Query 005784
Match_columns 677
No_of_seqs 216 out of 1212
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 13:42:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03131 hypothetical protein; 100.0 1.5E-67 3.3E-72 576.8 39.7 254 1-257 1-322 (705)
2 PLN03119 putative ADP-ribosyla 100.0 3.6E-58 7.8E-63 500.2 34.0 252 1-257 1-305 (648)
3 KOG0702 Predicted GTPase-activ 100.0 1.4E-43 3E-48 381.3 29.0 467 1-555 1-523 (524)
4 KOG0703 Predicted GTPase-activ 100.0 1.1E-37 2.3E-42 321.1 12.0 118 6-126 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 9.5E-36 2.1E-40 271.4 8.3 111 13-124 2-115 (116)
6 smart00105 ArfGap Putative GTP 100.0 5.4E-34 1.2E-38 258.7 10.1 106 22-127 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 2.9E-31 6.3E-36 278.7 10.1 117 9-125 5-125 (319)
8 PLN03114 ADP-ribosylation fact 99.9 5.7E-26 1.2E-30 239.1 15.7 116 12-127 10-130 (395)
9 KOG0704 ADP-ribosylation facto 99.9 4E-25 8.6E-30 231.5 8.5 114 9-122 4-124 (386)
10 KOG0706 Predicted GTPase-activ 99.9 1.7E-24 3.7E-29 232.4 7.4 82 11-92 10-94 (454)
11 KOG0705 GTPase-activating prot 99.9 9.1E-24 2E-28 231.5 8.7 114 14-128 503-619 (749)
12 KOG0521 Putative GTPase activa 99.8 1.2E-20 2.7E-25 217.7 3.8 116 14-129 416-535 (785)
13 KOG1117 Rho- and Arf-GTPase ac 99.7 3.1E-17 6.7E-22 186.1 4.8 111 14-125 288-403 (1186)
14 KOG0818 GTPase-activating prot 99.7 2.7E-17 5.8E-22 178.8 4.0 108 20-127 4-121 (669)
15 KOG0702 Predicted GTPase-activ 98.4 4.5E-05 9.9E-10 84.9 22.7 75 180-254 153-248 (524)
16 KOG0521 Putative GTPase activa 91.4 0.022 4.7E-07 68.0 -3.4 71 19-91 625-699 (785)
17 PF00643 zf-B_box: B-box zinc 86.5 0.54 1.2E-05 35.5 2.3 40 23-64 2-42 (42)
18 PRK12495 hypothetical protein; 80.9 1.3 2.7E-05 46.1 2.9 36 14-53 29-67 (226)
19 PRK00085 recO DNA repair prote 80.3 2.5 5.4E-05 43.0 4.8 32 21-52 146-178 (247)
20 TIGR00613 reco DNA repair prot 76.2 4.6 0.0001 40.9 5.3 33 21-53 144-177 (241)
21 COG1734 DksA DnaK suppressor p 64.7 2.3 4.9E-05 40.4 0.2 46 9-54 63-111 (120)
22 PF11781 RRN7: RNA polymerase 55.5 7.8 0.00017 29.6 1.6 28 21-51 5-32 (36)
23 COG1381 RecO Recombinational D 50.9 8.1 0.00018 40.4 1.5 30 22-51 152-182 (251)
24 PF08271 TF_Zn_Ribbon: TFIIB z 50.2 8.1 0.00018 29.9 1.0 27 26-53 2-28 (43)
25 TIGR02419 C4_traR_proteo phage 46.3 10 0.00023 32.0 1.2 33 21-54 28-62 (63)
26 PRK11019 hypothetical protein; 46.1 9.4 0.0002 34.6 0.9 31 24-55 36-68 (88)
27 PF01286 XPA_N: XPA protein N- 41.4 8.7 0.00019 29.3 -0.0 27 25-51 4-31 (34)
28 TIGR02890 spore_yteA sporulati 41.0 15 0.00032 36.4 1.5 31 24-54 86-117 (159)
29 KOG2057 Predicted equilibrativ 38.6 4.8E+02 0.01 29.5 12.4 27 227-255 313-339 (499)
30 KOG3362 Predicted BBOX Zn-fing 38.4 12 0.00026 37.0 0.4 34 22-56 116-150 (156)
31 cd03031 GRX_GRX_like Glutaredo 37.9 18 0.00038 35.4 1.5 42 7-57 82-123 (147)
32 TIGR00100 hypA hydrogenase nic 36.6 19 0.00042 33.6 1.5 43 21-67 67-113 (115)
33 PRK00420 hypothetical protein; 36.4 58 0.0013 30.9 4.5 44 7-53 4-49 (112)
34 PRK13715 conjugal transfer pro 35.7 16 0.00034 32.0 0.7 31 24-54 34-65 (73)
35 PRK10778 dksA RNA polymerase-b 35.4 22 0.00048 35.0 1.7 35 21-55 108-143 (151)
36 PHA00080 DksA-like zinc finger 35.0 19 0.00042 31.3 1.1 32 22-54 29-62 (72)
37 PF14376 Haem_bd: Haem-binding 33.5 30 0.00065 33.3 2.2 23 12-38 33-55 (137)
38 smart00401 ZnF_GATA zinc finge 32.1 35 0.00076 27.8 2.1 36 23-58 2-39 (52)
39 PRK00564 hypA hydrogenase nick 29.5 22 0.00049 33.3 0.6 43 22-67 69-115 (117)
40 PF02318 FYVE_2: FYVE-type zin 29.4 79 0.0017 29.5 4.2 32 23-54 53-89 (118)
41 PRK00423 tfb transcription ini 28.2 34 0.00074 36.9 1.9 35 21-56 8-42 (310)
42 KOG2236 Uncharacterized conser 27.6 1.5E+02 0.0032 34.5 6.6 19 511-535 411-429 (483)
43 KOG0119 Splicing factor 1/bran 27.1 1.1E+03 0.024 28.0 18.7 60 505-572 459-520 (554)
44 PF04189 Gcd10p: Gcd10p family 26.4 58 0.0013 35.5 3.2 46 67-120 106-151 (299)
45 PRK12380 hydrogenase nickel in 25.4 41 0.00088 31.4 1.6 42 21-66 67-112 (113)
46 cd07171 NR_DBD_ER DNA-binding 25.4 38 0.00083 30.0 1.3 31 23-56 2-32 (82)
47 KOG1985 Vesicle coat complex C 24.9 1.1E+03 0.024 29.6 13.4 12 614-625 84-95 (887)
48 PRK03681 hypA hydrogenase nick 24.8 27 0.00058 32.7 0.3 44 20-66 66-113 (114)
49 PF14803 Nudix_N_2: Nudix N-te 23.6 34 0.00073 26.0 0.6 30 25-55 1-33 (34)
50 PF01258 zf-dskA_traR: Prokary 23.5 12 0.00027 27.9 -1.8 29 26-54 5-34 (36)
51 cd06968 NR_DBD_ROR DNA-binding 23.1 43 0.00094 30.5 1.3 31 23-56 4-34 (95)
52 COG1997 RPL43A Ribosomal prote 22.9 84 0.0018 28.9 3.0 29 22-52 33-61 (89)
53 COG0353 RecR Recombinational D 22.5 73 0.0016 33.0 2.8 66 7-85 36-102 (198)
54 PRK03824 hypA hydrogenase nick 22.1 53 0.0012 31.6 1.7 25 43-67 106-134 (135)
55 PF10764 Gin: Inhibitor of sig 21.7 48 0.001 26.7 1.1 26 26-52 1-26 (46)
56 cd07173 NR_DBD_AR DNA-binding 21.4 48 0.001 29.4 1.1 31 23-56 2-32 (82)
57 PRK00762 hypA hydrogenase nick 21.3 42 0.0009 31.8 0.8 47 20-67 66-119 (124)
58 PF00320 GATA: GATA zinc finge 20.9 65 0.0014 24.3 1.6 30 27-56 1-32 (36)
59 COG2174 RPL34A Ribosomal prote 20.5 59 0.0013 30.0 1.5 33 20-52 30-79 (93)
60 COG5145 RAD14 DNA excision rep 20.2 41 0.00089 35.6 0.6 33 21-54 113-147 (292)
61 PLN03131 hypothetical protein; 20.0 1.8E+02 0.0039 35.0 5.6 52 521-572 601-652 (705)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-67 Score=576.77 Aligned_cols=254 Identities=51% Similarity=0.857 Sum_probs=231.2
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCCcceeecccccCCHHHHHHHHhc
Q 005784 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (677)
Q Consensus 1 M~sr~ke~ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~LgHrVKSIsLD~WT~eEV~~mq~g 80 (677)
|++| |++|++|++|++|+++++|++||||++++|+|||+|||||||++|+||||+|+||||||+||+|+.+||++|+.+
T Consensus 1 m~Sk-kqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLghRVKSVTLD~WtdeEV~~Mk~g 79 (705)
T PLN03131 1 MGSR-KEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFTHRVKSVSMSKFTSQDVEALQNG 79 (705)
T ss_pred Ccch-HHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccCcccccccCCCCCHHHHHHHHHh
Confidence 8898 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCCCCCCCccCCCCcccccccc-cCCCCCCCC---
Q 005784 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRS--- 156 (677)
Q Consensus 81 GN~raN~i~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e~~~d~ppr~k~~~keds~e~Rr-~sy~~gs~S--- 156 (677)
||+++|+|||++|+..+.+.|+..+.+++|+|||.|||+|||+.....+++++.....+.+..|+|| ++|++|+||
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr~~syh~~SqSPpY 159 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRRACSYHSYSQSPPY 159 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccccccccCCCcCCCc
Confidence 9999999999999988778888888888999999999999999999999999887666667778999 899988775
Q ss_pred ---------------------------------------------------------CCCC------CC-CCCCCCCCCC
Q 005784 157 ---------------------------------------------------------PISD------GD-SKLEGRSPEQ 172 (677)
Q Consensus 157 ---------------------------------------------------------r~sd------~~-~k~~~kS~~s 172 (677)
|.+| ++ ++++.++++.
