Query 025621
Match_columns 250
No_of_seqs 137 out of 1392
Neff 9.5
Searched_HMMs 46136
Date Fri Mar 29 07:43:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1315 Predicted DHHC-type Zn 100.0 5.8E-37 1.3E-41 252.4 9.0 230 8-245 13-285 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 1.5E-33 3.3E-38 229.1 15.3 225 3-246 10-283 (414)
3 KOG1311 DHHC-type Zn-finger pr 99.9 4.9E-27 1.1E-31 198.0 15.4 171 65-243 79-295 (299)
4 PF01529 zf-DHHC: DHHC palmito 99.9 1.2E-23 2.6E-28 164.0 7.7 130 57-186 2-174 (174)
5 COG5273 Uncharacterized protei 99.9 4.2E-22 9.1E-27 166.8 14.6 202 41-242 55-304 (309)
6 KOG1313 DHHC-type Zn-finger pr 99.9 5.6E-22 1.2E-26 157.0 13.3 145 94-240 101-304 (309)
7 KOG0509 Ankyrin repeat and DHH 99.7 3.5E-18 7.7E-23 150.0 8.5 162 54-218 380-585 (600)
8 KOG1312 DHHC-type Zn-finger pr 99.7 2.3E-17 5E-22 131.7 8.9 80 40-122 96-175 (341)
9 COG5273 Uncharacterized protei 94.8 0.05 1.1E-06 46.2 4.7 98 92-189 120-248 (309)
10 PF01529 zf-DHHC: DHHC palmito 93.7 0.026 5.6E-07 43.6 0.8 28 92-119 59-86 (174)
11 KOG1315 Predicted DHHC-type Zn 93.6 0.11 2.5E-06 43.7 4.5 50 200-249 248-298 (307)
12 KOG1311 DHHC-type Zn-finger pr 93.3 0.034 7.3E-07 47.1 0.9 27 93-119 125-151 (299)
13 KOG1314 DHHC-type Zn-finger pr 93.0 0.088 1.9E-06 44.6 3.0 62 57-119 68-129 (414)
14 PF13240 zinc_ribbon_2: zinc-r 91.8 0.091 2E-06 26.1 1.0 21 97-117 1-21 (23)
15 PF10571 UPF0547: Uncharacteri 89.1 0.19 4.1E-06 25.8 0.8 22 96-117 1-22 (26)
16 PF13248 zf-ribbon_3: zinc-rib 88.3 0.28 6.1E-06 25.1 1.1 22 96-117 3-24 (26)
17 KOG1313 DHHC-type Zn-finger pr 87.9 0.2 4.3E-06 41.1 0.6 64 51-119 77-140 (309)
18 PRK04136 rpl40e 50S ribosomal 86.3 0.36 7.8E-06 28.5 0.9 24 94-117 13-36 (48)
19 PF07010 Endomucin: Endomucin; 85.0 2.3 5E-05 34.0 5.0 38 43-80 195-232 (259)
20 KOG0509 Ankyrin repeat and DHH 84.1 0.35 7.5E-06 44.1 0.2 29 91-119 430-458 (600)
21 PRK15103 paraquat-inducible me 83.9 28 0.0006 31.1 12.0 29 94-122 220-248 (419)
22 PTZ00303 phosphatidylinositol 79.6 0.83 1.8E-05 43.0 1.0 22 96-117 461-489 (1374)
23 PHA02680 ORF090 IMV phosphoryl 77.4 12 0.00026 25.2 5.6 27 159-185 57-83 (91)
24 KOG1312 DHHC-type Zn-finger pr 77.1 0.51 1.1E-05 39.0 -1.0 30 93-122 160-189 (341)
25 COG2093 DNA-directed RNA polym 75.1 1.4 3.1E-05 27.5 0.8 23 95-117 4-26 (64)
26 COG1552 RPL40A Ribosomal prote 73.8 0.73 1.6E-05 27.2 -0.7 24 94-117 13-36 (50)
27 PF12773 DZR: Double zinc ribb 71.4 3 6.5E-05 24.8 1.6 23 94-116 28-50 (50)
28 PF00641 zf-RanBP: Zn-finger i 69.0 1.7 3.8E-05 22.8 0.2 20 97-116 6-25 (30)
29 TIGR00155 pqiA_fam integral me 68.7 43 0.00093 29.7 8.9 29 94-122 214-243 (403)
30 PF01363 FYVE: FYVE zinc finge 67.2 1.5 3.4E-05 28.0 -0.3 26 94-119 8-35 (69)
31 KOG1842 FYVE finger-containing 66.3 1.4 3.1E-05 38.6 -0.7 29 94-122 179-209 (505)
32 PF14127 DUF4294: Domain of un 65.7 5.9 0.00013 30.0 2.5 33 173-218 102-134 (157)
33 PF09889 DUF2116: Uncharacteri 65.1 11 0.00024 23.5 3.3 23 95-117 3-26 (59)
34 smart00064 FYVE Protein presen 64.4 4.3 9.4E-05 25.8 1.4 25 95-119 10-36 (68)
35 PF01020 Ribosomal_L40e: Ribos 59.7 4.5 9.8E-05 24.3 0.8 25 94-118 16-42 (52)
36 cd00065 FYVE FYVE domain; Zinc 55.2 7.3 0.00016 23.6 1.2 23 96-118 3-27 (57)
37 PRK02251 putative septation in 54.8 64 0.0014 21.8 6.6 32 4-35 29-60 (87)
38 cd01995 ExsB ExsB is a transcr 54.3 7.1 0.00015 29.7 1.3 26 94-122 139-164 (169)
39 PF08113 CoxIIa: Cytochrome c 53.8 26 0.00056 19.0 2.9 23 1-23 1-23 (34)
40 COG4640 Predicted membrane pro 53.1 28 0.0006 30.5 4.7 28 95-122 1-28 (465)
41 KOG1841 Smad anchor for recept 53.1 7.2 0.00016 38.5 1.3 23 95-117 557-581 (1287)
42 PRK03681 hypA hydrogenase nick 52.5 6.6 0.00014 28.1 0.8 24 94-117 69-95 (114)
43 KOG1819 FYVE finger-containing 51.5 4.4 9.4E-05 36.3 -0.3 24 94-117 900-925 (990)
44 PF06781 UPF0233: Uncharacteri 50.4 78 0.0017 21.5 6.2 30 3-32 27-56 (87)
45 PF07649 C1_3: C1-like domain; 49.4 4.2 9.1E-05 21.3 -0.5 21 97-117 2-23 (30)
46 PF07282 OrfB_Zn_ribbon: Putat 48.5 8.1 0.00018 24.6 0.7 27 94-120 27-57 (69)
47 KOG1818 Membrane trafficking a 47.7 7.7 0.00017 36.1 0.6 24 94-117 164-189 (634)
48 PF02150 RNA_POL_M_15KD: RNA p 45.8 5.4 0.00012 21.9 -0.4 7 96-102 2-8 (35)
49 PRK00432 30S ribosomal protein 44.9 9.9 0.00021 22.8 0.6 23 94-116 19-44 (50)
50 PF09297 zf-NADH-PPase: NADH p 44.3 6.9 0.00015 20.9 -0.1 22 95-116 3-28 (32)
51 PF03503 Chlam_OMP3: Chlamydia 43.4 15 0.00032 21.6 1.2 21 96-116 24-44 (55)
52 PRK02935 hypothetical protein; 42.1 1.2E+02 0.0026 21.3 6.9 8 96-103 87-94 (110)
53 PF05814 DUF843: Baculovirus p 41.7 1.1E+02 0.0023 20.5 5.4 23 165-188 38-60 (83)
54 smart00661 RPOL9 RNA polymeras 40.8 10 0.00023 22.5 0.3 9 96-104 21-29 (52)
55 TIGR00364 exsB protein. This p 38.3 16 0.00035 28.7 1.1 23 96-121 179-201 (201)
56 smart00547 ZnF_RBZ Zinc finger 38.1 14 0.00031 18.4 0.5 20 97-116 4-23 (26)
57 COG1579 Zn-ribbon protein, pos 37.3 32 0.0007 28.1 2.6 27 94-120 196-232 (239)
58 PF04161 Arv1: Arv1-like famil 36.9 1.2E+02 0.0025 24.2 5.8 16 107-122 22-37 (208)
59 PF06508 QueC: Queuosine biosy 36.8 19 0.0004 28.8 1.2 28 94-122 176-203 (209)
60 TIGR00155 pqiA_fam integral me 36.8 1.2E+02 0.0026 26.9 6.4 29 94-122 12-46 (403)
61 COG1852 Uncharacterized conser 36.6 14 0.00031 28.9 0.5 23 100-122 102-124 (209)
62 PRK14559 putative protein seri 36.2 19 0.00041 34.0 1.3 28 95-122 27-54 (645)
63 PF07754 DUF1610: Domain of un 35.8 20 0.00043 17.9 0.8 19 98-116 1-23 (24)
64 PHA02942 putative transposase; 35.0 17 0.00038 31.9 0.8 26 94-119 324-352 (383)
65 PHA02898 virion envelope prote 34.8 1.5E+02 0.0032 20.1 6.3 25 157-181 54-79 (92)
66 PRK13130 H/ACA RNA-protein com 34.0 21 0.00045 22.0 0.8 22 94-117 4-25 (56)
67 TIGR02745 ccoG_rdxA_fixG cytoc 33.2 1.5E+02 0.0032 26.7 6.4 12 110-121 255-266 (434)
68 PF06143 Baculo_11_kDa: Baculo 32.9 1.6E+02 0.0034 19.9 4.9 8 170-177 56-63 (84)
69 COG2956 Predicted N-acetylgluc 32.1 18 0.0004 31.0 0.5 26 93-118 352-377 (389)
70 KOG0230 Phosphatidylinositol-4 31.3 22 0.00048 36.4 1.0 24 94-118 4-27 (1598)
71 KOG1729 FYVE finger containing 31.0 11 0.00024 31.7 -1.0 26 94-119 167-195 (288)
72 PRK14559 putative protein seri 30.9 26 0.00057 33.1 1.4 23 94-118 14-36 (645)
73 PRK12380 hydrogenase nickel in 30.7 23 0.00051 25.2 0.8 24 94-117 69-94 (113)
74 KOG2927 Membrane component of 30.4 1.1E+02 0.0024 26.5 4.8 16 98-113 266-281 (372)
75 PRK15103 paraquat-inducible me 30.1 1.8E+02 0.0039 26.0 6.3 27 96-122 11-43 (419)
76 PRK00159 putative septation in 29.9 1.8E+02 0.0039 19.7 6.6 29 4-32 28-56 (87)
77 KOG4606 Uncharacterized conser 29.7 1.4E+02 0.0031 21.0 4.4 55 1-55 24-78 (126)
78 PF03107 C1_2: C1 domain; Int 29.0 23 0.00051 18.5 0.4 20 97-116 2-22 (30)
79 TIGR00100 hypA hydrogenase nic 29.0 27 0.00058 25.0 0.8 24 94-117 69-94 (115)
80 PRK10692 hypothetical protein; 28.8 1.9E+02 0.0041 19.6 5.9 18 40-57 40-57 (92)
81 PF12172 DUF35_N: Rubredoxin-l 28.7 13 0.00029 20.4 -0.6 22 94-116 10-32 (37)
82 PRK00564 hypA hydrogenase nick 28.1 29 0.00063 24.9 0.9 24 94-117 70-96 (117)
83 PF12837 Fer4_6: 4Fe-4S bindin 27.8 26 0.00055 17.4 0.4 9 112-120 9-17 (24)
84 PLN00186 ribosomal protein S26 27.8 18 0.0004 25.4 -0.2 14 109-122 20-33 (109)
85 COG1600 Uncharacterized Fe-S p 27.3 31 0.00067 29.8 1.1 17 105-121 180-196 (337)
86 COG1645 Uncharacterized Zn-fin 25.5 22 0.00047 26.1 -0.1 9 109-117 28-36 (131)
87 PF10762 DUF2583: Protein of u 25.4 2.2E+02 0.0047 19.2 5.8 17 41-57 41-57 (89)
88 KOG1710 MYND Zn-finger and ank 25.2 33 0.00071 28.9 0.8 21 94-116 318-338 (396)
89 PF12798 Fer4_3: 4Fe-4S bindin 25.0 32 0.0007 14.9 0.4 9 112-120 1-9 (15)
90 COG0603 Predicted PP-loop supe 25.0 43 0.00092 27.1 1.4 18 105-122 188-205 (222)
91 PF11023 DUF2614: Protein of u 24.7 2.7E+02 0.0058 19.9 5.6 8 97-104 71-78 (114)
92 PF00037 Fer4: 4Fe-4S binding 24.7 30 0.00065 17.0 0.3 10 111-120 7-16 (24)
93 PRK09335 30S ribosomal protein 24.6 21 0.00046 24.5 -0.3 14 109-122 20-33 (95)
94 KOG4399 C2HC-type Zn-finger pr 24.5 36 0.00079 28.0 0.9 23 95-118 261-283 (325)
95 PF12387 Peptidase_C74: Pestiv 24.4 36 0.00079 26.1 0.8 22 96-118 163-184 (200)
96 PRK11106 queuosine biosynthesi 24.3 45 0.00097 27.1 1.4 25 96-122 183-207 (231)
97 PF08772 NOB1_Zn_bind: Nin one 24.2 32 0.00069 22.5 0.5 25 94-118 8-33 (73)
98 PF06689 zf-C4_ClpX: ClpX C4-t 24.2 48 0.001 18.8 1.1 27 96-122 2-34 (41)
99 PTZ00172 40S ribosomal protein 24.0 23 0.00049 25.0 -0.3 14 109-122 20-33 (108)
100 cd00350 rubredoxin_like Rubred 22.6 59 0.0013 17.3 1.3 21 97-117 3-25 (33)
101 PRK06393 rpoE DNA-directed RNA 22.4 42 0.00092 21.3 0.7 22 94-117 4-25 (64)
102 PF14319 Zn_Tnp_IS91: Transpos 22.0 50 0.0011 23.4 1.2 27 92-118 39-69 (111)
103 KOG4800 Neuronal membrane glyc 21.6 2E+02 0.0044 23.2 4.5 16 111-126 113-128 (248)
104 PF01976 DUF116: Protein of un 21.0 55 0.0012 24.9 1.3 22 101-122 56-77 (158)
105 PF13829 DUF4191: Domain of un 20.7 2.8E+02 0.0061 22.5 5.2 16 2-17 20-35 (224)
106 PF00130 C1_1: Phorbol esters/ 20.5 28 0.00062 20.6 -0.3 26 94-119 10-38 (53)
107 PRK14132 riboflavin kinase; Pr 20.1 38 0.00083 24.7 0.2 16 98-113 84-99 (126)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.8e-37 Score=252.37 Aligned_cols=230 Identities=32% Similarity=0.565 Sum_probs=174.8
Q ss_pred chhHHHHHHHHHHHHHHHHHhhhccccccCCcchhHHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCCCCCCcCCCCcchh
Q 025621 8 SLPVSVVVLAIFYIYFTTVFIFIDRWFGLMSSPGLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHE 87 (250)
Q Consensus 8 ~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~~~l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~ 87 (250)
|+|++++...+++.|+++++.+...+.... +...+..++++.+.++.+|+|++++++|||.+|..+.++.++++.....
