Query 025379
Match_columns 253
No_of_seqs 239 out of 1651
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 05:12:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025379.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025379hhsearch_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 8.7E-56 1.9E-60 384.1 17.9 221 2-232 48-271 (307)
2 KOG1314 DHHC-type Zn-finger pr 100.0 8.3E-49 1.8E-53 336.6 11.3 206 4-253 52-282 (414)
3 KOG1311 DHHC-type Zn-finger pr 100.0 1.1E-44 2.3E-49 319.8 19.0 224 5-247 58-291 (299)
4 PF01529 zf-DHHC: DHHC palmito 100.0 9E-43 1.9E-47 284.4 12.9 173 14-197 1-174 (174)
5 COG5273 Uncharacterized protei 100.0 3.4E-40 7.4E-45 290.1 14.7 219 2-249 58-303 (309)
6 KOG1313 DHHC-type Zn-finger pr 100.0 4.9E-39 1.1E-43 268.5 15.3 175 71-251 101-307 (309)
7 KOG1312 DHHC-type Zn-finger pr 100.0 3.2E-33 7E-38 234.9 8.2 111 5-137 103-213 (341)
8 KOG0509 Ankyrin repeat and DHH 100.0 7.8E-29 1.7E-33 228.2 8.9 140 73-219 421-585 (600)
9 KOG1311 DHHC-type Zn-finger pr 94.0 0.3 6.5E-06 43.1 8.2 44 85-128 112-166 (299)
10 PF01529 zf-DHHC: DHHC palmito 93.5 0.84 1.8E-05 36.5 9.5 33 69-101 59-91 (174)
11 PF13240 zinc_ribbon_2: zinc-r 89.0 0.22 4.8E-06 26.4 1.0 21 74-94 1-21 (23)
12 PRK04136 rpl40e 50S ribosomal 88.8 0.23 5.1E-06 31.2 1.2 26 69-94 11-36 (48)
13 PF13248 zf-ribbon_3: zinc-rib 84.8 0.51 1.1E-05 25.7 1.0 22 73-94 3-24 (26)
14 COG5273 Uncharacterized protei 84.4 3.2 7E-05 37.0 6.5 109 82-194 105-224 (309)
15 KOG0509 Ankyrin repeat and DHH 80.8 1.2 2.6E-05 42.7 2.5 53 70-123 323-375 (600)
16 COG1552 RPL40A Ribosomal prote 78.3 0.5 1.1E-05 29.8 -0.6 26 69-94 11-36 (50)
17 PTZ00303 phosphatidylinositol 77.5 1.3 2.9E-05 43.7 1.7 22 73-94 461-489 (1374)
18 PF12773 DZR: Double zinc ribb 76.3 2.2 4.8E-05 26.8 2.0 34 71-104 11-47 (50)
19 PHA02680 ORF090 IMV phosphoryl 76.2 18 0.00039 25.8 6.6 36 158-196 48-83 (91)
20 PF10571 UPF0547: Uncharacteri 71.3 2.3 5E-05 23.2 1.0 21 73-93 1-21 (26)
21 KOG1313 DHHC-type Zn-finger pr 70.1 76 0.0016 27.8 10.6 55 67-132 111-165 (309)
22 PF01020 Ribosomal_L40e: Ribos 69.2 2.2 4.7E-05 27.3 0.7 27 69-95 14-42 (52)
23 PF12773 DZR: Double zinc ribb 66.9 4.2 9.1E-05 25.5 1.7 24 70-93 27-50 (50)
24 KOG1842 FYVE finger-containing 65.1 2.2 4.7E-05 39.5 0.1 27 70-96 178-206 (505)
25 PF06906 DUF1272: Protein of u 64.3 4.3 9.3E-05 26.4 1.3 35 75-112 8-50 (57)
26 KOG1315 Predicted DHHC-type Zn 60.4 50 0.0011 29.4 7.8 32 85-116 108-139 (307)
27 PF00641 zf-RanBP: Zn-finger i 59.2 3.1 6.8E-05 23.2 0.0 21 74-94 6-26 (30)
28 PRK11875 psbT photosystem II r 59.1 23 0.00049 20.1 3.4 28 3-30 3-31 (31)
29 CHL00031 psbT photosystem II p 58.5 20 0.00043 20.6 3.2 28 3-30 3-31 (33)
30 smart00064 FYVE Protein presen 57.1 7.2 0.00016 26.1 1.6 24 73-96 11-36 (68)
31 PF01363 FYVE: FYVE zinc finge 53.9 3.2 6.9E-05 27.9 -0.6 25 72-96 9-35 (69)
32 PF02150 RNA_POL_M_15KD: RNA p 51.2 3.6 7.8E-05 24.1 -0.6 8 73-80 2-9 (35)
33 PF07649 C1_3: C1-like domain; 49.8 5.3 0.00011 22.3 -0.1 21 74-94 2-23 (30)
34 PF09297 zf-NADH-PPase: NADH p 45.6 7.7 0.00017 22.0 0.2 22 72-93 3-28 (32)
35 PF07010 Endomucin: Endomucin; 45.3 38 0.00083 28.7 4.3 27 3-29 197-223 (259)
36 smart00661 RPOL9 RNA polymeras 44.1 11 0.00023 23.6 0.8 7 74-80 2-8 (52)
37 PRK00432 30S ribosomal protein 42.2 14 0.00029 23.6 1.0 23 71-93 19-44 (50)
38 KOG3183 Predicted Zn-finger pr 41.5 12 0.00026 31.9 0.8 21 87-107 24-49 (250)
39 PF00751 DM: DM DNA binding do 41.2 10 0.00022 23.9 0.3 22 86-107 2-28 (47)
40 PF03107 C1_2: C1 domain; Int 38.4 19 0.00041 20.0 1.1 20 74-93 2-22 (30)
41 PF01405 PsbT: Photosystem II 36.9 62 0.0013 18.1 2.9 24 3-26 3-27 (29)
42 PF01437 PSI: Plexin repeat; 36.8 12 0.00026 23.6 0.1 22 90-111 6-30 (51)
43 cd00065 FYVE FYVE domain; Zinc 35.3 17 0.00037 23.1 0.7 22 74-95 4-27 (57)
44 COG2093 DNA-directed RNA polym 34.9 21 0.00045 23.9 1.0 23 72-94 4-26 (64)
45 PF07282 OrfB_Zn_ribbon: Putat 34.9 21 0.00046 23.8 1.1 26 70-95 26-55 (69)
46 KOG1729 FYVE finger containing 34.9 12 0.00027 32.9 -0.1 27 72-98 168-197 (288)
47 TIGR00155 pqiA_fam integral me 34.6 3.8E+02 0.0082 24.8 11.0 32 72-103 215-247 (403)
48 PRK12286 rpmF 50S ribosomal pr 34.5 25 0.00053 23.1 1.3 22 70-93 25-47 (57)
49 PRK13130 H/ACA RNA-protein com 34.0 21 0.00045 23.4 0.9 22 71-94 4-25 (56)
50 smart00547 ZnF_RBZ Zinc finger 33.4 20 0.00042 19.0 0.6 21 74-94 4-24 (26)
51 COG4640 Predicted membrane pro 32.5 22 0.00047 32.6 1.1 25 72-96 1-25 (465)
52 PRK03681 hypA hydrogenase nick 32.5 21 0.00046 26.8 0.8 26 69-94 67-95 (114)
53 KOG1819 FYVE finger-containing 31.9 15 0.00033 34.7 -0.1 22 73-94 902-925 (990)
54 PRK13743 conjugal transfer pro 31.8 2.4E+02 0.0052 21.8 6.5 22 113-134 36-57 (141)
55 smart00423 PSI domain found in 31.6 25 0.00054 21.5 0.9 17 90-106 5-21 (46)
56 KOG1398 Uncharacterized conser 30.9 25 0.00055 32.2 1.2 27 81-113 9-35 (460)
57 cd01995 ExsB ExsB is a transcr 29.4 23 0.00051 28.0 0.7 23 74-99 142-164 (169)
58 PLN00186 ribosomal protein S26 29.1 20 0.00044 26.6 0.2 16 85-100 19-34 (109)
59 KOG3611 Semaphorins [Signal tr 28.9 23 0.00049 35.5 0.6 39 86-124 491-537 (737)
60 COG0603 Predicted PP-loop supe 28.5 26 0.00056 29.7 0.8 19 81-99 187-205 (222)
61 PF14127 DUF4294: Domain of un 28.4 49 0.0011 26.4 2.3 32 185-219 103-134 (157)
62 PRK14559 putative protein seri 27.2 40 0.00086 33.3 1.9 22 73-94 28-49 (645)
63 PRK14559 putative protein seri 27.0 35 0.00075 33.7 1.5 40 70-111 13-52 (645)
64 PF09889 DUF2116: Uncharacteri 26.8 90 0.0019 20.6 3.0 22 73-94 4-26 (59)
65 PF08600 Rsm1: Rsm1-like; Int 26.1 30 0.00064 24.9 0.6 12 100-111 55-66 (91)
66 COG1579 Zn-ribbon protein, pos 26.0 60 0.0013 27.8 2.6 27 72-98 197-233 (239)
67 PF09788 Tmemb_55A: Transmembr 25.9 3.1E+02 0.0067 23.8 6.8 21 109-129 188-209 (256)
68 KOG1841 Smad anchor for recept 25.8 64 0.0014 33.7 3.0 39 72-122 554-597 (1287)
69 PRK09335 30S ribosomal protein 25.6 24 0.00052 25.6 0.1 20 85-104 19-38 (95)
70 TIGR01031 rpmF_bact ribosomal 25.2 44 0.00095 21.7 1.2 22 70-93 24-46 (55)
71 PTZ00172 40S ribosomal protein 25.1 25 0.00054 26.1 0.1 17 85-101 19-35 (108)
72 PHA02942 putative transposase; 23.6 44 0.00094 30.7 1.4 25 70-94 323-350 (383)
73 TIGR00364 exsB protein. This p 23.4 41 0.0009 27.5 1.1 13 86-98 189-201 (201)
74 PF07754 DUF1610: Domain of un 23.3 50 0.0011 17.6 1.0 7 87-93 17-23 (24)
75 PF14952 zf-tcix: Putative tre 23.1 50 0.0011 20.4 1.1 21 70-90 9-29 (44)
76 KOG1710 MYND Zn-finger and ank 23.0 35 0.00075 30.2 0.6 22 70-93 317-338 (396)
77 smart00301 DM Doublesex DNA-bi 23.0 45 0.00098 21.6 1.0 6 102-107 23-28 (54)
78 PF14319 Zn_Tnp_IS91: Transpos 22.5 36 0.00079 25.4 0.6 24 71-94 41-68 (111)
79 PF06508 QueC: Queuosine biosy 22.4 35 0.00076 28.5 0.5 26 72-99 177-203 (209)
80 PF00130 C1_1: Phorbol esters/ 22.3 52 0.0011 20.5 1.2 34 70-103 9-50 (53)
81 PF09538 FYDLN_acid: Protein o 21.8 53 0.0012 24.5 1.3 25 70-94 7-34 (108)
82 PF12760 Zn_Tnp_IS1595: Transp 21.7 45 0.00097 20.5 0.8 22 73-94 19-45 (46)
83 PF13842 Tnp_zf-ribbon_2: DDE_ 21.4 61 0.0013 18.4 1.2 6 88-93 18-23 (32)
84 KOG1818 Membrane trafficking a 21.1 38 0.00082 33.1 0.5 22 73-94 166-189 (634)
85 PRK11106 queuosine biosynthesi 20.5 47 0.001 28.3 0.9 13 87-99 195-207 (231)
86 PF03842 Silic_transp: Silicon 20.3 7.2E+02 0.016 23.3 9.4 16 116-131 171-186 (512)
No 1
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=8.7e-56 Score=384.06 Aligned_cols=221 Identities=41% Similarity=0.733 Sum_probs=175.6
Q ss_pred ChhhHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccccccccccccccccc
Q 025379 2 LVLNFVMQLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQF 81 (253)
Q Consensus 2 ~li~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 81 (253)
++++++++++|.+|+|++++++|||.+|..|.++.+++...+... + .++.......+..++.|+|.+|+.+
T Consensus 48 ~ll~~~~ll~m~~~sy~~~vf~~pg~vp~~~~~~~~~~~~~~~~~---~------~~~~~~~~~~~~~g~~R~C~kC~~i 118 (307)
T KOG1315|consen 48 LLLLFHLLLIMFLWSYFRTVFTDPGRVPDSYRPSVEDEDSLENGS---D------NERDLPGYTRTSDGAVRYCDKCKCI 118 (307)
T ss_pred HHHHHHHHHHHHHHHHHheeEecCCCCccccCCCcCccccccccC---c------ccccceeeEecCCCCceeecccccc
Confidence 578999999999999999999999999999988776543221100 0 0011111234667899999999999
Q ss_pred CCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcchhHHHH
Q 025379 82 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESPGNLAASFI 161 (253)
Q Consensus 82 kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (253)
||+|||||++|+|||+||||||||+|||||.+|||+|++|++|+.+++++..+.....++.++... ...+......+++
T Consensus 119 KPdRaHHCsvC~rCvLKmDHHCpWi~nCVgf~NyKfF~lfl~y~~l~~~~~lv~~~~~~~~~~~~~-~~~~~~~~~~~~~ 197 (307)
T KOG1315|consen 119 KPDRAHHCSVCNRCVLKMDHHCPWINNCVGFRNYKFFLLFLFYTNLYSIYVLVTTLIGFTKYFQGG-AGPSSLLLFFIVF 197 (307)
T ss_pred cCCccccchhhhhhhhccccCCcceeceecccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccCchhHHHHHHH
Confidence 999999999999999999999999999999999999999999999999888888877777777332 2223333445555
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhhcCCCCCCCchhH---HHHHHhccCCCccceeecCccCCC
Q 025379 162 TFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKTSPKWRYDLGW---KINFEQVFGKNKKYWLIPAYSKDD 232 (253)
Q Consensus 162 ~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~~~~~yd~G~---~~N~~~vfG~~~~~W~~P~~~~~~ 232 (253)
.+++++.+++++++++++|++||++|+||+|.++......+.++.+- ..|++|+||.++..|++|+.++.+
T Consensus 198 ~~~~~~~f~i~l~~~l~~h~~Li~~N~TTiE~~~~~~~~~~~~~~~~~~~~~n~~~vfg~~~~~wl~P~~~s~~ 271 (307)
T KOG1315|consen 198 LFLVAIAFSISLSGLLCFHTYLILKNKTTIEAYKSPVFRSGLHNKNGFNLYVNFREVFGSNLLYWLLPIDSSWG 271 (307)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhhccccccccccccCCcceeecHHHHhCCCceEEeccccCccc
Confidence 66777888888888999999999999999999987533323333332 569999999999999999988764
No 2
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=8.3e-49 Score=336.60 Aligned_cols=206 Identities=32% Similarity=0.661 Sum_probs=157.4
Q ss_pred hhHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccCCCCCCCCCCCCCcccccccccccccccccccccccccccCC
Q 025379 4 LNFVMQLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKP 83 (253)
Q Consensus 4 i~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP 83 (253)
+.|-+...|++++|+.+++++||+||++|.|.... +..-.+||.+|+.+|+
T Consensus 52 i~f~~~~~m~~~ny~~A~~~gPG~vp~~wkPe~~~-----------------------------D~~~lqfCk~CqgYKa 102 (414)
T KOG1314|consen 52 ITFLLWTSMILYNYFNAIFTGPGFVPLGWKPENPK-----------------------------DEMFLQFCKKCQGYKA 102 (414)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCCCCCh-----------------------------hHHHHHHHhhccCcCC
Confidence 45667788999999999999999999999885432 1234689999999999
Q ss_pred CCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHH----HHHHHh----cCCCCCC---C
Q 025379 84 PRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLP----IFIALF----TDDEIPE---S 152 (253)
Q Consensus 84 ~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~----~~~~~~----~~~~~~~---~ 152 (253)
||||||+.|||||.+|||||||+|||||..||.||+.||++..++|+..++++.. .+...| .....+. .
T Consensus 103 pRSHHCrkCnrCvmkMDHHCPWinnCVG~aNh~~F~~FLlf~ivG~ih~tiI~~~~~~~~Iy~~W~~~~g~~hlp~v~ft 182 (414)
T KOG1314|consen 103 PRSHHCRKCNRCVMKMDHHCPWINNCVGWANHAYFLRFLLFSIVGCIHGTIILVCAQYRGIYFRWYIKYGLRHLPIVFFT 182 (414)
T ss_pred CccccchHHHHHHHhhccCCcchhhcccccccHHHHHHHHHHHHhcccceeeehhHHHHHHHHHHHhhcccccCceeecc
Confidence 9999999999999999999999999999999999999999998877655443332 222223 1122211 2
Q ss_pred CcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhhc--------------CCCCCCCchhHHHHHHhccCC
Q 025379 153 PGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK--------------TSPKWRYDLGWKINFEQVFGK 218 (253)
Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~--------------~~~~~~yd~G~~~N~~~vfG~ 218 (253)
+.++..+++++.++++..+.+..|++.|+..|.+|+|.+|.+.-+ .....|||+|++.|+++||-.
T Consensus 183 ~~~li~~vfslgla~gv~la~t~Lf~~qlk~Il~nrt~IE~wi~~Ka~~rr~~~~~d~~~~f~ypydlgWr~n~r~vf~~ 262 (414)
T KOG1314|consen 183 LSSLIALVFSLGLAIGVVLALTMLFFIQLKQILNNRTGIESWIVEKAMDRREYYFNDDEGEFTYPYDLGWRINLREVFFQ 262 (414)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHHHHHHHHHHhhccCCCCceeeeccccccccHHHHhhh
Confidence 223334444445555566666778889999999999999986411 123469999999999999965
Q ss_pred CccceeecCccCCCCCCCCCCCCeeecCCCCCCCC
Q 025379 219 NKKYWLIPAYSKDDLEWLPSFQCVEYPTRPDSDDL 253 (253)
Q Consensus 219 ~~~~W~~P~~~~~~~~~~p~~dG~~~~~~~~~~~~ 253 (253)
+. .+.|||++||+.++++|.
T Consensus 263 ~~---------------~~~gdg~~wPv~~gc~qy 282 (414)
T KOG1314|consen 263 NK---------------KEEGDGIEWPVVEGCVQY 282 (414)
T ss_pred cc---------------ccCCCCccccccCccccc
Confidence 42 245999999999999873
No 3
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=1.1e-44 Score=319.79 Aligned_cols=224 Identities=27% Similarity=0.498 Sum_probs=154.7
Q ss_pred hHHHHHHHHHHHHHHHhhc---CCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccccccccccccccccc
Q 025379 5 NFVMQLVMLVWSYFSVVIT---DPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQF 81 (253)
Q Consensus 5 ~~~~l~~~~~~sy~~~~~t---dPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 81 (253)
+..++++..+.....+.++ |||++|++.....+.. ++.++ ......++...+.+||.+|+.+
T Consensus 58 ~~~if~~~~~~~~~~~~~~~~sdpg~~p~~~~~~~~~~--~~~~~-------------~~~~~~~~~~~~~~~C~~C~~~ 122 (299)
T KOG1311|consen 58 LGAIFFLLNILNLMLACFRMLSDPGIVPRADDEQIEDP--ERAPL-------------YKNVDVNGIQVEWKYCDTCQLY 122 (299)
T ss_pred HHHHHHHHHHHHHHHHHhcccCCCceecCcccCCCCCc--ccccc-------------CCCcccCCcccceEEcCcCccc
Confidence 3344444445555555555 9999998641111110 00000 0011234566789999999999
Q ss_pred CCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CC--CCCcchh
Q 025379 82 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDE--IP--ESPGNLA 157 (253)
Q Consensus 82 kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--~~~~~~~ 157 (253)
||||||||+.||+||+||||||||+|||||++|||+|+.|++++.+++++..+.....+........ .. .......
T Consensus 123 rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (299)
T KOG1311|consen 123 RPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYLALGVLLALAFLFYELLQRADNLKVNLTPVLIPAGTF 202 (299)
T ss_pred CCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccchhHH
Confidence 9999999999999999999999999999999999999999999888888777766555444332211 11 1122222
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhh-cCCCC-CCCchhHHHHHHhccCCCc-cceeecCccCCCCC
Q 025379 158 ASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEK-KTSPK-WRYDLGWKINFEQVFGKNK-KYWLIPAYSKDDLE 234 (253)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~-~~~~~-~~yd~G~~~N~~~vfG~~~-~~W~~P~~~~~~~~ 234 (253)
..++..++++++.+.+++++.+|++++.+|+||+|.++. +.... ++||.|.++|++++||.+. +.|.-|...+.
T Consensus 203 ~~~~l~~~~~~~~~~~~~l~~fh~~li~~~~Tt~e~~~~~~~~~~~~~~~~g~~~n~~~~~~~~~~~~~~~p~~~~~--- 279 (299)
T KOG1311|consen 203 LSALLGLLSALFLAFTSALLCFHIYLIKSGSTTYESIKSLDFVSRSNPYDLGLLKNLQEVFGGPLPLSWLSPFARSG--- 279 (299)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhheeeEecCcchhhhhhccccccccCCCchhHHHHHHHHhCCCCCcccccccccCC---
Confidence 333344556666777778999999999999999999874 33333 7999999999999999875 67988876542
Q ss_pred CCCCCCCeeecCC
Q 025379 235 WLPSFQCVEYPTR 247 (253)
Q Consensus 235 ~~p~~dG~~~~~~ 247 (253)
.+..||-.+...
