSPEELEELRKLID 114 (115)
T ss_dssp HHHHHHHHHHHHHHSTT--HHHHHHHHHHHCT-S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCC--CHHHHHHHHHhcCCCCHHHHHHHHHHHc
Confidence 45555555566655543 466666665543 678899999998875
No 12
>PF05596 Taeniidae_ag: Taeniidae antigen; InterPro: IPR008860 This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species.
Probab=60.13 E-value=7.1 Score=19.26 Aligned_cols=17 Identities=18% Similarity=0.263 Sum_probs=13.1
Q ss_pred CHHHHHHHHHHHhhcCC
Q psy13041 65 TQERLDEVSEKSLKNLL 81 (81)
Q Consensus 65 t~~~~~~~~~f~~~~~~ 81 (81)
+...++++..||...|+
T Consensus 12 ~kK~i~~v~~FF~~DPl 28 (64)
T PF05596_consen 12 VKKWIEEVRNFFYEDPL 28 (64)
T ss_pred HHHHHHHHHHHhccCch
Confidence 34678889999988774
No 13
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=56.79 E-value=15 Score=17.68 Aligned_cols=18 Identities=17% Similarity=-0.023 Sum_probs=14.0
Q ss_pred cCCHHHHHHHHHHHhhcC
Q psy13041 63 FTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 63 ~~t~~~~~~~~~f~~~~~ 80 (81)
.-|.++++++++||+..+
T Consensus 7 ~Ft~~Q~~~Le~~fe~~~ 24 (58)
T TIGR01565 7 KFTAEQKEKMRDFAEKLG 24 (58)
T ss_pred CCCHHHHHHHHHHHHHcC
Confidence 346799999999997653
No 14
>COG3251 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.20 E-value=7.9 Score=19.39 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=18.3
Q ss_pred hcCCchHHHHHHHHHHhHHHHH
Q psy13041 21 AGNPKGLPVAWDYVKKNWDYLL 42 (81)
Q Consensus 21 ~~n~~~~~~~~~f~~~n~~~i~ 42 (81)
.+.+..++...+|+..||..+.
T Consensus 39 v~~~~sr~aCldyve~~Wtdmr 60 (71)
T COG3251 39 VHEPGSREACLDYVEVHWTDMR 60 (71)
T ss_pred ecccccHHHHHHHHHHHhccCC
Confidence 4567888999999999998763
No 15
>PF04320 DUF469: Protein with unknown function (DUF469); InterPro: IPR007416 This entry represents a family of uncharacterised proteins which are predicted to function as phosphotransferases.
Probab=53.00 E-value=18 Score=19.52 Aligned_cols=29 Identities=10% Similarity=-0.145 Sum_probs=22.3
Q ss_pred hhchHHHhhcccCCHHHHHHHHHHHhhcC
Q psy13041 52 FGRIIPSVCGKFTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 52 l~~~i~~~~~~~~t~~~~~~~~~f~~~~~ 80 (81)
+..+|..--..-||+++.+.+++|++.+|
T Consensus 58 ~eG~vc~~~~gs~tee~R~~v~~WL~~~~ 86 (101)
T PF04320_consen 58 WEGFVCLQRYGSCTEEDRAAVEAWLKARP 86 (101)
T ss_pred EeEEEEeccCCCCCHHHHHHHHHHHHhCC
Confidence 44555443446899999999999999887
No 16
>KOG1756|consensus
Probab=50.22 E-value=39 Score=19.07 Aligned_cols=53 Identities=15% Similarity=0.123 Sum_probs=30.9
Q ss_pred hcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHH
Q psy13041 21 AGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVS 73 (81)
Q Consensus 21 ~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~ 73 (81)
++.|+-...+++|+..+.-++......+..-..-....+--.+|+++++..+-
T Consensus 48 ~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL 100 (131)
T KOG1756|consen 48 AGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLL 100 (131)
T ss_pred CCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHh
Confidence 46677778888999888776655544321111111222233578888777653
No 17
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=50.02 E-value=29 Score=18.11 Aligned_cols=17 Identities=12% Similarity=0.391 Sum_probs=9.9
Q ss_pred hhcccCCHHHHHHHHHH
Q psy13041 59 VCGKFTTQERLDEVSEK 75 (81)
Q Consensus 59 ~~~~~~t~~~~~~~~~f 75 (81)
+..-+||+.+++++.+-
T Consensus 22 f~~dL~T~~E~~~l~~R 38 (87)
T PF01371_consen 22 FFEDLCTPDELEALAQR 38 (87)
T ss_dssp HHHHHSSHHHHHHHHHH
T ss_pred HHHHhCCHHHHHHHHHH
Confidence 34456666666666543
No 18
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=48.80 E-value=39 Score=17.57 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=26.1
Q ss_pred HHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 31 WDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 31 ~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
|+-++.|+..+.+.+... ..+..++ ....-|+++.+++.+
T Consensus 2 ~~~L~~~R~~L~~~l~~~-~l~d~L~---q~~VLt~~d~EeI~~ 41 (86)
T cd08785 2 WEALEGMRHRLTRKINPS-RLTPYLR---QCKVLDEQDEEEVLS 41 (86)
T ss_pred HHHHHHHHHHHHHHhhHH-HHHHHHH---hcCCCCHHHHHHHhC
Confidence 677788888887777653 2344444 335777777777765
No 19
>PF13475 DUF4116: Domain of unknown function (DUF4116)
Probab=47.43 E-value=27 Score=15.31 Aligned_cols=35 Identities=26% Similarity=0.227 Sum_probs=23.9
Q ss_pred HHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCC
Q psy13041 14 FTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLN 48 (81)
Q Consensus 14 ~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~ 48 (81)
-.++.++..++.....+-+-++.+.+.+......+
T Consensus 3 e~v~~~v~~~~~~l~~~~~~lk~D~e~vl~av~~~ 37 (49)
T PF13475_consen 3 EFVLEAVKKNGYALQYASEELKNDKEFVLKAVKQN 37 (49)
T ss_pred HHHHHHHHhCCHHHHHhCHHHhCCHHHHHHHHHhC
Confidence 34566677777766666667777887777776643
No 20
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=47.35 E-value=40 Score=17.94 Aligned_cols=38 Identities=11% Similarity=0.219 Sum_probs=18.8
Q ss_pred HhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHH
Q psy13041 36 KNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEK 75 (81)
Q Consensus 36 ~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f 75 (81)
++|+.+...+... ..- ..+..+...++|+++.+.+..-
T Consensus 7 ~~w~~~~~ll~~~-~~~-~~l~~~l~~lLTp~E~~~l~~R 44 (94)
T TIGR01321 7 QAWEAFLKLLKKA-DSE-DDMQLLLELILTRSEREDLGDR 44 (94)
T ss_pred HHHHHHHHHHHHc-CCH-HHHHHHHHHhCCHHHHHHHHHH
Confidence 5566665555431 111 1222334456777777666543
No 21
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=46.52 E-value=51 Score=18.29 Aligned_cols=45 Identities=13% Similarity=0.166 Sum_probs=25.7
Q ss_pred HHHHhHHHHHHHhCCCchhhhchHHHhh-cccCCHHHHHHHHHHHhhc
Q psy13041 33 YVKKNWDYLLKRFGLNHRVFGRIIPSVC-GKFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 33 f~~~n~~~i~~~~~~~~~~l~~~i~~~~-~~~~t~~~~~~~~~f~~~~ 79 (81)
|....-..+..++-++ ....++..+. +.-.+++++++++++++..
T Consensus 72 ~~~~~~~~~~~~~f~g--s~~~ll~~l~~~~~ls~eele~L~~li~~~ 117 (130)
T TIGR02698 72 AVENAAQELFSRICSR--KVGAVIADLIEESPLSQTDIEKLEKLLSEK 117 (130)
T ss_pred HHHHHHHHHHHHHHCC--CHHHHHHHHHhcCCCCHHHHHHHHHHHHhc
Confidence 3344444454444332 2344444443 3457789999999998764
No 22
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=45.76 E-value=30 Score=15.75 Aligned_cols=17 Identities=29% Similarity=0.223 Sum_probs=12.5
Q ss_pred CCHHHHHHHHHHHhhcC
Q psy13041 64 TTQERLDEVSEKSLKNL 80 (81)
Q Consensus 64 ~t~~~~~~~~~f~~~~~ 80 (81)
-|.++++.|+++|..++
T Consensus 7 ~t~~q~~~L~~~f~~~~ 23 (57)
T PF00046_consen 7 FTKEQLKVLEEYFQENP 23 (57)
T ss_dssp SSHHHHHHHHHHHHHSS
T ss_pred CCHHHHHHHHHHHHHhc
Confidence 45788888888887643
No 23
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=45.44 E-value=29 Score=16.47 Aligned_cols=16 Identities=25% Similarity=0.162 Sum_probs=11.8
Q ss_pred cCCHHHHHHHHHHHhh
Q psy13041 63 FTTQERLDEVSEKSLK 78 (81)
Q Consensus 63 ~~t~~~~~~~~~f~~~ 78 (81)
--|+++++++.+|+++
T Consensus 16 ~ft~~El~~i~~FY~S 31 (64)
T PF09832_consen 16 HFTEEELDAILAFYES 31 (64)
T ss_dssp HS-HHHHHHHHHHHHS
T ss_pred HCCHHHHHHHHHHHCC
Confidence 3467889999999864
No 24
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=44.30 E-value=47 Score=17.23 Aligned_cols=37 Identities=14% Similarity=0.192 Sum_probs=20.5
Q ss_pred HHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 34 VKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 34 ~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
++.|+..+.+-+... ..+..++ ..+.-|.++.+++++
T Consensus 3 Lr~~R~~L~~dL~v~-~ild~L~---~~gvlt~~~~e~I~~ 39 (86)
T cd08323 3 LLRHRQALEKDIKTS-YIMDHMI---SDGVLTLDEEEKVKS 39 (86)
T ss_pred HHHHHHHHHHHccHH-HHHHHHH---hcCCCCHHHHHHHHc
Confidence 456666666666532 2445454 234666666666654
No 25
>PRK11702 hypothetical protein; Provisional
Probab=40.83 E-value=21 Score=19.49 Aligned_cols=29 Identities=14% Similarity=-0.155 Sum_probs=21.7
Q ss_pred hhchHHHhhcccCCHHHHHHHHHHHhhcC
Q psy13041 52 FGRIIPSVCGKFTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 52 l~~~i~~~~~~~~t~~~~~~~~~f~~~~~ 80 (81)
+..+|..-...-||+++.+.+++|++.+.
