Query psy5133
Match_columns 313
No_of_seqs 191 out of 244
Neff 4.5
Searched_HMMs 46136
Date Fri Aug 16 18:11:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5133.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5133hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4017|consensus 100.0 2.9E-81 6.2E-86 576.5 13.8 253 14-307 15-274 (274)
2 TIGR00598 rad14 DNA repair pro 100.0 2.1E-70 4.6E-75 483.9 12.7 172 135-307 1-172 (172)
3 COG5145 RAD14 DNA excision rep 100.0 6.5E-61 1.4E-65 438.1 8.1 214 89-306 55-291 (292)
4 PF05181 XPA_C: XPA protein C- 99.9 1.5E-26 3.2E-31 169.1 2.6 52 164-216 1-52 (52)
5 PF01286 XPA_N: XPA protein N- 99.1 6.7E-12 1.5E-16 85.0 -0.5 30 133-162 4-33 (34)
6 KOG2802|consensus 99.0 4.4E-10 9.6E-15 110.8 5.2 92 165-262 109-200 (503)
7 PF12677 DUF3797: Domain of un 82.2 0.62 1.4E-05 34.3 0.9 17 286-303 33-49 (49)
8 PF01412 ArfGap: Putative GTPa 71.2 1.2 2.6E-05 37.1 -0.2 29 132-161 13-41 (116)
9 PF11261 IRF-2BP1_2: Interfero 68.4 2.8 6.1E-05 31.4 1.2 31 134-164 5-35 (54)
10 smart00105 ArfGap Putative GTP 54.7 4 8.6E-05 33.8 -0.1 29 133-162 4-32 (112)
11 PF12269 zf-CpG_bind_C: CpG bi 50.7 28 0.00062 33.2 4.9 91 215-307 7-99 (236)
12 PRK11032 hypothetical protein; 50.3 25 0.00054 31.7 4.3 105 176-307 34-139 (160)
13 PF07295 DUF1451: Protein of u 50.0 39 0.00085 29.8 5.4 19 289-307 109-127 (146)
14 PF01258 zf-dskA_traR: Prokary 49.1 5.7 0.00012 26.6 0.0 27 135-161 6-32 (36)
15 TIGR00515 accD acetyl-CoA carb 47.0 9.8 0.00021 36.9 1.3 46 133-185 27-72 (285)
16 COG5347 GTPase-activating prot 45.9 6.7 0.00015 38.8 -0.0 31 131-162 19-49 (319)
17 PF04161 Arv1: Arv1-like famil 42.0 12 0.00026 34.3 0.9 33 134-167 2-38 (208)
18 COG2191 Formylmethanofuran deh 40.6 14 0.0003 34.6 1.2 30 133-162 173-202 (206)
19 PF14446 Prok-RING_1: Prokaryo 37.4 20 0.00043 27.0 1.3 27 131-162 4-30 (54)
20 KOG1701|consensus 34.6 12 0.00025 38.8 -0.4 46 133-183 335-389 (468)
21 PF08412 Ion_trans_N: Ion tran 34.6 28 0.0006 27.7 1.8 25 212-236 6-30 (77)
22 cd07160 NR_DBD_LXR DNA-binding 33.9 22 0.00047 29.5 1.2 26 133-162 19-44 (101)
23 PLN03114 ADP-ribosylation fact 33.4 17 0.00037 36.9 0.6 29 133-162 23-51 (395)
24 PF11240 DUF3042: Protein of u 33.4 41 0.00088 25.4 2.4 20 19-38 33-52 (54)
25 PF03991 Prion_octapep: Copper 31.6 27 0.0006 17.0 0.8 8 200-207 1-8 (8)
26 TIGR03826 YvyF flagellar opero 31.6 8.9 0.00019 33.6 -1.5 27 135-167 6-33 (137)
27 KOG3134|consensus 30.3 11 0.00025 35.6 -1.1 34 134-167 2-38 (225)
28 PF12760 Zn_Tnp_IS1595: Transp 29.7 19 0.00042 25.2 0.2 27 133-161 19-45 (46)
29 CHL00174 accD acetyl-CoA carbo 29.7 25 0.00055 34.5 1.1 60 133-202 39-98 (296)
30 PF00096 zf-C2H2: Zinc finger, 29.5 22 0.00047 20.7 0.4 15 134-148 2-16 (23)
31 smart00834 CxxC_CXXC_SSSS Puta 29.2 47 0.001 22.0 2.0 19 290-308 3-21 (41)
32 PF08274 PhnA_Zn_Ribbon: PhnA 28.9 22 0.00049 23.6 0.4 25 133-161 3-27 (30)
33 PRK05654 acetyl-CoA carboxylas 28.3 28 0.0006 34.0 1.1 67 133-211 28-94 (292)
34 smart00661 RPOL9 RNA polymeras 28.2 24 0.00052 24.7 0.5 28 134-162 2-29 (52)
35 PLN03119 putative ADP-ribosyla 28.0 23 0.00051 37.9 0.5 28 133-161 24-51 (648)
36 PF13451 zf-trcl: Probable zin 26.5 21 0.00046 26.3 -0.1 29 134-162 6-42 (49)
37 PF09297 zf-NADH-PPase: NADH p 26.3 36 0.00078 22.1 1.0 16 287-302 16-31 (32)
38 PRK06424 transcription factor; 25.6 15 0.00032 32.3 -1.2 28 135-162 3-32 (144)
39 PF09845 DUF2072: Zn-ribbon co 24.6 38 0.00083 29.7 1.2 38 134-176 3-40 (131)
40 PRK12495 hypothetical protein; 23.8 36 0.00078 32.4 0.9 25 133-162 43-67 (226)
