Query 004239
Match_columns 766
No_of_seqs 187 out of 210
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 19:58:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004239.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004239hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2295 C2H2 Zn-finger protein 100.0 5.7E-86 1.2E-90 719.8 17.0 522 43-600 27-575 (648)
2 PF04959 ARS2: Arsenite-resist 100.0 5.2E-37 1.1E-41 310.3 6.6 129 456-594 2-136 (214)
3 PF12066 DUF3546: Domain of un 99.9 3.4E-25 7.3E-30 204.0 9.0 85 227-311 1-85 (110)
4 KOG2295 C2H2 Zn-finger protein 99.0 3.7E-10 8.1E-15 126.5 5.6 92 220-311 42-133 (648)
5 PF13821 DUF4187: Domain of un 98.0 2E-06 4.3E-11 71.5 2.0 32 426-457 8-39 (55)
6 PF13894 zf-C2H2_4: C2H2-type 88.9 0.3 6.6E-06 32.2 1.9 24 531-556 1-24 (24)
7 PF00096 zf-C2H2: Zinc finger, 88.4 0.25 5.4E-06 33.3 1.2 23 531-556 1-23 (23)
8 KOG1994 Predicted RNA binding 81.0 1.5 3.2E-05 46.5 3.5 82 366-457 167-251 (268)
9 PF12756 zf-C2H2_2: C2H2 type 80.8 0.8 1.7E-05 39.7 1.3 31 530-562 50-81 (100)
10 PF12171 zf-C2H2_jaz: Zinc-fin 79.5 0.76 1.6E-05 32.6 0.6 24 530-555 1-24 (27)
11 KOG3973 Uncharacterized conser 76.1 7.8 0.00017 43.6 7.3 24 172-197 376-399 (465)
12 KOG1924 RhoA GTPase effector D 74.9 6.6 0.00014 48.0 6.8 18 290-307 135-152 (1102)
13 PF12874 zf-met: Zinc-finger o 74.0 2.1 4.6E-05 29.3 1.6 23 531-555 1-23 (25)
14 smart00355 ZnF_C2H2 zinc finge 72.2 3.1 6.8E-05 27.3 2.0 24 531-557 1-24 (26)
15 PHA00616 hypothetical protein 72.0 1.6 3.6E-05 35.4 0.7 26 531-558 2-27 (44)
16 smart00451 ZnF_U1 U1-like zinc 71.7 2.8 6E-05 30.7 1.8 29 530-560 3-32 (35)
17 KOG0717 Molecular chaperone (D 68.8 4.9 0.00011 46.5 3.8 43 527-571 289-332 (508)
18 PF04959 ARS2: Arsenite-resist 67.3 1.2 2.6E-05 46.6 -1.2 43 511-554 62-104 (214)
19 PF13912 zf-C2H2_6: C2H2-type 61.3 5.4 0.00012 27.7 1.5 25 531-557 2-26 (27)
20 PF04780 DUF629: Protein of un 49.6 16 0.00035 42.6 3.6 43 514-562 44-87 (466)
21 PF02892 zf-BED: BED zinc fing 49.0 12 0.00026 29.1 1.8 27 529-557 15-45 (45)
22 KOG2654 Uncharacterized conser 47.3 41 0.00088 38.8 6.2 24 67-94 105-128 (461)
23 KOG3875 Peroxisomal biogenesis 41.8 59 0.0013 36.5 6.3 15 112-127 4-18 (362)
24 KOG3993 Transcription factor ( 41.0 9.8 0.00021 43.8 0.3 27 530-558 356-382 (500)
25 PF05605 zf-Di19: Drought indu 39.7 23 0.00051 29.0 2.2 26 530-558 2-27 (54)
26 PF13465 zf-H2C2_2: Zinc-finge 39.6 18 0.00038 25.7 1.3 24 515-543 2-25 (26)
27 KOG0921 Dosage compensation co 39.5 1.3E+02 0.0029 38.3 9.2 19 122-143 1156-1174(1282)
28 KOG4173 Alpha-SNAP protein [In 38.2 17 0.00037 38.5 1.5 49 507-556 122-170 (253)
29 KOG2482 Predicted C2H2-type Zn 38.0 6.3 0.00014 44.2 -1.7 59 529-592 194-252 (423)
30 COG5192 BMS1 GTP-binding prote 37.3 35 0.00075 41.1 3.8 37 235-274 506-542 (1077)
31 KOG2893 Zn finger protein [Gen 36.3 1.8E+02 0.0039 31.8 8.6 33 530-565 34-67 (341)
32 PF04423 Rad50_zn_hook: Rad50 34.9 63 0.0014 26.5 4.0 46 513-566 7-52 (54)
33 KOG1924 RhoA GTPase effector D 33.7 89 0.0019 39.0 6.5 11 512-522 425-435 (1102)
34 PF13913 zf-C2HC_2: zinc-finge 32.2 34 0.00074 24.4 1.8 20 532-554 4-23 (25)
35 PF13909 zf-H2C2_5: C2H2-type 30.8 30 0.00065 23.6 1.3 24 531-557 1-24 (24)
36 PHA00733 hypothetical protein 30.5 37 0.00079 32.9 2.3 26 530-557 99-124 (128)
37 PF01715 IPPT: IPP transferase 28.5 92 0.002 33.3 5.1 48 225-273 203-250 (253)
38 smart00805 AGTRAP Angiotensin 24.2 69 0.0015 32.6 3.0 13 746-758 133-145 (159)
39 KOG3623 Homeobox transcription 23.8 31 0.00067 42.4 0.5 29 529-559 280-308 (1007)
40 PHA02768 hypothetical protein; 23.5 53 0.0012 28.1 1.7 24 531-557 6-29 (55)
41 PF05605 zf-Di19: Drought indu 23.3 96 0.0021 25.4 3.2 24 530-557 31-54 (54)
42 KOG4702 Uncharacterized conser 23.2 1.5E+02 0.0032 26.8 4.5 35 227-261 30-64 (77)
43 PRK00091 miaA tRNA delta(2)-is 22.9 1.2E+02 0.0025 33.6 4.7 49 225-274 239-287 (307)
44 PF05443 ROS_MUCR: ROS/MUCR tr 21.8 63 0.0014 31.9 2.2 36 525-565 67-102 (132)
45 COG0324 MiaA tRNA delta(2)-iso 21.0 1.7E+02 0.0037 32.6 5.5 50 224-274 239-288 (308)
46 TIGR00174 miaA tRNA isopenteny 20.4 1.4E+02 0.003 32.8 4.6 41 225-266 235-275 (287)
47 TIGR00570 cdk7 CDK-activating 20.3 2.4E+02 0.0051 31.7 6.4 87 224-311 91-194 (309)
No 1
>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]
Probab=100.00 E-value=5.7e-86 Score=719.83 Aligned_cols=522 Identities=27% Similarity=0.273 Sum_probs=446.8
Q ss_pred CCCCCCCCCCCC---CCcccccchhhhhhccCCCCCCCCCCCCCCCCcCCCCCCCCCCCccchhhhhccCCCCCCCCCCC
Q 004239 43 NNSAPQSSPPPP---PPPARRRERDSRERRDDRDLDRPPPNRRGPDYYDRNRSPPPPMPRERDRDYKRRSTVSPPPPPLP 119 (766)
Q Consensus 43 ~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (766)
.-++|-|++|+- -+++-++.+++|.+++++|+++++..++ |-|+..-|+ +.+.+++..+.++++ +
T Consensus 27 ~r~~p~S~sp~geqs~~~p~r~t~kkr~~~~dddi~e~~p~kr---ynd~k~dp~------~qq~~~~f~a~k~ee---w 94 (648)
T KOG2295|consen 27 ERSQPRSQSPPGEQSAYHPERSTFKKRLNSYDDDIRESGPYKR---YNDYKIDPR------TQQNAVFFEAHKDEE---W 94 (648)
T ss_pred CCCCccccCCCccccccCcccchHHHhhcccccccccCCCccc---ccccCCCCc------hhhhHHHHHhcCCcc---h
Confidence 334444444444 3355678899999999999999966654 777777666 237888888877776 9
Q ss_pred CCCCCCCCC--CCCCCCccCccCCCCCCCCCCCCCCCCCCC-CCCCcccCCCCccccCCCCCCCCCCCCCCCCCCCCCCC
Q 004239 120 YRDRRHSPP--PRRSPPYKRSRRDDGGYEPRRGSPRGGFGP-DRRFGYDYTGGYEREMGGRPGYGDERPHGRFAGRSSGG 196 (766)
Q Consensus 120 ~~~rr~SP~--~~~spp~kr~rr~~~g~d~~~g~p~~~~g~-d~~~g~~~~~g~~~~~gg~~~~~~~~~~g~~~~~~~~g 196 (766)
||+++|+++ -++++++++.+++..+|+++.+.+.++++. |.+|+|++..++.++|++..+++....++.++++..