T Consensus 65 ~eG~vc~~~~gs~tEe~R~~V~~WL~~r~ 93 (108)
T PRK11702 65 WEGLICLQKIGKCTEEHRALVKKWLEGRK 93 (108)
T ss_pred EEEEEeecccCCCCHHHHHHHHHHHHhCC
Confidence 44555443346899999999999998764
No 26
>TIGR03765 ICE_PFL_4695 integrating conjugative element protein, PFL_4695 family. This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
Probab=39.99 E-value=65 Score=17.57 Aligned_cols=39 Identities=10% Similarity=0.088 Sum_probs=27.5
Q ss_pred HHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHh
Q psy13041 29 VAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSL 77 (81)
Q Consensus 29 ~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~ 77 (81)
...+|+++|-+.+.++-..+ + .-+..|.+.++++++...
T Consensus 35 ~S~~WL~~~~~~L~~l~AvG------l----VVnV~t~~~l~~Lr~lap 73 (105)
T TIGR03765 35 ASRQWLQQNAAALKSLGAVG------L----VVNVETAAALQRLRALAP 73 (105)
T ss_pred HHHHHHHHHHHHHHHCCCeE------E----EEecCCHHHHHHHHHHcC
Confidence 45589999999997765432 2 235677888888887653
No 27
>PRK01381 Trp operon repressor; Provisional
Probab=37.57 E-value=68 Score=17.29 Aligned_cols=38 Identities=5% Similarity=0.135 Sum_probs=20.6
Q ss_pred HhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHH
Q psy13041 36 KNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEK 75 (81)
Q Consensus 36 ~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f 75 (81)
++|..+...+... ..-. .+..+..-++|+++.+.+..-
T Consensus 7 ~~W~~~v~ll~~a-~~~~-~~~~~l~~llTp~Er~al~~R 44 (99)
T PRK01381 7 QEWQRFVDLLKQA-FEED-LHLPLLTLLLTPDEREALGTR 44 (99)
T ss_pred hhHHHHHHHHHHh-ccHH-HHHHHHHHhCCHHHHHHHHHH
Confidence 5666666665432 1122 223344567888887776644
No 28
>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus
Probab=37.56 E-value=14 Score=17.66 Aligned_cols=37 Identities=14% Similarity=0.343 Sum_probs=27.3
Q ss_pred chHHHHHHHh-hcCCchHHHHHHHHHHhHHHHHHHhCC
Q psy13041 11 QDYFTVIVMV-AGNPKGLPVAWDYVKKNWDYLLKRFGL 47 (81)
Q Consensus 11 qd~~~~~~~~-~~n~~~~~~~~~f~~~n~~~i~~~~~~ 47 (81)
.+...++..+ +++-...--.|+|..+.++.+.++...
T Consensus 9 ~~lI~vFK~~pSr~YD~~Tr~W~F~L~Dy~~L~~~~~~ 46 (55)
T PF07443_consen 9 EELIAVFKQMPSRNYDPKTRKWNFSLEDYSTLMKKVRN 46 (55)
T ss_pred HHHHHHHHcCcccccCccceeeeeeHHHHHHHHHHHhc
Confidence 3456677776 466666667899999999998877653
No 29
>cd08163 MPP_Cdc1 Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain. Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. Cdc1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site
Probab=37.49 E-value=69 Score=19.96 Aligned_cols=23 Identities=22% Similarity=0.585 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhHHHHHHHhCCCc
Q psy13041 27 LPVAWDYVKKNWDYLLKRFGLNH 49 (81)
Q Consensus 27 ~~~~~~f~~~n~~~i~~~~~~~~ 49 (81)
+.++=.|++.||..+...+.++.
T Consensus 26 ~~~~D~ylr~~~~~~~~~l~PD~ 48 (257)
T cd08163 26 EHFVDNYLRRNWRYMQKQLKPDS 48 (257)
T ss_pred HHhhHHHHHHHHHHHHHhcCCCE
Confidence 34445788999999999887753
No 30
>PF10384 Scm3: Centromere protein Scm3; InterPro: IPR018465 The centromere protein Scm3 is a non-histone component of centromeric chromatin that binds to CenH3-H4 histones, which are required for kinetochore assembly. Scm3 is required for Cse4 localisation and is required for its centromeric association [, ]. The histone H3 variant Cse4 replaces conventional histone H3 in centromeric chromatin and helps direct the assembly of the kinetochore. In addition, Scm3 has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for G2/M progression []. Scm3 is required to maintain kinetochore function throughout the cell cycle. Scm3 contains a nuclear export signal (NES). The N-terminal region of Scm3 is well conserved and functions as the CenH3-interacting domain, while the C-terminal region is variable in size and sometimes consists of DNA binding motifs [].; GO: 0005634 nucleus; PDB: 3R45_C 2YFV_C 2L5A_A.
Probab=35.95 E-value=42 Score=16.17 Aligned_cols=16 Identities=19% Similarity=0.779 Sum_probs=13.7
Q ss_pred HHHHHhHHHHHHHhCC
Q psy13041 32 DYVKKNWDYLLKRFGL 47 (81)
Q Consensus 32 ~f~~~n~~~i~~~~~~ 47 (81)
.-|+..|+.|.++|+.
T Consensus 12 ~r~k~~~e~I~~KY~~ 27 (58)
T PF10384_consen 12 QRFKSRWESIIEKYGQ 27 (58)
T ss_dssp HHHHHHHHHHHHHHCS
T ss_pred HHHHHHHHHHHHHhcC
Confidence 4478999999999986
No 31
>PF04691 ApoC-I: Apolipoprotein C-I (ApoC-1); InterPro: IPR006781 Exchangeable apolipoproteins are water-soluble protein components of lipoproteins that solubilise lipids and regulate their metabolism by binding to cell receptors or activating specific enzymes. Apolipoprotein C-I (ApoC-1) is the smallest exchangeable apolipoprotein and transfers among HDL (high density lipoprotein), VLDL (very low-density lipoprotein) and chlylomicrons. ApoC-1 activates lecithin:choline acetyltransferase (LCAT), inhibits cholesteryl ester transfer protein, can inhibit hepatic lipase and phospholipase 2 and can stimulate cell growth. ApoC-1 delays the clearance of beta-VLDL by inhibiting its uptake via the LDL receptor-related pathway []. ApoC-1 has been implicated in hypertriglyceridemia [], and Alzheimer s disease []. ApoC-1 is believed to comprise of two dynamic helices that are stabilised by interhelical interactions and are connected by a short linker region. The minimal folding unit in the lipid-free state of this and other exchangeable apolipoproteins comprises the helix-turn-helix motif formed of four 11-mer sequence repeats.; GO: 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 1ALF_A 1ALE_A 1OPP_A 1IOJ_A 1EZE_A.
Probab=35.50 E-value=60 Score=15.88 Aligned_cols=19 Identities=0% Similarity=0.169 Sum_probs=16.0
Q ss_pred HHHHHHHHhHHHHHHHhCC
Q psy13041 29 VAWDYVKKNWDYLLKRFGL 47 (81)
Q Consensus 29 ~~~~f~~~n~~~i~~~~~~ 47 (81)
-.++||.+.++.+.+++..
T Consensus 41 KTrnWfsEtf~kvKeK~~~ 59 (61)
T PF04691_consen 41 KTRNWFSETFEKVKEKVKE 59 (61)
T ss_dssp CCHHHHHHHHHHHHHHSSS
T ss_pred HHHHHHHHHHHHHHHHhhc
Confidence 3579999999999998864
No 32
>PF05106 Phage_holin_3: Phage holin family (Lysis protein S); InterPro: IPR006481 This entry is represented by the Bacteriophage lambda, GpS. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
Probab=35.11 E-value=75 Score=16.92 Aligned_cols=22 Identities=14% Similarity=0.360 Sum_probs=16.7
Q ss_pred cCCchHHHHHHHHHHhHHHHHH
Q psy13041 22 GNPKGLPVAWDYVKKNWDYLLK 43 (81)
Q Consensus 22 ~n~~~~~~~~~f~~~n~~~i~~ 43 (81)
.+|..-...++|+++||+.+..
T Consensus 3 k~P~~W~~ll~wl~~~~~~~~~ 24 (100)
T PF05106_consen 3 KNPDFWAQLLAWLQSHWPQIYG 24 (100)
T ss_pred CCccHHHHHHHHHHHHHHHHHH
Confidence 4677777888999999976543
No 33
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=33.17 E-value=56 Score=15.64 Aligned_cols=17 Identities=6% Similarity=0.098 Sum_probs=14.2
Q ss_pred cCCHHHHHHHHHHHhhc
Q psy13041 63 FTTQERLDEVSEKSLKN 79 (81)
Q Consensus 63 ~~t~~~~~~~~~f~~~~ 79 (81)
.-|+++++.|-+|+++.
