Query psy62
Match_columns 262
No_of_seqs 225 out of 1108
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 20:13:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy62.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/62hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0704|consensus 100.0 4.7E-70 1E-74 506.3 14.5 210 1-219 21-231 (386)
2 COG5347 GTPase-activating prot 100.0 1.1E-37 2.3E-42 291.3 10.5 104 1-104 22-125 (319)
3 KOG0706|consensus 100.0 1.3E-34 2.9E-39 276.5 7.0 99 1-101 25-123 (454)
4 PLN03114 ADP-ribosylation fact 100.0 9.5E-34 2.1E-38 265.5 8.8 100 1-101 24-123 (395)
5 smart00105 ArfGap Putative GTP 100.0 1.4E-33 3.1E-38 227.5 8.0 105 1-109 5-109 (112)
6 PF01412 ArfGap: Putative GTPa 100.0 2.2E-33 4.7E-38 227.6 4.6 102 1-107 15-116 (116)
7 KOG0703|consensus 100.0 5E-32 1.1E-36 248.6 5.4 70 1-70 27-96 (287)
8 PLN03131 hypothetical protein; 99.9 1E-27 2.2E-32 236.6 8.9 105 1-112 25-129 (705)
9 PLN03119 putative ADP-ribosyla 99.9 3.7E-27 8.1E-32 231.0 10.1 107 1-114 25-131 (648)
10 KOG0705|consensus 99.8 4.2E-21 9.1E-26 188.7 4.7 69 1-69 515-583 (749)
11 KOG0521|consensus 99.8 6.9E-20 1.5E-24 188.4 1.6 104 1-110 428-534 (785)
12 KOG0818|consensus 99.7 1.3E-18 2.7E-23 169.2 1.3 70 1-70 10-79 (669)
13 KOG1117|consensus 99.6 6E-16 1.3E-20 157.6 2.3 71 1-71 300-372 (1186)
14 KOG0702|consensus 99.2 2E-11 4.3E-16 119.2 6.0 106 1-111 27-133 (524)
15 KOG0521|consensus 91.9 0.031 6.6E-07 59.0 -1.4 66 1-68 632-698 (785)
16 PF00643 zf-B_box: B-box zinc 80.0 1.6 3.4E-05 28.5 2.2 31 1-31 5-36 (42)
17 PRK00085 recO DNA repair prote 77.2 1.1 2.3E-05 40.0 1.0 27 1-27 151-178 (247)
18 KOG0704|consensus 76.6 0.95 2.1E-05 43.8 0.5 37 192-228 247-293 (386)
19 TIGR00613 reco DNA repair prot 71.0 2.7 5.8E-05 37.3 1.9 28 1-28 149-177 (241)
20 PF08271 TF_Zn_Ribbon: TFIIB z 69.1 3.3 7.1E-05 27.7 1.6 25 1-26 2-26 (43)
21 COG1381 RecO Recombinational D 63.4 3.2 7E-05 37.9 0.9 26 1-26 156-182 (251)
22 PF10764 Gin: Inhibitor of sig 57.0 6.4 0.00014 27.2 1.3 26 1-27 1-26 (46)
23 COG1997 RPL43A Ribosomal prote 55.7 8.2 0.00018 30.4 1.8 26 1-28 37-62 (89)
24 PF00320 GATA: GATA zinc finge 54.1 8.6 0.00019 24.9 1.5 30 2-31 1-32 (36)
25 PF14471 DUF4428: Domain of un 54.0 4.1 8.9E-05 28.7 -0.1 43 1-44 1-45 (51)
26 PF01286 XPA_N: XPA protein N- 52.4 4.6 9.9E-05 26.4 -0.1 26 1-26 5-31 (34)
27 PF11781 RRN7: RNA polymerase 47.1 14 0.0003 24.2 1.6 21 2-25 11-31 (36)
28 PRK12495 hypothetical protein; 40.4 14 0.0003 33.8 1.1 24 1-28 44-67 (226)
29 smart00401 ZnF_GATA zinc finge 37.2 26 0.00056 24.5 1.8 34 1-34 5-40 (52)
30 smart00290 ZnF_UBP Ubiquitin C 34.3 26 0.00057 23.4 1.5 16 1-16 1-16 (50)
31 PF01258 zf-dskA_traR: Prokary 34.2 5.5 0.00012 25.6 -1.8 29 1-29 5-34 (36)
32 COG2158 Uncharacterized protei 33.9 26 0.00057 28.7 1.6 31 2-34 45-77 (112)
33 PF07282 OrfB_Zn_ribbon: Putat 33.5 25 0.00054 25.3 1.3 23 1-25 30-52 (69)
34 PF12156 ATPase-cat_bd: Putati 32.4 25 0.00053 27.2 1.2 32 1-32 2-39 (88)
35 PTZ00255 60S ribosomal protein 30.8 33 0.00071 27.2 1.7 25 1-27 38-62 (90)
36 PF10310 DUF2413: Protein of u 30.7 31 0.00066 34.6 1.9 30 195-224 117-148 (444)
37 PRK00423 tfb transcription ini 30.7 33 0.00072 32.2 2.0 28 1-29 13-40 (310)
38 smart00659 RPOLCX RNA polymera 30.6 22 0.00048 24.2 0.6 22 1-25 4-25 (44)
39 PF14376 Haem_bd: Haem-binding 30.0 24 0.00052 29.4 0.9 38 1-48 43-84 (137)
40 PF08274 PhnA_Zn_Ribbon: PhnA 30.0 26 0.00056 22.2 0.8 24 1-27 4-27 (30)
41 PTZ00074 60S ribosomal protein 25.3 37 0.0008 28.8 1.2 26 1-26 43-85 (135)
42 cd07162 NR_DBD_PXR DNA-binding 24.6 49 0.0011 25.5 1.6 27 1-30 1-27 (87)
43 PF14803 Nudix_N_2: Nudix N-te 23.7 38 0.00082 22.0 0.7 27 2-29 3-32 (34)
44 PRK14714 DNA polymerase II lar 23.0 40 0.00086 38.0 1.2 28 81-108 844-871 (1337)
45 PF01780 Ribosomal_L37ae: Ribo 22.9 52 0.0011 26.0 1.5 24 1-26 37-60 (90)
46 cd07156 NR_DBD_VDR_like The DN 22.7 54 0.0012 24.2 1.5 27 2-31 1-27 (72)
47 cd07170 NR_DBD_ERR DNA-binding 22.5 45 0.00098 26.4 1.1 27 1-30 6-32 (97)
48 smart00399 ZnF_C4 c4 zinc fing 22.1 48 0.001 24.2 1.2 27 1-30 1-27 (70)
49 cd06966 NR_DBD_CAR DNA-binding 21.4 47 0.001 26.0 1.0 28 1-31 2-29 (94)
50 PHA02540 61 DNA primase; Provi 21.3 56 0.0012 31.6 1.7 56 1-60 29-92 (337)
51 cd07165 NR_DBD_DmE78_like DNA- 21.1 49 0.0011 25.1 1.0 27 2-31 1-27 (81)
52 PF06827 zf-FPG_IleRS: Zinc fi 21.1 40 0.00086 20.6 0.4 27 1-27 3-29 (30)
53 cd07157 2DBD_NR_DBD1 The first 21.0 47 0.001 25.6 0.9 28 1-31 2-29 (86)
54 cd00202 ZnF_GATA Zinc finger D 20.4 59 0.0013 23.0 1.3 34 1-34 1-36 (54)
No 1
>KOG0704|consensus
Probab=100.00 E-value=4.7e-70 Score=506.31 Aligned_cols=210 Identities=49% Similarity=0.855 Sum_probs=174.7
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+||||+++|||||||+|||||||+|+|+||+||||||||||||||+|++.||++|++|||.++++||+.++++++.++|+
T Consensus 21 ~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~~eFL~s~~~~~e~~~i~ 100 (386)
T KOG0704|consen 21 KCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERFREFLSSQGIYKETWPIR 100 (386)
T ss_pred ceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhHHHHHhhCccccccccHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccCCCCCCCCC-CCCcccccCCCCCCCCCCCCCCCCCCCcchhhhhHHHHhhhhhc
