Query 012405
Match_columns 464
No_of_seqs 258 out of 1136
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 02:17:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012405.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012405hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0704 ADP-ribosylation facto 100.0 1.5E-95 3E-100 728.7 21.1 374 3-458 6-386 (386)
2 COG5347 GTPase-activating prot 100.0 1.6E-36 3.4E-41 305.6 10.4 119 3-121 7-126 (319)
3 KOG0706 Predicted GTPase-activ 100.0 6E-36 1.3E-40 308.0 9.8 114 3-117 10-123 (454)
4 PLN03114 ADP-ribosylation fact 100.0 2E-35 4.4E-40 298.4 11.2 115 4-118 10-124 (395)
5 PF01412 ArfGap: Putative GTPa 100.0 2E-34 4.4E-39 251.7 9.0 114 5-122 2-115 (116)
6 KOG0703 Predicted GTPase-activ 100.0 2.7E-34 5.8E-39 284.4 9.2 115 3-124 12-127 (287)
7 smart00105 ArfGap Putative GTP 100.0 3.5E-33 7.6E-38 242.8 9.7 107 14-123 1-107 (112)
8 PLN03119 putative ADP-ribosyla 99.9 3.3E-28 7.1E-33 256.8 10.6 114 3-122 10-123 (648)
9 PLN03131 hypothetical protein; 99.9 3.6E-28 7.7E-33 258.2 10.3 114 3-122 10-123 (705)
10 KOG0705 GTPase-activating prot 99.8 1.8E-21 3.9E-26 206.0 7.2 83 4-86 501-583 (749)
11 KOG0521 Putative GTPase activa 99.8 1.7E-19 3.8E-24 200.0 2.6 83 7-89 417-499 (785)
12 KOG0818 GTPase-activating prot 99.6 2E-16 4.3E-21 165.9 3.3 108 11-122 3-118 (669)
13 KOG1117 Rho- and Arf-GTPase ac 99.5 2.5E-15 5.4E-20 164.8 3.0 82 9-90 291-374 (1186)
14 KOG0702 Predicted GTPase-activ 99.3 9.8E-13 2.1E-17 138.4 6.7 117 4-124 13-130 (524)
15 KOG0521 Putative GTPase activa 86.1 0.17 3.7E-06 58.0 -0.9 69 12-82 626-695 (785)
16 PRK00085 recO DNA repair prote 82.7 0.81 1.8E-05 44.3 2.2 40 5-44 138-178 (247)
17 KOG0704 ADP-ribosylation facto 78.4 2.3 5E-05 44.9 3.9 24 258-281 247-278 (386)
18 TIGR00613 reco DNA repair prot 76.3 2.1 4.5E-05 41.3 2.7 40 6-45 137-177 (241)
19 PRK12495 hypothetical protein; 75.3 2.2 4.8E-05 42.4 2.6 28 14-45 40-67 (226)
20 COG1997 RPL43A Ribosomal prote 70.1 4.4 9.6E-05 35.1 2.9 41 3-45 21-62 (89)
21 PF00643 zf-B_box: B-box zinc 66.7 5.6 0.00012 28.4 2.5 34 15-48 2-36 (42)
22 COG1381 RecO Recombinational D 64.7 3.7 8.1E-05 40.8 1.7 37 7-43 145-182 (251)
23 PF08271 TF_Zn_Ribbon: TFIIB z 53.1 8 0.00017 28.4 1.3 27 18-45 2-28 (43)
24 PF10764 Gin: Inhibitor of sig 51.9 8.9 0.00019 29.3 1.4 26 18-44 1-26 (46)
25 PRK11019 hypothetical protein; 49.0 7.6 0.00017 33.5 0.8 37 15-52 35-73 (88)
26 PTZ00255 60S ribosomal protein 48.4 17 0.00037 31.7 2.8 40 3-44 22-62 (90)
27 TIGR02419 C4_traR_proteo phage 44.8 9 0.0002 30.8 0.6 35 12-46 27-62 (63)
28 PF11781 RRN7: RNA polymerase 44.1 18 0.00038 26.2 1.9 27 14-43 6-32 (36)
29 PF00320 GATA: GATA zinc finge 41.9 18 0.00039 25.9 1.7 32 19-50 1-34 (36)
30 smart00401 ZnF_GATA zinc finge 41.6 23 0.00051 27.3 2.4 38 15-52 2-41 (52)
31 KOG0457 Histone acetyltransfer 39.3 25 0.00054 38.3 2.9 39 36-74 38-86 (438)
32 PF10310 DUF2413: Protein of u 37.8 16 0.00034 39.9 1.2 40 261-300 117-158 (444)
33 PF01780 Ribosomal_L37ae: Ribo 37.8 19 0.0004 31.4 1.4 40 3-44 21-61 (90)
34 PF01286 XPA_N: XPA protein N- 37.6 12 0.00027 27.0 0.3 27 17-43 4-31 (34)
35 cd07171 NR_DBD_ER DNA-binding 37.3 22 0.00047 29.9 1.7 31 15-48 2-32 (82)
36 PRK13715 conjugal transfer pro 35.6 15 0.00032 30.5 0.5 34 16-49 34-68 (73)
37 COG1734 DksA DnaK suppressor p 35.5 12 0.00025 34.0 -0.2 31 17-47 81-112 (120)
38 PF12760 Zn_Tnp_IS1595: Transp 34.9 44 0.00096 24.8 2.9 39 3-43 6-44 (46)
39 cd06968 NR_DBD_ROR DNA-binding 34.0 26 0.00056 30.3 1.7 31 15-48 4-34 (95)
40 PF07282 OrfB_Zn_ribbon: Putat 33.8 24 0.00052 27.8 1.4 28 15-44 27-54 (69)
41 PF14803 Nudix_N_2: Nudix N-te 33.1 19 0.00041 25.9 0.6 30 17-47 1-33 (34)
42 cd07173 NR_DBD_AR DNA-binding 32.8 26 0.00057 29.5 1.5 32 14-48 1-32 (82)
43 cd07170 NR_DBD_ERR DNA-binding 32.1 26 0.00057 30.4 1.5 30 16-48 4-33 (97)
44 PF01258 zf-dskA_traR: Prokary 31.3 8.3 0.00018 27.3 -1.5 29 18-46 5-34 (36)
45 PTZ00218 40S ribosomal protein 30.6 21 0.00044 28.5 0.5 39 14-57 14-52 (54)
46 cd07160 NR_DBD_LXR DNA-binding 30.1 34 0.00073 30.1 1.8 31 15-48 17-47 (101)
47 cd06966 NR_DBD_CAR DNA-binding 28.9 27 0.00059 30.1 1.0 29 17-48 1-29 (94)
48 PRK00423 tfb transcription ini 28.7 37 0.00079 34.9 2.1 33 13-46 8-40 (310)
49 KOG3507 DNA-directed RNA polym 28.6 28 0.0006 28.4 0.9 22 18-43 22-44 (62)
50 cd07169 NR_DBD_GCNF_like DNA-b 28.3 35 0.00075 29.2 1.6 32 14-48 4-35 (90)
51 COG4647 AcxC Acetone carboxyla 27.9 25 0.00054 32.9 0.6 35 3-47 97-131 (165)
52 COG2174 RPL34A Ribosomal prote 27.8 40 0.00087 29.5 1.8 34 11-44 29-79 (93)
53 KOG3362 Predicted BBOX Zn-fing 27.1 27 0.00058 33.0 0.7 34 14-48 116-150 (156)
54 COG0675 Transposase and inacti 26.9 28 0.00061 34.0 0.8 22 16-44 309-330 (364)
55 TIGR00382 clpX endopeptidase C 25.9 34 0.00073 36.9 1.3 30 15-44 6-37 (413)
56 TIGR02890 spore_yteA sporulati 25.5 31 0.00066 32.6 0.8 34 14-48 84-119 (159)
57 COG2158 Uncharacterized protei 24.6 30 0.00065 31.1 0.5 25 28-52 52-78 (112)
58 PRK10778 dksA RNA polymerase-b 24.3 45 0.00097 31.3 1.6 39 12-50 107-146 (151)
59 PHA00080 DksA-like zinc finger 24.1 40 0.00086 27.9 1.1 34 13-47 28-63 (72)
60 TIGR00280 L37a ribosomal prote 23.8 73 0.0016 27.9 2.7 40 3-44 21-61 (91)
61 PF14471 DUF4428: Domain of un 23.6 28 0.00061 27.0 0.1 44 18-62 1-46 (51)
62 cd07161 NR_DBD_EcR DNA-binding 23.5 49 0.0011 28.4 1.6 29 17-48 2-30 (91)
63 cd07163 NR_DBD_TLX DNA-binding 23.2 38 0.00082 29.1 0.9 30 16-48 6-35 (92)
64 PRK03976 rpl37ae 50S ribosomal 22.7 67 0.0014 28.0 2.3 40 3-44 22-62 (90)
65 cd07162 NR_DBD_PXR DNA-binding 22.7 53 0.0011 27.8 1.6 28 18-48 1-28 (87)
66 PF02993 MCPVI: Minor capsid p 22.5 29 0.00062 35.1 0.0 65 262-328 32-96 (238)
67 cd06956 NR_DBD_RXR DNA-binding 22.1 58 0.0013 26.9 1.7 28 18-48 2-29 (77)
