Query psy2450
Match_columns 254
No_of_seqs 273 out of 1137
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 16:38:06 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2450.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2450hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0154|consensus 99.9 3.4E-26 7.5E-31 226.7 8.4 233 1-246 311-573 (573)
2 PF01585 G-patch: G-patch doma 99.5 1.5E-14 3.3E-19 99.1 4.7 45 182-226 1-45 (45)
3 smart00443 G_patch glycine ric 99.4 4.7E-13 1E-17 92.0 4.5 45 181-225 2-46 (47)
4 KOG2809|consensus 99.3 7.4E-12 1.6E-16 116.9 6.1 71 175-245 18-90 (326)
5 KOG0965|consensus 99.2 5.5E-12 1.2E-16 127.1 5.2 73 178-250 901-975 (988)
6 KOG2384|consensus 99.1 1.5E-10 3.2E-15 101.8 5.2 93 82-228 81-173 (223)
7 PF12656 G-patch_2: DExH-box s 98.8 4.1E-09 8.9E-14 80.1 2.9 49 179-227 26-74 (77)
8 KOG2184|consensus 98.7 1E-08 2.2E-13 104.7 3.3 51 180-230 113-163 (767)
9 KOG3673|consensus 98.4 1.5E-07 3.2E-12 93.5 3.4 47 182-228 82-128 (845)
10 KOG1996|consensus 98.2 1.4E-06 3.1E-11 81.0 5.5 39 184-222 213-251 (378)
11 KOG2185|consensus 98.1 1.1E-06 2.3E-11 84.6 2.3 45 180-224 294-338 (486)
12 KOG1994|consensus 97.9 1.1E-05 2.3E-10 72.7 4.0 55 175-229 73-130 (268)
13 KOG4315|consensus 97.4 0.00012 2.7E-09 70.8 3.1 49 178-227 149-197 (455)
14 KOG4368|consensus 96.9 0.00053 1.2E-08 68.9 2.7 60 178-246 682-745 (757)
15 PF12171 zf-C2H2_jaz: Zinc-fin 96.4 0.0018 4E-08 39.2 1.5 27 85-112 1-27 (27)
16 smart00451 ZnF_U1 U1-like zinc 96.4 0.0031 6.7E-08 39.7 2.6 33 84-117 2-34 (35)
17 KOG0717|consensus 96.3 0.003 6.5E-08 62.2 3.1 35 86-121 293-327 (508)
18 KOG2138|consensus 94.8 0.015 3.2E-07 59.9 2.0 21 182-202 147-167 (883)
19 PF12874 zf-met: Zinc-finger o 94.4 0.019 4.1E-07 33.6 1.0 25 86-111 1-25 (25)
20 KOG1994|consensus 93.7 0.028 6E-07 51.1 1.1 48 182-229 37-84 (268)
21 PTZ00448 hypothetical protein; 92.4 0.093 2E-06 50.6 2.7 35 84-119 313-347 (373)
22 KOG2505|consensus 92.3 0.16 3.5E-06 50.9 4.2 39 80-119 61-99 (591)
23 PF00096 zf-C2H2: Zinc finger, 92.2 0.065 1.4E-06 30.6 0.8 20 87-106 2-21 (23)
24 PF13913 zf-C2HC_2: zinc-finge 91.6 0.12 2.7E-06 31.0 1.6 21 85-106 2-22 (25)
25 KOG3408|consensus 91.3 0.13 2.9E-06 42.6 2.1 43 77-120 49-91 (129)
26 PF13894 zf-C2H2_4: C2H2-type 90.2 0.13 2.9E-06 28.8 0.8 20 87-106 2-21 (24)
27 PF13912 zf-C2H2_6: C2H2-type 89.6 0.13 2.8E-06 30.5 0.4 21 86-106 2-22 (27)
28 smart00355 ZnF_C2H2 zinc finge 85.4 0.64 1.4E-05 26.0 1.7 20 87-106 2-21 (26)
29 PLN02748 tRNA dimethylallyltra 83.7 0.94 2E-05 45.1 3.1 42 79-121 412-454 (468)
30 PF12756 zf-C2H2_2: C2H2 type 83.7 0.38 8.2E-06 35.9 0.3 30 85-115 50-79 (100)
31 KOG2785|consensus 82.9 0.79 1.7E-05 44.5 2.1 33 85-118 3-35 (390)
32 PF07808 RED_N: RED-like prote 79.7 0.81 1.8E-05 41.7 1.0 19 131-149 19-37 (238)
33 PF05443 ROS_MUCR: ROS/MUCR tr 74.9 1.4 3.1E-05 36.9 1.0 27 77-106 64-90 (132)
34 PHA00616 hypothetical protein 72.1 1.5 3.3E-05 30.1 0.4 26 86-113 2-27 (44)
35 PF12756 zf-C2H2_2: C2H2 type 69.3 1.5 3.3E-05 32.5 0.0 27 88-116 2-28 (100)
36 PF09237 GAGA: GAGA factor; I 68.7 2.5 5.5E-05 30.2 1.0 23 84-106 23-45 (54)
37 PHA02768 hypothetical protein; 62.9 4.4 9.6E-05 29.1 1.3 22 86-107 6-27 (55)
38 PF04959 ARS2: Arsenite-resist 62.8 4.5 9.7E-05 36.5 1.7 38 81-120 73-110 (214)
39 COG5112 UFD2 U1-like Zn-finger 62.7 3.2 7E-05 33.9 0.7 43 78-121 48-90 (126)
40 KOG2785|consensus 62.4 4.1 8.9E-05 39.7 1.4 35 85-120 68-102 (390)
41 COG5246 PRP11 Splicing factor 58.2 7.6 0.00016 34.6 2.2 55 55-118 31-85 (222)
42 KOG3032|consensus 52.1 14 0.00031 34.0 3.0 38 80-119 30-67 (264)
43 PHA00732 hypothetical protein 50.2 11 0.00023 28.7 1.7 21 86-106 2-22 (79)
44 KOG3576|consensus 43.9 9 0.0002 34.9 0.5 31 76-106 108-138 (267)
45 PF04423 Rad50_zn_hook: Rad50 42.8 8.1 0.00018 26.8 -0.0 11 87-97 22-32 (54)
46 PF04988 AKAP95: A-kinase anch 42.1 18 0.00038 31.5 2.0 32 86-118 1-32 (165)
47 PF15337 Vasculin: Vascular pr 40.3 16 0.00034 29.2 1.2 14 185-198 11-24 (97)
48 PF05605 zf-Di19: Drought indu 39.2 23 0.00049 24.5 1.8 26 85-113 2-27 (54)
49 COG4957 Predicted transcriptio 36.1 15 0.00033 31.2 0.6 28 76-106 67-94 (148)
50 smart00734 ZnF_Rad18 Rad18-lik 33.5 31 0.00067 20.8 1.5 20 86-106 2-21 (26)
51 PHA00733 hypothetical protein 33.1 30 0.00064 28.5 1.9 22 85-106 99-120 (128)
52 KOG4173|consensus 31.2 22 0.00048 32.4 0.9 40 77-118 98-137 (253)
53 TIGR00606 rad50 rad50. This fa 30.9 26 0.00057 39.0 1.6 18 83-100 675-692 (1311)
54 KOG1074|consensus 26.8 32 0.00069 37.0 1.2 38 83-120 877-928 (958)
55 smart00586 ZnF_DBF Zinc finger 25.7 38 0.00083 23.8 1.1 29 81-113 1-29 (49)
56 COG4049 Uncharacterized protei 24.2 36 0.00078 24.9 0.8 33 85-117 17-49 (65)
57 PF07535 zf-DBF: DBF zinc fing 23.9 56 0.0012 22.8 1.7 26 84-113 4-29 (49)
58 KOG1146|consensus 23.8 42 0.00091 37.8 1.5 29 84-113 1327-1355(1406)
59 PF13465 zf-H2C2_2: Zinc-finge 22.7 26 0.00057 20.7 -0.1 18 80-97 9-26 (26)
60 PF06220 zf-U1: U1 zinc finger 22.4 64 0.0014 21.2 1.6 32 85-117 3-36 (38)
61 PHA00733 hypothetical protein 20.8 67 0.0014 26.4 1.8 22 85-106 73-94 (128)
No 1
>KOG0154|consensus
Probab=99.93 E-value=3.4e-26 Score=226.73 Aligned_cols=233 Identities=34% Similarity=0.490 Sum_probs=175.2
Q ss_pred ChhhhhhhhhhhccccC--CCCcccccCCCCCccccCCCCccccccccccccc-------------------cchhhhhh
Q psy2450 1 MEKWAKTLNHRKEISKV--ANNTEQAASESPSQSTQGSADVCFSVVGNNREEK-------------------TKKSLVAA 59 (254)
Q Consensus 1 me~wak~ln~~ke~~~~--~~~~~~~~~~~~~~~~~~~ad~gf~~~e~k~~~~-------------------~~~~l~~~ 59 (254)
|++|++.++.+++.... .+.. ....+....+..+..+.-..+++.... ...+|+..
T Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 387 (573)
T KOG0154|consen 311 MEKWAKYLSKEKDSYLLSSTPAH---EGVHTGVNTSKGAEPGPVKKEKKLYKKKEKFVNPELSKRGSHVSPSKNLKLIDV 387 (573)
T ss_pred HHhhhhhhhcccccccccccccc---eecccccccccccCchhhhhhccccccchhccCccccccccccCcccccccccc
Confidence 89999999988886655 2221 122334444444555544333322111 13578999
Q ss_pred ccCCCCchhhhccccccccccccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhhhcCCCCCchhccccccchh
Q psy2450 60 YESDEEPEVQEETVSGEEKQQIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYTCRNLDPNDAVHRAVQYRDR 139 (254)
Q Consensus 60 y~~~sd~e~~~~~~~~~e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~~k~~~~~~~~~~~~~YRDR 139 (254)
|.|.++++.+.+.. ..+++|.+++|+||+|+|++.+.+++|...|.+|++||..++.....+ .........|+||
T Consensus 388 ~~~~~~~~~~~~~~----~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~s~~h~~n~~~~~~~~~~~-~~~~~~~~~~~~~ 462 (573)
T KOG0154|consen 388 STGLSDSELEQEKS----LKLVDKLKLMCLLCRRQFPSKGSLQKHLTPSDLHKENLDKHRRPSTLE-EASAEGPLAYRDR 462 (573)
T ss_pred ccCCCchHhhhhhh----hhccccchhhhhhhhccCCchHHHhhhcccccchhhhHHhhccchhhh-hhccccccccchH
Confidence 99999998876542 289999999999999999999999999999999999999999876543 2233456899999
Q ss_pred HHHHhhhcCCCCCCcccccccc-cccccccccccCC--------CccCCCCCCcHHHHHHHHcCCCCCCCCCCCCCCccc
Q psy2450 140 AKERRLKYGEPEVPPACKLKAK-YSKVKEATVTFEE--------PTKKGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTS 210 (254)
Q Consensus 140 A~ERR~~~G~~~~P~~~~~r~k-~~~~~~~~~~~e~--------~~~~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~ 210 (254)
+.+||..+|...++.+....-. |.. ....... -...+|+.+|+|.+||++|||.+|+|||...+|++.
T Consensus 463 ~~~~~~~~g~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~sn~~~~~l~~~gw~~g~Glg~~~~g~~~ 539 (573)
T KOG0154|consen 463 AKERRKSMGIVEGRGPGRSKPDSFEP---ISVLLESRQKSSRGATEEPPIDTSNVGNRMLQSMGWKEGSGLGKKNQGIKE 539 (573)
T ss_pred HHhHHHHhcCCCCCCCCcccCCCccc---ceeeccccccchhhccccccCCCCccchhhhhccCcccccccccccCCCcc
Confidence 9999999999987665521111 111 1111111 123358899999999999999999999999999999
Q ss_pred cceeeeecCCceecccCCCCCCCCCchHHHHHHHHH
Q psy2450 211 IIEAEARISSAGLGTNAIGMTPAPGETYKDCVKKMM 246 (254)
Q Consensus 211 PI~~~~~~~~~GLG~~~~~~~~~~~d~Y~~~vrk~~ 246 (254)
||++..+..++|||+. ..+.....+ |+++++++|
T Consensus 540 ~~e~~~~~~~~~lg~~-~~~~~~~~~-~~~~~~k~~ 573 (573)
T KOG0154|consen 540 PIEAEGRDRGAGLGAK-SKQGVKGND-YKEAKRKKM 573 (573)
T ss_pred cccccccccCCCCCcc-cccccCCcc-hhhhhhccC
Confidence 9999999999999999 777778888 999999875
No 2
>PF01585 G-patch: G-patch domain; InterPro: IPR000467 The D111/G-patch domain [] is a short conserved region of about 40 amino acids which occurs in a number of putative RNA-binding proteins, including tumor suppressor and DNA-damage-repair proteins, suggesting that this domain may have an RNA binding function. This domain has seven highly conserved glycines. A multiple alignment of a small subset of D111/G-patch domains is shown in Fig. 2b of [].; GO: 0003676 nucleic acid binding, 0005622 intracellular
Probab=99.51 E-value=1.5e-14 Score=99.11 Aligned_cols=45 Identities=44% Similarity=0.827 Sum_probs=42.9
Q ss_pred CCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceeccc
Q psy2450 182 ADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTN 226 (254)
Q Consensus 182 ~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~ 226 (254)
+++||.+||.+|||++|+|||++.+|+++||++..+.++.|||++
T Consensus 1 t~~~g~~lm~kmGw~~G~GLGk~~~G~~~pi~~~~~~~~~GlG~~ 45 (45)
T PF01585_consen 1 TSSIGFKLMKKMGWKPGQGLGKNGQGIAEPIEVKKKKDRKGLGAE 45 (45)
T ss_pred CCcHHHHHHHHCCCCCCcCCCcCCccCCcceEEeeEcCCccccCC
Confidence 368999999999999999999999999999999999999999974
No 3
>smart00443 G_patch glycine rich nucleic binding domain. A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.