T Consensus 95 yr~k~h~d~~~k~r~~~~g~yqn~~q~f~~r~e~~~~~~~~~D~~fada~~~~~d~~vv~~~g~te~~~r~~l~qk~e-- 172 (648)
T KOG2295|consen 95 YRKKYHPDATEKLRNSLHGTYQNRLQVFYARTERGFFESHCLDAWFADAIWVMLDQGVVKEEGGTEKSLRRALYQKFE-- 172 (648)
T ss_pred hhhccCCChHHHHHHHHHHHHHHHHHHHHHhhcccccccCCcccchhhhHhhhhhhhhhcccCCCcccHHHHHHHHhh--
Confidence 999999999 778999999998888999999999999998 999999999999999999999999999998888776
Q ss_pred CCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhc
Q 004239 197 YQSGPSEWDSSRGGYGDASNTGSTQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDK 276 (766)
Q Consensus 197 ~~~~p~~~~~~~~g~~~~~~~~~~~~~~lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEK 276 (766)
| ..+.+||.++..++..+....|++|+ +|++++..+...|++| .+|. .|..+||+.||...||..+
T Consensus 173 ------D-e~~~~gy~De~~~gt~e~e~kkssk~-----ddd~d~s~~ee~e~e~-se~~-tqksa~~n~hke~sll~rn 238 (648)
T KOG2295|consen 173 ------D-EGLDAGYKDEFQLGTAEDEIKKSSKP-----DDDTDDSILEENEPEL-SEWG-TQKSANDNTHKECSLLVRN 238 (648)
T ss_pred ------h-ccccccccccccCCCcchhhhcccCc-----ccccCcccccccchhh-hhhh-hhhhhhhhhhHHHHHHHhc
Confidence 3 45678999999889999999999998 9999999999999999 7887 8999999999999999999
Q ss_pred cCCcchHHHHHHH-------------HHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCcccc
Q 004239 277 YHPTNLVAVIERR-------------NDLARKVAKDFLLDLQSGTLDLGPSVNASSSNKLGQTSEPNSDDDVDNGGKRRR 343 (766)
Q Consensus 277 Y~P~~l~~~~erR-------------~E~~~~aak~F~~dLesG~fD~~pgv~~~~sdksG~~sdpnse~e~~~~~Kr~R 343 (766)
|+|.++.+.++.. +.++...+..|+-.+.++++++++.+.+. ++.+-++.++++.+...+.+|.|
T Consensus 239 i~Pnis~aeIe~~ck~i~~~lrfals~~~aek~~~r~lwv~fk~~~ni~~a~~aL--n~irl~s~~~se~en~~i~rrvr 316 (648)
T KOG2295|consen 239 ILPNISVAEIENLCKGIPGFLRFALSTINAEKNFERRLWVTFKRGTNIKEACWAL--NGIRLRSNFLSESENPDITRRVR 316 (648)
T ss_pred cCCcccHHHHHHHhccCchheeeeccCchHHHHHHHHhhHhhccccchHHHHHHh--hhccccccccccccccCccceec
Confidence 9999988777643 33667778888888999999998766655 34444577888888777888888
Q ss_pred cCCCCCCcccccc-cCCCCCCCCCChhHHHHHHHHHHHHHHHHhhhccccccccCCCCcccccccccC-CCCCCceeecc
Q 004239 344 HGRGPAKETDLLS-AAPKAHPISSEPRRIQVDIEQAQALVRKLDSEKGITENILCGSDNDKMNREKSH-GSTGPVIIIRG 421 (766)
Q Consensus 344 ~Gwv~~kesD~~s-~aPkahPi~S~p~RI~~DLeqAr~LV~kLDaEkGIe~n~L~~~d~~~~d~dks~-~s~gP~~i~rg 421 (766)
++-+-.+...+++ +|+|.+.+.+.+-||..+.+|+..|+.+|++++-|..||+.......+..++.+ ++.+|++++++
T Consensus 317 ~~~Gia~~keiasn~a~k~~~lldk~irl~~~a~~t~al~tkl~s~n~i~kni~d~l~te~S~eE~e~~gssg~e~p~eg 396 (648)
T KOG2295|consen 317 PINGIAKHKEIASNAAQKLKNLLDKLIRLIDRASQTQALVTKLSSPNPIAKNIEDRLKTEASMEEDELLGSSGPEVPIEG 396 (648)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHhhhHHHhhcccccccchhhccCCCHHHHHHHHHhhhhcchhhhhhcCCCCCcCcccc
Confidence 8877666666555 799999999999999999999999999999999998888665443333334444 47889999999
Q ss_pred cccccCcchhhHHHHHHHHHHHHhhcccccccccc------cccccccccCCCCCCCcCCchhhHHHhhHHHHHHHhhcC
Q 004239 422 LTSVKGLEGVELLDTLITYLWRIHGVDYYGMVETS------EAKGLRHVRAEGKSSDITNNGAEWEKKLDFRWQERLRSQ 495 (766)
Q Consensus 422 ~~~v~~le~ik~LDllI~YLRrVHsvDYY~~~E~d------ercgl~HvR~~~k~~~~~s~~~eW~KklD~~~q~rL~~~ 495 (766)
++.++++..+++||+||+|||+||++|||+.+||+ ++||++|||+++..+. .+..+|+++|++.|+.+|...
T Consensus 397 ~~~er~d~~lk~LDll~~YLr~VhslDfyn~~ey~~e~~mpnrcgl~hvR~~~~vs~--~ev~e~es~f~s~le~~l~~~ 474 (648)
T KOG2295|consen 397 LTSERDDIRLKLLDLLAEYLRIVHSLDFYNSKEYESEDAMPNRCGLIHVRGKGFVSS--KEVGEEESIFLSDLENNLACL 474 (648)
T ss_pred CccccchhHHHHHHHHHHHHHHHHhcccccccccchhhhcccccCceeecccCCCCc--ccchhHHHHHHHHhhhccccc
Confidence 99999999999999999999999999999999987 4899999999854432 247789999999999999988
Q ss_pred ChhhHhhhhhhHHHHHHHhhhhHHHhhhhcccCcccccCCCCCcccccchhHHHHHHhhhChHHHHHHHhhHHHHHHHhh
Q 004239 496 DPLEIMTAKDKIDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQN 575 (766)
Q Consensus 496 dple~l~~kekid~el~e~ve~fVkk~~dEk~g~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~kv~E~~yFNN 575 (766)
++++.+-++.++++..+++|++||.+|++|+++|||+|+|++|+|||||||||+|||++||.|||+++++ |++||||
T Consensus 475 ~~lee~eakkkg~k~~e~eve~~v~s~t~e~~kdKy~C~lsgc~KlF~gpEFvrKHi~~KH~d~leeirk---ea~ffnn 551 (648)
T KOG2295|consen 475 LELEEEEAKKKGAKDVEDEVENFVDSNTMELDKDKYLCPLSGCAKLFKGPEFVRKHINKKHKDKLEEIRK---EAIFFNN 551 (648)
T ss_pred ccchHHHHHHhcccCHHHHHHHHHHHHHHHhhcccccCCCcchHhhccCHHHHHHHHHHHHHHHHHHHHH---HHHHHHh
Confidence 8888888888888889999999999999999999999999999999999999999999999999999997 8999999
Q ss_pred hccCCCCCCCCCCCCCCCCCCcccc
Q 004239 576 YMNDPDAPGGTPVMQQPMPKDRPLR 600 (766)
Q Consensus 576 Yl~DP~RP~~~p~~~q~~~~~~~~~ 600 (766)
||+|||||..+++ +++.+.+..+.