T Consensus 280 -~~p~~~~~~~~~ 291 (299)
T KOG1311|consen 280 -PLPHDGEGGPPT 291 (299)
T ss_pred -CCCCCCCCCCcc
Confidence 122455555443
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=100.00 E-value=9e-43 Score=284.38 Aligned_cols=173 Identities=29% Similarity=0.598 Sum_probs=122.4
Q ss_pred HHHHHHHhhcCCCCCCCCCCCCCcccccCCCCCCCCCCCCCcccccccccccccccccccccccccccCCCCCcCCcccc
Q 025379 14 VWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPPRCHHCSVCR 93 (253)
Q Consensus 14 ~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~Rs~HC~~C~ 93 (253)
+++|++++++|||++|+....+...+. +.+. .. ..+......+...+.++|.+|+.+||+|||||+.||
T Consensus 1 ~~~~~~~~~~dPG~~~~~~~~~~~~~~-~~~~---~~-------~~~~~~~~~~~~~~~~~C~~C~~~kp~Rs~HC~~C~ 69 (174)
T PF01529_consen 1 IWSYFLTIFIDPGYVPRSNPDEDQRQE-EKEE---EQ-------NQSIDSPEDDENGELKYCSTCKIIKPPRSHHCRVCN 69 (174)
T ss_pred CEEehhhheECCcccCCcccccccccc-cccc---cc-------chhhhhhccccCCCCEECcccCCcCCCcceeccccc
Confidence 368999999999999986221111100 0000 00 000111223466789999999999999999999999
Q ss_pred hhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-cchhHHHHHHHHHHHHHHH
Q 025379 94 RCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESP-GNLAASFITFVLNLAFALS 172 (253)
Q Consensus 94 ~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 172 (253)
+||+||||||||+|||||++|||+|++|+++..+.+++..+..+..+............. ......++.+++++++.++
T Consensus 70 ~CV~~~DHHC~w~~~cIG~~N~~~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (174)
T PF01529_consen 70 RCVLRFDHHCPWLGNCIGRRNHRYFLLFLLYLCLYCLYFFILSLYYLVRYIPSISFSSFWIFSNFSSIFLLIISIFFFIF 149 (174)
T ss_pred cccccccccchhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccchhhhHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999888877776665555443332111111 1111113444555667777
Q ss_pred HHHHHHHHHHHHhcCcchHhhHhhc
Q 025379 173 ILGFLIMHISLVAGNTTTIEAFEKK 197 (253)
Q Consensus 173 ~~~l~~~h~~li~~n~Tt~E~~~~~ 197 (253)
++.+++.|++++++|+||+|.++++
T Consensus 150 ~~~l~~~~~~~i~~n~Tt~E~~~~~ 174 (174)
T PF01529_consen 150 VGFLLIFQLYLILRNITTYERIKRK 174 (174)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHcC
Confidence 7889999999999999999999864
No 5
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=100.00 E-value=3.4e-40 Score=290.09 Aligned_cols=219 Identities=33% Similarity=0.617 Sum_probs=155.3
Q ss_pred ChhhHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccCCCCCCCCCCCCCccccccccccccccccccccccccccc
Q 025379 2 LVLNFVMQLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQF 81 (253)
Q Consensus 2 ~li~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~ 81 (253)
+.+.+.+.+.+...+|++.+++|||+.+++-.....++.. ......+..+..++|.+|+.+
T Consensus 58 ~~i~~~~i~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~C~~C~~~ 118 (309)
T COG5273 58 FIILFIVILVLASFSYLLLLVSDPGYLGENITLSGYRETI-------------------SRLLDDGKFGTENFCSTCNIY 118 (309)
T ss_pred hhhhhhhhhhhHHHhhHHHhhcCCCccCccccccchhhhh-------------------hhhhhcCccccceeccccccc
Confidence 4567778888899999999999999998542211111110 001234567889999999999
Q ss_pred CCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCcch-hHHH
Q 025379 82 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPESPGNL-AASF 160 (253)
Q Consensus 82 kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 160 (253)
||+|||||+.||+||+||||||||+|||||++|||+|++|++++...++...+.....+...+.... .+... ..++
T Consensus 119 KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~li 195 (309)
T COG5273 119 KPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYIAGIFSIRH---DTSLAICFLI 195 (309)
T ss_pred cCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccC---ChHHHHHHHH
Confidence 9999999999999999999999999999999999999999999877766665554444443332211 12111 1111
Q ss_pred HH-HHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhhcCC------------C-------------CCCCchhHHHHHHh
Q 025379 161 IT-FVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKKTS------------P-------------KWRYDLGWKINFEQ 214 (253)
Q Consensus 161 ~~-~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~~~------------~-------------~~~yd~G~~~N~~~ 214 (253)
.+ ..+++.+.+.+.+++.++.+++..|+|++|.++..+. . ..|++.|.-+|+..
T Consensus 196 ~~~~~~~~~~f~~~~~~~~~~~~~~~~~~t~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~ 275 (309)
T COG5273 196 FGCSLLGVVFFIITTLLLLFLIYLILNNLTTIEFIQISRGGSTLEFFPLCRESNLPFTNIFDSSEGALPLDLGIGQNLST 275 (309)
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHhccceecccccchhccCCcCceeccCCCccccccccCcccccee
Confidence 11 2333444555667888999999999999998654321 1 14677888889999
Q ss_pred ccCCCccceeecCccCCCCCCCCCCCCeeecCCCC
Q 025379 215 VFGKNKKYWLIPAYSKDDLEWLPSFQCVEYPTRPD 249 (253)
Q Consensus 215 vfG~~~~~W~~P~~~~~~~~~~p~~dG~~~~~~~~ 249 (253)
++|.+...|..|..+.. .++.+|+.+++
T Consensus 276 i~~~~~~~~~~~~~~~~-------~~~~~~~~~~~ 303 (309)
T COG5273 276 IKGSNALYWLTPLHTNY-------CNSYDFSLRSD 303 (309)
T ss_pred ecCCCceeeccccccCC-------CCccCcccchh
Confidence 99999889988854432 36667766654
No 6
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=4.9e-39 Score=268.52 Aligned_cols=175 Identities=31% Similarity=0.609 Sum_probs=129.7
Q ss_pred cccccccccccCCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCC
Q 025379 71 GVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTD-DEI 149 (253)
Q Consensus 71 ~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 149 (253)
...+|.+|..+||||+|||+.|||||++|||||||+|||||.+|||||++|++|+.+++.++.+...+..+..... .+.
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 4579999999999999999999999999999999999999999999999999999999998777665555443211 111
Q ss_pred CC---------CCcchh---------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhhc--------CCCCCC
Q 025379 150 PE---------SPGNLA---------ASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEKK--------TSPKWR 203 (253)
Q Consensus 150 ~~---------~~~~~~---------~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~~--------~~~~~~ 203 (253)
.. .+..+. -..-..++++.+.++++.+..+|.++|.+|.|++|+.... +...+|
T Consensus 181 tay~~d~~h~~Pp~~i~r~~~~i~~t~~~~~~fls~~~lv~vg~l~~W~~vlI~~G~tsi~~~~~~~e~k~~~a~~R~~~ 260 (309)
T KOG1313|consen 181 TAYASDVAHVAPPPSILRVYKNITRTSIANLWFLSVRVLVAVGLLTAWHAVLISRGETSIEQLINIKERKRYLAHLRSNP 260 (309)
T ss_pred ccccCcccccCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhheeeehhhhhHHHHHHHHHhHhHHHhccCCC
Confidence 10 011111 0111334445566677788899999999999999986421 123689
Q ss_pred CchhHHHHHHhccCCCc-c-cee---ecCccCCCCCCCCCCCCeeecCCCCCC
Q 025379 204 YDLGWKINFEQVFGKNK-K-YWL---IPAYSKDDLEWLPSFQCVEYPTRPDSD 251 (253)
Q Consensus 204 yd~G~~~N~~~vfG~~~-~-~W~---~P~~~~~~~~~~p~~dG~~~~~~~~~~ 251 (253)
++.|.++||+.++|-.. . .|. +|.. ..|.+.|.+++.++.+|
T Consensus 261 ~n~g~k~nWr~fLg~~~~r~~wk~v~lPt~------~~p~~~~~~~~~~da~~ 307 (309)
T KOG1313|consen 261 TNFGGKANWRNFLGLFRGRHFWKTVLLPTI------RKPVKYGDSKEKSDAYD 307 (309)
T ss_pred cccchHHHHHHhhccccCCceeEEEecccc------ccccccCCcccccchhh
Confidence 99999999999998753 2 564 4542 24668999999776654
No 7
>KOG1312 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=100.00 E-value=3.2e-33 Score=234.86 Aligned_cols=111 Identities=29% Similarity=0.527 Sum_probs=83.3
Q ss_pred hHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccCCCCCCCCCCCCCcccccccccccccccccccccccccccCCC
Q 025379 5 NFVMQLVMLVWSYFSVVITDPGGVPPNWIPNLDEESGGAGQWAGSDNDGVDLGANQSAMLIEPKHQGVRFCQKCNQFKPP 84 (253)
Q Consensus 5 ~~~~l~~~~~~sy~~~~~tdPG~vp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~kP~ 84 (253)
.-..+.++-..++..++.+|||.+.++-... .. ++++ .+.........|+||+..||+
T Consensus 103 l~~l~vivp~i~f~ltc~snpg~i~k~n~s~----~~-------~~yp-----------YDy~if~k~~kCSTCki~KPA 160 (341)
T KOG1312|consen 103 LPYLLVIVPLIFFTLTCGSNPGIITKANESL----FL-------HVYP-----------YDYVIFPKNVKCSTCKIRKPA 160 (341)
T ss_pred HHHHHHHHHHHHHhhhhcCCCCccchhhhcc----ce-------eccC-----------ccceeecCCCccccccCCCcc
Confidence 3344555556788899999999998641110 00 0110 011223444789999999999
Q ss_pred CCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHH
Q 025379 85 RCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLL 137 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~ 137 (253)
||+|||.|||||.|+||||.|+|||||++|.|||++||++...++.++.+.+.
T Consensus 161 RSKHCsiCNrCV~rfDHHCiWiNNCIG~~N~ryF~lFLL~~i~l~~yaivrlg 213 (341)
T KOG1312|consen 161 RSKHCSICNRCVHRFDHHCIWINNCIGAWNIRYFLLFLLTLISLATYAIVRLG 213 (341)
T ss_pred ccccchHHHHHHHHhccceEeeecccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999998777766665443
No 8
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=99.95 E-value=7.8e-29 Score=228.24 Aligned_cols=140 Identities=28% Similarity=0.454 Sum_probs=93.2
Q ss_pred cccccccccCCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 025379 73 RFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIPES 152 (253)
Q Consensus 73 ~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (253)
+||.+|.++||.|||||+.|||||.||||||||++||||.+|||+|+.|++.+...+.+...... .++...+...