T Consensus 160 ~~~yedrRygk~~~~~~R~pg~d~~~~~~k~~~~~~SP~r~~d~~~eDrf~ne~~~~r~~d~s~ss~~~~~r~~~~SP~~ 239 (705)
T PLN03131 160 DFQYEDRRYGKQAGILTRKPGSDRGLNVGKMASFICSPTRLNDRMFEDRFANEGSVSGVSDYSVSSGGDLVRSGAESPNF 239 (705)
T ss_pred ccccccccccccccccccCCccccccccccccccccCchhhhhhhhhcccccCCCCcccccccccccccccccCCCCCCc
Confidence 1111 12 4556678888
Q ss_pred CCCCCCCCCCCCCccccccCCCCCCCCcCCCCCCCCCCcCCCCCccccccCCCCCCCCCCCcchhhhcccCCccCCCCCC
Q 005784 173 PKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVKLETTGSLIDFDADP 252 (677)
Q Consensus 173 ~kd~~ssSpP~v~Pv~dlLG~daPpl~i~~~~k~~~~~~~~gs~~~qr~sssss~~s~~~~~~~~K~~~s~sLiDf~sdp 252 (677)
+|+... +|+++|+++|||+|+|++||.++++++..+++++..+.||++++++++|++++..++|++++.+||||..|+
T Consensus 240 ~k~~~~--Sp~v~p~r~ilg~n~~~~~v~~~s~~~~~~~~~~~~~~Qrt~Ssgs~gS~dg~s~s~Ks~~s~sL~D~~~e~ 317 (705)
T PLN03131 240 QKDIAF--SPPIQPPKDILGEDVQQRRIDLFSAALCKQGAEGCPHIQRSASLGSIGSFDSLSVSIKSFNSGSLADIVAEA 317 (705)
T ss_pred ccccCC--CCCcccchhhccccccccccCCCcccccccccccccccccccccCcccccCCCccceeecccccccccccCc
Confidence 888753 356799999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCChh
Q 005784 253 KPSPA 257 (677)
Q Consensus 253 ~p~~~ 257 (677)
++.-+
T Consensus 318 ~~~~~ 322 (705)
T PLN03131 318 EQAAG 322 (705)
T ss_pred ccccc
Confidence 96544
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=3.6e-58 Score=500.17 Aligned_cols=252 Identities=47% Similarity=0.766 Sum_probs=187.4
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCCcceeecccccCCHHHHHHHHhc
Q 005784 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (677)
Q Consensus 1 M~sr~ke~ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~LgHrVKSIsLD~WT~eEV~~mq~g 80 (677)
|++| |++||++++|++|+++++|++||||++++|+|||+|||||||++|+||||+|+||||||+||+|+.+||++|+.+
T Consensus 1 M~SK-R~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLGhRVKSLSLDkWT~EEVe~Mk~g 79 (648)
T PLN03119 1 MGSK-REEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFTHRVKSVSMSKFTSKEVEVLQNG 79 (648)
T ss_pred Ccch-HHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCCceeeccccCCCCHHHHHHHHHh
Confidence 8998 899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCCCCCCCccCCCCcccccccc-cCCCCCCCCCC-
Q 005784 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPI- 158 (677)
Q Consensus 81 GN~raN~i~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e~~~d~ppr~k~~~keds~e~Rr-~sy~~gs~Sr~- 158 (677)
||+++|+|||++|+..+.+.|+..+.+++|+|||+|||+|||++....|++++.....+....++|+ .+|+++++++.
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~~~s~h~~s~sp~y 159 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRRANSYHSYSQSPPY 159 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccccccCCCCCCCCCc
Confidence 9999999999999987777788888888999999999999999999999988754344444445677 88998887622
Q ss_pred -------------------CCCCCCCCCCC---------------CCC---------CCCCCCCCCCCCCccc-cccCCC
Q 005784 159 -------------------SDGDSKLEGRS---------------PEQ---------PKDPESSSPPVVRPVR-EILGDN 194 (677)
Q Consensus 159 -------------------sd~~~k~~~kS---------------~~s---------~kd~~ssSpP~v~Pv~-dlLG~d 194 (677)
..-+..+.+|. +|. ..|...+ ....+++ +++.-+
T Consensus 160 ~~~ye~rr~~~~~~~~~~~~~s~r~~~~k~~~~~~s~~~~~~~m~ed~f~~e~~~~r~sd~s~s--s~g~~~~~~~~sp~ 237 (648)
T PLN03119 160 DYQYEERRYGKIPLGFTGKSASVKGLHAKASSFVYSPGRFSDHMFEDQFSNEDSAPRASDYSVS--SAGDPFRSDIQSPN 237 (648)
T ss_pred ccchhhhhccccccccccCCCccccccccccceeeccchHHHHhhhhhcccCCCCCcccccccc--cCCcccccCcCCCC
Confidence 10000111110 010 0010001 1111221 111111
Q ss_pred -------CCCCCcCCCCCCCCCCcCCCCCccccccCCCCCCCCCCCcchhhhcccCCccCCCCCCCCChh
Q 005784 195 -------VLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVKLETTGSLIDFDADPKPSPA 257 (677)
Q Consensus 195 -------aPpl~i~~~~k~~~~~~~~gs~~~qr~sssss~~s~~~~~~~~K~~~s~sLiDf~sdp~p~~~ 257 (677)
-|+++-...-. +...-.+ ..+.|||++++++++.|++..++|++++++|.|+..|.+..-+
T Consensus 238 ~~~~~~~~~~~~~~~~~~-~~~~~~~-~~~sqRT~SsGs~gSfDs~s~S~ks~~Sg~l~d~~~E~~~~~~ 305 (648)
T PLN03119 238 FQQEAEFRSPQFQHSNAP-PSENLFP-GRQHQRTTSSGSVRSVDSNFMSIKSYTSGGLGEAVSESRQNTG 305 (648)
T ss_pred cccccccCCcccccccCc-chhhccc-ccccccccccccccccccccccccccccCCccccccccccccc
Confidence 11111110000 0001111 4678999999999999999999999999999999999885433
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.4e-43 Score=381.30 Aligned_cols=467 Identities=30% Similarity=0.375 Sum_probs=324.9
Q ss_pred CcchhhhhHHH-HHHHHHHHcCCCCCCCcCCCCCCC-CeeEecceeheehhhhhhhccCC--cceeecccccCCHHHHHH
Q 005784 1 MANRLKEDEKN-ERIIRGLLKLQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHREFT--HRVKSVSMAKFTSQEVKA 76 (677)
Q Consensus 1 M~sr~ke~ern-ekiLr~Llk~pgNk~CADCga~~P-~WaSin~GVFVC~~CSGIHR~Lg--HrVKSIsLD~WT~eEV~~ 76 (677)
|++++||+|++ |++||+|+++++||+|+||+.+.. +|+++..|-|||+.|+|+.|.|. ||||+|+|.+|+..||..