68 PHA02942 putative transposase; 21.8 45 0.00097 35.5 1.2 26 16-44 325-350 (383)
69 PF06689 zf-C4_ClpX: ClpX C4-t 21.5 79 0.0017 23.3 2.1 28 17-44 2-32 (41)
70 cd06955 NR_DBD_VDR DNA-binding 21.1 45 0.00097 29.6 0.9 30 16-48 6-35 (107)
71 cd07168 NR_DBD_DHR4_like DNA-b 20.8 60 0.0013 27.7 1.6 31 15-48 5-35 (90)
72 cd07156 NR_DBD_VDR_like The DN 20.7 61 0.0013 26.4 1.6 27 19-48 1-27 (72)
73 cd07172 NR_DBD_GR_PR DNA-bindi 20.2 63 0.0014 26.9 1.6 29 17-48 3-31 (78)
74 cd07158 NR_DBD_Ppar_like The D 20.2 57 0.0012 26.5 1.3 27 19-48 1-27 (73)
No 1
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=100.00 E-value=1.5e-95 Score=728.74 Aligned_cols=374 Identities=51% Similarity=0.873 Sum_probs=316.9
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
+||+|++|+...+|++||||+++|||||||+|||||||+|+|+||+||||||||||||||+|+++||++|++|||+++++
T Consensus 6 trr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~e 85 (386)
T KOG0704|consen 6 TRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFRE 85 (386)
T ss_pred HHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHH
Confidence 77888888888899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCCC-CcccccCChhHHHHHHHHHHHHcCCCCCCCchhhhhcccCCCCCCCCCcccCCCCCcCCCCCCCCCCC
Q 012405 83 FLSQYGIPKET-DIVTKYNTNAASIYRDRIQAIAEGRPWRDPPVVKETLNAGKSSSRPPLAQSASVGGVGRNGNYGNHGG 161 (464)
Q Consensus 83 f~ea~~~~~e~-~I~~KY~s~aa~~YrekL~a~~eGr~w~~pP~~~E~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~ 161 (464)
||+.+++.++. +|++||++++|++||+||++++|||+|.+||+++|..++ +..+|. .
T Consensus 86 FL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w~d~~~~k~~~p~--~syt~a---~----------------- 143 (386)
T KOG0704|consen 86 FLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREWNDPPYLKEDNPA--QSYTSA---A----------------- 143 (386)
T ss_pred HHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcccccccccccCcc--cccccC---C-----------------
Confidence 99998866655 999999999999999999999999999999999998753 222320 0
Q ss_pred CCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCchhhhhHHHHHHHhhhchhhhhHhhhhhccCCCCCCCCC
Q 012405 162 WDSWDNDDFRSSNDMRRNQSVSDFRGGSGGMGGMPASRSKSTEDIYTRAELEASAANKEGFFSRKIAENEARPEGLPPSQ 241 (464)
Q Consensus 162 ~~~w~~~~~~~~~~~~r~~s~~~~~~~~~~~~~~p~~~s~s~~~~y~~~q~~~s~~~~e~yFa~~g~~NasrPe~lpPSQ 241 (464)
+ ..+.++..+|+..|++++++.+|.||++++.+|++|||+|||||
T Consensus 144 ----------------------------------~-~~~~ss~~~~~~sq~~~~~~~ke~~fa~~~~~n~srpd~lppsQ 188 (386)
T KOG0704|consen 144 ----------------------------------Q-LGSKSSETIYTISQLSNSAAGKESYFAKRLSENQSRPDGLPPSQ 188 (386)
T ss_pred ----------------------------------C-cCCCcCCcccccccchhhhcchhHHHHHhcccccCCCCCCCccc
Confidence 0 11112223456667788889999999999999999999999999
Q ss_pred CCcccccCCCCCCCCCCCCCccchhHHHhhchhhhHhhHHHHHHHHHHHhhhhhhhhhhhhccCccccccccceeeeeee
Q 012405 242 GGKYVGFGSTPPPTQRNTNSQGDVLSAVSQGFGRISLVAASAAQSAATVVQAGTREFTSKVREGGYDHKVNETVNVVTAK 321 (464)
Q Consensus 242 GGKY~GFGntp~p~~~~~~~~~d~~ssls~Gwg~fS~~a~~aa~~a~~~~~~~~~~~~~kv~eg~~~~~v~~~v~~~a~K 321 (464)
||||+|||+|+.|||+... ++|+|++|+.||++||++|++||+ |++.++..+. ||||| |++.|++.|++||.|
T Consensus 189 ggkY~GFGst~~~ppqs~~-~~~~~s~ls~Gws~~s~~as~~a~----~~~~~~~~~s-kvkeg-l~~~~s~~v~~va~k 261 (386)
T KOG0704|consen 189 GGKYQGFGSTNAPPPQSNS-QDDAMSVLSSGWSRLSTGASSAAS----VGQTATQKAS-KVKEG-LDDFVSDPVGTVASK 261 (386)
T ss_pred CCcccccCCCCCCCCcccc-ccchhhhhccccccccchhhhhhh----hhhhhhhhhh-hhhhh-hhhhcccchhhhhhh
Confidence 9999999999888886432 338999999999999999998775 7777777776 99999 999999999999999
Q ss_pred ccccccccccchhhhHHhhhhhhhhhhccCCCCcccccccCCCCcccccccCCCCCCCCCCCCCC-CCCCCCCCC-CCCC
Q 012405 322 TSEIGQRTWGIMKGVMAMASQKVEEYTKEGWNNDNWQRNESESNGYYQEFNHGNKGQDSPAGGGQ-YSAGHHNSY-GSSS 399 (464)
Q Consensus 322 ~~e~g~~gw~~~~~~~~~~~~k~e~~~~~~~~~~~~~~~~~~~~~~yq~~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~ 399 (464)
|+|||+|||++|+ ++++|++|++ |+++..+++|||.+.++|..=|+..++.+ ++-+|.+++ ++++
T Consensus 262 ~t~vG~r~W~~ls---~~~sq~~e~f----------q~~~s~g~~~~qn~~~~n~~sn~~~g~~q~~~~~~~~s~~~s~s 328 (386)
T KOG0704|consen 262 VTEVGTRGWGLLS---AAVSQSVEDF----------QDSESVGGPYYQNSGQGNFSSNSKRGGWQFSSKGHEKSSLPSNS 328 (386)
T ss_pred cccccccchhhhH---Hhhccccccc----------cccCccCCccccccccccccccccccccccccccccccCCCCcc
Confidence 9999999999887 8899999988 78888899999999998876566655555 345666555 8999
Q ss_pred CCcCCcCCCC-CCCCCCCC-CCCCCCCcccc--CCCCCCccccccccccccccCCCCCCCCcc
Q 012405 400 WDDWDQKDKK-EDTPKGTG-SGNNDAWAGWD--DAKDDGYDNFYQSASDKKALGHNGKSDATW 458 (464)
Q Consensus 400 w~~w~~~~~~-~~~~~~~~-~~~~~~w~g~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w 458 (464)
|+.|...+.. ....++++ ..++.+|+||| ++++| +-+|+.+++| .|+|+.|.+|
T Consensus 329 ~s~~~~n~~~~~s~~~gta~~~~ds~~~g~e~~~~k~~--~~~~~~a~dk---s~~g~~d~aw 386 (386)
T KOG0704|consen 329 FSCFTENDQNSSSDSKGTASADDDSGWSGFEASDAKDD--ETSYQNAPDK---SHDGWDDDAW 386 (386)
T ss_pred ccccccCcccCcccccCccccCCCCcccccccCCCCcc--cccccccccc---ccCCccccCC
Confidence 9999997544 22333554 44456799999 77777 4588888877 4999999999
No 2
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=100.00 E-value=1.6e-36 Score=305.60 Aligned_cols=119 Identities=39% Similarity=0.721 Sum_probs=111.2
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
.+++|..|++.++|++||||++++|+|||++||||||++||||||+|||||||||||+||.|+++||++|+.+||.++++
T Consensus 7 ~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~ 86 (319)
T COG5347 7 DRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANR 86 (319)
T ss_pred HHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhh
Confidence 57888889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCC-CCCcccccCChhHHHHHHHHHHHHcCCCCC
Q 012405 83 FLSQYGIPK-ETDIVTKYNTNAASIYRDRIQAIAEGRPWR 121 (464)
Q Consensus 83 f~ea~~~~~-e~~I~~KY~s~aa~~YrekL~a~~eGr~w~ 121 (464)
||+.++... ..+|+.||++.+++.|++++..+.....|.