Probab=99.38 E-value=4.7e-13 Score=91.98 Aligned_cols=45 Identities=51% Similarity=0.886 Sum_probs=43.1
Q ss_pred CCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecc
Q psy2450 181 GADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGT 225 (254)
Q Consensus 181 ~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~ 225 (254)
+.+++|.+||.+|||++|+|||++.+|+++||++..+.++.|||+
T Consensus 2 ~~~~~g~~~l~~mGw~~G~GLG~~~~g~~~pi~~~~~~~~~GlG~ 46 (47)
T smart00443 2 STSNIGYKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDRKGLGA 46 (47)
T ss_pred CcccHHHHHHHHcCCCCCCcCCCCCCcCccceeEeeccCCcCcCC
Confidence 467999999999999999999999999999999999999999997
No 4
>KOG2809|consensus
Probab=99.25 E-value=7.4e-12 Score=116.93 Aligned_cols=71 Identities=32% Similarity=0.536 Sum_probs=63.4
Q ss_pred CccCCCCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccCCC--CCCCCCchHHHHHHHH
Q psy2450 175 PTKKGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNAIG--MTPAPGETYKDCVKKM 245 (254)
Q Consensus 175 ~~~~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~~~--~~~~~~d~Y~~~vrk~ 245 (254)
.+...++.+.+|++||.+|||++|.|||++.||++.||.|.++.++.|||+.... .|+.+.+.|+.++.++
T Consensus 18 n~~w~nd~~~fg~KlLekmGW~eG~GLG~~~qG~~~~IKvs~K~d~~GLGa~~~ned~W~~h~d~Fn~lla~L 90 (326)
T KOG2809|consen 18 NTAWSNDDSRFGKKLLEKMGWSEGDGLGKNEQGITDPIKVSLKNDTLGLGADKNNEDQWIAHQDDFNALLAKL 90 (326)
T ss_pred cchhcccchHHHHHHHHHcCCccCCcccccccCCccceEEEeccCCcccCccccccccchhhcccHHHHHHHh
Confidence 3456788999999999999999999999999999999999999999999999876 5667788898887664
No 5
>KOG0965|consensus
Probab=99.24 E-value=5.5e-12 Score=127.13 Aligned_cols=73 Identities=32% Similarity=0.566 Sum_probs=63.6
Q ss_pred CCCCCCcHHHHHHHHcCCCCCCCCCCCCCCcccccee-eeecCCceecccCCCCCCCCCchHHHHHHHHHHH-HH
Q psy2450 178 KGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEA-EARISSAGLGTNAIGMTPAPGETYKDCVKKMMRA-RY 250 (254)
Q Consensus 178 ~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~-~~~~~~~GLG~~~~~~~~~~~d~Y~~~vrk~~~~-Ry 250 (254)
..+...|||++||+||||++|+|||..++||.+||.+ .+...+.|+|...+.-.-...|.|..+-++||++ ||
T Consensus 901 ~KLt~dNiGfQMLqKMGWKEGeGLGS~gkGI~dPVnkg~~~~~g~G~G~s~pael~peDdeYeayrKRMMLaYrf 975 (988)
T KOG0965|consen 901 QKLTDDNIGFQMLQKMGWKEGEGLGSLGKGIRDPVNKGAAGSLGWGWGGSQPAELQPEDDEYEAYRKRMMLAYRF 975 (988)
T ss_pred hhccccchHHHHHHHhCccccccccccCcccccchhhcccccCCcccccCCccccCchhhHHHHHHHHHHHhhhc
Confidence 3578899999999999999999999999999999985 5778899999888764445678999999999987 55
No 6
>KOG2384|consensus
Probab=99.07 E-value=1.5e-10 Score=101.78 Aligned_cols=93 Identities=26% Similarity=0.408 Sum_probs=75.7
Q ss_pred cccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhhhcCCCCCchhccccccchhHHHHhhhcCCCCCCcccccccc
Q psy2450 82 DWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYTCRNLDPNDAVHRAVQYRDRAKERRLKYGEPEVPPACKLKAK 161 (254)
Q Consensus 82 D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~~k~~~~~~~~~~~~~YRDRA~ERR~~~G~~~~P~~~~~r~k 161 (254)
|..-.+|-+|.+=|+. .....|+. |.-|.-||+.+-. + +
T Consensus 81 ~e~lfyCE~Cd~~ip~-~~~snH~t-SttHllsl~~~pa-------------------------------~---k----- 119 (223)
T KOG2384|consen 81 DEALFYCEVCDIYIPN-SKKSNHFT-STTHLLSLQHIPA-------------------------------N---K----- 119 (223)
T ss_pred CCccchhhhhhhhccC-CCCccchh-hHHHHhhhccCCC-------------------------------C---C-----
Confidence 4456789999999985 44567886 8999998875321 1 1
Q ss_pred cccccccccccCCCccCCCCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccCC
Q psy2450 162 YSKVKEATVTFEEPTKKGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNAI 228 (254)
Q Consensus 162 ~~~~~~~~~~~e~~~~~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~~ 228 (254)
+. ...|..+|+|++||.+.||+++.|||.+++|+..||.+.++.++.|||+...
T Consensus 120 ~~-------------p~~i~pks~GyrLl~~~GW~pe~GLGp~~~Grr~PvrTvlkkdr~GLG~e~~ 173 (223)
T KOG2384|consen 120 FQ-------------PHLIKPKSLGYRLLSQYGWSPEAGLGPENQGRRAPVRTVLKKDRIGLGTEID 173 (223)
T ss_pred CC-------------CCcCCCCCchHHHHHhcCCCcccCCCccccCcccchhHHHhhcccccchhhc
Confidence 11 1247788999999999999999999999999999999999999999999865
No 7
>PF12656 G-patch_2: DExH-box splicing factor binding site
Probab=98.77 E-value=4.1e-09 Score=80.13 Aligned_cols=49 Identities=31% Similarity=0.677 Sum_probs=46.0
Q ss_pred CCCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccC
Q psy2450 179 GIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNA 227 (254)
Q Consensus 179 ~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~ 227 (254)
.++.+.||..||..|||++|+|+|++.++.+.|+....|..+.|||+..
T Consensus 26 ~vPVe~FG~AlLRGMGW~~~~~~g~~~~~~~~~~~~~~Rp~~lGLGA~~ 74 (77)
T PF12656_consen 26 AVPVEEFGAALLRGMGWKPGEGIGKNKKKSVKPVEPKRRPKGLGLGAKP 74 (77)
T ss_pred hCCHHHHHHHHHHHcCCCCCCCCCCCcccccCcccccccccCcCCCcCC
Confidence 3667899999999999999999999999999999999999999999875
No 8
>KOG2184|consensus
Probab=98.67 E-value=1e-08 Score=104.75 Aligned_cols=51 Identities=43% Similarity=0.721 Sum_probs=47.2
Q ss_pred CCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccCCCC
Q psy2450 180 IGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNAIGM 230 (254)
Q Consensus 180 ~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~~~~ 230 (254)
....+||.+||++|||++|.|||++.|||++||++++|+.+.|||+-+...
T Consensus 113 ~~t~gig~Kll~kMGYkpG~GLGkn~qGIv~Pieaq~Rp~rgg~Gay~~e~ 163 (767)
T KOG2184|consen 113 KGTKGIGAKLLEKMGYKPGKGLGKNAQGIVAPIEAQLRPGRGGLGAYGFET 163 (767)
T ss_pred hcccchhHHHHHHcCCccccccCccccccccHHhcccCccCcccccccccc
Confidence 456799999999999999999999999999999999999999999987643
No 9
>KOG3673|consensus
Probab=98.41 E-value=1.5e-07 Score=93.54 Aligned_cols=47 Identities=40% Similarity=0.609 Sum_probs=44.6
Q ss_pred CCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccCC
Q psy2450 182 ADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNAI 228 (254)
Q Consensus 182 ~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~~ 228 (254)
.+++..+||.|||++.|+|||+.+||+.+||.+....++.|||..-.
