Query psy4090
Match_columns 112
No_of_seqs 108 out of 275
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 16:37:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5101 CRM1 Importin beta-rel 99.9 5.4E-28 1.2E-32 206.0 8.5 95 11-105 1-95 (1053)
2 KOG2020|consensus 99.8 4.2E-19 9.1E-24 158.1 6.6 94 13-107 1-95 (1041)
3 PF03810 IBN_N: Importin-beta 99.4 3.2E-12 6.9E-17 80.9 7.9 63 44-106 1-73 (77)
4 KOG1410|consensus 99.3 6.7E-12 1.5E-16 108.8 9.4 84 22-106 3-87 (1082)
5 KOG2022|consensus 98.9 7.1E-09 1.5E-13 91.6 9.4 87 21-107 4-91 (982)
6 KOG2021|consensus 98.5 7.5E-07 1.6E-11 78.4 8.5 79 25-103 4-85 (980)
7 KOG2171|consensus 98.2 1.5E-05 3.2E-10 72.3 10.1 85 22-106 2-86 (1075)
8 KOG2081|consensus 97.6 9.7E-05 2.1E-09 63.2 4.8 63 42-104 2-64 (559)
9 KOG1991|consensus 96.7 0.018 3.8E-07 52.4 10.2 85 22-106 2-96 (1010)
10 COG5656 SXM1 Importin, protein 95.9 0.036 7.7E-07 49.7 7.8 79 28-106 4-91 (970)
11 KOG1992|consensus 93.2 0.54 1.2E-05 42.7 8.2 80 26-105 4-94 (960)
12 KOG1241|consensus 92.7 0.54 1.2E-05 42.3 7.4 78 29-106 6-97 (859)
13 KOG2023|consensus 91.0 0.52 1.1E-05 42.2 5.4 83 23-105 12-96 (885)
14 KOG1993|consensus 86.2 1.5 3.4E-05 39.8 5.2 78 29-106 5-88 (978)
15 PF13646 HEAT_2: HEAT repeats; 83.8 3.4 7.3E-05 25.5 4.7 58 23-81 30-87 (88)
16 PF00790 VHS: VHS domain; Int 83.8 10 0.00022 26.5 7.6 20 68-87 53-72 (140)
17 cd00197 VHS_ENTH_ANTH VHS, ENT 83.0 11 0.00025 25.1 8.3 51 22-87 17-67 (115)
18 cd03567 VHS_GGA VHS domain fam 82.7 10 0.00022 27.0 7.4 53 20-87 16-68 (139)
19 smart00288 VHS Domain present 78.7 13 0.00029 25.9 6.7 52 21-87 16-67 (133)
20 cd03568 VHS_STAM VHS domain fa 77.3 15 0.00032 26.2 6.7 52 21-87 16-67 (144)
21 PF10391 DNA_pol_lambd_f: Fing 77.0 1.8 4E-05 26.0 1.6 26 77-103 22-47 (52)
22 PF13646 HEAT_2: HEAT repeats; 76.8 8 0.00017 23.7 4.7 57 26-84 1-58 (88)
23 cd03569 VHS_Hrs_Vps27p VHS dom 71.8 30 0.00065 24.5 7.1 53 20-87 19-71 (142)
24 PF04994 TfoX_C: TfoX C-termin 70.9 10 0.00022 24.5 4.2 28 74-104 53-81 (81)
25 PLN03060 inositol phosphatase- 70.1 21 0.00047 27.3 6.4 59 23-82 72-147 (206)
26 PRK13266 Thf1-like protein; Re 69.3 22 0.00048 27.6 6.4 60 23-83 74-151 (225)
27 COG5657 CSE1 CAS/CSE protein i 68.6 26 0.00057 32.4 7.5 70 35-104 15-90 (947)
28 cd03565 VHS_Tom1 VHS domain fa 68.1 40 0.00086 23.8 7.5 15 22-36 18-32 (141)
29 PF02376 CUT: CUT domain; Int 65.6 21 0.00045 23.5 4.9 50 37-100 26-82 (87)
30 PF12348 CLASP_N: CLASP N term 64.4 52 0.0011 24.0 7.4 64 26-89 96-163 (228)
31 COG1043 LpxA Acyl-[acyl carrie 64.3 13 0.00029 29.4 4.3 48 22-69 209-256 (260)
32 KOG2274|consensus 63.1 23 0.0005 32.9 6.1 75 33-107 13-94 (1005)
33 TIGR03060 PS_II_psb29 photosys 60.8 39 0.00085 26.1 6.3 60 23-83 74-149 (214)
34 smart00337 BCL BCL (B-Cell lym 57.9 52 0.0011 21.7 8.1 54 25-87 15-69 (100)
35 PF11264 ThylakoidFormat: Thyl 54.5 60 0.0013 25.0 6.4 60 23-83 69-146 (216)
36 cd07064 AlkD_like_1 A new stru 52.0 91 0.002 23.2 7.0 72 33-109 20-94 (208)
37 PF07875 Coat_F: Coat F domain 49.4 57 0.0012 19.6 5.1 59 41-111 3-61 (64)
38 PF11698 V-ATPase_H_C: V-ATPas 49.0 30 0.00066 24.2 3.7 30 60-90 90-119 (119)
39 PF01602 Adaptin_N: Adaptin N 49.0 45 0.00097 27.3 5.2 62 26-88 233-298 (526)
40 PF01417 ENTH: ENTH domain; I 48.7 82 0.0018 21.3 8.5 62 22-101 20-82 (125)
41 PRK09687 putative lyase; Provi 48.3 78 0.0017 24.7 6.3 60 25-84 55-118 (280)
42 cd00084 HMG-box High Mobility 46.7 25 0.00055 20.3 2.6 24 80-103 30-53 (66)
43 PF00505 HMG_box: HMG (high mo 46.2 18 0.00039 21.4 2.0 26 80-105 30-55 (69)
44 TIGR03504 FimV_Cterm FimV C-te 44.3 38 0.00082 19.5 3.0 24 24-50 20-43 (44)
45 COG5215 KAP95 Karyopherin (imp 43.4 84 0.0018 28.4 6.2 71 34-105 15-100 (858)
46 KOG1087|consensus 43.3 21 0.00045 30.6 2.5 51 22-87 18-68 (470)
47 PF08578 DUF1765: Protein of u 42.9 59 0.0013 22.3 4.4 51 57-111 50-103 (126)
48 TIGR00865 bcl-2 Apoptosis regu 42.5 1.5E+02 0.0033 22.6 7.8 57 9-65 66-125 (213)
49 PF15581 Imm35: Immunity prote 42.2 18 0.00038 24.4 1.5 18 80-97 34-51 (93)
50 cd05502 Bromo_tif1_like Bromod 42.0 31 0.00068 23.1 2.8 25 38-62 3-27 (109)
51 cd01390 HMGB-UBF_HMG-box HMGB- 41.6 26 0.00056 20.5 2.1 22 80-101 30-51 (66)
52 PF14846 DUF4485: Domain of un 41.4 28 0.00061 22.7 2.4 53 38-95 23-75 (85)
53 smart00398 HMG high mobility g 41.2 28 0.0006 20.4 2.2 23 79-101 30-52 (70)
54 KOG4646|consensus 39.6 68 0.0015 23.8 4.4 39 23-61 15-54 (173)
55 PRK09687 putative lyase; Provi 39.0 1.4E+02 0.003 23.3 6.4 58 25-84 24-81 (280)
56 COG5493 Uncharacterized conser 38.9 45 0.00098 25.8 3.5 31 80-110 102-133 (231)
57 COG2854 Ttg2D ABC-type transpo 37.8 1.1E+02 0.0024 23.4 5.5 56 41-100 34-95 (202)
58 PRK12330 oxaloacetate decarbox 35.2 34 0.00074 29.5 2.6 49 56-104 325-375 (499)
59 PF09372 PRANC: PRANC domain; 34.5 40 0.00086 21.9 2.4 27 79-105 60-88 (97)
60 PLN00047 photosystem II biogen 33.4 2E+02 0.0043 23.2 6.5 58 24-82 126-200 (283)
61 PF08620 RPAP1_C: RPAP1-like, 33.3 59 0.0013 20.9 2.9 24 64-87 46-69 (73)
62 PF13309 HTH_22: HTH domain 33.2 66 0.0014 19.6 3.1 26 86-111 15-40 (64)
63 PF12830 Nipped-B_C: Sister ch 31.8 2E+02 0.0044 20.9 7.4 77 26-102 10-90 (187)
64 cd05500 Bromo_BDF1_2_I Bromodo 30.1 65 0.0014 21.2 2.8 25 38-62 3-27 (103)
65 PF08389 Xpo1: Exportin 1-like 29.8 1.5E+02 0.0032 19.6 4.6 56 52-107 18-79 (148)
66 PF09058 L27_1: L27_1; InterP 29.8 50 0.0011 20.8 2.1 32 23-54 12-44 (64)
67 PRK12581 oxaloacetate decarbox 28.6 49 0.0011 28.3 2.5 37 68-104 348-385 (468)
68 PF13720 Acetyltransf_11: Udp 28.5 1.4E+02 0.003 19.2 4.1 44 22-65 32-75 (83)
69 PF10047 DUF2281: Protein of u 28.2 49 0.0011 20.4 1.9 22 84-105 4-25 (66)
70 PF09011 HMG_box_2: HMG-box do 28.1 42 0.00091 20.6 1.5 21 81-101 35-55 (73)
71 PF08568 Kinetochor_Ybp2: Unch 28.0 3.5E+02 0.0077 23.5 7.7 60 33-93 451-514 (633)
72 cd03562 CID CID (CTD-Interacti 27.4 1.4E+02 0.0031 19.5 4.2 78 23-104 21-103 (114)
73 PTZ00199 high mobility group p 27.1 44 0.00096 21.9 1.6 19 81-99 55-73 (94)
74 PHA02878 ankyrin repeat protei 25.9 71 0.0015 26.2 2.9 29 77-105 431-463 (477)
75 PHA02875 ankyrin repeat protei 25.7 72 0.0016 25.4 2.9 28 78-105 373-403 (413)
76 cd01388 SOX-TCF_HMG-box SOX-TC 25.2 51 0.0011 20.1 1.5 20 80-99 31-50 (72)
77 cd01389 MATA_HMG-box MATA_HMG- 25.0 70 0.0015 19.7 2.2 22 79-100 30-51 (77)
78 KOG4368|consensus 24.9 2E+02 0.0044 25.9 5.5 39 9-48 90-129 (757)
79 COG5016 Pyruvate/oxaloacetate 24.7 46 0.001 28.5 1.6 38 67-104 338-376 (472)
80 PF11626 Rap1_C: TRF2-interact 24.6 2E+02 0.0043 18.4 4.7 43 26-69 11-61 (87)
81 PLN02999 photosystem II oxygen 24.6 1.8E+02 0.0038 22.2 4.5 55 41-105 94-150 (190)
82 PF11304 DUF3106: Protein of u 23.8 48 0.001 22.5 1.3 17 88-104 55-71 (107)
83 PRK13800 putative oxidoreducta 23.8 3.8E+02 0.0083 24.4 7.3 60 22-83 619-678 (897)
84 TIGR03481 HpnM hopanoid biosyn 23.1 2.6E+02 0.0057 20.7 5.3 53 41-100 31-89 (198)
85 KOG1086|consensus 23.1 1.7E+02 0.0037 25.5 4.7 36 20-60 23-62 (594)
86 PF06183 DinI: DinI-like famil 23.1 61 0.0013 20.2 1.6 23 37-59 42-64 (65)
87 PF11864 DUF3384: Domain of un 22.8 1.2E+02 0.0025 25.4 3.7 36 55-90 27-62 (464)
88 PF04826 Arm_2: Armadillo-like 22.7 3.7E+02 0.008 20.8 9.4 42 57-105 55-96 (254)
89 PF13867 SAP30_Sin3_bdg: Sin3 22.5 92 0.002 18.4 2.2 25 81-105 26-50 (53)
90 PF10188 Oscp1: Organic solute 22.1 3.4E+02 0.0074 20.2 5.7 51 58-111 100-150 (173)
91 PRK12331 oxaloacetate decarbox 21.8 80 0.0017 26.7 2.5 50 53-104 326-376 (448)
92 cd05505 Bromo_WSTF_like Bromod 21.0 75 0.0016 21.0 1.8 21 41-61 2-22 (97)
93 PF10508 Proteasom_PSMB: Prote 20.5 5.3E+02 0.011 21.8 8.1 20 91-110 470-490 (503)
94 PRK14041 oxaloacetate decarbox 20.2 71 0.0015 27.2 1.9 49 56-104 321-372 (467)
95 cd03571 ENTH_epsin ENTH domain 20.1 3.1E+02 0.0067 19.0 8.1 53 22-88 18-70 (123)
No 1
>COG5101 CRM1 Importin beta-related nuclear transport receptor [Nuclear structure / Intracellular trafficking and secretion]
Probab=99.95 E-value=5.4e-28 Score=206.02 Aligned_cols=95 Identities=40% Similarity=0.690 Sum_probs=93.3
Q ss_pred HHHhhcccccCCHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhccc
Q psy4090 11 FKKLLDFNQKLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWK 90 (112)
Q Consensus 11 ~~~lld~~~~~dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~ 90 (112)
||.||+|+..+||++||+||+.||+|.|.++++||++|.+||++||||+++++||++|+.|++||.|||+|+++|+++|+
T Consensus 1 MEgIL~fd~dLdiallDkVVttfyqg~g~~q~qAq~iLtkFq~~PdaWtkad~IL~~S~~pqskyiALs~LdklIttkWk 80 (1053)
T COG5101 1 MEGILEFDKDLDIALLDKVVTTFYQGDGRKQEQAQRILTKFQELPDAWTKADYILNNSKLPQSKYIALSLLDKLITTKWK 80 (1053)
T ss_pred CcchhhcccccCHHHHHHHHHHhcCCCchhHHHHHHHHHHHHhCchHHHHHHHHHhcccCcchhhhHHHHHHHHHHhhhh
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHhH
Q psy4090 91 ALPREQCDVKEEKER 105 (112)
Q Consensus 91 ~Lp~eqr~~IRnyv~ 105 (112)
.||+++|.||||||-
T Consensus 81 llp~~~r~GiRnyvv 95 (1053)
T COG5101 81 LLPEGMRQGIRNYVV 95 (1053)
T ss_pred hCCcHHHHHHHHHHH
Confidence 999999999999984
No 2
>KOG2020|consensus
Probab=99.77 E-value=4.2e-19 Score=158.09 Aligned_cols=94 Identities=43% Similarity=0.637 Sum_probs=89.3
Q ss_pred HhhcccccCCHHHHHHHHHHHhC-CChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccC
Q psy4090 13 KLLDFNQKLDITLLDNIVECMYT-GMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKA 91 (112)
Q Consensus 13 ~lld~~~~~dv~~Ld~vv~~~y~-~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~ 91 (112)
+++| ++++|+..||.++..+|. |++.+|.+|+++|.+||+.|++|..|+.||+.|+++.+||||||+||++|+++|+.