T Consensus 87 ~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~ 126 (319)
T COG5347 87 FYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDS 126 (319)
T ss_pred HhccCCCcccccccccccCHHHHHHHHHHHHHhhhccccc
Confidence 999988774 489999999999999998887777766663
No 3
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=6e-36 Score=307.96 Aligned_cols=114 Identities=46% Similarity=0.927 Sum_probs=108.4
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
.-++++.|+.+++||+||||++++|.|+||+||||||++|+++||.||||||||||+.||.|+..||++|+.|||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCCCCcccccCChhHHHHHHHHHHHHcC
Q 012405 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEG 117 (464)
Q Consensus 83 f~ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eG 117 (464)
||++|+... ..++.||++++|..||++|..++..
T Consensus 90 FFkqhg~~t-~d~~aKY~SraA~~Yr~kl~~lv~k 123 (454)
T KOG0706|consen 90 FFKQHGCVT-LDANAKYNSRAAKLYREKLKKLVQK 123 (454)
T ss_pred HHHHcCCcc-hhhhhhhccHHHHHHHHHHHHHHHH
Confidence 999998864 4899999999999999999888754
No 4
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=2e-35 Score=298.37 Aligned_cols=115 Identities=45% Similarity=0.877 Sum_probs=110.2
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 012405 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (464)
Q Consensus 4 ~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f 83 (464)
.++|++|+..|+|++||||++++|+|||++||||||++|+|+||.||+||||||||+||.|++++|++|+.+||.++|+|
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~f 89 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVF 89 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHH
Confidence 45699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCCCCCCCCcccccCChhHHHHHHHHHHHHcCC
Q 012405 84 LSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGR 118 (464)
Q Consensus 84 ~ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eGr 118 (464)
|++|++.....|++||++++|..||++|.++++..
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~ 124 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKS 124 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHh
Confidence 99999887788999999999999999999988764
No 5
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=2e-34 Score=251.69 Aligned_cols=114 Identities=41% Similarity=0.804 Sum_probs=91.0
Q ss_pred HHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHH
Q 012405 5 RRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFL 84 (464)
Q Consensus 5 r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f~ 84 (464)
++|+.|++.|+|++||||++++|+|||++||||||++|+++||.||+|||+||||+||.|+++||++|+.+||.++|+||
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCCCCcccccCChhHHHHHHHHHHHHcCCCCCC
Q 012405 85 SQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (464)
Q Consensus 85 ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eGr~w~~ 122 (464)
+++ .+....+ -.......|+++|+++|+.+.|..
T Consensus 82 e~~-~~~~~~~---~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EAN-SPPPKKP---PPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTT-STTTTTH---CTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcC-CCCCCCC---CCCCcHHHHHHHHHHHHHhhhhcc
Confidence 987 2111111 123455688999999999999974
No 6
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-34 Score=284.45 Aligned_cols=115 Identities=40% Similarity=0.761 Sum_probs=101.4
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
.+++|++|++.|+|++|+||+++.|+|||+++|||||+.|+||||.||||||+||||+||.|++|||+.|+..||.++|.
T Consensus 12 ~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~ 91 (287)
T KOG0703|consen 12 NKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANS 91 (287)
T ss_pred HHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhh
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhCCCCCCCCcccccCChhH-HHHHHHHHHHHcCCCCCCCc
Q 012405 83 FLSQYGIPKETDIVTKYNTNAA-SIYRDRIQAIAEGRPWRDPP 124 (464)
Q Consensus 83 f~ea~~~~~e~~I~~KY~s~aa-~~YrekL~a~~eGr~w~~pP 124 (464)
|||+..+. . |...-. .....+|++|||-++|.+++
T Consensus 92 ~~ea~~p~-~------~~~p~~d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 92 YYEAKLPD-P------FRRPGPDDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hccccCCc-c------ccCCChHHHHHHHHHHHHhhhhhccch
Confidence 99987332 1 111111 14566899999999999875
No 7
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=3.5e-33 Score=242.77 Aligned_cols=107 Identities=43% Similarity=0.779 Sum_probs=95.0
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhCCCCCCC
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIPKET 93 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f~ea~~~~~e~ 93 (464)
|+|++||||++++|+|||++||||||++|+|+||.||+|||+||||+||+|++++|++|+.+||.++|+||+++..+...
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999988764322
Q ss_pred CcccccCChhHHHHHHHHHHHHcCCCCCCC
Q 012405 94 DIVTKYNTNAASIYRDRIQAIAEGRPWRDP 123 (464)
Q Consensus 94 ~I~~KY~s~aa~~YrekL~a~~eGr~w~~p 123 (464)
... .......|+.+|+.+|+.+.|.++
T Consensus 81 ~~~---~~~~~~~~~~fI~~KY~~k~f~~~ 107 (112)
T smart00105 81 KPP---DSDDQQKYESFIAAKYEEKLFVPP 107 (112)
T ss_pred CCC---CCchHHHHHHHHHHHHHhhhcccc
Confidence 221 122456899999999999999864
No 8
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.95 E-value=3.3e-28 Score=256.82 Aligned_cols=114 Identities=23% Similarity=0.496 Sum_probs=98.6
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
.+++|++|+++|+|++|+||++++|+|||++||||||++|+||||.|| ++||||+||+|+++||++|+.+||+++|+
T Consensus 10 nekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG---hRVKSLSLDkWT~EEVe~Mk~gGN~~AN~ 86 (648)
T PLN03119 10 NEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFT---HRVKSVSMSKFTSKEVEVLQNGGNQRARE 86 (648)
T ss_pred HHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCC---ceeeccccCCCCHHHHHHHHHhchHHHHH
Confidence 467899999999999999999999999999999999999999999998 38999999999999999999999999999
Q ss_pred HHhhCCCCCCCCcccccCChhHHHHHHHHHHHHcCCCCCC
Q 012405 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (464)
Q Consensus 83 f~ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eGr~w~~ 122 (464)
||+++.......+.. ....+..|++|+.+|+.|.|..
T Consensus 87 iyeanw~~~~~~~P~---~sD~e~lr~FIR~KYVeKRF~~ 123 (648)
T PLN03119 87 IYLKNWDHQRQRLPE---NSNAERVREFIKNVYVQKKYAG 123 (648)
T ss_pred HHHhhcccccCCCCC---CccHHHHHHHHHHHHhhhhccC
Confidence 999865433222222 1223456889999999999975
No 9
>PLN03131 hypothetical protein; Provisional
Probab=99.95 E-value=3.6e-28 Score=258.23 Aligned_cols=114 Identities=24% Similarity=0.517 Sum_probs=98.2
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
.+++|++|++.|+|++|+||++++|+|||++||||||++|+||||.|| | +||||+||.|+++||++|+.+||+++|+
T Consensus 10 nekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk~gGN~~AN~ 86 (705)
T PLN03131 10 NEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQNGGNQRARE 86 (705)
T ss_pred HHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHHHhccHHHHH
Confidence 467899999999999999999999999999999999999999999997 3 8999999999999999999999999999
Q ss_pred HHhhCCCCCCCCcccccCChhHHHHHHHHHHHHcCCCCCC
Q 012405 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (464)
Q Consensus 83 f~ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eGr~w~~ 122 (464)
||+++.......+... ......|++|+.+|+.|.|..