T Consensus 82 y~~va~~lMakMG~~~geGLGK~~QGr~epi~as~Q~GRrGlGl~l~ 128 (845)
T KOG3673|consen 82 YLTVAERLMAKMGHKAGEGLGKHGQGRSEPIAASTQRGRRGLGLNLK 128 (845)
T ss_pred cchHHHHHHHHhCccccccccccCCCccchhhhhhhccccccCccch
Confidence 67999999999999999999999999999999999999999998764
No 10
>KOG1996|consensus
Probab=98.24 E-value=1.4e-06 Score=81.00 Aligned_cols=39 Identities=38% Similarity=0.725 Sum_probs=36.3
Q ss_pred cHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCce
Q psy2450 184 NVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAG 222 (254)
Q Consensus 184 n~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~G 222 (254)
.+.++||+||||++|+|||+++|||..++.++....+.|
T Consensus 213 tvA~~im~k~G~keGqGLGKsEQGlsTalsveKT~~rgG 251 (378)
T KOG1996|consen 213 TVAHKIMQKYGFKEGQGLGKSEQGLSTALSVEKTSKRGG 251 (378)
T ss_pred hHHHHHHHHhCcccccCcCccccccccceeeeeccccCc
Confidence 578999999999999999999999999999988777777
No 11
>KOG2185|consensus
Probab=98.13 E-value=1.1e-06 Score=84.59 Aligned_cols=45 Identities=33% Similarity=0.522 Sum_probs=40.2
Q ss_pred CCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceec
Q psy2450 180 IGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLG 224 (254)
Q Consensus 180 ~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG 224 (254)
..+-+||.+||.||||..|.|||+.++||++||.+.+-+.+..|-
T Consensus 294 ~hTRGIgsKLM~kMGY~~G~GLG~~g~GiV~pI~a~vlp~grSLD 338 (486)
T KOG2185|consen 294 NHTRGIGSKLMAKMGYREGMGLGVSGQGIVNPILAKVLPAGRSLD 338 (486)
T ss_pred cccchHHHHHHHHhchhhccccCcCCCccccchhhhhccCCCCHH
Confidence 345589999999999999999999999999999999888777664
No 12
>KOG1994|consensus
Probab=97.89 E-value=1.1e-05 Score=72.74 Aligned_cols=55 Identities=27% Similarity=0.473 Sum_probs=50.4
Q ss_pred CccCCCCCCcHHHHHHHHcCCCCCCCCCCCCCC---ccccceeeeecCCceecccCCC
Q psy2450 175 PTKKGIGADNVGNKLLQKMGWTQGQGLGKTNQG---RTSIIEAEARISSAGLGTNAIG 229 (254)
Q Consensus 175 ~~~~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG---~~~PI~~~~~~~~~GLG~~~~~ 229 (254)
+...+|..+++|+.+|.+||+++|.-||++..+ +++||...++..+.|||.....
T Consensus 73 ~~~~~i~~e~~gf~lm~~Mg~kpg~~lgkq~e~~~~r~epI~~dI~~~r~g~G~ed~~ 130 (268)
T KOG1994|consen 73 TKRRGIRAEKPGFSLMNDMGMKPGRFLGKQSEMKNKRLEPIWYDIQVAREGMGDEDLY 130 (268)
T ss_pred hccccccccCcChHHHHHhCCCccchhccccccccccccceeehHHHHhhccCccccc
Confidence 445578999999999999999999999999999 9999999999999999988654
No 13
>KOG4315|consensus
Probab=97.36 E-value=0.00012 Score=70.83 Aligned_cols=49 Identities=35% Similarity=0.647 Sum_probs=42.3
Q ss_pred CCCCCCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccC
Q psy2450 178 KGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNA 227 (254)
Q Consensus 178 ~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~ 227 (254)
..|+...||..||.-|||++|.|+|+++|+ +.+.....|+.+.|||+..
T Consensus 149 eaiPVe~FGlAmLrG~GWkpg~gigk~~q~-v~~~~~~~rpkglGLGa~~ 197 (455)
T KOG4315|consen 149 EAIPVEGFGLAMLRGMGWKPGPGIGKNKQD-VKIKEPFLRPKGLGLGADP 197 (455)
T ss_pred ccCchhHHHHHHHhcCCCCCCCCcCcCCcc-ccccccccCCCCcccCCCc
Confidence 357788999999999999999999999664 5566678999999999984
No 14
>KOG4368|consensus
Probab=96.92 E-value=0.00053 Score=68.89 Aligned_cols=60 Identities=35% Similarity=0.660 Sum_probs=45.5
Q ss_pred CCCCCCcHHHHHHHHcCCCCCCCCCCCCCCcccccee-eeecC---CceecccCCCCCCCCCchHHHHHHHHH
Q psy2450 178 KGIGADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEA-EARIS---SAGLGTNAIGMTPAPGETYKDCVKKMM 246 (254)
Q Consensus 178 ~~~~~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~-~~~~~---~~GLG~~~~~~~~~~~d~Y~~~vrk~~ 246 (254)
..+.++|+|.+||.||||. |.|||..++||.+||-+ .++.. ..|+|+.- |-|..+.+.++
T Consensus 682 ~~lse~NKGhQml~KMGWs-G~GLGak~qGI~DPiSGGEVRdR~E~yKGvG~~l--------DP~E~FRKnK~ 745 (757)
T KOG4368|consen 682 APLGEENKGHQMLVKMGWS-GSGLGAKEQGIQDPISGGEVRDRWEQYKGVGVAL--------DPYENFRKNKS 745 (757)
T ss_pred CccccccchhhhHhhcCcc-cCCcccccccccCcccCccccchhhhhcccCccc--------CcHHHHHHhhc
Confidence 3488999999999999999 89999999999999974 34433 34665543 45666666543
No 15
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.40 E-value=0.0018 Score=39.17 Aligned_cols=27 Identities=37% Similarity=0.725 Sum_probs=23.6
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHH
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHK 112 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk 112 (254)
+..|.+|.+.|.+...|..|.+ |..||
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~-sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMK-SKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTT-SHHHH
T ss_pred CCCcccCCCCcCCHHHHHHHHc-cCCCC
Confidence 3689999999999999999997 77775
No 16
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=96.39 E-value=0.0031 Score=39.73 Aligned_cols=33 Identities=24% Similarity=0.505 Sum_probs=29.6
Q ss_pred cCccccccccCCCCHHHHHhhhhhhHHHHhhhhh
Q psy2450 84 DKLACLICKRQFNSKDILKKHTQLSELHKSNLKM 117 (254)
Q Consensus 84 ~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~ 117 (254)
+...|.+|...|.+...+..|.+ |..|+.|++.
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H~~-gk~H~~~~~~ 34 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAHLK-GKKHKKNVKK 34 (35)
T ss_pred cCeEccccCCccCCHHHHHHHHC-hHHHHHHHHc
Confidence 45789999999999999999997 8999999875
No 17
>KOG0717|consensus
Probab=96.28 E-value=0.003 Score=62.24 Aligned_cols=35 Identities=34% Similarity=0.631 Sum_probs=33.0
Q ss_pred ccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQLSELHKSNLKMWYTC 121 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~~ 121 (254)
+.|..|...|+|.-+|..|++ |..|+.||..|++.
T Consensus 293 lyC~vCnKsFKseKq~kNHEn-SKKHkenv~eLrqe 327 (508)
T KOG0717|consen 293 LYCVVCNKSFKSEKQLKNHEN-SKKHKENVAELRQE 327 (508)
T ss_pred eEEeeccccccchHHHHhhHH-HHHHHHHHHHHHHH
Confidence 999999999999999999997 99999999999864
No 18
>KOG2138|consensus
Probab=94.84 E-value=0.015 Score=59.90 Aligned_cols=21 Identities=52% Similarity=1.243 Sum_probs=19.9
Q ss_pred CCcHHHHHHHHcCCCCCCCCC
Q psy2450 182 ADNVGNKLLQKMGWTQGQGLG 202 (254)
Q Consensus 182 ~sn~G~kmL~kMGW~~G~GLG 202 (254)
...||.+||.+|||++|+|+|
T Consensus 147 s~sIgvrlLrsMGWr~GqgIg 167 (883)
T KOG2138|consen 147 SDSIGVRLLRSMGWREGQGIG 167 (883)
T ss_pred hhhHHHHHHHHhcCccCCCcC
Confidence 468999999999999999999
No 19
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.44 E-value=0.019 Score=33.63 Aligned_cols=25 Identities=36% Similarity=0.798 Sum_probs=21.3
Q ss_pred ccccccccCCCCHHHHHhhhhhhHHH
Q psy2450 86 LACLICKRQFNSKDILKKHTQLSELH 111 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~~S~LH 111 (254)
..|.+|.+.|.+...|..|.+ |..|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~-s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLR-SKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHT-THHH
T ss_pred CCCCCCCCCcCCHHHHHHHHC-cCCC
Confidence 369999999999999999987 5444
No 20
>KOG1994|consensus
Probab=93.71 E-value=0.028 Score=51.11 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=44.1
Q ss_pred CCcHHHHHHHHcCCCCCCCCCCCCCCccccceeeeecCCceecccCCC
Q psy2450 182 ADNVGNKLLQKMGWTQGQGLGKTNQGRTSIIEAEARISSAGLGTNAIG 229 (254)
Q Consensus 182 ~sn~G~kmL~kMGW~~G~GLGk~~qG~~~PI~~~~~~~~~GLG~~~~~ 229 (254)
...++.+||.-|||++|.-||.+...+-+||++-.+.-..|||+....