T Consensus 421 ~FC~~clirKp~rSkhc~vcnrcVarfDHhCPwi~ncVG~kNh~~F~~Fl~~l~~~~~~~l~~~~----~y~~~~~~~~- 495 (600)
T KOG0509|consen 421 RFCLTCLIRKPLRSKHCSVCNRCVARFDHHCPWIGNCVGLKNHRLFVFFLLTLLTVIVFYLYLCL----YYIMNLENAS- 495 (600)
T ss_pred cceeeeeeecCCccchhhhhHHHHhccccCCCccccccCccchHHHHHHHHHHHHHHHHHHHHHH----HHHhhcchhH-
Confidence 79999999999999999999999999999999999999999999999999987665554444332 2222211110
Q ss_pred CcchhHHHHHHHHHHHH--HH-------------HHH-HHHHHHHHHHhcCcchHhhHhhcC---------CCCCCCchh
Q 025379 153 PGNLAASFITFVLNLAF--AL-------------SIL-GFLIMHISLVAGNTTTIEAFEKKT---------SPKWRYDLG 207 (253)
Q Consensus 153 ~~~~~~~~~~~~~~~~~--~~-------------~~~-~l~~~h~~li~~n~Tt~E~~~~~~---------~~~~~yd~G 207 (253)
.....++.++..+.. .+ ... ..-..|-..++.+.||+|+++..+ ..+.|++.|
T Consensus 496 --~~~~~~l~~~~~~~~~~~~~~~~~~n~~~~~t~~~~~~~~~~~~~~c~~~tt~e~~n~~r~~~~~~~~~~~~~~~s~g 573 (600)
T KOG0509|consen 496 --TIYVGFLIAVQAFRIPKPVTGNLLGNEDLNPTWGSTSTKCQHYNCACLHLTTNEQINVKRYEHLGIKRGPTRSPFSPG 573 (600)
T ss_pred --HHHHHHHHHHHHHhCCccceeeeeeccccccccccccccccccceeeecccHHHHHHHHHhhccccccCcCCCCCCch
Confidence 000111111111000 00 000 011223445789999999986533 245799999
Q ss_pred HHHHHHhccCCC
Q 025379 208 WKINFEQVFGKN 219 (253)
Q Consensus 208 ~~~N~~~vfG~~ 219 (253)
+.+|+.+++-.+
T Consensus 574 ~~~Nl~df~~~~ 585 (600)
T KOG0509|consen 574 PIRNLVDFFLCS 585 (600)
T ss_pred hhhcchheeecc
Confidence 999999988554
No 9
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=93.98 E-value=0.3 Score=43.10 Aligned_cols=44 Identities=23% Similarity=0.522 Sum_probs=37.9
Q ss_pred CCcCCcccchhhccccccCccccccccccch-----------HHHHHHHHHHHHH
Q 025379 85 RCHHCSVCRRCILKMDHHCVWVVNCVGAFNY-----------KYFLLFLFYTFLE 128 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~-----------r~F~~fl~~~~~~ 128 (253)
+.++|..|+.-+...-|||..=|+||-+.-| |-+-.|+.+++..
T Consensus 112 ~~~~C~~C~~~rPpRs~HCsvC~~CV~rfDHHC~WvnnCVG~rNyr~F~~f~~~~ 166 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHCSVCNNCVLRFDHHCPWLNNCIGERNYRYFVLFLFYL 166 (299)
T ss_pred ceEEcCcCcccCCCCcccchhhcccccccCCCCCCccceECCCchHHHHHHHHHH
Confidence 3899999999999999999999999988865 6688898766633
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=93.50 E-value=0.84 Score=36.53 Aligned_cols=33 Identities=27% Similarity=0.532 Sum_probs=17.7
Q ss_pred cccccccccccccCCCCCcCCcccchhhccccc
Q 025379 69 HQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDH 101 (253)
Q Consensus 69 ~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DH 101 (253)
..+.+.|+.|+.--..+-|||.--+.||.+-.|
T Consensus 59 p~Rs~HC~~C~~CV~~~DHHC~w~~~cIG~~N~ 91 (174)
T PF01529_consen 59 PPRSHHCRVCNRCVLRFDHHCPWLGNCIGRRNH 91 (174)
T ss_pred CCcceeccccccccccccccchhhccccccccH
Confidence 344555555555555555555555555555444
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.97 E-value=0.22 Score=26.41 Aligned_cols=21 Identities=19% Similarity=0.673 Sum_probs=17.3
Q ss_pred ccccccccCCCCCcCCcccch
Q 025379 74 FCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 74 ~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
+|+.|...-++.+..|..||.
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 688888888888888888874
No 12
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=88.80 E-value=0.23 Score=31.16 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=22.8
Q ss_pred cccccccccccccCCCCCcCCcccch
Q 025379 69 HQGVRFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 69 ~~~~~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
......|.+|...-|+|+..|+.||.
T Consensus 11 ~~~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 11 VFNKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred hhcccchhcccCCCCccccccccCCC
Confidence 34568999999999999999998875
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.80 E-value=0.51 Score=25.70 Aligned_cols=22 Identities=27% Similarity=0.762 Sum_probs=18.0
Q ss_pred cccccccccCCCCCcCCcccch
Q 025379 73 RFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
++|+.|...-++-++.|+.||.
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCcccccChhhCC
Confidence 5788898877888888888874
No 14
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=84.42 E-value=3.2 Score=36.96 Aligned_cols=109 Identities=19% Similarity=0.253 Sum_probs=59.9
Q ss_pred CCCCCcCCcccchhhccccccCccccccccccchH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 025379 82 KPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYK-----------YFLLFLFYTFLETTLVTVSLLPIFIALFTDDEIP 150 (253)
Q Consensus 82 kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r-----------~F~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (253)
+-.+.+.|++|+.-....-|||.--|.||-+.-|- -.=.|..++......+.++.+...+.. ....
T Consensus 105 ~~~~~~~C~~C~~~KP~RS~HC~~Cn~CV~k~DHHC~Wi~nCVG~~N~r~F~~Fl~~~~~~~~~~~~~~~~~~---~~~~ 181 (309)
T COG5273 105 KFGTENFCSTCNIYKPPRSHHCSICNRCVLKFDHHCPWINNCVGFRNYRFFYQFLLYTILVALVVLLSTAYYI---AGIF 181 (309)
T ss_pred ccccceeccccccccCCCCccchhhcchhhccCccCcccccccCcchHHHHHHHHHHHHHHHHHHHHHHHHHH---Hhhc
Confidence 34577899999999999999999999999888764 344566555443333333333322221 1222
Q ss_pred CCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhH
Q 025379 151 ESPGNLAASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAF 194 (253)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~ 194 (253)
........ ...+++.....+.+..+......++..+....+..
T Consensus 182 ~~~~~~~~-~~~~li~~~~~~~~~~f~~~~~~~~~~~~~~~~~~ 224 (309)
T COG5273 182 SIRHDTSL-AICFLIFGCSLLGVVFFIITTLLLLFLIYLILNNL 224 (309)
T ss_pred cccCChHH-HHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence 33333322 22323222223333344444555555555555543
No 15
>KOG0509 consensus Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only]
Probab=80.80 E-value=1.2 Score=42.67 Aligned_cols=53 Identities=6% Similarity=-0.111 Sum_probs=46.0
Q ss_pred ccccccccccccCCCCCcCCcccchhhccccccCccccccccccchHHHHHHHH
Q 025379 70 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLF 123 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~ 123 (253)
.-...|.+|....+.+..++..+-.++..+++||+|+. +|+.+|-..|....+
T Consensus 323 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fw~~~~w~~-~i~~~~~~~~~~~~i 375 (600)
T KOG0509|consen 323 VLTCLCATRKIVGFLLRPPLLSGFFLSTLFWFYYFWFS-KITPYTLFDFHYCFI 375 (600)
T ss_pred hhheeccchhhccccccchhHHHHHHHHHHHHHHhhhe-eccchhhhhhHHHHH
Confidence 44567889999999999999999999999999999999 999999886544443
No 16
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=78.31 E-value=0.5 Score=29.78 Aligned_cols=26 Identities=27% Similarity=0.770 Sum_probs=22.4
Q ss_pred cccccccccccccCCCCCcCCcccch
Q 025379 69 HQGVRFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 69 ~~~~~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
....+.|..|...-|+|+.-|+.|+.
T Consensus 11 ~~~kkIC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 11 LFNKKICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred HhhHHHHHHhcCCCCcchhHHhhccC
Confidence 34568999999999999999998864
No 17
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=77.47 E-value=1.3 Score=43.66 Aligned_cols=22 Identities=32% Similarity=0.745 Sum_probs=18.1
Q ss_pred cccccccccCC-------CCCcCCcccch
Q 025379 73 RFCQKCNQFKP-------PRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~kP-------~Rs~HC~~C~~ 94 (253)
..|..|+..-. -|-|||+.||+
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGr 489 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGI 489 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCcc
Confidence 57999987664 39999999976
No 18
>PF12773 DZR: Double zinc ribbon
Probab=76.32 E-value=2.2 Score=26.75 Aligned_cols=34 Identities=21% Similarity=0.483 Sum_probs=20.8
Q ss_pred cccccccccccCC---CCCcCCcccchhhccccccCc
Q 025379 71 GVRFCQKCNQFKP---PRCHHCSVCRRCILKMDHHCV 104 (253)
Q Consensus 71 ~~~~C~~C~~~kP---~Rs~HC~~C~~CV~~~DHHC~ 104 (253)
..+||+.|...-+ .....|..|+.=+...+.+|+
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcCCCcCCcCccC
Confidence 3567777766555 234567777766666666665
No 19
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=76.23 E-value=18 Score=25.78 Aligned_cols=36 Identities=14% Similarity=0.335 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcchHhhHhh
Q 025379 158 ASFITFVLNLAFALSILGFLIMHISLVAGNTTTIEAFEK 196 (253)
Q Consensus 158 ~~~~~~~~~~~~~~~~~~l~~~h~~li~~n~Tt~E~~~~ 196 (253)
..+++|+++++ .+.+++++..|--+++.++.|+++.
T Consensus 48 lSii~FIlG~v---l~lGilifs~y~~C~~~~~~~r~n~ 83 (91)
T PHA02680 48 LSVTCFIVGAV---LLLGLFVFSMYRKCSGSMPYERLNN 83 (91)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHhcccCCCceeecccC
Confidence 44455554433 3344666777767778887787754
No 20
>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=71.29 E-value=2.3 Score=23.22 Aligned_cols=21 Identities=24% Similarity=0.752 Sum_probs=16.7
Q ss_pred cccccccccCCCCCcCCcccc
Q 025379 73 RFCQKCNQFKPPRCHHCSVCR 93 (253)
Q Consensus 73 ~~C~~C~~~kP~Rs~HC~~C~ 93 (253)
+.|+.|...-|.-++-|..||
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG 21 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCG 21 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCC
Confidence 458888888888888888776
No 21
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=70.12 E-value=76 Score=27.83 Aligned_cols=55 Identities=24% Similarity=0.484 Sum_probs=41.0
Q ss_pred cccccccccccccccCCCCCcCCcccchhhccccccCccccccccccchHHHHHHHHHHHHHHHHH
Q 025379 67 PKHQGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFLFYTFLETTLV 132 (253)
Q Consensus 67 ~~~~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl~~~~~~~~~~ 132 (253)
.+..+..-|+.|+.=--.--|||.-=|+||--..| +-.=.|+.++.-...+..+.