T Consensus 87 iyeanwd~~r~~lP~~---sd~ekrr~FIR~KYVeKRFa~ 123 (705)
T PLN03131 87 IYLKDWDQQRQRLPDN---SKVDKIREFIKDIYVDKKYAG 123 (705)
T ss_pred HHHhhcccccCCCCCC---ccHHHHHHHHHHHHhhhhhhc
Confidence 9997654332222221 223456889999999999864
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.84 E-value=1.8e-21 Score=205.98 Aligned_cols=83 Identities=45% Similarity=0.847 Sum_probs=80.2
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHH
Q 012405 4 TRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTF 83 (464)
Q Consensus 4 ~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f 83 (464)
+-.|+.|+..++|..|+||+.++|.|||+++||.||++|+||||.||.|||+||+|.||.|..|.+..|..+||+.||.+
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~v 580 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSV 580 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHH
Confidence 44688899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhh
Q 012405 84 LSQ 86 (464)
Q Consensus 84 ~ea 86 (464)
||.
T Consensus 581 WE~ 583 (749)
T KOG0705|consen 581 WEG 583 (749)
T ss_pred hhh
Confidence 994
No 11
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.76 E-value=1.7e-19 Score=200.00 Aligned_cols=83 Identities=43% Similarity=0.833 Sum_probs=80.0
Q ss_pred HHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 012405 7 LRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQ 86 (464)
Q Consensus 7 L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f~ea 86 (464)
+.++++.|+|.+|+|||++.|.|+|+++||.+|++|+|+||.||||||+||||+||.|.++.+..|+..||..+|.+|++
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred CCC
Q 012405 87 YGI 89 (464)
Q Consensus 87 ~~~ 89 (464)
...
T Consensus 497 ~l~ 499 (785)
T KOG0521|consen 497 LLP 499 (785)
T ss_pred ccc
Confidence 543
No 12
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.61 E-value=2e-16 Score=165.93 Aligned_cols=108 Identities=29% Similarity=0.510 Sum_probs=88.2
Q ss_pred hcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHHHHhhCCCC
Q 012405 11 QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNTFLSQYGIP 90 (464)
Q Consensus 11 ~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~f~ea~~~~ 90 (464)
++...-++|+||++++|.||||+-|||||.+|..+||.||.|||.||+|....|.++.|+++...-|..+|.+||.+.++
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 34456689999999999999999999999999999999999999999999999999999999999999999999976654
Q ss_pred CCC--------CcccccCChhHHHHHHHHHHHHcCCCCCC
Q 012405 91 KET--------DIVTKYNTNAASIYRDRIQAIAEGRPWRD 122 (464)
Q Consensus 91 ~e~--------~I~~KY~s~aa~~YrekL~a~~eGr~w~~ 122 (464)
... ..++|.... -.++|+++|+-..|+.
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~----K~eFIkaKy~~LtFv~ 118 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPN----KAEFIRAKYQMLAFVH 118 (669)
T ss_pred chhhhcccCCCCCcCCCCcc----HHHHHHHHHHheeeec
Confidence 311 122333322 2356777777777776
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.53 E-value=2.5e-15 Score=164.79 Aligned_cols=82 Identities=38% Similarity=0.661 Sum_probs=75.8
Q ss_pred HHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCcccceeecccC--CCCHHHHHHHHhcChHHHHHHHhh
Q 012405 9 DLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMD--SWSEIQIKKMEAGGNERLNTFLSQ 86 (464)
Q Consensus 9 ~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD--~Ws~~eL~~Mk~GGN~~an~f~ea 86 (464)
.+=....|+.|+||+++.|.|||+|++|.||-.|+|-||+||..+|+|||++|| .|+.+-|+++...||.++|+||..
T Consensus 291 riW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~ 370 (1186)
T KOG1117|consen 291 RIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAG 370 (1186)
T ss_pred HHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccccccc
Confidence 344567899999999999999999999999999999999999999999999999 799999999999999999999986
Q ss_pred CCCC
Q 012405 87 YGIP 90 (464)
Q Consensus 87 ~~~~ 90 (464)
+..+
T Consensus 371 nl~~ 374 (1186)
T KOG1117|consen 371 NLPP 374 (1186)
T ss_pred CCCC
Confidence 6544
No 14
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.35 E-value=9.8e-13 Score=138.37 Aligned_cols=117 Identities=18% Similarity=0.365 Sum_probs=97.1
Q ss_pred HHHHHHHhcCCCCCCccCCCCCCC-CceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 4 TRRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 4 ~r~L~~L~~~pgNk~CaDCGA~nP-qWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
+++||.|+++|+|++|++|....+ .|++++-|-|+|+.|+|.-|+|.. -.+||+|.|-.+++.||..++.+||+.+++
T Consensus 13 ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~k~ 91 (524)
T KOG0702|consen 13 EKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVCKE 91 (524)
T ss_pred HHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhhhh
Confidence 678999999999999999999887 999999999999999999999953 358999999999999999999999999999
Q ss_pred HHhhCCCCCCCCcccccCChhHHHHHHHHHHHHcCCCCCCCc
Q 012405 83 FLSQYGIPKETDIVTKYNTNAASIYRDRIQAIAEGRPWRDPP 124 (464)
Q Consensus 83 f~ea~~~~~e~~I~~KY~s~aa~~YrekL~a~~eGr~w~~pP 124 (464)
+|-.--.....-+.+ .+-...-|++|+.+|+++.|+.++
T Consensus 92 i~fkl~D~q~S~vPD---~rn~~~~kef~q~~y~~kr~~v~~ 130 (524)
T KOG0702|consen 92 IWFKLFDFQRSNVPD---SRNPQKVKEFQQEKYVKKRYYVPK 130 (524)
T ss_pred hhhcchhhhhccCCC---cccchhhHHHHhhhhccceeecCc
Confidence 886321111112222 233446789999999999998764
No 15
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=86.13 E-value=0.17 Score=58.02 Aligned_cols=69 Identities=14% Similarity=0.289 Sum_probs=55.5
Q ss_pred cCCCCCCccCCCC-CCCCceEeccceeEehhhhhhhccCCCcccceeecccCCCCHHHHHHHHhcChHHHHH
Q 012405 12 SQPGNKICVDCAQ-KNPQWASVSYGVFMCLECSGKHRGLGVHISFVRSVTMDSWSEIQIKKMEAGGNERLNT 82 (464)
Q Consensus 12 ~~pgNk~CaDCGA-~nPqWASv~~GIFICleCSGiHR~LGvHISfVRSvtmD~Ws~~eL~~Mk~GGN~~an~ 82 (464)
....+-.|++|.+ ..-.|+++++.+-+|..|+++|+.++.|++.++++.++...+ |.....-|+..++.
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~ 695 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHH 695 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchh
Confidence 3345778999987 577899999999999999999999999999999999988777 44444445554444
No 16
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=82.68 E-value=0.81 Score=44.29 Aligned_cols=40 Identities=25% Similarity=0.419 Sum_probs=31.4
Q ss_pred HHHHHHhcCCCCCCccCCCCCCC-CceEeccceeEehhhhh
Q 012405 5 RRLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSG 44 (464)
Q Consensus 5 r~L~~L~~~pgNk~CaDCGA~nP-qWASv~~GIFICleCSG 44 (464)
+.|..+--.|.-..|+-||.+.. .+.++..|.|+|..|..
T Consensus 138 ~lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 138 RLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred HHHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 34444555667789999998755 78899999999999973
No 17
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=78.37 E-value=2.3 Score=44.88 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=19.3
Q ss_pred CCCCccchhHHHh-h----c---hhhhHhhHH
Q 012405 258 NTNSQGDVLSAVS-Q----G---FGRISLVAA 281 (464)
Q Consensus 258 ~~~~~~d~~ssls-~----G---wg~fS~~a~ 281 (464)
.++++++||++|+ + | |++|+.+++
T Consensus 247 l~~~~s~~v~~va~k~t~vG~r~W~~ls~~~s 278 (386)
T KOG0704|consen 247 LDDFVSDPVGTVASKVTEVGTRGWGLLSAAVS 278 (386)
T ss_pred hhhhcccchhhhhhhcccccccchhhhHHhhc
Confidence 4778999999999 5 4 999995443
No 18
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=76.31 E-value=2.1 Score=41.32 Aligned_cols=40 Identities=28% Similarity=0.501 Sum_probs=31.1
Q ss_pred HHHHHhcCCCCCCccCCCCCCC-CceEeccceeEehhhhhh
Q 012405 6 RLRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECSGK 45 (464)
Q Consensus 6 ~L~~L~~~pgNk~CaDCGA~nP-qWASv~~GIFICleCSGi 45 (464)
.|..+--.|.-..|+.||...+ .+.++..|.|+|.+|...