T Consensus 37 ~~r~e~k~~~n~~~~e~r~l~~~e~~~ee~~~~la~~~~~~i~~e~~g 84 (268)
T KOG1994|consen 37 IMRREYKMMENMGYKEGRTLGSNESALEEPIKVLANTKRRGIRAEKPG 84 (268)
T ss_pred hhhhHHHHHHhcCCCCCCccchhhhhhcchHHHhhhhccccccccCcC
Confidence 356888999999999999999999999999999999999999998764
No 21
>PTZ00448 hypothetical protein; Provisional
Probab=92.43 E-value=0.093 Score=50.61 Aligned_cols=35 Identities=31% Similarity=0.405 Sum_probs=30.9
Q ss_pred cCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhh
Q psy2450 84 DKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWY 119 (254)
Q Consensus 84 ~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~ 119 (254)
..++|..|.-+|.+.+.-+-|.+ |++|+.||+..-
T Consensus 313 ~~~tC~~C~v~F~~~~~qR~H~K-SDwHrYNLKRkl 347 (373)
T PTZ00448 313 NMLLCRKCNIQLMDHNAFKQHYR-SEWHIFNTKRNA 347 (373)
T ss_pred CCccccccccccCCHHHHHHHhh-hhHHHHHHHHHh
Confidence 46789999999999899999998 999999998643
No 22
>KOG2505|consensus
Probab=92.33 E-value=0.16 Score=50.88 Aligned_cols=39 Identities=26% Similarity=0.386 Sum_probs=34.2
Q ss_pred cccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhh
Q psy2450 80 QIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWY 119 (254)
Q Consensus 80 ~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~ 119 (254)
.|-.+.+.|.-|.--|.+.....-|.+ |+.|+-|++.--
T Consensus 61 ~v~sd~~~CstCq~~F~s~~eqr~Hyk-sD~HR~N~Krkl 99 (591)
T KOG2505|consen 61 SVISDSDQCSTCQIPFGSRQEQREHYK-SDWHRFNTKRKL 99 (591)
T ss_pred hhhcccccccccCCccccHHHHHHHHH-HHHHHHHHHHHh
Confidence 355589999999999999999999997 999999998643
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=92.18 E-value=0.065 Score=30.64 Aligned_cols=20 Identities=45% Similarity=0.898 Sum_probs=18.9
Q ss_pred cccccccCCCCHHHHHhhhh
Q psy2450 87 ACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 87 ~ClLC~RqF~s~e~L~kH~~ 106 (254)
.|..|.+.|.+...|.+|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 2 KCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCccCCHHHHHHHHh
Confidence 69999999999999999996
No 24
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=91.62 E-value=0.12 Score=31.03 Aligned_cols=21 Identities=48% Similarity=0.922 Sum_probs=18.0
Q ss_pred CccccccccCCCCHHHHHhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
...|..|.|.|. .+.|.+|++
T Consensus 2 l~~C~~CgR~F~-~~~l~~H~~ 22 (25)
T PF13913_consen 2 LVPCPICGRKFN-PDRLEKHEK 22 (25)
T ss_pred CCcCCCCCCEEC-HHHHHHHHH
Confidence 357999999995 699999986
No 25
>KOG3408|consensus
Probab=91.32 E-value=0.13 Score=42.56 Aligned_cols=43 Identities=23% Similarity=0.410 Sum_probs=36.9
Q ss_pred ccccccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhh
Q psy2450 77 EKQQIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYT 120 (254)
Q Consensus 77 e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~ 120 (254)
+.++--.+.+.|+.|.|-|.+.-+|.-|-+ +..||.-|+.++.
T Consensus 49 D~dlPG~GqfyCi~CaRyFi~~~~l~~H~k-tK~HKrRvK~l~~ 91 (129)
T KOG3408|consen 49 DPDLPGGGQFYCIECARYFIDAKALKTHFK-TKVHKRRVKELRE 91 (129)
T ss_pred CCCCCCCceeehhhhhhhhcchHHHHHHHh-ccHHHHHHHhccc
Confidence 444555678999999999999999999997 9999999998874
No 26
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=90.16 E-value=0.13 Score=28.76 Aligned_cols=20 Identities=40% Similarity=0.864 Sum_probs=16.9
Q ss_pred cccccccCCCCHHHHHhhhh
Q psy2450 87 ACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 87 ~ClLC~RqF~s~e~L~kH~~ 106 (254)
.|.+|...|.+...|..|+.
T Consensus 2 ~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 2 QCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp E-SSTS-EESSHHHHHHHHH
T ss_pred CCcCCCCcCCcHHHHHHHHH
Confidence 69999999999999999986
No 27
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=89.63 E-value=0.13 Score=30.55 Aligned_cols=21 Identities=29% Similarity=0.684 Sum_probs=19.3
Q ss_pred ccccccccCCCCHHHHHhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~ 106 (254)
..|..|...|.+...|..|.+
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~~ 22 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHKR 22 (27)
T ss_dssp EEETTTTEEESSHHHHHHHHC
T ss_pred CCCCccCCccCChhHHHHHhH
Confidence 479999999999999999985
No 28
>smart00355 ZnF_C2H2 zinc finger.
Probab=85.40 E-value=0.64 Score=26.00 Aligned_cols=20 Identities=40% Similarity=0.762 Sum_probs=18.6
Q ss_pred cccccccCCCCHHHHHhhhh
Q psy2450 87 ACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 87 ~ClLC~RqF~s~e~L~kH~~ 106 (254)
.|..|...|.+...|..|++
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 69999999999999999986
No 29
>PLN02748 tRNA dimethylallyltransferase
Probab=83.72 E-value=0.94 Score=45.15 Aligned_cols=42 Identities=14% Similarity=0.321 Sum_probs=37.0
Q ss_pred ccccccCcccccccc-CCCCHHHHHhhhhhhHHHHhhhhhhhhh
Q psy2450 79 QQIDWDKLACLICKR-QFNSKDILKKHTQLSELHKSNLKMWYTC 121 (254)
Q Consensus 79 ~~~D~~kl~ClLC~R-qF~s~e~L~kH~~~S~LHk~NL~~~~~~ 121 (254)
.-..|...+|-+|.+ -|...+.+..|.+ |.-||.+++..+++
T Consensus 412 ~~~~~~~~~Ce~C~~~~~~G~~eW~~Hlk-sr~Hk~~~~~~~k~ 454 (468)
T PLN02748 412 SRELWTQYVCEACGNKVLRGAHEWEQHKQ-GRGHRKRVQRLKQK 454 (468)
T ss_pred cccccccccccCCCCcccCCHHHHHHHhc-chHHHHHHhHHHhh
Confidence 344699999999997 7999999999997 99999999988765
No 30
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=83.67 E-value=0.38 Score=35.88 Aligned_cols=30 Identities=30% Similarity=0.676 Sum_probs=24.0
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHHhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHKSNL 115 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL 115 (254)
.+.|.+|...|.+.+.|..|.+ +.-|+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~-~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMR-SKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHH-HTTTTC-S
T ss_pred CCCCCccCCCCcCHHHHHHHHc-CccCCCcc
Confidence 6999999999999999999997 45566643
No 31
>KOG2785|consensus
Probab=82.93 E-value=0.79 Score=44.51 Aligned_cols=33 Identities=30% Similarity=0.564 Sum_probs=29.1
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHHhhhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHKSNLKMW 118 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~ 118 (254)
-+||.-|.-.|.+.|.-+-|-+ |++|+-||+-.