T Consensus 1 ~~~~-~~~l~~~lldavv~~~~~~~s~~~r~eA~~~l~~lke~~~~~~~~~~iL~~s~~~~~k~f~Lqlle~vik~~W~~ 79 (1041)
T KOG2020|consen 1 QLLD-DNKLDSELLDAVVVTLNPEGSNEERGEAQQILEELKEEPDSWLQVYLILKLSTNPILKYFALQLLENVIKFRWNS 79 (1041)
T ss_pred CCcc-chhHHHHHHHhHHHHhCcccchHHHHHHHHHHHHHHhCcchHHHHHHHHhccCCchhheeeHHHHHHHHHHhccc
Confidence 3678 899999999999999998 77789999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHhHhh
Q psy4090 92 LPREQCDVKEEKEREQ 107 (112)
Q Consensus 92 Lp~eqr~~IRnyv~~~ 107 (112)
+|.++|.|||+||-+-
T Consensus 80 ~~~~~r~glk~~v~~~ 95 (1041)
T KOG2020|consen 80 LPVEERVGLKNYVLTL 95 (1041)
T ss_pred CCccccHHHHHHHHHH
Confidence 9999999999999763
No 3
>PF03810 IBN_N: Importin-beta N-terminal domain; InterPro: IPR001494 Karyopherins are a group of proteins involved in transporting molecules through the pores of the nuclear envelope. Karyopherins, which may act as importins or exportins, are part of the Importin-beta super-family, which all share a similar three-dimensional structure. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins [, ], which is important for importin-beta mediated transport. Ran GTPase helps to control the unidirectional transfer of cargo. The cytoplasm contains primarily RanGDP and the nucleus RanGTP through the actions of RanGAP and RanGEF, respectively. In the nucleus, RanGTP binds to importin-beta within the importin/cargo complex, causing a conformational change in importin-beta that releases it from importin-alpha-bound cargo. As a result, the N-terminal auto-inhibitory region on importin-alpha is free to loop back and bind to the major NLS-binding site, causing the cargo to be released []. There are additional release factors as well. This entry represents the N-terminal domain of karyopherins that is important for the binding of the Ran protein []. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport; PDB: 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 1IBR_D 1QGR_A 3LWW_A 1F59_A 2Q5D_A ....
Probab=99.38 E-value=3.2e-12 Score=80.87 Aligned_cols=63 Identities=24% Similarity=0.463 Sum_probs=60.0
Q ss_pred HHHHHHHHhcC-CccHHHHHHHh-ccCchHHHHHHHHHHHHHHHhhccc--------CCCHHHHHHHHHHhHh
Q psy4090 44 AQEVLTALKEH-PDAWTRVDTIL-EYSSNQQTKFYALQILEQVIKTRWK--------ALPREQCDVKEEKERE 106 (112)
Q Consensus 44 A~~iL~~fk~~-pdaw~~v~~IL-~~S~~~~tk~fALqiLe~~I~~~W~--------~Lp~eqr~~IRnyv~~ 106 (112)
|++.|.+|+.+ |++|..|..|+ +.+.++++|+||+.+|.+.|+++|+ .+|+++|..||+++.+
T Consensus 1 AE~~L~~~~~~~p~~~~~l~~il~~~~~~~~~R~~A~i~LKn~I~~~W~~~~~~~~~~~~~~~k~~Ik~~ll~ 73 (77)
T PF03810_consen 1 AEQQLKQFQKQNPGFWQYLLQILSSNSQDPEVRQLAAILLKNLIKKNWSPSKQKGWSQLPEEEKEQIKSQLLQ 73 (77)
T ss_dssp HHHHHHHHHHSCTCHHHHHHHHHHCTTSCHHHHHHHHHHHHHHHHHSGGHHHHHHHHGSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhhHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHcCchhhccCCCCCCHHHHHHHHHHHHH
Confidence 78999999999 99999999999 7777999999999999999999999 9999999999999875
No 4
>KOG1410|consensus
Probab=99.33 E-value=6.7e-12 Score=108.75 Aligned_cols=84 Identities=19% Similarity=0.285 Sum_probs=79.3
Q ss_pred CHHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHH
Q psy4090 22 DITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~I 100 (112)
..+.|+.+|..+|.+++. +|.+|++-|.+|.++||+.++|..+|++++.||+.+.|.+.|.+++..+- .||-+||.+|
T Consensus 3 sLaqLe~lCk~LY~s~D~~~R~~AE~~L~e~s~speclskCqlll~~gs~pYs~mlAst~L~Klvs~~t-~lpl~qrldi 81 (1082)
T KOG1410|consen 3 SLAQLESLCKDLYESTDPTARHRAEKALAELSESPECLSKCQLLLERGSYPYSQMLASTCLMKLVSRKT-PLPLEQRLDI 81 (1082)
T ss_pred cHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHccCHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHcCCC-CCcHHHHHHH
Confidence 478999999999999875 79999999999999999999999999999999999999999999998874 7999999999
Q ss_pred HHHhHh
Q psy4090 101 EEKERE 106 (112)
Q Consensus 101 Rnyv~~ 106 (112)
|+|+.+
T Consensus 82 r~Yiln 87 (1082)
T KOG1410|consen 82 RNYILN 87 (1082)
T ss_pred HHHHHH
Confidence 999986
No 5
>KOG2022|consensus
Probab=98.91 E-value=7.1e-09 Score=91.61 Aligned_cols=87 Identities=16% Similarity=0.249 Sum_probs=79.9
Q ss_pred CCHHHHHHHHHHHhCCCh-HHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHH
Q psy4090 21 LDITLLDNIVECMYTGMG-VEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDV 99 (112)
Q Consensus 21 ~dv~~Ld~vv~~~y~~~~-~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~ 99 (112)
-+|..++.++..+|.+.+ +..+.++++|.+.+.+|++|..-+.+|+..+++.++|||..+|+..|++||..+|++++..
T Consensus 4 ~~Ia~v~~~v~~lY~~~~~~~~a~~qk~Lq~aq~S~Q~w~~s~~llQ~~k~~evqyFGAltL~~ki~~~~e~~~~~~~~q 83 (982)
T KOG2022|consen 4 DLIATVEELVTTLYSHRNHENDAITQKWLQDAQCSQQGWHFSWQLLQPDKSSEVQYFGALTLHDKINTRWEECPANEAVQ 83 (982)
T ss_pred hHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHhhHHHHHHHHHHcCCCchhHHHHHhHHHHHHHHHhhhccCChhHHHH
Confidence 378999999999999855 5699999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhHhh
Q psy4090 100 KEEKEREQ 107 (112)
Q Consensus 100 IRnyv~~~ 107 (112)
++-.+.++
T Consensus 84 L~~klf~~ 91 (982)
T KOG2022|consen 84 LKLKLFLI 91 (982)
T ss_pred HHHHHHHH
Confidence 88766543
No 6
>KOG2021|consensus
Probab=98.46 E-value=7.5e-07 Score=78.38 Aligned_cols=79 Identities=22% Similarity=0.372 Sum_probs=68.8
Q ss_pred HHHHHHHHHhCC-Ch-HHHHHHHHHHHHHhcCCccHHHHHHHhccC-chHHHHHHHHHHHHHHHhhcccCCCHHHHHHHH
Q psy4090 25 LLDNIVECMYTG-MG-VEQKAAQEVLTALKEHPDAWTRVDTILEYS-SNQQTKFYALQILEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 25 ~Ld~vv~~~y~~-~~-~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S-~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IR 101 (112)
.++++|.+..+| .+ ..|++|-..+.++|.+|++|.-|-.+|.++ +++.+|||+||+|+++++.+.+..+..+..-||
T Consensus 4 diEqav~a~ndp~vdsa~KqqA~~y~~qiKsSp~aw~Icie~l~~~ts~d~vkf~clqtL~e~vrekyne~nl~elqlvR 83 (980)
T KOG2021|consen 4 DIEQAVNAVNDPRVDSATKQQAIEYLNQIKSSPNAWEICIELLINETSNDLVKFYCLQTLIELVREKYNEANLNELQLVR 83 (980)
T ss_pred HHHHHHHhhCCCcccHHHHHHHHHHHHhhcCCccHHHHHHHHHHhhcccchhhhhhHHHHHHHHHHhhccCCHHHHHHHH
Confidence 578888888888 33 469999999999999999999999999555 999999999999999999999988888866665
Q ss_pred HH
Q psy4090 102 EK 103 (112)
Q Consensus 102 ny 103 (112)
.-
T Consensus 84 ~s 85 (980)
T KOG2021|consen 84 FS 85 (980)
T ss_pred HH
Confidence 43
No 7
>KOG2171|consensus
Probab=98.17 E-value=1.5e-05 Score=72.27 Aligned_cols=85 Identities=19% Similarity=0.277 Sum_probs=77.1
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHH
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IR 101 (112)
|.+.|.+++..+..|++..|++|++.|...--.+..-.....|+..+.+|.+|=+|+-.+.+++++.|+.|+.|.|..||
T Consensus 2 ~~~~l~qLl~~l~spDn~vr~~Ae~~l~~~~~~~~~l~~L~~i~~~~~~p~~Rq~aaVl~Rkl~~~~w~~l~~e~~~sik 81 (1075)
T KOG2171|consen 2 DSAPLEQLLQQLLSPDNEVRRQAEEALETLAKTEPLLPALAHILATSADPQVRQLAAVLLRKLLTKHWSRLSAEVQQSIK 81 (1075)
T ss_pred chhHHHHHHHHhcCCCchHHHHHHHHHHHhhcccchHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Confidence 56789999999999988899999999995544455888889999999999999999999999999999999999999999
Q ss_pred HHhHh
Q psy4090 102 EKERE 106 (112)
Q Consensus 102 nyv~~ 106 (112)
+-+++
T Consensus 82 s~lL~ 86 (1075)
T KOG2171|consen 82 SSLLE 86 (1075)
T ss_pred HHHHH
Confidence 98875
No 8
>KOG2081|consensus
Probab=97.58 E-value=9.7e-05 Score=63.16 Aligned_cols=63 Identities=21% Similarity=0.329 Sum_probs=58.7
Q ss_pred HHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHh
Q psy4090 42 KAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKE 104 (112)
Q Consensus 42 ~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv 104 (112)
.+|.++|..||.++++|..|..||..-...++.+||.|+|.+.|++-.+.||+.+-...|+-+
T Consensus 2 ~~A~~~L~~FQ~S~~aW~i~~eiL~~~~~~~~~~FaaqTlr~Ki~~~F~~Lp~~~~~slrdsl 64 (559)
T KOG2081|consen 2 EKANNWLGNFQKSNDAWQICEEILSQKCDVEALLFAAQTLRNKIQYDFSELPPLTHASLRDSL 64 (559)
T ss_pred chHhHHHHHhCCChHHHHHHHHHHcccchHHHHHHHHHHHHHHHHhhHHhcCcchhHHHHHHH
Confidence 468999999999999999999999999999999999999999999999999998888887743
No 9
>KOG1991|consensus
Probab=96.69 E-value=0.018 Score=52.40 Aligned_cols=85 Identities=24% Similarity=0.261 Sum_probs=68.2
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCch-HHHHHHHHHHHHHHHhhcccCC--------
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSN-QQTKFYALQILEQVIKTRWKAL-------- 92 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~-~~tk~fALqiLe~~I~~~W~~L-------- 92 (112)
|...|-++..+-..++...|+.|++-|.++...|.....|-.|...... -.+|--|.--|.+.|.+.|++.
T Consensus 2 d~~~l~~~~~~T~d~d~~~R~~AE~~L~q~~K~pgFv~~lLqIi~~d~~~l~vrqaaaIYlKN~I~~~W~~~~~~g~~~~ 81 (1010)
T KOG1991|consen 2 DLQSLLQIFRATIDSDAKERKAAEQQLNQLEKQPGFVSSLLQIIMDDGVPLPVRQAAAIYLKNKITKSWSSHEAPGRPFG 81 (1010)
T ss_pred ChHHHHHHHHHhcCCChHHHHHHHHHHHHhhcCCcHHHHHHHHHHccCCchhHHHHHHHHHHHHHHhcCCccCCCCCcCC
Confidence 5556666666666666678999999999999999999999998855554 4559999999999999999986
Q ss_pred -CHHHHHHHHHHhHh
Q psy4090 93 -PREQCDVKEEKERE 106 (112)
Q Consensus 93 -p~eqr~~IRnyv~~ 106 (112)
++++|.-||+=+.+
T Consensus 82 I~e~dk~~irenIl~ 96 (1010)
T KOG1991|consen 82 IPEEDKAVIRENILE 96 (1010)
T ss_pred CChHHHHHHHHHHHH
Confidence 67887777765544
No 10
>COG5656 SXM1 Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones]
Probab=95.95 E-value=0.036 Score=49.70 Aligned_cols=79 Identities=14% Similarity=0.215 Sum_probs=65.0
Q ss_pred HHHHHHhCC---ChHHHHHHHHHHHHHhcCCccHHHHHHHhccC-chHHHHHHHHHHHHHHHhhcccCC-----CHHHHH
Q psy4090 28 NIVECMYTG---MGVEQKAAQEVLTALKEHPDAWTRVDTILEYS-SNQQTKFYALQILEQVIKTRWKAL-----PREQCD 98 (112)
Q Consensus 28 ~vv~~~y~~---~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S-~~~~tk~fALqiLe~~I~~~W~~L-----p~eqr~ 98 (112)
.++++|-++ ....|..|+..|.++.-.|.....|-.|+... -++++|.-|.--|.+.|.+.|.++ +.+.+.
T Consensus 4 ellqcf~qTldada~~rt~AE~~Lk~leKqPgFv~all~i~s~de~~lnvklsAaIYfKNkI~rsWss~~d~~i~~Dek~ 83 (970)
T COG5656 4 ELLQCFLQTLDADAGKRTIAEAMLKDLEKQPGFVMALLHICSKDEGDLNVKLSAAIYFKNKIIRSWSSKRDDGIKADEKS 83 (970)
T ss_pred HHHHHHHHHhccCcchhhHHHHHHHHhhcCCcHHHHHHHHHhhccCCchhhHHHHHHHhhhhhhhhhhcccCCCCCcccH
Confidence 345554443 33469999999999999999999999999655 889999999999999999999983 446788
Q ss_pred HHHHHhHh
Q psy4090 99 VKEEKERE 106 (112)
Q Consensus 99 ~IRnyv~~ 106 (112)
++|.|+.|
T Consensus 84 e~K~~lie 91 (970)
T COG5656 84 EAKKYLIE 91 (970)
T ss_pred HHHHHHHH
Confidence 88888776
No 11
>KOG1992|consensus
Probab=93.20 E-value=0.54 Score=42.68 Aligned_cols=80 Identities=14% Similarity=0.171 Sum_probs=63.4
Q ss_pred HHHHHHHHhC---CChHHHHHHHHHHHHHhcCCccHHHHHHHhccCc-hHHHHHHHHHHHHHHHhhcccC-------CCH
Q psy4090 26 LDNIVECMYT---GMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSS-NQQTKFYALQILEQVIKTRWKA-------LPR 94 (112)
Q Consensus 26 Ld~vv~~~y~---~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~-~~~tk~fALqiLe~~I~~~W~~-------Lp~ 94 (112)
|+.+..++-. |....|+-|++.|.+...++..-..+-.++.+++ .+++|.-|.--+.+-||++|-. ++.