T Consensus 137 lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 137 LLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 4444555677789999998544 678999999999999764
No 19
>PRK12495 hypothetical protein; Provisional
Probab=75.26 E-value=2.2 Score=42.42 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=23.0
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhhhh
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCSGi 45 (464)
..+..|-+||.|-|. + -|+.+|..|..+
T Consensus 40 msa~hC~~CG~PIpa---~-pG~~~Cp~CQ~~ 67 (226)
T PRK12495 40 MTNAHCDECGDPIFR---H-DGQEFCPTCQQP 67 (226)
T ss_pred cchhhcccccCcccC---C-CCeeECCCCCCc
Confidence 368999999999992 2 699999999744
No 20
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=70.05 E-value=4.4 Score=35.10 Aligned_cols=41 Identities=22% Similarity=0.656 Sum_probs=30.1
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeEehhhhhh
Q 012405 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGK 45 (464)
Q Consensus 3 a~r~L~~L-~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGi 45 (464)
.|+..++| .....--.|-.|+.+ .---+..|||.|..|--.
T Consensus 21 ~Rrrv~~ie~~~~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 21 LRRRVKEIEAQQRAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred HHHHHHHHHHHHhcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 45556665 344566789999998 455788999999999544
No 21
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=66.65 E-value=5.6 Score=28.44 Aligned_cols=34 Identities=18% Similarity=0.387 Sum_probs=28.9
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhhh-hcc
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGK-HRG 48 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSGi-HR~ 48 (464)
.+..|..|......+-..+-.++||..|... |+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3578999998878889999999999999987 987
No 22
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=64.75 E-value=3.7 Score=40.83 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=29.3
Q ss_pred HHHHhcCCCCCCccCCCCCCC-CceEeccceeEehhhh
Q 012405 7 LRDLQSQPGNKICVDCAQKNP-QWASVSYGVFMCLECS 43 (464)
Q Consensus 7 L~~L~~~pgNk~CaDCGA~nP-qWASv~~GIFICleCS 43 (464)
|..+--.|.=..|+.||.+.+ ...++..|-+||.+|+
T Consensus 145 L~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 145 LGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 333334455679999999855 6999999999999998
No 23
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=53.08 E-value=8 Score=28.39 Aligned_cols=27 Identities=22% Similarity=0.502 Sum_probs=21.0
Q ss_pred CccCCCCCCCCceEeccceeEehhhhhh
Q 012405 18 ICVDCAQKNPQWASVSYGVFMCLECSGK 45 (464)
Q Consensus 18 ~CaDCGA~nPqWASv~~GIFICleCSGi 45 (464)
+|-.|++.. .-.....|-+||..|.-+
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 699999977 455677899999999543
No 24
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=51.90 E-value=8.9 Score=29.29 Aligned_cols=26 Identities=27% Similarity=0.836 Sum_probs=20.4
Q ss_pred CccCCCCCCCCceEeccceeEehhhhh
Q 012405 18 ICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 18 ~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
+|+=|+.+.+. --.=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 58889988777 444589999999954
No 25
>PRK11019 hypothetical protein; Provisional
Probab=49.00 E-value=7.6 Score=33.51 Aligned_cols=37 Identities=19% Similarity=0.480 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCC--ceEeccceeEehhhhhhhccCCCc
Q 012405 15 GNKICVDCAQKNPQ--WASVSYGVFMCLECSGKHRGLGVH 52 (464)
Q Consensus 15 gNk~CaDCGA~nPq--WASv~~GIFICleCSGiHR~LGvH 52 (464)
.-..|.+||.+=|. +.-+ -++-.|++|...+-..+.|
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~-P~a~~Cv~Cq~~~E~~~k~ 73 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAI-PGVRLCVACQQEKDLQQAA 73 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhc-CCccccHHHHHHHHHHHhH
Confidence 45799999997553 3222 2678899999876655444
No 26
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.41 E-value=17 Score=31.66 Aligned_cols=40 Identities=20% Similarity=0.549 Sum_probs=29.8
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 3 a~r~L~~L-~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
.|+++++| ..+..--.|.-|+........+ ||+-|..|.-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~~ 62 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCKK 62 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCCC
Confidence 45666666 4556678999999877665554 9999999953
No 27
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=44.81 E-value=9 Score=30.80 Aligned_cols=35 Identities=26% Similarity=0.510 Sum_probs=23.4
Q ss_pred cCCCCCCccCCCCCCCCce-EeccceeEehhhhhhh
Q 012405 12 SQPGNKICVDCAQKNPQWA-SVSYGVFMCLECSGKH 46 (464)
Q Consensus 12 ~~pgNk~CaDCGA~nPqWA-Sv~~GIFICleCSGiH 46 (464)
..++...|.|||.+=|.=- -.--++..|.+|...+
T Consensus 27 ~~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 27 IGPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred cCCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 4456789999999755311 1223778899998654
No 28
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=44.10 E-value=18 Score=26.24 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=23.0
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhh
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCS 43 (464)
..|..|..|++. |....=|-|+|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 346679999998 888999999999994
No 29
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=41.88 E-value=18 Score=25.85 Aligned_cols=32 Identities=28% Similarity=0.726 Sum_probs=23.0
Q ss_pred ccCCCC-CCCCceEecccee-EehhhhhhhccCC
Q 012405 19 CVDCAQ-KNPQWASVSYGVF-MCLECSGKHRGLG 50 (464)
Q Consensus 19 CaDCGA-~nPqWASv~~GIF-ICleCSGiHR~LG 50 (464)
|..|+. ..|+|=....|-. ||-.|--.+|..+
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk~~ 34 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKKYG 34 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHHHS
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHHhC
Confidence 889988 4899998888888 9999987776543
No 30
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=41.56 E-value=23 Score=27.30 Aligned_cols=38 Identities=21% Similarity=0.531 Sum_probs=30.5
Q ss_pred CCCCccCCCC-CCCCceEeccce-eEehhhhhhhccCCCc
Q 012405 15 GNKICVDCAQ-KNPQWASVSYGV-FMCLECSGKHRGLGVH 52 (464)
Q Consensus 15 gNk~CaDCGA-~nPqWASv~~GI-FICleCSGiHR~LGvH 52 (464)
....|..|+. .-|+|=.-..|- +||-.|.-..+..+..
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~~ 41 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGGL 41 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCCC
Confidence 3578999997 578898888886 9999998877765543
No 31
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=39.28 E-value=25 Score=38.26 Aligned_cols=39 Identities=26% Similarity=0.490 Sum_probs=22.6
Q ss_pred eeEehhhhhhhccCCCcc-----cceeeccc----CCCCH-HHHHHHHh
Q 012405 36 VFMCLECSGKHRGLGVHI-----SFVRSVTM----DSWSE-IQIKKMEA 74 (464)
Q Consensus 36 IFICleCSGiHR~LGvHI-----SfVRSvtm----D~Ws~-~eL~~Mk~ 74 (464)
.+||+.|-..--.+|+|- -.|...+. -.|+. +||++++.
T Consensus 38 fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea 86 (438)
T KOG0457|consen 38 FDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEA 86 (438)
T ss_pred cchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHH
Confidence 479999986544555542 12333222 26876 67777764
No 32
>PF10310 DUF2413: Protein of unknown function (DUF2413); InterPro: IPR018814 This entry represents a family of proteins conserved in fungi. Their function is not known.