T Consensus 552 Yl~Dp~rp~~pe~-~~q~prd~qIl 575 (648)
T KOG2295|consen 552 YLLDPCRPMDPEV-VSQSPRDLQIL 575 (648)
T ss_pred hccCccccCCCcc-ccCCCCccccc
Confidence 9999999999988 66666666553
No 2
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=100.00 E-value=5.2e-37 Score=310.28 Aligned_cols=129 Identities=34% Similarity=0.560 Sum_probs=67.6
Q ss_pred ccccccccccCCCCCCCcC-CchhhHHHhhHHHHHHHhhcCCh-----hhHhhhhhhHHHHHHHhhhhHHHhhhhcccCc
Q 004239 456 SEAKGLRHVRAEGKSSDIT-NNGAEWEKKLDFRWQERLRSQDP-----LEIMTAKDKIDAAAVDALDPFVRKIRDEKYGW 529 (766)
Q Consensus 456 dercgl~HvR~~~k~~~~~-s~~~eW~KklD~~~q~rL~~~dp-----le~l~~kekid~el~e~ve~fVkk~~dEk~g~ 529 (766)
.+||||+|||++.+++.++ .++.+|+|+|+++|+.+|+..+. +.+|++++ + +++|++||.++++|++++
T Consensus 2 p~rcGi~HvRg~~p~~~~~~~e~~~w~k~~e~kl~~~L~~~~~l~~~~~~klG~k~-~----e~eve~~v~~~~~e~~~~ 76 (214)
T PF04959_consen 2 PNRCGIIHVRGPPPSNRVTSDEVSEWVKTFEEKLQQLLEPRETLSEEELKKLGGKD-P----EEEVEKFVQKNTKEEDED 76 (214)
T ss_dssp ------------------------HHHHHHHHHHHHHHHS--HHHHHH-HHHHHHH-H----HHHHGGGEEEEE-SSSSE
T ss_pred cccccccccccccccCccCHHHHHHHHHHHHHHHHHHcCCcCcCChHHHHHHccCc-H----HHHHHHHHHHHHHHHcCC
Confidence 4699999999998876654 36689999999999999976543 34444443 4 555666666666667778
Q ss_pred ccccCCCCCcccccchhHHHHHHhhhChHHHHHHHhhHHHHHHHhhhccCCCCCCCCCCCCCCCC
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQPMP 594 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~kv~E~~yFNNYl~DP~RP~~~p~~~q~~~ 594 (766)
||+|++ |+|||||+|||+|||+|||+|||+++++ |+.||||||+||+||+.+.+++++.+
T Consensus 77 K~~C~l--c~KlFkg~eFV~KHI~nKH~e~ve~~~~---ev~~fnnY~~Dp~rp~~~~~~~~~~p 136 (214)
T PF04959_consen 77 KWRCPL--CGKLFKGPEFVRKHIFNKHPEKVEEVKK---EVEYFNNYLLDPKRPQPPEANPNQHP 136 (214)
T ss_dssp EEEE-S--SS-EESSHHHHHHHHHHH-HHHHHHHHH---HHHHHHHH------------------
T ss_pred EECCCC--CCcccCChHHHHHHHhhcCHHHHHHHHH---HHHHHHHHhcCcccCCCCcccccCcc
Confidence 999985 9999999999999999999999999988 66899999999999987776665444
No 3
>PF12066 DUF3546: Domain of unknown function (DUF3546); InterPro: IPR021933 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 93 to 114 amino acids in length. This domain has two completely conserved Y residues that may be functionally important. ; PDB: 3AX1_A.
Probab=99.92 E-value=3.4e-25 Score=203.97 Aligned_cols=85 Identities=46% Similarity=0.868 Sum_probs=76.7
Q ss_pred CHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhccCCcchHHHHHHHHHHHHHHHHHHHHHhhc
Q 004239 227 SYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKDFLLDLQS 306 (766)
Q Consensus 227 sFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEKY~P~~l~~~~erR~E~~~~aak~F~~dLes 306 (766)
|||||++.++|+|++++|+++|++||.+|+++|+++||++||+++||+|||||+.+..+.+++++.+++++++|+++|++
T Consensus 1 tfK~F~~~~~D~i~~~ea~~~Y~eYK~e~~~~q~~~FF~~HK~eeWFreKY~P~~~~~~~~~~~~~~~~~~~~F~~~l~~ 80 (110)
T PF12066_consen 1 TFKQFLEQQDDDITPEEAQKRYDEYKEEFQRKQLRAFFEQHKDEEWFREKYHPEELDKRREERKEFRKGRADVFMEDLES 80 (110)
T ss_dssp -HHHHGGGTTTS--HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHhcCcHhhHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCC
Q 004239 307 GTLDL 311 (766)
Q Consensus 307 G~fD~ 311 (766)
|+||.
T Consensus 81 G~~d~ 85 (110)
T PF12066_consen 81 GKFDE 85 (110)
T ss_dssp T----
T ss_pred CCCcc
Confidence 99995
No 4
>KOG2295 consensus C2H2 Zn-finger protein [General function prediction only]
Probab=98.99 E-value=3.7e-10 Score=126.52 Aligned_cols=92 Identities=27% Similarity=0.490 Sum_probs=80.2
Q ss_pred CCCCCCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhccCCcchHHHHHHHHHHHHHHHHH
Q 004239 220 TQREGLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDLARKVAKD 299 (766)
Q Consensus 220 ~~~~~lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEKY~P~~l~~~~erR~E~~~~aak~ 299 (766)
.+.+.+-|||.|+.+++|+|...++.++|++||.++..+|...||.+||+|+||+.||||....+.+..-....++....
T Consensus 42 ~~~p~r~t~kkr~~~~dddi~e~~p~krynd~k~dp~~qq~~~~f~a~k~eewyr~k~h~d~~~k~r~~~~g~yqn~~q~ 121 (648)
T KOG2295|consen 42 AYHPERSTFKKRLNSYDDDIRESGPYKRYNDYKIDPRTQQNAVFFEAHKDEEWYRKKYHPDATEKLRNSLHGTYQNRLQV 121 (648)
T ss_pred ccCcccchHHHhhcccccccccCCCcccccccCCCCchhhhHHHHHhcCCcchhhhccCCChHHHHHHHHHHHHHHHHHH
Confidence 46677889999999999999999999999999999999999999999999999999999988655544445556666778
Q ss_pred HHHHhhcCCCCC
Q 004239 300 FLLDLQSGTLDL 311 (766)
Q Consensus 300 F~~dLesG~fD~ 311 (766)
|....++|.|+.