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTKGIFDFSQS-GGSTVTSSYQGGGGGYQSGGGGGMVNSASFQSEKEAFFSRKQQE 159 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~~~~~~~~s-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~Fa~~g~~ 159 (262)
+||++++|+.||+||.++++||+|..++....+.+ ..-++..... ..+.... ....+....+..+|.||++++.+
T Consensus 101 eKYns~aAa~yRdki~~laegr~w~d~~~~k~~~p~~syt~a~~~~--~~ss~~~--~~~sq~~~~~~~ke~~fa~~~~~ 176 (386)
T KOG0704|consen 101 EKYNSRAAALYRDKIAALAEGREWNDPPYLKEDNPAQSYTSAAQLG--SKSSETI--YTISQLSNSAAGKESYFAKRLSE 176 (386)
T ss_pred HhhccHHHHHHHHHHHHHhcCCcccccccccccCcccccccCCCcC--CCcCCcc--cccccchhhhcchhHHHHHhccc
Confidence 99999999999999999999999977665543321 1111100000 0000000 01122334567788999999999
Q ss_pred ccCCCCCCCCCCCCccccccCCCCCCCCCCCCccccccchhhhhhhhhhHHHHHHHHHHH
Q psy62 160 NLSRPDHLPPSQGGRYAGFGNSVESPPPRSVSSQELFGGAVSSLTSGWSMFSSSATKLAS 219 (262)
Q Consensus 160 N~sRp~~lpPsQggkY~GFGnt~~~p~~~~~~~~~~~~~~~~~l~~Gw~~fs~~~~k~a~ 219 (262)
|.+||++|||+|||||+|||+|+. |||+++ .+| |+|++|+.||++||.+|+++|+
T Consensus 177 n~srpd~lppsQggkY~GFGst~~-~ppqs~-~~~---~~~s~ls~Gws~~s~~as~~a~ 231 (386)
T KOG0704|consen 177 NQSRPDGLPPSQGGKYQGFGSTNA-PPPQSN-SQD---DAMSVLSSGWSRLSTGASSAAS 231 (386)
T ss_pred ccCCCCCCCcccCCcccccCCCCC-CCCccc-ccc---chhhhhccccccccchhhhhhh
Confidence 999999999999999999999988 666654 333 8999999999999999999887
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=1.1e-37 Score=291.29 Aligned_cols=104 Identities=39% Similarity=0.753 Sum_probs=97.3
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|||||+++|+|+|++||||||++||||||+|||||||||||+||.|+++||++|+.+||.++++||+.+......++|+
T Consensus 22 ~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a~~~~e~~~~~~~~~~~k 101 (319)
T COG5347 22 KCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNANRFYEKNLLDQLLLPIK 101 (319)
T ss_pred ccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhhhhHhccCCCcccccccc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999986643458999
Q ss_pred hhhccHHHHHHHHHHhcccCCCCc
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTF 104 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~ 104 (262)
+||++..++.|+.++..++....|
T Consensus 102 ~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 102 AKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred cccCHHHHHHHHHHHHHhhhcccc
Confidence 999999999999999888777776
No 3
>KOG0706|consensus
Probab=100.00 E-value=1.3e-34 Score=276.51 Aligned_cols=99 Identities=48% Similarity=0.927 Sum_probs=93.1
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|||||+++|.|+||+||||||++|+++||.||||||||||++||.|+..||++|+.|||.+|+.||..|... ...++
T Consensus 25 vCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~FFkqhg~~--t~d~~ 102 (454)
T KOG0706|consen 25 VCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARVFFKQHGCV--TLDAN 102 (454)
T ss_pred eecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHHHHHHcCCc--chhhh
Confidence 5999999999999999999999999999999999999999999999999999999999999999999998543 34899
Q ss_pred hhhccHHHHHHHHHHhcccCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMF 101 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~g 101 (262)
.||+++++.+||++|..++.+
T Consensus 103 aKY~SraA~~Yr~kl~~lv~k 123 (454)
T KOG0706|consen 103 AKYNSRAAKLYREKLKKLVQK 123 (454)
T ss_pred hhhccHHHHHHHHHHHHHHHH
Confidence 999999999999999987654
No 4
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=100.00 E-value=9.5e-34 Score=265.46 Aligned_cols=100 Identities=46% Similarity=0.936 Sum_probs=95.0
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|+|||+++|+|+|++||||||++|+|+||+||+|||+||||+||.|+++||++|+.+||.++++||+.+ ++.....|+
T Consensus 24 ~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~fF~qh-G~~~~~~~~ 102 (395)
T PLN03114 24 ICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVFFKQY-GWSDGGKTE 102 (395)
T ss_pred cCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHHHHHc-CCCCCCCcc
Confidence 5999999999999999999999999999999999999999999999999999999999999999999986 455567899
Q ss_pred hhhccHHHHHHHHHHhcccCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMF 101 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~g 101 (262)
+||+++++++||++|.+++++
T Consensus 103 ~KY~S~aA~~Yre~L~keVa~ 123 (395)
T PLN03114 103 AKYTSRAADLYKQILAKEVAK 123 (395)
T ss_pred cccCCHHHHHHHHHHHHHHHH
Confidence 999999999999999998875
No 5
>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=1.4e-33 Score=227.53 Aligned_cols=105 Identities=37% Similarity=0.736 Sum_probs=88.9
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|+|||+++|+|||++||||||++|+|+||.||+|||+||||+||+|+++||++|+.+||+++|+||+++.......+
T Consensus 5 ~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~~~-- 82 (112)
T smart00105 5 KCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSLKP-- 82 (112)
T ss_pred cccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCccccCC--
Confidence 599999999999999999999999999999999999999999999999999999999999999999999754221111
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccCCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTKGI 109 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~~~ 109 (262)
-.......|+++|+++|+.++|+.+..