Probab=37.84 E-value=16 Score=39.88 Aligned_cols=40 Identities=25% Similarity=0.302 Sum_probs=29.5
Q ss_pred CccchhHHHhhch--hhhHhhHHHHHHHHHHHhhhhhhhhhh
Q 012405 261 SQGDVLSAVSQGF--GRISLVAASAAQSAATVVQAGTREFTS 300 (464)
Q Consensus 261 ~~~d~~ssls~Gw--g~fS~~a~~aa~~a~~~~~~~~~~~~~ 300 (464)
...+|.++++.|| |.+++.|+++++.|.+.+....++|++
T Consensus 117 ~~~~p~~s~ggwWsWGs~~stAss~~~~a~kqAe~~~k~i~q 158 (444)
T PF10310_consen 117 EEPDPIASSGGWWSWGSIWSTASSAAEQAMKQAEAAVKEIQQ 158 (444)
T ss_pred CCCCcccccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4668899999988 577777877777776666666666655
No 33
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=37.82 E-value=19 Score=31.39 Aligned_cols=40 Identities=23% Similarity=0.563 Sum_probs=29.0
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 3 a~r~L~~L-~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
.|+++.+| ..+...-.|.-|+.... --+..|||-|..|.-
T Consensus 21 lRK~vkkie~~q~~ky~Cp~Cgk~~v--kR~a~GIW~C~~C~~ 61 (90)
T PF01780_consen 21 LRKRVKKIEISQHAKYTCPFCGKTSV--KRVATGIWKCKKCGK 61 (90)
T ss_dssp HHHHHHHHHHHHHS-BEESSSSSSEE--EEEETTEEEETTTTE
T ss_pred HHHHHHHHHHHHhCCCcCCCCCCcee--EEeeeEEeecCCCCC
Confidence 35556665 45557789999999773 457789999999953
No 34
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=37.64 E-value=12 Score=27.03 Aligned_cols=27 Identities=15% Similarity=0.533 Sum_probs=16.4
Q ss_pred CCccCCCCC-CCCceEeccceeEehhhh
Q 012405 17 KICVDCAQK-NPQWASVSYGVFMCLECS 43 (464)
Q Consensus 17 k~CaDCGA~-nPqWASv~~GIFICleCS 43 (464)
..|.+|+.+ .-.|..-+|+.-||..|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 479999985 667999999999999994
No 35
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv
Probab=37.30 E-value=22 Score=29.93 Aligned_cols=31 Identities=23% Similarity=0.643 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
.|..|.-|+.+.- ...||++.|..|.++.|-
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997553 579999999999998764
No 36
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=35.62 E-value=15 Score=30.53 Aligned_cols=34 Identities=24% Similarity=0.551 Sum_probs=22.7
Q ss_pred CCCccCCCCCCCCc-eEeccceeEehhhhhhhccC
Q 012405 16 NKICVDCAQKNPQW-ASVSYGVFMCLECSGKHRGL 49 (464)
Q Consensus 16 Nk~CaDCGA~nPqW-ASv~~GIFICleCSGiHR~L 49 (464)
...|.|||.+=|.= .-.--|+..|.+|...+-..
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~E~~ 68 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQERQ 68 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHHHHH
Confidence 45899999975521 11223788999998765443
No 37
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=35.48 E-value=12 Score=34.03 Aligned_cols=31 Identities=23% Similarity=0.632 Sum_probs=20.5
Q ss_pred CCccCCCCCCCC-ceEeccceeEehhhhhhhc
Q 012405 17 KICVDCAQKNPQ-WASVSYGVFMCLECSGKHR 47 (464)
Q Consensus 17 k~CaDCGA~nPq-WASv~~GIFICleCSGiHR 47 (464)
-+|.+||.+=|. =.-.--+..+|++|.-.|-
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E 112 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERAE 112 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHHH
Confidence 389999997442 1122235788999987653
No 38
>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=34.88 E-value=44 Score=24.84 Aligned_cols=39 Identities=18% Similarity=0.527 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhh
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECS 43 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCS 43 (464)
+++.|.+|+ -|..-+|.-||....-+.. +.+.|-|-.|.
T Consensus 6 c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 6 CREYLEEIR-WPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHhc-CCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 455566654 4444789999998443333 26899999984
No 39
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=34.00 E-value=26 Score=30.34 Aligned_cols=31 Identities=32% Similarity=0.684 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
++..|.-||.+.- ...||++.|..|.++.|-
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 5678999998654 568999999999998873
No 40
>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=33.80 E-value=24 Score=27.83 Aligned_cols=28 Identities=29% Similarity=0.623 Sum_probs=23.5
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
--+.|..||..... ..+--+|.|..|--
T Consensus 27 TSq~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCccccccc--ccccceEEcCCCCC
Confidence 35789999998887 77888999999953
No 41
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=33.09 E-value=19 Score=25.91 Aligned_cols=30 Identities=20% Similarity=0.404 Sum_probs=15.7
Q ss_pred CCccCCCCCCCCceEe---ccceeEehhhhhhhc
Q 012405 17 KICVDCAQKNPQWASV---SYGVFMCLECSGKHR 47 (464)
Q Consensus 17 k~CaDCGA~nPqWASv---~~GIFICleCSGiHR 47 (464)
|.|-.||.+ .++..+ +.--++|..|.-||-
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEEe
Confidence 578999987 233333 455679999988883
No 42
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=32.81 E-value=26 Score=29.50 Aligned_cols=32 Identities=25% Similarity=0.657 Sum_probs=26.0
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
|..+.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 1 ~~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 1 PPQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 34677999997654 578999999999998774
No 43
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=32.11 E-value=26 Score=30.44 Aligned_cols=30 Identities=23% Similarity=0.666 Sum_probs=24.6
Q ss_pred CCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 16 Nk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
+..|.-|+.+.- ...||++.|..|.++.|-
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 357999998654 568999999999998874
No 44
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=31.28 E-value=8.3 Score=27.34 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=16.5
Q ss_pred CccCCCCCCCC-ceEeccceeEehhhhhhh
Q 012405 18 ICVDCAQKNPQ-WASVSYGVFMCLECSGKH 46 (464)
Q Consensus 18 ~CaDCGA~nPq-WASv~~GIFICleCSGiH 46 (464)
+|.+||.+=|. =.-+--+..+|..|+..|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 59999985221 111223678899998765
No 45
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=30.63 E-value=21 Score=28.48 Aligned_cols=39 Identities=26% Similarity=0.571 Sum_probs=27.8
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhhhhhccCCCccccee
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRGLGVHISFVR 57 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~LGvHISfVR 57 (464)
++-+.|.-||.+. =+--.||+.||..|- |.+-..|.|||
T Consensus 14 kGsr~C~vCg~~~--gliRkygL~~CRqCF---Re~A~~iGF~K 52 (54)
T PTZ00218 14 KGSRQCRVCSNRH--GLIRKYGLNVCRQCF---RENAELIGFHK 52 (54)
T ss_pred CCCCeeecCCCcc--hhhhhcCcchhhHHH---HHhhHhcCeee
Confidence 4678999999853 334589999999995 44445555654
No 46
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=30.08 E-value=34 Score=30.05 Aligned_cols=31 Identities=35% Similarity=0.832 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
.+..|.-|+.+.- ...||+..|..|.++.|-
T Consensus 17 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKAS---GFHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCc---ceEECcceehhhhhhhhh
Confidence 4678999998654 579999999999998774
No 47
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=28.89 E-value=27 Score=30.07 Aligned_cols=29 Identities=28% Similarity=0.615 Sum_probs=23.5
Q ss_pred CCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 17 k~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
+.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 1 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 1 KICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCCeeCCCcCc---ceEECcceeeeehheehh
Confidence 46888987544 569999999999998774
No 48
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.69 E-value=37 Score=34.87 Aligned_cols=33 Identities=15% Similarity=0.440 Sum_probs=23.6
Q ss_pred CCCCCCccCCCCCCCCceEeccceeEehhhhhhh
Q 012405 13 QPGNKICVDCAQKNPQWASVSYGVFMCLECSGKH 46 (464)
Q Consensus 13 ~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiH 46 (464)
.....+|.+||..+. =....-|-.||.+|--|.
T Consensus 8 ~~~~~~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 8 EEEKLVCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred cccCCcCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 345578999997432 224567999999998754
No 49
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=28.65 E-value=28 Score=28.38 Aligned_cols=22 Identities=45% Similarity=0.942 Sum_probs=15.0
Q ss_pred CccCCCCCCCCceEec-cceeEehhhh
Q 012405 18 ICVDCAQKNPQWASVS-YGVFMCLECS 43 (464)
Q Consensus 18 ~CaDCGA~nPqWASv~-~GIFICleCS 43 (464)
+|.||++.|. ++ --++-|.+|.