T Consensus 74 ~ls~~e~~~l~ayl~sl 90 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSL 90 (91)
T ss_dssp TSSHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 46789999999999864
No 34
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=33.13 E-value=31 Score=17.28 Aligned_cols=14 Identities=21% Similarity=0.695 Sum_probs=10.1
Q ss_pred CchHHHHHHHHHHh
Q psy13041 24 PKGLPVAWDYVKKN 37 (81)
Q Consensus 24 ~~~~~~~~~f~~~n 37 (81)
+.....+|+|+++|
T Consensus 23 ~ev~~~lw~YIk~n 36 (77)
T smart00151 23 TEIIKRLWEYIKEH 36 (77)
T ss_pred HHHHHHHHHHHHHh
Confidence 34556789999866
No 35
>KOG2959|consensus
Probab=32.49 E-value=1.2e+02 Score=18.58 Aligned_cols=46 Identities=13% Similarity=0.067 Sum_probs=33.1
Q ss_pred HHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhh
Q psy13041 32 DYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLK 78 (81)
Q Consensus 32 ~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~ 78 (81)
.-|......++.+...+...+.+++.. -..|.++.-++.|.+|..-
T Consensus 129 ~eL~~KI~k~y~~k~k~~mdmnrliq~-~keFRNPsiydkLi~FcdI 174 (238)
T KOG2959|consen 129 TELEKKIKKFYKLKAKGIMDMNRLIQD-NKEFRNPSIYDKLIDFCDI 174 (238)
T ss_pred HHHHHHHHHHHHHHhhcchhHHHHHhh-hhhccCcHHHHHHHHHhcc
Confidence 346666777766665443467888865 3579999999999999754
No 36
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=31.97 E-value=25 Score=14.59 Aligned_cols=11 Identities=27% Similarity=0.093 Sum_probs=6.3
Q ss_pred HHHHHHHHhhc
Q psy13041 69 LDEVSEKSLKN 79 (81)
Q Consensus 69 ~~~~~~f~~~~ 79 (81)
.+++++|++.+
T Consensus 19 ~eeir~FL~~~ 29 (30)
T PF08671_consen 19 KEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhC
Confidence 35566666543
No 37
>PF14778 ODR4-like: Olfactory receptor 4-like
Probab=31.28 E-value=37 Score=22.30 Aligned_cols=28 Identities=11% Similarity=0.163 Sum_probs=21.4
Q ss_pred HHHHHHHHhHHHHHHHhCCCchhhhchH
Q psy13041 29 VAWDYVKKNWDYLLKRFGLNHRVFGRII 56 (81)
Q Consensus 29 ~~~~f~~~n~~~i~~~~~~~~~~l~~~i 56 (81)
+=-+|+.+|+..+...++||...++-++
T Consensus 43 id~~WVaeHA~qVsRMLPGGi~VlGifv 70 (362)
T PF14778_consen 43 IDEEWVAEHARQVSRMLPGGISVLGIFV 70 (362)
T ss_pred cCHHHHHHHHHHHHhhCCCCcEEEEEEE
Confidence 4448999999999999999854455443
No 38
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=31.27 E-value=1.1e+02 Score=17.86 Aligned_cols=62 Identities=16% Similarity=0.154 Sum_probs=32.3
Q ss_pred cccchHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhhccc---CCHHHHHHHHHHH
Q psy13041 8 IRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKF---TTQERLDEVSEKS 76 (81)
Q Consensus 8 v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~---~t~~~~~~~~~f~ 76 (81)
|...|...+++++..+|.... |.-+.+-.+. +.....+.-++..+.... .+++++.+.-+.|
T Consensus 37 I~~~el~~ilr~lg~~~s~~e--i~~l~~~~d~-----~~~~idf~~Fl~~ms~~~~~~~~~Eel~~aF~~f 101 (160)
T COG5126 37 IDRNELGKILRSLGFNPSEAE--INKLFEEIDA-----GNETVDFPEFLTVMSVKLKRGDKEEELREAFKLF 101 (160)
T ss_pred CcHHHHHHHHHHcCCCCcHHH--HHHHHHhccC-----CCCccCHHHHHHHHHHHhccCCcHHHHHHHHHHh
Confidence 888888888887766666432 2333333332 223345555554444333 3344444444444
No 39
>PF10859 DUF2660: Protein of unknown function (DUF2660); InterPro: IPR022589 This is a bacterial group of proteins with unknown function found in Rickettsiales.
Probab=31.25 E-value=82 Score=16.17 Aligned_cols=22 Identities=14% Similarity=0.521 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHhHHHHHHHhCC
Q psy13041 26 GLPVAWDYVKKNWDYLLKRFGL 47 (81)
Q Consensus 26 ~~~~~~~f~~~n~~~i~~~~~~ 47 (81)
-.+..|+|+.+=-+.|.++|+.
T Consensus 43 ~iElSWkFLYDiTe~ILnkFsk 64 (86)
T PF10859_consen 43 RIELSWKFLYDITETILNKFSK 64 (86)
T ss_pred HHHHHHHHHHHHHHHHHHhhcH
Confidence 3467888888887888877764
No 40
>PF13864 Enkurin: Calmodulin-binding
Probab=31.01 E-value=87 Score=16.41 Aligned_cols=24 Identities=29% Similarity=0.344 Sum_probs=19.6
Q ss_pred chHHHHHHHHHHhHHHHHHHhCCC
Q psy13041 25 KGLPVAWDYVKKNWDYLLKRFGLN 48 (81)
Q Consensus 25 ~~~~~~~~f~~~n~~~i~~~~~~~ 48 (81)
.-+..+++=++.||+.+...|..-
T Consensus 40 eER~~lL~~Lk~~~~el~~ey~~l 63 (98)
T PF13864_consen 40 EERQELLEGLKKNWDELNKEYQKL 63 (98)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhC
Confidence 446678888999999999998763
No 41
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=30.86 E-value=91 Score=16.55 Aligned_cols=42 Identities=12% Similarity=0.064 Sum_probs=28.1
Q ss_pred HHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHh
Q psy13041 34 VKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSL 77 (81)
Q Consensus 34 ~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~ 77 (81)
+.+.++.+.+....+ ..+...|.. ...|.++.-++.+.+|+.
T Consensus 13 l~~Ki~~fl~lk~~G-~~fN~~L~~-s~~frNP~i~ekLi~~~~ 54 (96)
T PF07818_consen 13 LQAKIAKFLELKRQG-IHFNDRLQN-SKSFRNPSILEKLIEFFG 54 (96)
T ss_pred HHHHHHHHHHHHHcC-CCHHHHHHH-ccccCChHHHHHHHHHcC
Confidence 445555555554433 457666655 357999999999999875
No 42
>PF08203 RNA_polI_A14: Yeast RNA polymerase I subunit RPA14; InterPro: IPR013239 Saccharomyces cerevisiae RNA polymerase I (Pol I) is a complex consisting of 14 subunits. Subunit RPA14 forms part of a Pol I subcomplex consisting of RPA14 and and RPA43. The RPA14 and RPA43 heterodimer is proposed to play a role in the recruitment of Pol I to the promoter []. ; PDB: 2RF4_F.
Probab=30.53 E-value=54 Score=16.77 Aligned_cols=16 Identities=6% Similarity=-0.076 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHhhcCC
Q psy13041 66 QERLDEVSEKSLKNLL 81 (81)
Q Consensus 66 ~~~~~~~~~f~~~~~~ 81 (81)
-.++++++..|+..||
T Consensus 58 LSQLKRiQRdlrGLPP 73 (76)
T PF08203_consen 58 LSQLKRIQRDLRGLPP 73 (76)
T ss_dssp HHHHHHHHHHHHHS--
T ss_pred HHHHHHHHHhhCCCCC
Confidence 5788999999998876
No 43
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=30.52 E-value=59 Score=14.34 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=16.5
Q ss_pred chHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhC
Q psy13041 11 QDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFG 46 (81)
Q Consensus 11 qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~ 46 (81)
+|-..++.++...+.+ ||+.|...++
T Consensus 7 eE~~~l~~~v~~~g~~----------~W~~Ia~~~~ 32 (48)
T PF00249_consen 7 EEDEKLLEAVKKYGKD----------NWKKIAKRMP 32 (48)
T ss_dssp HHHHHHHHHHHHSTTT----------HHHHHHHHHS
T ss_pred HHHHHHHHHHHHhCCc----------HHHHHHHHcC
Confidence 4444555555433333 8999998888
No 44
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=30.45 E-value=36 Score=17.00 Aligned_cols=13 Identities=31% Similarity=0.772 Sum_probs=8.8
Q ss_pred chHHHHHHHHHHh
Q psy13041 25 KGLPVAWDYVKKN 37 (81)
Q Consensus 25 ~~~~~~~~f~~~n 37 (81)
......|+|+++|
T Consensus 24 ~v~~~lw~YIk~~ 36 (76)
T PF02201_consen 24 EVVKRLWQYIKEN 36 (76)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHh
Confidence 3445778888765
No 45
>PF11894 DUF3414: Protein of unknown function (DUF3414); InterPro: IPR021827 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 764 to 2011 amino acids in length. This protein has a conserved LLG sequence motif.
Probab=29.80 E-value=1.5e+02 Score=23.90 Aligned_cols=26 Identities=15% Similarity=0.503 Sum_probs=22.1
Q ss_pred HHHHHHHhhcCCchHHHHHHHHHHhH
Q psy13041 13 YFTVIVMVAGNPKGLPVAWDYVKKNW 38 (81)
Q Consensus 13 ~~~~~~~~~~n~~~~~~~~~f~~~n~ 38 (81)
+..++.+++.++.+...+|+|+.+|-
T Consensus 499 f~~ML~sLs~g~~~A~~a~~~L~~~~ 524 (1691)
T PF11894_consen 499 FLEMLASLSSGPECASAAFNFLKDNS 524 (1691)
T ss_pred HHHHHHHHcCChHHHHHHHHHHhhcc
Confidence 34567889999999999999999876
No 46
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=29.36 E-value=60 Score=19.11 Aligned_cols=14 Identities=7% Similarity=0.060 Sum_probs=10.9
Q ss_pred HHHHHHHHHhHHHH
Q psy13041 28 PVAWDYVKKNWDYL 41 (81)
Q Consensus 28 ~~~~~f~~~n~~~i 41 (81)
..+.+++.+||+.|
T Consensus 181 ~~~~~~LI~~~~~i 194 (195)
T cd04404 181 NTFTKFLLDHQDEI 194 (195)
T ss_pred HHHHHHHHHhHHhh
Confidence 45778889998875
No 47
>PF11637 UvsW: ATP-dependant DNA helicase UvsW; InterPro: IPR020975 This entry represents the DNA helicase UvsW from Enterobacteria phage T4. The protein is a member of the monomeric SF2 helicase superfamily and shows structural homology to the eukaryotic SF2 helicase Rad54. UvsW is thought to have a role in recombination and the rescue of stalled replication forks []. ; PDB: 2JPN_A.