T Consensus 122 f~~r~e~~~~~~ 133 (648)
T KOG2295|consen 122 FYARTERGFFES 133 (648)
T ss_pred HHHhhccccccc
Confidence 888888888874
No 5
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=98.05 E-value=2e-06 Score=71.48 Aligned_cols=32 Identities=25% Similarity=0.374 Sum_probs=28.3
Q ss_pred cCcchhhHHHHHHHHHHHHhhccccccccccc
Q 004239 426 KGLEGVELLDTLITYLWRIHGVDYYGMVETSE 457 (766)
Q Consensus 426 ~~le~ik~LDllI~YLRrVHsvDYY~~~E~de 457 (766)
..+...++|+++|.|||.+|++||||+++|++
T Consensus 8 ~~l~~~e~L~~l~~YLR~~~~YC~~Cg~~Y~d 39 (55)
T PF13821_consen 8 EELSPEERLDKLLSYLREEHNYCFWCGTKYDD 39 (55)
T ss_pred hccCHHHHHHHHHHHHHhhCceeeeeCCccCC
Confidence 34556789999999999999999999999975
No 6
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=88.94 E-value=0.3 Score=32.18 Aligned_cols=24 Identities=25% Similarity=0.695 Sum_probs=20.0
Q ss_pred cccCCCCCcccccchhHHHHHHhhhC
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKH 556 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH 556 (766)
|.|.+ |++.|....=+++|+.+.|
T Consensus 1 ~~C~~--C~~~~~~~~~l~~H~~~~H 24 (24)
T PF13894_consen 1 FQCPI--CGKSFRSKSELRQHMRTHH 24 (24)
T ss_dssp EE-SS--TS-EESSHHHHHHHHHHHS
T ss_pred CCCcC--CCCcCCcHHHHHHHHHhhC
Confidence 67985 9999999999999999877
No 7
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=88.37 E-value=0.25 Score=33.26 Aligned_cols=23 Identities=30% Similarity=0.704 Sum_probs=20.7
Q ss_pred cccCCCCCcccccchhHHHHHHhhhC
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKH 556 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH 556 (766)
|.|. .|+|.|....-+.+||++ |
T Consensus 1 y~C~--~C~~~f~~~~~l~~H~~~-H 23 (23)
T PF00096_consen 1 YKCP--ICGKSFSSKSNLKRHMRR-H 23 (23)
T ss_dssp EEET--TTTEEESSHHHHHHHHHH-H
T ss_pred CCCC--CCCCccCCHHHHHHHHhH-C
Confidence 5788 599999999999999987 5
No 8
>KOG1994 consensus Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification]
Probab=81.04 E-value=1.5 Score=46.54 Aligned_cols=82 Identities=13% Similarity=0.121 Sum_probs=50.3
Q ss_pred CChhHHHHHHHHHHHHHHHHhhhcccc-ccccCCCCcccccccccCCCCCCceeecccc--cccCcchhhHHHHHHHHHH
Q 004239 366 SEPRRIQVDIEQAQALVRKLDSEKGIT-ENILCGSDNDKMNREKSHGSTGPVIIIRGLT--SVKGLEGVELLDTLITYLW 442 (766)
Q Consensus 366 S~p~RI~~DLeqAr~LV~kLDaEkGIe-~n~L~~~d~~~~d~dks~~s~gP~~i~rg~~--~v~~le~ik~LDllI~YLR 442 (766)
+.-.++..|+.-|++..-.|+-++|.- ...|.--+ +++.+ -.+..++. +.+.+-..+.|-.+.-|||
T Consensus 167 ~~kk~~i~~vr~~~~a~~~l~~~~g~~~ps~~kk~e--~~~~e--------~~~~k~~e~~E~eeei~Ee~lt~in~~LR 236 (268)
T KOG1994|consen 167 EDKKNMIPMVRESLEASPALKGEKGFGRPSTLKKCE--TSIIE--------SRITKDTELAELEEEIIEERLTKINIFLR 236 (268)
T ss_pred hhhhhhHHHHHHHHHhhHHhcCccccCCcchhhhcc--ccchh--------hhccCccchhHHHHHHHHHHHHHHHHHHh
Confidence 556799999999999999999888752 11121111 00000 00001111 1111122477999999999
Q ss_pred HHhhccccccccccc
Q 004239 443 RIHGVDYYGMVETSE 457 (766)
Q Consensus 443 rVHsvDYY~~~E~de 457 (766)
--|-+||||++.|..
T Consensus 237 ~eh~YC~fCG~~y~~ 251 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKD 251 (268)
T ss_pred ccceEEEEeccccCC
Confidence 999999999999864
No 9
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=80.78 E-value=0.8 Score=39.75 Aligned_cols=31 Identities=29% Similarity=0.603 Sum_probs=23.8
Q ss_pred ccccCCCCCcccccchhHHHHHHhhh-ChHHHHH
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLK-HPELVIE 562 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nK-H~E~Vee 562 (766)
+|.|.+ |.|.|+..+=+.+||..+ |..+..+
T Consensus 50 ~~~C~~--C~~~f~s~~~l~~Hm~~~~H~~~~~~ 81 (100)
T PF12756_consen 50 SFRCPY--CNKTFRSREALQEHMRSKHHKKRNSE 81 (100)
T ss_dssp SEEBSS--SS-EESSHHHHHHHHHHTTTTC-S--
T ss_pred CCCCCc--cCCCCcCHHHHHHHHcCccCCCcccc
Confidence 699985 999999999999999976 6665443
No 10
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=79.53 E-value=0.76 Score=32.57 Aligned_cols=24 Identities=33% Similarity=0.757 Sum_probs=20.8
Q ss_pred ccccCCCCCcccccchhHHHHHHhhh
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLK 555 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nK 555 (766)
+|.|.+ |.|-|+...-+..|+..|
T Consensus 1 q~~C~~--C~k~f~~~~~~~~H~~sk 24 (27)
T PF12171_consen 1 QFYCDA--CDKYFSSENQLKQHMKSK 24 (27)
T ss_dssp -CBBTT--TTBBBSSHHHHHCCTTSH
T ss_pred CCCccc--CCCCcCCHHHHHHHHccC
Confidence 478986 999999999999999874
No 11
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=76.11 E-value=7.8 Score=43.56 Aligned_cols=24 Identities=25% Similarity=0.506 Sum_probs=14.9
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCCCCC
Q 004239 172 REMGGRPGYGDERPHGRFAGRSSGGY 197 (766)
Q Consensus 172 ~~~gg~~~~~~~~~~g~~~~~~~~g~ 197 (766)
++.||+++|. +|++.+..|.+++|
T Consensus 376 gG~GGGggyq--qp~~~~~~hqn~~y 399 (465)
T KOG3973|consen 376 GGRGGGGGYQ--QPQQQQQQHQNQSY 399 (465)
T ss_pred CCCCCCCCCc--Cchhhhhccccccc
Confidence 4456667777 67666666655444
No 12
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=74.93 E-value=6.6 Score=48.00 Aligned_cols=18 Identities=22% Similarity=0.621 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHhhcC
Q 004239 290 NDLARKVAKDFLLDLQSG 307 (766)
Q Consensus 290 ~E~~~~aak~F~~dLesG 307 (766)
+..+....-.|+..|.+|
T Consensus 135 ~ne~~~~s~eyV~~l~~g 152 (1102)
T KOG1924|consen 135 DNEAKGSSPEYVVELRSG 152 (1102)
T ss_pred hhhhccCChHHHHHHHcc
Confidence 334556677899999998
No 13
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=74.05 E-value=2.1 Score=29.27 Aligned_cols=23 Identities=30% Similarity=0.706 Sum_probs=20.6
Q ss_pred cccCCCCCcccccchhHHHHHHhhh
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLK 555 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nK 555 (766)
|.|.+ |.+.|....-++.|+.-|
T Consensus 1 ~~C~~--C~~~f~s~~~~~~H~~s~ 23 (25)
T PF12874_consen 1 FYCDI--CNKSFSSENSLRQHLRSK 23 (25)
T ss_dssp EEETT--TTEEESSHHHHHHHHTTH
T ss_pred CCCCC--CCCCcCCHHHHHHHHCcC
Confidence 67986 999999999999999764
No 14
>smart00355 ZnF_C2H2 zinc finger.