T Consensus 83 --~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 83 --PDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred --CCCchHHHHHHHHHHHHHhhhcccccc
Confidence 111134567888888888888877654
No 6
>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=99.98 E-value=2.2e-33 Score=227.61 Aligned_cols=102 Identities=39% Similarity=0.756 Sum_probs=77.7
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|+|||+++|+|||++||||||++|+|+||.||+|||+||||+||+|+++||++|+.+||.++|++|+++... ...+
T Consensus 15 ~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~e~~~~~--~~~~- 91 (116)
T PF01412_consen 15 VCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIWEANSPP--PKKP- 91 (116)
T ss_dssp B-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHHTTTSTT--TTTH-
T ss_pred cCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHHHcCCCC--CCCC-
Confidence 5999999999999999999999999999999999999999999999999999999999999999999998211 1111
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccC
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTK 107 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~ 107 (262)
-.......|+++|+++|+.+.|..+
T Consensus 92 --~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 92 --PPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp --CTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred --CCCCcHHHHHHHHHHHHHhhhhccC
Confidence 1123355788899999999999753
No 7
>KOG0703|consensus
Probab=99.97 E-value=5e-32 Score=248.62 Aligned_cols=70 Identities=43% Similarity=0.935 Sum_probs=69.0
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQ 70 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~ 70 (262)
.|+|||++.|.|||+|+|||||+.|+||||.||||||+||||+||.|++|||+.|...||.++|+|||++
T Consensus 27 ~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN~~an~~~ea~ 96 (287)
T KOG0703|consen 27 VCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGNAKANSYYEAK 96 (287)
T ss_pred cccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcchhhhhhcccc
Confidence 5999999999999999999999999999999999999999999999999999999999999999999997
No 8
>PLN03131 hypothetical protein; Provisional
Probab=99.94 E-value=1e-27 Score=236.63 Aligned_cols=105 Identities=26% Similarity=0.527 Sum_probs=88.8
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|+||++++|+|||++||||||++|+||||.|| | |||||+||+|+++||+.|+.+||+++|+||+++.+.. ...+.
T Consensus 25 ~CADCga~~P~WASiNlGIFICi~CSGIHRsLg-h--RVKSVTLD~WtdeEV~~Mk~gGN~~AN~iyeanwd~~-r~~lP 100 (705)
T PLN03131 25 RCINCNSLGPQFVCTNFWTFICMTCSGIHREFT-H--RVKSVSMSKFTSQDVEALQNGGNQRAREIYLKDWDQQ-RQRLP 100 (705)
T ss_pred ccccCCCCCCCeeEeccceEEchhchhhhcccC-c--ccccccCCCCCHHHHHHHHHhccHHHHHHHHhhcccc-cCCCC
Confidence 599999999999999999999999999999998 4 9999999999999999999999999999999875422 11222
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccCCCCCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTKGIFDF 112 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~~~~~~ 112 (262)
... .....+++|+.+|+.|+|..+.....
T Consensus 101 ~~s---d~ekrr~FIR~KYVeKRFa~~~s~d~ 129 (705)
T PLN03131 101 DNS---KVDKIREFIKDIYVDKKYAGGKTHDK 129 (705)
T ss_pred CCc---cHHHHHHHHHHHHhhhhhhcCCCCCC
Confidence 222 24457899999999999998875544
No 9
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=99.94 E-value=3.7e-27 Score=231.05 Aligned_cols=107 Identities=28% Similarity=0.550 Sum_probs=90.0
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTIQ 80 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I~ 80 (262)
+|+|||+.+|+|||++||||||++|+||||.|| | +||||+||+|+++||+.|+.+||+++|+||+++.+... ..+.
T Consensus 25 ~CADCgs~~P~WASiNlGIFICi~CSGIHRsLG-h--RVKSLSLDkWT~EEVe~Mk~gGN~~AN~iyeanw~~~~-~~~P 100 (648)
T PLN03119 25 RCINCNSLGPQYVCTTFWTFVCMACSGIHREFT-H--RVKSVSMSKFTSKEVEVLQNGGNQRAREIYLKNWDHQR-QRLP 100 (648)
T ss_pred ccccCCCCCCCceeeccceEEeccchhhhccCC-c--eeeccccCCCCHHHHHHHHHhchHHHHHHHHhhccccc-CCCC
Confidence 599999999999999999999999999999998 4 99999999999999999999999999999999754221 1111
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccCCCCCCCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTKGIFDFSQ 114 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~~~~~~~~ 114 (262)
...+ .+..+++|+.+|+.|+|..+...+..+
T Consensus 101 ~~sD---~e~lr~FIR~KYVeKRF~~~~~~d~p~ 131 (648)
T PLN03119 101 ENSN---AERVREFIKNVYVQKKYAGANDADKPS 131 (648)
T ss_pred CCcc---HHHHHHHHHHHHhhhhccCcCCCCCCc
Confidence 1122 345689999999999999887666544
No 10
>KOG0705|consensus
Probab=99.82 E-value=4.2e-21 Score=188.74 Aligned_cols=69 Identities=43% Similarity=0.885 Sum_probs=68.1
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNA 69 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~ 69 (262)
.|+||++++|.|||+|+|+.||++|+|+||.||.|+|+||||.+|.|..|.+..|..+||+.+|.+||.