T Consensus 4 le~l~~~l~qTl~pdps~rk~aEr~L~~~e~q~~y~l~lL~Lv~~~~~d~~~r~aaav~fKN~iKr~W~~~~~~~~~i~~ 83 (960)
T KOG1992|consen 4 LETLANYLLQTLSPDPSVRKPAERALRSLEGQQNYPLLLLNLVANGQQDPQIRVAAAVYFKNYIKRNWIPAEDSPIKIIE 83 (960)
T ss_pred HHHHHHHHHhcCCCCCccCchHHHHHHHhccCCCchHHHHHHHhccCcChhHHHHHHHHHHHHHHhccCcCCCCccccch
Confidence 4444444433 3345699999999999999999888888888877 9999999999999999999964 455
Q ss_pred HHHHHHHHHhH
Q psy4090 95 EQCDVKEEKER 105 (112)
Q Consensus 95 eqr~~IRnyv~ 105 (112)
+.|+-||.-+-
T Consensus 84 ~~~e~ikslIv 94 (960)
T KOG1992|consen 84 EDREQIKSLIV 94 (960)
T ss_pred hHHHHHHHHHH
Confidence 57788877553
No 12
>KOG1241|consensus
Probab=92.67 E-value=0.54 Score=42.30 Aligned_cols=78 Identities=17% Similarity=0.196 Sum_probs=58.9
Q ss_pred HHHHHhCCChHHHHHHHHHHHHHhcCC--ccHHHHHHHh-ccCchHHHHHHHHHHHHHHHh-----------hcccCCCH
Q psy4090 29 IVECMYTGMGVEQKAAQEVLTALKEHP--DAWTRVDTIL-EYSSNQQTKFYALQILEQVIK-----------TRWKALPR 94 (112)
Q Consensus 29 vv~~~y~~~~~~r~~A~~iL~~fk~~p--daw~~v~~IL-~~S~~~~tk~fALqiLe~~I~-----------~~W~~Lp~ 94 (112)
++...-+|..+.|+.|++.|.++++.. ........+| ...+++++|+.|--+|.+.+. .||-.+|.
T Consensus 6 ~le~tlSpD~n~~~~Ae~~l~~~~~~nf~~F~~~Ls~vl~n~~~~~~~R~~AGL~LKN~L~akd~~~k~~~~qRWl~l~~ 85 (859)
T KOG1241|consen 6 LLEKTLSPDQNVRKRAEKQLEQAQSQNFPQFLVLLSEVLANDNSSDVARMAAGLQLKNSLTAKDPERKQQYQQRWLQLPA 85 (859)
T ss_pred HHHHHcCCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHhccCCcHHHHHHHhHHHhhhhccCCHHHHHHHHHHHHcCCH
Confidence 333345666678999999999988653 2333333444 677788899998888887765 78999999
Q ss_pred HHHHHHHHHhHh
Q psy4090 95 EQCDVKEEKERE 106 (112)
Q Consensus 95 eqr~~IRnyv~~ 106 (112)
|-|+.||++++.
T Consensus 86 e~reqVK~~il~ 97 (859)
T KOG1241|consen 86 EIREQVKNNILR 97 (859)
T ss_pred HHHHHHHHHHHH
Confidence 999999999864
No 13
>KOG2023|consensus
Probab=90.99 E-value=0.52 Score=42.18 Aligned_cols=83 Identities=18% Similarity=0.199 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHh--ccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTIL--EYSSNQQTKFYALQILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL--~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~I 100 (112)
+.++-++++.-.+|+...|+.++..|++|+..||.=-..-+|| -.|.+..+|-.|=-+|.+-|+-+|+.+|.+....|
T Consensus 12 l~ql~~lLk~s~Spn~~~~~~~~~~leq~~~~pdfnnYL~~IL~~~~~~d~~~Rs~aGLlLKNnvr~~~~~~~~~~~~yi 91 (885)
T KOG2023|consen 12 LQQLAQLLKNSQSPNSETRNNVQEKLEQFNLFPDFNNYLIYILIRAKSEDVPTRSLAGLLLKNNVRGHYNSIPSEVLDYI 91 (885)
T ss_pred HHHHHHHHHhccCCChHHHHHHHHHHHHHhcccchhceeeEEEecccccchhHHHHhhhhHhccccccccCCChHHHHHH
Confidence 3445555555556666789999999999999999988888888 55666777888888999999999999999888877
Q ss_pred HHHhH
Q psy4090 101 EEKER 105 (112)
Q Consensus 101 Rnyv~ 105 (112)
|.-+.
T Consensus 92 Ks~~l 96 (885)
T KOG2023|consen 92 KSECL 96 (885)
T ss_pred HHHHH
Confidence 76543
No 14
>KOG1993|consensus
Probab=86.16 E-value=1.5 Score=39.84 Aligned_cols=78 Identities=15% Similarity=0.279 Sum_probs=63.1
Q ss_pred HHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHh-ccCchHHHHHHHHHHHHHHHhhccc-----CCCHHHHHHHHH
Q psy4090 29 IVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTIL-EYSSNQQTKFYALQILEQVIKTRWK-----ALPREQCDVKEE 102 (112)
Q Consensus 29 vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL-~~S~~~~tk~fALqiLe~~I~~~W~-----~Lp~eqr~~IRn 102 (112)
+.++.-+|...-++-|+.-|.+-+..|...+....|. +.+.+-.+|..|.--+.+-|.+.|. .||+|+|.-||.
T Consensus 5 ~Lq~Ats~d~~v~k~AE~qLr~WEtqPGF~~~L~sI~l~~t~dv~vRWmAviyfKNgIdryWR~~~~~sl~~EEK~~iR~ 84 (978)
T KOG1993|consen 5 VLQQATSQDHIVVKPAEAQLRQWETQPGFFSKLYSIFLSKTNDVSVRWMAVIYFKNGIDRYWRRNTKMSLPPEEKDFIRC 84 (978)
T ss_pred HHHHhcCCCcccchhHHHHHHhhccCCcHHHHHHHHHhccccceeeeeehhhhHhcchhHHhhcCCcccCCHHHHHHHHH
Confidence 3344334444468999999999999999999877776 7777788999999999999999995 689999999997
Q ss_pred HhHh
Q psy4090 103 KERE 106 (112)
Q Consensus 103 yv~~ 106 (112)
-+.+
T Consensus 85 ~Ll~ 88 (978)
T KOG1993|consen 85 NLLL 88 (978)
T ss_pred HHHH
Confidence 6543
No 15
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=83.80 E-value=3.4 Score=25.48 Aligned_cols=58 Identities=16% Similarity=0.202 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQIL 81 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiL 81 (112)
...++.++..+.+++..-|..|=..|..++ +|+++..+...|..+.+..++.-|...|
T Consensus 30 ~~~~~~L~~~l~d~~~~vr~~a~~aL~~i~-~~~~~~~L~~~l~~~~~~~vr~~a~~aL 87 (88)
T PF13646_consen 30 PEAIPALIELLKDEDPMVRRAAARALGRIG-DPEAIPALIKLLQDDDDEVVREAAAEAL 87 (88)
T ss_dssp HHHHHHHHHHHTSSSHHHHHHHHHHHHCCH-HHHTHHHHHHHHTC-SSHHHHHHHHHHH
T ss_pred HhHHHHHHHHHcCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHcCCCcHHHHHHHHhhc
Confidence 345555665554444445777777777765 4667777777777776666676666554
No 16
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=83.80 E-value=10 Score=26.52 Aligned_cols=20 Identities=25% Similarity=0.539 Sum_probs=16.7
Q ss_pred CchHHHHHHHHHHHHHHHhh
Q psy4090 68 SSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 68 S~~~~tk~fALqiLe~~I~~ 87 (112)
+.+|.+.++||.+|+.+++.
T Consensus 53 ~~~~~vq~~aL~lld~lvkN 72 (140)
T PF00790_consen 53 HGNPNVQLLALTLLDALVKN 72 (140)
T ss_dssp TSSHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHc
Confidence 37888889999988888885
No 17
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=83.02 E-value=11 Score=25.05 Aligned_cols=51 Identities=20% Similarity=0.246 Sum_probs=29.3
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
|...+..+|+..+......+..+..+...+ .++++.+.+.||.+||.+++.
T Consensus 17 ~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl---------------~~~~~~~~lkaL~lLe~lvkN 67 (115)
T cd00197 17 DWPLIMEICDLINETNVGPKEAVDAIKKRI---------------NNKNPHVVLKALTLLEYCVKN 67 (115)
T ss_pred CHHHHHHHHHHHHCCCccHHHHHHHHHHHh---------------cCCcHHHHHHHHHHHHHHHHH
Confidence 566777777777654322233333332222 233677777777777777776
No 18
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=82.72 E-value=10 Score=26.96 Aligned_cols=53 Identities=19% Similarity=0.219 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 20 KLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 20 ~~dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
.-|......+|+......... +.|-+.|.. =| ++.||++.++||++|+.+++.
T Consensus 16 ~~dw~~ileicD~In~~~~~~-k~a~rai~k-------------rl-~~~n~~v~l~AL~LLe~~vkN 68 (139)
T cd03567 16 EEDWEAIQAFCEQINKEPEGP-QLAVRLLAH-------------KI-QSPQEKEALQALTVLEACMKN 68 (139)
T ss_pred CCCHHHHHHHHHHHHcCCccH-HHHHHHHHH-------------HH-cCCCHHHHHHHHHHHHHHHHH
Confidence 347888888888875432222 233333321 11 377888899999999999885
No 19
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=78.67 E-value=13 Score=25.85 Aligned_cols=52 Identities=19% Similarity=0.267 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 21 LDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 21 ~dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
-|....-.+|+..-......+..+..+...++ +.+|++.++||.+|+.+++.
T Consensus 16 ~dw~~~l~icD~i~~~~~~~k~a~r~l~krl~---------------~~n~~v~l~AL~lLe~~vkN 67 (133)
T smart00288 16 EDWELILEICDLINSTPDGPKDAVRLLKKRLN---------------NKNPHVALLALTLLDACVKN 67 (133)
T ss_pred cCHHHHHHHHHHHhCCCccHHHHHHHHHHHHc---------------CCCHHHHHHHHHHHHHHHHH
Confidence 46777777787765442222333333333222 35566666777777666664
No 20
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=77.33 E-value=15 Score=26.22 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 21 LDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 21 ~dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
-|....-.+|+..-..... =+.|-+.|.. =| .+++|++.++||.+|+.+++.
T Consensus 16 ~dw~~il~icD~I~~~~~~-~k~a~ral~K-------------Rl-~~~n~~v~l~AL~LLe~~vkN 67 (144)
T cd03568 16 ENWGLILDVCDKVKSDENG-AKDCLKAIMK-------------RL-NHKDPNVQLRALTLLDACAEN 67 (144)
T ss_pred cCHHHHHHHHHHHhcCCcc-HHHHHHHHHH-------------HH-cCCCHHHHHHHHHHHHHHHHH
Confidence 3677777888876543222 2334333331 11 246788888888888888875
No 21
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=76.96 E-value=1.8 Score=25.98 Aligned_cols=26 Identities=19% Similarity=0.098 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhcccCCCHHHHHHHHHH
Q psy4090 77 ALQILEQVIKTRWKALPREQCDVKEEK 103 (112)
Q Consensus 77 ALqiLe~~I~~~W~~Lp~eqr~~IRny 103 (112)
|.-+|+.+.+.++ .|+..|+.|+|-|
T Consensus 22 G~rtl~Dl~~~~~-~Lt~~Q~iGl~yy 47 (52)
T PF10391_consen 22 GIRTLEDLRKSKS-KLTWQQQIGLKYY 47 (52)
T ss_dssp T--SHHHHHHGGC-GS-HHHHHHHHTH
T ss_pred CCCCHHHHhhhhc-cCCHHHHHHHHHH
Confidence 5568899977788 9999999999976
No 22
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=76.79 E-value=8 Score=23.72 Aligned_cols=57 Identities=14% Similarity=0.178 Sum_probs=42.1
Q ss_pred HHHHHHHH-hCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHH
Q psy4090 26 LDNIVECM-YTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQV 84 (112)
Q Consensus 26 Ld~vv~~~-y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~ 84 (112)
++.+++.+ -++....|..|-..|.++. +|++....-..| .+.++.++.-|...|...
T Consensus 1 i~~L~~~l~~~~~~~vr~~a~~~L~~~~-~~~~~~~L~~~l-~d~~~~vr~~a~~aL~~i 58 (88)
T PF13646_consen 1 IPALLQLLQNDPDPQVRAEAARALGELG-DPEAIPALIELL-KDEDPMVRRAAARALGRI 58 (88)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHCCT-HHHHHHHHHHHH-TSSSHHHHHHHHHHHHCC
T ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHcC-CHhHHHHHHHHH-cCCCHHHHHHHHHHHHHh
Confidence 35566666 3444456888988888664 667777777777 689999999999888753
No 23
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=71.81 E-value=30 Score=24.50 Aligned_cols=53 Identities=26% Similarity=0.327 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 20 KLDITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 20 ~~dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
.-|....-++|+..-..... -++|-+.|.. =| .+++|++.++||.+|+.+++.