Probab=72.24 E-value=3.1 Score=27.33 Aligned_cols=24 Identities=29% Similarity=0.830 Sum_probs=20.4
Q ss_pred cccCCCCCcccccchhHHHHHHhhhCh
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
|.|. .|.|.|....-+..|+. +|.
T Consensus 1 ~~C~--~C~~~f~~~~~l~~H~~-~H~ 24 (26)
T smart00355 1 YRCP--ECGKVFKSKSALKEHMR-THX 24 (26)
T ss_pred CCCC--CCcchhCCHHHHHHHHH-Hhc
Confidence 4687 49999999999999998 654
No 15
>PHA00616 hypothetical protein
Probab=72.00 E-value=1.6 Score=35.40 Aligned_cols=26 Identities=31% Similarity=0.548 Sum_probs=23.9
Q ss_pred cccCCCCCcccccchhHHHHHHhhhChH
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKHPE 558 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~E 558 (766)
|.|. .|+|.|.-.--+.+||.+.|.+
T Consensus 2 YqC~--~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCL--RCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred Cccc--hhhHHHhhHHHHHHHHHHhcCC
Confidence 5787 5999999999999999999988
No 16
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=71.68 E-value=2.8 Score=30.72 Aligned_cols=29 Identities=34% Similarity=0.478 Sum_probs=23.4
Q ss_pred ccccCCCCCcccccchhHHHHHHhhh-ChHHH
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLK-HPELV 560 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nK-H~E~V 560 (766)
+|.|.+ |.+-|.....+..|+..| |.+.|
T Consensus 3 ~~~C~~--C~~~~~~~~~~~~H~~gk~H~~~~ 32 (35)
T smart00451 3 GFYCKL--CNVTFTDEISVEAHLKGKKHKKNV 32 (35)
T ss_pred CeEccc--cCCccCCHHHHHHHHChHHHHHHH
Confidence 688986 999999999999999764 44443
No 17
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=68.83 E-value=4.9 Score=46.51 Aligned_cols=43 Identities=33% Similarity=0.425 Sum_probs=37.4
Q ss_pred cCcccccCCCCCcccccchhHHHHHHh-hhChHHHHHHHhhHHHHH
Q 004239 527 YGWKYGCGAKGCTKLFHAAEFVHKHLK-LKHPELVIELTSKVREEL 571 (766)
Q Consensus 527 ~g~K~rC~l~gCtKLFKgpEFVrKHI~-nKH~E~Veev~~kv~E~~ 571 (766)
+++-+-|.| |+|.||..-=+..|+. +||-+.|.++++++.|..
T Consensus 289 ~ge~lyC~v--CnKsFKseKq~kNHEnSKKHkenv~eLrqemEEEe 332 (508)
T KOG0717|consen 289 EGEVLYCVV--CNKSFKSEKQLKNHENSKKHKENVAELRQEMEEEE 332 (508)
T ss_pred cCCceEEee--ccccccchHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 455589997 9999999999999996 579999999999887665
No 18
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=67.34 E-value=1.2 Score=46.64 Aligned_cols=43 Identities=14% Similarity=0.121 Sum_probs=26.6
Q ss_pred HHHhhhhHHHhhhhcccCcccccCCCCCcccccchhHHHHHHhh
Q 004239 511 AVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKL 554 (766)
Q Consensus 511 l~e~ve~fVkk~~dEk~g~K~rC~l~gCtKLFKgpEFVrKHI~n 554 (766)
++++|+++|+++.+.+|.- =.|.-+.=+--|.-.+...||-..
T Consensus 62 ve~~v~~~~~e~~~~K~~C-~lc~KlFkg~eFV~KHI~nKH~e~ 104 (214)
T PF04959_consen 62 VEKFVQKNTKEEDEDKWRC-PLCGKLFKGPEFVRKHIFNKHPEK 104 (214)
T ss_dssp HGGGEEEEE-SSSSEEEEE--SSS-EESSHHHHHHHHHHH-HHH
T ss_pred HHHHHHHHHHHHcCCEECC-CCCCcccCChHHHHHHHhhcCHHH
Confidence 4557888888876777764 346554555778777888888643
No 19
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=61.30 E-value=5.4 Score=27.75 Aligned_cols=25 Identities=20% Similarity=0.542 Sum_probs=21.3
Q ss_pred cccCCCCCcccccchhHHHHHHhhhCh
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
|.|.. |.|.|....=+.+|++..|.
T Consensus 2 ~~C~~--C~~~F~~~~~l~~H~~~h~~ 26 (27)
T PF13912_consen 2 FECDE--CGKTFSSLSALREHKRSHCS 26 (27)
T ss_dssp EEETT--TTEEESSHHHHHHHHCTTTT
T ss_pred CCCCc--cCCccCChhHHHHHhHHhcC
Confidence 57874 99999999999999977653
No 20
>PF04780 DUF629: Protein of unknown function (DUF629); InterPro: IPR006865 This domain represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family.
Probab=49.55 E-value=16 Score=42.58 Aligned_cols=43 Identities=26% Similarity=0.561 Sum_probs=33.7
Q ss_pred hhhhHHHhhhhcccCcc-cccCCCCCcccccchhHHHHHHhhhChHHHHH
Q 004239 514 ALDPFVRKIRDEKYGWK-YGCGAKGCTKLFHAAEFVHKHLKLKHPELVIE 562 (766)
Q Consensus 514 ~ve~fVkk~~dEk~g~K-~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Vee 562 (766)
.+..|++++. .|+ |.|+. |.|+|...+=...||.++|...+..