Probab=29.12 E-value=71 Score=15.15 Aligned_cols=18 Identities=22% Similarity=0.239 Sum_probs=12.8
Q ss_pred ccCCHHHHHHHHHHHhhc
Q psy13041 62 KFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 62 ~~~t~~~~~~~~~f~~~~ 79 (81)
...|.+-++|+++|.+.+
T Consensus 3 sC~T~~Gl~ELEkyY~kR 20 (54)
T PF11637_consen 3 SCQTLDGLEELEKYYKKR 20 (54)
T ss_dssp T--SHHHHHHHHHHHHHH
T ss_pred cccccccHHHHHHHHHHh
Confidence 456788899999998653
No 48
>COG5448 Uncharacterized conserved protein [Function unknown]
Probab=28.83 E-value=68 Score=18.92 Aligned_cols=20 Identities=15% Similarity=-0.019 Sum_probs=16.2
Q ss_pred hcccCCHHHHHHHHHHHhhc
Q psy13041 60 CGKFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 60 ~~~~~t~~~~~~~~~f~~~~ 79 (81)
.....+..+++|+-+||+.+
T Consensus 25 ~ta~rsl~el~evlaFFeAR 44 (184)
T COG5448 25 GTARRSLDELEEVLAFFEAR 44 (184)
T ss_pred ccCcccHHHHHHHHHHHHHh
Confidence 45677788999999999864
No 49
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=28.79 E-value=66 Score=14.34 Aligned_cols=16 Identities=38% Similarity=0.470 Sum_probs=10.5
Q ss_pred CCHHHHHHHHHHHhhc
Q psy13041 64 TTQERLDEVSEKSLKN 79 (81)
Q Consensus 64 ~t~~~~~~~~~f~~~~ 79 (81)
-+++++..+++.|..+
T Consensus 7 ~~~~~~~~L~~~f~~~ 22 (56)
T smart00389 7 FTPEQLEELEKEFQKN 22 (56)
T ss_pred CCHHHHHHHHHHHHhC
Confidence 3566777777777654
No 50
>PF08687 ASD2: Apx/Shroom domain ASD2; InterPro: IPR014799 Cell shape changes require the coordination of actin and microtubule cytoskeletons. The Shroom family is a small group of related proteins that are defined by sequence similarity and in most cases by some link to the actin cytoskeleton. The Shroom (Shrm) protein family is found only in animals. Proteins of this family are predicted to be utilised in multiple morphogenic and developmental processes across animal phyla to regulate cells shape or intracellular architecture in an actin and myosin-dependent manner []. While the founding member of the Shrm family is Shrm1 (formerly Apx), it appears that this protein is found only in Xenopus []. In mice and humans, the Shrm family of proteins consists of: Shrm2 (formerly Apxl), a protein involved in the morphogenesis, maintenance, and/or function of vascular endothelial cells. Shrm3 (formerly Shroom), a protein necessary for neural tube closure in vertebrate development as deficiency in Shrm results in spina bifida. Shrm3 is also conserved in some invertebrates, as orthologues can be found in sea urchins. Shrm4, a regulator of cyto-skeletal architecture that may play an important role in vertebrate development. It is implicated in X-linked mental retardation in humans. This protein family is based on the conservation of a specific arrangement of an N-terminal PDZ domain, a centrally positioned sequence motif termed ASD1 (Apx/Shrm Domain 1) and a C-terminal motif termed ASD2 [, , ]. Shrm2 and Shrm3 contain all three domains, while Shrm4 contains the PDZ and ASD2 domains, but lacks a discernible ASD1 element. To date, the ASD1 and ASD2 elements have only been found in Shrm-related proteins and do not appear in combination with other conserved domains. ASD1 is required for targeting actin, while ASD2 is capable of eliciting an actomyosin based constriction event [, ]. ASD2 is the most highly conserved sequence element shared by Shrm1, Shrm2, Shrm3, and Shrm4. It possesses a well conserved series of leucine residues that exhibit spacing consistent with that of a leucine zipper motif []. Shroom2 is both necessary and sufficient to govern the localization of pigment granules at the apical surface of epithelial cells. Shroom2 is a central regulator of RPE pigmentation. Despite their diverse biological roles, Shroom family proteins share a common activity. Since the locus encoding human SHROOM2 lies within the critical region for two distinct forms of ocular albinism, it is possible that SHROOM2 mutations may contribute to human visual system disorders [].; GO: 0000902 cell morphogenesis, 0005737 cytoplasm; PDB: 3THF_B.
Probab=28.50 E-value=1.1e+02 Score=19.52 Aligned_cols=27 Identities=11% Similarity=0.274 Sum_probs=21.1
Q ss_pred hhchHHHhhcccCCHHHHHHHHHHHhh
Q psy13041 52 FGRIIPSVCGKFTTQERLDEVSEKSLK 78 (81)
Q Consensus 52 l~~~i~~~~~~~~t~~~~~~~~~f~~~ 78 (81)
-.+.|..+...+-+++++.+...|++.
T Consensus 209 Re~~v~~iL~~~L~~eq~~dy~~fv~m 235 (264)
T PF08687_consen 209 RERVVSEILARYLSEEQLADYRHFVKM 235 (264)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 446777777888899999999999864
No 51
>PF06240 COXG: Carbon monoxide dehydrogenase subunit G (CoxG); InterPro: IPR010419 The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source [].; PDB: 2NS9_A 2PCS_A.
Probab=27.62 E-value=1e+02 Score=17.03 Aligned_cols=23 Identities=13% Similarity=0.276 Sum_probs=15.5
Q ss_pred CchHHHHHHHHHHhHHHHHHHhCC
Q psy13041 24 PKGLPVAWDYVKKNWDYLLKRFGL 47 (81)
Q Consensus 24 ~~~~~~~~~f~~~n~~~i~~~~~~ 47 (81)
|...+.+|+|| .|.+.+..-+++
T Consensus 6 ~a~~~~vw~~l-~D~~~l~~ciPG 28 (140)
T PF06240_consen 6 PAPPEKVWAFL-SDPENLARCIPG 28 (140)
T ss_dssp CS-HHHHHHHH-T-HHHHHHHSTT
T ss_pred cCCHHHHHHHh-cCHHHHHhhCCC
Confidence 45678899987 678877776665
No 52
>PF07349 DUF1478: Protein of unknown function (DUF1478); InterPro: IPR009949 This family consists of several hypothetical Sapovirus VP3 proteins of around 165 residues in length. The function of this family is unknown.
Probab=27.26 E-value=36 Score=19.72 Aligned_cols=19 Identities=26% Similarity=0.740 Sum_probs=15.1
Q ss_pred HHHhhcCCchHHHHHHHHH
Q psy13041 17 IVMVAGNPKGLPVAWDYVK 35 (81)
Q Consensus 17 ~~~~~~n~~~~~~~~~f~~ 35 (81)
+--+..||-|..-||+|+.
T Consensus 31 l~lI~nNpmgp~nAW~WLL 49 (162)
T PF07349_consen 31 LLLIRNNPMGPHNAWSWLL 49 (162)
T ss_pred hhhhhcCCCCCchHHHHhc
Confidence 3445689999999999974
No 53
>PF11256 DUF3055: Protein of unknown function (DUF3055); InterPro: IPR021415 This family of proteins with unknown function appear to be restricted to Firmicutes.
Probab=27.14 E-value=69 Score=16.61 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=12.0
Q ss_pred CHHHHHHHHHHHhh
Q psy13041 65 TQERLDEVSEKSLK 78 (81)
Q Consensus 65 t~~~~~~~~~f~~~ 78 (81)
++++.+++.+|+..
T Consensus 67 ~~eea~eL~~fl~~ 80 (81)
T PF11256_consen 67 SEEEAEELREFLYE 80 (81)
T ss_pred CHHHHHHHHHHHhh
Confidence 78999999999863
No 54
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=26.86 E-value=56 Score=12.85 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=4.7
Q ss_pred HHHHHHHH
Q psy13041 29 VAWDYVKK 36 (81)
Q Consensus 29 ~~~~f~~~ 36 (81)
.+++||.+
T Consensus 6 lI~~YL~~ 13 (27)
T PF08513_consen 6 LIYDYLVE 13 (27)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 45666654
No 55
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=26.77 E-value=1.2e+02 Score=20.19 Aligned_cols=49 Identities=14% Similarity=0.174 Sum_probs=32.8
Q ss_pred cchHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCchhhhchHHHhh
Q psy13041 10 SQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVC 60 (81)
Q Consensus 10 ~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~ 60 (81)
..++......+..+.......|..+.+++..+...+|+ +.-..++++..