T Consensus 515 ~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE~ 583 (749)
T KOG0705|consen 515 HCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWEG 583 (749)
T ss_pred eeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhhh
Confidence 599999999999999999999999999999999999999999999999999999999999999999997
No 11
>KOG0521|consensus
Probab=99.77 E-value=6.9e-20 Score=188.43 Aligned_cols=104 Identities=33% Similarity=0.589 Sum_probs=84.7
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCC---CCc
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWD---DTM 77 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~---~~~ 77 (262)
+|+|||++.|.|+|+|+||.+|++|+|+||.||||||+|||++||.|.++.+..|+.+||..+|.+||++.... ...
T Consensus 428 ~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~~l~~~~~~~~~ 507 (785)
T KOG0521|consen 428 QCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEALLPSYDSSKPT 507 (785)
T ss_pred hhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhcccccccccCCC
Confidence 59999999999999999999999999999999999999999999999999999999999999999999863211 111
Q ss_pred hhhhhhccHHHHHHHHHHhcccCCCCcccCCCC
Q psy62 78 TIQQKYNTKAAALYRDKVSSSYMFNTFTTKGIF 110 (262)
Q Consensus 78 ~I~~KY~~~aa~~yr~kl~~~~~gr~~~~~~~~ 110 (262)
.... ...-+.+|+++|..+.|....+.
T Consensus 508 ~~~~------~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 508 ASSS------RQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred Cccc------hhhhhHhhhcccceeeEeecccc
Confidence 1111 22345567777777777665543
No 12
>KOG0818|consensus
Probab=99.71 E-value=1.3e-18 Score=169.19 Aligned_cols=70 Identities=33% Similarity=0.694 Sum_probs=68.3
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQ 70 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~ 70 (262)
.|.|||+++|.||||+-|+|||.+|..+||.||.|||.||+|....|.++.|++.....|..+|.+||+.
T Consensus 10 vC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~ 79 (669)
T KOG0818|consen 10 VCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHS 79 (669)
T ss_pred hhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhh
Confidence 5999999999999999999999999999999999999999999999999999999999999999999984
No 13
>KOG1117|consensus
Probab=99.57 E-value=6e-16 Score=157.60 Aligned_cols=71 Identities=38% Similarity=0.733 Sum_probs=68.9
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCC--CCHHHHHhhhcCChHHHHHHHhhCC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDK--WKDIELEKMKVGGNKAAHDFLNAQP 71 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~--W~~~el~~m~~gGN~~~n~f~e~~~ 71 (262)
.|+|||++.|.|||+|+++.||-.|+|-||+||.-+|+|||++||. |+.+-|+++-..||.++|+||..+.
T Consensus 300 ~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~nl 372 (1186)
T KOG1117|consen 300 ECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAGNL 372 (1186)
T ss_pred cccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccccCC
Confidence 4999999999999999999999999999999999999999999998 9999999999999999999999864
No 14
>KOG0702|consensus
Probab=99.19 E-value=2e-11 Score=119.18 Aligned_cols=106 Identities=21% Similarity=0.364 Sum_probs=88.8
Q ss_pred CCCCCCCCCC-CeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHhhCCCCCCCchh
Q psy62 1 KCFECNAHNP-QWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLNAQPDWDDTMTI 79 (262)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e~~~~~~~~~~I 79 (262)
||++|....+ .|++.+-|.|+|+.|+|..|+|.. -.+||||+|.+|++.|+..++.+||+..+++|-.-.|...+...
T Consensus 27 rC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~-ahRvksiSmttft~qevs~lQshgNq~~k~i~fkl~D~q~S~vP 105 (524)
T KOG0702|consen 27 RCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNP-AHRVKSISMTTFTDQEVSFLQSHGNQVCKEIWFKLFDFQRSNVP 105 (524)
T ss_pred ceeeccccccceEEEeeccceeeeccchhhccCCC-ccccceeeeeeccccchHHHhhcchhhhhhhhhcchhhhhccCC
Confidence 7999999888 999999999999999999999964 24999999999999999999999999999999976554433322
Q ss_pred hhhhccHHHHHHHHHHhcccCCCCcccCCCCC
Q psy62 80 QQKYNTKAAALYRDKVSSSYMFNTFTTKGIFD 111 (262)
Q Consensus 80 ~~KY~~~aa~~yr~kl~~~~~gr~~~~~~~~~ 111 (262)
-.+| ...-|++++.+|++++|+.+.-..
T Consensus 106 D~rn----~~~~kef~q~~y~~kr~~v~~n~~ 133 (524)
T KOG0702|consen 106 DSRN----PQKVKEFQQEKYVKKRYYVPKNQM 133 (524)
T ss_pred Cccc----chhhHHHHhhhhccceeecCcccc
Confidence 2223 455699999999999999887543
No 15
>KOG0521|consensus
Probab=91.88 E-value=0.031 Score=58.99 Aligned_cols=66 Identities=17% Similarity=0.261 Sum_probs=54.0
Q ss_pred CCCCCCC-CCCCeeEcccceeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCChHHHHHHHh
Q psy62 1 KCFECNA-HNPQWASVTYGIWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGNKAAHDFLN 68 (262)
Q Consensus 1 ~C~DCga-~~P~WaSv~~GifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN~~~n~f~e 68 (262)
.|++|++ ..-.|+++++.+-+|..|+++|+.++.|++..+++.+|...+ |.....-|+...+.-+.