T Consensus 44 eal~fak~n~----sWrFWiCp~--CskkF~d~~~~~~H~~~eH~~~l~P 87 (466)
T PF04780_consen 44 EALSFAKENK----SWRFWICPR--CSKKFSDAESCLSHMEQEHPAGLKP 87 (466)
T ss_pred HHHHHHHhcC----ceeEeeCCc--ccceeCCHHHHHHHHHHhhhhhcCh
Confidence 3446887632 233 78985 9999999999999999999997754
No 21
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=48.98 E-value=12 Score=29.11 Aligned_cols=27 Identities=37% Similarity=0.619 Sum_probs=19.8
Q ss_pred cccccCCCCCcccccc----hhHHHHHHhhhCh
Q 004239 529 WKYGCGAKGCTKLFHA----AEFVHKHLKLKHP 557 (766)
Q Consensus 529 ~K~rC~l~gCtKLFKg----pEFVrKHI~nKH~ 557 (766)
.+..|.. |.|.|++ ..=+..||.+|||
T Consensus 15 ~~a~C~~--C~~~~~~~~~~ts~l~~HL~~~hp 45 (45)
T PF02892_consen 15 KKAKCKY--CGKVIKYSSGGTSNLKRHLKKKHP 45 (45)
T ss_dssp S-EEETT--TTEE-----SSTHHHHHHHHHTTH
T ss_pred CeEEeCC--CCeEEeeCCCcHHHHHHhhhhhCc
Confidence 4789985 9999997 4788999999996
No 22
>KOG2654 consensus Uncharacterized conserved protein [Function unknown]
Probab=47.25 E-value=41 Score=38.83 Aligned_cols=24 Identities=46% Similarity=0.859 Sum_probs=12.1
Q ss_pred hhccCCCCCCCCCCCCCCCCcCCCCCCC
Q 004239 67 ERRDDRDLDRPPPNRRGPDYYDRNRSPP 94 (766)
Q Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (766)
.++ |-|...|..+|. ..|-..|||
T Consensus 105 ~~~-dsd~spprp~rk---r~dsd~spp 128 (461)
T KOG2654|consen 105 QDR-DSDMSPPRPNRK---RTDSDMSPP 128 (461)
T ss_pred ccc-ccCCCCCCCccc---cCCCCCCCC
Confidence 444 556666644442 235555555
No 23
>KOG3875 consensus Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.85 E-value=59 Score=36.48 Aligned_cols=15 Identities=40% Similarity=0.767 Sum_probs=7.1
Q ss_pred CCCCCCCCCCCCCCCC
Q 004239 112 SPPPPPLPYRDRRHSP 127 (766)
Q Consensus 112 ~~~~~~~~~~~rr~SP 127 (766)
+||++++|| .-|-+|
T Consensus 4 ~pp~~~~p~-n~~~~p 18 (362)
T KOG3875|consen 4 SPPQDSRPE-NTRTNP 18 (362)
T ss_pred CCCCCCchh-hhcCCC
Confidence 344455555 444444
No 24
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=41.04 E-value=9.8 Score=43.76 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=23.6
Q ss_pred ccccCCCCCcccccchhHHHHHHhhhChH
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHPE 558 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nKH~E 558 (766)
.|-|. .|.|+|+-.-|++||...-|--
T Consensus 356 i~~C~--~C~KkFrRqAYLrKHqlthq~~ 382 (500)
T KOG3993|consen 356 IFSCH--TCGKKFRRQAYLRKHQLTHQRA 382 (500)
T ss_pred eeecH--HhhhhhHHHHHHHHhHHhhhcc
Confidence 89998 6999999999999998776644
No 25
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=39.73 E-value=23 Score=28.96 Aligned_cols=26 Identities=23% Similarity=0.442 Sum_probs=19.9
Q ss_pred ccccCCCCCcccccchhHHHHHHhhhChH
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHPE 558 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nKH~E 558 (766)
.|.|+. |+|.|.. .-+.+||..+|..
T Consensus 2 ~f~CP~--C~~~~~~-~~L~~H~~~~H~~ 27 (54)
T PF05605_consen 2 SFTCPY--CGKGFSE-SSLVEHCEDEHRS 27 (54)
T ss_pred CcCCCC--CCCccCH-HHHHHHHHhHCcC
Confidence 688984 9996655 4577899999886
No 26
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=39.55 E-value=18 Score=25.73 Aligned_cols=24 Identities=38% Similarity=0.610 Sum_probs=18.5
Q ss_pred hhhHHHhhhhcccCcccccCCCCCccccc
Q 004239 515 LDPFVRKIRDEKYGWKYGCGAKGCTKLFH 543 (766)
Q Consensus 515 ve~fVkk~~dEk~g~K~rC~l~gCtKLFK 543 (766)
+..+++..+.|+ .|.|. .|.|.|+
T Consensus 2 l~~H~~~H~~~k---~~~C~--~C~k~F~ 25 (26)
T PF13465_consen 2 LRRHMRTHTGEK---PYKCP--YCGKSFS 25 (26)
T ss_dssp HHHHHHHHSSSS---SEEES--SSSEEES
T ss_pred HHHHhhhcCCCC---CCCCC--CCcCeeC
Confidence 345777777775 79998 4999996
No 27
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=39.48 E-value=1.3e+02 Score=38.25 Aligned_cols=19 Identities=37% Similarity=0.545 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCCCccCccCCCC
Q 004239 122 DRRHSPPPRRSPPYKRSRRDDG 143 (766)
Q Consensus 122 ~rr~SP~~~~spp~kr~rr~~~ 143 (766)
.+||+=.++ |-|+-|-|||
T Consensus 1156 StrygDGp~---PPKmaryDnG 1174 (1282)
T KOG0921|consen 1156 STRYGDGPG---PPKMARYDNG 1174 (1282)
T ss_pred cccccCCCC---CcccccccCC
Confidence 466664332 3355555544
No 28
>KOG4173 consensus Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.22 E-value=17 Score=38.50 Aligned_cols=49 Identities=24% Similarity=0.365 Sum_probs=36.3
Q ss_pred HHHHHHHhhhhHHHhhhhcccCcccccCCCCCcccccchhHHHHHHhhhC
Q 004239 507 IDAAAVDALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKH 556 (766)
Q Consensus 507 id~el~e~ve~fVkk~~dEk~g~K~rC~l~gCtKLFKgpEFVrKHI~nKH 556 (766)
++.-|.||-+.|..+ ..|...+-|.|.|-+||-|||..-=-+.|+-.+|
T Consensus 122 Ld~HI~E~HDs~Fqa-~veRG~dMy~ClvEgCt~KFkT~r~RkdH~I~~H 170 (253)
T KOG4173|consen 122 LDAHILEWHDSLFQA-LVERGQDMYQCLVEGCTEKFKTSRDRKDHMIRMH 170 (253)
T ss_pred hhHHHHHHHHHHHHH-HHHcCccHHHHHHHhhhhhhhhhhhhhhHHHHhc
Confidence 444567787777666 4677678999999999999998766666665444
No 29
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=38.03 E-value=6.3 Score=44.20 Aligned_cols=59 Identities=19% Similarity=0.330 Sum_probs=46.7
Q ss_pred cccccCCCCCcccccchhHHHHHHhhhChHHHHHHHhhHHHHHHHhhhccCCCCCCCCCCCCCC
Q 004239 529 WKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSKVREELYFQNYMNDPDAPGGTPVMQQP 592 (766)
Q Consensus 529 ~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~kv~E~~yFNNYl~DP~RP~~~p~~~q~ 592 (766)
+.++|- .|.|-|+...-++.|+++|.=-.|.....+ .+.-|.-||+.=++++ ++|.++-
T Consensus 194 ~r~~CL--yCekifrdkntLkeHMrkK~HrrinPknre-YDkfyiINY~ev~ks~--t~~~~e~ 252 (423)
T KOG2482|consen 194 ERLRCL--YCEKIFRDKNTLKEHMRKKRHRRINPKNRE-YDKFYIINYLEVGKSW--TIVHSED 252 (423)
T ss_pred hhheee--eeccccCCcHHHHHHHHhccCcccCCCccc-cceEEEEeHhhcCCcc--chhhhhh
Confidence 478997 599999999999999999977777665443 2556888999999996 5666554
No 30
>COG5192 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=37.26 E-value=35 Score=41.11 Aligned_cols=37 Identities=16% Similarity=0.370 Sum_probs=22.8
Q ss_pred hcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHh
Q 004239 235 LEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLK 274 (766)
Q Consensus 235 ~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFr 274 (766)