T Consensus 107 ~~~m~~f~~dL~~G~~qkhP~l~~v~~~l~~~lr~fGp--F~s~~IikSTL 155 (357)
T cd00686 107 YPTMVNYFDDLQAGREQAHPWWALVNEHFPNVLRHFGP--FCSLNLIRSTL 155 (357)
T ss_pred chHHHHHHHHHhcCCCCCCcHHHHHHHHHHHHHHHhhh--hhHHHHHHHHH
Confidence 34555666666555566667899999999999998886 33344444443
No 56
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=26.70 E-value=75 Score=14.24 Aligned_cols=17 Identities=35% Similarity=0.374 Sum_probs=10.5
Q ss_pred CCHHHHHHHHHHHhhcC
Q psy13041 64 TTQERLDEVSEKSLKNL 80 (81)
Q Consensus 64 ~t~~~~~~~~~f~~~~~ 80 (81)
.++++.+.++++|..++
T Consensus 7 ~~~~~~~~Le~~f~~~~ 23 (59)
T cd00086 7 FTPEQLEELEKEFEKNP 23 (59)
T ss_pred CCHHHHHHHHHHHHhCC
Confidence 34566677777776543
No 57
>PRK00944 hypothetical protein; Provisional
Probab=26.46 E-value=22 Score=21.35 Aligned_cols=29 Identities=14% Similarity=0.311 Sum_probs=20.7
Q ss_pred hHHHHHHHHHHhHHHHHHHhCCCchhhhch
Q psy13041 26 GLPVAWDYVKKNWDYLLKRFGLNHRVFGRI 55 (81)
Q Consensus 26 ~~~~~~~f~~~n~~~i~~~~~~~~~~l~~~ 55 (81)
..+.+|+ +.||-+.+.+||...+.++++.
T Consensus 98 ~iE~aWE-i~ENsp~II~RYR~aTisldY~ 126 (195)
T PRK00944 98 LIESAWE-LLENSPLIIERYRAATISLDYY 126 (195)
T ss_pred HHhhhhH-hhcCCHHHHHHHHHhhhhcccc
Confidence 3467888 5699999999998654444433
No 58
>PF10755 DUF2585: Protein of unknown function (DUF2585); InterPro: IPR019691 This family is conserved in Proteobacteria. The function is not known, but it is thought to be a transmembrane protein. ; GO: 0005886 plasma membrane
Probab=25.97 E-value=22 Score=20.87 Aligned_cols=27 Identities=15% Similarity=0.428 Sum_probs=19.1
Q ss_pred hHHHHHHHHHHhHHHHHHHhCCCchhhh
Q psy13041 26 GLPVAWDYVKKNWDYLLKRFGLNHRVFG 53 (81)
Q Consensus 26 ~~~~~~~f~~~n~~~i~~~~~~~~~~l~ 53 (81)
..+.+|+. .||-+.+.+||...+..++
T Consensus 69 ~iEa~WEi-~ENsp~II~rYR~~Tia~~ 95 (165)
T PF10755_consen 69 LIEAAWEI-VENSPFIIERYRAATIALD 95 (165)
T ss_pred Hhhhhhhh-hhCCHHHHHHHHHhhhccc
Confidence 34568994 5999999999876543333
No 59
>PF05338 DUF717: Protein of unknown function (DUF717); InterPro: IPR008002 This entry is represented by the Human herpesvirus 8, Orf30 protein; it is a family of uncharacterised viral proteins.
Probab=25.93 E-value=74 Score=15.22 Aligned_cols=14 Identities=7% Similarity=0.138 Sum_probs=11.3
Q ss_pred CHHHHHHHHHHHhh
Q psy13041 65 TQERLDEVSEKSLK 78 (81)
Q Consensus 65 t~~~~~~~~~f~~~ 78 (81)
+++++++-.+||+.
T Consensus 3 se~Df~eC~~FF~r 16 (55)
T PF05338_consen 3 SENDFEECLKFFSR 16 (55)
T ss_pred cHHHHHHHHHHHcC
Confidence 57888888899864
No 60
>PLN02620 indole-3-acetic acid-amido synthetase
Probab=25.83 E-value=1.5e+02 Score=21.39 Aligned_cols=22 Identities=18% Similarity=0.431 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhHHHHHHHhCCC
Q psy13041 27 LPVAWDYVKKNWDYLLKRFGLN 48 (81)
Q Consensus 27 ~~~~~~f~~~n~~~i~~~~~~~ 48 (81)
.-.+++|+.+||+.+..-+..+
T Consensus 236 ll~a~~~Le~~w~~L~~DI~~G 257 (612)
T PLN02620 236 FIRAIRFLEKHWTLLCRDIRTG 257 (612)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC
Confidence 5567899999999998877765
No 61
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=25.81 E-value=78 Score=16.43 Aligned_cols=14 Identities=0% Similarity=0.314 Sum_probs=11.2
Q ss_pred HHHHHHHHHhHHHH
Q psy13041 28 PVAWDYVKKNWDYL 41 (81)
Q Consensus 28 ~~~~~f~~~n~~~i 41 (81)
..+.+||.+||..|
T Consensus 77 ~~~~~fl~~~f~eI 90 (91)
T PF05595_consen 77 KKMKEFLEEHFEEI 90 (91)
T ss_pred HHHHHHHHHhHHhh
Confidence 46778999999876
No 62
>COG3543 Uncharacterized conserved protein [Function unknown]
Probab=25.51 E-value=70 Score=18.19 Aligned_cols=16 Identities=19% Similarity=0.376 Sum_probs=13.4
Q ss_pred HHHhHHHHHHHhCCCc
Q psy13041 34 VKKNWDYLLKRFGLNH 49 (81)
Q Consensus 34 ~~~n~~~i~~~~~~~~ 49 (81)
|.+|+++|..++..+.
T Consensus 25 FveN~d~I~~rL~~ge 40 (135)
T COG3543 25 FVENYDAIAERLKAGE 40 (135)
T ss_pred HHHHHHHHHHHhhcCC
Confidence 4699999999998753
No 63
>PF09499 RE_ApaLI: ApaLI-like restriction endonuclease; InterPro: IPR019036 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognises and cleaves the sequence GTGCAC.
Probab=25.00 E-value=78 Score=19.04 Aligned_cols=30 Identities=40% Similarity=0.416 Sum_probs=19.8
Q ss_pred cccchH-HHHHHHhhcCCchHHHHHHHHHHh
Q psy13041 8 IRSQDY-FTVIVMVAGNPKGLPVAWDYVKKN 37 (81)
Q Consensus 8 v~~qd~-~~~~~~~~~n~~~~~~~~~f~~~n 37 (81)
+|.|.. ..+..++.+.-...+.||+|+++.
T Consensus 159 ~~iq~~L~tlY~gvgG~yY~Gd~AW~y~~~~ 189 (191)
T PF09499_consen 159 IRIQTTLKTLYNGVGGEYYYGDAAWEYVKKE 189 (191)
T ss_pred HHHHHHHHHHHHhcCceEeccHHHHHHHHHh
Confidence 444443 344566766667888999998764
No 64
>PF05484 LRV_FeS: LRV protein FeS4 cluster; InterPro: IPR008665 This iron sulphur cluster is found at the N terminus of some proteins containing leucine-repeat variant (LRV) repeats (IPR004830 from INTERPRO). These proteins have a two-domain structure, composed of a small N-terminal domain containing a cluster of four Cys residues that houses the 4Fe:4S cluster, and a larger C-terminal domain containing the LRV repeats []. Biochemical studies revealed that the 4Fe:4S cluster is sensitive to oxygen, but does not appear to have reversible redox activity.; PDB: 1LRV_A.
Probab=24.90 E-value=59 Score=15.68 Aligned_cols=14 Identities=7% Similarity=-0.206 Sum_probs=9.2
Q ss_pred HHHHHHHHHHhhcC
Q psy13041 67 ERLDEVSEKSLKNL 80 (81)
Q Consensus 67 ~~~~~~~~f~~~~~ 80 (81)
.....++.||.-||
T Consensus 38 ryaRrIdRFF~~NP 51 (57)
T PF05484_consen 38 RYARRIDRFFRWNP 51 (57)
T ss_dssp S-HHHHHHHHHH-G
T ss_pred hHHHHHHHHHHhCh
Confidence 34577889998776
No 65
>TIGR01592 holin_SPP1 holin, SPP1 family. This model represents one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others.
Probab=24.59 E-value=1.1e+02 Score=15.56 Aligned_cols=28 Identities=21% Similarity=0.253 Sum_probs=15.6
Q ss_pred cccchHHHHHHHhhcCCchHHHHHHHHHHhH
Q psy13041 8 IRSQDYFTVIVMVAGNPKGLPVAWDYVKKNW 38 (81)
Q Consensus 8 v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~ 38 (81)
+...++..++.++ -......|.|.++|+
T Consensus 31 ide~~i~~~v~~v---~t~~~~l~~wwKNN~ 58 (75)
T TIGR01592 31 VDEEGISTVVDAV---FTIGVSLWTWWKNNY 58 (75)
T ss_pred ccHHHHHHHHHHH---HHHHHHHHHHHHcCc
Confidence 3333444444443 244466778888776
No 66
>PHA02692 hypothetical protein; Provisional
Probab=24.58 E-value=47 Score=16.69 Aligned_cols=6 Identities=17% Similarity=0.069 Sum_probs=2.8
Q ss_pred HHHHHH
Q psy13041 71 EVSEKS 76 (81)
Q Consensus 71 ~~~~f~ 76 (81)
++++|.
T Consensus 19 DF~~Fi 24 (70)
T PHA02692 19 DFEEFL 24 (70)
T ss_pred HHHHHH
Confidence 444444
No 67
>PF15186 TEX13: Testis-expressed sequence 13 protein family
Probab=24.46 E-value=89 Score=18.18 Aligned_cols=41 Identities=12% Similarity=0.189 Sum_probs=33.0
Q ss_pred ccccchHHHHHHH-hhcCCchHHHHHHHHHHhHHHHHHHhCC
Q psy13041 7 NIRSQDYFTVIVM-VAGNPKGLPVAWDYVKKNWDYLLKRFGL 47 (81)
Q Consensus 7 ~v~~qd~~~~~~~-~~~n~~~~~~~~~f~~~n~~~i~~~~~~ 47 (81)
+++-.++...++- ++.|..|.+.=..|+-.-|+.|-.++..