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~ 80 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSF 80 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHH
Confidence 78899999997 999999999999999999999988 99999999999999999999996 999999999999999999
Q ss_pred HHhcCcHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCCCCCC-Ccc--CCCCcccccc-cccC---
Q 005784 77 LQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPP-RVK--MGDKEDSYDI-RRDT--- 149 (677)
Q Consensus 77 mq~gGN~raN~i~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e~~~d~pp-r~k--~~~keds~e~-Rr~s--- 149 (677)
|+++||+.+++||++..+.++...||++|.+++|+|||+||++|||+.++..++-+ -.+ ++.++-.++. |.+.
T Consensus 81 lQshgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~tr~s~s~~s~~~~~s~~~~~~l 160 (524)
T KOG0702|consen 81 LQSHGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSYTRGSLSEDSRPVSESRPETKSL 160 (524)
T ss_pred HhhcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccccccccccccCCcccccCCCcccc
Confidence 99999999999999999999999999999999999999999999999876654422 111 1111111111 1110
Q ss_pred --CCCC-----------CCC--------C--CCCCCC-CCCC--------CCCCCCCCCCCCCCCCCCccccccCCCCCC
Q 005784 150 --YQGG-----------SRS--------P--ISDGDS-KLEG--------RSPEQPKDPESSSPPVVRPVREILGDNVLP 197 (677)
Q Consensus 150 --y~~g-----------s~S--------r--~sd~~~-k~~~--------kS~~s~kd~~ssSpP~v~Pv~dlLG~daPp 197 (677)
+-+. +++ | +.++++ .|.. .+..+.+.+.+++++.-+++..++++..-.
T Consensus 161 rs~~gd~~P~~~~~t~np~~~~~~~~~~~~~~~~~rfdlfg~~k~sd~~s~s~~qss~~~~ssp~~~~~~~~~~~~s~an 240 (524)
T KOG0702|consen 161 RSLLGDHAPLLAESTKNPRSRGLPKSPIRFEIVDDRFDLFGLPKASDAQSQSTFQSSIAPSSSPPNHQSVPQAYSDSPAN 240 (524)
T ss_pred ccccCCCCcchhhcccCccccCCCCCCchhhhhhhhhhhhcCcCcccccccCcccccccccCCCCccccchhhccccccc
Confidence 1000 100 0 111111 1111 223445666677778888999999987778
Q ss_pred CCcCCCCCCCCCCcCCCCCccccccCCCCCCCCCCCcchhhhcccCCccCCCCCCCCC--hhhhhcccccccccccccCC
Q 005784 198 LRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVKLETTGSLIDFDADPKPS--PAVAQAQQKTVAQSVVQPAS 275 (677)
Q Consensus 198 l~i~~~~k~~~~~~~~gs~~~qr~sssss~~s~~~~~~~~K~~~s~sLiDf~sdp~p~--~~~~~a~qt~~~~~~~q~~~ 275 (677)
+...++.+....+....+...--...+.+..+.+++..+.+..+..+++||+.+.|-+ ..+.+.+.-+.++.+-|+++
T Consensus 241 ~~~ge~~k~P~~~~~~asapk~eg~~s~sd~pvne~~~e~~i~s~~~~~~f~k~~e~paps~a~qlp~~ss~~~~~q~t~ 320 (524)
T KOG0702|consen 241 IFAGEPFKQPVSRPSFASAPKNEGWASLSDNPVNEAKSENVITSPGSFADFLKFEEIPAPSVAMQLPPYSSTVDQHQPTI 320 (524)
T ss_pred ccccCCCCCCccCccccccccccCCcccccCccccccccccccCcccchhhcccccccCcchhhhcCCcCCCccccCCCC
Confidence 8888887766666777777766555555778888999999999999999999886544 22223333333333334433
Q ss_pred -CCCCCCcccccCcccccc---ccCCCCCCchHHHhhhcCCCCCCCCCCCCCCCCCCCCcccCCCcccccCCCCCCCccc
Q 005784 276 -SANDNNWASFDLAPQVKV---SQTSSNLNTLETVFSQLSVPASVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASV 351 (677)
Q Consensus 276 -~s~~~nWasfd~~~~~~~---~~~~~~~N~le~~l~qls~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 351 (677)
+.+.++|.+|+....... ...++..+.|.+.+.+|.|.++++|+. +.+.++
T Consensus 321 ~~~~nd~~ssf~~~~~Ap~~~~~s~p~i~s~~~s~~~~l~~~~s~~gsa-------------------------~~~~~~ 375 (524)
T KOG0702|consen 321 PSPWNDQGSSFGATPVAPPLWVASPPSIGSNLLSSSRALAVQSSVFGSA-------------------------GYVPPH 375 (524)
T ss_pred CCcccccCcccccccccCCccccCCCCcccccccccccccccccccccc-------------------------ccCCCC
Confidence 578999999998776543 333466677888888888888876521 122222
Q ss_pred CCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCccccCCCCCCccCCCC--CCcCCCCCCccccccCCCCcCC
Q 005784 352 GHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLPVSVNAGNSFSMQHQP--PLFPTAGGQFTASQFTPPVAGS 429 (677)
Q Consensus 352 ~~~~~~~~~~~~~~~~~~~~~~~f~~s~~s~~s~~~~~~~~~~~~~~~~~~~q~~q--~~f~~~~~~~~~q~~t~~~~~~ 429 (677)
+++-.++ ..-..+...|..+-+.+. .+||.+-+. + -+
T Consensus 376 ~~~n~~~-------------------------------~e~~~~s~~q~~s~ft~~~ts~~p~~~~~------~----ps 414 (524)
T KOG0702|consen 376 QPVNLGV-------------------------------LEELSNSTTQTFSAFTNESTSGFPAPIGM------A----PS 414 (524)
T ss_pred ccccccc-------------------------------ccccccccccccccccCcccccCcccccc------C----Cc
Confidence 2221000 000123333434433333 455544433 1 12
Q ss_pred CCCcccccccccCCCCCCCCCCCCCCCCcccccCCCCCCCCCCccccccCCccCc-ccccccccCCCCCCCCCCCCCCCC
Q 005784 430 SNNQQWNTSLAQNAQGPPAAQPAQSVPKPALESASGGLSQPSPVEVKSTGRTALP-EDLFTANYSSFPASVPGWQTVPPH 508 (677)
Q Consensus 430 ~n~q~w~~~~~qg~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~e~k~sgr~eLP-~DlFt~~y~~~p~~vpgwq~~pp~ 508 (677)
.| +|-.. ..+..+.+..+ + ....+.+..+|.++| .++|++.|.-...|+++||...+|
T Consensus 415 sn--------~~~~~---~~Q~~~~~~~~--g--------~~~~sl~~~~~~~~P~~~~fa~s~~qp~fP~qt~~~q~~~ 473 (524)
T KOG0702|consen 415 SN--------HHQDD---EFQPNHRNPQP--G--------AAMSSLPYGFEFASPFDMFFAMSFPQPAFPIQTPQVQQPG 473 (524)
T ss_pred cc--------ccccc---cccccccCCCC--c--------cccccCCCCCCcCCCccccccccCcCcCCCCccccccCCC
Confidence 22 12222 11222222211 1 134678899999999 999999999988999999999999
Q ss_pred Cceeeee-ccCCCCCCC--cccCCCCCCCCcCCCCCCCCcccC-CCCcccc
Q 005784 509 GMVYAMQ-YNTAAPMPN--FVHSKSTTNPFDVNNDSHPVQAQT-FPSMASL 555 (677)
Q Consensus 509 gmg~~mq-Y~~~~~~~~--~~~~~ks~npfd~~~~~~~~Q~~~-fPsm~~l 555 (677)
||+|+|+ |.+....|+ .++.-+|+|||+.+-. .+.|.+. ||+|.++
T Consensus 474 ~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~~-S~aq~~~~~p~~nPF 523 (524)
T KOG0702|consen 474 GSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASPN-SAAQFPVAFPGTNPF 523 (524)
T ss_pred CCCccccccCCcccCccccccccccccCccccCCC-CcccccccCCCCCCC
Confidence 9999999 888776666 9999999999999754 4456554 7887765
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-37 Score=321.07 Aligned_cols=118 Identities=28% Similarity=0.588 Sum_probs=107.0
Q ss_pred hhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCc
Q 005784 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGN 82 (677)
Q Consensus 6 ke~ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN 82 (677)
...++++++|++||+.++|++||||++++|+|||||+|||||++|+||||+|| | |||||+||.|++|+|+.|+.+||
T Consensus 7 ~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 7 GSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGN 86 (287)
T ss_pred cccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcc
Confidence 44678999999999999999999999999999999999999999999999998 6 99999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCC
Q 005784 83 QRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (677)
Q Consensus 83 ~raN~i~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e~ 126 (677)
.+||++||++++.. ..+|..+ +.++.|||+|||+|+|+...