+.++|+|+||+++ ||-+-...--...+.+--.+.+|+
T Consensus 506 y~e~lspeeci~e---~kge~~~s~e~~~v~~D~~edff~ 542 (1077)
T COG5192 506 YDESLSPEECIEE---YKGESAKSSESDLVVQDEPEDFFD 542 (1077)
T ss_pred ccccCCHHHHHHH---hccccccccccccccccCchhhhh
Confidence 4678999998655 455544444445555555555665
No 31
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=36.32 E-value=1.8e+02 Score=31.78 Aligned_cols=33 Identities=24% Similarity=0.505 Sum_probs=23.1
Q ss_pred ccccCCCCCc-ccccchhHHHHHHhhhChHHHHHHHh
Q 004239 530 KYGCGAKGCT-KLFHAAEFVHKHLKLKHPELVIELTS 565 (766)
Q Consensus 530 K~rC~l~gCt-KLFKgpEFVrKHI~nKH~E~Veev~~ 565 (766)
-|.|.+ |- |||.|+-.-+ |-..-|-|-|+.+-+
T Consensus 34 hfkchi--chkkl~sgpglsi-hcmqvhketid~ip~ 67 (341)
T KOG2893|consen 34 HFKCHI--CHKKLFSGPGLSI-HCMQVHKETIDKIPA 67 (341)
T ss_pred cceeee--ehhhhccCCCcee-ehhhhhhhhhhcccc
Confidence 578875 75 5788887654 667778887777644
No 32
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=34.85 E-value=63 Score=26.53 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=28.0
Q ss_pred HhhhhHHHhhhhcccCcccccCCCCCcccccchhHHHHHHhhhChHHHHHHHhh
Q 004239 513 DALDPFVRKIRDEKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTSK 566 (766)
Q Consensus 513 e~ve~fVkk~~dEk~g~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~k 566 (766)
+++.++|..+... +=.|+| |+--|-..+. .+|..++.+.++.+.++
T Consensus 7 ~~~~k~i~~l~~~----~~~CPl--C~r~l~~e~~--~~li~~~~~~i~~~~~~ 52 (54)
T PF04423_consen 7 EELKKYIEELKEA----KGCCPL--CGRPLDEEHR--QELIKKYKSEIEELPEK 52 (54)
T ss_dssp HHHHHHHHHHTT-----SEE-TT--T--EE-HHHH--HHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHhcC----CCcCCC--CCCCCCHHHH--HHHHHHHHHHHHhhhhc
Confidence 4556666665443 228997 9999998887 77777777777776553
No 33
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=33.69 E-value=89 Score=38.95 Aligned_cols=11 Identities=9% Similarity=0.329 Sum_probs=7.9
Q ss_pred HHhhhhHHHhh
Q 004239 512 VDALDPFVRKI 522 (766)
Q Consensus 512 ~e~ve~fVkk~ 522 (766)
-+.||.||.+|
T Consensus 425 ykLIEecISqI 435 (1102)
T KOG1924|consen 425 YKLIEECISQI 435 (1102)
T ss_pred HHHHHHHHHHH
Confidence 35677788876
No 34
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.20 E-value=34 Score=24.38 Aligned_cols=20 Identities=30% Similarity=0.599 Sum_probs=16.7
Q ss_pred ccCCCCCcccccchhHHHHHHhh
Q 004239 532 GCGAKGCTKLFHAAEFVHKHLKL 554 (766)
Q Consensus 532 rC~l~gCtKLFKgpEFVrKHI~n 554 (766)
.|+ .|+.+| .++-+.||+..
T Consensus 4 ~C~--~CgR~F-~~~~l~~H~~~ 23 (25)
T PF13913_consen 4 PCP--ICGRKF-NPDRLEKHEKI 23 (25)
T ss_pred cCC--CCCCEE-CHHHHHHHHHh
Confidence 587 599999 88999999863
No 35
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=30.75 E-value=30 Score=23.57 Aligned_cols=24 Identities=33% Similarity=0.683 Sum_probs=17.3
Q ss_pred cccCCCCCcccccchhHHHHHHhhhCh
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
|.|.. |.=..+ ..-+.+|++.+|+
T Consensus 1 y~C~~--C~y~t~-~~~l~~H~~~~H~ 24 (24)
T PF13909_consen 1 YKCPH--CSYSTS-KSNLKRHLKRHHP 24 (24)
T ss_dssp EE-SS--SS-EES-HHHHHHHHHHHHS
T ss_pred CCCCC--CCCcCC-HHHHHHHHHhhCc
Confidence 56874 886666 7778999999885
No 36
>PHA00733 hypothetical protein
Probab=30.47 E-value=37 Score=32.88 Aligned_cols=26 Identities=27% Similarity=0.425 Sum_probs=23.4
Q ss_pred ccccCCCCCcccccchhHHHHHHhhhCh
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
.|.|.. |+|.|....-+.+|+..||.
T Consensus 99 ~~~C~~--CgK~F~~~~sL~~H~~~~h~ 124 (128)
T PHA00733 99 SKVCPV--CGKEFRNTDSTLDHVCKKHN 124 (128)
T ss_pred CccCCC--CCCccCCHHHHHHHHHHhcC
Confidence 578984 99999999999999999996
No 37
>PF01715 IPPT: IPP transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) [].; GO: 0005524 ATP binding, 0008033 tRNA processing; PDB: 2ZXU_A 3FOZ_A 2ZM5_B 3D3Q_A 3EXA_B 2QGN_A 3A8T_A 3EPK_B 3EPH_A 3EPJ_A ....
Probab=28.51 E-value=92 Score=33.26 Aligned_cols=48 Identities=29% Similarity=0.575 Sum_probs=37.5
Q ss_pred CCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHH
Q 004239 225 LMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWL 273 (766)
Q Consensus 225 lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWF 273 (766)
.+=||||+..+...++-+||......==..|.++|+ +||....+-.||
T Consensus 203 aIGYkE~~~~l~g~~~~~e~~e~i~~~TrqyAKRQ~-TWfr~~~~~~w~ 250 (253)
T PF01715_consen 203 AIGYKEFIDYLEGEISLEEAIERIKTNTRQYAKRQR-TWFRNQPNIHWI 250 (253)
T ss_dssp STTHHHHHHHHTTSSCHHHHHHHHHHHHHHHHHHHH-HHHHTTSSEEEE
T ss_pred eeehHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHH-HHhCCCCCCeee
Confidence 678999999999999999998887666667777764 566666555565
No 38
>smart00805 AGTRAP Angiotensin II, type I receptor-associated protein. This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the C-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear.
Probab=24.19 E-value=69 Score=32.62 Aligned_cols=13 Identities=54% Similarity=0.879 Sum_probs=11.1
Q ss_pred CccccCCCCCCCc
Q 004239 746 RSYQDLDAPEDEV 758 (766)
Q Consensus 746 r~Y~DLDaP~~~~ 758 (766)
+||||+|+|.+.-
T Consensus 133 ~sYqdID~p~qp~ 145 (159)
T smart00805 133 SSYQTIDAPADPF 145 (159)
T ss_pred cccccccCCCCCC
Confidence 8999999998753
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=23.77 E-value=31 Score=42.35 Aligned_cols=29 Identities=28% Similarity=0.600 Sum_probs=24.8
Q ss_pred cccccCCCCCcccccchhHHHHHHhhhChHH
Q 004239 529 WKYGCGAKGCTKLFHAAEFVHKHLKLKHPEL 559 (766)
Q Consensus 529 ~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~ 559 (766)
-||-|+ +|+|-||=.+-++.||+.--+||
T Consensus 280 RKFKCt--ECgKAFKfKHHLKEHlRIHSGEK 308 (1007)
T KOG3623|consen 280 RKFKCT--ECGKAFKFKHHLKEHLRIHSGEK 308 (1007)
T ss_pred cccccc--ccchhhhhHHHHHhhheeecCCC
Confidence 489998 89999999999999998766664
No 40
>PHA02768 hypothetical protein; Provisional
Probab=23.48 E-value=53 Score=28.06 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=21.2
Q ss_pred cccCCCCCcccccchhHHHHHHhhhCh
Q 004239 531 YGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 531 ~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
|.|. .|+|.|.-..-+.+|+++ |.