T Consensus 8 GFrH~~Vv~FINee~~~n~~GpeFYl~~~S~sW~eVEdkLra 49 (152)
T PF15186_consen 8 GFRHGEVVAFINEEMLRNGGGPEFYLENRSLSWEEVEDKLRA 49 (152)
T ss_pred CccccHHHHHHHHHHHhcCCCchHHHHhccCCHHHHHHHHHH
Confidence 5888888877766 7888889888778888889988887653
No 68
>PF14680 FANCI_HD2: FANCI helical domain 2; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=24.36 E-value=86 Score=19.41 Aligned_cols=36 Identities=19% Similarity=0.250 Sum_probs=28.0
Q ss_pred cccchHHHHHHHhhcCCchHHHHHHHHHHhHHHHHH
Q psy13041 8 IRSQDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLK 43 (81)
Q Consensus 8 v~~qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~ 43 (81)
||..-+..+...+..||.-.+.+++++..|+.....
T Consensus 49 VR~~LY~gl~~~v~~n~~l~~~iLd~L~~hf~~y~~ 84 (234)
T PF14680_consen 49 VRLMLYEGLYDVVTRNPQLAPHILDMLLSHFKQYYE 84 (234)
T ss_dssp HHHHHHHHHHHHHHHSGGGHHHHHHHHHHHHHHHB-
T ss_pred HHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHHHhC
Confidence 555556666777889999999999999999876555
No 69
>PHA02609 uvsW.1 hypothetical protein; Provisional
Probab=24.26 E-value=1.1e+02 Score=15.46 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=18.2
Q ss_pred hhchHHHhhcccCCHHHHHHHHHHHhhc
Q psy13041 52 FGRIIPSVCGKFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 52 l~~~i~~~~~~~~t~~~~~~~~~f~~~~ 79 (81)
+..++.-++ ...|.+-+++++++.+.+
T Consensus 13 Id~Fm~Kia-sC~T~eGl~ELEkyY~kR 39 (76)
T PHA02609 13 IDSFMSKIA-SCQTLEGLEELEKYYKKR 39 (76)
T ss_pred HHHHHHHHh-ccchhhhHHHHHHHHHHH
Confidence 344444443 577889999999987653
No 70
>PHA02819 hypothetical protein; Provisional
Probab=24.24 E-value=50 Score=16.64 Aligned_cols=6 Identities=0% Similarity=0.468 Sum_probs=2.3
Q ss_pred HHHHHH
Q psy13041 66 QERLDE 71 (81)
Q Consensus 66 ~~~~~~ 71 (81)
+++.++
T Consensus 17 DdDFnn 22 (71)
T PHA02819 17 DDDFNN 22 (71)
T ss_pred hhHHHH
Confidence 344333
No 71
>KOG4519|consensus
Probab=24.07 E-value=1.1e+02 Score=20.49 Aligned_cols=52 Identities=15% Similarity=0.224 Sum_probs=35.0
Q ss_pred HHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHhhcCC
Q psy13041 29 VAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSLKNLL 81 (81)
Q Consensus 29 ~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~~~~~ 81 (81)
.+---.++.|+....-+.-. ..+.-++-...+.-+|+.....+++|.+++||
T Consensus 250 l~~~V~k~~W~~~~~~f~LP-~~~~L~mGd~~gGSsTp~mV~kVk~Wq~s~~p 301 (459)
T KOG4519|consen 250 LIGTVLKGKWDNKRTEFSLP-PLMNLFMGDGSGGSSTPSMVGKVKKWQMSDPP 301 (459)
T ss_pred HHHHhhhhhcccccccccCC-ceeeeeeecCCCCCCcHHHHHHHHHHhhcCCh
Confidence 33334567787665544422 23555555667789999999999999988864
No 72
>PF11072 DUF2859: Protein of unknown function (DUF2859); InterPro: IPR021300 This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE.
Probab=23.92 E-value=1.6e+02 Score=16.98 Aligned_cols=38 Identities=11% Similarity=0.197 Sum_probs=27.0
Q ss_pred HHHHHHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHH
Q psy13041 29 VAWDYVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKS 76 (81)
Q Consensus 29 ~~~~f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~ 76 (81)
...+|+++|-+.+.++-..+ + .-+..|.+.++++++..
T Consensus 73 ~S~~WL~~~~~~L~~l~AvG------l----VVNV~t~~~L~~Lr~la 110 (142)
T PF11072_consen 73 LSRQWLQQNAEELKQLGAVG------L----VVNVATEAALQRLRQLA 110 (142)
T ss_pred HHHHHHHHHHHHHHHCCCeE------E----EEecCCHHHHHHHHHHc
Confidence 45589999999987765432 2 23667788888888765
No 73
>TIGR02217 chp_TIGR02217 conserved hypothetical protein TIGR02217. This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes.
Probab=23.06 E-value=84 Score=19.32 Aligned_cols=18 Identities=17% Similarity=0.130 Sum_probs=14.8
Q ss_pred ccCCHHHHHHHHHHHhhc
Q psy13041 62 KFTTQERLDEVSEKSLKN 79 (81)
Q Consensus 62 ~~~t~~~~~~~~~f~~~~ 79 (81)
.+.+.++++++.+||+.+
T Consensus 51 g~rs~~dl~~liaFFeaR 68 (210)
T TIGR02217 51 GLRSNEDLEQVLAFFEAR 68 (210)
T ss_pred ccCCHHHHHHHHHHHHHh
Confidence 566689999999999864
No 74
>PF02993 MCPVI: Minor capsid protein VI; InterPro: IPR004243 This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. Residues at the C-terminal end of the protein may act as a protease cofactor leading to activation of the adenovirus proteinase [].; GO: 0019028 viral capsid; PDB: 1AVP_B.
Probab=22.68 E-value=28 Score=21.73 Aligned_cols=41 Identities=15% Similarity=0.232 Sum_probs=0.0
Q ss_pred hHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHHHHh
Q psy13041 37 NWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSEKSL 77 (81)
Q Consensus 37 n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~f~~ 77 (81)
||..|-..+..+...+++.|...++++.+..-.+++++=++
T Consensus 31 NWgsLwS~is~glkn~Gs~l~n~g~k~wnS~tgq~lrq~Lk 71 (238)
T PF02993_consen 31 NWGSLWSSISSGLKNFGSFLKNYGSKAWNSQTGQQLRQGLK 71 (238)
T ss_dssp -----------------------------------------
T ss_pred ccccchhhhhhhhhhHhHHHHHhhhhhhhhhHHHHHHHHHh
Confidence 44444443333323455556555555555555555554443
No 75
>COG3405 CelA Endoglucanase Y [Carbohydrate transport and metabolism]
Probab=22.67 E-value=1.2e+02 Score=20.02 Aligned_cols=30 Identities=17% Similarity=0.416 Sum_probs=25.2
Q ss_pred chHHHHHHHhhcCCchHHHHHHHHHHhHHH
Q psy13041 11 QDYFTVIVMVAGNPKGLPVAWDYVKKNWDY 40 (81)
Q Consensus 11 qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~ 40 (81)
|-+...+..++.+....+.+|+|-++|-..
T Consensus 58 qsYgM~~Av~addk~~F~rIwnwT~~nL~~ 87 (360)
T COG3405 58 QSYGMFFAVLADDKDAFDRIWNWTQNNLAQ 87 (360)
T ss_pred chhHHHHHHHhCCHHHHHHHHHHHHHHHhh
Confidence 667677777788999999999999999854
No 76
>COG1962 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme metabolism]
Probab=22.63 E-value=51 Score=21.08 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=18.2
Q ss_pred hcCCchHHHHHHHHHHhHHHHHHHhC
Q psy13041 21 AGNPKGLPVAWDYVKKNWDYLLKRFG 46 (81)
Q Consensus 21 ~~n~~~~~~~~~f~~~n~~~i~~~~~ 46 (81)
.+..++...+|+||++-.+.......
T Consensus 227 Gsg~HN~psaWdwlr~~~kk~~e~~~ 252 (313)
T COG1962 227 GSGIHNAPSAWDWLREFKKKLPEAGA 252 (313)
T ss_pred CcccccCchHHHHHHHHHhhCccccc
Confidence 35667788999999877665544433
No 77
>CHL00088 apcB allophycocyanin beta subunit
Probab=22.52 E-value=1e+02 Score=17.97 Aligned_cols=18 Identities=11% Similarity=0.303 Sum_probs=15.4
Q ss_pred cccCCHHHHHHHHHHHhh
Q psy13041 61 GKFTTQERLDEVSEKSLK 78 (81)
Q Consensus 61 ~~~~t~~~~~~~~~f~~~ 78 (81)
.+|-+..+++.++.||+.
T Consensus 16 gRyls~~eL~~l~~~~~~ 33 (161)
T CHL00088 16 GKYLDDNSVEKLRSYFQT 33 (161)
T ss_pred CCCCCHHHHHHHHHHHHH
Confidence 578888999999999874
No 78
>KOG0859|consensus
Probab=22.41 E-value=1.9e+02 Score=17.82 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=23.3
Q ss_pred hcCCchHHHHHHHHHHhHHHHHHHhCCC
Q psy13041 21 AGNPKGLPVAWDYVKKNWDYLLKRFGLN 48 (81)
Q Consensus 21 ~~n~~~~~~~~~f~~~n~~~i~~~~~~~ 48 (81)
+.+..|+.+.+.|+.+=-+++.++||+.