T Consensus 22 iCgdC~~en~----lk~~D~irCReCG 44 (62)
T KOG3507|consen 22 ICGDCGQENT----LKRGDVIRCRECG 44 (62)
T ss_pred Eecccccccc----ccCCCcEehhhcc
Confidence 6899988764 22 2367788883
No 50
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=28.33 E-value=35 Score=29.21 Aligned_cols=32 Identities=22% Similarity=0.742 Sum_probs=26.2
Q ss_pred CCCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
.+.+.|.-|+.+. ....||+..|..|..+.|-
T Consensus 4 ~~~~~C~VCg~~a---~g~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRA---TGLHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcC---cceEECcceehhhHHHHHH
Confidence 4567899999865 3578999999999998764
No 51
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.90 E-value=25 Score=32.86 Aligned_cols=35 Identities=29% Similarity=0.685 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCCCCccCCCCCCCCceEeccceeEehhhhhhhc
Q 012405 3 ATRRLRDLQSQPGNKICVDCAQKNPQWASVSYGVFMCLECSGKHR 47 (464)
Q Consensus 3 a~r~L~~L~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSGiHR 47 (464)
|++.|+++--. --.++|+|- -+--|||.+|.-+|-
T Consensus 97 tee~lreiyp~--------s~ipdp~wm--e~reficpecg~l~e 131 (165)
T COG4647 97 TEEKLREIYPK--------SDIPDPQWM--EIREFICPECGILHE 131 (165)
T ss_pred hHHHHHHhCcc--------cCCCCchHH--HHHHhhCccccceee
Confidence 55666666322 236789994 566899999988775
No 52
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=27.85 E-value=40 Score=29.55 Aligned_cols=34 Identities=21% Similarity=0.627 Sum_probs=23.9
Q ss_pred hcCCCCCCccCCCCCC--------CCce---------EeccceeEehhhhh
Q 012405 11 QSQPGNKICVDCAQKN--------PQWA---------SVSYGVFMCLECSG 44 (464)
Q Consensus 11 ~~~pgNk~CaDCGA~n--------PqWA---------Sv~~GIFICleCSG 44 (464)
++.+.--+|++||.+- ++.. +=.||-.+|..|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 4567777999999851 1121 33499999999964
No 53
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=27.14 E-value=27 Score=33.05 Aligned_cols=34 Identities=26% Similarity=0.654 Sum_probs=26.5
Q ss_pred CCCCCccCCCCCCCCceEeccceeEeh-hhhhhhcc
Q 012405 14 PGNKICVDCAQKNPQWASVSYGVFMCL-ECSGKHRG 48 (464)
Q Consensus 14 pgNk~CaDCGA~nPqWASv~~GIFICl-eCSGiHR~ 48 (464)
|--+.|+-||- ...+.+++.|.-+|. .|-.+|..
T Consensus 116 P~r~fCaVCG~-~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCGY-DSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcCC-CchhHHHhcCCceeechhhhhccc
Confidence 55678999994 445999999998885 67777764
No 54
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=26.92 E-value=28 Score=33.97 Aligned_cols=22 Identities=32% Similarity=0.695 Sum_probs=19.0
Q ss_pred CCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 16 NKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 16 Nk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
-+.|.-||. +.-..|.|..|..
T Consensus 309 S~~C~~cg~-------~~~r~~~C~~cg~ 330 (364)
T COG0675 309 SKTCPCCGH-------LSGRLFKCPRCGF 330 (364)
T ss_pred cccccccCC-------ccceeEECCCCCC
Confidence 489999999 6678999999975
No 55
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=25.91 E-value=34 Score=36.91 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=21.4
Q ss_pred CCCCccCCCCCCCCceEecc--ceeEehhhhh
Q 012405 15 GNKICVDCAQKNPQWASVSY--GVFMCLECSG 44 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~--GIFICleCSG 44 (464)
++..|--||.+..+--.+-. ++|||.+|..
T Consensus 6 ~~~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 6 ETLYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred CCeecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 34589999997665443333 4899999975
No 56
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=25.48 E-value=31 Score=32.62 Aligned_cols=34 Identities=21% Similarity=0.498 Sum_probs=21.4
Q ss_pred CCCCCccCCCCCCC--CceEeccceeEehhhhhhhcc
Q 012405 14 PGNKICVDCAQKNP--QWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 14 pgNk~CaDCGA~nP--qWASv~~GIFICleCSGiHR~ 48 (464)
+.=-+|.+||.+=| ...-+ -.+-.|+.|...+-.
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~-P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAI-PTATTCVECQNRKEV 119 (159)
T ss_pred CCCCeecccCCcccHHHHhhC-CCcchhHHHHHHhhh
Confidence 34457999998522 12122 246689999987644
No 57
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=24.60 E-value=30 Score=31.14 Aligned_cols=25 Identities=40% Similarity=0.781 Sum_probs=21.9
Q ss_pred CceEeccc--eeEehhhhhhhccCCCc
Q 012405 28 QWASVSYG--VFMCLECSGKHRGLGVH 52 (464)
Q Consensus 28 qWASv~~G--IFICleCSGiHR~LGvH 52 (464)
.|++-.-| |+-|.+|--|||.-++.
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~~~ 78 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEGAE 78 (112)
T ss_pred ceeEcCCCCEEeeccccceecccchHH
Confidence 89999999 99999999999976553
No 58
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=24.28 E-value=45 Score=31.26 Aligned_cols=39 Identities=10% Similarity=0.176 Sum_probs=24.4
Q ss_pred cCCCCCCccCCCCCCCC-ceEeccceeEehhhhhhhccCC
Q 012405 12 SQPGNKICVDCAQKNPQ-WASVSYGVFMCLECSGKHRGLG 50 (464)
Q Consensus 12 ~~pgNk~CaDCGA~nPq-WASv~~GIFICleCSGiHR~LG 50 (464)
..+.--+|-+||.+=|. =.-+--.+..|++|...|-...
T Consensus 107 ~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~~ 146 (151)
T PRK10778 107 EDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIRE 146 (151)
T ss_pred hCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHHh
Confidence 34566899999986321 1111224678999998776443
No 59
>PHA00080 DksA-like zinc finger domain containing protein
Probab=24.08 E-value=40 Score=27.89 Aligned_cols=34 Identities=24% Similarity=0.622 Sum_probs=22.5
Q ss_pred CCCCCCccCCCCCCCC--ceEeccceeEehhhhhhhc
Q 012405 13 QPGNKICVDCAQKNPQ--WASVSYGVFMCLECSGKHR 47 (464)
Q Consensus 13 ~pgNk~CaDCGA~nPq--WASv~~GIFICleCSGiHR 47 (464)
.+....|.+||.+=|. +.-+. ++..|.+|...+-
T Consensus 28 ~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~E 63 (72)
T PHA00080 28 APSATHCEECGDPIPEARREAVP-GCRTCVSCQEILE 63 (72)
T ss_pred CCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHHH
Confidence 3455689999996442 32222 5677999988654
No 60
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=23.81 E-value=73 Score=27.86 Aligned_cols=40 Identities=23% Similarity=0.582 Sum_probs=29.4
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 3 a~r~L~~L-~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
.|+++++| ..+..--.|.-|+..... -+..||+.|..|.-
T Consensus 21 lRK~v~kie~~q~a~y~CpfCgk~~vk--R~a~GIW~C~~C~~ 61 (91)
T TIGR00280 21 LRRQVKKIEIQQKAKYVCPFCGKKTVK--RGSTGIWTCRKCGA 61 (91)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceE--EEeeEEEEcCCCCC
Confidence 45666665 455567799999976544 56789999999953
No 61
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.64 E-value=28 Score=26.96 Aligned_cols=44 Identities=20% Similarity=0.565 Sum_probs=26.7
Q ss_pred CccCCCCCCCCce--EeccceeEehhhhhhhccCCCcccceeecccC
Q 012405 18 ICVDCAQKNPQWA--SVSYGVFMCLECSGKHRGLGVHISFVRSVTMD 62 (464)
Q Consensus 18 ~CaDCGA~nPqWA--Sv~~GIFICleCSGiHR~LGvHISfVRSvtmD 62 (464)
.|+=||..-.-.- -+.=| +||-.|...-..+-..+..++.+|++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~~~~~~t~~ 46 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVKIKKNLTLE 46 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchhhhhhccHH
Confidence 4888887654433 34557 89999997655543333344455543
No 62
>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs h
Probab=23.54 E-value=49 Score=28.38 Aligned_cols=29 Identities=24% Similarity=0.750 Sum_probs=23.4
Q ss_pred CCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 17 k~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
..|.-|+.+.- ...||++.|..|.++.|-
T Consensus 2 ~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 30 (91)
T cd07161 2 ELCLVCGDRAS---GYHYNALTCEGCKGFFRR 30 (91)
T ss_pred CCCeeCCCcCc---ceEECceeehhhHHHHHH
Confidence 35888987654 569999999999998763
No 63
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=23.21 E-value=38 Score=29.06 Aligned_cols=30 Identities=27% Similarity=0.744 Sum_probs=24.9
Q ss_pred CCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 16 Nk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
+..|.-|+.+.- ...||+..|..|.++.|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (92)
T cd07163 6 DIPCKVCGDRSS---GKHYGIYACDGCSGFFKR 35 (92)
T ss_pred CCCCcccCCcCc---ccEECceeeeeeeeEEee
Confidence 677999998654 479999999999998764
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=22.74 E-value=67 Score=28.04 Aligned_cols=40 Identities=20% Similarity=0.635 Sum_probs=29.2
Q ss_pred HHHHHHHH-hcCCCCCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 3 ATRRLRDL-QSQPGNKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 3 a~r~L~~L-~~~pgNk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
.|+++.+| ..+..--.|.-|+..... -+..||+-|..|.-
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vk--R~a~GIW~C~~C~~ 62 (90)
T PRK03976 22 IRKRVADIEEKMRAKHVCPVCGRPKVK--RVGTGIWECRKCGA 62 (90)
T ss_pred HHHHHHHHHHHHhcCccCCCCCCCceE--EEEEEEEEcCCCCC
Confidence 45666665 455667799999876655 46679999999953
No 65
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=22.73 E-value=53 Score=27.79 Aligned_cols=28 Identities=25% Similarity=0.692 Sum_probs=22.5
Q ss_pred CccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 18 ~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
+|.-|+.+.. ...||++.|..|.++.|-
T Consensus 1 ~C~VCg~~~~---g~hygv~sC~aC~~FFRR 28 (87)
T cd07162 1 ICRVCGDRAT---GYHFNAMTCEGCKGFFRR 28 (87)
T ss_pred CCcccCCcCc---ceEECcceehhhHHHHHh
Confidence 4778887655 468999999999998764
No 66
>PF02993 MCPVI: Minor capsid protein VI; InterPro: IPR004243 This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. Residues at the C-terminal end of the protein may act as a protease cofactor leading to activation of the adenovirus proteinase [].; GO: 0019028 viral capsid; PDB: 1AVP_B.