T Consensus 3 ~ftC~tC~v~F~~ad~Qr~HyK-SdWHRYNLKRk 35 (390)
T KOG2785|consen 3 GFTCNTCNVEFDDADEQRAHYK-SDWHRYNLKRK 35 (390)
T ss_pred cceeeceeeeeccHHHHHHHhh-hhHHHhhHHhH
Confidence 4799999999999887788986 99999999863
No 32
>PF07808 RED_N: RED-like protein N-terminal region; InterPro: IPR012916 This domain contains sequences that are similar to the N-terminal region of Red protein (Q13123 from SWISSPROT). This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements []. The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region [], suggesting that these proteins are expressed in the nucleus []. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated, or that the protein self-aggregates extremely efficiently []. ; GO: 0005634 nucleus
Probab=79.71 E-value=0.81 Score=41.71 Aligned_cols=19 Identities=53% Similarity=0.615 Sum_probs=15.5
Q ss_pred ccccccchhHHHHhhhcCC
Q psy2450 131 HRAVQYRDRAKERRLKYGE 149 (254)
Q Consensus 131 ~~~~~YRDRA~ERR~~~G~ 149 (254)
....+|||||+|||.-...
T Consensus 19 ~~~~~YrDRA~eRR~~~~~ 37 (238)
T PF07808_consen 19 KLAPGYRDRAKERREGEND 37 (238)
T ss_pred ccccchhhHHHHHHcccCc
Confidence 4568999999999987553
No 33
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=74.89 E-value=1.4 Score=36.86 Aligned_cols=27 Identities=33% Similarity=0.717 Sum_probs=17.0
Q ss_pred ccccccccCccccccccCCCCHHHHHhhhh
Q psy2450 77 EKQQIDWDKLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 77 e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
-..=|-.+.++|+.|.+.|++ |.+|.+
T Consensus 64 i~kSI~~d~i~clecGk~~k~---LkrHL~ 90 (132)
T PF05443_consen 64 IRKSITPDYIICLECGKKFKT---LKRHLR 90 (132)
T ss_dssp SSTTB-SS-EE-TBT--EESB---HHHHHH
T ss_pred HhhccccCeeEEccCCcccch---HHHHHH
Confidence 344457789999999999997 588875
No 34
>PHA00616 hypothetical protein
Probab=72.06 E-value=1.5 Score=30.14 Aligned_cols=26 Identities=31% Similarity=0.567 Sum_probs=21.6
Q ss_pred ccccccccCCCCHHHHHhhhhhhHHHHh
Q psy2450 86 LACLICKRQFNSKDILKKHTQLSELHKS 113 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~~S~LHk~ 113 (254)
..|+.|...|...-.|.+|++ .-|.+
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r--~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLL--SVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHH--HhcCC
Confidence 469999999999999999996 44444
No 35
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=69.27 E-value=1.5 Score=32.52 Aligned_cols=27 Identities=33% Similarity=0.671 Sum_probs=0.0
Q ss_pred ccccccCCCCHHHHHhhhhhhHHHHhhhh
Q psy2450 88 CLICKRQFNSKDILKKHTQLSELHKSNLK 116 (254)
Q Consensus 88 ClLC~RqF~s~e~L~kH~~~S~LHk~NL~ 116 (254)
|++|...|.+.+.|..|.. .-|..++.
T Consensus 2 C~~C~~~f~~~~~l~~H~~--~~H~~~~~ 28 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK--KKHGFDIP 28 (100)
T ss_dssp -----------------------------
T ss_pred ccccccccccccccccccc--cccccccc
Confidence 9999999999999999985 77777665
No 36
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=68.75 E-value=2.5 Score=30.18 Aligned_cols=23 Identities=22% Similarity=0.515 Sum_probs=16.4
Q ss_pred cCccccccccCCCCHHHHHhhhh
Q psy2450 84 DKLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 84 ~kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
.--+|.+|.+.+.....|.+|..
T Consensus 23 ~PatCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 23 QPATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp --EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCCCcchhhccchhhHHHHHH
Confidence 45699999999999999999974
No 37
>PHA02768 hypothetical protein; Provisional
Probab=62.88 E-value=4.4 Score=29.12 Aligned_cols=22 Identities=18% Similarity=0.468 Sum_probs=20.0
Q ss_pred ccccccccCCCCHHHHHhhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQL 107 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~~ 107 (254)
..|..|.+.|...+.|.+|++.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~ 27 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRK 27 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHh
Confidence 4799999999999999999973
No 38
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=62.76 E-value=4.5 Score=36.47 Aligned_cols=38 Identities=24% Similarity=0.450 Sum_probs=28.3
Q ss_pred ccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhh
Q psy2450 81 IDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYT 120 (254)
Q Consensus 81 ~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~ 120 (254)
.|-.|.-|.||..-|+..+=+.||+. .-|-+-|+.+++
T Consensus 73 ~~~~K~~C~lc~KlFkg~eFV~KHI~--nKH~e~ve~~~~ 110 (214)
T PF04959_consen 73 EDEDKWRCPLCGKLFKGPEFVRKHIF--NKHPEKVEEVKK 110 (214)
T ss_dssp SSSEEEEE-SSS-EESSHHHHHHHHH--HH-HHHHHHHHH
T ss_pred HcCCEECCCCCCcccCChHHHHHHHh--hcCHHHHHHHHH
Confidence 35568899999999999999999996 667777776653
No 39
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=62.73 E-value=3.2 Score=33.89 Aligned_cols=43 Identities=21% Similarity=0.370 Sum_probs=36.5
Q ss_pred cccccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhhh
Q psy2450 78 KQQIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYTC 121 (254)
Q Consensus 78 ~~~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~~ 121 (254)
..+--.+...|.-|.|=|.+.-+|.-|.+ +..||.-++.++..
T Consensus 48 p~lPGlGqhYCieCaryf~t~~aL~~Hkk-gkvHkRR~KelRev 90 (126)
T COG5112 48 PELPGLGQHYCIECARYFITEKALMEHKK-GKVHKRRAKELREV 90 (126)
T ss_pred CCCCCCceeeeehhHHHHHHHHHHHHHhc-cchhHHHHHHHhcC
Confidence 33455678999999999999999999997 89999999988854
No 40
>KOG2785|consensus
Probab=62.43 E-value=4.1 Score=39.70 Aligned_cols=35 Identities=26% Similarity=0.421 Sum_probs=31.2
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHHhhhhhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHKSNLKMWYT 120 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~~ 120 (254)
-..|.+|.++|.+..+-.+|.. |.-|+.|+.++.+
T Consensus 68 ~~~c~~c~k~~~s~~a~~~hl~-Sk~h~~~~~~~~r 102 (390)
T KOG2785|consen 68 VVYCEACNKSFASPKAHENHLK-SKKHVENLSNHQR 102 (390)
T ss_pred ceehHHhhccccChhhHHHHHH-Hhhcchhhhhhhc
Confidence 3589999999999888899996 9999999999775
No 41
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=58.22 E-value=7.6 Score=34.60 Aligned_cols=55 Identities=25% Similarity=0.331 Sum_probs=37.2
Q ss_pred hhhhhccCCCCchhhhccccccccccccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhh
Q psy2450 55 SLVAAYESDEEPEVQEETVSGEEKQQIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMW 118 (254)
Q Consensus 55 ~l~~~y~~~sd~e~~~~~~~~~e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~ 118 (254)
-++++||-|-..|.- -.--|.+++.|+||.-.--+.-...+|.. -.-|+.|+...