T Consensus 13 ~~~~~~i~~~~~~~yy~~v~~~c~~~i~~~-~~~~~~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~ 91 (307)
T KOG1315|consen 13 WIPVLIILLVIGWTYYVYVAVLCILSISLT-IPSVLLLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENG 91 (307)
T ss_pred chhheeeeeeEEEEEEEeehhhhHHHHhhh-hHHHHHHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCcccccccc
Confidence 899999999999999999998888776653 5667778899999999999999999999999999988777766433221
Q ss_pred ----------hhhcCCCcccccccccccCCCCCCCcchhhhhhhH---------------------HHHHHHHHH-----
Q 025621 88 ----------IKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM---------------------VLLVGSLTN----- 131 (250)
Q Consensus 88 ----------~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~---------------------~~~~~~~~~----- 131 (250)
..+..+..++|.+|+.+||+|||||++|+|||+|| +++.+.++.
T Consensus 92 ~~~~~~~~~~~~~~~g~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv 171 (307)
T KOG1315|consen 92 SDNERDLPGYTRTSDGAVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLV 171 (307)
T ss_pred CcccccceeeEecCCCCceeecccccccCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHH
Confidence 13345688999999999999999999999999999 112221111
Q ss_pred ----hhhhhhhc---cCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHhhhhHHHHHHhCCCcccCCCC
Q 025621 132 ----DSLEDELQ---TGGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGGTVYKHPYD 204 (250)
Q Consensus 132 ----~~~~~~~~---~~~~~~~~~~~~~~l~~~~~~~~~~ll~~~~~li~~n~TT~E~~~~~~~~~~~~~~~~~~~n~yd 204 (250)
.+...+.. .........+++++++..+++.++.++++|+++|++|+||+|..+..... .+...+|.|+
T Consensus 172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~-----~~~~~~~~~~ 246 (307)
T KOG1315|consen 172 TTLIGFTKYFQGGAGPSSLLLFFIVFLFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFR-----SGLHNKNGFN 246 (307)
T ss_pred HHHHHHHHHHhccccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhcccccc-----ccccccCCcc
Confidence 11111111 11222344556667777888888889999999999999999999874221 1223456666
Q ss_pred hhHHHhHHHhcCCCccceeccCcCCCCCCeeeccccCCccC
Q 025621 205 LGIFENLTSVLGPNIFSWVCPSSRHIGSGLNFRTAYHNAVG 245 (250)
Q Consensus 205 ~G~~~N~~~vfg~~~~~w~~P~~~~~~~g~~~~~~~~~~~~ 245 (250)
. ..|++++||.++..|++|...+.+||..++.+.+.-.+
T Consensus 247 ~--~~n~~~vfg~~~~~wl~P~~~s~~~~~~~~~~~~~~~~ 285 (307)
T KOG1315|consen 247 L--YVNFREVFGSNLLYWLLPIDSSWGDGVSFPLRGDGLDF 285 (307)
T ss_pred e--eecHHHHhCCCceEEeccccCccccCccccccccCCcc
Confidence 6 88999999999999999999888888888887664433
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.5e-33 Score=229.10 Aligned_cols=225 Identities=30% Similarity=0.445 Sum_probs=161.7
Q ss_pred CCcccchhHHHHHHHHHHHHHHHHHhhhccccccCCcchhHHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCCCCCCcCCC
Q 025621 3 KGFTFSLPVSVVVLAIFYIYFTTVFIFIDRWFGLMSSPGLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQ 82 (250)
Q Consensus 3 ~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~~~l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~~~ 82 (250)
|+.+.|-|+..+.. +.++.....+.-...|.+..+..+..+.+.|.+...+.+++|+.+++++||++|.++.|+...++
T Consensus 10 rr~~hwGpi~alsi-it~i~~~~~~~n~lww~p~ss~~g~~n~i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~D~ 88 (414)
T KOG1314|consen 10 RRFLHWGPITALSI-ITIITSTTGYMNSLWWFPLSSFLGVPNQITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPKDE 88 (414)
T ss_pred hheeccccHHHHHH-HHHHHHHHHHhhhhhhccccchhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCChhH
Confidence 46677878776543 44444444444444556666778889999999999999999999999999999999988766553
Q ss_pred CcchhhhhcCCCcccccccccccCCCCCCCcchhhhhhhH---------------------HH---HHHHH---------
Q 025621 83 NPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM---------------------VL---LVGSL--------- 129 (250)
Q Consensus 83 ~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~---------------------~~---~~~~~--------- 129 (250)
...+||.+|+..|++|||||+.|||||.+| ++ .++++
T Consensus 89 ----------~~lqfCk~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~ 158 (414)
T KOG1314|consen 89 ----------MFLQFCKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCA 158 (414)
T ss_pred ----------HHHHHHhhccCcCCCccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhH
Confidence 267999999999999999999999999999 11 12211
Q ss_pred -HHhhhhhhhc-------cCCchhHHH----HHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHhhhhHHHHH----H
Q 025621 130 -TNDSLEDELQ-------TGGSFRTAY----VISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLA----E 193 (250)
Q Consensus 130 -~~~~~~~~~~-------~~~~~~~~~----~~~~~l~~~~~~~~~~ll~~~~~li~~n~TT~E~~~~~~~~~~~----~ 193 (250)
+..++..|.. ....+.... ++..-+++...+++++|++.|+..|.+|+|.+|.+.-.++..++ .
T Consensus 159 ~~~~Iy~~W~~~~g~~hlp~v~ft~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~ 238 (414)
T KOG1314|consen 159 QYRGIYFRWYIKYGLRHLPIVFFTLSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFN 238 (414)
T ss_pred HHHHHHHHHHhhcccccCceeeccHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhcc
Confidence 2222333311 111111111 22222335667888899999999999999999998754443332 2
Q ss_pred hCCCcccCCCChhHHHhHHHhcCCCccceeccCcCCCCCCeeeccccCCccCC
Q 025621 194 KGGTVYKHPYDLGIFENLTSVLGPNIFSWVCPSSRHIGSGLNFRTAYHNAVGA 246 (250)
Q Consensus 194 ~~~~~~~n~yd~G~~~N~~~vfg~~~~~w~~P~~~~~~~g~~~~~~~~~~~~~ 246 (250)
+...+..-|||.|++.|+++||-... ...|||++||..+++.++.
T Consensus 239 d~~~~f~ypydlgWr~n~r~vf~~~~--------~~~gdg~~wPv~~gc~qyt 283 (414)
T KOG1314|consen 239 DDEGEFTYPYDLGWRINLREVFFQNK--------KEEGDGIEWPVVEGCVQYT 283 (414)
T ss_pred CCCCceeeeccccccccHHHHhhhcc--------ccCCCCccccccCcccccc
Confidence 22245788999998899999997543 4689999999999998764
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.95 E-value=4.9e-27 Score=197.96 Aligned_cols=171 Identities=32% Similarity=0.480 Sum_probs=114.8
Q ss_pred cCCCCCCCCCCCCCcC----CCCcchhhhhcCCCcccccccccccCCCCCCCcchhhhhhhH------------------
Q 025621 65 RDPGRVPADYMPDVED----DQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM------------------ 122 (250)
Q Consensus 65 ~dPG~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~------------------ 122 (250)
+|||.+|++.....+. ......+.++...+.++|.+|+..||+|||||+.||+||.||
T Consensus 79 sdpg~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~ 158 (299)
T KOG1311|consen 79 SDPGIVPRADDEQIEDPERAPLYKNVDVNGIQVEWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRY 158 (299)
T ss_pred CCCceecCcccCCCCCccccccCCCcccCCcccceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHH
Confidence 4999999963111111 111223345555689999999999999999999999999999
Q ss_pred -HHHHH-----HHHHhh---hhhh--------hcc---CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHH
Q 025621 123 -VLLVG-----SLTNDS---LEDE--------LQT---GGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEY 182 (250)
Q Consensus 123 -~~~~~-----~~~~~~---~~~~--------~~~---~~~~~~~~~~~~~l~~~~~~~~~~ll~~~~~li~~n~TT~E~ 182 (250)
+.++. +++... .... ... ........++++++++++...++.|+.+|++++.+|+||+|+
T Consensus 159 F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~ 238 (299)
T KOG1311|consen 159 FVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTFLSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYES 238 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhh
Confidence 11111 111100 0000 001 112223334555666777788889999999999999999999
Q ss_pred HhhhhHHHHHHhCCCcccCCCChhHHHhHHHhcCCC-ccceeccCc---CCCCCCeeeccccCCc
Q 025621 183 HEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN-IFSWVCPSS---RHIGSGLNFRTAYHNA 243 (250)
Q Consensus 183 ~~~~~~~~~~~~~~~~~~n~yd~G~~~N~~~vfg~~-~~~w~~P~~---~~~~~g~~~~~~~~~~ 243 (250)
+++.+ .+...++||+|.++|++++||.+ ...|+.|.. +.+.+|-.|+.....+
T Consensus 239 ~~~~~--------~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~~~~p~~~~~~~~~~~~~ 295 (299)
T KOG1311|consen 239 IKSLD--------FVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARSGPLPHDGEGGPPTPHVS 295 (299)
T ss_pred hhccc--------cccccCCCchhHHHHHHHHhCCCCCcccccccccCCCCCCCCCCCCcccccc
Confidence 88611 11125899999999999999975 489999986 4667788777666554
No 4
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.89 E-value=1.2e-23 Score=164.01 Aligned_cols=130 Identities=32% Similarity=0.540 Sum_probs=83.5
Q ss_pred HHHhHHHhcCCCCCCCCCCCCCcCCC--------CcchhhhhcCCCcccccccccccCCCCCCCcchhhhhhhH------
Q 025621 57 FSYTVAILRDPGRVPADYMPDVEDDQ--------NPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVLRM------ 122 (250)
Q Consensus 57 ~~~~~~~~~dPG~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~------ 122 (250)
++|++++++|||++|.....+.+.++ ..+....+.....++|.+|+..||+|||||+.||+||.+|
T Consensus 2 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~DHHC~w 81 (174)
T PF01529_consen 2 WSYFLTIFIDPGYVPRSNPDEDQRQEEKEEEQNQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCNRCVLRFDHHCPW 81 (174)
T ss_pred EEehhhheECCcccCCccccccccccccccccchhhhhhccccCCCCEECcccCCcCCCcceeccccccccccccccchh
Confidence 57889999999999987211111110 1111233345688999999999999999999999999999
Q ss_pred -----------H--H--HHHHHHH---------hhhhhhhc-cCCc---hhHH-HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025621 123 -----------V--L--LVGSLTN---------DSLEDELQ-TGGS---FRTA-YVISGLLLVPLSVALSVLLGWHIYLI 173 (250)
Q Consensus 123 -----------~--~--~~~~~~~---------~~~~~~~~-~~~~---~~~~-~~~~~~l~~~~~~~~~~ll~~~~~li 173 (250)
+ + +...+.. .+...... .... .... .+++.++++++.++++.++++|++++
T Consensus 82 ~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i 161 (174)
T PF01529_consen 82 LGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIFVGFLLIFQLYLI 161 (174)
T ss_pred hccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1 1 1111100 01011000 1111 1111 14445555777888899999999999
Q ss_pred ccCcchHHHHhhh
Q 025621 174 FHNKTTIEYHEGV 186 (250)
Q Consensus 174 ~~n~TT~E~~~~~ 186 (250)
++|+||+|.++++
T Consensus 162 ~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 162 LRNITTYERIKRK 174 (174)
T ss_pred HcCCcHHHHHHcC
Confidence 9999999999863
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=99.88 E-value=4.2e-22 Score=166.81 Aligned_cols=202 Identities=27% Similarity=0.426 Sum_probs=131.0
Q ss_pred hhHHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCCCCCCcCCCCcchhhhhcCCCcccccccccccCCCCCCCcchhhhhh
Q 025621 41 GLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCVL 120 (250)
Q Consensus 41 ~~~~~ii~~~l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV~ 120 (250)
.....+.+.+...+..++++...+.|||+.+++.....-++..+..-..++.+..++|.+|+.+||+|||||+.||+||.