T Consensus 111 pK~prTHHCsiC~kCVL~MDHHCPwinnCVG~~NH-----------ryFFlFl~~ltlat~~~~i~ 165 (309)
T KOG1313|consen 111 PKSPRTHHCSICNKCVLKMDHHCPWINNCVGAHNH-----------RYFFLFLFYLTLATSYAAIM 165 (309)
T ss_pred CCCCCcchhhHHhhHhhccccCCchhhcccccccc-----------hhHHHHHHHHHHHHHHHHHH
Confidence 44556677888886556667999999999999888 56667888887665555544
No 22
>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=69.21 E-value=2.2 Score=27.33 Aligned_cols=27 Identities=30% Similarity=0.733 Sum_probs=17.9
Q ss_pred cccccccccccccCCCCCcCCcc--cchh
Q 025379 69 HQGVRFCQKCNQFKPPRCHHCSV--CRRC 95 (253)
Q Consensus 69 ~~~~~~C~~C~~~kP~Rs~HC~~--C~~C 95 (253)
+-....|.+|...-|+|+..|+. ||.+
T Consensus 14 n~~k~ICrkCyarl~~~A~nCRKkkCGhs 42 (52)
T PF01020_consen 14 NCDKMICRKCYARLPPRATNCRKKKCGHS 42 (52)
T ss_dssp HTS-EEETTT--EE-TTSSS-TSSSCTS-
T ss_pred cccceecccccCcCCCCccceecccCCCC
Confidence 34568899999999999999998 8754
No 23
>PF12773 DZR: Double zinc ribbon
Probab=66.92 E-value=4.2 Score=25.47 Aligned_cols=24 Identities=29% Similarity=0.868 Sum_probs=21.3
Q ss_pred ccccccccccccCCCCCcCCcccc
Q 025379 70 QGVRFCQKCNQFKPPRCHHCSVCR 93 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~HC~~C~ 93 (253)
....+|+.|....++.+..|..|+
T Consensus 27 ~~~~~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 27 QSKKICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCCCCcCCcCCCcCCcCccCccc
Confidence 456899999999999999999886
No 24
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=65.08 E-value=2.2 Score=39.48 Aligned_cols=27 Identities=37% Similarity=0.929 Sum_probs=20.6
Q ss_pred ccccccccccccC--CCCCcCCcccchhh
Q 025379 70 QGVRFCQKCNQFK--PPRCHHCSVCRRCI 96 (253)
Q Consensus 70 ~~~~~C~~C~~~k--P~Rs~HC~~C~~CV 96 (253)
....+|+.|...= --|-|||+.||+-+
T Consensus 178 s~V~~CP~Ca~~F~l~rRrHHCRLCG~Vm 206 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRRRHHCRLCGRVM 206 (505)
T ss_pred CcccccccccchhhhHHHhhhhhhcchHH
Confidence 4578999997543 45889999999854
No 25
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=64.35 E-value=4.3 Score=26.45 Aligned_cols=35 Identities=34% Similarity=0.927 Sum_probs=25.7
Q ss_pred cccccccCCCC-------CcCCcccchhhccc-cccCccccccccc
Q 025379 75 CQKCNQFKPPR-------CHHCSVCRRCILKM-DHHCVWVVNCVGA 112 (253)
Q Consensus 75 C~~C~~~kP~R-------s~HC~~C~~CV~~~-DHHC~w~~nCIG~ 112 (253)
|..|..--|+- |+-|..|..|+..+ +++|| ||=|.
T Consensus 8 CE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CP---NCgGe 50 (57)
T PF06906_consen 8 CECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCP---NCGGE 50 (57)
T ss_pred ccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCc---CCCCc
Confidence 55555554443 36788999999998 99998 77664
No 26
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=60.41 E-value=50 Score=29.41 Aligned_cols=32 Identities=22% Similarity=0.453 Sum_probs=24.9
Q ss_pred CCcCCcccchhhccccccCccccccccccchH
Q 025379 85 RCHHCSVCRRCILKMDHHCVWVVNCVGAFNYK 116 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r 116 (253)
+.+.|.+|+.-....-|||.--+.||.+.-|.
T Consensus 108 ~~R~C~kC~~iKPdRaHHCsvC~rCvLKmDHH 139 (307)
T KOG1315|consen 108 AVRYCDKCKCIKPDRAHHCSVCNRCVLKMDHH 139 (307)
T ss_pred CceeecccccccCCccccchhhhhhhhccccC
Confidence 66778888888888888888888888776553
No 27
>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=59.24 E-value=3.1 Score=23.22 Aligned_cols=21 Identities=24% Similarity=0.735 Sum_probs=14.0
Q ss_pred ccccccccCCCCCcCCcccch
Q 025379 74 FCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 74 ~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
.|..|...-++++.+|..|+.
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--
T ss_pred cCCCCcCCchHHhhhhhCcCC
Confidence 477888777888888877763
No 28
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=59.11 E-value=23 Score=20.08 Aligned_cols=28 Identities=14% Similarity=0.490 Sum_probs=20.5
Q ss_pred hhhHHHHHHHHHH-HHHHHhhcCCCCCCC
Q 025379 3 VLNFVMQLVMLVW-SYFSVVITDPGGVPP 30 (253)
Q Consensus 3 li~~~~l~~~~~~-sy~~~~~tdPG~vp~ 30 (253)
.++|.+++++.+- .++...++||-.+++
T Consensus 3 al~Ytfll~~tlgiiFFAIfFRepPri~k 31 (31)
T PRK11875 3 SFAYILILTLALVTLFFAIAFRDPPKIDK 31 (31)
T ss_pred hHHHHHHHHHHHHHHHHhhhccCCCCCCC
Confidence 4678888887765 567777899977763
No 29
>CHL00031 psbT photosystem II protein T
Probab=58.49 E-value=20 Score=20.62 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=21.2
Q ss_pred hhhHHHHHHHHHH-HHHHHhhcCCCCCCC
Q 025379 3 VLNFVMQLVMLVW-SYFSVVITDPGGVPP 30 (253)
Q Consensus 3 li~~~~l~~~~~~-sy~~~~~tdPG~vp~ 30 (253)
.++|.+++++.+- .+|...++||-.+++
T Consensus 3 alvYtfll~~tlgilFFAI~FRePPri~k 31 (33)
T CHL00031 3 ALVYTFLLVSTLGIIFFAIFFREPPKVPT 31 (33)
T ss_pred hhHHHHHHHHHHHHHHHhheecCCCCCCC
Confidence 4678888888765 567777899988875
No 30
>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 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=53.88 E-value=3.2 Score=27.92 Aligned_cols=25 Identities=32% Similarity=0.672 Sum_probs=12.0
Q ss_pred cccccccccc--CCCCCcCCcccchhh
Q 025379 72 VRFCQKCNQF--KPPRCHHCSVCRRCI 96 (253)
Q Consensus 72 ~~~C~~C~~~--kP~Rs~HC~~C~~CV 96 (253)
...|..|+.. --.|-|||+.||+.|
T Consensus 9 ~~~C~~C~~~F~~~~rrhhCr~CG~~v 35 (69)
T PF01363_consen 9 ASNCMICGKKFSLFRRRHHCRNCGRVV 35 (69)
T ss_dssp -SB-TTT--B-BSSS-EEE-TTT--EE
T ss_pred CCcCcCcCCcCCCceeeEccCCCCCEE
Confidence 4667777633 246889999999854
No 32
>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=51.24 E-value=3.6 Score=24.09 Aligned_cols=8 Identities=50% Similarity=1.531 Sum_probs=4.6
Q ss_pred cccccccc
Q 025379 73 RFCQKCNQ 80 (253)
Q Consensus 73 ~~C~~C~~ 80 (253)
+||++|+.
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 56777753
No 33
>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=49.81 E-value=5.3 Score=22.28 Aligned_cols=21 Identities=24% Similarity=0.474 Sum_probs=8.8
Q ss_pred ccccccccCCC-CCcCCcccch
Q 025379 74 FCQKCNQFKPP-RCHHCSVCRR 94 (253)
Q Consensus 74 ~C~~C~~~kP~-Rs~HC~~C~~ 94 (253)
.|..|+..... ..++|..|+-
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 47777776666 7788888864
No 34
>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=45.64 E-value=7.7 Score=21.98 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=10.3
Q ss_pred cccccccccc----CCCCCcCCcccc
Q 025379 72 VRFCQKCNQF----KPPRCHHCSVCR 93 (253)
Q Consensus 72 ~~~C~~C~~~----kP~Rs~HC~~C~ 93 (253)
.+||..|... .-.++..|..|+
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 4788888643 233555565554
No 35
>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=45.31 E-value=38 Score=28.69 Aligned_cols=27 Identities=26% Similarity=0.316 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHHHHHHHhhcCCCCCC
Q 025379 3 VLNFVMQLVMLVWSYFSVVITDPGGVP 29 (253)
Q Consensus 3 li~~~~l~~~~~~sy~~~~~tdPG~vp 29 (253)
+||..++.+.++-.|..|.-+|||..-
T Consensus 197 liVitl~vf~LvgLyr~C~k~dPg~p~ 223 (259)
T PF07010_consen 197 LIVITLSVFTLVGLYRMCWKTDPGTPE 223 (259)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 455556666666677788889999743
No 36
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=44.12 E-value=11 Score=23.64 Aligned_cols=7 Identities=57% Similarity=1.621 Sum_probs=3.9
Q ss_pred ccccccc
Q 025379 74 FCQKCNQ 80 (253)
Q Consensus 74 ~C~~C~~ 80 (253)
||+.|+.
T Consensus 2 FCp~Cg~ 8 (52)
T smart00661 2 FCPKCGN 8 (52)
T ss_pred CCCCCCC
Confidence 5666653
No 37
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=42.18 E-value=14 Score=23.55 Aligned_cols=23 Identities=30% Similarity=0.888 Sum_probs=14.8
Q ss_pred cccccccccc-cCCC--CCcCCcccc
Q 025379 71 GVRFCQKCNQ-FKPP--RCHHCSVCR 93 (253)
Q Consensus 71 ~~~~C~~C~~-~kP~--Rs~HC~~C~ 93 (253)
..++|+.|.. .-.+ ...+|..|+
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcC
Confidence 3569999987 3222 356777776
No 38
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=41.54 E-value=12 Score=31.88 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=13.9
Q ss_pred cCCcccch-----hhccccccCcccc
Q 025379 87 HHCSVCRR-----CILKMDHHCVWVV 107 (253)
Q Consensus 87 ~HC~~C~~-----CV~~~DHHC~w~~ 107 (253)
.||..|+. =..+.+|||||..
T Consensus 24 f~Cd~C~~~FC~eHrsye~H~Cp~~~ 49 (250)
T KOG3183|consen 24 FKCDGCSGIFCLEHRSYESHHCPKGL 49 (250)
T ss_pred eeeCCccchhhhccchHhhcCCCccc
Confidence 45555532 3567899999974
No 39
>PF00751 DM: DM DNA binding domain; InterPro: IPR001275 This domain was first discovered in the doublesex proteins of Drosophila melanogaster and is also seen in proteins from Caenorhabditis elegans []. In D. melanogaster the doublesex gene controls somatic sexual differentiation by producing alternatively spliced mRNAs encoding related sex-specific polypeptides []. These proteins are believed to function as transcription factors on downstream sex-determination genes, especially on neuroblast differentiation and yolk protein genes transcription [, ]. The DM domain binds DNA as a dimer, allowing the recognition of pseudopalindromic sequences [, , ]. The NMR analysis of the DSX DM domain [] revealed a novel zinc module containing 'intertwined' CCHC and HCCC zinc-binding sites. The recognition of the DNA requires the carboxy-terminal basic tail which contacts the minor groove of the target sequence.; GO: 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007548 sex differentiation, 0005634 nucleus; PDB: 1LPV_A.