T Consensus 632 ~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 632 ECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred cchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 3788887 457899999999999999999999999999999999998888 56565556555554433
No 16
>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=79.95 E-value=1.6 Score=28.54 Aligned_cols=31 Identities=26% Similarity=0.410 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhh-hcC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGK-HRG 31 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csgv-HR~ 31 (262)
.|..|......+-+.+-.++||..|... |++
T Consensus 5 ~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 5 KCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp B-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 3777777778889999999999999987 887
No 17
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=77.24 E-value=1.1 Score=40.01 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=23.4
Q ss_pred CCCCCCCCCC-CeeEcccceeEehhhhh
Q psy62 1 KCFECNAHNP-QWASVTYGIWICLECSG 27 (262)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GifiC~~Csg 27 (262)
.|+-||.+.. .|.++..|.++|..|..
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred hHhcCCCCCCceEEecccCCcccccccC
Confidence 4999998755 78899999999999973
No 18
>KOG0704|consensus
Probab=76.59 E-value=0.95 Score=43.81 Aligned_cols=37 Identities=14% Similarity=0.357 Sum_probs=33.3
Q ss_pred ccccccchhhhhh-h----h---hhHHHHHHHHHHHHH--hhhhhcc
Q psy62 192 SQELFGGAVSSLT-S----G---WSMFSSSATKLASKA--TENAIKY 228 (262)
Q Consensus 192 ~~~~~~~~~~~l~-~----G---w~~fs~~~~k~a~~~--~e~~~k~ 228 (262)
+++|+++|+++|+ + | |++|+..+++.+..+ +++++++
T Consensus 247 l~~~~s~~v~~va~k~t~vG~r~W~~ls~~~sq~~e~fq~~~s~g~~ 293 (386)
T KOG0704|consen 247 LDDFVSDPVGTVASKVTEVGTRGWGLLSAAVSQSVEDFQDSESVGGP 293 (386)
T ss_pred hhhhcccchhhhhhhcccccccchhhhHHhhccccccccccCccCCc
Confidence 5889999999998 5 4 999999999999999 8888885
No 19
>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=70.95 E-value=2.7 Score=37.29 Aligned_cols=28 Identities=36% Similarity=0.772 Sum_probs=23.5
Q ss_pred CCCCCCCCCC-CeeEcccceeEehhhhhh
Q psy62 1 KCFECNAHNP-QWASVTYGIWICLECSGK 28 (262)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GifiC~~Csgv 28 (262)
.|+.||..++ .+.++..|.++|.+|...
T Consensus 149 ~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 149 KCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred ccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 4999998554 788999999999999764
No 20
>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=69.10 E-value=3.3 Score=27.67 Aligned_cols=25 Identities=24% Similarity=0.595 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECS 26 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Cs 26 (262)
+|-.||+.. .-....-|-++|..|-
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCG 26 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCC
Confidence 599999976 4556788999999994
No 21
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=63.40 E-value=3.2 Score=37.87 Aligned_cols=26 Identities=23% Similarity=0.626 Sum_probs=23.6
Q ss_pred CCCCCCCCCC-CeeEcccceeEehhhh
Q psy62 1 KCFECNAHNP-QWASVTYGIWICLECS 26 (262)
Q Consensus 1 ~C~DCga~~P-~WaSv~~GifiC~~Cs 26 (262)
+|+.||.+.+ ...|+..|-++|.+|+
T Consensus 156 ~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 156 SCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHhCcCCcCCCcceeeccCcccchhcc
Confidence 5999999865 7999999999999998
No 22
>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=56.96 E-value=6.4 Score=27.24 Aligned_cols=26 Identities=31% Similarity=0.841 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSG 27 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csg 27 (262)
+|+=|+.+.+. .=.=+|.|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 58889988776 334478999999943
No 23
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=55.74 E-value=8.2 Score=30.44 Aligned_cols=26 Identities=31% Similarity=0.775 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGK 28 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csgv 28 (262)
.|-.|+.+ .--=+..|||.|..|--.
T Consensus 37 ~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 37 VCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred cCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 48899987 555678899999999443
No 24
>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=54.10 E-value=8.6 Score=24.90 Aligned_cols=30 Identities=27% Similarity=0.664 Sum_probs=21.6
Q ss_pred CCCCCCC-CCCeeEccccee-EehhhhhhhcC
Q psy62 2 CFECNAH-NPQWASVTYGIW-ICLECSGKHRG 31 (262)
Q Consensus 2 C~DCga~-~P~WaSv~~Gif-iC~~CsgvHR~ 31 (262)
|..|++. .|+|=....|-. ||-.|--.+|.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHH
Confidence 8899985 699998888888 99999765554
No 25
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=53.96 E-value=4.1 Score=28.66 Aligned_cols=43 Identities=21% Similarity=0.546 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCee--EcccceeEehhhhhhhcCCCCCccceeeccc
Q psy62 1 KCFECNAHNPQWA--SVTYGIWICLECSGKHRGLGVHLSFVRSISM 44 (262)
Q Consensus 1 ~C~DCga~~P~Wa--Sv~~GifiC~~CsgvHR~LGvhiS~VrSitm 44 (262)
+|+=||.+-.-.- -+.=| +||-.|...-.++-.....++.+|+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~~~~~~t~ 45 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVKIKKNLTL 45 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchhhhhhccH
Confidence 5888888755443 34457 8999999765444322233344444
No 26
>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=52.36 E-value=4.6 Score=26.41 Aligned_cols=26 Identities=23% Similarity=0.599 Sum_probs=15.7
Q ss_pred CCCCCCCC-CCCeeEcccceeEehhhh
Q psy62 1 KCFECNAH-NPQWASVTYGIWICLECS 26 (262)
Q Consensus 1 ~C~DCga~-~P~WaSv~~GifiC~~Cs 26 (262)
+|.+|+.+ .-.|..-+|+.-||..|.