T Consensus 55 ~~~~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~ 134 (309)
T COG5273 55 VVLFIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETISRLLDDGKFGTENFCSTCNIYKPPRSHHCSICNRCVL 134 (309)
T ss_pred hhhhhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhhhhhhhcCccccceeccccccccCCCCccchhhcchhh
Confidence 33445666667778889999999999999986543333333222223444556889999999999999999999999999
Q ss_pred hH-------------------HHHHHHH-----------HHhhhhhhhccCCchhH-HHHHH--HHHHHHHHHHHHHHHH
Q 025621 121 RM-------------------VLLVGSL-----------TNDSLEDELQTGGSFRT-AYVIS--GLLLVPLSVALSVLLG 167 (250)
Q Consensus 121 ~~-------------------~~~~~~~-----------~~~~~~~~~~~~~~~~~-~~~~~--~~l~~~~~~~~~~ll~ 167 (250)
|| +.|+.+. ...+............. ..++. ..+...+++.+..++.
T Consensus 135 k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~~~~~~f~~~~~~~~ 214 (309)
T COG5273 135 KFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCSLLGVVFFIITTLLLL 214 (309)
T ss_pred ccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 99 1111111 11111222222222222 22222 2333555667788999
Q ss_pred HHHHHhccCcchHHHHhhhhHHHHHH-------h--------CCCcccCCCChhHHHhHHHhcCCCccceeccCcCCCCC
Q 025621 168 WHIYLIFHNKTTIEYHEGVRALWLAE-------K--------GGTVYKHPYDLGIFENLTSVLGPNIFSWVCPSSRHIGS 232 (250)
Q Consensus 168 ~~~~li~~n~TT~E~~~~~~~~~~~~-------~--------~~~~~~n~yd~G~~~N~~~vfg~~~~~w~~P~~~~~~~ 232 (250)
++.+++..|+||+|.....|..+..+ . +..+...|++.|.-+|+..+++.+...|..|......+
T Consensus 215 ~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~ 294 (309)
T COG5273 215 FLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLSTIKGSNALYWLTPLHTNYCN 294 (309)
T ss_pred HHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCccccceeecCCCceeeccccccCCCC
Confidence 99999999999999998766533211 1 11123467788888999999999888999885422256
Q ss_pred CeeeccccCC
Q 025621 233 GLNFRTAYHN 242 (250)
Q Consensus 233 g~~~~~~~~~ 242 (250)
+.+++.+.+.
T Consensus 295 ~~~~~~~~~~ 304 (309)
T COG5273 295 SYDFSLRSDT 304 (309)
T ss_pred ccCcccchhh
Confidence 6666665543
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.88 E-value=5.6e-22 Score=157.04 Aligned_cols=145 Identities=26% Similarity=0.360 Sum_probs=101.1
Q ss_pred CcccccccccccCCCCCCCcchhhhhhhH-------------------HHHH-----HHH-------HHhhhhhhh----
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRM-------------------VLLV-----GSL-------TNDSLEDEL---- 138 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~-------------------~~~~-----~~~-------~~~~~~~~~---- 138 (250)
...+|.+|..+||+|+|||++|||||++| ++|+ ++. +.|......
T Consensus 101 ~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NHryFFlFl~~ltlat~~~~i~~~~~w~~~le~~~~~ 180 (309)
T KOG1313|consen 101 NDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNHRYFFLFLFYLTLATSYAAIMCVYTWIDHLEPIEEI 180 (309)
T ss_pred cccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhcccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHhcchHhhc
Confidence 44899999999999999999999999999 1111 111 111110000
Q ss_pred --ccCC----------------chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHhhhhHHHHHHhCCCccc
Q 025621 139 --QTGG----------------SFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRALWLAEKGGTVYK 200 (250)
Q Consensus 139 --~~~~----------------~~~~~~~~~~~l~~~~~~~~~~ll~~~~~li~~n~TT~E~~~~~~~~~~~~~~~~~~~ 200 (250)
...+ ........+.++++.+.++++.+..+|..+|.+|.|++|+....++++...+.+ ..
T Consensus 181 tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~--R~ 258 (309)
T KOG1313|consen 181 TAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHL--RS 258 (309)
T ss_pred ccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhc--cC
Confidence 0000 001112345566667788889999999999999999999998877766555544 38
Q ss_pred CCCChhHHHhHHHhcCC-C-c---cceeccCc-CCCCCCeeecccc
Q 025621 201 HPYDLGIFENLTSVLGP-N-I---FSWVCPSS-RHIGSGLNFRTAY 240 (250)
Q Consensus 201 n~yd~G~~~N~~~vfg~-~-~---~~w~~P~~-~~~~~g~~~~~~~ 240 (250)
||++.|..+||+.++|- + + ..-++|.. +..+.|-.||..+
T Consensus 259 ~~~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~~~p~~~~~~~~~~d 304 (309)
T KOG1313|consen 259 NPTNFGGKANWRNFLGLFRGRHFWKTVLLPTIRKPVKYGDSKEKSD 304 (309)
T ss_pred CCcccchHHHHHHhhccccCCceeEEEeccccccccccCCcccccc
Confidence 99999999999999984 2 2 23388986 6666788888443
No 7
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.75 E-value=3.5e-18 Score=149.97 Aligned_cols=162 Identities=21% Similarity=0.243 Sum_probs=91.7
Q ss_pred HHHHHHhHHHhcCCCCCCCCCCCCCcCCCCcchhhhhcCCCc-ccccccccccCCCCCCCcchhhhhhhH----------
Q 025621 54 MCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDL-RYCQKCSHYKPPRAHHCRVCKRCVLRM---------- 122 (250)
Q Consensus 54 ~~~~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~C~~C~~~kp~Rs~HC~~C~~CV~~~---------- 122 (250)
..++.+.+...+|||++|...... .+.+......++.... ++|.+|.++||.|||||+.|||||.||
T Consensus 380 ~~~~~f~~~~rsDPg~i~~~~~~~--~~tIs~l~d~gkf~~en~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~nc 457 (600)
T KOG0509|consen 380 AYFITFGLFLRSDPGFIPTSTEVG--RETISQLIDFGKFDLENRFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNC 457 (600)
T ss_pred HHHHHHHHHhccCCCCCCCchhhH--HHHHHHhhccccccccccceeeeeeecCCccchhhhhHHHHhccccCCCccccc
Confidence 334455556669999999763222 1111111111222233 799999999999999999999999999
Q ss_pred ---------HHHHHHHHH------hh-hhhhhccCCchhHHH-HHHHHHHHHH----------------HHHHHHHHHHH
Q 025621 123 ---------VLLVGSLTN------DS-LEDELQTGGSFRTAY-VISGLLLVPL----------------SVALSVLLGWH 169 (250)
Q Consensus 123 ---------~~~~~~~~~------~~-~~~~~~~~~~~~~~~-~~~~~l~~~~----------------~~~~~~ll~~~ 169 (250)
.+++.++.. +. ...+........+.. .+..+.+... ....+..-+.|
T Consensus 458 VG~kNh~~F~~Fl~~l~~~~~~~l~~~~~y~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~ 537 (600)
T KOG0509|consen 458 VGLKNHRLFVFFLLTLLTVIVFYLYLCLYYIMNLENASTIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQH 537 (600)
T ss_pred cCccchHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccc
Confidence 111111100 00 001111111101111 1111111000 01111222334
Q ss_pred HHHhccCcchHHHHhhhhHHHHHHhCCCcccCCCChhHHHhHHHhcCCC
Q 025621 170 IYLIFHNKTTIEYHEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN 218 (250)
Q Consensus 170 ~~li~~n~TT~E~~~~~~~~~~~~~~~~~~~n~yd~G~~~N~~~vfg~~ 218 (250)
...++.+.||+|+++.+|+++...+.+. ..+|++.|..+|+.+|+-.+
T Consensus 538 ~~~~c~~~tt~e~~n~~r~~~~~~~~~~-~~~~~s~g~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 538 YNCACLHLTTNEQINVKRYEHLGIKRGP-TRSPFSPGPIRNLVDFFLCS 585 (600)
T ss_pred cceeeecccHHHHHHHHHhhccccccCc-CCCCCCchhhhcchheeecc
Confidence 4568999999999999999877755543 67999999999999999643
No 8
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=99.72 E-value=2.3e-17 Score=131.71 Aligned_cols=80 Identities=23% Similarity=0.344 Sum_probs=57.5
Q ss_pred chhHHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCCCCCCcCCCCcchhhhhcCCCcccccccccccCCCCCCCcchhhhh
Q 025621 40 PGLMNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 40 ~~~~~~ii~~~l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
.+..+.+....++++-..++..++.+|||.+.++.........+-+.... -+...|+||++.||.|||||+.||+||
T Consensus 96 lsl~~~il~~l~vivp~i~f~ltc~snpg~i~k~n~s~~~~~ypYDy~if---~k~~kCSTCki~KPARSKHCsiCNrCV 172 (341)
T KOG1312|consen 96 LSLHYLILPYLLVIVPLIFFTLTCGSNPGIITKANESLFLHVYPYDYVIF---PKNVKCSTCKIRKPARSKHCSICNRCV 172 (341)
T ss_pred hhHHHHHHHHHHHHHHHHHHhhhhcCCCCccchhhhccceeccCccceee---cCCCccccccCCCccccccchHHHHHH
Confidence 45566666666666777888889999999998753322222222111111 134899999999999999999999999
Q ss_pred hhH
Q 025621 120 LRM 122 (250)
Q Consensus 120 ~~~ 122 (250)
.||
T Consensus 173 ~rf 175 (341)
T KOG1312|consen 173 HRF 175 (341)
T ss_pred HHh
Confidence 999
No 9
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=94.76 E-value=0.05 Score=46.17 Aligned_cols=98 Identities=18% Similarity=0.191 Sum_probs=57.8
Q ss_pred CCCcccccccccccCCCCCCCcchhhhh--------hhH-----------HHHHHHHHHhhhhh------h---hc-c--
Q 025621 92 GGDLRYCQKCSHYKPPRAHHCRVCKRCV--------LRM-----------VLLVGSLTNDSLED------E---LQ-T-- 140 (250)
Q Consensus 92 ~~~~~~C~~C~~~kp~Rs~HC~~C~~CV--------~~~-----------~~~~~~~~~~~~~~------~---~~-~-- 140 (250)
..+.++|..|+......+|||..-|+|| ..| +......+...... . .. .