T Consensus 31 ~~L~~~gqDl~dDPy--------l~knh~Gk~vC~LC~T~H~~e~Sy~~H~~-GKKH~~n~~rr 85 (222)
T COG5246 31 LLLEAYGQDLMDDPY--------LSKNHTGKYVCLLCKTKHLTEMSYVKHRE-GKKHKENSSRR 85 (222)
T ss_pred HHHHhcCcccccCcc--------hhhcCCCcEEeeeeccccccHHHHHHhhc-cchhhhhHHHH
Confidence 456778844432211 11136789999999999888888888875 45677777644
No 42
>KOG3032|consensus
Probab=52.09 E-value=14 Score=34.00 Aligned_cols=38 Identities=16% Similarity=0.332 Sum_probs=30.2
Q ss_pred cccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhhh
Q psy2450 80 QIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMWY 119 (254)
Q Consensus 80 ~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~~ 119 (254)
|--.+.++|++|.--.+ .-.+.-|+ .|.-|+.++..++
T Consensus 30 yn~sgql~C~vCn~piK-p~lW~vHv-nsKkHre~id~lK 67 (264)
T KOG3032|consen 30 YNESGQLVCRVCNVPIK-PSLWDVHV-NSKKHREAIDSLK 67 (264)
T ss_pred cCCCCCeeEEEecCccc-HHHHHHHh-ccHHHHHHHHHHH
Confidence 33457899999998888 44456688 4999999999998
No 43
>PHA00732 hypothetical protein
Probab=50.24 E-value=11 Score=28.71 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=19.1
Q ss_pred ccccccccCCCCHHHHHhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~ 106 (254)
..|..|.+.|.+...|..|++
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r 22 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHAR 22 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhh
Confidence 369999999999999999986
No 44
>KOG3576|consensus
Probab=43.88 E-value=9 Score=34.87 Aligned_cols=31 Identities=23% Similarity=0.579 Sum_probs=26.1
Q ss_pred cccccccccCccccccccCCCCHHHHHhhhh
Q psy2450 76 EEKQQIDWDKLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 76 ~e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
...+-.|-+.++|-+|...|.-.-.|++|.+
T Consensus 108 t~gsssd~d~ftCrvCgK~F~lQRmlnrh~k 138 (267)
T KOG3576|consen 108 TIGSSSDQDSFTCRVCGKKFGLQRMLNRHLK 138 (267)
T ss_pred cccCCCCCCeeeeehhhhhhhHHHHHHHHhh
Confidence 3445567789999999999998899999987
No 45
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=42.84 E-value=8.1 Score=26.82 Aligned_cols=11 Identities=27% Similarity=0.963 Sum_probs=6.3
Q ss_pred cccccccCCCC
Q psy2450 87 ACLICKRQFNS 97 (254)
Q Consensus 87 ~ClLC~RqF~s 97 (254)
.|.||.|-|..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 99999999974
No 46
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=42.10 E-value=18 Score=31.53 Aligned_cols=32 Identities=31% Similarity=0.563 Sum_probs=27.2
Q ss_pred ccccccccCCCCHHHHHhhhhhhHHHHhhhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQLSELHKSNLKMW 118 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~ 118 (254)
++|-+|+=.--..+.+..|.. |..|++-|+-+
T Consensus 1 F~Cs~CKfrtf~~~ei~~Hle-S~~H~E~~~~i 32 (165)
T PF04988_consen 1 FTCSFCKFRTFEEKEIEKHLE-SKFHKETLKYI 32 (165)
T ss_pred CccceeeeecccHHHHHHHHc-cchHHHHHHHH
Confidence 489999966556788999996 99999999887
No 47
>PF15337 Vasculin: Vascular protein family Vasculin-like 1
Probab=40.31 E-value=16 Score=29.16 Aligned_cols=14 Identities=36% Similarity=0.835 Sum_probs=11.6
Q ss_pred HHHHHHHHcCCCCC
Q psy2450 185 VGNKLLQKMGWTQG 198 (254)
Q Consensus 185 ~G~kmL~kMGW~~G 198 (254)
.-++||+.|||.+-
T Consensus 11 aEhRLLk~MGWqEy 24 (97)
T PF15337_consen 11 AEHRLLKAMGWQEY 24 (97)
T ss_pred HHHHHHHHhccccc
Confidence 35789999999985
No 48
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=39.21 E-value=23 Score=24.49 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=19.9
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHHh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHKS 113 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk~ 113 (254)
.++|..|... .+...|..|.. +.|..
T Consensus 2 ~f~CP~C~~~-~~~~~L~~H~~--~~H~~ 27 (54)
T PF05605_consen 2 SFTCPYCGKG-FSESSLVEHCE--DEHRS 27 (54)
T ss_pred CcCCCCCCCc-cCHHHHHHHHH--hHCcC
Confidence 5789999995 45788999986 56655
No 49
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=36.12 E-value=15 Score=31.16 Aligned_cols=28 Identities=32% Similarity=0.497 Sum_probs=22.8
Q ss_pred cccccccccCccccccccCCCCHHHHHhhhh
Q psy2450 76 EEKQQIDWDKLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 76 ~e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
.-.+-|..+-++||-|.+.|+| |.+|..
T Consensus 67 ~~kKSVtpD~IicLEDGkkfKS---LKRHL~ 94 (148)
T COG4957 67 PIKKSVTPDYIICLEDGKKFKS---LKRHLT 94 (148)
T ss_pred CcccccCCCeEEEeccCcchHH---HHHHHh
Confidence 3556677789999999999997 778864
No 50
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=33.51 E-value=31 Score=20.80 Aligned_cols=20 Identities=20% Similarity=0.742 Sum_probs=16.5
Q ss_pred ccccccccCCCCHHHHHhhhh
Q psy2450 86 LACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 86 l~ClLC~RqF~s~e~L~kH~~ 106 (254)
..|.+|.+.+ +...++.|.-
T Consensus 2 v~CPiC~~~v-~~~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREV-PENLINSHLD 21 (26)
T ss_pred CcCCCCcCcc-cHHHHHHHHH
Confidence 4799999999 5678888875
No 51
>PHA00733 hypothetical protein
Probab=33.11 E-value=30 Score=28.46 Aligned_cols=22 Identities=23% Similarity=0.563 Sum_probs=18.3
Q ss_pred CccccccccCCCCHHHHHhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
...|..|.+.|.....|.+|+.
T Consensus 99 ~~~C~~CgK~F~~~~sL~~H~~ 120 (128)
T PHA00733 99 SKVCPVCGKEFRNTDSTLDHVC 120 (128)
T ss_pred CccCCCCCCccCCHHHHHHHHH
Confidence 3689999999988888888874
No 52
>KOG4173|consensus
Probab=31.18 E-value=22 Score=32.38 Aligned_cols=40 Identities=28% Similarity=0.464 Sum_probs=31.3
Q ss_pred ccccccccCccccccccCCCCHHHHHhhhhhhHHHHhhhhhh
Q psy2450 77 EKQQIDWDKLACLICKRQFNSKDILKKHTQLSELHKSNLKMW 118 (254)
Q Consensus 77 e~~~~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~~ 118 (254)
|..|--...+.|..|+|.|++--.|.-|+ ++.|..=.+.+
T Consensus 98 E~hY~~~h~~sCs~C~r~~Pt~hLLd~HI--~E~HDs~Fqa~ 137 (253)
T KOG4173|consen 98 EHHYHTLHGNSCSFCKRAFPTGHLLDAHI--LEWHDSLFQAL 137 (253)
T ss_pred HHhhhhcccchhHHHHHhCCchhhhhHHH--HHHHHHHHHHH
Confidence 55666667889999999999988889998 47887755443
No 53
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.87 E-value=26 Score=38.97 Aligned_cols=18 Identities=22% Similarity=0.625 Sum_probs=14.5
Q ss_pred ccCccccccccCCCCHHH
Q psy2450 83 WDKLACLICKRQFNSKDI 100 (254)
Q Consensus 83 ~~kl~ClLC~RqF~s~e~ 100 (254)
-...+|.||.|.|.+.+.