T Consensus 19 ~~dw~~ileicD~In~~~~~-~k~a~ral~k-------------rl-~~~n~~vql~AL~LLe~~vkN 71 (142)
T cd03569 19 EPDLASILEICDMIRSKDVQ-PKYAMRALKK-------------RL-LSKNPNVQLYALLLLESCVKN 71 (142)
T ss_pred ccCHHHHHHHHHHHhCCCCC-HHHHHHHHHH-------------HH-cCCChHHHHHHHHHHHHHHHH
Confidence 34677777778776443222 2333333321 12 336788899999999988885
No 24
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=70.88 E-value=10 Score=24.54 Aligned_cols=28 Identities=36% Similarity=0.445 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHH-hhcccCCCHHHHHHHHHHh
Q psy4090 74 KFYALQILEQVI-KTRWKALPREQCDVKEEKE 104 (112)
Q Consensus 74 k~fALqiLe~~I-~~~W~~Lp~eqr~~IRnyv 104 (112)
.+|| |+-+| ..+|..||++.|.+++.++
T Consensus 53 ~L~a---L~gAi~g~~~~~L~~~~K~~L~~~~ 81 (81)
T PF04994_consen 53 LLYA---LEGAIQGIHWADLPDEEKQELLEWF 81 (81)
T ss_dssp HHHH---HHHHHCTS-GGGS-HHHHHHHHH--
T ss_pred HHHH---HHHHHcCCCHHHCCHHHHHHHHhcC
Confidence 3555 56655 4789999999999999864
No 25
>PLN03060 inositol phosphatase-like protein; Provisional
Probab=70.13 E-value=21 Score=27.32 Aligned_cols=59 Identities=8% Similarity=0.175 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCcc----HHH------------HHHHhccCchHHHHHHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDA----WTR------------VDTILEYSSNQQTKFYALQILE 82 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pda----w~~------------v~~IL~~S~~~~tk~fALqiLe 82 (112)
-..|+.+|.+. +...+ -|+.|++.....+..+-. |.. ...+-.+++-.|+|+||.-++.
T Consensus 72 ~~IF~Alc~a~-~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~f~YSRl~AIGL~~ 147 (206)
T PLN03060 72 DAIFKAYIEAL-GEDPDQYRKDAKKLEEWASSQSASGIADFNSGDGEVEAVLKDIAERAAGKTKFHYSRFFAIGLFR 147 (206)
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcccccchHHHHHHHHhhcCCCcchHHHHHHHHHH
Confidence 34566666664 22233 499999999888876654 332 2223367888999999987543
No 26
>PRK13266 Thf1-like protein; Reviewed
Probab=69.29 E-value=22 Score=27.61 Aligned_cols=60 Identities=10% Similarity=0.118 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCcc-----------------HHHHHHHhccCchHHHHHHHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDA-----------------WTRVDTILEYSSNQQTKFYALQILEQ 83 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pda-----------------w~~v~~IL~~S~~~~tk~fALqiLe~ 83 (112)
-..|+.+|.+. +...+ -|+.|++.+...+..+-. |..+..|-.+++-.|+|+||.-++.-
T Consensus 74 ~~IF~Alc~a~-~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~~~l~~ia~~~~f~YSRl~AIGL~~L 151 (225)
T PRK13266 74 DSIFNALCQAV-GFDPEQLRQDAERLLELAKGKSLKEILSWLTQKALGEPGGLLATLLAIANNSKFKYSRLFAIGLYTL 151 (225)
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccccchhHHHHHHHHhcCCCCchHHHHHHHHHHH
Confidence 34566666664 22233 489999998888776433 23344455678888999999876543
No 27
>COG5657 CSE1 CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning]
Probab=68.57 E-value=26 Score=32.40 Aligned_cols=70 Identities=13% Similarity=0.144 Sum_probs=55.0
Q ss_pred CCChHHHHHHHHHHHHHhcCCccHHHHHHHh-ccCchHHHHHHHHHHHHHHHhhcccC-----CCHHHHHHHHHHh
Q psy4090 35 TGMGVEQKAAQEVLTALKEHPDAWTRVDTIL-EYSSNQQTKFYALQILEQVIKTRWKA-----LPREQCDVKEEKE 104 (112)
Q Consensus 35 ~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL-~~S~~~~tk~fALqiLe~~I~~~W~~-----Lp~eqr~~IRnyv 104 (112)
++.+..++.|++-|.+.+-.++.-.+...|- +.+.+-.+|.-|+--+.+-|.++|.. ++++.+.-||.=+
T Consensus 15 s~~p~s~k~AE~~Lrqwe~q~gF~~kL~~I~~~~~~~m~lR~~a~i~fkn~I~~~W~~~~~~~i~p~e~v~IR~~l 90 (947)
T COG5657 15 SPDPPSVKCAEERLRQWEKQHGFALKLLSINLSAFNSMSLRWAALIQFKNYIDKHWREENGNSILPDENVLIRDEL 90 (947)
T ss_pred CCCCchHhhHHHHHHhhhccccHHHHHHHHHhccccchhHHHHHHHHHHhhHHHHhhhhcccCCCCccchHHHHHH
Confidence 3455679999999999999999777666665 56688899999999999999999976 5555555666543
No 28
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=68.14 E-value=40 Score=23.83 Aligned_cols=15 Identities=20% Similarity=0.140 Sum_probs=10.8
Q ss_pred CHHHHHHHHHHHhCC
Q psy4090 22 DITLLDNIVECMYTG 36 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~ 36 (112)
|....=.+|+..-.+
T Consensus 18 dw~~ileicD~In~~ 32 (141)
T cd03565 18 DWGLNMEICDIINET 32 (141)
T ss_pred CHHHHHHHHHHHhCC
Confidence 677777788887554
No 29
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=65.58 E-value=21 Score=23.49 Aligned_cols=50 Identities=22% Similarity=0.430 Sum_probs=34.1
Q ss_pred ChHHHHHHHHH-------HHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHH
Q psy4090 37 MGVEQKAAQEV-------LTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 37 ~~~~r~~A~~i-------L~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~I 100 (112)
...++--|..| |..+-.+|.-|.. +...++.+++++| .|=.+|+++|..|
T Consensus 26 ~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~---L~~~gre~y~RM~-----------nWL~~~e~~r~~i 82 (87)
T PF02376_consen 26 NISQRVFAKKVLNRSQGTLSDLLRKPKPWNK---LKPKGREPYIRMY-----------NWLSLPEEERMEI 82 (87)
T ss_dssp T--HHHHHHHTTSS-HHHHHHHHHSCCTTCH---HHHHHHHHHHHHH-----------HHHCSTHHHHHHH
T ss_pred CCCHHHHHHHHhccChhHHHHHhCCCCCHHH---cCccccHHHHHHH-----------HHhcCCHHHHHHH
Confidence 33455556665 5667778888875 4447778888877 6778888887766
No 30
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=64.43 E-value=52 Score=23.95 Aligned_cols=64 Identities=19% Similarity=0.125 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHH-HHHh---ccCchHHHHHHHHHHHHHHHhhcc
Q psy4090 26 LDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRV-DTIL---EYSSNQQTKFYALQILEQVIKTRW 89 (112)
Q Consensus 26 Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v-~~IL---~~S~~~~tk~fALqiLe~~I~~~W 89 (112)
+..++..+-+++..-+..|...|..+-++-..-+.+ ..++ ..++||.+|..++..|..+|..-.
T Consensus 96 l~~Ll~~~~~~~~~i~~~a~~~L~~i~~~~~~~~~~~~~~l~~~~~~Kn~~vR~~~~~~l~~~l~~~~ 163 (228)
T PF12348_consen 96 LPPLLKKLGDSKKFIREAANNALDAIIESCSYSPKILLEILSQGLKSKNPQVREECAEWLAIILEKWG 163 (228)
T ss_dssp HHHHHHGGG---HHHHHHHHHHHHHHHTTS-H--HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHHccccHHHHHHHHHHHHHHHHHCCcHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHcc
Confidence 333444444444456899999999999987744444 4444 789999999999999999998865
No 31
>COG1043 LpxA Acyl-[acyl carrier protein]
Probab=64.30 E-value=13 Score=29.43 Aligned_cols=48 Identities=17% Similarity=0.222 Sum_probs=39.5
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCc
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSS 69 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~ 69 (112)
++..|.++-..+|.+...-++.+++++.++.++|..-..|++|.+.|+
T Consensus 209 ~i~alr~ayk~lfr~~~~~~e~~~~i~~~~~~~~~v~~~~dFi~~s~r 256 (260)
T COG1043 209 EIHALRKAYKLLFRSGLTLREALEEIAEEYADNPEVKEFIDFIASSSR 256 (260)
T ss_pred HHHHHHHHHHHHeeCCCCHHHHHHHHHHHhcCChHHHHHHHHHhhccc
Confidence 366666666778988777788889999999999999999999987665
No 32
>KOG2274|consensus
Probab=63.05 E-value=23 Score=32.86 Aligned_cols=75 Identities=15% Similarity=0.113 Sum_probs=53.2
Q ss_pred HhCCChHHHHHHHHHHHHHhcCCccHHH-HHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHH------HHHHHHHhH
Q psy4090 33 MYTGMGVEQKAAQEVLTALKEHPDAWTR-VDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQ------CDVKEEKER 105 (112)
Q Consensus 33 ~y~~~~~~r~~A~~iL~~fk~~pdaw~~-v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eq------r~~IRnyv~ 105 (112)
..++....|.+|+.-|.++--.++.-.. |+-+++...+-..+=+|+-.|...|.++|....+.- -+..|..||
T Consensus 13 ~ls~d~~vr~~AE~~l~qle~~~~f~~aL~~va~~~~~sl~lRQ~A~v~L~~yie~hW~~~~E~fr~~~~~~e~~K~~IR 92 (1005)
T KOG2274|consen 13 SLSADQNVRSQAETQLKQLELTEGFGVALAEVAANKDASLPLRQIALVLLKRYIEKHWSPNFEAFRYPLIVSEEVKALIR 92 (1005)
T ss_pred hcCCChhHHHHHHHHHhccccchHHHHHHHHHHhCcccCchHHHHHHHHHHHHHHHhCCChHhhccCCCcccHHHHHHHH
Confidence 3344445799999999988777774443 344446657778899999999999999998764432 234566666
Q ss_pred hh
Q psy4090 106 EQ 107 (112)
Q Consensus 106 ~~ 107 (112)
||
T Consensus 93 e~ 94 (1005)
T KOG2274|consen 93 EQ 94 (1005)
T ss_pred HH
Confidence 65
No 33
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=60.80 E-value=39 Score=26.05 Aligned_cols=60 Identities=13% Similarity=0.180 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCc----cHH-----------HHHHHhccCchHHHHHHHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPD----AWT-----------RVDTILEYSSNQQTKFYALQILEQ 83 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pd----aw~-----------~v~~IL~~S~~~~tk~fALqiLe~ 83 (112)
-..|+.+|.+. +...+ -|+.|++.+...+..+- +|. ....|-.+++-.|+|+||.-++.-
T Consensus 74 ~~IF~Alc~a~-~~dp~~~r~dA~~l~~~a~~~s~~~i~~~l~~~~~~~~~~l~l~~ia~n~~f~YSRl~AIGL~~L 149 (214)
T TIGR03060 74 DALFDALCNSN-GFDPEQLREDAKQLLEQAKGKGLDEILSWLTQANLSNGGGDTLQGIAGRHKFKYSRLFAIGLYSL 149 (214)
T ss_pred HHHHHHHHHhc-CCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhccccCCcchhHHHHHhcCCCcchHHHHHHHHHHH
Confidence 34566666663 22233 49999999988877543 233 233444677778999999875543
No 34
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=57.91 E-value=52 Score=21.72 Aligned_cols=54 Identities=17% Similarity=0.210 Sum_probs=32.1
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhcCC-ccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 25 LLDNIVECMYTGMGVEQKAAQEVLTALKEHP-DAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 25 ~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~p-daw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
.+..+|..+.-+++..+..-.++..++-++. -.|-++-.++ .||-.+-.++++.
T Consensus 15 ~f~~~~~~l~~~~~~~~~~f~~Va~~lf~dg~inWGRIval~---------~F~~~la~~~~~~ 69 (100)
T smart00337 15 AFSSFSAQLHVTPGTAIELFGEVATELFSDGNINWGRVVALL---------SFGGALAVKLVQK 69 (100)
T ss_pred HHHHHHHHhCCCcccHHHHHHHHHHHHHccCCCCHHHHHHHH---------HHHHHHHHHHHHc
Confidence 4566666643222223444444555555555 7999999888 6666666666554
No 35
>PF11264 ThylakoidFormat: Thylakoid formation protein; InterPro: IPR017499 Psp29, originally designated sll1414 (P73956 from SWISSPROT) in Synechocystis sp. (strain PCC 6803), is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.; GO: 0010027 thylakoid membrane organization, 0015979 photosynthesis, 0009523 photosystem II
Probab=54.52 E-value=60 Score=25.01 Aligned_cols=60 Identities=10% Similarity=0.200 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCcc----HH---------HHHHHh----ccCchHHHHHHHHHHHHH
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDA----WT---------RVDTIL----EYSSNQQTKFYALQILEQ 83 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pda----w~---------~v~~IL----~~S~~~~tk~fALqiLe~ 83 (112)
...++.+|.+. +...+ -|+.|+++....+..+-. |. .+..++ .+++-.|+|+||.-++.-
T Consensus 69 ~~If~Alc~a~-~~dp~~~r~dA~~l~~~a~~~s~~~l~~~l~~~~~~~~~~l~~~~~~ia~~~~f~YSRl~AIGL~~L 146 (216)
T PF11264_consen 69 DSIFNALCQAL-GFDPEQYRQDAEKLEEWAKGKSIEDLLSWLSQKGGEGDNPLAAILQAIASNPKFKYSRLFAIGLFRL 146 (216)
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHHHHHHHcCCHHHHHHHHhccccccchHHHHHHHHHhcCCCCchHHHHHHHHHHH
Confidence 44666677663 22333 489999998887776543 22 122233 577889999999876543
No 36
>cd07064 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this fa
Probab=52.04 E-value=91 Score=23.21 Aligned_cols=72 Identities=18% Similarity=0.283 Sum_probs=45.6
Q ss_pred HhCCChH-HHHHHHHHHHHHhcC--CccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHhHhhhh
Q psy4090 33 MYTGMGV-EQKAAQEVLTALKEH--PDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKEREQNW 109 (112)
Q Consensus 33 ~y~~~~~-~r~~A~~iL~~fk~~--pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv~~~~~ 109 (112)
|++=+.+ .|+.|..++...+.. ++.|..+..++ .|..-+.+++|+.+|....+. ++++.-..+..|+..-+|
T Consensus 20 f~Gv~~P~~R~lak~~~~~~~~~~~~~~~~l~~~Lw-~~~~~E~r~~al~~l~~~~~~----~~~~~~~~~~~~l~~~~~ 94 (208)
T cd07064 20 FYGIKTPERRALSKPFLKESKLPDKEELWELVLELW-QQPEREYQYVAIDLLRKYKKF----LTPEDLPLLEELITTKSW 94 (208)
T ss_pred cCCCChHHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-cchHHHHHHHHHHHHHHHHhc----CCHHHHHHHHHHHcCCch
Confidence 4544444 466677776544432 34555555555 444468999999988886543 577777777777776655
No 37
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=49.38 E-value=57 Score=19.62 Aligned_cols=59 Identities=15% Similarity=0.196 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHhHhhhhhc
Q psy4090 41 QKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKEREQNWFQ 111 (112)
Q Consensus 41 r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv~~~~~~~ 111 (112)
|..|...|...|....... . ..-.+.+|..|=.-.++|...+ +....|=+|..+.||++
T Consensus 3 ~~i~~d~L~~~K~~~~~y~--~-a~~E~~np~lR~~l~~~~~~~~---------~~~~~l~~~m~~kGwY~ 61 (64)
T PF07875_consen 3 KDIANDLLNSEKAAARNYA--T-AALECANPELRQILQQILNECQ---------QMQYELFNYMNQKGWYQ 61 (64)
T ss_pred HHHHHHHHHHHHHHHHHHH--H-HHHHHCCHHHHHHHHHHHHHHH---------HHHHHHHHHHHHcCCcC
Confidence 5566677766666555444 2 4446667777766566666554 44667889999999986
No 38
>PF11698 V-ATPase_H_C: V-ATPase subunit H; InterPro: IPR011987 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C-terminal domain of subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=49.02 E-value=30 Score=24.21 Aligned_cols=30 Identities=17% Similarity=0.535 Sum_probs=22.3
Q ss_pred HHHHHhccCchHHHHHHHHHHHHHHHhhccc
Q psy4090 60 RVDTILEYSSNQQTKFYALQILEQVIKTRWK 90 (112)
Q Consensus 60 ~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~ 90 (112)
.+..+|+ +.++.+||-||..+-.++.++|.