T Consensus 120 P~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~ 199 (309)
T COG5273 120 PPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRHDTSLAICFLIFGCS 199 (309)
T ss_pred CCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCChHHHHHHHHHhhh
Confidence 4578999999999999999999999998 555 22223322211100 0 00 0
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCcchHHHHhhhhHH
Q 025621 141 GGSFRTAYVISGLLLVPLSVALSVLLGWHIYLIFHNKTTIEYHEGVRAL 189 (250)
Q Consensus 141 ~~~~~~~~~~~~~l~~~~~~~~~~ll~~~~~li~~n~TT~E~~~~~~~~ 189 (250)
......+++...++......++-.....+.+.+.++.++-|...-.++.
T Consensus 200 ~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~ 248 (309)
T COG5273 200 LLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRES 248 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccC
Confidence 0111111222222223344555567777888999999998886554444
No 10
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=93.70 E-value=0.026 Score=43.56 Aligned_cols=28 Identities=21% Similarity=0.483 Sum_probs=25.6
Q ss_pred CCCcccccccccccCCCCCCCcchhhhh
Q 025621 92 GGDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 92 ~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
..+.++|..|+.....++|||..-|+||
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cI 86 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCI 86 (174)
T ss_pred CCcceeccccccccccccccchhhcccc
Confidence 3478999999999999999999999994
No 11
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=93.62 E-value=0.11 Score=43.73 Aligned_cols=50 Identities=30% Similarity=0.199 Sum_probs=36.2
Q ss_pred cCCCChhHHHhHHHhcCCCccceeccCc-CCCCCCeeeccccCCccCCCCC
Q 025621 200 KHPYDLGIFENLTSVLGPNIFSWVCPSS-RHIGSGLNFRTAYHNAVGASMS 249 (250)
Q Consensus 200 ~n~yd~G~~~N~~~vfg~~~~~w~~P~~-~~~~~g~~~~~~~~~~~~~~~~ 249 (250)
.+.|+..+-.|+...+++....|-.+.. +..++|+++..+.+...-++.+
T Consensus 248 ~~n~~~vfg~~~~~wl~P~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 298 (307)
T KOG1315|consen 248 YVNFREVFGSNLLYWLLPIDSSWGDGVSFPLRGDGLDFRTASDSKPDNSST 298 (307)
T ss_pred eecHHHHhCCCceEEeccccCccccCccccccccCCccccccccCcccCcc
Confidence 4577778888888889887777777764 7778888887776655544443
No 12
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=93.26 E-value=0.034 Score=47.08 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=25.6
Q ss_pred CCcccccccccccCCCCCCCcchhhhh
Q 025621 93 GDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 93 ~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
.+.++|..|+.....++|||+.-|+||
T Consensus 125 pRs~HCsvC~~CV~rfDHHC~WvnnCV 151 (299)
T KOG1311|consen 125 PRSSHCSVCNNCVLRFDHHCPWLNNCI 151 (299)
T ss_pred CCcccchhhcccccccCCCCCCccceE
Confidence 478999999999999999999999997
No 13
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=93.04 E-value=0.088 Score=44.55 Aligned_cols=62 Identities=19% Similarity=0.211 Sum_probs=39.2
Q ss_pred HHHhHHHhcCCCCCCCCCCCCCcCCCCcchhhhhcCCCcccccccccccCCCCCCCcchhhhh
Q 025621 57 FSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 57 ~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
..+.---+..||.-|.....+.--+. ...-..=+..+..+|.+|+..+-...|||+.-|.||
T Consensus 68 A~~~gPG~vp~~wkPe~~~D~~~lqf-Ck~CqgYKapRSHHCrkCnrCvmkMDHHCPWinnCV 129 (414)
T KOG1314|consen 68 AIFTGPGFVPLGWKPENPKDEMFLQF-CKKCQGYKAPRSHHCRKCNRCVMKMDHHCPWINNCV 129 (414)
T ss_pred HHhcCCCCCCCCCCCCCChhHHHHHH-HhhccCcCCCccccchHHHHHHHhhccCCcchhhcc
Confidence 33455568889998865322121110 000000011267999999999999999999999997
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=91.81 E-value=0.091 Score=26.11 Aligned_cols=21 Identities=29% Similarity=0.733 Sum_probs=18.5
Q ss_pred cccccccccCCCCCCCcchhh
Q 025621 97 YCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 97 ~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
+|..|....++.++.|+.||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 689999999999999999874
No 15
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=89.13 E-value=0.19 Score=25.77 Aligned_cols=22 Identities=27% Similarity=0.712 Sum_probs=19.5
Q ss_pred ccccccccccCCCCCCCcchhh
Q 025621 96 RYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
+.|..|....|.-++-|+.||-
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 4699999999999999999973
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.32 E-value=0.28 Score=25.06 Aligned_cols=22 Identities=27% Similarity=0.750 Sum_probs=19.6
Q ss_pred ccccccccccCCCCCCCcchhh
Q 025621 96 RYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
.+|..|....++.++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 6899999988999999999984
No 17
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=87.93 E-value=0.2 Score=41.09 Aligned_cols=64 Identities=23% Similarity=0.340 Sum_probs=40.2
Q ss_pred HHHHHHHHHhHHHhcCCCCCCCCCCCCCcCCCCcchhhhhcCCCcccccccccccCCCCCCCcchhhhh
Q 025621 51 VALMCVFSYTVAILRDPGRVPADYMPDVEDDQNPMHEIKRKGGDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 51 l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
+....++.|+++..+.|=-.| ..+.+..-..-...+..+...|..|+...-..+|||+.-|+||
T Consensus 77 ~l~nvi~hy~ka~t~pPvgn~-----~~~~~SfC~KC~~pK~prTHHCsiC~kCVL~MDHHCPwinnCV 140 (309)
T KOG1313|consen 77 LLSNVIFHYYKARTKPPVGNP-----GLENDSFCNKCNYPKSPRTHHCSICNKCVLKMDHHCPWINNCV 140 (309)
T ss_pred HHHHHHHhheeecccCCcCCC-----CCccccHHhhcCCCCCCCcchhhHHhhHhhccccCCchhhccc
Confidence 344456667777766651111 1111111111123334477999999999999999999999998
No 18
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=86.32 E-value=0.36 Score=28.46 Aligned_cols=24 Identities=33% Similarity=0.819 Sum_probs=21.9
Q ss_pred CcccccccccccCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
....|..|...-|+|+..|+.||.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 568999999999999999998874
No 19
>PF07010 Endomucin: Endomucin; InterPro: IPR010740 This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells.
Probab=85.00 E-value=2.3 Score=33.97 Aligned_cols=38 Identities=24% Similarity=0.212 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHhHHHhcCCCCCCCCCCCCCcC
Q 025621 43 MNAIVFTAVALMCVFSYTVAILRDPGRVPADYMPDVED 80 (250)
Q Consensus 43 ~~~ii~~~l~~~~~~~~~~~~~~dPG~~~~~~~~~~~~ 80 (250)
+.++++.++.+..+.+|.+|..+|||.........+.+
T Consensus 195 IaliVitl~vf~LvgLyr~C~k~dPg~p~~g~~qpqsd 232 (259)
T PF07010_consen 195 IALIVITLSVFTLVGLYRMCWKTDPGTPENGPDQPQSD 232 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCcccCCCCCCcc
Confidence 45566677777888889999999999766554333333
No 20
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=84.12 E-value=0.35 Score=44.14 Aligned_cols=29 Identities=28% Similarity=0.518 Sum_probs=25.9
Q ss_pred cCCCcccccccccccCCCCCCCcchhhhh
Q 025621 91 KGGDLRYCQKCSHYKPPRAHHCRVCKRCV 119 (250)
Q Consensus 91 ~~~~~~~C~~C~~~kp~Rs~HC~~C~~CV 119 (250)
+..+.++|..|+...---.|||+.-++||
T Consensus 430 Kp~rSkhc~vcnrcVarfDHhCPwi~ncV 458 (600)
T KOG0509|consen 430 KPLRSKHCSVCNRCVARFDHHCPWIGNCV 458 (600)
T ss_pred cCCccchhhhhHHHHhccccCCCcccccc
Confidence 34578999999999999999999999997
No 21
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=83.88 E-value=28 Score=31.07 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=24.5
Q ss_pred CcccccccccccCCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
....|+.|+...+....||+.||.-..+.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~ 248 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVR 248 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCC
Confidence 45679999999888888999999888666
No 22
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=79.59 E-value=0.83 Score=43.00 Aligned_cols=22 Identities=41% Similarity=0.848 Sum_probs=18.2
Q ss_pred ccccccccccC-------CCCCCCcchhh
Q 025621 96 RYCQKCSHYKP-------PRAHHCRVCKR 117 (250)
Q Consensus 96 ~~C~~C~~~kp-------~Rs~HC~~C~~ 117 (250)
..|..|+..-. .|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 57999997764 48999999877
No 23
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=77.41 E-value=12 Score=25.18 Aligned_cols=27 Identities=19% Similarity=0.169 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHhccCcchHHHHhh
Q 025621 159 SVALSVLLGWHIYLIFHNKTTIEYHEG 185 (250)
Q Consensus 159 ~~~~~~ll~~~~~li~~n~TT~E~~~~ 185 (250)
.+.+.+++++.+|--+++.++.|++++
T Consensus 57 ~vl~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 57 AVLLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHHHhcccCCCceeecccC
Confidence 334445888888878888888887764
No 24
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=77.08 E-value=0.51 Score=39.02 Aligned_cols=30 Identities=20% Similarity=0.452 Sum_probs=28.1
Q ss_pred CCcccccccccccCCCCCCCcchhhhhhhH
Q 025621 93 GDLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 93 ~~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
.+.++|+.|+..+-.-.|||-.-|+||...
T Consensus 160 ARSKHCsiCNrCV~rfDHHCiWiNNCIG~~ 189 (341)
T KOG1312|consen 160 ARSKHCSICNRCVHRFDHHCIWINNCIGAW 189 (341)
T ss_pred cccccchHHHHHHHHhccceEeeecccccc
Confidence 477999999999999999999999999987
No 25
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=75.14 E-value=1.4 Score=27.52 Aligned_cols=23 Identities=26% Similarity=0.777 Sum_probs=20.8
Q ss_pred cccccccccccCCCCCCCcchhh
Q 025621 95 LRYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 95 ~~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
.+-|..|+...|+.+.-|+.||.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 46799999999999999999985
No 26
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=73.77 E-value=0.73 Score=27.23 Aligned_cols=24 Identities=38% Similarity=0.989 Sum_probs=21.3
Q ss_pred CcccccccccccCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
..+.|..|...-|+++.-|+.|+.
T Consensus 13 ~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 13 NKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred hHHHHHHhcCCCCcchhHHhhccC
Confidence 458999999999999999998863
No 27
>PF12773 DZR: Double zinc ribbon
Probab=71.43 E-value=3 Score=24.76 Aligned_cols=23 Identities=30% Similarity=0.853 Sum_probs=18.2
Q ss_pred CcccccccccccCCCCCCCcchh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCK 116 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~ 116 (250)
...+|..|....++.++.|..||
T Consensus 28 ~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 28 SKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCcCCcCCCcCCcCccCccc
Confidence 45788888888888888888775
No 28
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=69.03 E-value=1.7 Score=22.83 Aligned_cols=20 Identities=25% Similarity=0.838 Sum_probs=12.5
Q ss_pred cccccccccCCCCCCCcchh
Q 025621 97 YCQKCSHYKPPRAHHCRVCK 116 (250)
Q Consensus 97 ~C~~C~~~kp~Rs~HC~~C~ 116 (250)
.|..|...-+.++.||..|+
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~ 25 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACG 25 (30)
T ss_dssp EETTTTEEEESSSSB-TTT-
T ss_pred cCCCCcCCchHHhhhhhCcC
Confidence 46777777777777777665
No 29
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=68.67 E-value=43 Score=29.73 Aligned_cols=29 Identities=24% Similarity=0.553 Sum_probs=22.4
Q ss_pred Cccccccccc-ccCCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSH-YKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~-~kp~Rs~HC~~C~~CV~~~ 122 (250)
...-|+.|+. ..+....||+.||.-..+.