Probab=22.54 E-value=29 Score=35.09 Aligned_cols=65 Identities=17% Similarity=0.264 Sum_probs=0.0
Q ss_pred ccchhHHHhhchhhhHhhHHHHHHHHHHHhhhhhhhhhhhhccCccccccccceeeeeeeccccccc
Q 012405 262 QGDVLSAVSQGFGRISLVAASAAQSAATVVQAGTREFTSKVREGGYDHKVNETVNVVTAKTSEIGQR 328 (464)
Q Consensus 262 ~~d~~ssls~Gwg~fS~~a~~aa~~a~~~~~~~~~~~~~kv~eg~~~~~v~~~v~~~a~K~~e~g~~ 328 (464)
...-.|+||+|+.-|-+.....+..|-+ ...-+.|.+++||-+|.++|-+.+..--.-+.|||+.
T Consensus 32 WgsLwS~is~glkn~Gs~l~n~g~k~wn--S~tgq~lrq~LkDsg~~~kVv~g~~~gi~g~vDIgrq 96 (238)
T PF02993_consen 32 WGSLWSSISSGLKNFGSFLKNYGSKAWN--SQTGQQLRQGLKDSGLQEKVVEGAGSGINGLVDIGRQ 96 (238)
T ss_dssp -------------------------------------------------------------------
T ss_pred cccchhhhhhhhhhHhHHHHHhhhhhhh--hhHHHHHHHHHhhhhHHHHHHHHHhhhhhHHHHHHHH
Confidence 3455778888988888766655544422 1122466778888888887777777766667777765
No 67
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=22.09 E-value=58 Score=26.88 Aligned_cols=28 Identities=32% Similarity=0.856 Sum_probs=23.0
Q ss_pred CccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 18 ICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 18 ~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 2 ~C~VC~~~~~---g~hygv~sC~aC~~FFRR 29 (77)
T cd06956 2 ICAICGDRAS---GKHYGVYSCEGCKGFFKR 29 (77)
T ss_pred CCcccCCcCc---ceEECceeehhHHHHHHH
Confidence 5888887654 479999999999998763
No 68
>PHA02942 putative transposase; Provisional
Probab=21.76 E-value=45 Score=35.47 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=20.2
Q ss_pred CCCccCCCCCCCCceEeccceeEehhhhh
Q 012405 16 NKICVDCAQKNPQWASVSYGVFMCLECSG 44 (464)
Q Consensus 16 Nk~CaDCGA~nPqWASv~~GIFICleCSG 44 (464)
-+.|..||...+ .++-.+|.|..|--
T Consensus 325 Sq~Cs~CG~~~~---~l~~r~f~C~~CG~ 350 (383)
T PHA02942 325 SVSCPKCGHKMV---EIAHRYFHCPSCGY 350 (383)
T ss_pred CccCCCCCCccC---cCCCCEEECCCCCC
Confidence 478999998765 34566999999964
No 69
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=21.54 E-value=79 Score=23.30 Aligned_cols=28 Identities=29% Similarity=0.646 Sum_probs=16.6
Q ss_pred CCccCCCCCCCC---ceEeccceeEehhhhh
Q 012405 17 KICVDCAQKNPQ---WASVSYGVFMCLECSG 44 (464)
Q Consensus 17 k~CaDCGA~nPq---WASv~~GIFICleCSG 44 (464)
++|.=||.+..+ -++-.-+++||.+|.-
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 468889987553 3344557999999975
No 70
>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core
Probab=21.15 E-value=45 Score=29.61 Aligned_cols=30 Identities=23% Similarity=0.665 Sum_probs=24.8
Q ss_pred CCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 16 NKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 16 Nk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
.+.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 6 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 35 (107)
T cd06955 6 PRICGVCGDRAT---GFHFNAMTCEGCKGFFRR 35 (107)
T ss_pred CCCCeecCCcCc---ccEECcceeeeecceecc
Confidence 467999997654 469999999999998774
No 71
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=20.78 E-value=60 Score=27.73 Aligned_cols=31 Identities=29% Similarity=0.773 Sum_probs=25.2
Q ss_pred CCCCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 15 GNKICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 15 gNk~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
..+.|.-|+.+.- ...||+..|..|..+.|-
T Consensus 5 ~~~~C~VCg~~~~---g~hyGv~sC~aCk~FFRR 35 (90)
T cd07168 5 SPKLCSICEDKAT---GLHYGIITCEGCKGFFKR 35 (90)
T ss_pred cCCCCcccCCcCc---ceEECceehhhhhHhhhh
Confidence 3567999997653 579999999999998864
No 72
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=20.65 E-value=61 Score=26.37 Aligned_cols=27 Identities=22% Similarity=0.652 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 19 CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
|.-|+.+.- ...||++.|..|.++.|-
T Consensus 1 C~VC~~~~~---g~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRAT---GYHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCc---ccEECcceehhhhhhhch
Confidence 556776544 358999999999998774
No 73
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=20.20 E-value=63 Score=26.87 Aligned_cols=29 Identities=31% Similarity=0.755 Sum_probs=23.6
Q ss_pred CCccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 17 KICVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 17 k~CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
+.|.-|+.+.- ...||++.|..|.++.|-
T Consensus 3 ~~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 31 (78)
T cd07172 3 KICLVCSDEAS---GCHYGVLTCGSCKVFFKR 31 (78)
T ss_pred CCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 46888987654 479999999999998763
No 74
>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=20.17 E-value=57 Score=26.51 Aligned_cols=27 Identities=37% Similarity=0.816 Sum_probs=21.0
Q ss_pred ccCCCCCCCCceEeccceeEehhhhhhhcc
Q 012405 19 CVDCAQKNPQWASVSYGVFMCLECSGKHRG 48 (464)
Q Consensus 19 CaDCGA~nPqWASv~~GIFICleCSGiHR~ 48 (464)
|.-|+.+.- ...||++.|..|..+.|-
T Consensus 1 C~VCg~~~~---g~hyGv~~C~aC~~FFRR 27 (73)
T cd07158 1 CKVCGDKAS---GFHYGVHSCEGCKGFFRR 27 (73)
T ss_pred CcccCccCc---ceEECcchhhHHHHHHhh
Confidence 556776544 368999999999998874
Done!