T Consensus 67 adds~gR~ipfaFLe~Ik~~F~k~YG~~ 94 (217)
T KOG0859|consen 67 ADDSAGRQIPFAFLERIKEDFKKRYGGG 94 (217)
T ss_pred EeccccccccHHHHHHHHHHHHHHhccc
Confidence 4567899999999987778999999874
No 79
>cd04386 RhoGAP_nadrin RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.19 E-value=91 Score=18.54 Aligned_cols=15 Identities=7% Similarity=0.200 Sum_probs=11.0
Q ss_pred HHHHHHHHHHhHHHH
Q psy13041 27 LPVAWDYVKKNWDYL 41 (81)
Q Consensus 27 ~~~~~~f~~~n~~~i 41 (81)
...+.+++.+||+.|
T Consensus 184 ~~~iv~~LI~~~~~i 198 (203)
T cd04386 184 VVAIVELIISHADWF 198 (203)
T ss_pred HHHHHHHHHHhHHHh
Confidence 456677888888876
No 80
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=22.14 E-value=1.4e+02 Score=15.68 Aligned_cols=8 Identities=25% Similarity=0.476 Sum_probs=3.0
Q ss_pred hHHHHHHH
Q psy13041 37 NWDYLLKR 44 (81)
Q Consensus 37 n~~~i~~~ 44 (81)
|-+.+.++
T Consensus 6 hRe~LV~r 13 (85)
T cd08324 6 NRELLVTH 13 (85)
T ss_pred HHHHHHHH
Confidence 33333333
No 81
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=22.13 E-value=1.2e+02 Score=18.67 Aligned_cols=30 Identities=17% Similarity=0.150 Sum_probs=23.4
Q ss_pred hhhchHHHhhcccCCHHHHHHHHHHHhhcC
Q psy13041 51 VFGRIIPSVCGKFTTQERLDEVSEKSLKNL 80 (81)
Q Consensus 51 ~l~~~i~~~~~~~~t~~~~~~~~~f~~~~~ 80 (81)
-+..+++.+.+..|+.+-++++.+..+.+.
T Consensus 51 HlrNVLrrlls~qcs~~ii~ell~lm~kn~ 80 (225)
T PHA03074 51 HLRNVLRRLLSNQCSGEIISELLELMNKNQ 80 (225)
T ss_pred eHHHHHHHHHHhHhhHHHHHHHHHHHHHcc
Confidence 467777777778888888888888877654
No 82
>PF02224 Cytidylate_kin: Cytidylate kinase; InterPro: IPR011994 Cytidylate kinase (2.7.4.14 from EC) catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP. ; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase-containing compound metabolic process; PDB: 3R20_A 4DIE_A 3R8C_B 2H92_B 1KDT_A 1KDP_B 2FEO_A 1KDO_B 2CMK_A 1KDR_A ....
Probab=22.08 E-value=1.3e+02 Score=17.53 Aligned_cols=26 Identities=19% Similarity=0.160 Sum_probs=22.2
Q ss_pred cccchHHHHHHHhhcCCchHHHHHHH
Q psy13041 8 IRSQDYFTVIVMVAGNPKGLPVAWDY 33 (81)
Q Consensus 8 v~~qd~~~~~~~~~~n~~~~~~~~~f 33 (81)
++.+++....+.++..|.-+..+.++
T Consensus 30 ir~~eV~~~aS~vA~~~~VR~~l~~~ 55 (157)
T PF02224_consen 30 IRTEEVSKAASKVAAIPEVREALVEI 55 (157)
T ss_dssp GGSHHHHHHHHHHHTSHHHHHHHHHH
T ss_pred hccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 89999999999999999988765554
No 83
>PHA02650 hypothetical protein; Provisional
Probab=21.90 E-value=64 Score=16.67 Aligned_cols=6 Identities=0% Similarity=0.468 Sum_probs=2.2
Q ss_pred HHHHHH
Q psy13041 66 QERLDE 71 (81)
Q Consensus 66 ~~~~~~ 71 (81)
+++.++
T Consensus 17 DdDFnn 22 (81)
T PHA02650 17 DDDFNN 22 (81)
T ss_pred HHHHHH
Confidence 333333
No 84
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=21.86 E-value=1.3e+02 Score=15.21 Aligned_cols=17 Identities=24% Similarity=0.489 Sum_probs=10.1
Q ss_pred HHHHHHHHHhHHHHHHH
Q psy13041 28 PVAWDYVKKNWDYLLKR 44 (81)
Q Consensus 28 ~~~~~f~~~n~~~i~~~ 44 (81)
++.-+|+.+|-..+.++
T Consensus 45 PmLkeWLD~nLP~lVEr 61 (73)
T PF10691_consen 45 PMLKEWLDENLPGLVER 61 (73)
T ss_pred HHHHHHHHhccHHHHHH
Confidence 45556776666655544
No 85
>smart00315 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Probab=21.84 E-value=1.2e+02 Score=15.59 Aligned_cols=18 Identities=11% Similarity=0.339 Sum_probs=11.4
Q ss_pred HhhcCCchHHHHHHHHHH
Q psy13041 19 MVAGNPKGLPVAWDYVKK 36 (81)
Q Consensus 19 ~~~~n~~~~~~~~~f~~~ 36 (81)
.+..+|.++..+.+|+..
T Consensus 4 ~il~d~~~~~~F~~fl~~ 21 (118)
T smart00315 4 SLLSDPIGRLLFREFLES 21 (118)
T ss_pred HHhcChHHHHHHHHHHHH
Confidence 344667777777776664
No 86
>PF04930 FUN14: FUN14 family; InterPro: IPR007014 This is a family of short proteins found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices.
Probab=21.72 E-value=1.2e+02 Score=15.98 Aligned_cols=14 Identities=50% Similarity=0.859 Sum_probs=8.7
Q ss_pred HHHHhHHHHHHHhC
Q psy13041 33 YVKKNWDYLLKRFG 46 (81)
Q Consensus 33 f~~~n~~~i~~~~~ 46 (81)
|+.-||+++.....
T Consensus 42 ~i~Vnw~kl~~~~~ 55 (100)
T PF04930_consen 42 YIKVNWDKLEKDVK 55 (100)
T ss_pred eEEECHHHHHHHHH
Confidence 34567877766654
No 87
>PF07707 BACK: BTB And C-terminal Kelch; InterPro: IPR011705 This domain is found associated with (IPR000210 from INTERPRO) and (IPR006652 from INTERPRO). BTB (broad-complex, tramtrack and bric a brac) is a Kelch related domain, also known as the POZ domain []. BTB proteins are divided into subgroups depending on what domain lies at the C terminus. Despite the divergence in sequences, the BTB fold is highly conserved. BTB-Kelch proteins have Kelch repeats that form a beta-propeller that can interact with actin filaments []. BTB and C-terminal Kelch (BACK) together constitute a novel conserved domain, which is thought to have a possible role in substrate orientation in Cullin3-based E3 ligase complexes. Four domains, namely the BTB domain, a kelch domain, a BACK domain, and an intervening region (IVR) make up the aryl hydrocarbon receptor (AHR); a ligand-activated transcription factor []. This entry represents the domain associated with BTB and Kelch.; PDB: 3HVE_A 2EQX_A 3I3N_A 4AP2_A 4APF_A.
Probab=21.61 E-value=1.2e+02 Score=15.18 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=16.8
Q ss_pred cCCchHHHHHHHHHHhHHHHHH
Q psy13041 22 GNPKGLPVAWDYVKKNWDYLLK 43 (81)
Q Consensus 22 ~n~~~~~~~~~f~~~n~~~i~~ 43 (81)
+-+.-...+++|+..|+..+.+
T Consensus 12 ~~~~L~~~~~~~i~~nf~~v~~ 33 (103)
T PF07707_consen 12 GLEELAEACLRFIAKNFNEVSK 33 (103)
T ss_dssp T-HHHHHHHHHHHHHTHHHHTT
T ss_pred ChHHHHHHHHHHHHHHHHHHcc
Confidence 4456677899999999998753
No 88
>PF11220 DUF3015: Protein of unknown function (DUF3015); InterPro: IPR021383 This bacterial family of proteins has no known function.
Probab=21.38 E-value=1.8e+02 Score=16.76 Aligned_cols=33 Identities=3% Similarity=-0.007 Sum_probs=20.0
Q ss_pred HHHHHHHhh-cCCchHHHHHHHHHHhHHHHHHHh
Q psy13041 13 YFTVIVMVA-GNPKGLPVAWDYVKKNWDYLLKRF 45 (81)
Q Consensus 13 ~~~~~~~~~-~n~~~~~~~~~f~~~n~~~i~~~~ 45 (81)
....+..+. -.+..+..+-..+++||..|...-
T Consensus 85 ~L~ala~llgv~~~d~~~f~~~~q~nF~~if~s~ 118 (144)
T PF11220_consen 85 HLDALAELLGVPAEDRAAFGAVLQENFASIFPSE 118 (144)
T ss_pred hHHHHHHHhCCCHhhHHHHHHHHHHHHHHhcccC
Confidence 334444443 345667777788888888774443
No 89
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=21.33 E-value=1e+02 Score=14.01 Aligned_cols=17 Identities=12% Similarity=0.024 Sum_probs=11.9
Q ss_pred cCCHHHHHHHHHHHhhc
Q psy13041 63 FTTQERLDEVSEKSLKN 79 (81)
Q Consensus 63 ~~t~~~~~~~~~f~~~~ 79 (81)
-.+..+++.++++++.+
T Consensus 23 ~~s~~~L~k~~~wld~r 39 (45)
T PF12123_consen 23 PLSDAELDKFTAWLDER 39 (45)
T ss_dssp ---HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHhc
Confidence 34458999999999865
No 90
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=21.32 E-value=82 Score=12.81 Aligned_cols=6 Identities=33% Similarity=0.490 Sum_probs=2.4
Q ss_pred HHHHHH
Q psy13041 70 DEVSEK 75 (81)
Q Consensus 70 ~~~~~f 75 (81)
+++++|
T Consensus 17 k~Ike~ 22 (28)
T PF12108_consen 17 KEIKEY 22 (28)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 334443
No 91
>PF05939 Phage_min_tail: Phage minor tail protein; InterPro: IPR010265 This entry is represented by Bacteriophage lambda, GpM, the minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.