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred hHhHhCCHHHHHHHHHhCCcccccccc
Confidence 49999985 458999999999999994
No 27
>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=47.06 E-value=14 Score=24.20 Aligned_cols=21 Identities=29% Similarity=0.888 Sum_probs=18.8
Q ss_pred CCCCCCCCCCeeEcccceeEehhh
Q psy62 2 CFECNAHNPQWASVTYGIWICLEC 25 (262)
Q Consensus 2 C~DCga~~P~WaSv~~GifiC~~C 25 (262)
|..|++. |....=|-++|.+|
T Consensus 11 C~~C~~~---~~~~~dG~~yC~~c 31 (36)
T PF11781_consen 11 CPVCGSR---WFYSDDGFYYCDRC 31 (36)
T ss_pred CCCCCCe---EeEccCCEEEhhhC
Confidence 8888887 88889999999998
No 28
>PRK12495 hypothetical protein; Provisional
Probab=40.44 E-value=14 Score=33.79 Aligned_cols=24 Identities=25% Similarity=0.451 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGK 28 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csgv 28 (262)
.|.+||.|=|. + -|+-+|..|..+
T Consensus 44 hC~~CG~PIpa---~-pG~~~Cp~CQ~~ 67 (226)
T PRK12495 44 HCDECGDPIFR---H-DGQEFCPTCQQP 67 (226)
T ss_pred hcccccCcccC---C-CCeeECCCCCCc
Confidence 49999999982 2 599999999643
No 29
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=37.18 E-value=26 Score=24.53 Aligned_cols=34 Identities=24% Similarity=0.535 Sum_probs=26.8
Q ss_pred CCCCCCCC-CCCeeEcccce-eEehhhhhhhcCCCC
Q psy62 1 KCFECNAH-NPQWASVTYGI-WICLECSGKHRGLGV 34 (262)
Q Consensus 1 ~C~DCga~-~P~WaSv~~Gi-fiC~~CsgvHR~LGv 34 (262)
.|..|+.. .|+|=.-..|- +||-.|--..+..+.
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 59999985 58998888886 999999776665444
No 30
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=34.31 E-value=26 Score=23.45 Aligned_cols=16 Identities=25% Similarity=0.742 Sum_probs=11.0
Q ss_pred CCCCCCCCCCCeeEcc
Q psy62 1 KCFECNAHNPQWASVT 16 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~ 16 (262)
+|.+|+..+.-|+++.
T Consensus 1 ~C~~C~~~~~l~~CL~ 16 (50)
T smart00290 1 RCSVCGTIENLWLCLT 16 (50)
T ss_pred CcccCCCcCCeEEecC
Confidence 6999998775454444
No 31
>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=34.23 E-value=5.5 Score=25.62 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=15.4
Q ss_pred CCCCCCCCCCC-eeEcccceeEehhhhhhh
Q psy62 1 KCFECNAHNPQ-WASVTYGIWICLECSGKH 29 (262)
Q Consensus 1 ~C~DCga~~P~-WaSv~~GifiC~~CsgvH 29 (262)
.|.+||.+=|. =.-+--+..+|.+|+..|
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 37888875331 111222677899998764
No 32
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=33.94 E-value=26 Score=28.66 Aligned_cols=31 Identities=32% Similarity=0.766 Sum_probs=25.9
Q ss_pred CCCCCCCCCCeeEcccc--eeEehhhhhhhcCCCC
Q psy62 2 CFECNAHNPQWASVTYG--IWICLECSGKHRGLGV 34 (262)
Q Consensus 2 C~DCga~~P~WaSv~~G--ifiC~~CsgvHR~LGv 34 (262)
|.||+-- .|++-.-| |+-|.+|-=+||.-++
T Consensus 45 c~~~~~g--ewi~~~~G~~VwSC~dC~~iH~ke~~ 77 (112)
T COG2158 45 CENEELG--EWISDSNGRKVWSCSDCHWIHRKEGA 77 (112)
T ss_pred ccccccC--ceeEcCCCCEEeeccccceecccchH
Confidence 5666655 89999999 9999999999997655
No 33
>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=33.46 E-value=25 Score=25.25 Aligned_cols=23 Identities=22% Similarity=0.676 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCeeEcccceeEehhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLEC 25 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~C 25 (262)
.|..||..... ..+--+|.|..|
T Consensus 30 ~C~~CG~~~~~--~~~~r~~~C~~C 52 (69)
T PF07282_consen 30 TCPRCGHRNKK--RRSGRVFTCPNC 52 (69)
T ss_pred CccCccccccc--ccccceEEcCCC
Confidence 48889988777 777889999998
No 34
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=32.42 E-value=25 Score=27.22 Aligned_cols=32 Identities=22% Similarity=0.548 Sum_probs=23.5
Q ss_pred CCCCCCCCCCC---eeEcccc---eeEehhhhhhhcCC
Q psy62 1 KCFECNAHNPQ---WASVTYG---IWICLECSGKHRGL 32 (262)
Q Consensus 1 ~C~DCga~~P~---WaSv~~G---ifiC~~CsgvHR~L 32 (262)
.|+-||.+-|. +...--| .|-|..|.+|+..|
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i 39 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLI 39 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHH
Confidence 59999998873 3333334 89999999998653
No 35
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=30.78 E-value=33 Score=27.16 Aligned_cols=25 Identities=36% Similarity=0.821 Sum_probs=19.1
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSG 27 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csg 27 (262)
.|.-||........+ |||-|..|--
T Consensus 38 ~CpfCgk~~vkR~a~--GIW~C~~C~~ 62 (90)
T PTZ00255 38 FCPFCGKHAVKRQAV--GIWRCKGCKK 62 (90)
T ss_pred cCCCCCCCceeeeee--EEEEcCCCCC
Confidence 488899777665544 9999999943
No 36
>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=30.72 E-value=31 Score=34.57 Aligned_cols=30 Identities=20% Similarity=0.190 Sum_probs=21.4
Q ss_pred cccchhhhhhhhh--hHHHHHHHHHHHHHhhh
Q psy62 195 LFGGAVSSLTSGW--SMFSSSATKLASKATEN 224 (262)
Q Consensus 195 ~~~~~~~~l~~Gw--~~fs~~~~k~a~~~~e~ 224 (262)
-..+|.++++.|| |.++++|+++++++.+.
T Consensus 117 ~~~~p~~s~ggwWsWGs~~stAss~~~~a~kq 148 (444)
T PF10310_consen 117 EEPDPIASSGGWWSWGSIWSTASSAAEQAMKQ 148 (444)
T ss_pred CCCCcccccCCcccccchhhHHHHHHHHHHHH
Confidence 4577788888887 68888888666555443
No 37
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=30.69 E-value=33 Score=32.22 Aligned_cols=28 Identities=21% Similarity=0.439 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKH 29 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvH 29 (262)
+|.+||..+. =....-|-.||.+|--|.