T Consensus 90 ~vM~Lm~-h~d~eVr~eAL~avQklm~~~w~ 119 (119)
T PF11698_consen 90 RVMELMN-HEDPEVRYEALLAVQKLMVNNWE 119 (119)
T ss_dssp HHHHHTS--SSHHHHHHHHHHHHHHHHHS--
T ss_pred HHHHHhc-CCCHHHHHHHHHHHHHHHHhcCC
Confidence 3344444 58999999999999999999994
No 39
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=48.99 E-value=45 Score=27.28 Aligned_cols=62 Identities=16% Similarity=0.309 Sum_probs=41.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHH----HHHHhccCchHHHHHHHHHHHHHHHhhc
Q psy4090 26 LDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTR----VDTILEYSSNQQTKFYALQILEQVIKTR 88 (112)
Q Consensus 26 Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~----v~~IL~~S~~~~tk~fALqiLe~~I~~~ 88 (112)
++.+...+.+.+..-.-+|-+.+..+..++..+.. ...+|. |++++++|.||..|...+...
T Consensus 233 i~~l~~~l~s~~~~V~~e~~~~i~~l~~~~~~~~~~~~~L~~lL~-s~~~nvr~~~L~~L~~l~~~~ 298 (526)
T PF01602_consen 233 IEPLLNLLQSSSPSVVYEAIRLIIKLSPSPELLQKAINPLIKLLS-SSDPNVRYIALDSLSQLAQSN 298 (526)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHHHT-SSSHHHHHHHHHHHHHHCCHC
T ss_pred HHHHHHHhhccccHHHHHHHHHHHHhhcchHHHHhhHHHHHHHhh-cccchhehhHHHHHHHhhccc
Confidence 33333334333334466777777777777774443 344456 889999999999999998886
No 40
>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....
Probab=48.66 E-value=82 Score=21.28 Aligned_cols=62 Identities=23% Similarity=0.294 Sum_probs=37.8
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHH-hcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHH
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTAL-KEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~f-k~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~I 100 (112)
....|..++...|++ ........-+...+ ..++..|. ..|=||.+|+.++.+- |++-..++
T Consensus 20 ~~~~l~eIa~~t~~~-~~~~~I~~~l~kRL~~~~~k~wr-------------~~~KaL~ll~yLl~nG----~~~~~~~~ 81 (125)
T PF01417_consen 20 PGKLLAEIAQLTYNS-KDCQEIMDVLWKRLSKSDGKNWR-------------HVYKALTLLEYLLKNG----SERFVDEL 81 (125)
T ss_dssp -HHHHHHHHHHTTSC-HHHHHHHHHHHHHHHSSTSSGHH-------------HHHHHHHHHHHHHHHS-----HHHHHHH
T ss_pred CHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhcCCcchh-------------HHHHHHHHHHHHHHHC----CHHHHHHH
Confidence 566788888887776 33344444454444 45555555 5677888888888874 44444444
Q ss_pred H
Q psy4090 101 E 101 (112)
Q Consensus 101 R 101 (112)
|
T Consensus 82 ~ 82 (125)
T PF01417_consen 82 R 82 (125)
T ss_dssp H
T ss_pred H
Confidence 4
No 41
>PRK09687 putative lyase; Provisional
Probab=48.26 E-value=78 Score=24.74 Aligned_cols=60 Identities=8% Similarity=0.123 Sum_probs=32.0
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhcCC----ccHHHHHHHhccCchHHHHHHHHHHHHHH
Q psy4090 25 LLDNIVECMYTGMGVEQKAAQEVLTALKEHP----DAWTRVDTILEYSSNQQTKFYALQILEQV 84 (112)
Q Consensus 25 ~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~p----daw~~v~~IL~~S~~~~tk~fALqiLe~~ 84 (112)
.++.+...+-+++...|..|-.+|.+++..+ .+......++....++.++.-|...|-+.
T Consensus 55 ~~~~l~~ll~~~d~~vR~~A~~aLg~lg~~~~~~~~a~~~L~~l~~~D~d~~VR~~A~~aLG~~ 118 (280)
T PRK09687 55 VFRLAIELCSSKNPIERDIGADILSQLGMAKRCQDNVFNILNNLALEDKSACVRASAINATGHR 118 (280)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHhcCCCHHHHHHHHHHHhcc
Confidence 3444444333333345666666666666532 34444444445666666666666666553
No 42
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=46.65 E-value=25 Score=20.30 Aligned_cols=24 Identities=29% Similarity=0.524 Sum_probs=18.7
Q ss_pred HHHHHHhhcccCCCHHHHHHHHHH
Q psy4090 80 ILEQVIKTRWKALPREQCDVKEEK 103 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eqr~~IRny 103 (112)
-+...+..+|+.+|+++|..-+.-
T Consensus 30 ~i~~~~~~~W~~l~~~~k~~y~~~ 53 (66)
T cd00084 30 EISKILGEMWKSLSEEEKKKYEEK 53 (66)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHH
Confidence 456777899999999998765543
No 43
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=46.21 E-value=18 Score=21.44 Aligned_cols=26 Identities=19% Similarity=0.414 Sum_probs=19.8
Q ss_pred HHHHHHhhcccCCCHHHHHHHHHHhH
Q psy4090 80 ILEQVIKTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eqr~~IRnyv~ 105 (112)
-+...|...|+.||+++|...+....
T Consensus 30 ~i~~~~~~~W~~l~~~eK~~y~~~a~ 55 (69)
T PF00505_consen 30 EISKILAQMWKNLSEEEKAPYKEEAE 55 (69)
T ss_dssp HHHHHHHHHHHCSHHHHHHHHHHHHH
T ss_pred cchhhHHHHHhcCCHHHHHHHHHHHH
Confidence 45567789999999999877655443
No 44
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=44.34 E-value=38 Score=19.48 Aligned_cols=24 Identities=25% Similarity=0.541 Sum_probs=16.3
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy4090 24 TLLDNIVECMYTGMGVEQKAAQEVLTA 50 (112)
Q Consensus 24 ~~Ld~vv~~~y~~~~~~r~~A~~iL~~ 50 (112)
..|+.|+. .++.++|.+|++.|.+
T Consensus 20 ~lL~evl~---~~~~~q~~eA~~LL~~ 43 (44)
T TIGR03504 20 ELLEEVIE---EGDEAQRQEARALLAQ 43 (44)
T ss_pred HHHHHHHH---cCCHHHHHHHHHHHhc
Confidence 45666663 4666778888888764
No 45
>COG5215 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]
Probab=43.42 E-value=84 Score=28.40 Aligned_cols=71 Identities=18% Similarity=0.178 Sum_probs=52.9
Q ss_pred hCCChHHHHHHHHHHHHHhcCCccHHH----HHHHhccCchHHHHHHHHHHHHHHHh-----------hcccCCCHHHHH
Q psy4090 34 YTGMGVEQKAAQEVLTALKEHPDAWTR----VDTILEYSSNQQTKFYALQILEQVIK-----------TRWKALPREQCD 98 (112)
Q Consensus 34 y~~~~~~r~~A~~iL~~fk~~pdaw~~----v~~IL~~S~~~~tk~fALqiLe~~I~-----------~~W~~Lp~eqr~ 98 (112)
..|..+.|..|++-|.++++.. .-++ +.-+.+..++++.|+.|--+|.+.|. .||-.++.|-|+
T Consensus 15 LspD~n~rl~aE~ql~~l~~~d-F~qf~~ll~qvl~d~ns~~~~Rm~agl~LKN~l~a~d~~~~~~~~qrW~~~~~E~k~ 93 (858)
T COG5215 15 LSPDPNARLRAEAQLLELQSGD-FEQFISLLVQVLCDLNSNDQLRMVAGLILKNSLHANDPELQKGCSQRWLGMRHESKE 93 (858)
T ss_pred CCCCCCccccHHHHHHHhcccc-HHHHHHHHHHHHhccCCcHHHHHHHHHHHhhhhhcCCHHHHHHHHHhhccCCHHHHH
Confidence 4555567888999998877643 2222 23333788899999999999988775 689999999998
Q ss_pred HHHHHhH
Q psy4090 99 VKEEKER 105 (112)
Q Consensus 99 ~IRnyv~ 105 (112)
.+|.-.+
T Consensus 94 qvK~~al 100 (858)
T COG5215 94 QVKGMAL 100 (858)
T ss_pred HHHHHHH
Confidence 8887554
No 46
>KOG1087|consensus
Probab=43.28 E-value=21 Score=30.57 Aligned_cols=51 Identities=27% Similarity=0.332 Sum_probs=31.2
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
|-..-=.+|+.+....++.+ +|-+.|.+ -| +++++.+.++||++||.+++.
T Consensus 18 DWa~NleIcD~IN~~~~~~~-eAvralkK-------------Ri-~~k~s~vq~lALtlLE~cvkN 68 (470)
T KOG1087|consen 18 DWALNLEICDLINSTEGGPK-EAVRALKK-------------RL-NSKNSKVQLLALTLLETCVKN 68 (470)
T ss_pred cHHHHHHHHHHHhcCccCcH-HHHHHHHH-------------Hh-ccCCcHHHHHHHHHHHHHHHh
Confidence 56666677777654433322 33333321 12 345558999999999998885
No 47
>PF08578 DUF1765: Protein of unknown function (DUF1765); InterPro: IPR013887 This entry represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae.
Probab=42.90 E-value=59 Score=22.35 Aligned_cols=51 Identities=24% Similarity=0.345 Sum_probs=37.7
Q ss_pred cHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHH---HHHhHhhhhhc
Q psy4090 57 AWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVK---EEKEREQNWFQ 111 (112)
Q Consensus 57 aw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~I---Rnyv~~~~~~~ 111 (112)
-|..+-..+=.|.+.++..-+++.|= ..|..+|.+.|..+ -+++.+-+||.
T Consensus 50 fwl~~i~~ml~s~n~~~~~r~l~fLy----n~w~~~~~~~~~~~~~~~~~Ll~~~~f~ 103 (126)
T PF08578_consen 50 FWLDGIRMMLESDNVQSEIRALSFLY----NIWDLFPSESRRKISLCLDWLLSEKWFF 103 (126)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHH----HHHHHcChhHHHHHHHHHHHHcCchHHH
Confidence 35544444433999998888887654 56888999999999 88998877764
No 48
>TIGR00865 bcl-2 Apoptosis regulator. in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
Probab=42.46 E-value=1.5e+02 Score=22.62 Aligned_cols=57 Identities=9% Similarity=0.121 Sum_probs=34.7
Q ss_pred HHHHHhhcccccCC---HHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHh
Q psy4090 9 EQFKKLLDFNQKLD---ITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTIL 65 (112)
Q Consensus 9 ~~~~~lld~~~~~d---v~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL 65 (112)
+..+.|......++ -..|..+|..+.-.....+..-.+|..++-++.=.|-++-.++
T Consensus 66 ~v~~~Lr~igdEle~~~~~~f~~m~~qL~it~~~a~~~F~~Va~elF~DGiNWGRIVaLf 125 (213)
T TIGR00865 66 AVHQALRRAGDEFERRYRRAFSDMTSQLHITPFTARQSFFQVAAELFRDGVNWGRIVAFF 125 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHhcCCCCHHHHHHHH
Confidence 34555555555444 3467777776543222334445556666666669999988888
No 49
>PF15581 Imm35: Immunity protein 35
Probab=42.25 E-value=18 Score=24.43 Aligned_cols=18 Identities=44% Similarity=0.885 Sum_probs=16.2
Q ss_pred HHHHHHhhcccCCCHHHH
Q psy4090 80 ILEQVIKTRWKALPREQC 97 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eqr 97 (112)
.|+.+|-+.|..||.+|-
T Consensus 34 ~l~~lIe~eWRGl~~~qV 51 (93)
T PF15581_consen 34 NLESLIEHEWRGLPEEQV 51 (93)
T ss_pred HHHHHHHHHHcCCCHHHH
Confidence 588999999999999984
No 50
>cd05502 Bromo_tif1_like Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=41.99 E-value=31 Score=23.06 Aligned_cols=25 Identities=16% Similarity=0.198 Sum_probs=21.7
Q ss_pred hHHHHHHHHHHHHHhcCCccHHHHH
Q psy4090 38 GVEQKAAQEVLTALKEHPDAWTRVD 62 (112)
Q Consensus 38 ~~~r~~A~~iL~~fk~~pdaw~~v~ 62 (112)
..+++.++++|.++.+++.||.+..
T Consensus 3 ~~~~~~c~~il~~l~~~~~s~~F~~ 27 (109)
T cd05502 3 PIDQRKCERLLLELYCHELSLPFHE 27 (109)
T ss_pred HHHHHHHHHHHHHHHhCCCChhhcC
Confidence 4578999999999999999999743
No 51
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=41.59 E-value=26 Score=20.50 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=17.3
Q ss_pred HHHHHHhhcccCCCHHHHHHHH
Q psy4090 80 ILEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eqr~~IR 101 (112)
-+...|...|+.|++++|....