T Consensus 214 ~~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~ 243 (403)
T TIGR00155 214 KLRSCSACHTTILPAQEPVCPRCSTPLYVR 243 (403)
T ss_pred CCCcCCCCCCccCCCCCcCCcCCCCcccCC
Confidence 4566999998 4566667999999887666
No 30
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=67.16 E-value=1.5 Score=28.02 Aligned_cols=26 Identities=38% Similarity=0.775 Sum_probs=12.4
Q ss_pred Ccccccccccc--cCCCCCCCcchhhhh
Q 025621 94 DLRYCQKCSHY--KPPRAHHCRVCKRCV 119 (250)
Q Consensus 94 ~~~~C~~C~~~--kp~Rs~HC~~C~~CV 119 (250)
....|..|... --.|-|||+.||+-|
T Consensus 8 ~~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp G-SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 34677777744 347888999998743
No 31
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=66.29 E-value=1.4 Score=38.64 Aligned_cols=29 Identities=34% Similarity=0.935 Sum_probs=23.0
Q ss_pred Ccccccccccc--cCCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSHY--KPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~~--kp~Rs~HC~~C~~CV~~~ 122 (250)
.-.+|+.|... -..|-|||+.||+-+=+.
T Consensus 179 ~V~~CP~Ca~~F~l~rRrHHCRLCG~VmC~~ 209 (505)
T KOG1842|consen 179 SVQFCPECANSFGLTRRRHHCRLCGRVMCRD 209 (505)
T ss_pred cccccccccchhhhHHHhhhhhhcchHHHHH
Confidence 56899999855 456899999999865555
No 32
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=65.75 E-value=5.9 Score=30.00 Aligned_cols=33 Identities=9% Similarity=0.099 Sum_probs=28.2
Q ss_pred hccCcchHHHHhhhhHHHHHHhCCCcccCCCChhHHHhHHHhcCCC
Q 025621 173 IFHNKTTIEYHEGVRALWLAEKGGTVYKHPYDLGIFENLTSVLGPN 218 (250)
Q Consensus 173 i~~n~TT~E~~~~~~~~~~~~~~~~~~~n~yd~G~~~N~~~vfg~~ 218 (250)
--+|.|++|.++. ..++|..|+++..+.+||-+
T Consensus 102 Retg~TsyelIK~-------------~rgg~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 102 RETGSTSYELIKE-------------LRGGWRAFWYQTFAWLFGIS 134 (157)
T ss_pred HhcCCcHHHHHHH-------------hhCChhHHHHHHHHHHhCcc
Confidence 4479999999986 56788889999999999964
No 33
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=65.11 E-value=11 Score=23.46 Aligned_cols=23 Identities=26% Similarity=0.787 Sum_probs=17.9
Q ss_pred cccccccccccCCCCCCCc-chhh
Q 025621 95 LRYCQKCSHYKPPRAHHCR-VCKR 117 (250)
Q Consensus 95 ~~~C~~C~~~kp~Rs~HC~-~C~~ 117 (250)
-+.|..|....|+.-.-|| .|..
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHH
Confidence 4789999988888888885 5654
No 34
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=59.72 E-value=4.5 Score=24.32 Aligned_cols=25 Identities=44% Similarity=0.934 Sum_probs=17.4
Q ss_pred CcccccccccccCCCCCCCcc--hhhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRV--CKRC 118 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~--C~~C 118 (250)
....|..|...-|+|+..|+. ||.+
T Consensus 16 ~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 16 DKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp S-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cceecccccCcCCCCccceecccCCCC
Confidence 568999999999999999998 8765
No 36
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=55.23 E-value=7.3 Score=23.63 Aligned_cols=23 Identities=39% Similarity=0.839 Sum_probs=14.2
Q ss_pred ccccccccc--cCCCCCCCcchhhh
Q 025621 96 RYCQKCSHY--KPPRAHHCRVCKRC 118 (250)
Q Consensus 96 ~~C~~C~~~--kp~Rs~HC~~C~~C 118 (250)
+.|..|+.. .-.|.|||+.||+-
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred CcCcccCccccCCccccccCcCcCC
Confidence 345556532 35677888888763
No 37
>PRK02251 putative septation inhibitor protein; Reviewed
Probab=54.84 E-value=64 Score=21.85 Aligned_cols=32 Identities=13% Similarity=0.063 Sum_probs=20.1
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHhhhccccc
Q 025621 4 GFTFSLPVSVVVLAIFYIYFTTVFIFIDRWFG 35 (250)
Q Consensus 4 ~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~ 35 (250)
+...|..++.+.++++.+.+..++++...-++
T Consensus 29 ~sP~W~~~~m~~lm~~Gl~WlvvyYl~~~~~P 60 (87)
T PRK02251 29 SNPRWFVPLFVALMIIGLIWLVVYYLSNGSLP 60 (87)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHHhhhCCCcC
Confidence 45667777777776666666666666543333
No 38
>cd01995 ExsB ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown
Probab=54.30 E-value=7.1 Score=29.72 Aligned_cols=26 Identities=31% Similarity=0.692 Sum_probs=19.6
Q ss_pred CcccccccccccCCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
......+|... ..+||..|..|+.|+
T Consensus 139 ~~~~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 139 PLELTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred ChhheeeccCC---CCCCCCCCHHHHHHH
Confidence 44556677665 338999999999986
No 39
>PF08113 CoxIIa: Cytochrome c oxidase subunit IIa family; InterPro: IPR012538 This family consists of the cytochrome c oxidase subunit IIa family. The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix, subunit IIa, spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases [].; PDB: 2QPD_C 3QJR_C 3EH5_C 3BVD_C 3S39_C 3QJU_C 3QJS_C 4EV3_C 3QJT_C 4FA7_C ....
Probab=53.84 E-value=26 Score=18.96 Aligned_cols=23 Identities=17% Similarity=0.330 Sum_probs=8.8
Q ss_pred CCCCcccchhHHHHHHHHHHHHH
Q 025621 1 MTKGFTFSLPVSVVVLAIFYIYF 23 (250)
Q Consensus 1 ~~~~~~~~~p~~~~~~l~~~~~~ 23 (250)
|+.|.-+-+-++.++.+.+.+++
T Consensus 1 meekp~Gal~vv~iLt~~ILvFW 23 (34)
T PF08113_consen 1 MEEKPKGALGVVMILTAFILVFW 23 (34)
T ss_dssp ---STHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCcceeeeHHHHHHHHHHHH
Confidence 44554444444444444333333
No 40
>COG4640 Predicted membrane protein [Function unknown]
Probab=53.14 E-value=28 Score=30.50 Aligned_cols=28 Identities=21% Similarity=0.615 Sum_probs=24.4
Q ss_pred cccccccccccCCCCCCCcchhhhhhhH
Q 025621 95 LRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 95 ~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
+++|..|...+-+.+..|..||.=+..+
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccccccccccccccCCcCCch
Confidence 3789999999999999999999877765
No 41
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=53.13 E-value=7.2 Score=38.50 Aligned_cols=23 Identities=35% Similarity=0.820 Sum_probs=17.2
Q ss_pred cccccccc--cccCCCCCCCcchhh
Q 025621 95 LRYCQKCS--HYKPPRAHHCRVCKR 117 (250)
Q Consensus 95 ~~~C~~C~--~~kp~Rs~HC~~C~~ 117 (250)
..-|..|. -.--.|-|||+.||+
T Consensus 557 ~pncm~clqkft~ikrrhhcRacgk 581 (1287)
T KOG1841|consen 557 APNCMDCLQKFTPIKRRHHCRACGK 581 (1287)
T ss_pred CchHHHHHhhcccccccccchhccc
Confidence 45566666 445678999999997
No 42
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=52.48 E-value=6.6 Score=28.11 Aligned_cols=24 Identities=21% Similarity=0.685 Sum_probs=18.8
Q ss_pred CcccccccccccCCCCCC---Ccchhh
Q 025621 94 DLRYCQKCSHYKPPRAHH---CRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~H---C~~C~~ 117 (250)
..-+|..|+..-|...++ |+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCC
Confidence 458999999888776555 999884
No 43
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=51.46 E-value=4.4 Score=36.34 Aligned_cols=24 Identities=38% Similarity=0.750 Sum_probs=17.5
Q ss_pred Ccccccccccc--cCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHY--KPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~--kp~Rs~HC~~C~~ 117 (250)
....|..|+.. .--|-|||+-||.
T Consensus 900 ~a~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 900 DAEQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred cchhhhhccCcHHHHHHhhhhcccCc
Confidence 44678888865 3457899998875
No 44
>PF06781 UPF0233: Uncharacterised protein family (UPF0233); InterPro: IPR009619 This is a group of proteins of unknown function.
Probab=50.39 E-value=78 Score=21.47 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=19.5
Q ss_pred CCcccchhHHHHHHHHHHHHHHHHHhhhcc
Q 025621 3 KGFTFSLPVSVVVLAIFYIYFTTVFIFIDR 32 (250)
Q Consensus 3 ~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~ 32 (250)
+++..|..++.+.++++.+.+..++++...
T Consensus 27 ~~sp~W~~p~m~~lmllGL~WiVvyYi~~~ 56 (87)
T PF06781_consen 27 KPSPRWYAPLMLGLMLLGLLWIVVYYISGG 56 (87)
T ss_pred CCCCccHHHHHHHHHHHHHHHHhhhhcccC
Confidence 345667777777676666666666666654
No 45
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=49.39 E-value=4.2 Score=21.33 Aligned_cols=21 Identities=19% Similarity=0.444 Sum_probs=7.7
Q ss_pred cccccccccCC-CCCCCcchhh
Q 025621 97 YCQKCSHYKPP-RAHHCRVCKR 117 (250)
Q Consensus 97 ~C~~C~~~kp~-Rs~HC~~C~~ 117 (250)
.|..|+..... ...||..|+-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 46667766655 6667777763
No 46
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.55 E-value=8.1 Score=24.60 Aligned_cols=27 Identities=22% Similarity=0.504 Sum_probs=20.1
Q ss_pred CcccccccccccC----CCCCCCcchhhhhh
Q 025621 94 DLRYCQKCSHYKP----PRAHHCRVCKRCVL 120 (250)
Q Consensus 94 ~~~~C~~C~~~kp----~Rs~HC~~C~~CV~ 120 (250)
..+.|+.|..... .|.++|+.||.-..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEEC
Confidence 5688999997654 47778998886443
No 47
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=47.72 E-value=7.7 Score=36.07 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=19.0
Q ss_pred Ccccccccccc--cCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHY--KPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~--kp~Rs~HC~~C~~ 117 (250)
...-|..|... --.|.|||+.||+
T Consensus 164 D~~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 164 DSEECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccccceeeeeeeeccccccccccch
Confidence 45788888854 3459999999998
No 48
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=45.76 E-value=5.4 Score=21.95 Aligned_cols=7 Identities=43% Similarity=1.626 Sum_probs=3.4
Q ss_pred ccccccc
Q 025621 96 RYCQKCS 102 (250)
Q Consensus 96 ~~C~~C~ 102 (250)
++|..|.