T Consensus 13 ~Cp~Cg~~~i-v~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 13 VCPECGSDKL-IYDYERGEIVCADCGLVI 40 (310)
T ss_pred cCcCCCCCCe-eEECCCCeEeecccCCcc
Confidence 5999997432 223567999999996643
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.64 E-value=22 Score=24.24 Aligned_cols=22 Identities=32% Similarity=0.597 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCeeEcccceeEehhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLEC 25 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~C 25 (262)
+|.+||...... .....-|.+|
T Consensus 4 ~C~~Cg~~~~~~---~~~~irC~~C 25 (44)
T smart00659 4 ICGECGRENEIK---SKDVVRCREC 25 (44)
T ss_pred ECCCCCCEeecC---CCCceECCCC
Confidence 599999965433 4577889999
No 39
>PF14376 Haem_bd: Haem-binding domain
Probab=30.00 E-value=24 Score=29.39 Aligned_cols=38 Identities=16% Similarity=0.671 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCee---EcccceeEehhhhhhhcCCCCCccc-eeecccCCCC
Q psy62 1 KCFECNAHNPQWA---SVTYGIWICLECSGKHRGLGVHLSF-VRSISMDKWK 48 (262)
Q Consensus 1 ~C~DCga~~P~Wa---Sv~~GifiC~~CsgvHR~LGvhiS~-VrSitmD~W~ 48 (262)
.|.||++.+..|. .+.-..+ -+..||.. .|.+.++.|.
T Consensus 43 ~CydCHSn~T~~PwYa~i~p~s~----------l~~~dI~~Gr~~lNfs~~~ 84 (137)
T PF14376_consen 43 SCYDCHSNNTRYPWYANIAPASW----------LMEKDIKEGRRHLNFSEWG 84 (137)
T ss_pred cccccCCCCCCCccceecCchHH----------HHHHHHHHHHHHhCcchhh
Confidence 4999999886665 3322222 12224332 4677778874
No 40
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=29.95 E-value=26 Score=22.22 Aligned_cols=24 Identities=25% Similarity=0.641 Sum_probs=12.3
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSG 27 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csg 27 (262)
+|--|++... | ..-.+|||.+|..
T Consensus 4 ~Cp~C~se~~-y--~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYT-Y--EDGELLVCPECGH 27 (30)
T ss_dssp --TTT------E--E-SSSEEETTTTE
T ss_pred CCCCCCCcce-e--ccCCEEeCCcccc
Confidence 4777777654 3 5667999999953
No 41
>PTZ00074 60S ribosomal protein L34; Provisional
Probab=25.33 E-value=37 Score=28.77 Aligned_cols=26 Identities=35% Similarity=0.726 Sum_probs=18.2
Q ss_pred CCCCCCCCC-------C----------CeeEcccceeEehhhh
Q psy62 1 KCFECNAHN-------P----------QWASVTYGIWICLECS 26 (262)
Q Consensus 1 ~C~DCga~~-------P----------~WaSv~~GifiC~~Cs 26 (262)
+|.|||.+- | .-++=.||-.+|..|-
T Consensus 43 kC~~cg~~L~GI~~~Rp~e~~rlsK~~KtvsRaYGG~lC~~CV 85 (135)
T PTZ00074 43 KCGDCGKVLAGIKALRPTEYKQLSRRERTVSRAYGGVLCHKCV 85 (135)
T ss_pred CCCCCCCccCCccCCchHHHHHccccCCCccCCCccchhHHHH
Confidence 599999752 1 1245678888998884
No 42
>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=24.58 E-value=49 Score=25.45 Aligned_cols=27 Identities=22% Similarity=0.549 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhc
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHR 30 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR 30 (262)
.|.=||.+... ..||++.|..|++..|
T Consensus 1 ~C~VCg~~~~g---~hygv~sC~aC~~FFR 27 (87)
T cd07162 1 ICRVCGDRATG---YHFNAMTCEGCKGFFR 27 (87)
T ss_pred CCcccCCcCcc---eEECcceehhhHHHHH
Confidence 47778876554 4899999999999876
No 43
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.71 E-value=38 Score=21.96 Aligned_cols=27 Identities=19% Similarity=0.390 Sum_probs=13.8
Q ss_pred CCCCCCCCCCeeEc---ccceeEehhhhhhh
Q psy62 2 CFECNAHNPQWASV---TYGIWICLECSGKH 29 (262)
Q Consensus 2 C~DCga~~P~WaSv---~~GifiC~~CsgvH 29 (262)
|-.||.+ -++.-+ +.--++|..|.-||
T Consensus 3 C~~CG~~-l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCGGP-LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT--B--EEE--TT-SS-EEEETTTTEEE
T ss_pred cccccCh-hhhhcCCCCCccceECCCCCCEE
Confidence 6778876 233322 44567899998877
No 44
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.00 E-value=40 Score=38.02 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=14.3
Q ss_pred hhhccHHHHHHHHHHhcccCCCCcccCC
Q psy62 81 QKYNTKAAALYRDKVSSSYMFNTFTTKG 108 (262)
Q Consensus 81 ~KY~~~aa~~yr~kl~~~~~gr~~~~~~ 108 (262)
.+|--+++.+.-+.|..-|-=.+|+.-+
T Consensus 844 a~yl~~va~fiDdLL~k~Ygl~~fYn~~ 871 (1337)
T PRK14714 844 AEYLLKVAKFVDDLLEKFYGLPRFYNVE 871 (1337)
T ss_pred HHHHHHHHHHHHHHHHHhhCCCcccCCC
Confidence 3555555555555555555544555433
No 45
>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=22.88 E-value=52 Score=26.03 Aligned_cols=24 Identities=33% Similarity=0.845 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECS 26 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Cs 26 (262)
.|.-||.... --+..|||-|..|-
T Consensus 37 ~Cp~Cgk~~v--kR~a~GIW~C~~C~ 60 (90)
T PF01780_consen 37 TCPFCGKTSV--KRVATGIWKCKKCG 60 (90)
T ss_dssp EESSSSSSEE--EEEETTEEEETTTT
T ss_pred cCCCCCCcee--EEeeeEEeecCCCC
Confidence 3888988763 44577999999994
No 46
>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=22.73 E-value=54 Score=24.21 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=20.5
Q ss_pred CCCCCCCCCCeeEcccceeEehhhhhhhcC