T Consensus 30 ~i~~~~~~~W~~ls~~eK~~y~ 51 (66)
T cd01390 30 EVTKILGEKWKELSEEEKKKYE 51 (66)
T ss_pred HHHHHHHHHHHhCCHHHHHHHH
Confidence 4556778999999999986543
No 52
>PF14846 DUF4485: Domain of unknown function (DUF4485)
Probab=41.44 E-value=28 Score=22.66 Aligned_cols=53 Identities=15% Similarity=0.165 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHH
Q psy4090 38 GVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPRE 95 (112)
Q Consensus 38 ~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~e 95 (112)
..+|..|..|+..+.+-+. ...-...+|.|++++..++-...+....+..|++
T Consensus 23 ~~~k~~a~~Wl~KL~~~~~-----~~~~~~~RN~Y~~~Ll~~l~~~~L~~PF~~~Pp~ 75 (85)
T PF14846_consen 23 KSEKQRAALWLKKLCEPPH-----NVEEKKNRNEYASLLLHCLQQGRLEGPFTKPPPD 75 (85)
T ss_pred HHHHHHHHHHHHHHcCCCC-----CHHHHHHHHHHHHHHHHHHhcCccCCCCCCCCCC
Confidence 4579999999999998652 2344578999999998888888888777777765
No 53
>smart00398 HMG high mobility group.
Probab=41.21 E-value=28 Score=20.38 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=18.2
Q ss_pred HHHHHHHhhcccCCCHHHHHHHH
Q psy4090 79 QILEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 79 qiLe~~I~~~W~~Lp~eqr~~IR 101 (112)
.-+...|...|+.||+++|.-..
T Consensus 30 ~~i~~~~~~~W~~l~~~ek~~y~ 52 (70)
T smart00398 30 AEISKKLGERWKLLSEEEKAPYE 52 (70)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHH
Confidence 34567789999999999987654
No 54
>KOG4646|consensus
Probab=39.59 E-value=68 Score=23.79 Aligned_cols=39 Identities=13% Similarity=0.296 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCccHHHH
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDAWTRV 61 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pdaw~~v 61 (112)
..-|-.+|+.||+.++. .+++.-.-|-.|.-+|-.|++.
T Consensus 15 l~Ylq~LV~efq~tt~~eakeqv~ANLANFAYDP~Nys~L 54 (173)
T KOG4646|consen 15 LEYLQHLVDEFQTTTNIEAKEQVTANLANFAYDPINYSHL 54 (173)
T ss_pred HHHHHHHHHHHHHhccHHHHHHHHHHHHhhccCcchHHHH
Confidence 44567889999998886 4777888899999999999974
No 55
>PRK09687 putative lyase; Provisional
Probab=38.98 E-value=1.4e+02 Score=23.30 Aligned_cols=58 Identities=16% Similarity=0.105 Sum_probs=30.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHH
Q psy4090 25 LLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQV 84 (112)
Q Consensus 25 ~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~ 84 (112)
..+.+...+.+++...|..|...|.++ ..++.+..+..++ .|.++.++.+|..+|-.+
T Consensus 24 ~~~~L~~~L~d~d~~vR~~A~~aL~~~-~~~~~~~~l~~ll-~~~d~~vR~~A~~aLg~l 81 (280)
T PRK09687 24 NDDELFRLLDDHNSLKRISSIRVLQLR-GGQDVFRLAIELC-SSKNPIERDIGADILSQL 81 (280)
T ss_pred cHHHHHHHHhCCCHHHHHHHHHHHHhc-CcchHHHHHHHHH-hCCCHHHHHHHHHHHHhc
Confidence 344444444444445566666666533 3455555544433 455666666666555553
No 56
>COG5493 Uncharacterized conserved protein containing a coiled-coil domain [Function unknown]
Probab=38.89 E-value=45 Score=25.82 Aligned_cols=31 Identities=19% Similarity=0.292 Sum_probs=26.4
Q ss_pred HHHHHHhhcccCCCHHH-HHHHHHHhHhhhhh
Q psy4090 80 ILEQVIKTRWKALPREQ-CDVKEEKEREQNWF 110 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eq-r~~IRnyv~~~~~~ 110 (112)
+.-+.|-.||..|+++- |+|+|.-++|-||-
T Consensus 102 ~~i~~lgaRwGilsEdAFR~gv~eil~e~g~~ 133 (231)
T COG5493 102 TIITGLGARWGILSEDAFRQGVREILREVGYV 133 (231)
T ss_pred HHHHHHHHHhccccHHHHHHHHHHHHHHhchh
Confidence 55567789999999886 99999999998873
No 57
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=37.75 E-value=1.1e+02 Score=23.36 Aligned_cols=56 Identities=25% Similarity=0.240 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHhcC----CccHHHHHHHhccCchHHH--HHHHHHHHHHHHhhcccCCCHHHHHHH
Q psy4090 41 QKAAQEVLTALKEH----PDAWTRVDTILEYSSNQQT--KFYALQILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 41 r~~A~~iL~~fk~~----pdaw~~v~~IL~~S~~~~t--k~fALqiLe~~I~~~W~~Lp~eqr~~I 100 (112)
+.-|.+.|..+|.+ .......-.+.+.-=.|++ ++-|..+| .+.|+..+++|++.+
T Consensus 34 ~~~a~~~ls~lk~~~~~~k~dp~~l~~~v~~~l~p~vd~~~~a~~vL----Gk~~k~aspeQ~~~F 95 (202)
T COG2854 34 QEAADKVLSILKNNQAKIKQDPQYLRQIVDQELLPYVDFKYAAKLVL----GKYYKTASPEQRQAF 95 (202)
T ss_pred HHHHHHHHHHHhccchhhccCHHHHHHHHHHHhhhhhcHHHHHHHHh----ccccccCCHHHHHHH
Confidence 77899999999998 6666777777755555554 66665554 478999999998864
No 58
>PRK12330 oxaloacetate decarboxylase; Provisional
Probab=35.22 E-value=34 Score=29.46 Aligned_cols=49 Identities=20% Similarity=0.187 Sum_probs=36.2
Q ss_pred ccHHHHHHHhcc--CchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHh
Q psy4090 56 DAWTRVDTILEY--SSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKE 104 (112)
Q Consensus 56 daw~~v~~IL~~--S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv 104 (112)
+..++|...|.. .-.|-+|+.|-|.+-++++.||+.+|.|-+.-+++|+
T Consensus 325 ~e~~~Vr~~lG~~~~VTP~Sqivg~qA~~nv~~gry~~~~~e~~~~~~G~y 375 (499)
T PRK12330 325 EEVPRVRKDAGYPPLVTPSSQIVGTQAVFNVLMGRYKVLTGEFADLMLGYY 375 (499)
T ss_pred HHHHHHHHHcCCCCeeCChhHHHHHHHHHHHHcCccccCCHHHHHHhCcCC
Confidence 334444444422 3467789999999999999999999999877776654
No 59
>PF09372 PRANC: PRANC domain; InterPro: IPR018272 This presumed domain is found at the C terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin, C-terminal) domain is also found on its own in some proteins []. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role.
Probab=34.54 E-value=40 Score=21.91 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=19.2
Q ss_pred HHHHHHHh--hcccCCCHHHHHHHHHHhH
Q psy4090 79 QILEQVIK--TRWKALPREQCDVKEEKER 105 (112)
Q Consensus 79 qiLe~~I~--~~W~~Lp~eqr~~IRnyv~ 105 (112)
..++..+. ..|+.||.|-|--|=+|+.
T Consensus 60 ~~i~~~~~~~~~w~~LP~EIk~~Il~~L~ 88 (97)
T PF09372_consen 60 EVIDNICDDNNYWNILPIEIKYKILEYLS 88 (97)
T ss_pred HHHHhhcCCCCchhhCCHHHHHHHHHcCC
Confidence 34444443 7899999999888776653
No 60
>PLN00047 photosystem II biogenesis protein Psb29; Provisional
Probab=33.44 E-value=2e+02 Score=23.19 Aligned_cols=58 Identities=9% Similarity=0.222 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhCCChH-HHHHHHHHHHHHhcCCcc----HHH--------HHHHh----ccCchHHHHHHHHHHHH
Q psy4090 24 TLLDNIVECMYTGMGV-EQKAAQEVLTALKEHPDA----WTR--------VDTIL----EYSSNQQTKFYALQILE 82 (112)
Q Consensus 24 ~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~pda----w~~--------v~~IL----~~S~~~~tk~fALqiLe 82 (112)
.+|+.+|.+. +...+ -|+.|++.....+..+-. |.. +..|- .+++-.|+||||.-++.
T Consensus 126 ~IF~Alc~a~-g~Dp~qyr~dA~~l~~~A~~~s~~~l~~~l~~~~~l~~~l~~IA~~a~~~~~f~YSRlfAIGLf~ 200 (283)
T PLN00047 126 AIFKAYIKAL-GEDPEQYRKDAAKLEEWARSQTGSSLVDFSSKEGEIEGILKDIAERAGSKGKFSYSRFFAIGLFR 200 (283)
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHHHHHHhcCCHHHHHHHHhcchHHHHHHHHHHHhhccCCCcchHHHHHHHHHH
Confidence 4555566553 11223 489999998888764432 332 22333 45788999999987543
No 61
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=33.32 E-value=59 Score=20.88 Aligned_cols=24 Identities=29% Similarity=0.285 Sum_probs=20.6
Q ss_pred HhccCchHHHHHHHHHHHHHHHhh
Q psy4090 64 ILEYSSNQQTKFYALQILEQVIKT 87 (112)
Q Consensus 64 IL~~S~~~~tk~fALqiLe~~I~~ 87 (112)
.|.+|+.|.=+..|+++|-..+.+
T Consensus 46 ~L~RSsv~~QR~~al~~L~~Il~~ 69 (73)
T PF08620_consen 46 HLSRSSVPSQRCIALQTLGRILYR 69 (73)
T ss_pred HHHhcCcHHHHHHHHHHHHHHHHH
Confidence 468999999999999999988764
No 62
>PF13309 HTH_22: HTH domain
Probab=33.20 E-value=66 Score=19.64 Aligned_cols=26 Identities=15% Similarity=0.043 Sum_probs=22.8
Q ss_pred hhcccCCCHHHHHHHHHHhHhhhhhc
Q psy4090 86 KTRWKALPREQCDVKEEKEREQNWFQ 111 (112)
Q Consensus 86 ~~~W~~Lp~eqr~~IRnyv~~~~~~~ 111 (112)
...+..++.++|..|=..+.++|-|+
T Consensus 15 ~~~~~~l~~~~k~~iV~~L~~~G~F~ 40 (64)
T PF13309_consen 15 GKPPSRLSKEEKKEIVRQLYEKGIFL 40 (64)
T ss_pred CCChhhCCHHHHHHHHHHHHHCCCcc
Confidence 36678899999999999999999885
No 63
>PF12830 Nipped-B_C: Sister chromatid cohesion C-terminus
Probab=31.82 E-value=2e+02 Score=20.87 Aligned_cols=77 Identities=19% Similarity=0.119 Sum_probs=54.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhcCCcc-HHHHHH---HhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHH
Q psy4090 26 LDNIVECMYTGMGVEQKAAQEVLTALKEHPDA-WTRVDT---ILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 26 Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pda-w~~v~~---IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IR 101 (112)
|+.+++...++.+.-|..|-+++...-+.-=. +..|-. -|+.|.++..+--|..+|..+-.++=+.+...-.+|||
T Consensus 10 l~~Il~~~~~~~~~vr~~Al~~l~~il~qGLvnP~~cvp~lIAL~ts~~~~ir~~A~~~l~~l~eK~~s~v~~~~~~gi~ 89 (187)
T PF12830_consen 10 LKNILELCLSSDDSVRLAALQVLELILRQGLVNPKQCVPTLIALETSPNPSIRSRAYQLLKELHEKHESLVESRYSEGIR 89 (187)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHhcCCCChHHHHhHhhhhhCCCChHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 56777777777777788888888766553322 223333 24899999999999999999888776666666677776
Q ss_pred H
Q psy4090 102 E 102 (112)
Q Consensus 102 n 102 (112)
.
T Consensus 90 ~ 90 (187)
T PF12830_consen 90 L 90 (187)
T ss_pred H
Confidence 4
No 64
>cd05500 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=30.09 E-value=65 Score=21.24 Aligned_cols=25 Identities=20% Similarity=0.098 Sum_probs=21.5
Q ss_pred hHHHHHHHHHHHHHhcCCccHHHHH
Q psy4090 38 GVEQKAAQEVLTALKEHPDAWTRVD 62 (112)
Q Consensus 38 ~~~r~~A~~iL~~fk~~pdaw~~v~ 62 (112)
..+++.+.+++..+.++|+||.+..
T Consensus 3 ~~~~~~~~~ii~~l~~~~~a~~F~~ 27 (103)
T cd05500 3 KHQHKFLLSSIRSLKRLKDARPFLV 27 (103)
T ss_pred HHHHHHHHHHHHHHHcCCCChhhcC
Confidence 4568889999999999999999754
No 65
>PF08389 Xpo1: Exportin 1-like protein; InterPro: IPR013598 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found close to the N terminus of yeast exportin 1 (Xpo1, Crm1, P14068 from SWISSPROT), as well as adjacent to the N-terminal domain of importin-beta (IPR001494 from INTERPRO). Exportin 1 is a nuclear export receptor that translocates proteins out of the nucleus; it interacts with leucine-rich nuclear export signal (NES) sequences in proteins to be transported, as well as with RanGTP [, ]. Importin-beta is a nuclear import receptor that translocates proteins into the nucleus; it interacts with RanGTP and importin-alpha, the latter binding with the nuclear localisation signal (NLS) sequences in proteins to be transported []. More information about these proteins can be found at Protein of the Month: Importins [].; PDB: 3IBV_A 3ICQ_U 3M1I_C 3NC1_A 3NBY_D 3NBZ_D 3NC0_A 3GJX_D 2XWU_B 2X19_B ....
Probab=29.83 E-value=1.5e+02 Score=19.62 Aligned_cols=56 Identities=21% Similarity=0.390 Sum_probs=33.2
Q ss_pred hcCCccHH-HHHHHhccCc-hHHHHHHHHHHHHHH---Hhh-cccCCCHHHHHHHHHHhHhh
Q psy4090 52 KEHPDAWT-RVDTILEYSS-NQQTKFYALQILEQV---IKT-RWKALPREQCDVKEEKEREQ 107 (112)
Q Consensus 52 k~~pdaw~-~v~~IL~~S~-~~~tk~fALqiLe~~---I~~-~W~~Lp~eqr~~IRnyv~~~ 107 (112)
++-|+.|+ ....+++..+ ++....++|.+|..+ |.. +=..++.+.|..++.-++++
T Consensus 18 ~~~P~~Wp~~l~~l~~~~~~~~~~~~~~L~iL~~l~eEi~~~~~~~~~~~r~~~l~~~l~~~ 79 (148)
T PF08389_consen 18 RDWPQQWPDFLEDLLQLLQSSPQHLELVLRILRILPEEITDFRRSSLSQERRRELKDALRSN 79 (148)
T ss_dssp HHTTTTSTTHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHTSHCCHSHHHHHHHHHHHHHHH
T ss_pred HHChhhCchHHHHHHHHhccchhHHHHHHHHHHHHHHHHHhhhchhhhHHHHHHHHHHHHHH
Confidence 34478888 4466664433 355565666555443 332 22466778888888877765
No 66
>PF09058 L27_1: L27_1; InterPro: IPR015143 The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organisation centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices []. ; PDB: 3LRA_A 1RSO_A.