T Consensus 6 y~C~--~CGK~Fs~~~~L~~H~r~-H~ 29 (55)
T PHA02768 6 YECP--ICGEIYIKRKSMITHLRK-HN 29 (55)
T ss_pred cCcc--hhCCeeccHHHHHHHHHh-cC
Confidence 7898 599999999999999998 44
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=23.33 E-value=96 Score=25.38 Aligned_cols=24 Identities=21% Similarity=0.423 Sum_probs=19.4
Q ss_pred ccccCCCCCcccccchhHHHHHHhhhCh
Q 004239 530 KYGCGAKGCTKLFHAAEFVHKHLKLKHP 557 (766)
Q Consensus 530 K~rC~l~gCtKLFKgpEFVrKHI~nKH~ 557 (766)
.+.|++ |.+.|.. =+..||...|.
T Consensus 31 ~v~CPi--C~~~~~~--~l~~Hl~~~H~ 54 (54)
T PF05605_consen 31 NVVCPI--CSSRVTD--NLIRHLNSQHR 54 (54)
T ss_pred CccCCC--chhhhhh--HHHHHHHHhcC
Confidence 689996 9998875 56679998884
No 42
>KOG4702 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.19 E-value=1.5e+02 Score=26.83 Aligned_cols=35 Identities=20% Similarity=0.429 Sum_probs=28.9
Q ss_pred CHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHH
Q 004239 227 SYKQFIQELEDDILPAEAERRYQEYKSEYISTQKR 261 (766)
Q Consensus 227 sFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r 261 (766)
=|++|+....-.++|-|+.++-+||+.-..+++++
T Consensus 30 ~Fee~v~~~krel~ppe~~~~~EE~~~~lRe~~a~ 64 (77)
T KOG4702|consen 30 IFEEFVRGYKRELSPPEATKRKEEYENFLREQMAF 64 (77)
T ss_pred HHHHHHHhccccCCChHHHhhHHHHHHHHHHHHHH
Confidence 48999988888888999999999998877776543
No 43
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=22.89 E-value=1.2e+02 Score=33.56 Aligned_cols=49 Identities=24% Similarity=0.495 Sum_probs=36.9
Q ss_pred CCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHh
Q 004239 225 LMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLK 274 (766)
Q Consensus 225 lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFr 274 (766)
.+=||||+.++...+|-++|...-..==..|.++|+ ++|....+-.||-
T Consensus 239 aIGykE~~~yl~g~~s~~e~~e~i~~~Tr~yAKRQ~-TWfr~~~~~~w~~ 287 (307)
T PRK00091 239 AIGYKELLAYLDGEISLEEAIEKIKQATRQYAKRQL-TWFRRQPDIHWLD 287 (307)
T ss_pred eecHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH-HHhCCCCCCeeec
Confidence 677999999999999999998877666667777774 5555555555654
No 44
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=21.77 E-value=63 Score=31.89 Aligned_cols=36 Identities=22% Similarity=0.210 Sum_probs=21.5
Q ss_pred cccCcccccCCCCCcccccchhHHHHHHhhhChHHHHHHHh
Q 004239 525 EKYGWKYGCGAKGCTKLFHAAEFVHKHLKLKHPELVIELTS 565 (766)
Q Consensus 525 Ek~g~K~rC~l~gCtKLFKgpEFVrKHI~nKH~E~Veev~~ 565 (766)
....+...|- .|+|.||.- .+||...|.=-.++-++
T Consensus 67 SI~~d~i~cl--ecGk~~k~L---krHL~~~~gltp~eYR~ 102 (132)
T PF05443_consen 67 SITPDYIICL--ECGKKFKTL---KRHLRTHHGLTPEEYRA 102 (132)
T ss_dssp TB-SS-EE-T--BT--EESBH---HHHHHHTT-S-HHHHHH
T ss_pred ccccCeeEEc--cCCcccchH---HHHHHHccCCCHHHHHH
Confidence 3344688997 699999976 99999998765555433
No 45
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=21.00 E-value=1.7e+02 Score=32.65 Aligned_cols=50 Identities=24% Similarity=0.422 Sum_probs=36.1
Q ss_pred CCCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHh
Q 004239 224 GLMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLK 274 (766)
Q Consensus 224 ~lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFr 274 (766)
..+=||||+.+++-.+|-+||..+=..=-..|.++|+ +||..-.+..||.
T Consensus 239 ~~iGy~e~~~yl~g~~~~~ea~~~~~~~TRqyAKRQ~-TWfr~~~~~~w~~ 288 (308)
T COG0324 239 QAIGYKEILAYLDGGISLEEAIERIKTATRQYAKRQL-TWFRNQLGVHWLD 288 (308)
T ss_pred HhcCHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH-HHhccCcccceec
Confidence 3678999999998779999998766555566777764 5555555555543
No 46
>TIGR00174 miaA tRNA isopentenyltransferase (miaA). Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine.
Probab=20.44 E-value=1.4e+02 Score=32.84 Aligned_cols=41 Identities=24% Similarity=0.401 Sum_probs=30.7
Q ss_pred CCCHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 004239 225 LMSYKQFIQELEDDILPAEAERRYQEYKSEYISTQKRVFFDA 266 (766)
Q Consensus 225 lmsFKqFl~~~eD~IspeEA~~rY~eYK~ef~~kq~r~FF~~ 266 (766)
.+=||||+.++...++-+||...-..=-..|.++|+ ++|..
T Consensus 235 aIGYkE~~~~l~g~~~~~e~ie~i~~~Tr~yAKRQ~-TWfR~ 275 (287)
T TIGR00174 235 AIGYKEFLLYLEGTVSLEDAIERIKCNTRQYAKRQL-TWFRK 275 (287)
T ss_pred hccHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH-HHhCC
Confidence 678999999999999999987766555556777764 34443
No 47
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.34 E-value=2.4e+02 Score=31.71 Aligned_cols=87 Identities=22% Similarity=0.326 Sum_probs=56.1
Q ss_pred CCCCHHHHHHhhcC-------CCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCChhHHhhccCCcchHHHHHHHHHH----
Q 004239 224 GLMSYKQFIQELED-------DILPAEAERRYQEYKSEYISTQKRVFFDAHKDEEWLKDKYHPTNLVAVIERRNDL---- 292 (766)
Q Consensus 224 ~lmsFKqFl~~~eD-------~IspeEA~~rY~eYK~ef~~kq~r~FF~~HK~EeWFrEKY~P~~l~~~~erR~E~---- 292 (766)
.+.-|-.||+..+| .|+.++++..-++|+.+++..-.+..-......+||.+.=.=+. +...++|++.
T Consensus 91 ~l~~yNdYLE~vEdii~nL~~~~d~~~te~~l~~y~~~n~~~I~~n~~~~~~e~~~~~~~~~~E~-~~~~~rr~~~~~~e 169 (309)
T TIGR00570 91 SLREYNDYLEEVEDIVYNLTNNIDLENTKKKIETYQKENKDVIQKNKEKSTREQEELEEALEFEK-EEEEQRRLLLQKEE 169 (309)
T ss_pred CHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHhHHHHHHHHHHHHhHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 56778888876554 46778888999999999998888777788888888866542111 1111222221
Q ss_pred ------HHHHHHHHHHHhhcCCCCC
Q 004239 293 ------ARKVAKDFLLDLQSGTLDL 311 (766)
Q Consensus 293 ------~~~aak~F~~dLesG~fD~ 311 (766)
.+..-.+.+.+|++|..+.
T Consensus 170 ~ee~~~~~~~~~~~ld~L~~s~~~~ 194 (309)
T TIGR00570 170 EEQQMNKRKNKQALLDELETSTLPA 194 (309)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCH
Confidence 1222347788887766443
Done!