Q psy62 2 CFECNAHNPQWASVTYGIWICLECSGKHRG 31 (262)
Q Consensus 2 C~DCga~~P~WaSv~~GifiC~~CsgvHR~ 31 (262)
|.=||.+.-. ..||++.|..|.+..|-
T Consensus 1 C~VC~~~~~g---~hygv~sC~aC~~FFRR 27 (72)
T cd07156 1 CGVCGDRATG---YHFNAMTCEGCKGFFRR 27 (72)
T ss_pred CCccCccCcc---cEECcceehhhhhhhch
Confidence 5557765543 58999999999998773
No 47
>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=22.47 E-value=45 Score=26.37 Aligned_cols=27 Identities=22% Similarity=0.620 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhc
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHR 30 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR 30 (262)
.|.=||.+.- ...||++.|..|.+..|
T Consensus 6 ~C~VCg~~a~---g~hyGv~sC~aCk~FFR 32 (97)
T cd07170 6 LCLVCGDIAS---GYHYGVASCEACKAFFK 32 (97)
T ss_pred CCeecCCcCc---ceEECceeehhhhHHHH
Confidence 3677887553 45899999999999877
No 48
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=22.11 E-value=48 Score=24.16 Aligned_cols=27 Identities=26% Similarity=0.732 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhc
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHR 30 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR 30 (262)
.|.-||.+.- ...||++.|..|.+..|
T Consensus 1 ~C~vC~~~~~---~~hygv~~C~aC~~FFR 27 (70)
T smart00399 1 LCCVCGDHAS---GFHFGVCSCRACKAFFR 27 (70)
T ss_pred CCeEeCCcCc---ccEeCCcEechhhhhhh
Confidence 3667876654 34899999999999876
No 49
>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=21.35 E-value=47 Score=26.03 Aligned_cols=28 Identities=18% Similarity=0.421 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRG 31 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~ 31 (262)
.|.=||.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aC~~FFRR 29 (94)
T cd06966 2 ICGVCGDKAL---GYNFNAITCESCKAFFRR 29 (94)
T ss_pred CCeeCCCcCc---ceEECcceeeeehheehh
Confidence 3677886543 458999999999998763
No 50
>PHA02540 61 DNA primase; Provisional
Probab=21.32 E-value=56 Score=31.55 Aligned_cols=56 Identities=21% Similarity=0.551 Sum_probs=40.9
Q ss_pred CCCCCCCCCC------CeeEcccc--eeEehhhhhhhcCCCCCccceeecccCCCCHHHHHhhhcCCh
Q psy62 1 KCFECNAHNP------QWASVTYG--IWICLECSGKHRGLGVHLSFVRSISMDKWKDIELEKMKVGGN 60 (262)
Q Consensus 1 ~C~DCga~~P------~WaSv~~G--ifiC~~CsgvHR~LGvhiS~VrSitmD~W~~~el~~m~~gGN 60 (262)
+|.=|+...+ =|++..-+ +|-|..| |.| |--|.||....-..|.+.--++.+..|+
T Consensus 29 ~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgC-Ga~---Gd~i~Flme~e~lsf~Eav~~la~~~g~ 92 (337)
T PHA02540 29 RCPICGDSQKDKNKARGWIYEKKDGGVFKCHNC-GYH---RPFGNFLKDYEPDLYREYIMERFKERGT 92 (337)
T ss_pred cCCCCCCccccCcCCcEEEeccCCceEEEecCC-CCC---CCHHHHHHHhcCCChHHHHHHHHHHhCC
Confidence 4777887554 48888888 9999999 555 4557788887777787765556666664
No 51
>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,
Probab=21.14 E-value=49 Score=25.08 Aligned_cols=27 Identities=30% Similarity=0.694 Sum_probs=20.9
Q ss_pred CCCCCCCCCCeeEcccceeEehhhhhhhcC
Q psy62 2 CFECNAHNPQWASVTYGIWICLECSGKHRG 31 (262)
Q Consensus 2 C~DCga~~P~WaSv~~GifiC~~CsgvHR~ 31 (262)
|.=||.+.- ...||++.|..|....|-
T Consensus 1 C~VCg~~~~---g~hyG~~sC~aC~~FFRR 27 (81)
T cd07165 1 CKVCGDKAS---GYHYGVTSCEGCKGFFRR 27 (81)
T ss_pred CCccCccCc---ceEECchhhhhHHHHHHh
Confidence 556776553 458999999999998773
No 52
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=21.11 E-value=40 Score=20.57 Aligned_cols=27 Identities=19% Similarity=0.409 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhh
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSG 27 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~Csg 27 (262)
+|.-|+..-+.=.--....++|..|..
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 366677665554455667889988864
No 53
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) 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. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=20.99 E-value=47 Score=25.58 Aligned_cols=28 Identities=18% Similarity=0.501 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCeeEcccceeEehhhhhhhcC
Q psy62 1 KCFECNAHNPQWASVTYGIWICLECSGKHRG 31 (262)
Q Consensus 1 ~C~DCga~~P~WaSv~~GifiC~~CsgvHR~ 31 (262)
.|.=||.+.- ...||++.|..|.+..|-
T Consensus 2 ~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 29 (86)
T cd07157 2 TCQVCGEPAA---GFHHGAYVCEACKKFFMR 29 (86)
T ss_pred CCcccCCcCc---ccEECcceeeEeeeEEec
Confidence 3777887553 469999999999998763
No 54
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=20.41 E-value=59 Score=22.96 Aligned_cols=34 Identities=26% Similarity=0.599 Sum_probs=26.3
Q ss_pred CCCCCCCC-CCCeeEcc-cceeEehhhhhhhcCCCC
Q psy62 1 KCFECNAH-NPQWASVT-YGIWICLECSGKHRGLGV 34 (262)
Q Consensus 1 ~C~DCga~-~P~WaSv~-~GifiC~~CsgvHR~LGv 34 (262)
.|..|+.. -|+|=.-. -+..||-.|--..+..|.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~~~ 36 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKHGV 36 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhcCC
Confidence 59999985 58998755 788999999766666553
Done!