T Consensus 87 ~~an~~~ea~~p~~-~~~p~~d--~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDP-FRRPGPD--DLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCcc-ccCCChH--HHHHHHHHHHHhhhhhccch
Confidence 99999999997655 3445432 36889999999999999754
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=9.5e-36 Score=271.43 Aligned_cols=111 Identities=34% Similarity=0.707 Sum_probs=92.1
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC---cceeecccccCCHHHHHHHHhcCcHHHHHHH
Q 005784 13 RIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVL 89 (677)
Q Consensus 13 kiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg---HrVKSIsLD~WT~eEV~~mq~gGN~raN~i~ 89 (677)
++|++|++.++|++||||++++|+|||++||||||++|+||||+|| |+||||+||+|+.+||++|+.+||.++|++|
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 6899999999999999999999999999999999999999999998 6999999999999999999999999999999
Q ss_pred hhcCCCCCCCCCCCChHHHHHHHHHHHHhhccccc
Q 005784 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTG 124 (677)
Q Consensus 90 ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~ 124 (677)
|++... ..+.+..++.+++++||++||++|+|+.
T Consensus 82 e~~~~~-~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANSPP-PKKPPPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTSTT-TTTHCTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCCCC-CCCCCCCCcHHHHHHHHHHHHHhhhhcc
Confidence 999333 3445556788889999999999999985
No 6
>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=5.4e-34 Score=258.69 Aligned_cols=106 Identities=28% Similarity=0.644 Sum_probs=97.5
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHHHHhhcCCCCCC
Q 005784 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQ 98 (677)
Q Consensus 22 pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~i~ea~~~p~~~ 98 (677)
++|++||||++++|+|||++||||||++|+||||+|| | +||||+||+|+++||++|+.+||.++|++||++++....
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 5899999999999999999999999999999999998 5 699999999999999999999999999999999987766
Q ss_pred CCCCCChHHHHHHHHHHHHhhcccccCCC
Q 005784 99 SFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (677)
Q Consensus 99 ~~Pdssd~~~lreFIr~KYeeKrF~~e~~ 127 (677)
+.+..++.+.+++||+.||++|+|+.++.
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 66666667788999999999999987654
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=2.9e-31 Score=278.74 Aligned_cols=117 Identities=21% Similarity=0.538 Sum_probs=102.4
Q ss_pred HHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHH
Q 005784 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (677)
Q Consensus 9 ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~ra 85 (677)
...++++..|.+.++|++||||++++|+|||||||||||++||||||+|| | +||||+||+|+.+||++|+.+||++|
T Consensus 5 ~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a 84 (319)
T COG5347 5 SEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNA 84 (319)
T ss_pred hHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhh
Confidence 34567788888899999999999999999999999999999999999998 5 99999999999999999999999999
Q ss_pred HHHHhhcCCCCC-CCCCCCChHHHHHHHHHHHHhhcccccC
Q 005784 86 KEVLLKEWDPQR-QSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (677)
Q Consensus 86 N~i~ea~~~p~~-~~~Pdssd~~~lreFIr~KYeeKrF~~e 125 (677)
|+||+++.-... .+.-...|...+++||++||++++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999999865431 2222345666789999999999999875
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.93 E-value=5.7e-26 Score=239.08 Aligned_cols=116 Identities=23% Similarity=0.405 Sum_probs=96.4
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHHH
Q 005784 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (677)
Q Consensus 12 ekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~i 88 (677)
.++|++|+++++|++|+||++++|+||++|||||||++|+||||.|| | +||||+||+|+.++|++|+.+||.++|.+
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 35799999999999999999999999999999999999999999998 4 89999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCC--CChHHHHHHHHHHHHhhcccccCCC
Q 005784 89 LLKEWDPQRQSFPD--SSNVERLRNFIKHVYVDRRYTGERN 127 (677)
Q Consensus 89 ~ea~~~p~~~~~Pd--ssd~~~lreFIr~KYeeKrF~~e~~ 127 (677)
|+.+--........ .+...++.+.+.+|++++.+..+..
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 98753211111111 2444555566888999999976543
No 9
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.91 E-value=4e-25 Score=231.46 Aligned_cols=114 Identities=28% Similarity=0.543 Sum_probs=90.5
Q ss_pred HHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHH
Q 005784 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (677)
Q Consensus 9 ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~ra 85 (677)
-+++|.|.+|....+|+.|+||++.+|+|||++||||||++|+|+||.|| | +||||+||+|++.||++|+.+||+++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 46778888888888999999999999999999999999999999999998 5 99999999999999999999999999
Q ss_pred HHHHhhcCCCCCC-CCC---CCChHHHHHHHHHHHHhhccc
Q 005784 86 KEVLLKEWDPQRQ-SFP---DSSNVERLRNFIKHVYVDRRY 122 (677)
Q Consensus 86 N~i~ea~~~p~~~-~~P---dssd~~~lreFIr~KYeeKrF 122 (677)
++|++..-+-... ++- ++.-....|+-|..--+.+.|
T Consensus 84 ~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 84 REFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 9998775322111 111 111223345556555555555
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.90 E-value=1.7e-24 Score=232.44 Aligned_cols=82 Identities=22% Similarity=0.589 Sum_probs=79.0
Q ss_pred HHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHH
Q 005784 11 NERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKE 87 (677)
Q Consensus 11 nekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~ 87 (677)
.++++++|...++||+||||++++|+|++++|||||||+|+++||+|| | +|||++||+|+.+||++|+.+||.+|+.
T Consensus 10 ~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~~ 89 (454)
T KOG0706|consen 10 IQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANARV 89 (454)
T ss_pred HHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHHH
Confidence 467899999999999999999999999999999999999999999999 5 9999999999999999999999999999
Q ss_pred HHhhc
Q 005784 88 VLLKE 92 (677)
Q Consensus 88 i~ea~ 92 (677)
|+..+
T Consensus 90 FFkqh 94 (454)
T KOG0706|consen 90 FFKQH 94 (454)
T ss_pred HHHHc
Confidence 99876
No 11
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.89 E-value=9.1e-24 Score=231.47 Aligned_cols=114 Identities=24% Similarity=0.485 Sum_probs=104.6
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC---cceeecccccCCHHHHHHHHhcCcHHHHHHHh
Q 005784 14 IIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVLL 90 (677)
Q Consensus 14 iLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg---HrVKSIsLD~WT~eEV~~mq~gGN~raN~i~e 90 (677)
.|+.|...++|.+|+||+.++|.||++|+|++||++|+||||.|| +|||++.||.|..|.+..|..+||+.||.+||
T Consensus 503 a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vWE 582 (749)
T KOG0705|consen 503 ALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVWE 582 (749)
T ss_pred HHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHhh
Confidence 578888999999999999999999999999999999999999998 49999999999999999999999999999999
Q ss_pred hcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCC
Q 005784 91 KEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (677)
Q Consensus 91 a~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e~~~ 128 (677)
.....++++.|++..++ +|+|||.|||+|.|......
T Consensus 583 ~~~~G~~KPs~~s~REE-kErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 583 GSSQGQTKPSPDSSREE-KERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred hhccCCcCCCccccHHH-HHHHHHHHHHHHhhcCCCCC
Confidence 97777778888876554 68999999999999976554
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.80 E-value=1.2e-20 Score=217.75 Aligned_cols=116 Identities=23% Similarity=0.468 Sum_probs=101.2
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHHHHh
Q 005784 14 IIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLL 90 (677)
Q Consensus 14 iLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~i~e 90 (677)
.+..+.+.++|.+|+||+++.|+|+++|+||.+||+|+||||+|| | ||+|++||.|..+.+..++++||..+|.|||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 367888999999999999999999999999999999999999998 4 9999999999999999999999999999999
Q ss_pred hcCCCCCCCCCC-CChHHHHHHHHHHHHhhcccccCCCCC
Q 005784 91 KEWDPQRQSFPD-SSNVERLRNFIKHVYVDRRYTGERNYD 129 (677)
Q Consensus 91 a~~~p~~~~~Pd-ssd~~~lreFIr~KYeeKrF~~e~~~d 129 (677)
+++.....+.|. ..+...++.||++||++++|..+..+.