T Consensus 2 ~FCp~C~ 8 (35)
T PF02150_consen 2 RFCPECG 8 (35)
T ss_dssp -BETTTT
T ss_pred eeCCCCC
Confidence 4555555
No 49
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=44.88 E-value=9.9 Score=22.80 Aligned_cols=23 Identities=22% Similarity=0.832 Sum_probs=15.0
Q ss_pred Cccccccccc-c--cCCCCCCCcchh
Q 025621 94 DLRYCQKCSH-Y--KPPRAHHCRVCK 116 (250)
Q Consensus 94 ~~~~C~~C~~-~--kp~Rs~HC~~C~ 116 (250)
..++|+.|.. . .-....||..|+
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcC
Confidence 4579999977 2 222355777776
No 50
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=44.32 E-value=6.9 Score=20.86 Aligned_cols=22 Identities=27% Similarity=0.717 Sum_probs=10.2
Q ss_pred cccccccccc----cCCCCCCCcchh
Q 025621 95 LRYCQKCSHY----KPPRAHHCRVCK 116 (250)
Q Consensus 95 ~~~C~~C~~~----kp~Rs~HC~~C~ 116 (250)
.+||..|... ...++..|+.|+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg 28 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCG 28 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS
T ss_pred CcccCcCCccccCCCCcCEeECCCCc
Confidence 4778888744 233455555554
No 51
>PF03503 Chlam_OMP3: Chlamydia cysteine-rich outer membrane protein 3; InterPro: IPR003517 Three cysteine-rich proteins (also believed to be lipoproteins) make up the extracellular matrix of the Chlamydial outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. As these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism. The largest of these is the major outer membrane protein (MOMP), and constitutes around 60% of the total protein for the membrane []. OMP2 is the second largest, with a molecular mass of 58kDa, while the OMP3 protein is ~15kDa []. MOMP is believed to elicit the strongest immune response, and has recently been linked to heart disease through its sequence similarity to a murine heart-muscle specific alpha myosin []. The OMP3 family plays a structural role in the outer membrane during the EB stage of the Chlamydial cell, and different biovars show a small, yet highly significant, change at peptide charge level []. Members of this family include Chlamydia trachomatis, Chlamydia pneumoniae, and Chlamydia psittaci.; GO: 0005201 extracellular matrix structural constituent
Probab=43.41 E-value=15 Score=21.63 Aligned_cols=21 Identities=24% Similarity=0.626 Sum_probs=9.3
Q ss_pred ccccccccccCCCCCCCcchh
Q 025621 96 RYCQKCSHYKPPRAHHCRVCK 116 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~ 116 (250)
+-|..|+..|-+++--|+.||
T Consensus 24 ~sc~pc~~~kkd~~~g~n~cg 44 (55)
T PF03503_consen 24 KSCNPCEVNKKDVSCGCNPCG 44 (55)
T ss_pred CcccccccccccccCCccccc
Confidence 344444444444444444443
No 52
>PRK02935 hypothetical protein; Provisional
Probab=42.11 E-value=1.2e+02 Score=21.32 Aligned_cols=8 Identities=25% Similarity=0.924 Sum_probs=3.6
Q ss_pred cccccccc
Q 025621 96 RYCQKCSH 103 (250)
Q Consensus 96 ~~C~~C~~ 103 (250)
..|..|+.
T Consensus 87 D~CM~C~~ 94 (110)
T PRK02935 87 DACMHCNQ 94 (110)
T ss_pred eecCcCCC
Confidence 34444443
No 53
>PF05814 DUF843: Baculovirus protein of unknown function (DUF843); InterPro: IPR008561 This family consists of several unidentified baculovirus proteins of around 85 residues long with no known function.
Probab=41.73 E-value=1.1e+02 Score=20.55 Aligned_cols=23 Identities=17% Similarity=0.250 Sum_probs=14.1
Q ss_pred HHHHHHHHhccCcchHHHHhhhhH
Q 025621 165 LLGWHIYLIFHNKTTIEYHEGVRA 188 (250)
Q Consensus 165 ll~~~~~li~~n~TT~E~~~~~~~ 188 (250)
++..|+|.+ +.+++.+.+...+.
T Consensus 38 ~~~L~~yy~-kteS~~~dL~t~k~ 60 (83)
T PF05814_consen 38 FCVLQVYYI-KTESTPQDLQTEKA 60 (83)
T ss_pred HHHHHHHHc-CCCCcHHHHhhhhh
Confidence 455577777 66777666644333
No 54
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.85 E-value=10 Score=22.46 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=4.7
Q ss_pred ccccccccc
Q 025621 96 RYCQKCSHY 104 (250)
Q Consensus 96 ~~C~~C~~~ 104 (250)
..|..|...
T Consensus 21 ~vC~~Cg~~ 29 (52)
T smart00661 21 FVCRKCGYE 29 (52)
T ss_pred EECCcCCCe
Confidence 455555543
No 55
>TIGR00364 exsB protein. This protein family is represented by a single member in nearly every completed large ( 1000 genes) prokaryotic genome. In Rhizobium meliloti, a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA. In Arthrobacter viscosus, the homologous gene is designated ALU1 and is associated with an aluminum tolerance phenotype. The function is unknown.
Probab=38.32 E-value=16 Score=28.69 Aligned_cols=23 Identities=26% Similarity=0.655 Sum_probs=15.9
Q ss_pred ccccccccccCCCCCCCcchhhhhhh
Q 025621 96 RYCQKCSHYKPPRAHHCRVCKRCVLR 121 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~~CV~~ 121 (250)
..=..|... ..+||..|..|+.|
T Consensus 179 ~~t~sC~~~---~~~~CG~C~~C~~r 201 (201)
T TIGR00364 179 KLTYSCYAG---GGEGCGKCPSCMLR 201 (201)
T ss_pred hhCCcCCCc---CCCCCCCChhhhcc
Confidence 444456554 24699999999875
No 56
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=38.13 E-value=14 Score=18.36 Aligned_cols=20 Identities=20% Similarity=0.614 Sum_probs=14.4
Q ss_pred cccccccccCCCCCCCcchh
Q 025621 97 YCQKCSHYKPPRAHHCRVCK 116 (250)
Q Consensus 97 ~C~~C~~~kp~Rs~HC~~C~ 116 (250)
.|..|......++..|..|+
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~ 23 (26)
T smart00547 4 ECPACTFLNFASRSKCFACG 23 (26)
T ss_pred cCCCCCCcChhhhccccccC
Confidence 47777777777777777775
No 57
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=37.30 E-value=32 Score=28.09 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=19.9
Q ss_pred Ccccccccccc----------cCCCCCCCcchhhhhh
Q 025621 94 DLRYCQKCSHY----------KPPRAHHCRVCKRCVL 120 (250)
Q Consensus 94 ~~~~C~~C~~~----------kp~Rs~HC~~C~~CV~ 120 (250)
..+.|.-|++. +++.-.||+.|||-.+
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy 232 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILY 232 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHH
Confidence 44788888854 4566789999998654
No 58
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=36.91 E-value=1.2e+02 Score=24.21 Aligned_cols=16 Identities=19% Similarity=0.445 Sum_probs=13.3
Q ss_pred CCCCCCcchhhhhhhH
Q 025621 107 PRAHHCRVCKRCVLRM 122 (250)
Q Consensus 107 ~Rs~HC~~C~~CV~~~ 122 (250)
.|--+|+.||+.++++
T Consensus 22 irLt~C~~C~~vaDkY 37 (208)
T PF04161_consen 22 IRLTKCPNCGKVADKY 37 (208)
T ss_pred EEEeeccccCCcccce
Confidence 4556899999999988
No 59
>PF06508 QueC: Queuosine biosynthesis protein QueC; InterPro: IPR018317 This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti (Sinorhizobium meliloti), a species in which the exo genes make succinoglycan, a symbiotically important exopolysaccharide, exsB is located nearby and affects succinoglycan levels, probably through polar effects on exsA expression or the same polycistronic mRNA [, ]. In Arthrobacter viscosus, the homologous gene is designated alu1 and is associated with an aluminum tolerance phenotype. When expressed in Escherichia coli, it conferred aliminium tolerance []. The entry also contains the gene queC, which is responsible for the conversion of GTP to 7-cyano-7-deazaguanine (preQ0). The biosynthesis of hypermodified tRNA nucleoside queuosine only occurs in eubacteria. It occupies the wobble position for all known tRNAs that are specific for Asp, Asn, His or Tyr [].; PDB: 3BL5_B 2PG3_A.
Probab=36.84 E-value=19 Score=28.78 Aligned_cols=28 Identities=29% Similarity=0.649 Sum_probs=18.5
Q ss_pred CcccccccccccCCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
....-.+|..-. ....||..|..|+.|.
T Consensus 176 ~~~~T~SCy~~~-~~~~~CG~C~~C~~R~ 203 (209)
T PF06508_consen 176 PLELTWSCYRGG-EKGKHCGRCPSCLLRR 203 (209)
T ss_dssp HHHH-B-STTS---BTTTTSSSHHHHHHH
T ss_pred CHHHccCCCCCC-CCCCCCCCCHHHHHHH
Confidence 456777774333 4568999999999985
No 60
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=36.83 E-value=1.2e+02 Score=26.95 Aligned_cols=29 Identities=14% Similarity=0.346 Sum_probs=19.2
Q ss_pred Cccccccccccc------CCCCCCCcchhhhhhhH
Q 025621 94 DLRYCQKCSHYK------PPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 94 ~~~~C~~C~~~k------p~Rs~HC~~C~~CV~~~ 122 (250)
...-|+.|+... +...-||+.||.-..+.
T Consensus 12 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~ 46 (403)
T TIGR00155 12 KHILCSQCDMLVALPRIESGQKAACPRCGTTLTVG 46 (403)
T ss_pred CeeeCCCCCCcccccCCCCCCeeECCCCCCCCcCC
Confidence 345699999543 22334688888877665
No 61
>COG1852 Uncharacterized conserved protein [Function unknown]
Probab=36.58 E-value=14 Score=28.91 Aligned_cols=23 Identities=30% Similarity=0.817 Sum_probs=18.4
Q ss_pred ccccccCCCCCCCcchhhhhhhH
Q 025621 100 KCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 100 ~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
.|+..-.+--.-|+.||+||..-
T Consensus 102 ~CeA~~t~~G~~Ck~CgkCvi~e 124 (209)
T COG1852 102 KCEAKLTPTGYECKKCGKCVIGE 124 (209)
T ss_pred CCccccccccceecccCCeehHH
Confidence 47777666688999999999753
No 62
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.18 E-value=19 Score=34.03 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=24.7
Q ss_pred cccccccccccCCCCCCCcchhhhhhhH
Q 025621 95 LRYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 95 ~~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
.+.|..|....|+.+++|..||.=....
T Consensus 27 ~~~Cp~CG~~~~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 27 HKPCPQCGTEVPVDEAHCPNCGAETGTI 54 (645)
T ss_pred CCcCCCCCCCCCcccccccccCCcccch
Confidence 3679999999999999999999887776
No 63
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=35.78 E-value=20 Score=17.94 Aligned_cols=19 Identities=32% Similarity=0.861 Sum_probs=9.6
Q ss_pred ccccccccCCCC----CCCcchh
Q 025621 98 CQKCSHYKPPRA----HHCRVCK 116 (250)
Q Consensus 98 C~~C~~~kp~Rs----~HC~~C~ 116 (250)
|..|...-.+|- ..|+.||
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 455554444443 3566665
No 64
>PHA02942 putative transposase; Provisional
Probab=34.98 E-value=17 Score=31.94 Aligned_cols=26 Identities=31% Similarity=0.545 Sum_probs=19.8
Q ss_pred CcccccccccccCC---CCCCCcchhhhh
Q 025621 94 DLRYCQKCSHYKPP---RAHHCRVCKRCV 119 (250)
Q Consensus 94 ~~~~C~~C~~~kp~---Rs~HC~~C~~CV 119 (250)
..+.|+.|....+. |.++|..||-=.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 56899999976543 778999888633
No 65
>PHA02898 virion envelope protein; Provisional
Probab=34.77 E-value=1.5e+02 Score=20.14 Aligned_cols=25 Identities=16% Similarity=0.052 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHH-hccCcchHH
Q 025621 157 PLSVALSVLLGWHIYL-IFHNKTTIE 181 (250)
Q Consensus 157 ~~~~~~~~ll~~~~~l-i~~n~TT~E 181 (250)
+..+.+.+++++.+|- -+++.++.|
T Consensus 54 lgivl~lG~~ifs~y~r~C~~~~~~e 79 (92)
T PHA02898 54 LAIILILGIIFFKGYNMFCGGNTTDE 79 (92)
T ss_pred HHHHHHHHHHHHHHHhhhcCCCcccc
Confidence 3344455677777776 667776664
No 66
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.98 E-value=21 Score=22.04 Aligned_cols=22 Identities=36% Similarity=0.865 Sum_probs=16.5
Q ss_pred CcccccccccccCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
..+.|..|...-- ...|+.||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4578888888776 677888774
No 67
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=33.19 E-value=1.5e+02 Score=26.68 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=9.7
Q ss_pred CCCcchhhhhhh
Q 025621 110 HHCRVCKRCVLR 121 (250)
Q Consensus 110 ~HC~~C~~CV~~ 121 (250)
..|..|+.|+..
T Consensus 255 ~~Ci~Cg~Cida 266 (434)
T TIGR02745 255 LECINCGLCIDA 266 (434)
T ss_pred hhChhhhHHHHh
Confidence 469999999875
No 68
>PF06143 Baculo_11_kDa: Baculovirus 11 kDa family; InterPro: IPR009313 This is a family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Probab=32.88 E-value=1.6e+02 Score=19.88 Aligned_cols=8 Identities=38% Similarity=0.522 Sum_probs=3.8
Q ss_pred HHHhccCc
Q 025621 170 IYLIFHNK 177 (250)
Q Consensus 170 ~~li~~n~ 177 (250)
++.|.+|.