Probab=29.76 E-value=50 Score=20.84 Aligned_cols=32 Identities=13% Similarity=0.187 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhCCChH-HHHHHHHHHHHHhcC
Q psy4090 23 ITLLDNIVECMYTGMGV-EQKAAQEVLTALKEH 54 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~-~r~~A~~iL~~fk~~ 54 (112)
+.+|+..+..+-.|++. -|..+++++.-||.+
T Consensus 12 LelLe~y~~~L~~~~D~~lr~~ierli~ifkS~ 44 (64)
T PF09058_consen 12 LELLEEYHNKLSRPEDEELRTAIERLINIFKSR 44 (64)
T ss_dssp HHHHHHHHHTTSSSS-CCHHHHHHHHHHHHHSH
T ss_pred HHHHHHHHHhcCCcccHHHHHHHHHHHHHHHHH
Confidence 45677777776667665 488899999988864
No 67
>PRK12581 oxaloacetate decarboxylase; Provisional
Probab=28.56 E-value=49 Score=28.28 Aligned_cols=37 Identities=11% Similarity=0.042 Sum_probs=31.0
Q ss_pred CchHHHHHHHHHHHHHHHhh-cccCCCHHHHHHHHHHh
Q psy4090 68 SSNQQTKFYALQILEQVIKT-RWKALPREQCDVKEEKE 104 (112)
Q Consensus 68 S~~~~tk~fALqiLe~~I~~-~W~~Lp~eqr~~IRnyv 104 (112)
.-.|-+|+.|-|.+-+++.. ||+.+|.|-+.-+++|+
T Consensus 348 ~VTP~Sqivg~qA~~nV~~g~ry~~~~~ev~~~~~G~y 385 (468)
T PRK12581 348 LVTPLSQMVGTQAAMNVILGKPYQMVSKEIKQYLAGDY 385 (468)
T ss_pred EECChhHHHHHHHHHHHHcCCCchhCCHHHHHHhCcCC
Confidence 34577899999999999988 99999999877776654
No 68
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=28.50 E-value=1.4e+02 Score=19.18 Aligned_cols=44 Identities=18% Similarity=0.229 Sum_probs=29.8
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHh
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTIL 65 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL 65 (112)
++..+.++...+|.++..-.+.++++..++.++|+.=..|++|-
T Consensus 32 ~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~~v~~~~~Fi~ 75 (83)
T PF13720_consen 32 EISALRRAYRILFRSGLTLEEALEELEEEYPDSPEVREIVDFIR 75 (83)
T ss_dssp HHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 46677777777887665545556666666777777777777665
No 69
>PF10047 DUF2281: Protein of unknown function (DUF2281); InterPro: IPR018739 This domain is found in putative uncharacterised proteins, though some proteins contaning this domain are described as a transcritional regulator of the Xre family.
Probab=28.23 E-value=49 Score=20.44 Aligned_cols=22 Identities=14% Similarity=0.065 Sum_probs=17.2
Q ss_pred HHhhcccCCCHHHHHHHHHHhH
Q psy4090 84 VIKTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 84 ~I~~~W~~Lp~eqr~~IRnyv~ 105 (112)
.|-..+..||++.+.++-.||.
T Consensus 4 ~l~~~i~~LP~~~~~Evldfi~ 25 (66)
T PF10047_consen 4 ELLEKIQQLPEELQQEVLDFIE 25 (66)
T ss_pred HHHHHHHHCCHHHHHHHHHHHH
Confidence 4455666799999999998874
No 70
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=28.09 E-value=42 Score=20.55 Aligned_cols=21 Identities=33% Similarity=0.577 Sum_probs=15.4
Q ss_pred HHHHHhhcccCCCHHHHHHHH
Q psy4090 81 LEQVIKTRWKALPREQCDVKE 101 (112)
Q Consensus 81 Le~~I~~~W~~Lp~eqr~~IR 101 (112)
.-..|..+|..|++++|....
T Consensus 35 ~~k~~~~~Wk~Ls~~EK~~Y~ 55 (73)
T PF09011_consen 35 VMKEISERWKSLSEEEKEPYE 55 (73)
T ss_dssp HHHHHHHHHHHS-HHHHHHHH
T ss_pred HHHHHHHHHHhcCHHHHHHHH
Confidence 335688999999999986543
No 71
>PF08568 Kinetochor_Ybp2: Uncharacterised protein family, YAP/Alf4/glomulin; InterPro: IPR013877 This is a family of proteins integrally involved in the central kinetochore. In baker's yeast the protein seems to be part of a macromolecular kinetochore complex and appears to contribute to the proper associations among the central kinetochore sub-complexes and the kinetochore-specific nucleosome. The family is localised in such a way as to bridge the COMA and Ndc80 complexes onto the centromeric nucleosome []. This family also includes aberrant root formation protein 4 and glomulin. Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress) is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation []. Glomulin (FAP68) is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 [, ].
Probab=28.04 E-value=3.5e+02 Score=23.52 Aligned_cols=60 Identities=20% Similarity=0.181 Sum_probs=44.2
Q ss_pred HhCCChHHHHHHHHHHHH----HhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCC
Q psy4090 33 MYTGMGVEQKAAQEVLTA----LKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALP 93 (112)
Q Consensus 33 ~y~~~~~~r~~A~~iL~~----fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp 93 (112)
.++|...-|..+-+++.. +-+.. .......+|+.+..+.+|=+++.+|...|...++.-+
T Consensus 451 ~~~p~~~lR~~~~~ll~~iL~~~p~~~-rf~~i~dlLe~c~~~~~k~~~I~~lKd~i~~a~~~~~ 514 (633)
T PF08568_consen 451 VYCPSPELRKIAFTLLTRILHLFPEET-RFKFIRDLLENCPFESLKASAIGWLKDEILKALQSSD 514 (633)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHCCcHh-HHHHHHHHHhcCCCHhHHHHHHHHHHHHHHHHhccCC
Confidence 456655557666555544 44433 7778888899999999999999999999877665543
No 72
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=27.39 E-value=1.4e+02 Score=19.53 Aligned_cols=78 Identities=10% Similarity=0.132 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCcc-----HHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHH
Q psy4090 23 ITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDA-----WTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQC 97 (112)
Q Consensus 23 v~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pda-----w~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr 97 (112)
|..|-..|.... ......++-+...++..|.. .--++.|+.++..++..+|+-.+ ......-....+++.|
T Consensus 21 I~~lt~~a~~~~---~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~~~~~~-~~~f~~~~~~~~~~~r 96 (114)
T cd03562 21 IQTLTKLAIENR---KHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEFFSEFL-VPLFLDAYEKVDEKTR 96 (114)
T ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHHHHHHH-HHHHHHHHHhCCHHHH
Confidence 455555554432 23345566667777776642 23467788999999998887653 3333433446788888
Q ss_pred HHHHHHh
Q psy4090 98 DVKEEKE 104 (112)
Q Consensus 98 ~~IRnyv 104 (112)
..|+.=+
T Consensus 97 ~kl~rl~ 103 (114)
T cd03562 97 KKLERLL 103 (114)
T ss_pred HHHHHHH
Confidence 8877654
No 73
>PTZ00199 high mobility group protein; Provisional
Probab=27.14 E-value=44 Score=21.85 Aligned_cols=19 Identities=16% Similarity=0.443 Sum_probs=15.4
Q ss_pred HHHHHhhcccCCCHHHHHH
Q psy4090 81 LEQVIKTRWKALPREQCDV 99 (112)
Q Consensus 81 Le~~I~~~W~~Lp~eqr~~ 99 (112)
+...|..+|+.||+++|.-
T Consensus 55 vsk~ige~Wk~ls~eeK~~ 73 (94)
T PTZ00199 55 VGKMVGEAWNKLSEEEKAP 73 (94)
T ss_pred HHHHHHHHHHcCCHHHHHH
Confidence 4467899999999999753
No 74
>PHA02878 ankyrin repeat protein; Provisional
Probab=25.86 E-value=71 Score=26.20 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=21.6
Q ss_pred HHHHHHHHH----hhcccCCCHHHHHHHHHHhH
Q psy4090 77 ALQILEQVI----KTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 77 ALqiLe~~I----~~~W~~Lp~eqr~~IRnyv~ 105 (112)
|+.+|++.+ ++.|+.||.|-|--|=+|+.
T Consensus 431 ~~~~i~~~~~~~~~~~w~~lP~Eik~~Il~~l~ 463 (477)
T PHA02878 431 AIYSLDNIFFEKQNYMWNRLPLEIKHYIMELLD 463 (477)
T ss_pred HHHHHHHHhcccccCcHhhCCHHHHHHHHHHcC
Confidence 345566655 46899999999888877764
No 75
>PHA02875 ankyrin repeat protein; Provisional
Probab=25.69 E-value=72 Score=25.37 Aligned_cols=28 Identities=25% Similarity=0.522 Sum_probs=21.3
Q ss_pred HHHHHHHH---hhcccCCCHHHHHHHHHHhH
Q psy4090 78 LQILEQVI---KTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 78 LqiLe~~I---~~~W~~Lp~eqr~~IRnyv~ 105 (112)
..+++..+ ++.|+.||.|-|--|=.|+.
T Consensus 373 ~~~i~~~~~~~~~~w~~LP~Eik~~Il~~l~ 403 (413)
T PHA02875 373 IRVIDDEITGDESKWNILPHEIKYLILEKIG 403 (413)
T ss_pred HHHHHhhccccccchhcCcHHHHHHHHHHhc
Confidence 44555555 68899999999988877763
No 76
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=25.23 E-value=51 Score=20.10 Aligned_cols=20 Identities=30% Similarity=0.655 Sum_probs=15.8
Q ss_pred HHHHHHhhcccCCCHHHHHH
Q psy4090 80 ILEQVIKTRWKALPREQCDV 99 (112)
Q Consensus 80 iLe~~I~~~W~~Lp~eqr~~ 99 (112)
-+...|...|+.+++++|.-
T Consensus 31 eisk~l~~~Wk~ls~~eK~~ 50 (72)
T cd01388 31 AISKILGDRWKALSNEEKQP 50 (72)
T ss_pred HHHHHHHHHHHcCCHHHHHH
Confidence 34567789999999999754
No 77
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=25.04 E-value=70 Score=19.70 Aligned_cols=22 Identities=14% Similarity=0.261 Sum_probs=16.9
Q ss_pred HHHHHHHhhcccCCCHHHHHHH
Q psy4090 79 QILEQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 79 qiLe~~I~~~W~~Lp~eqr~~I 100 (112)
+-+...|...|+.|+++.|.--
T Consensus 30 ~eisk~~g~~Wk~ls~eeK~~y 51 (77)
T cd01389 30 NEISRIIGRMWRSESPEVKAYY 51 (77)
T ss_pred HHHHHHHHHHHhhCCHHHHHHH
Confidence 3455677899999999997643
No 78
>KOG4368|consensus
Probab=24.86 E-value=2e+02 Score=25.86 Aligned_cols=39 Identities=23% Similarity=0.393 Sum_probs=26.5
Q ss_pred HHHHHhhcccccCCHHHHHHHHHHHhCCCh-HHHHHHHHHH
Q psy4090 9 EQFKKLLDFNQKLDITLLDNIVECMYTGMG-VEQKAAQEVL 48 (112)
Q Consensus 9 ~~~~~lld~~~~~dv~~Ld~vv~~~y~~~~-~~r~~A~~iL 48 (112)
..|+++|. ...+|+..||.+++.+.+... .-..+|.++.
T Consensus 90 ~~~~k~l~-~~~l~~~~~~~~l~~~~~~c~kd~is~~k~w~ 129 (757)
T KOG4368|consen 90 QQMQKLLE-ETQLDMNEFDNLLQPIIDTCTKDAISAGKNWM 129 (757)
T ss_pred HHHHHHHH-hccCCHHHHHHHHHHHHHHHhHHHHHHhhhhh
Confidence 35777886 456899999999999876422 2344555554
No 79
>COG5016 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]
Probab=24.67 E-value=46 Score=28.45 Aligned_cols=38 Identities=16% Similarity=0.169 Sum_probs=31.7
Q ss_pred cCchHHHHHHHHHHHHHHHhh-cccCCCHHHHHHHHHHh
Q psy4090 67 YSSNQQTKFYALQILEQVIKT-RWKALPREQCDVKEEKE 104 (112)
Q Consensus 67 ~S~~~~tk~fALqiLe~~I~~-~W~~Lp~eqr~~IRnyv 104 (112)
..-.|-++++|.|..-+++.- ||+.++.|-+.-+|++.
T Consensus 338 PLVTPtSQiVGtQAvlNVl~GerYK~It~E~~~yv~G~Y 376 (472)
T COG5016 338 PLVTPTSQIVGTQAVLNVLTGERYKVITKETKDYVKGLY 376 (472)
T ss_pred CccCchhhhhhHHHHHHHHhcchhhHHHHHHHHHhcccc
Confidence 356788999999999999998 99999999876666543
No 80
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=24.63 E-value=2e+02 Score=18.43 Aligned_cols=43 Identities=26% Similarity=0.404 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChHHHHHHHH-HHHHHh-------cCCccHHHHHHHhccCc
Q psy4090 26 LDNIVECMYTGMGVEQKAAQE-VLTALK-------EHPDAWTRVDTILEYSS 69 (112)
Q Consensus 26 Ld~vv~~~y~~~~~~r~~A~~-iL~~fk-------~~pdaw~~v~~IL~~S~ 69 (112)
.+.|++++|..++.- ..|.. +|..++ +.|.-|+..+..+=.+.