T Consensus 675 ~~~~~C~LC~R~f~~eee 692 (1311)
T TIGR00606 675 ENQSCCPVCQRVFQTEAE 692 (1311)
T ss_pred ccCCcCCCCCCCCCChhH
Confidence 356799999999987554
No 54
>KOG1074|consensus
Probab=26.83 E-value=32 Score=37.03 Aligned_cols=38 Identities=26% Similarity=0.447 Sum_probs=29.2
Q ss_pred ccCccccccccCCCCHHHHHhhhhh--------------hHHHHhhhhhhhh
Q psy2450 83 WDKLACLICKRQFNSKDILKKHTQL--------------SELHKSNLKMWYT 120 (254)
Q Consensus 83 ~~kl~ClLC~RqF~s~e~L~kH~~~--------------S~LHk~NL~~~~~ 120 (254)
.++-.|..|.++|.+-.+|.+|++. -.+-+-|||.+..
T Consensus 877 nn~h~C~vCgk~FsSSsALqiH~rTHtg~KPF~C~fC~~aFttrgnLKvHMg 928 (958)
T KOG1074|consen 877 NNAHVCNVCGKQFSSSAALEIHMRTHTGPKPFFCHFCEEAFTTRGNLKVHMG 928 (958)
T ss_pred cchhhhccchhcccchHHHHHhhhcCCCCCCccchhhhhhhhhhhhhhhhhc
Confidence 3578999999999999999999872 2445666766653
No 55
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=25.72 E-value=38 Score=23.76 Aligned_cols=29 Identities=24% Similarity=0.463 Sum_probs=21.8
Q ss_pred ccccCccccccccCCCCHHHHHhhhhhhHHHHh
Q psy2450 81 IDWDKLACLICKRQFNSKDILKKHTQLSELHKS 113 (254)
Q Consensus 81 ~D~~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~ 113 (254)
+|...-.|-.|+-.|.+ |..|+. |.-|+.
T Consensus 1 ~~~k~GYCE~Cr~kfd~---l~~Hi~-s~~Hr~ 29 (49)
T smart00586 1 EEKKPGYCENCREKYDD---LETHLL-SEKHRR 29 (49)
T ss_pred CCCCCcccccHhHHHhh---HHHHhc-cHHHHH
Confidence 35677899999999875 666775 777765
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=24.20 E-value=36 Score=24.91 Aligned_cols=33 Identities=15% Similarity=0.132 Sum_probs=27.8
Q ss_pred CccccccccCCCCHHHHHhhhhhhHHHHhhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQLSELHKSNLKM 117 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~~S~LHk~NL~~ 117 (254)
-+-|.-|.--|...-...+|+..|-+|+.|--+
T Consensus 17 ~lrCPRC~~~FR~~K~Y~RHVNKaH~~~~~r~k 49 (65)
T COG4049 17 FLRCPRCGMVFRRRKDYIRHVNKAHGWLFGRGK 49 (65)
T ss_pred eeeCCchhHHHHHhHHHHHHhhHHhhhhhcCCc
Confidence 367999999998888899999999999886444
No 57
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=23.89 E-value=56 Score=22.83 Aligned_cols=26 Identities=31% Similarity=0.612 Sum_probs=20.6
Q ss_pred cCccccccccCCCCHHHHHhhhhhhHHHHh
Q psy2450 84 DKLACLICKRQFNSKDILKKHTQLSELHKS 113 (254)
Q Consensus 84 ~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~ 113 (254)
..-.|-.|+-.|.+ |..|+. |.-|+.
T Consensus 4 k~GYCE~C~~ky~~---l~~Hi~-s~~Hr~ 29 (49)
T PF07535_consen 4 KPGYCENCRVKYDD---LEEHIQ-SEKHRK 29 (49)
T ss_pred CCccCccccchhhh---HHHHhC-CHHHHH
Confidence 45679999999975 788885 887876
No 58
>KOG1146|consensus
Probab=23.84 E-value=42 Score=37.78 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=24.4
Q ss_pred cCccccccccCCCCHHHHHhhhhhhHHHHh
Q psy2450 84 DKLACLICKRQFNSKDILKKHTQLSELHKS 113 (254)
Q Consensus 84 ~kl~ClLC~RqF~s~e~L~kH~~~S~LHk~ 113 (254)
...+|+.|.++|.+.+.|.+|.+ |.+|+.
T Consensus 1327 ~~~~c~~c~~~~~~~~alqihm~-~~~~~~ 1355 (1406)
T KOG1146|consen 1327 CTYHCLACEVLLSGREALQIHMR-SSAHRR 1355 (1406)
T ss_pred ccccchHHHhhcchhHHHHHHHH-Hhhhcc
Confidence 34459999999999999999997 677765
No 59
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=22.75 E-value=26 Score=20.71 Aligned_cols=18 Identities=17% Similarity=0.492 Sum_probs=13.9
Q ss_pred cccccCccccccccCCCC
Q psy2450 80 QIDWDKLACLICKRQFNS 97 (254)
Q Consensus 80 ~~D~~kl~ClLC~RqF~s 97 (254)
++......|..|.+.|.+
T Consensus 9 H~~~k~~~C~~C~k~F~~ 26 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKSFSN 26 (26)
T ss_dssp HSSSSSEEESSSSEEESS
T ss_pred cCCCCCCCCCCCcCeeCc
Confidence 455567899999999863
No 60
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=22.39 E-value=64 Score=21.16 Aligned_cols=32 Identities=28% Similarity=0.511 Sum_probs=17.5
Q ss_pred CccccccccCCC-CHHHH-HhhhhhhHHHHhhhhh
Q psy2450 85 KLACLICKRQFN-SKDIL-KKHTQLSELHKSNLKM 117 (254)
Q Consensus 85 kl~ClLC~RqF~-s~e~L-~kH~~~S~LHk~NL~~ 117 (254)
+-.|.-|..-|. +.-.. ..|++ +.-|+.|.+.
T Consensus 3 ryyCdyC~~~~~~d~~~~Rk~H~~-G~kH~~nv~~ 36 (38)
T PF06220_consen 3 RYYCDYCKKYLTHDSPSIRKQHER-GWKHKENVKR 36 (38)
T ss_dssp S-B-TTT--B-S--SHHHHHHHT---THHHHHHHH
T ss_pred CeecccccceecCCChHHHHHhhc-cHHHHHHHHH
Confidence 567999999994 43334 66775 7889999875
No 61
>PHA00733 hypothetical protein
Probab=20.82 E-value=67 Score=26.36 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=20.2
Q ss_pred CccccccccCCCCHHHHHhhhh
Q psy2450 85 KLACLICKRQFNSKDILKKHTQ 106 (254)
Q Consensus 85 kl~ClLC~RqF~s~e~L~kH~~ 106 (254)
...|..|.+.|.+...|..|++
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r 94 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIR 94 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHh
Confidence 4789999999999999999986
Done!