T Consensus 56 l~~i~~~~ 63 (84)
T PF06143_consen 56 LYNINKNA 63 (84)
T ss_pred HHHHHHHH
Confidence 34444554
No 69
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=32.12 E-value=18 Score=30.98 Aligned_cols=26 Identities=23% Similarity=0.499 Sum_probs=22.3
Q ss_pred CCcccccccccccCCCCCCCcchhhh
Q 025621 93 GDLRYCQKCSHYKPPRAHHCRVCKRC 118 (250)
Q Consensus 93 ~~~~~C~~C~~~kp~Rs~HC~~C~~C 118 (250)
.....|..|.--.-.--.||+.|++-
T Consensus 352 ~~~YRC~~CGF~a~~l~W~CPsC~~W 377 (389)
T COG2956 352 KPRYRCQNCGFTAHTLYWHCPSCRAW 377 (389)
T ss_pred cCCceecccCCcceeeeeeCCCcccc
Confidence 46788999998888888899999873
No 70
>KOG0230 consensus Phosphatidylinositol-4-phosphate 5-kinase and related FYVE finger-containing proteins [Signal transduction mechanisms]
Probab=31.32 E-value=22 Score=36.44 Aligned_cols=24 Identities=42% Similarity=0.919 Sum_probs=17.2
Q ss_pred CcccccccccccCCCCCCCcchhhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRC 118 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~C 118 (250)
..+.|..|. -+-.|.|||+.||+|
T Consensus 4 s~~~~~~~~-t~~~~~~~~~~~g~~ 27 (1598)
T KOG0230|consen 4 SSNVCYDCD-TSVNRRHHCRVCGRV 27 (1598)
T ss_pred cccchhccc-cccccCCCCcccCce
Confidence 346677777 666778888888884
No 71
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=30.95 E-value=11 Score=31.65 Aligned_cols=26 Identities=35% Similarity=0.723 Sum_probs=17.5
Q ss_pred Ccccccccccc---cCCCCCCCcchhhhh
Q 025621 94 DLRYCQKCSHY---KPPRAHHCRVCKRCV 119 (250)
Q Consensus 94 ~~~~C~~C~~~---kp~Rs~HC~~C~~CV 119 (250)
....|..|... --.|-|||+.||.=|
T Consensus 167 ea~~C~~C~~~~Ftl~~RRHHCR~CG~iv 195 (288)
T KOG1729|consen 167 EATECMVCGCTEFTLSERRHHCRNCGDIV 195 (288)
T ss_pred cceecccCCCccccHHHHHHHHHhcchHh
Confidence 44677777762 246778988888743
No 72
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=30.95 E-value=26 Score=33.08 Aligned_cols=23 Identities=30% Similarity=0.712 Sum_probs=13.7
Q ss_pred CcccccccccccCCCCCCCcchhhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKRC 118 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~C 118 (250)
..+||..|...-+ .+.|+.||.=
T Consensus 14 ~akFC~~CG~~l~--~~~Cp~CG~~ 36 (645)
T PRK14559 14 NNRFCQKCGTSLT--HKPCPQCGTE 36 (645)
T ss_pred CCccccccCCCCC--CCcCCCCCCC
Confidence 4578888866533 2456666543
No 73
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.73 E-value=23 Score=25.21 Aligned_cols=24 Identities=25% Similarity=0.645 Sum_probs=16.5
Q ss_pred CcccccccccccCCCCCC--Ccchhh
Q 025621 94 DLRYCQKCSHYKPPRAHH--CRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~H--C~~C~~ 117 (250)
..-+|..|...-+....+ |+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQHDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCCcCccCcCCCC
Confidence 457899998765554333 888873
No 74
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.43 E-value=1.1e+02 Score=26.47 Aligned_cols=16 Identities=19% Similarity=0.251 Sum_probs=9.2
Q ss_pred ccccccccCCCCCCCc
Q 025621 98 CQKCSHYKPPRAHHCR 113 (250)
Q Consensus 98 C~~C~~~kp~Rs~HC~ 113 (250)
|-.|...+|.-++|=.
T Consensus 266 vGfleSF~PLy~~~~~ 281 (372)
T KOG2927|consen 266 VGFLESFKPLYEYHYK 281 (372)
T ss_pred hhHHHhhcccccccCC
Confidence 5556666666555543
No 75
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=30.11 E-value=1.8e+02 Score=26.04 Aligned_cols=27 Identities=15% Similarity=0.388 Sum_probs=19.1
Q ss_pred cccccccccc------CCCCCCCcchhhhhhhH
Q 025621 96 RYCQKCSHYK------PPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 96 ~~C~~C~~~k------p~Rs~HC~~C~~CV~~~ 122 (250)
.-|+.|+... +...-||+.||.-..+.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcCC
Confidence 5599999653 23345788888888766
No 76
>PRK00159 putative septation inhibitor protein; Reviewed
Probab=29.87 E-value=1.8e+02 Score=19.71 Aligned_cols=29 Identities=10% Similarity=-0.003 Sum_probs=17.7
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHhhhcc
Q 025621 4 GFTFSLPVSVVVLAIFYIYFTTVFIFIDR 32 (250)
Q Consensus 4 ~~~~~~p~~~~~~l~~~~~~~~~~~~~~~ 32 (250)
+...|..++.+.++++.+.+..++++...
T Consensus 28 ~sp~W~~~~m~glm~~GllWlvvyYl~~~ 56 (87)
T PRK00159 28 PSSVWYVVLMLGLMLIGLAWLVVNYLAGP 56 (87)
T ss_pred CCCccHHHHHHHHHHHHHHHHHHHhhccC
Confidence 34566666666666666666666665533
No 77
>KOG4606 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.67 E-value=1.4e+02 Score=21.00 Aligned_cols=55 Identities=11% Similarity=-0.161 Sum_probs=28.2
Q ss_pred CCCCcccchhHHHHHHHHHHHHHHHHHhhhccccccCCcchhHHHHHHHHHHHHH
Q 025621 1 MTKGFTFSLPVSVVVLAIFYIYFTTVFIFIDRWFGLMSSPGLMNAIVFTAVALMC 55 (250)
Q Consensus 1 ~~~~~~~~~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~~~l~~~~ 55 (250)
|+-..+.|=.++.++++......++.+..=|.........+.+....|++.++..
T Consensus 24 ~~Pst~RWRi~lvi~svc~gaigawywl~dpet~~vp~~~sLw~Hp~FTi~~~tL 78 (126)
T KOG4606|consen 24 MGPSTGRWRIALVIFSVCTGAIGAWYWLIDPETQKVPFFTSLWNHPFFTISFITL 78 (126)
T ss_pred cCCCccchhhHHHHHHHHHHhhhhhhhhcCcceeeeehHHHHhcCccHHHHHHHH
Confidence 4455666767777766666555566655544433322223334344455444443
No 78
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.02 E-value=23 Score=18.47 Aligned_cols=20 Identities=25% Similarity=0.610 Sum_probs=11.6
Q ss_pred cccccccccCCC-CCCCcchh
Q 025621 97 YCQKCSHYKPPR-AHHCRVCK 116 (250)
Q Consensus 97 ~C~~C~~~kp~R-s~HC~~C~ 116 (250)
.|..|+...... ..||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 356666555555 56666554
No 79
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=28.99 E-value=27 Score=24.98 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=17.7
Q ss_pred CcccccccccccCC--CCCCCcchhh
Q 025621 94 DLRYCQKCSHYKPP--RAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~--Rs~HC~~C~~ 117 (250)
..-+|..|...-+. +..+|+.|+.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcC
Confidence 45899999877655 3567999874
No 80
>PRK10692 hypothetical protein; Provisional
Probab=28.79 E-value=1.9e+02 Score=19.58 Aligned_cols=18 Identities=0% Similarity=0.008 Sum_probs=8.2
Q ss_pred chhHHHHHHHHHHHHHHH
Q 025621 40 PGLMNAIVFTAVALMCVF 57 (250)
Q Consensus 40 ~~~~~~ii~~~l~~~~~~ 57 (250)
....+..++.++....+|
T Consensus 40 ~~~~~gal~~IFiGAllW 57 (92)
T PRK10692 40 QFFAHGALLSIFVGALLW 57 (92)
T ss_pred HHHHhhHHHHHHHHHHHH
Confidence 334444555554444443
No 81
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.71 E-value=13 Score=20.42 Aligned_cols=22 Identities=32% Similarity=0.738 Sum_probs=12.7
Q ss_pred Ccccccccccc-cCCCCCCCcchh
Q 025621 94 DLRYCQKCSHY-KPPRAHHCRVCK 116 (250)
Q Consensus 94 ~~~~C~~C~~~-kp~Rs~HC~~C~ 116 (250)
..+.|..|..+ -|+| ..|+.|+
T Consensus 10 ~~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEEE-TTT--EEES---SEETTTT
T ss_pred EEEEcCCCCCEecCCC-cCCCCcC
Confidence 46899999988 4555 7787775
No 82
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.08 E-value=29 Score=24.88 Aligned_cols=24 Identities=33% Similarity=0.641 Sum_probs=17.0
Q ss_pred CcccccccccccCCCCC---CCcchhh
Q 025621 94 DLRYCQKCSHYKPPRAH---HCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~---HC~~C~~ 117 (250)
..-+|..|...-+.... +|+.||.
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCC
Confidence 45899999877655432 5998884
No 83
>PF12837 Fer4_6: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=27.85 E-value=26 Score=17.36 Aligned_cols=9 Identities=44% Similarity=1.058 Sum_probs=5.9
Q ss_pred Ccchhhhhh
Q 025621 112 CRVCKRCVL 120 (250)
Q Consensus 112 C~~C~~CV~ 120 (250)
|..|++|+.
T Consensus 9 C~~Cg~C~~ 17 (24)
T PF12837_consen 9 CIGCGDCVR 17 (24)
T ss_pred CcChhHHHH
Confidence 566777764
No 84
>PLN00186 ribosomal protein S26; Provisional
Probab=27.82 E-value=18 Score=25.41 Aligned_cols=14 Identities=29% Similarity=0.769 Sum_probs=11.6
Q ss_pred CCCCcchhhhhhhH
Q 025621 109 AHHCRVCKRCVLRM 122 (250)
Q Consensus 109 s~HC~~C~~CV~~~ 122 (250)
.-||..|++||-+=
T Consensus 20 ~V~C~nCgr~vPKD 33 (109)
T PLN00186 20 RIRCSNCGKCVPKD 33 (109)
T ss_pred ceeeCCCccccccc
Confidence 45899999999864
No 85
>COG1600 Uncharacterized Fe-S protein [Energy production and conversion]
Probab=27.33 E-value=31 Score=29.77 Aligned_cols=17 Identities=35% Similarity=1.001 Sum_probs=13.5
Q ss_pred cCCCCCCCcchhhhhhh
Q 025621 105 KPPRAHHCRVCKRCVLR 121 (250)
Q Consensus 105 kp~Rs~HC~~C~~CV~~ 121 (250)
+|....||..|.+|+..
T Consensus 180 ~p~~~~~Cg~C~~Clda 196 (337)
T COG1600 180 RPEEEDHCGSCTRCLDA 196 (337)
T ss_pred CCCCCccChhhHHHHhh
Confidence 45555899999999975
No 86
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.55 E-value=22 Score=26.10 Aligned_cols=9 Identities=44% Similarity=1.040 Sum_probs=6.6
Q ss_pred CCCCcchhh
Q 025621 109 AHHCRVCKR 117 (250)
Q Consensus 109 s~HC~~C~~ 117 (250)
++||+.||.
T Consensus 28 ~~hCp~Cg~ 36 (131)
T COG1645 28 AKHCPKCGT 36 (131)
T ss_pred HhhCcccCC
Confidence 678888774
No 87
>PF10762 DUF2583: Protein of unknown function (DUF2583) ; InterPro: IPR019698 Some members in this entry are annotated as YchH however currently no function is known.