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 998755333332 233666788999999999998665443
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.66 E-value=3.1e-17 Score=186.07 Aligned_cols=111 Identities=26% Similarity=0.538 Sum_probs=100.0
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC---cceeeccccc--CCHHHHHHHHhcCcHHHHHH
Q 005784 14 IIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAK--FTSQEVKALQEGGNQRAKEV 88 (677)
Q Consensus 14 iLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg---HrVKSIsLD~--WT~eEV~~mq~gGN~raN~i 88 (677)
.-.+++...+|+.|+||++..|.||++|++|.||-.|+|-||.|| ++|+|+.||. |+.+-|+++..+||.++|.|
T Consensus 288 vaeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~F 367 (1186)
T KOG1117|consen 288 VAERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRF 367 (1186)
T ss_pred HHHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccc
Confidence 345677889999999999999999999999999999999999998 6999999995 99999999999999999999
Q ss_pred HhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccC
Q 005784 89 LLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (677)
Q Consensus 89 ~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeKrF~~e 125 (677)
|.+++.+.....|+++- ..+++||+.||.+.+|...
T Consensus 368 wa~nl~~~e~lh~dssp-~~r~~fi~~Kykeg~fRk~ 403 (1186)
T KOG1117|consen 368 WAGNLPPNEHLHPDSSP-STRRQFIKEKYKEGKFRKE 403 (1186)
T ss_pred cccCCCCccccCCCCCc-chhhhHHHHHhhccccccc
Confidence 99999988777777644 4468999999999998654
No 14
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.66 E-value=2.7e-17 Score=178.84 Aligned_cols=108 Identities=19% Similarity=0.420 Sum_probs=91.2
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHHHHhhcC-CC
Q 005784 20 KLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEW-DP 95 (677)
Q Consensus 20 k~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~i~ea~~-~p 95 (677)
+...-+.|+||++++|.|||+|-|+|||.+|+.+||.|| | .||++....|.++.|+++..+.|..+|.|||..+ ++
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 445568999999999999999999999999999999999 4 8999999999999999999999999999999765 43
Q ss_pred C------CCCCCCCChHHHHHHHHHHHHhhcccccCCC
Q 005784 96 Q------RQSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (677)
Q Consensus 96 ~------~~~~Pdssd~~~lreFIr~KYeeKrF~~e~~ 127 (677)
. +++.|...-...+.+|||+||+...|+.+..
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~ 121 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLP 121 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCC
Confidence 2 3344443333346789999999999997443
No 15
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=98.41 E-value=4.5e-05 Score=84.85 Aligned_cols=75 Identities=21% Similarity=0.206 Sum_probs=44.4
Q ss_pred CCCCCCccccccCCCCCCCCcCCCCCCCCC------------------CcCC-CCCccccccCCCCCCC-CCCCcchhhh
Q 005784 180 SPPVVRPVREILGDNVLPLRISEPPKANGV------------------RVAD-GSTNTQRTASSGNLGS-ANENQAEVKL 239 (677)
Q Consensus 180 SpP~v~Pv~dlLG~daPpl~i~~~~k~~~~------------------~~~~-gs~~~qr~sssss~~s-~~~~~~~~K~ 239 (677)
+.+.+++++.+||+.+|.+...+....+.. .... .-++.|.+..++.+++ ...+....+.
T Consensus 153 s~~~~~~lrs~~gd~~P~~~~~t~np~~~~~~~~~~~~~~~~~rfdlfg~~k~sd~~s~s~~qss~~~~ssp~~~~~~~~ 232 (524)
T KOG0702|consen 153 SRPETKSLRSLLGDHAPLLAESTKNPRSRGLPKSPIRFEIVDDRFDLFGLPKASDAQSQSTFQSSIAPSSSPPNHQSVPQ 232 (524)
T ss_pred cCCCccccccccCCCCcchhhcccCccccCCCCCCchhhhhhhhhhhhcCcCcccccccCcccccccccCCCCccccchh
Confidence 347788999999999998886643221111 0001 1223344444444443 3334457777
Q ss_pred cccCCccCCC-CCCCC
Q 005784 240 ETTGSLIDFD-ADPKP 254 (677)
Q Consensus 240 ~~s~sLiDf~-sdp~p 254 (677)
.-.++++||. .|++.
T Consensus 233 ~~~~s~an~~~ge~~k 248 (524)
T KOG0702|consen 233 AYSDSPANIFAGEPFK 248 (524)
T ss_pred hcccccccccccCCCC
Confidence 8899999996 67663
No 16
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.44 E-value=0.022 Score=68.04 Aligned_cols=71 Identities=17% Similarity=0.280 Sum_probs=55.8
Q ss_pred HcCCCCCCCcCCCC-CCCCeeEecceeheehhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCcHHHHHHHhh
Q 005784 19 LKLQDNRRCINCNS-LGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (677)
Q Consensus 19 lk~pgNk~CADCga-~~P~WaSin~GVFVC~~CSGIHR~Lg-H--rVKSIsLD~WT~eEV~~mq~gGN~raN~i~ea 91 (677)
.+...+-.|++|.+ ..-.|+|+|+.+-+|+.|+++|+.++ | .+.++.|+...+ |..+...|+...+..|..
T Consensus 625 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 625 VKASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HHhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 34556889999998 57999999999999999999999996 4 666777776666 666777776666665544
No 17
>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=86.53 E-value=0.54 Score=35.54 Aligned_cols=40 Identities=15% Similarity=0.471 Sum_probs=34.0
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhh-hccCCcceeec
Q 005784 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGI-HREFTHRVKSV 64 (677)
Q Consensus 23 gNk~CADCga~~P~WaSin~GVFVC~~CSGI-HR~LgHrVKSI 64 (677)
.+..|..|......|.+.+=.++||..|... ||. |+|.+|
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~--H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG--HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT--SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC--CEEeEC
Confidence 4678999999889999999999999999988 887 887765
No 18
>PRK12495 hypothetical protein; Provisional
Probab=80.93 E-value=1.3 Score=46.13 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=27.0
Q ss_pred HHHHHHc---CCCCCCCcCCCCCCCCeeEecceeheehhhhhh
Q 005784 14 IIRGLLK---LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (677)
Q Consensus 14 iLr~Llk---~pgNk~CADCga~~P~WaSin~GVFVC~~CSGI 53 (677)
+|..||. ...+++|-+||.+=|.+ -|+.+|..|..+
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 4445544 46689999999988832 699999999754
No 19
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=80.29 E-value=2.5 Score=42.98 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=26.5
Q ss_pred CCCCCCCcCCCCCC-CCeeEecceeheehhhhh
Q 005784 21 LQDNRRCINCNSLG-TQYVCTNFWTFVCTNCSG 52 (677)
Q Consensus 21 ~pgNk~CADCga~~-P~WaSin~GVFVC~~CSG 52 (677)
.+.-..|+.||... ..|.+..-|.|+|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 35557999999864 478899999999999973
No 20
>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=76.18 E-value=4.6 Score=40.93 Aligned_cols=33 Identities=21% Similarity=0.481 Sum_probs=26.8
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeheehhhhhh
Q 005784 21 LQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGI 53 (677)
Q Consensus 21 ~pgNk~CADCga~~P-~WaSin~GVFVC~~CSGI 53 (677)
.+.-..|+.||..+. .|.+...|.|+|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 355679999998543 688999999999999764
No 21
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=64.70 E-value=2.3 Score=40.44 Aligned_cols=46 Identities=13% Similarity=0.258 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHcCCCCC--CCcCCCCC-CCCeeEecceeheehhhhhhh
Q 005784 9 EKNERIIRGLLKLQDNR--RCINCNSL-GTQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 9 ernekiLr~Llk~pgNk--~CADCga~-~P~WaSin~GVFVC~~CSGIH 54 (677)
....++-..|.+..... +|.+||.+ ...-.-..-+..+|+.|.-.|
T Consensus 63 ~~l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 63 KLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred HHHHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 33444444444444443 89999986 222223344678999998765
No 22
>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=55.50 E-value=7.8 Score=29.55 Aligned_cols=28 Identities=21% Similarity=0.505 Sum_probs=23.7
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhh
Q 005784 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCS 51 (677)
Q Consensus 21 ~pgNk~CADCga~~P~WaSin~GVFVC~~CS 51 (677)
...|..|..|++. |...+=|.++|.+|-
T Consensus 5 ~~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 5 RGPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred ccCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 3456779999987 888999999999994
No 23
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=50.90 E-value=8.1 Score=40.38 Aligned_cols=30 Identities=20% Similarity=0.580 Sum_probs=26.0
Q ss_pred CCCCCCcCCCCCC-CCeeEecceeheehhhh
Q 005784 22 QDNRRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (677)
Q Consensus 22 pgNk~CADCga~~-P~WaSin~GVFVC~~CS 51 (677)
+.=.+|+.|+... +.+++.-.|-+||.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3347999999975 57999999999999998
No 24
>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=50.17 E-value=8.1 Score=29.89 Aligned_cols=27 Identities=30% Similarity=0.563 Sum_probs=21.2
Q ss_pred CCcCCCCCCCCeeEecceeheehhhhhh
Q 005784 26 RCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (677)
Q Consensus 26 ~CADCga~~P~WaSin~GVFVC~~CSGI 53 (677)
+|-.|++.. ......-|-+||..|.-|
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 699999976 555677899999999544
No 25
>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=46.29 E-value=10 Score=32.04 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.7
Q ss_pred CCCCCCCcCCCCCCC--CeeEecceeheehhhhhhh
Q 005784 21 LQDNRRCINCNSLGT--QYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 21 ~pgNk~CADCga~~P--~WaSin~GVFVC~~CSGIH 54 (677)
..+...|.|||..=| ++. ..-|+..|+.|...+
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~-a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARRE-ALPGVTRCVSCQEIL 62 (63)
T ss_pred CCCCCeeccCCCcChHHHHh-hcCCcCCcHHHHhhc
Confidence 455679999998632 332 334788999998654
No 26
>PRK11019 hypothetical protein; Provisional
Probab=46.12 E-value=9.4 Score=34.63 Aligned_cols=31 Identities=13% Similarity=0.222 Sum_probs=22.1
Q ss_pred CCCCcCCCCCCC--CeeEecceeheehhhhhhhc
Q 005784 24 NRRCINCNSLGT--QYVCTNFWTFVCTNCSGIHR 55 (677)
Q Consensus 24 Nk~CADCga~~P--~WaSin~GVFVC~~CSGIHR 55 (677)
-.+|.|||..=| ++.-+ -++-.|++|...+.