T Consensus 11 ~~~v~~aL~~tSgd~-~~a~~~vl~~l~~g~~~P~n~~GiWT~eDD~~L~~~ 61 (87)
T PF11626_consen 11 REFVTHALYATSGDP-ELARRFVLNFLQAGKGIPDNMPGIWTPEDDEMLRSG 61 (87)
T ss_dssp HHHHHHHHHHTTTBH-HHHHHHHHHCHCHTTSS-TT-TT---HHHHHHHTS-
T ss_pred HHHHHHHHHHhCCCH-HHHHHHHHHHHHcCCCCCCCCCCCcCHHHHHHHHcC
Confidence 466788888766543 34555 666666 45789998877664444
No 81
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=24.60 E-value=1.8e+02 Score=22.17 Aligned_cols=55 Identities=13% Similarity=0.194 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhc--CCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHhH
Q psy4090 41 QKAAQEVLTALKE--HPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 41 r~~A~~iL~~fk~--~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv~ 105 (112)
|+.|+.++. +|. .+++|..|..-|..++ .|-+| =|..+|.. .|.++|..+|.--+
T Consensus 94 K~sA~dLl~-vK~LId~~aW~YVq~~LRlka-syLry----DL~tiIss----kP~~eK~~L~~Lan 150 (190)
T PLN02999 94 KQTAEGLRD-MREMLDHMSWRYVIFYIRLKQ-AYLSQ----DLTNAMNI----LPESRRNDYVQAAN 150 (190)
T ss_pred HHHHHHHHH-HHHHhccccHHHHHHHHHHHH-HHHHH----HHHHHHhc----CCHhhhHHHHHHHH
Confidence 455666543 444 5789999999984443 33333 36677776 59999999987544
No 82
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=23.80 E-value=48 Score=22.47 Aligned_cols=17 Identities=41% Similarity=0.581 Sum_probs=12.2
Q ss_pred cccCCCHHHHHHHHHHh
Q psy4090 88 RWKALPREQCDVKEEKE 104 (112)
Q Consensus 88 ~W~~Lp~eqr~~IRnyv 104 (112)
+|..||+++|..+|.=+
T Consensus 55 ~W~~LspeqR~~~R~~~ 71 (107)
T PF11304_consen 55 RWAALSPEQRQQARENY 71 (107)
T ss_pred HHHhCCHHHHHHHHHHH
Confidence 77788888877776533
No 83
>PRK13800 putative oxidoreductase/HEAT repeat-containing protein; Provisional
Probab=23.80 E-value=3.8e+02 Score=24.42 Aligned_cols=60 Identities=15% Similarity=0.060 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHH
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQ 83 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~ 83 (112)
+-+.++.++..+-++...-|+.|-+.|..+. .|.+-..+...| .+.++.++.-|+..|-.
T Consensus 619 ~~~~~~~L~~~L~D~d~~VR~~Av~~L~~~~-~~~~~~~L~~aL-~D~d~~VR~~Aa~aL~~ 678 (897)
T PRK13800 619 DAPSVAELAPYLADPDPGVRRTAVAVLTETT-PPGFGPALVAAL-GDGAAAVRRAAAEGLRE 678 (897)
T ss_pred cchhHHHHHHHhcCCCHHHHHHHHHHHhhhc-chhHHHHHHHHH-cCCCHHHHHHHHHHHHH
Confidence 4455666666655555556777777766654 344444444455 45566666666665543
No 84
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=23.14 E-value=2.6e+02 Score=20.73 Aligned_cols=53 Identities=17% Similarity=0.307 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhcCCc-----cHHHHHHHhccCchHHHHHHHHHHH-HHHHhhcccCCCHHHHHHH
Q psy4090 41 QKAAQEVLTALKEHPD-----AWTRVDTILEYSSNQQTKFYALQIL-EQVIKTRWKALPREQCDVK 100 (112)
Q Consensus 41 r~~A~~iL~~fk~~pd-----aw~~v~~IL~~S~~~~tk~fALqiL-e~~I~~~W~~Lp~eqr~~I 100 (112)
++.++++|..+++.+. .-..+..+++. +|-...+ ..++-.+|+.++++||...
T Consensus 31 ~~~~~~vl~~l~~~~~~~~~~~~~~l~~iv~~-------~~Df~~mar~vLG~~W~~~s~~Qr~~F 89 (198)
T TIGR03481 31 DALHGALLDVMKEAKKLGYQGRYTKLAPAVRE-------AFDLPAMARLTLGSSWTSLSPEQRRRF 89 (198)
T ss_pred HHHHHHHHHHHHhccccchhhHHHHHHHHHHH-------hCCHHHHHHHHhhhhhhhCCHHHHHHH
Confidence 6778888888887542 22344444433 2222222 3355679999999998874
No 85
>KOG1086|consensus
Probab=23.13 E-value=1.7e+02 Score=25.51 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=24.2
Q ss_pred cCCHHHHHHHHHHHhCC-ChH---HHHHHHHHHHHHhcCCccHHH
Q psy4090 20 KLDITLLDNIVECMYTG-MGV---EQKAAQEVLTALKEHPDAWTR 60 (112)
Q Consensus 20 ~~dv~~Ld~vv~~~y~~-~~~---~r~~A~~iL~~fk~~pdaw~~ 60 (112)
.-|...++..|+.+|.. .++ -|--||++ ++|+-|.-
T Consensus 23 eedw~ai~~fceqinkdp~gp~lAv~LlaHKi-----qSPqe~EA 62 (594)
T KOG1086|consen 23 EEDWKAIDGFCEQINKDPEGPLLAVRLLAHKI-----QSPQEWEA 62 (594)
T ss_pred HHHHHHHHHHHHHHhcCCCCchhHHHHHHhhc-----CChhHHHH
Confidence 45788999999998853 333 34445554 67888865
No 86
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=23.08 E-value=61 Score=20.18 Aligned_cols=23 Identities=22% Similarity=0.463 Sum_probs=18.4
Q ss_pred ChHHHHHHHHHHHHHhcCCccHH
Q psy4090 37 MGVEQKAAQEVLTALKEHPDAWT 59 (112)
Q Consensus 37 ~~~~r~~A~~iL~~fk~~pdaw~ 59 (112)
.+.++...+++|.+.=++.|.|.
T Consensus 42 ~~~~k~~i~~iLqe~we~aD~W~ 64 (65)
T PF06183_consen 42 KKDDKERIEEILQEMWEDADDWL 64 (65)
T ss_dssp -HHHHHHHHHHHHHHHHTHHHH-
T ss_pred CchHHHHHHHHHHHHHhccccCc
Confidence 33458999999999999999995
No 87
>PF11864 DUF3384: Domain of unknown function (DUF3384); InterPro: IPR024584 This entry represents the N-terminal domain of tuberin which is functionally uncharacterised.
Probab=22.77 E-value=1.2e+02 Score=25.40 Aligned_cols=36 Identities=17% Similarity=0.319 Sum_probs=32.1
Q ss_pred CccHHHHHHHhccCchHHHHHHHHHHHHHHHhhccc
Q psy4090 55 PDAWTRVDTILEYSSNQQTKFYALQILEQVIKTRWK 90 (112)
Q Consensus 55 pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~ 90 (112)
++-|.-+..+++..+++.+|.-|+..|..+|++.-.
T Consensus 27 ~~iW~~~~DLi~~~~p~e~R~~~~~ll~~~i~~~~~ 62 (464)
T PF11864_consen 27 EEIWYAAKDLIDPNQPSEARRAALELLIACIKRQDS 62 (464)
T ss_pred HHHHHHHhhhcCCCCCHHHHHHHHHHHHHHHHcccc
Confidence 346888999999999999999999999999999754
No 88
>PF04826 Arm_2: Armadillo-like; InterPro: IPR006911 This entry consists of mammalian proteins of unknown function.
Probab=22.74 E-value=3.7e+02 Score=20.85 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=22.2
Q ss_pred cHHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHhH
Q psy4090 57 AWTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 57 aw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv~ 105 (112)
....+..+|.. .+|.+|--|+..|.+. .-+.|.+.-|+.|+.
T Consensus 55 gi~lI~~lL~~-p~~~vr~~AL~aL~Nl------s~~~en~~~Ik~~i~ 96 (254)
T PF04826_consen 55 GISLIGSLLND-PNPSVREKALNALNNL------SVNDENQEQIKMYIP 96 (254)
T ss_pred CHHHHHHHcCC-CChHHHHHHHHHHHhc------CCChhhHHHHHHHHH
Confidence 33444444433 4566666666666654 223455555666654
No 89
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=22.53 E-value=92 Score=18.41 Aligned_cols=25 Identities=12% Similarity=0.274 Sum_probs=16.2
Q ss_pred HHHHHhhcccCCCHHHHHHHHHHhH
Q psy4090 81 LEQVIKTRWKALPREQCDVKEEKER 105 (112)
Q Consensus 81 Le~~I~~~W~~Lp~eqr~~IRnyv~ 105 (112)
|-..|+++++.+|-++.+-|-+|+.
T Consensus 26 La~~V~kHF~s~~v~E~evI~~Fly 50 (53)
T PF13867_consen 26 LANAVRKHFNSQPVDENEVIANFLY 50 (53)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHH
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 5567788888888888888888764
No 90
>PF10188 Oscp1: Organic solute transport protein 1; InterPro: IPR019332 Organic solute carrier protein 1, or Oscp1, is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red-nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein.
Probab=22.10 E-value=3.4e+02 Score=20.22 Aligned_cols=51 Identities=10% Similarity=0.212 Sum_probs=35.0
Q ss_pred HHHHHHHhccCchHHHHHHHHHHHHHHHhhcccCCCHHHHHHHHHHhHhhhhhc
Q psy4090 58 WTRVDTILEYSSNQQTKFYALQILEQVIKTRWKALPREQCDVKEEKEREQNWFQ 111 (112)
Q Consensus 58 w~~v~~IL~~S~~~~tk~fALqiLe~~I~~~W~~Lp~eqr~~IRnyv~~~~~~~ 111 (112)
|.|.+.|.+--.++.++...-.+...+ ..-|..|++.+-..||+-+. +|||
T Consensus 100 lnHld~i~~~v~~~~~~~~v~~~~~~~-~~~y~~ls~~~~~~iR~~ll--~flq 150 (173)
T PF10188_consen 100 LNHLDAIRDLVPDPEVQALVDEVFNRL-IEFYGKLSPGEFQLIRQTLL--NFLQ 150 (173)
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHH-HHHHhCCCHHHHHHHHHHHH--HHhC
Confidence 556666666556576666655444444 56689999999999998876 4554
No 91
>PRK12331 oxaloacetate decarboxylase; Provisional
Probab=21.76 E-value=80 Score=26.68 Aligned_cols=50 Identities=22% Similarity=0.199 Sum_probs=34.7
Q ss_pred cCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhh-cccCCCHHHHHHHHHHh
Q psy4090 53 EHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKT-RWKALPREQCDVKEEKE 104 (112)
Q Consensus 53 ~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~-~W~~Lp~eqr~~IRnyv 104 (112)
+-|..+..++++. .-.|-+|+.|-+.+-+++.. ||+.+|.+-+.-+++|+
T Consensus 326 e~~~v~~~lG~~~--~VTP~Sq~vg~~A~~nvl~g~r~~~~~~~~~~~~~G~~ 376 (448)
T PRK12331 326 EVPKVRADLGYPP--LVTPLSQMVGTQALMNVISGERYKMVPNEIKDYVRGLY 376 (448)
T ss_pred HHHHHHHHcCCCC--eeCChhHHHHHHHHHHHhcchhhccCCHHHHHHhCcCC
Confidence 3344444333333 34577899999998898887 78899999877776654
No 92
>cd05505 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=21.05 E-value=75 Score=20.96 Aligned_cols=21 Identities=14% Similarity=0.287 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHhcCCccHHHH
Q psy4090 41 QKAAQEVLTALKEHPDAWTRV 61 (112)
Q Consensus 41 r~~A~~iL~~fk~~pdaw~~v 61 (112)
.+.+.++|..+.++|.||.+.
T Consensus 2 ~~~c~~il~~l~~~~~s~~F~ 22 (97)
T cd05505 2 LQKCEEILSKILKYRFSWPFR 22 (97)
T ss_pred HHHHHHHHHHHHhCCCccccc
Confidence 467889999999999999864
No 93
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=20.52 E-value=5.3e+02 Score=21.81 Aligned_cols=20 Identities=15% Similarity=0.184 Sum_probs=10.8
Q ss_pred CCCHHHHH-HHHHHhHhhhhh
Q psy4090 91 ALPREQCD-VKEEKEREQNWF 110 (112)
Q Consensus 91 ~Lp~eqr~-~IRnyv~~~~~~ 110 (112)
.++...-. .+|.||+|-.|+
T Consensus 470 ~~~~~~~~~kL~~yv~eGpy~ 490 (503)
T PF10508_consen 470 VFDDPEYLGKLQEYVREGPYY 490 (503)
T ss_pred cCCCHHHHHHHHHHHHcCCcc
Confidence 33333333 666676666654
No 94
>PRK14041 oxaloacetate decarboxylase; Provisional
Probab=20.19 E-value=71 Score=27.20 Aligned_cols=49 Identities=16% Similarity=0.158 Sum_probs=35.0
Q ss_pred ccHHHHHHHhc--cCchHHHHHHHHHHHHHHHhh-cccCCCHHHHHHHHHHh
Q psy4090 56 DAWTRVDTILE--YSSNQQTKFYALQILEQVIKT-RWKALPREQCDVKEEKE 104 (112)
Q Consensus 56 daw~~v~~IL~--~S~~~~tk~fALqiLe~~I~~-~W~~Lp~eqr~~IRnyv 104 (112)
+..++|...|. -.-.|-+|+.|-|.+-++++. ||+.+|.+-+.-+++|+
T Consensus 321 ~e~~~v~~~lG~~~~VTP~Sq~vg~~A~~Nvl~g~r~~~~~~~~~~~~~G~~ 372 (467)
T PRK14041 321 EEVPRVRKDLGYPPLVTPTSQIVGVQAVLNVLTGERYKRVTNETKNYVKGLY 372 (467)
T ss_pred HHHHHHHHHcCCCCcCCChhHHHHHHHHHhhcChhheeeCCHHHHHHhCcCC
Confidence 34444444442 234677899999988899887 79999999877766654
No 95
>cd03571 ENTH_epsin ENTH domain, Epsin family; The epsin (Eps15 interactor) N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the trans-Golgi network, which suggests that E/ANTH domains are univ
Probab=20.14 E-value=3.1e+02 Score=18.97 Aligned_cols=53 Identities=25% Similarity=0.389 Sum_probs=34.5
Q ss_pred CHHHHHHHHHHHhCCChHHHHHHHHHHHHHhcCCccHHHHHHHhccCchHHHHHHHHHHHHHHHhhc
Q psy4090 22 DITLLDNIVECMYTGMGVEQKAAQEVLTALKEHPDAWTRVDTILEYSSNQQTKFYALQILEQVIKTR 88 (112)
Q Consensus 22 dv~~Ld~vv~~~y~~~~~~r~~A~~iL~~fk~~pdaw~~v~~IL~~S~~~~tk~fALqiLe~~I~~~ 88 (112)
.-..+..++...|+.. .-...-.-+...+.+++..|.+| |=||.+|+.+|++-
T Consensus 18 ~~~~m~eIa~~t~~~~-~~~~Im~~l~kRL~~~~k~WR~v-------------yKaL~lleyLl~nG 70 (123)
T cd03571 18 SGTLMAEIARATYNYV-EFQEIMSMLWKRLNDKGKNWRHV-------------YKALTLLEYLLKNG 70 (123)
T ss_pred CHHHHHHHHHHhCCHH-HHHHHHHHHHHHHHhccccHHHH-------------HHHHHHHHHHHHhC
Confidence 4567888888877752 22344445555666778888774 44667777777774
Done!