Probab=25.43 E-value=2.2e+02 Score=19.17 Aligned_cols=17 Identities=12% Similarity=0.131 Sum_probs=7.7
Q ss_pred hhHHHHHHHHHHHHHHH
Q 025621 41 GLMNAIVFTAVALMCVF 57 (250)
Q Consensus 41 ~~~~~ii~~~l~~~~~~ 57 (250)
...+..++.++....+|
T Consensus 41 ~~~~gal~~IFiGAllW 57 (89)
T PF10762_consen 41 FLAHGALFSIFIGALLW 57 (89)
T ss_pred HHHhhHHHHHHHHHHHH
Confidence 33444455544444443
No 88
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=25.17 E-value=33 Score=28.92 Aligned_cols=21 Identities=33% Similarity=0.963 Sum_probs=16.2
Q ss_pred CcccccccccccCCCCCCCcchh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCK 116 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~ 116 (250)
..+||++|...+|. |.|+.|.
T Consensus 318 d~~fCstCG~~ga~--KrCs~CK 338 (396)
T KOG1710|consen 318 DCQFCSTCGHPGAK--KRCSQCK 338 (396)
T ss_pred ecccccccCCCCcc--chhhhhH
Confidence 46999999998874 5666665
No 89
>PF12798 Fer4_3: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding
Probab=25.01 E-value=32 Score=14.90 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=4.6
Q ss_pred Ccchhhhhh
Q 025621 112 CRVCKRCVL 120 (250)
Q Consensus 112 C~~C~~CV~ 120 (250)
|..|+.|+.
T Consensus 1 C~~C~~C~~ 9 (15)
T PF12798_consen 1 CTGCGACVE 9 (15)
T ss_pred CCCchHHHH
Confidence 344566653
No 90
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=24.98 E-value=43 Score=27.06 Aligned_cols=18 Identities=39% Similarity=0.881 Sum_probs=14.0
Q ss_pred cCCCCCCCcchhhhhhhH
Q 025621 105 KPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 105 kp~Rs~HC~~C~~CV~~~ 122 (250)
.+.+-.||..|.-|+.|.
T Consensus 188 ~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 188 NGGEGDHCGECESCVLRE 205 (222)
T ss_pred CCCCCCCCCCCHHHHHHH
Confidence 344444999999999986
No 91
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=24.69 E-value=2.7e+02 Score=19.91 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=3.9
Q ss_pred cccccccc
Q 025621 97 YCQKCSHY 104 (250)
Q Consensus 97 ~C~~C~~~ 104 (250)
.|+.|+..
T Consensus 71 ~CP~C~K~ 78 (114)
T PF11023_consen 71 ECPNCGKQ 78 (114)
T ss_pred ECCCCCCh
Confidence 35555533
No 92
>PF00037 Fer4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1DUR_A 1H98_A 1BD6_A 1BQX_A 1BWE_A 1BC6_A 3BK7_A 1FCA_A 1FDN_A 2FDN_A ....
Probab=24.68 E-value=30 Score=16.96 Aligned_cols=10 Identities=50% Similarity=1.119 Sum_probs=5.5
Q ss_pred CCcchhhhhh
Q 025621 111 HCRVCKRCVL 120 (250)
Q Consensus 111 HC~~C~~CV~ 120 (250)
.|..|++|+.
T Consensus 7 ~C~~Cg~C~~ 16 (24)
T PF00037_consen 7 KCIGCGRCVE 16 (24)
T ss_dssp TSSS-THHHH
T ss_pred HCCCcchhhh
Confidence 4666677653
No 93
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=24.64 E-value=21 Score=24.50 Aligned_cols=14 Identities=36% Similarity=0.517 Sum_probs=11.8
Q ss_pred CCCCcchhhhhhhH
Q 025621 109 AHHCRVCKRCVLRM 122 (250)
Q Consensus 109 s~HC~~C~~CV~~~ 122 (250)
.-||..|++||-+-
T Consensus 20 ~V~C~nCgr~vPKD 33 (95)
T PRK09335 20 YVQCDNCGRRVPRD 33 (95)
T ss_pred cEEeCCCCCcCcCC
Confidence 45899999999876
No 94
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=24.46 E-value=36 Score=28.00 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=12.8
Q ss_pred cccccccccccCCCCCCCcchhhh
Q 025621 95 LRYCQKCSHYKPPRAHHCRVCKRC 118 (250)
Q Consensus 95 ~~~C~~C~~~kp~Rs~HC~~C~~C 118 (250)
.+.|..|+...-.| .||..|..|
T Consensus 261 ~~~C~iC~~~~~~R-~~C~~~kA~ 283 (325)
T KOG4399|consen 261 KHGCFICGELDHKR-STCPNIKAV 283 (325)
T ss_pred hcceeecccccccc-ccCccHHHH
Confidence 45566666666666 555554444
No 95
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=24.42 E-value=36 Score=26.10 Aligned_cols=22 Identities=23% Similarity=0.529 Sum_probs=12.7
Q ss_pred ccccccccccCCCCCCCcchhhh
Q 025621 96 RYCQKCSHYKPPRAHHCRVCKRC 118 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~~C 118 (250)
-.|..|+..+=.+. -|+.|||.
T Consensus 163 ilCtvCe~r~w~g~-~CPKCGr~ 184 (200)
T PF12387_consen 163 ILCTVCEGREWKGG-NCPKCGRH 184 (200)
T ss_pred EEEeeeecCccCCC-CCCcccCC
Confidence 45666665544333 38888764
No 96
>PRK11106 queuosine biosynthesis protein QueC; Provisional
Probab=24.26 E-value=45 Score=27.13 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=16.9
Q ss_pred ccccccccccCCCCCCCcchhhhhhhH
Q 025621 96 RYCQKCSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
..=.+|-. +.+..||..|+.|..|.
T Consensus 183 ~~T~SCy~--g~~g~~CG~C~sC~~R~ 207 (231)
T PRK11106 183 HETLTCYN--GIKGDGCGHCAACHLRA 207 (231)
T ss_pred CceeeccC--cCCCCCCCCCHHHHHHH
Confidence 45556654 22224999999999985
No 97
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=24.24 E-value=32 Score=22.48 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=12.0
Q ss_pred CcccccccccccCCCCC-CCcchhhh
Q 025621 94 DLRYCQKCSHYKPPRAH-HCRVCKRC 118 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~-HC~~C~~C 118 (250)
....|..|...-++.++ -|+.||.=
T Consensus 8 ~vlrC~aCf~~t~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 8 WVLRCHACFKITKDMTKQFCPKCGNA 33 (73)
T ss_dssp EEEE-SSS--EES-SS--S-SSS--S
T ss_pred eeEEccccccCcCCCCceeCcccCCC
Confidence 34678888888776665 78888764
No 98
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=24.18 E-value=48 Score=18.81 Aligned_cols=27 Identities=19% Similarity=0.559 Sum_probs=14.5
Q ss_pred ccccccccccCCCC------CCCcchhhhhhhH
Q 025621 96 RYCQKCSHYKPPRA------HHCRVCKRCVLRM 122 (250)
Q Consensus 96 ~~C~~C~~~kp~Rs------~HC~~C~~CV~~~ 122 (250)
++|+.|.....+-. .+-.+|+.||...
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 46777776654432 2577888888764
No 99
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=24.03 E-value=23 Score=24.95 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=11.5
Q ss_pred CCCCcchhhhhhhH
Q 025621 109 AHHCRVCKRCVLRM 122 (250)
Q Consensus 109 s~HC~~C~~CV~~~ 122 (250)
.-||..|++||-+=
T Consensus 20 ~V~C~nCgr~vPKD 33 (108)
T PTZ00172 20 PVRCSNCGRCVPKD 33 (108)
T ss_pred cEEeCCcccccccc
Confidence 45899999999864
No 100
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.58 E-value=59 Score=17.34 Aligned_cols=21 Identities=24% Similarity=0.581 Sum_probs=10.4
Q ss_pred cccccccc-cCC-CCCCCcchhh
Q 025621 97 YCQKCSHY-KPP-RAHHCRVCKR 117 (250)
Q Consensus 97 ~C~~C~~~-kp~-Rs~HC~~C~~ 117 (250)
.|..|.-. .+. ....|+.|+.
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCC
Confidence 35555544 332 3446666653
No 101
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.40 E-value=42 Score=21.27 Aligned_cols=22 Identities=32% Similarity=0.774 Sum_probs=15.5
Q ss_pred CcccccccccccCCCCCCCcchhh
Q 025621 94 DLRYCQKCSHYKPPRAHHCRVCKR 117 (250)
Q Consensus 94 ~~~~C~~C~~~kp~Rs~HC~~C~~ 117 (250)
..+-|..|+.... ..-|+.||.
T Consensus 4 ~~~AC~~C~~i~~--~~~Cp~Cgs 25 (64)
T PRK06393 4 QYRACKKCKRLTP--EKTCPVHGD 25 (64)
T ss_pred hhhhHhhCCcccC--CCcCCCCCC
Confidence 3467889998884 337777764
No 102
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=22.04 E-value=50 Score=23.42 Aligned_cols=27 Identities=30% Similarity=0.662 Sum_probs=17.8
Q ss_pred CCCccccccccccc----CCCCCCCcchhhh
Q 025621 92 GGDLRYCQKCSHYK----PPRAHHCRVCKRC 118 (250)
Q Consensus 92 ~~~~~~C~~C~~~k----p~Rs~HC~~C~~C 118 (250)
+.....|..|...+ .=|+.||+.|+.=
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 34567898898654 3355678877753
No 103
>KOG4800 consensus Neuronal membrane glycoprotein/Myelin proteolipid protein [Function unknown]
Probab=21.61 E-value=2e+02 Score=23.24 Aligned_cols=16 Identities=31% Similarity=0.713 Sum_probs=10.5
Q ss_pred CCcchhhhhhhHHHHH
Q 025621 111 HCRVCKRCVLRMVLLV 126 (250)
Q Consensus 111 HC~~C~~CV~~~~~~~ 126 (250)
.-+.|||||...+..+
T Consensus 113 k~r~cGr~Vs~~f~~l 128 (248)
T KOG4800|consen 113 KTRMCGRCVSGVFVGL 128 (248)
T ss_pred hceecCcchhhhhhHH
Confidence 3478999988843333
No 104
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=21.01 E-value=55 Score=24.89 Aligned_cols=22 Identities=18% Similarity=0.596 Sum_probs=18.6
Q ss_pred cccccCCCCCCCcchhhhhhhH
Q 025621 101 CSHYKPPRAHHCRVCKRCVLRM 122 (250)
Q Consensus 101 C~~~kp~Rs~HC~~C~~CV~~~ 122 (250)
|.......-..|+.||+|...-
T Consensus 56 C~~k~t~~g~~C~~Cg~C~Ig~ 77 (158)
T PF01976_consen 56 CPAKITSDGYNCKRCGKCDIGD 77 (158)
T ss_pred CCCccCCCCCcCCCCCCCchhH
Confidence 7777777888999999998764
No 105
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=20.70 E-value=2.8e+02 Score=22.46 Aligned_cols=16 Identities=19% Similarity=0.003 Sum_probs=7.8
Q ss_pred CCCcccchhHHHHHHH
Q 025621 2 TKGFTFSLPVSVVVLA 17 (250)
Q Consensus 2 ~~~~~~~~p~~~~~~l 17 (250)
+++.-.+++...+..+
T Consensus 20 trk~dp~l~~~ml~a~ 35 (224)
T PF13829_consen 20 TRKEDPKLPWLMLGAF 35 (224)
T ss_pred HHHHCcchHHHHHHHH
Confidence 4445555555544433
No 106
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=20.50 E-value=28 Score=20.60 Aligned_cols=26 Identities=19% Similarity=0.604 Sum_probs=17.8
Q ss_pred Cccccccccccc---CCCCCCCcchhhhh
Q 025621 94 DLRYCQKCSHYK---PPRAHHCRVCKRCV 119 (250)
Q Consensus 94 ~~~~C~~C~~~k---p~Rs~HC~~C~~CV 119 (250)
...+|..|+..- .....+|+.|+.-+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChH
Confidence 568899998776 55666888887644
No 107
>PRK14132 riboflavin kinase; Provisional
Probab=20.10 E-value=38 Score=24.70 Aligned_cols=16 Identities=13% Similarity=0.160 Sum_probs=13.0
Q ss_pred ccccccccCCCCCCCc
Q 025621 98 CQKCSHYKPPRAHHCR 113 (250)
Q Consensus 98 C~~C~~~kp~Rs~HC~ 113 (250)
.-.|.++.|.||||=.
T Consensus 84 ~i~~aiV~P~rT~h~~ 99 (126)
T PRK14132 84 EIDGAIVFPKKTDHSK 99 (126)
T ss_pred ceeEEEEEeccCCCCC
Confidence 4568889999999965
Done!