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~-P~a~~Cv~Cq~~~E 68 (88)
T PRK11019 36 LTECEECGEPIPEARRKAI-PGVRLCVACQQEKD 68 (88)
T ss_pred CCeeCcCCCcCcHHHHhhc-CCccccHHHHHHHH
Confidence 569999998633 34333 37789999998753
No 27
>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=41.40 E-value=8.7 Score=29.27 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCeeEecceeheehhhh
Q 005784 25 RRCINCNSL-GTQYVCTNFWTFVCTNCS 51 (677)
Q Consensus 25 k~CADCga~-~P~WaSin~GVFVC~~CS 51 (677)
..|.+|+.. .-+|..-+|+.-||.+|.
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 479999995 678999999999999994
No 28
>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=41.03 E-value=15 Score=36.44 Aligned_cols=31 Identities=13% Similarity=0.199 Sum_probs=19.5
Q ss_pred CCCCcCCCCC-CCCeeEecceeheehhhhhhh
Q 005784 24 NRRCINCNSL-GTQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 24 Nk~CADCga~-~P~WaSin~GVFVC~~CSGIH 54 (677)
=-+|.+||.. ...=.-+--++-.|+.|...+
T Consensus 86 YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 86 YGICEVCGKPIPYERLEAIPTATTCVECQNRK 117 (159)
T ss_pred CCeecccCCcccHHHHhhCCCcchhHHHHHHh
Confidence 3579999985 111122233567899998764
No 29
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=38.64 E-value=4.8e+02 Score=29.46 Aligned_cols=27 Identities=30% Similarity=0.380 Sum_probs=14.1
Q ss_pred CCCCCCCcchhhhcccCCccCCCCCCCCC
Q 005784 227 LGSANENQAEVKLETTGSLIDFDADPKPS 255 (677)
Q Consensus 227 ~~s~~~~~~~~K~~~s~sLiDf~sdp~p~ 255 (677)
+.+...+.+..|+ ++.|.|+.....|+
T Consensus 313 ~S~VkknaP~nks--sgdl~dLFDgsa~s 339 (499)
T KOG2057|consen 313 LSPVKKNAPRNKS--SGDLDDLFDGSAPS 339 (499)
T ss_pred CCcccccCCcccc--cccHHHHhcCcCCC
Confidence 3334444454444 77777775544443
No 30
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=38.37 E-value=12 Score=36.97 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=27.8
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheeh-hhhhhhcc
Q 005784 22 QDNRRCINCNSLGTQYVCTNFWTFVCT-NCSGIHRE 56 (677)
Q Consensus 22 pgNk~CADCga~~P~WaSin~GVFVC~-~CSGIHR~ 56 (677)
|--+.|+-|| -..-|.|++-|.-+|. .|-.+|.+
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 3457899999 6778999999998884 79899865
No 31
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=37.87 E-value=18 Score=35.38 Aligned_cols=42 Identities=19% Similarity=0.525 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccC
Q 005784 7 EDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF 57 (677)
Q Consensus 7 e~ernekiLr~Llk~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~L 57 (677)
++.+.+++|+.+........|.-||. ++..+|..|.|-||-+
T Consensus 82 e~G~L~~lL~~~~~~~~~~~C~~Cgg---------~rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 82 ESGELRKLLKGIRARAGGGVCEGCGG---------ARFVPCSECNGSCKVF 123 (147)
T ss_pred HcCCHHHHHhhcccccCCCCCCCCCC---------cCeEECCCCCCcceEE
Confidence 34445555665544556677999993 4455999999988764
No 32
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.56 E-value=19 Score=33.58 Aligned_cols=43 Identities=21% Similarity=0.471 Sum_probs=29.5
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccC--Cc--ceeecccc
Q 005784 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (677)
Q Consensus 21 ~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~L--gH--rVKSIsLD 67 (677)
.+..-+|.+|+. +..+..-.|.|-.|.+..-.+ |. +|++|.++
T Consensus 67 ~p~~~~C~~Cg~----~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~ie~~ 113 (115)
T TIGR00100 67 EPVECECEDCSE----EVSPEIDLYRCPKCHGIMLQVRAGKELNLKSIEVE 113 (115)
T ss_pred eCcEEEcccCCC----EEecCCcCccCcCCcCCCcEEecCCeEEEEEEEEE
Confidence 466779999994 233332358899999876555 32 88888765
No 33
>PRK00420 hypothetical protein; Validated
Probab=36.37 E-value=58 Score=30.89 Aligned_cols=44 Identities=16% Similarity=0.169 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHHHc--CCCCCCCcCCCCCCCCeeEecceeheehhhhhh
Q 005784 7 EDEKNERIIRGLLK--LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (677)
Q Consensus 7 e~ernekiLr~Llk--~pgNk~CADCga~~P~WaSin~GVFVC~~CSGI 53 (677)
+++..+++-+.|++ .--+..|-.||.+-.. ++-|-.+|-.|..+
T Consensus 4 ~~~~~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 4 SEDIVKKAAELLLKGAKMLSKHCPVCGLPLFE---LKDGEVVCPVHGKV 49 (112)
T ss_pred cHHHHHHHHHHHHhHHHHccCCCCCCCCccee---cCCCceECCCCCCe
Confidence 44555555555555 3346999999975433 36788999999753
No 34
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=35.73 E-value=16 Score=31.96 Aligned_cols=31 Identities=13% Similarity=0.181 Sum_probs=20.8
Q ss_pred CCCCcCCCCCCCC-eeEecceeheehhhhhhh
Q 005784 24 NRRCINCNSLGTQ-YVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 24 Nk~CADCga~~P~-WaSin~GVFVC~~CSGIH 54 (677)
...|.|||..=|. -.-.--|+..|+.|..++
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 3589999986332 222334788999998754
No 35
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=35.43 E-value=22 Score=34.98 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=22.5
Q ss_pred CCCCCCCcCCCCC-CCCeeEecceeheehhhhhhhc
Q 005784 21 LQDNRRCINCNSL-GTQYVCTNFWTFVCTNCSGIHR 55 (677)
Q Consensus 21 ~pgNk~CADCga~-~P~WaSin~GVFVC~~CSGIHR 55 (677)
...--+|-+||.. +..=.-.--++..|+.|...|-
T Consensus 108 ~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E 143 (151)
T PRK10778 108 DEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAE 143 (151)
T ss_pred CCCCceeccCCCcccHHHHhcCCCccccHHHHHHHH
Confidence 4455799999985 2222222335678999988664
No 36
>PHA00080 DksA-like zinc finger domain containing protein
Probab=35.02 E-value=19 Score=31.31 Aligned_cols=32 Identities=16% Similarity=0.337 Sum_probs=21.7
Q ss_pred CCCCCCcCCCCC--CCCeeEecceeheehhhhhhh
Q 005784 22 QDNRRCINCNSL--GTQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 22 pgNk~CADCga~--~P~WaSin~GVFVC~~CSGIH 54 (677)
.....|.|||.. ..+|.-+ -++..|+.|...+
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~-P~~~~Cv~Cq~~~ 62 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAV-PGCRTCVSCQEIL 62 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhC-CCccCcHHHHHHH
Confidence 445689999985 3344333 3667799998765
No 37
>PF14376 Haem_bd: Haem-binding domain
Probab=33.47 E-value=30 Score=33.26 Aligned_cols=23 Identities=30% Similarity=0.636 Sum_probs=16.0
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCee
Q 005784 12 ERIIRGLLKLQDNRRCINCNSLGTQYV 38 (677)
Q Consensus 12 ekiLr~Llk~pgNk~CADCga~~P~Wa 38 (677)
.+.++.|++ +.|.||++.+..|-
T Consensus 33 p~~v~~il~----~~CydCHSn~T~~P 55 (137)
T PF14376_consen 33 PEEVKIILK----NSCYDCHSNNTRYP 55 (137)
T ss_pred hHHHHHHHH----ccccccCCCCCCCc
Confidence 344555554 58999999877665
No 38
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=32.10 E-value=35 Score=27.75 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=28.9
Q ss_pred CCCCCcCCCCC-CCCeeEeccee-heehhhhhhhccCC
Q 005784 23 DNRRCINCNSL-GTQYVCTNFWT-FVCTNCSGIHREFT 58 (677)
Q Consensus 23 gNk~CADCga~-~P~WaSin~GV-FVC~~CSGIHR~Lg 58 (677)
..+.|.+|+.. -|.|=....|. +||-.|.-..|..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35799999985 58898888886 99999977666544
No 39
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.50 E-value=22 Score=33.31 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=27.6
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhhhhhccC--Cc--ceeecccc
Q 005784 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (677)
Q Consensus 22 pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~L--gH--rVKSIsLD 67 (677)
+.--+|-+||.. |-...+..+.|-.|.+..-.+ |. +|++|-++
T Consensus 69 p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~iE~~ 115 (117)