Probab=21.21 E-value=1.1e+02 Score=16.53 Aligned_cols=17 Identities=6% Similarity=-0.009 Sum_probs=13.2
Q ss_pred CCHHHHHHHHHHHhhcC
Q psy13041 64 TTQERLDEVSEKSLKNL 80 (81)
Q Consensus 64 ~t~~~~~~~~~f~~~~~ 80 (81)
.+.++..++++|++.|.
T Consensus 50 ~~~~~~~~I~~FL~~h~ 66 (109)
T PF05939_consen 50 GTEAEIRAIEAFLDRHG 66 (109)
T ss_pred ECHHHHHHHHHHHHHCC
Confidence 35677888999998763
No 92
>COG3644 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.04 E-value=1.9e+02 Score=17.11 Aligned_cols=36 Identities=14% Similarity=0.338 Sum_probs=23.6
Q ss_pred HHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHH
Q psy13041 34 VKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERL 69 (81)
Q Consensus 34 ~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~ 69 (81)
+-.||+.+...=|+.+..+.++|..--..-..++..
T Consensus 89 LPRHW~WLaAQPGGASvaLRkLve~arRa~~Gpdr~ 124 (194)
T COG3644 89 LPRHWDWLAAQPGGASVALRKLVEEARRAAEGPDRA 124 (194)
T ss_pred cchhHHHHhcCCCcchHHHHHHHHHHHhcccChhHH
Confidence 557888888887776667888886644444444433
No 93
>PF14658 EF-hand_9: EF-hand domain
Probab=20.97 E-value=1.3e+02 Score=14.91 Aligned_cols=26 Identities=12% Similarity=0.193 Sum_probs=15.2
Q ss_pred hhchHHHhhcccCCHHHHHHHHHHHh
Q psy13041 52 FGRIIPSVCGKFTTQERLDEVSEKSL 77 (81)
Q Consensus 52 l~~~i~~~~~~~~t~~~~~~~~~f~~ 77 (81)
+..++..++..-.++++++++.+-+.
T Consensus 20 l~~~Lra~~~~~p~e~~Lq~l~~elD 45 (66)
T PF14658_consen 20 LITYLRAVTGRSPEESELQDLINELD 45 (66)
T ss_pred HHHHHHHHcCCCCcHHHHHHHHHHhC
Confidence 44555666555666666666665543
No 94
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=20.71 E-value=1.5e+02 Score=15.63 Aligned_cols=39 Identities=10% Similarity=0.110 Sum_probs=21.2
Q ss_pred HHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 33 YVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 33 f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
-++.|+..+.+.+.........++ ...+-|.++.+++++
T Consensus 8 ~Lr~~R~~Lv~dl~~~~~v~~~L~---~~gIlT~~~~e~I~a 46 (94)
T cd08327 8 LLRSQRLELSAELLVDGLVIQYLY---QEGILTESHVEEIES 46 (94)
T ss_pred HHHHHHHHHHHHccchHHHHHHHH---hCCCCCHHHHHHHHc
Confidence 366777777776653211233333 234666666666654
No 95
>PF14228 MOR2-PAG1_mid: Cell morphogenesis central region
Probab=20.65 E-value=1.3e+02 Score=23.29 Aligned_cols=28 Identities=18% Similarity=0.373 Sum_probs=24.5
Q ss_pred cchHHHHHHHhhcCCchHHHHHHHHHHh
Q psy13041 10 SQDYFTVIVMVAGNPKGLPVAWDYVKKN 37 (81)
Q Consensus 10 ~qd~~~~~~~~~~n~~~~~~~~~f~~~n 37 (81)
+.++..+|.+++.++....++++|+.+.
T Consensus 681 ~~Eve~lW~~L~~~~~N~~~il~FLi~~ 708 (1120)
T PF14228_consen 681 PNEVEALWIALASNPQNIRVILDFLIEL 708 (1120)
T ss_pred HHHHHHHHHHHhcCcccHHHHHHHHHHH
Confidence 4688899999999999999999999854
No 96
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=20.58 E-value=90 Score=15.86 Aligned_cols=18 Identities=22% Similarity=0.571 Sum_probs=11.2
Q ss_pred HhhcCCchHHHHHHHHHH
Q psy13041 19 MVAGNPKGLPVAWDYVKK 36 (81)
Q Consensus 19 ~~~~n~~~~~~~~~f~~~ 36 (81)
.+..+|.+.....+|+.+
T Consensus 4 ~il~~~~~~~~F~~Fl~~ 21 (118)
T PF00615_consen 4 KILEDPEGLELFKEFLEK 21 (118)
T ss_dssp HHHHSHHHHHHHHHHHHH
T ss_pred HHHCChHHHHHHHHHHhH
Confidence 344566666666676664
No 97
>PF14317 YcxB: YcxB-like protein
Probab=20.51 E-value=82 Score=14.11 Aligned_cols=15 Identities=27% Similarity=0.313 Sum_probs=11.1
Q ss_pred ccCCHHHHHHHHHHHh
Q psy13041 62 KFTTQERLDEVSEKSL 77 (81)
Q Consensus 62 ~~~t~~~~~~~~~f~~ 77 (81)
.+. .++.+++.+|++
T Consensus 48 ~f~-~~e~~~f~~~lk 62 (62)
T PF14317_consen 48 AFS-EEEKEEFREFLK 62 (62)
T ss_pred HCC-HhHHHHHHHHhC
Confidence 455 888888888864
No 98
>PHA00440 host protein H-NS-interacting protein
Probab=20.38 E-value=1.4e+02 Score=16.06 Aligned_cols=43 Identities=7% Similarity=0.131 Sum_probs=26.5
Q ss_pred CCCccccchHHHHHHHhhcCCchHHHH--HHHHHHhHHHHHHHhC
Q psy13041 4 DEKNIRSQDYFTVIVMVAGNPKGLPVA--WDYVKKNWDYLLKRFG 46 (81)
Q Consensus 4 ~~~~v~~qd~~~~~~~~~~n~~~~~~~--~~f~~~n~~~i~~~~~ 46 (81)
+++.+.+.|...+..++.+++.|.-.+ -+=+++.......-++
T Consensus 38 ~GE~~~~~~re~lvqaLT~G~egai~F~~k~giRe~IKe~~~E~~ 82 (98)
T PHA00440 38 AGEEVNPKDKELLVQALTHGPEGAAAFAVRQGIREAIKDMHEEST 82 (98)
T ss_pred CcccCChHHHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHhHhhc
Confidence 345578888888889898777765432 2334455554444444
No 99
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=20.38 E-value=1.5e+02 Score=15.37 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=20.4
Q ss_pred HHHHhHHHHHHHhCCCchhhhchHHHhhcccCCHHHHHHHHH
Q psy13041 33 YVKKNWDYLLKRFGLNHRVFGRIIPSVCGKFTTQERLDEVSE 74 (81)
Q Consensus 33 f~~~n~~~i~~~~~~~~~~l~~~i~~~~~~~~t~~~~~~~~~ 74 (81)
-++.|+..+.+-+... ..+..++ ..+.-|+++.+++++
T Consensus 8 ~L~~~r~~Lv~~l~~~-~v~~~L~---~~gvlt~~~~~~I~~ 45 (90)
T cd08332 8 ALKKNRVKLAKELVLD-ELLIHLL---QKDILTDSMAESIMA 45 (90)
T ss_pred HHHHhHHHHHHHCCHH-HHHHHHH---HcCCCCHHHHHHHHc
Confidence 3667777776666432 2344443 234556666666554
No 100
>PF11004 Kdo_hydroxy: 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase; InterPro: IPR021266 This bacterial family of proteins has no known function.
Probab=20.13 E-value=36 Score=21.82 Aligned_cols=58 Identities=16% Similarity=0.261 Sum_probs=37.5
Q ss_pred chHHHHHHHhhcCCchHHHHHHHHHHhHHHHHHHhCCCc-------hhhhchHHHhhcccCCHHHHHHH
Q psy13041 11 QDYFTVIVMVAGNPKGLPVAWDYVKKNWDYLLKRFGLNH-------RVFGRIIPSVCGKFTTQERLDEV 72 (81)
Q Consensus 11 qd~~~~~~~~~~n~~~~~~~~~f~~~n~~~i~~~~~~~~-------~~l~~~i~~~~~~~~t~~~~~~~ 72 (81)
..+..++..+ ||.|..-+|. +=|.|+.+..+|.+.. ..+-+.+ .++....|+.+--++
T Consensus 140 ~RiLRvF~NI--NP~g~pRvWr-vGEpF~~~a~rflP~~~~~~p~~a~ll~~L-~iTK~~RS~YDh~ML 204 (281)
T PF11004_consen 140 ERILRVFTNI--NPDGEPRVWR-VGEPFEDMARRFLPAIKPPSPGSAWLLHAL-GITKSPRSEYDHLML 204 (281)
T ss_pred ceeeEEeecc--CCCCCCcccc-cCCChHHHHHHhcccCCCCCCchHHHHHHh-CCCcCCCCHHHHHHH
Confidence 3344555555 9999999999 7899999999987521 1122333 455566666654443
No 101
>PHA02975 hypothetical protein; Provisional
Probab=20.13 E-value=70 Score=16.03 Aligned_cols=6 Identities=0% Similarity=0.457 Sum_probs=2.2
Q ss_pred HHHHHH
Q psy13041 66 QERLDE 71 (81)
Q Consensus 66 ~~~~~~ 71 (81)
+++.++
T Consensus 17 DdDF~n 22 (69)
T PHA02975 17 DSDFED 22 (69)
T ss_pred hHHHHH
Confidence 333333
Done!