Probab=41.25 E-value=10 Score=23.88 Aligned_cols=22 Identities=18% Similarity=0.400 Sum_probs=8.3
Q ss_pred CcCCccc---chhhccccc--cCcccc
Q 025379 86 CHHCSVC---RRCILKMDH--HCVWVV 107 (253)
Q Consensus 86 s~HC~~C---~~CV~~~DH--HC~w~~ 107 (253)
..+|..| |.-+..-+| .|||-+
T Consensus 2 ~p~C~RCrnHG~~~~lKgHk~~C~~~~ 28 (47)
T PF00751_consen 2 SPTCARCRNHGVIVPLKGHKRYCPFRD 28 (47)
T ss_dssp -SS-HHHHTTT---TTTT-GGG-TTTT
T ss_pred CCcCcchhcCCcccchhhhccccCcCC
Confidence 3445555 445555666 577753
No 40
>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=38.44 E-value=19 Score=20.03 Aligned_cols=20 Identities=30% Similarity=0.680 Sum_probs=13.2
Q ss_pred ccccccccCCCC-CcCCcccc
Q 025379 74 FCQKCNQFKPPR-CHHCSVCR 93 (253)
Q Consensus 74 ~C~~C~~~kP~R-s~HC~~C~ 93 (253)
.|..|+..-... .+||+.|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCC
Confidence 366676555555 77887776
No 41
>PF01405 PsbT: Photosystem II reaction centre T protein; InterPro: IPR001743 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbT found in PSII, which is thought to be associated with the D1 (PsbA) - D2 (PsbD) heterodimer. PsbT may be involved in the formation and/or stabilisation of dimeric PSII complexes, because in the absence of this protein dimeric PSII complexes were found to be less abundant. Furthermore, although PsbT does not confer photo-protection, it is required for the efficient recovery of photo-damaged PSII [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3BZ1_T 1S5L_t 2AXT_t 3KZI_T 3PRQ_T 3BZ2_T 3PRR_T 4FBY_g 3A0H_t 3A0B_T ....
Probab=36.91 E-value=62 Score=18.11 Aligned_cols=24 Identities=17% Similarity=0.430 Sum_probs=14.9
Q ss_pred hhhHHHHHHHHHH-HHHHHhhcCCC
Q 025379 3 VLNFVMQLVMLVW-SYFSVVITDPG 26 (253)
Q Consensus 3 li~~~~l~~~~~~-sy~~~~~tdPG 26 (253)
.++|.++++..+- .++...++||-
T Consensus 3 a~vY~~ll~~tlgilffAI~FRePP 27 (29)
T PF01405_consen 3 ALVYTFLLIGTLGILFFAIFFREPP 27 (29)
T ss_dssp HHHHHHHHHHHHHHHHHHHHSS---
T ss_pred hhHHHHHHHHHHHHHHhhhhccCCC
Confidence 3677787777754 56777788884
No 42
>PF01437 PSI: Plexin repeat; InterPro: IPR002165 This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin (P70206 from SWISSPROT) []. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein (Q19981 from SWISSPROT) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.; GO: 0016020 membrane; PDB: 3NVQ_B 3NVN_B 3OL2_B 3OKT_A 3AL8_A 3OKW_A 3OKY_B 3AFC_B 1OLZ_B 1SHY_B ....
Probab=36.80 E-value=12 Score=23.62 Aligned_cols=22 Identities=32% Similarity=0.899 Sum_probs=16.0
Q ss_pred cccchhhccccccCccc---ccccc
Q 025379 90 SVCRRCILKMDHHCVWV---VNCVG 111 (253)
Q Consensus 90 ~~C~~CV~~~DHHC~w~---~nCIG 111 (253)
..|..|+.-.|-+|.|- +.|+-
T Consensus 6 ~sC~~Cl~~~dp~CgWc~~~~~C~~ 30 (51)
T PF01437_consen 6 TSCSSCLSSRDPYCGWCSSENRCVS 30 (51)
T ss_dssp SSHHHHHHSTCTTEEEETTTTEEEE
T ss_pred CcHHHHHcCCCcCccccCCCCcccC
Confidence 67888888888888883 34653
No 43
>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=35.34 E-value=17 Score=23.13 Aligned_cols=22 Identities=36% Similarity=0.797 Sum_probs=14.7
Q ss_pred ccccccc--cCCCCCcCCcccchh
Q 025379 74 FCQKCNQ--FKPPRCHHCSVCRRC 95 (253)
Q Consensus 74 ~C~~C~~--~kP~Rs~HC~~C~~C 95 (253)
-|..|.. -.-.|.|||+.|++-
T Consensus 4 ~C~~C~~~F~~~~rk~~Cr~Cg~~ 27 (57)
T cd00065 4 SCMGCGKPFTLTRRRHHCRNCGRI 27 (57)
T ss_pred cCcccCccccCCccccccCcCcCC
Confidence 4566652 135688999999874
No 44
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=34.94 E-value=21 Score=23.88 Aligned_cols=23 Identities=26% Similarity=0.845 Sum_probs=19.8
Q ss_pred ccccccccccCCCCCcCCcccch
Q 025379 72 VRFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 72 ~~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
.+-|..|+..-|+-+.-|..|+.
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs 26 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGS 26 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCC
Confidence 35699999999999999999985
No 45
>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=34.89 E-value=21 Score=23.79 Aligned_cols=26 Identities=19% Similarity=0.479 Sum_probs=18.7
Q ss_pred ccccccccccccC----CCCCcCCcccchh
Q 025379 70 QGVRFCQKCNQFK----PPRCHHCSVCRRC 95 (253)
Q Consensus 70 ~~~~~C~~C~~~k----P~Rs~HC~~C~~C 95 (253)
...+.|+.|.... ..|.++|..|+.-
T Consensus 26 ~TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 26 YTSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CCccCccCcccccccccccceEEcCCCCCE
Confidence 3567899998654 4477888888764
No 46
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=34.88 E-value=12 Score=32.92 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=14.8
Q ss_pred ccccccccc-cC--CCCCcCCcccchhhcc
Q 025379 72 VRFCQKCNQ-FK--PPRCHHCSVCRRCILK 98 (253)
Q Consensus 72 ~~~C~~C~~-~k--P~Rs~HC~~C~~CV~~ 98 (253)
..-|..|.. .. -.|-|||+.||+-|-.
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~ 197 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCA 197 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhh
Confidence 345555554 22 3366777777765543
No 47
>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=34.56 E-value=3.8e+02 Score=24.83 Aligned_cols=32 Identities=19% Similarity=0.509 Sum_probs=22.7
Q ss_pred ccccccccc-cCCCCCcCCcccchhhccccccC
Q 025379 72 VRFCQKCNQ-FKPPRCHHCSVCRRCILKMDHHC 103 (253)
Q Consensus 72 ~~~C~~C~~-~kP~Rs~HC~~C~~CV~~~DHHC 103 (253)
..-|+.|+. .+|....+|..|+.-..+..++.
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L~~~~~~s 247 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPLYVRRRNS 247 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcccCCCCCC
Confidence 456999997 45566678888888776655544
No 48
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=34.55 E-value=25 Score=23.05 Aligned_cols=22 Identities=36% Similarity=0.919 Sum_probs=15.5
Q ss_pred ccccccccccccCCCCCcC-Ccccc
Q 025379 70 QGVRFCQKCNQFKPPRCHH-CSVCR 93 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~H-C~~C~ 93 (253)
.....|+.|+..+.+ || |..||
T Consensus 25 ~~l~~C~~CG~~~~~--H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLP--HRVCPSCG 47 (57)
T ss_pred CcceECCCCCCccCC--eEECCCCC
Confidence 456679999976654 55 77776
No 49
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.97 E-value=21 Score=23.37 Aligned_cols=22 Identities=32% Similarity=0.779 Sum_probs=16.3
Q ss_pred cccccccccccCCCCCcCCcccch
Q 025379 71 GVRFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 71 ~~~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
..+.|+.|..+-- ...|..||.
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~ 25 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGG 25 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCC
Confidence 4677888888777 667777764
No 50
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=33.36 E-value=20 Score=18.97 Aligned_cols=21 Identities=19% Similarity=0.515 Sum_probs=15.4
Q ss_pred ccccccccCCCCCcCCcccch
Q 025379 74 FCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 74 ~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
.|..|...-.+++..|..|+.
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGA 24 (26)
T ss_pred cCCCCCCcChhhhccccccCC
Confidence 477787777777777777763
No 51
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.55 E-value=22 Score=32.65 Aligned_cols=25 Identities=28% Similarity=0.731 Sum_probs=21.0
Q ss_pred ccccccccccCCCCCcCCcccchhh
Q 025379 72 VRFCQKCNQFKPPRCHHCSVCRRCI 96 (253)
Q Consensus 72 ~~~C~~C~~~kP~Rs~HC~~C~~CV 96 (253)
.++|+.|+..+-.-+..|..||.=+
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~ 25 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKF 25 (465)
T ss_pred CCcccccccccccccccccccCCcC
Confidence 3789999999999998899998743
No 52
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=32.46 E-value=21 Score=26.80 Aligned_cols=26 Identities=19% Similarity=0.678 Sum_probs=18.3
Q ss_pred cccccccccccccCCCCCcC---Ccccch
Q 025379 69 HQGVRFCQKCNQFKPPRCHH---CSVCRR 94 (253)
Q Consensus 69 ~~~~~~C~~C~~~kP~Rs~H---C~~C~~ 94 (253)
....-+|..|+..-|...++ |..|+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCC
Confidence 34566899999877765444 888874
No 53
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=31.92 E-value=15 Score=34.71 Aligned_cols=22 Identities=32% Similarity=0.612 Sum_probs=14.4
Q ss_pred cccccccccC--CCCCcCCcccch
Q 025379 73 RFCQKCNQFK--PPRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~k--P~Rs~HC~~C~~ 94 (253)
..|..|...- --|-|||+.||.
T Consensus 902 ~~cmacq~pf~afrrrhhcrncgg 925 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGG 925 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCc
Confidence 3466665432 237899999886
No 54
>PRK13743 conjugal transfer protein TrbF; Provisional
Probab=31.78 E-value=2.4e+02 Score=21.76 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=15.1
Q ss_pred cchHHHHHHHHHHHHHHHHHHH
Q 025379 113 FNYKYFLLFLFYTFLETTLVTV 134 (253)
Q Consensus 113 ~N~r~F~~fl~~~~~~~~~~~~ 134 (253)
.--+||-+|+.++..+.++..+
T Consensus 36 ~~~~Y~~LfiVFl~AG~vLw~v 57 (141)
T PRK13743 36 VSDIYFDLFIVFLTAGIVLWVI 57 (141)
T ss_pred HHHHHHHHHHHHHHhhHHHHHH
Confidence 3447899999887776655443
No 55
>smart00423 PSI domain found in Plexins, Semaphorins and Integrins.