T PRK00564 69 KVELECKDCSHV---FKPNALDYGVCEKCHSKNVIITQGNEMRLLSLEML 115 (117)
T ss_pred CCEEEhhhCCCc---cccCCccCCcCcCCCCCceEEecCCEEEEEEEEEE
Confidence 445589999942 222234455699999866555 32 78888654
No 40
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=29.37 E-value=79 Score=29.46 Aligned_cols=32 Identities=25% Similarity=0.596 Sum_probs=21.6
Q ss_pred CCCCCcCCCCC-----CCCeeEecceeheehhhhhhh
Q 005784 23 DNRRCINCNSL-----GTQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 23 gNk~CADCga~-----~P~WaSin~GVFVC~~CSGIH 54 (677)
+.+.|+-|+.+ +..-.|..-.--||.+|...+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~ 89 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYS 89 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEET
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcC
Confidence 56899999974 445556777777888887764
No 41
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.24 E-value=34 Score=36.87 Aligned_cols=35 Identities=20% Similarity=0.318 Sum_probs=24.4
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhhhhhcc
Q 005784 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (677)
Q Consensus 21 ~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~ 56 (677)
.....+|-+||... --....-|..||.+|--|..+
T Consensus 8 ~~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 8 EEEKLVCPECGSDK-LIYDYERGEIVCADCGLVIEE 42 (310)
T ss_pred cccCCcCcCCCCCC-eeEECCCCeEeecccCCcccc
Confidence 34457899999732 222456799999999876543
No 42
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.57 E-value=1.5e+02 Score=34.46 Aligned_cols=19 Identities=11% Similarity=0.013 Sum_probs=12.6
Q ss_pred eeeeeccCCCCCCCcccCCCCCCCC
Q 005784 511 VYAMQYNTAAPMPNFVHSKSTTNPF 535 (677)
Q Consensus 511 g~~mqY~~~~~~~~~~~~~ks~npf 535 (677)
|..+||+| |+.++-+-|+|
T Consensus 411 ~p~pq~qN------yppp~p~f~m~ 429 (483)
T KOG2236|consen 411 GPSPQQQN------YPPPSPSFPMF 429 (483)
T ss_pred CCCcccCC------CCCCCCCCCcc
Confidence 55667665 66666666777
No 43
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=27.13 E-value=1.1e+03 Score=27.99 Aligned_cols=60 Identities=28% Similarity=0.370 Sum_probs=34.3
Q ss_pred CCCCCceeeeeccC--CCCCCCcccCCCCCCCCcCCCCCCCCcccCCCCccccccCCCCCCCCCCCCCCC
Q 005784 505 VPPHGMVYAMQYNT--AAPMPNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS 572 (677)
Q Consensus 505 ~pp~gmg~~mqY~~--~~~~~~~~~~~ks~npfd~~~~~~~~Q~~~fPsm~~l~galp~~~~~~~~~~~s 572 (677)
.|||+=-++||-.. -.|++.+ -.++-|||.. .|+.--|.+-.-.|+-..|+++.+|.+.+
T Consensus 459 ~pP~~p~Pg~~s~~~s~~P~q~s---~~~~pp~~r~-----a~~~a~Pg~p~~~~~~~~vPpp~g~~p~~ 520 (554)
T KOG0119|consen 459 LPPHPPPPGMQSAQSSSLPQQAS---TTSIPPGDRQ-----AQAAAPPGAPFHGGNYNAVPPPPGLQPAN 520 (554)
T ss_pred CCCCCCCCCccccccccCCcccc---cccCCccccc-----ccccCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 34443345555222 2244444 5677788874 24444466666666767777788887765
No 44
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=26.44 E-value=58 Score=35.47 Aligned_cols=46 Identities=26% Similarity=0.478 Sum_probs=29.1
Q ss_pred ccCCHHHHHHHHhcCcHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhc
Q 005784 67 AKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDR 120 (677)
Q Consensus 67 D~WT~eEV~~mq~gGN~raN~i~ea~~~p~~~~~Pdssd~~~lreFIr~KYeeK 120 (677)
.+.|.+||+.|++-|-. .++|-++.... +..-+.+.+|=++||++|
T Consensus 106 QkLt~eeIe~LK~~g~s-g~eII~kLien-------s~tF~~KT~FSqeKYlkr 151 (299)
T PF04189_consen 106 QKLTQEEIEELKKEGVS-GEEIIEKLIEN-------SSTFDKKTEFSQEKYLKR 151 (299)
T ss_pred ccCCHHHHHHHHHcCCC-HHHHHHHHHHh-------ccchhhhhHHHHHHHHHH
Confidence 46788999999976433 44455443321 122334567999999886
No 45
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.39 E-value=41 Score=31.42 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=27.8
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccC--Cc--ceeeccc
Q 005784 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (677)
Q Consensus 21 ~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~L--gH--rVKSIsL 66 (677)
.+..-+|-+|+.. ..+....|.|-.|-+....+ |. +|++|-+
T Consensus 67 vp~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 112 (113)
T PRK12380 67 KPAQAWCWDCSQV----VEIHQHDAQCPHCHGERLRVDTGDSLIVKSIEV 112 (113)
T ss_pred eCcEEEcccCCCE----EecCCcCccCcCCCCCCcEEccCCeEEEEEEEE
Confidence 4667799999942 22333456699998765555 32 7888764
No 46
>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=25.37 E-value=38 Score=30.00 Aligned_cols=31 Identities=16% Similarity=0.564 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhcc
Q 005784 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (677)
Q Consensus 23 gNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~ 56 (677)
+|..|.-|+... ....||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 577899999754 3478999999999998765
No 47
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.85 E-value=1.1e+03 Score=29.61 Aligned_cols=12 Identities=33% Similarity=0.567 Sum_probs=9.3
Q ss_pred CCCCCCcCCCCC
Q 005784 614 MPPRPYLGPQVP 625 (677)
Q Consensus 614 ~~p~~ymgqq~~ 625 (677)
+.+..|+.+|.|
T Consensus 84 ~~~~Sy~~~~~p 95 (887)
T KOG1985|consen 84 VGPPSYQQLQAP 95 (887)
T ss_pred CCCcchhhccCC
Confidence 557778888888
No 48
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.84 E-value=27 Score=32.67 Aligned_cols=44 Identities=11% Similarity=0.326 Sum_probs=30.2
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhccC--Cc--ceeeccc
Q 005784 20 KLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (677)
Q Consensus 20 k~pgNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~L--gH--rVKSIsL 66 (677)
..|..-+|-||+. .|....+..|.|-.|-+....+ |. +|++|-+
T Consensus 66 ~~p~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 113 (114)
T PRK03681 66 EQEAECWCETCQQ---YVTLLTQRVRRCPQCHGDMLRIVADDGLQIRRIEI 113 (114)
T ss_pred eeCcEEEcccCCC---eeecCCccCCcCcCcCCCCcEEccCCeEEEEEEEE
Confidence 3466779999995 3333344557899999876666 32 7888754
No 49
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=23.65 E-value=34 Score=25.98 Aligned_cols=30 Identities=23% Similarity=0.453 Sum_probs=15.2
Q ss_pred CCCcCCCCCCCCeeE---ecceeheehhhhhhhc
Q 005784 25 RRCINCNSLGTQYVC---TNFWTFVCTNCSGIHR 55 (677)
Q Consensus 25 k~CADCga~~P~WaS---in~GVFVC~~CSGIHR 55 (677)
|.|-.||.+ -.+.. -+.-=+||..|..||-
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 578899976 22221 1344568999999883
No 50
>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=23.49 E-value=12 Score=27.91 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=16.0
Q ss_pred CCcCCCCCC-CCeeEecceeheehhhhhhh
Q 005784 26 RCINCNSLG-TQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 26 ~CADCga~~-P~WaSin~GVFVC~~CSGIH 54 (677)
.|.+||..= ..-.-+--+..+|+.|+..|
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 499999741 11112223778999998765
No 51
>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=23.12 E-value=43 Score=30.47 Aligned_cols=31 Identities=19% Similarity=0.540 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhcc
Q 005784 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (677)
Q Consensus 23 gNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~ 56 (677)
++..|.-||... ....||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 577899999865 3468999999999998875
No 52
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=22.94 E-value=84 Score=28.87 Aligned_cols=29 Identities=14% Similarity=0.352 Sum_probs=22.9
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhhh
Q 005784 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (677)
Q Consensus 22 pgNk~CADCga~~P~WaSin~GVFVC~~CSG 52 (677)
-.--.|-+|+.+ .---+..||..|..|-.
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGA 61 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCC
Confidence 345689999988 44567889999999964
No 53
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=22.49 E-value=73 Score=33.03 Aligned_cols=66 Identities=29% Similarity=0.476 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHHcCCCC-CCCcCCCCCCCCeeEecceeheehhhhhhhccCCcceeecccccCCHHHHHHHHhcCcHHH
Q 005784 7 EDEKNERIIRGLLKLQDN-RRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEGGNQRA 85 (677)
Q Consensus 7 e~ernekiLr~Llk~pgN-k~CADCga~~P~WaSin~GVFVC~~CSGIHR~LgHrVKSIsLD~WT~eEV~~mq~gGN~ra 85 (677)
.++..+++.+.|.....| +.|..|+.-.-. -+|.-|+.--|.- ++-+--=+..+|..|+..|.-+.
T Consensus 36 ~~~~~~~la~al~~a~~~i~~C~~C~~~te~--------d~C~ICsd~~Rd~-----~~icVVe~p~Dv~a~E~~~~f~G 102 (198)
T COG0353 36 DREDVERLAKALLEAKENIKHCSVCGNLTES--------DPCDICSDESRDK-----SQLCVVEEPKDVLALEKTGEFRG 102 (198)
T ss_pred CHHHHHHHHHHHHHHHhcCccccccCCcCCC--------CcCcCcCCcccCC-----ceEEEEcchHHHHHHHHhcccCe
Confidence 445567788888775555 899999974322 1788888665552 22222235677778877664433
No 54
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.07 E-value=53 Score=31.56 Aligned_cols=25 Identities=12% Similarity=0.355 Sum_probs=17.3
Q ss_pred eeheehhhhhhhccC--Cc--ceeecccc
Q 005784 43 WTFVCTNCSGIHREF--TH--RVKSVSMA 67 (677)
Q Consensus 43 GVFVC~~CSGIHR~L--gH--rVKSIsLD 67 (677)
..+.|-.|-+.+-.+ |. +|++|-++
T Consensus 106 ~~~~CP~Cgs~~~~i~~G~el~i~~ie~e 134 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVKGRGVYIEEIKIE 134 (135)
T ss_pred cCcCCcCCCCCCcEEecCceEEEEEEEEe
Confidence 447799998765444 33 88888765
No 55
>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=21.68 E-value=48 Score=26.72 Aligned_cols=26 Identities=23% Similarity=0.701 Sum_probs=19.3
Q ss_pred CCcCCCCCCCCeeEecceeheehhhhh
Q 005784 26 RCINCNSLGTQYVCTNFWTFVCTNCSG 52 (677)
Q Consensus 26 ~CADCga~~P~WaSin~GVFVC~~CSG 52 (677)
.|+=|+..... --+=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48888887665 344579999999953
No 56
>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=21.41 E-value=48 Score=29.43 Aligned_cols=31 Identities=13% Similarity=0.555 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhcc
Q 005784 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (677)
Q Consensus 23 gNk~CADCga~~P~WaSin~GVFVC~~CSGIHR~ 56 (677)
..+.|.-|+...- ...||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4677999997553 468999999999998765
No 57
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.27 E-value=42 Score=31.84 Aligned_cols=47 Identities=15% Similarity=0.369 Sum_probs=29.4
Q ss_pred cCCCCCCCcCCCCCC-CCeeEec-ce-eheehhhhhhhccC--Cc--ceeecccc
Q 005784 20 KLQDNRRCINCNSLG-TQYVCTN-FW-TFVCTNCSGIHREF--TH--RVKSVSMA 67 (677)
Q Consensus 20 k~pgNk~CADCga~~-P~WaSin-~G-VFVC~~CSGIHR~L--gH--rVKSIsLD 67 (677)
..+.--+| +|+... ..+..+. +. .+.|-.|-+.+-.+ |. +|++|.++
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~Ieve 119 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECNVKNIKIE 119 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEEEEEEEEe
Confidence 34667799 999652 1111111 11 36799998776555 32 89998876
No 58
>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=20.87 E-value=65 Score=24.29 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=21.4
Q ss_pred CcCCCCC-CCCeeEecceeh-eehhhhhhhcc
Q 005784 27 CINCNSL-GTQYVCTNFWTF-VCTNCSGIHRE 56 (677)
Q Consensus 27 CADCga~-~P~WaSin~GVF-VC~~CSGIHR~ 56 (677)
|.+|+.. .|.|=....|-. ||-.|--.+|.
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 8999985 699998888887 99999765554
No 59
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=20.52 E-value=59 Score=30.00 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=22.8
Q ss_pred cCCCCCCCcCCCCC-----------------CCCeeEecceeheehhhhh
Q 005784 20 KLQDNRRCINCNSL-----------------GTQYVCTNFWTFVCTNCSG 52 (677)
Q Consensus 20 k~pgNk~CADCga~-----------------~P~WaSin~GVFVC~~CSG 52 (677)
+.+.--+|+|||.+ .-.-+.=.||-.+|.+|..
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred ccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 45666799999985 1112245689999999963
No 60
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=20.19 E-value=41 Score=35.57 Aligned_cols=33 Identities=21% Similarity=0.428 Sum_probs=25.7
Q ss_pred CCCCCCCcCCCC--CCCCeeEecceeheehhhhhhh
Q 005784 21 LQDNRRCINCNS--LGTQYVCTNFWTFVCTNCSGIH 54 (677)
Q Consensus 21 ~pgNk~CADCga--~~P~WaSin~GVFVC~~CSGIH 54 (677)
..-+.+|.+|.. .++.+-+ .||+-||..|..-|
T Consensus 113 i~~apkC~eC~~IelD~~l~d-~F~~~VC~~Cr~~~ 147 (292)
T COG5145 113 IALAPKCKECLQIELDDELED-TFGISVCRSCRHSM 147 (292)
T ss_pred hhhCccceeeeeeecchHHHh-hhcchhHHhhhhhc
Confidence 456899999997 4555544 58999999999877
No 61
>PLN03131 hypothetical protein; Provisional
Probab=20.05 E-value=1.8e+02 Score=35.03 Aligned_cols=52 Identities=29% Similarity=0.494 Sum_probs=43.7
Q ss_pred CCCCcccCCCCCCCCcCCCCCCCCcccCCCCccccccCCCCCCCCCCCCCCC
Q 005784 521 PMPNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS 572 (677)
Q Consensus 521 ~~~~~~~~~ks~npfd~~~~~~~~Q~~~fPsm~~l~galp~~~~~~~~~~~s 572 (677)
.|++--+..||+||||+-.|.-.-+.-+|=-|.+||++||+.--+..++-+.
T Consensus 601 ~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq~~lp~~~~~~~f~g~~ 652 (705)
T PLN03131 601 HAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLEAALPDAHLPSAFLGSG 652 (705)
T ss_pred ccccccCccCCCCCcCCccccccCcccceeehHHHHhhcCCCCCchhhhcCC
Confidence 4455557889999999999999999999999999999999887666665544
Done!