Probab=31.61 E-value=25 Score=21.50 Aligned_cols=17 Identities=35% Similarity=1.089 Sum_probs=9.8
Q ss_pred cccchhhccccccCccc
Q 025379 90 SVCRRCILKMDHHCVWV 106 (253)
Q Consensus 90 ~~C~~CV~~~DHHC~w~ 106 (253)
..|..|+...|-||.|=
T Consensus 5 ~sC~~C~~~~~~~C~Wc 21 (46)
T smart00423 5 TSCSECLLARDPYCAWC 21 (46)
T ss_pred CcHHHHHcCCCCCCCcc
Confidence 34566666666666663
No 56
>KOG1398 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.91 E-value=25 Score=32.22 Aligned_cols=27 Identities=37% Similarity=0.775 Sum_probs=20.1
Q ss_pred cCCCCCcCCcccchhhccccccCcccccccccc
Q 025379 81 FKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAF 113 (253)
Q Consensus 81 ~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~ 113 (253)
.+-.|..||..|+. .|| +|..||||..
T Consensus 9 ~sl~~p~l~~tC~e----~~h--~w~~~c~ga~ 35 (460)
T KOG1398|consen 9 RSLARPSLAETCDE----ADH--SWVANCIGAL 35 (460)
T ss_pred hhhcCchHhhhhhh----ccC--CcccchhHHH
Confidence 34556678888874 677 8999999964
No 57
>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=29.43 E-value=23 Score=27.97 Aligned_cols=23 Identities=26% Similarity=0.691 Sum_probs=16.2
Q ss_pred ccccccccCCCCCcCCcccchhhccc
Q 025379 74 FCQKCNQFKPPRCHHCSVCRRCILKM 99 (253)
Q Consensus 74 ~C~~C~~~kP~Rs~HC~~C~~CV~~~ 99 (253)
.-.+|... ...||..|..|+.|.
T Consensus 142 ~s~sC~~~---~~~~CG~C~~C~~r~ 164 (169)
T cd01995 142 LTWSCYNG---GEKHCGECDSCLLRK 164 (169)
T ss_pred heeeccCC---CCCCCCCCHHHHHHH
Confidence 34556543 238999999999874
No 58
>PLN00186 ribosomal protein S26; Provisional
Probab=29.12 E-value=20 Score=26.62 Aligned_cols=16 Identities=31% Similarity=0.762 Sum_probs=12.5
Q ss_pred CCcCCcccchhhcccc
Q 025379 85 RCHHCSVCRRCILKMD 100 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~D 100 (253)
+.-||..|++||.+=-
T Consensus 19 ~~V~C~nCgr~vPKDK 34 (109)
T PLN00186 19 KRIRCSNCGKCVPKDK 34 (109)
T ss_pred cceeeCCCcccccccc
Confidence 3568999999999733
No 59
>KOG3611 consensus Semaphorins [Signal transduction mechanisms]
Probab=28.92 E-value=23 Score=35.48 Aligned_cols=39 Identities=26% Similarity=0.525 Sum_probs=29.4
Q ss_pred CcCCc---ccchhhccccccCcccc---ccc--cccchHHHHHHHHH
Q 025379 86 CHHCS---VCRRCILKMDHHCVWVV---NCV--GAFNYKYFLLFLFY 124 (253)
Q Consensus 86 s~HC~---~C~~CV~~~DHHC~w~~---nCI--G~~N~r~F~~fl~~ 124 (253)
-|+|+ .|-.|++..|-||.|-+ .|+ +..|.|.+.+=+-.
T Consensus 491 l~~C~~y~~C~dcclarDPYCAWd~~~~~C~~~~~~~~rs~~Qd~~~ 537 (737)
T KOG3611|consen 491 LARCSRYGSCADCCLARDPYCAWDGVNSKCSLLSPTNRRSVIQDVSS 537 (737)
T ss_pred hhHhhcccchhhhhhccCCCccccCCCCcceECCCCcccchhhhhcc
Confidence 36677 89898888999999976 788 44567777665543
No 60
>COG0603 Predicted PP-loop superfamily ATPase [General function prediction only]
Probab=28.54 E-value=26 Score=29.69 Aligned_cols=19 Identities=26% Similarity=0.851 Sum_probs=15.5
Q ss_pred cCCCCCcCCcccchhhccc
Q 025379 81 FKPPRCHHCSVCRRCILKM 99 (253)
Q Consensus 81 ~kP~Rs~HC~~C~~CV~~~ 99 (253)
|++.+..||..|..|++|.
T Consensus 187 Y~g~~~~~CG~C~sC~~R~ 205 (222)
T COG0603 187 YNGGEGDHCGECESCVLRE 205 (222)
T ss_pred eCCCCCCCCCCCHHHHHHH
Confidence 4666666999999999984
No 61
>PF14127 DUF4294: Domain of unknown function (DUF4294)
Probab=28.40 E-value=49 Score=26.43 Aligned_cols=32 Identities=19% Similarity=0.351 Sum_probs=27.0
Q ss_pred hcCcchHhhHhhcCCCCCCCchhHHHHHHhccCCC
Q 025379 185 AGNTTTIEAFEKKTSPKWRYDLGWKINFEQVFGKN 219 (253)
Q Consensus 185 ~~n~Tt~E~~~~~~~~~~~yd~G~~~N~~~vfG~~ 219 (253)
-+|+|++|..+.-++ ++.-|+++.+..+||-+
T Consensus 103 etg~TsyelIK~~rg---g~~A~~~q~~A~~Fg~s 134 (157)
T PF14127_consen 103 ETGSTSYELIKELRG---GWRAFWYQTFAWLFGIS 134 (157)
T ss_pred hcCCcHHHHHHHhhC---ChhHHHHHHHHHHhCcc
Confidence 489999999886554 67788999999999986
No 62
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.22 E-value=40 Score=33.29 Aligned_cols=22 Identities=27% Similarity=0.686 Sum_probs=11.8
Q ss_pred cccccccccCCCCCcCCcccch
Q 025379 73 RFCQKCNQFKPPRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~kP~Rs~HC~~C~~ 94 (253)
+.|+.|+..-|+.+++|..||.
T Consensus 28 ~~Cp~CG~~~~~~~~fC~~CG~ 49 (645)
T PRK14559 28 KPCPQCGTEVPVDEAHCPNCGA 49 (645)
T ss_pred CcCCCCCCCCCcccccccccCC
Confidence 3455555555555555555554
No 63
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.04 E-value=35 Score=33.70 Aligned_cols=40 Identities=28% Similarity=0.510 Sum_probs=27.6
Q ss_pred ccccccccccccCCCCCcCCcccchhhccccccCcccccccc
Q 025379 70 QGVRFCQKCNQFKPPRCHHCSVCRRCILKMDHHCVWVVNCVG 111 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG 111 (253)
...+||..|+..-+ .+.|..||.=+..=..+|+==|.=.|
T Consensus 13 ~~akFC~~CG~~l~--~~~Cp~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 13 NNNRFCQKCGTSLT--HKPCPQCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred CCCccccccCCCCC--CCcCCCCCCCCCcccccccccCCccc
Confidence 45688999976543 35788888888888888874444333
No 64
>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=26.78 E-value=90 Score=20.60 Aligned_cols=22 Identities=36% Similarity=0.907 Sum_probs=15.4
Q ss_pred cccccccccCCCCCcCCc-ccch
Q 025379 73 RFCQKCNQFKPPRCHHCS-VCRR 94 (253)
Q Consensus 73 ~~C~~C~~~kP~Rs~HC~-~C~~ 94 (253)
+-|..|+..-|+--..|| .|+.
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 567888777777777774 6655
No 65
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=26.06 E-value=30 Score=24.87 Aligned_cols=12 Identities=25% Similarity=0.589 Sum_probs=8.8
Q ss_pred cccCcccccccc
Q 025379 100 DHHCVWVVNCVG 111 (253)
Q Consensus 100 DHHC~w~~nCIG 111 (253)
-.||||++.-..
T Consensus 55 r~~CPwv~~~~q 66 (91)
T PF08600_consen 55 REYCPWVNPSTQ 66 (91)
T ss_pred cccCCccCCccc
Confidence 367999987653
No 66
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=26.02 E-value=60 Score=27.84 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=19.2
Q ss_pred ccccccccc----------cCCCCCcCCcccchhhcc
Q 025379 72 VRFCQKCNQ----------FKPPRCHHCSVCRRCILK 98 (253)
Q Consensus 72 ~~~C~~C~~----------~kP~Rs~HC~~C~~CV~~ 98 (253)
.+-|.-|+. .++..--+|..|||-.+.
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~ 233 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYY 233 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHh
Confidence 456777764 456678899999986554
No 67
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=25.90 E-value=3.1e+02 Score=23.76 Aligned_cols=21 Identities=29% Similarity=0.488 Sum_probs=10.8
Q ss_pred cccc-cchHHHHHHHHHHHHHH
Q 025379 109 CVGA-FNYKYFLLFLFYTFLET 129 (253)
Q Consensus 109 CIG~-~N~r~F~~fl~~~~~~~ 129 (253)
-||. ...|-.++|++...+..
T Consensus 188 SVG~~faRkR~i~f~llgllfl 209 (256)
T PF09788_consen 188 SVGPRFARKRAIIFFLLGLLFL 209 (256)
T ss_pred cccchHhhhHHHHHHHHHHHHH
Confidence 3674 45555555555444433
No 68
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=25.77 E-value=64 Score=33.73 Aligned_cols=39 Identities=28% Similarity=0.443 Sum_probs=24.5
Q ss_pred cccccccc-----ccCCCCCcCCcccchhhccccccCccccccccccchHHHHHHH
Q 025379 72 VRFCQKCN-----QFKPPRCHHCSVCRRCILKMDHHCVWVVNCVGAFNYKYFLLFL 122 (253)
Q Consensus 72 ~~~C~~C~-----~~kP~Rs~HC~~C~~CV~~~DHHC~w~~nCIG~~N~r~F~~fl 122 (253)
..-|+.|. ..--.|-|||+.||+-- |-.-=|.|.++-|+
T Consensus 554 dse~pncm~clqkft~ikrrhhcRacgkVl------------cgvccnek~~leyl 597 (1287)
T KOG1841|consen 554 DSEAPNCMDCLQKFTPIKRRHHCRACGKVL------------CGVCCNEKSALEYL 597 (1287)
T ss_pred cccCchHHHHHhhcccccccccchhcccee------------ehhhcchhhhhhhc
Confidence 34455554 33456899999999832 22234667777776
No 69
>PRK09335 30S ribosomal protein S26e; Provisional
Probab=25.64 E-value=24 Score=25.63 Aligned_cols=20 Identities=25% Similarity=0.561 Sum_probs=14.8
Q ss_pred CCcCCcccchhhccccccCc
Q 025379 85 RCHHCSVCRRCILKMDHHCV 104 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~DHHC~ 104 (253)
+.-+|..|++||.+----+.
T Consensus 19 ~~V~C~nCgr~vPKDKAIkr 38 (95)
T PRK09335 19 GYVQCDNCGRRVPRDKAVCV 38 (95)
T ss_pred ccEEeCCCCCcCcCCceEEE
Confidence 45689999999998555443
No 70
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=25.15 E-value=44 Score=21.66 Aligned_cols=22 Identities=27% Similarity=0.809 Sum_probs=14.8
Q ss_pred ccccccccccccCCCCCcC-Ccccc
Q 025379 70 QGVRFCQKCNQFKPPRCHH-CSVCR 93 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~H-C~~C~ 93 (253)
.....|+.|+.+ -++|| |..|+
T Consensus 24 p~l~~C~~cG~~--~~~H~vc~~cG 46 (55)
T TIGR01031 24 PTLVVCPNCGEF--KLPHRVCPSCG 46 (55)
T ss_pred CcceECCCCCCc--ccCeeECCccC
Confidence 445679999864 45566 77776
No 71
>PTZ00172 40S ribosomal protein S26; Provisional
Probab=25.06 E-value=25 Score=26.14 Aligned_cols=17 Identities=35% Similarity=0.727 Sum_probs=12.8
Q ss_pred CCcCCcccchhhccccc
Q 025379 85 RCHHCSVCRRCILKMDH 101 (253)
Q Consensus 85 Rs~HC~~C~~CV~~~DH 101 (253)
+.-||..|++||.+=--
T Consensus 19 ~~V~C~nCgr~vPKDKA 35 (108)
T PTZ00172 19 KPVRCSNCGRCVPKDKA 35 (108)
T ss_pred ccEEeCCccccccccce
Confidence 35589999999997433
No 72
>PHA02942 putative transposase; Provisional
Probab=23.57 E-value=44 Score=30.73 Aligned_cols=25 Identities=28% Similarity=0.576 Sum_probs=18.2
Q ss_pred ccccccccccccCCC---CCcCCcccch
Q 025379 70 QGVRFCQKCNQFKPP---RCHHCSVCRR 94 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~---Rs~HC~~C~~ 94 (253)
...+.|+.|....++ |.+.|..||-
T Consensus 323 yTSq~Cs~CG~~~~~l~~r~f~C~~CG~ 350 (383)
T PHA02942 323 YSSVSCPKCGHKMVEIAHRYFHCPSCGY 350 (383)
T ss_pred CCCccCCCCCCccCcCCCCEEECCCCCC
Confidence 356789999866443 7788887775
No 73
>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=23.43 E-value=41 Score=27.49 Aligned_cols=13 Identities=31% Similarity=0.981 Sum_probs=10.9
Q ss_pred CcCCcccchhhcc
Q 025379 86 CHHCSVCRRCILK 98 (253)
Q Consensus 86 s~HC~~C~~CV~~ 98 (253)
..||..|..|+.|
T Consensus 189 ~~~CG~C~~C~~r 201 (201)
T TIGR00364 189 GEGCGKCPSCMLR 201 (201)
T ss_pred CCCCCCChhhhcc
Confidence 4599999999875
No 74
>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=23.29 E-value=50 Score=17.63 Aligned_cols=7 Identities=29% Similarity=0.904 Sum_probs=3.5
Q ss_pred cCCcccc
Q 025379 87 HHCSVCR 93 (253)
Q Consensus 87 ~HC~~C~ 93 (253)
+.|..||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4455554
No 75
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.08 E-value=50 Score=20.40 Aligned_cols=21 Identities=33% Similarity=0.882 Sum_probs=17.8
Q ss_pred ccccccccccccCCCCCcCCc
Q 025379 70 QGVRFCQKCNQFKPPRCHHCS 90 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~HC~ 90 (253)
-..+-|++|..+---|+--|+
T Consensus 9 RGirkCp~CGt~NG~R~~~CK 29 (44)
T PF14952_consen 9 RGIRKCPKCGTYNGTRGLSCK 29 (44)
T ss_pred hccccCCcCcCccCccccccc
Confidence 357889999999999997776
No 76
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=23.00 E-value=35 Score=30.25 Aligned_cols=22 Identities=27% Similarity=0.844 Sum_probs=16.4
Q ss_pred ccccccccccccCCCCCcCCcccc
Q 025379 70 QGVRFCQKCNQFKPPRCHHCSVCR 93 (253)
Q Consensus 70 ~~~~~C~~C~~~kP~Rs~HC~~C~ 93 (253)
....||++|...+|. +.|+.|+
T Consensus 317 ~d~~fCstCG~~ga~--KrCs~CK 338 (396)
T KOG1710|consen 317 ADCQFCSTCGHPGAK--KRCSQCK 338 (396)
T ss_pred EecccccccCCCCcc--chhhhhH
Confidence 347899999988875 4566665
No 77
>smart00301 DM Doublesex DNA-binding motif.
Probab=22.99 E-value=45 Score=21.62 Aligned_cols=6 Identities=17% Similarity=0.490 Sum_probs=3.3
Q ss_pred cCcccc
Q 025379 102 HCVWVV 107 (253)
Q Consensus 102 HC~w~~ 107 (253)
+|||-+
T Consensus 23 ~C~~r~ 28 (54)
T smart00301 23 ECPFRD 28 (54)
T ss_pred CCCCCC
Confidence 566643
No 78
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=22.54 E-value=36 Score=25.40 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=16.1
Q ss_pred cccccccccccC----CCCCcCCcccch
Q 025379 71 GVRFCQKCNQFK----PPRCHHCSVCRR 94 (253)
Q Consensus 71 ~~~~C~~C~~~k----P~Rs~HC~~C~~ 94 (253)
..-.|+.|+..+ -=|++||..|+.
T Consensus 41 ~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred ceeecCCCCceEEecCcccCcCCCCCCC
Confidence 345688887654 336678888875
No 79
>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=22.43 E-value=35 Score=28.46 Aligned_cols=26 Identities=23% Similarity=0.836 Sum_probs=17.4
Q ss_pred ccccccccccCC-CCCcCCcccchhhccc
Q 025379 72 VRFCQKCNQFKP-PRCHHCSVCRRCILKM 99 (253)
Q Consensus 72 ~~~C~~C~~~kP-~Rs~HC~~C~~CV~~~ 99 (253)
...-.+| +++ .+..||..|..|+.|.
T Consensus 177 ~~~T~SC--y~~~~~~~~CG~C~~C~~R~ 203 (209)
T PF06508_consen 177 LELTWSC--YRGGEKGKHCGRCPSCLLRR 203 (209)
T ss_dssp HHH-B-S--TTS--BTTTTSSSHHHHHHH
T ss_pred HHHccCC--CCCCCCCCCCCCCHHHHHHH
Confidence 4455667 455 4568999999999874
No 80
>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=22.31 E-value=52 Score=20.50 Aligned_cols=34 Identities=26% Similarity=0.762 Sum_probs=22.1
Q ss_pred ccccccccccccC---CCCCcCCcccc-----hhhccccccC
Q 025379 70 QGVRFCQKCNQFK---PPRCHHCSVCR-----RCILKMDHHC 103 (253)
Q Consensus 70 ~~~~~C~~C~~~k---P~Rs~HC~~C~-----~CV~~~DHHC 103 (253)
....+|..|+..- .....+|+.|+ +|..+.+.-|
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~~C 50 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPPSC 50 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSSBS
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCCCC
Confidence 4567899998655 45678899885 4555555544
No 81
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.83 E-value=53 Score=24.49 Aligned_cols=25 Identities=20% Similarity=0.333 Sum_probs=13.6
Q ss_pred ccccccccccccC--CC-CCcCCcccch
Q 025379 70 QGVRFCQKCNQFK--PP-RCHHCSVCRR 94 (253)
Q Consensus 70 ~~~~~C~~C~~~k--P~-Rs~HC~~C~~ 94 (253)
+..|.|++|..+= -. +.-+|..||.
T Consensus 7 GtKR~Cp~CG~kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDLNKDPIVCPKCGT 34 (108)
T ss_pred CCcccCCCCcchhccCCCCCccCCCCCC
Confidence 4567777776431 11 3355666664
No 82
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.75 E-value=45 Score=20.49 Aligned_cols=22 Identities=27% Similarity=0.711 Sum_probs=14.5
Q ss_pred ccccccccc-----CCCCCcCCcccch
Q 025379 73 RFCQKCNQF-----KPPRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~-----kP~Rs~HC~~C~~ 94 (253)
-.|+.|+.. +....+.|+.|++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 459999853 3445677887764
No 83
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.39 E-value=61 Score=18.41 Aligned_cols=6 Identities=50% Similarity=1.215 Sum_probs=2.9
Q ss_pred CCcccc
Q 025379 88 HCSVCR 93 (253)
Q Consensus 88 HC~~C~ 93 (253)
-|+.|+
T Consensus 18 ~C~~C~ 23 (32)
T PF13842_consen 18 MCSKCD 23 (32)
T ss_pred EccCCC
Confidence 355554
No 84
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.13 E-value=38 Score=33.15 Aligned_cols=22 Identities=32% Similarity=0.712 Sum_probs=17.0
Q ss_pred cccccccccC--CCCCcCCcccch
Q 025379 73 RFCQKCNQFK--PPRCHHCSVCRR 94 (253)
Q Consensus 73 ~~C~~C~~~k--P~Rs~HC~~C~~ 94 (253)
.-|.+|...= --|.|||+.||+
T Consensus 166 ~~C~rCr~~F~~~~rkHHCr~CG~ 189 (634)
T KOG1818|consen 166 EECLRCRVKFGLTNRKHHCRNCGQ 189 (634)
T ss_pred cccceeeeeeeeccccccccccch
Confidence 5688887432 339999999998
No 85
>PRK11106 queuosine biosynthesis protein QueC; Provisional
Probab=20.54 E-value=47 Score=28.28 Aligned_cols=13 Identities=31% Similarity=0.884 Sum_probs=11.4
Q ss_pred cCCcccchhhccc
Q 025379 87 HHCSVCRRCILKM 99 (253)
Q Consensus 87 ~HC~~C~~CV~~~ 99 (253)
.||..|+.|++|.
T Consensus 195 ~~CG~C~sC~~R~ 207 (231)
T PRK11106 195 DGCGHCAACHLRA 207 (231)
T ss_pred CCCCCCHHHHHHH
Confidence 4999999999874
No 86
>PF03842 Silic_transp: Silicon transporter; InterPro: IPR004693 Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterised member of the family (Sit1) functions in the energy-dependent uptake of either silicic acid [Si(OH)4] or silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms, which make their "glass houses" out of silicon.
Probab=20.32 E-value=7.2e+02 Score=23.33 Aligned_cols=16 Identities=31% Similarity=0.743 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHH
Q 025379 116 KYFLLFLFYTFLETTL 131 (253)
Q Consensus 116 r~F~~fl~~~~~~~~~ 131 (253)
-||.+|.+|+.+..=+
T Consensus 171 nyFalFTlyvam~IEf 186 (512)
T PF03842_consen 171 NYFALFTLYVAMAIEF 186 (512)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5899999997764433
Done!