41 PRK10363 cpxP periplasmic repr 23.5 97 0.0021 28.2 3.5 23 18-40 123-145 (166)
42 PF07739 TipAS: TipAS antibiot 22.9 96 0.0021 24.7 3.1 46 216-262 2-50 (118)
43 PLN03131 hypothetical protein; 22.8 32 0.0007 37.3 0.4 29 132-161 23-51 (705)
44 COG0777 AccD Acetyl-CoA carbox 22.1 74 0.0016 31.4 2.7 69 133-213 29-97 (294)
45 PF09538 FYDLN_acid: Protein o 21.9 40 0.00086 28.4 0.7 26 133-162 10-35 (108)
46 COG1656 Uncharacterized conser 20.5 55 0.0012 29.8 1.4 33 134-166 99-145 (165)
47 PRK00432 30S ribosomal protein 20.4 47 0.001 24.2 0.8 25 133-161 21-45 (50)
48 COG4957 Predicted transcriptio 20.3 69 0.0015 28.6 1.9 28 126-155 72-101 (148)
49 PRK00085 recO DNA repair prote 20.2 36 0.00078 31.0 0.1 28 134-161 151-178 (247)
50 PF05443 ROS_MUCR: ROS/MUCR tr 20.1 33 0.00071 29.9 -0.1 27 126-154 68-96 (132)
No 1
>KOG4017|consensus
Probab=100.00 E-value=2.9e-81 Score=576.51 Aligned_cols=253 Identities=45% Similarity=0.736 Sum_probs=225.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhccCCCCCCCcccccCCCCCCCCCCCCCCcccccccCCCCCCCcccceee
Q psy5133 14 SKTISLSAMQKEQIERNRQRAIQIQQTRTRDLYDPYPNPVKAGVRQTASAPSSCPQSPNLRSTTRLGGARSPGTIRSIIN 93 (313)
Q Consensus 14 ~~~~~lT~eq~~rIE~NR~kAl~lr~~r~~~~~~p~~~~~~~~~~~~~~~~s~~~~~~~~~~~~r~~~~~~~~~~~~~~k 93 (313)
..++.|+..++. |++++..|...+++.+ +.+||.++ ...+.++|+
T Consensus 15 eq~s~l~~~~k~-i~r~~~~a~~~~k~~l--~~rp~~~~--------------------------------s~~~~~~i~ 59 (274)
T KOG4017|consen 15 EQPSALPNTNKN-IERYGSGAVDGRKAVL--VKRPYDAA--------------------------------SERGQDYIE 59 (274)
T ss_pred cchhhhhhhhhh-hhhccchhhhhhhhhh--hcCccchh--------------------------------hhcCcccee
Confidence 355669999999 9999999999999999 78887631 011246788
Q ss_pred eecccceeecCCcccccCCChhh-----hhccCCCCC-CCC-cCCCcccccccccCCchhHHhhcCccccccccCCCccc
Q psy5133 94 AVGSKLFTDTGGGFLLDYDDKYE-----EKYIKQPAP-LLL-ESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKH 166 (313)
Q Consensus 94 ~y~~sk~~Dt~GGFl~ee~~~~~-----~~~~~ep~p-i~~-~~~~~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~ 166 (313)
|| ++|+|||||||+++++..+ ....+++.| ++. -...|+|.+|+++|||+||+++|||+||++||+..++|
T Consensus 60 -~~-~k~~d~~GGf~~e~~~~~~~~~~~~e~re~~~~~l~d~i~~~~~C~eC~~i~mDs~L~~~F~~~VCd~CRd~~eky 137 (274)
T KOG4017|consen 60 -YD-MKIIDTGGGFILEKDKVPESREFESEVREKEEPLLPDHIALAPKCEECDKIEMDSYLFDTFGCSVCDSCRDKDEKY 137 (274)
T ss_pred -ec-ceeecCCCceeccccccchhHHHHHHhhcccccccccchhhchhHHHhcCccchHHHHHhcCChhhhHhhhhhhhh
Confidence 99 9999999999999876433 233445555 431 12237799999999999999999999999999999999
Q ss_pred ccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhHH
Q psy5133 167 CLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNSKL 246 (313)
Q Consensus 167 ~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~QVe~~A~~~WGS~E~Le~E~erRe~~r~~~K~ 246 (313)
+||||||||++||||||||++++ +|+||.|+|||+++||+|+|||++|||+||++||||+|+|++++|+|++.++.+|+
T Consensus 138 kLlTkTEcK~eYLLtD~eL~~re-~l~~l~k~NPH~~~wg~MkLYL~~qVe~falekWGS~E~Le~~~e~Re~~ke~rke 216 (274)
T KOG4017|consen 138 KLLTKTECKSEYLLTDCELDDRE-LLRRLQKKNPHNGTWGDMKLYLRCQVEQFALEKWGSEEELEREKERREEMKEERKE 216 (274)
T ss_pred heeehhhhhhhhhccCccccchh-hhHHhhcCCCCCCchhhhhhHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999998 89999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhccccCCCCCCcccccCCccccCCCCceeeecCCCCCeeeeeeh
Q psy5133 247 KQYNKKIKALRMAVRSSLFNKISTSPSSHSHQFGMEVHNEEDDTYTRKCSTCDFEETFEKI 307 (313)
Q Consensus 247 Kkf~kklkeLRk~tR~s~~~k~~~~~~~H~H~fg~e~~~~e~~~y~k~C~~CG~ev~yEkm 307 (313)
|||+||||+||++||+|.|++. ....|+|+||+++ +.++|+|..+|++|||+++||||
T Consensus 217 kKfeKKiKeLR~~tRts~~~r~--~~~~H~Hef~~e~-~~eEd~y~~tc~~Cg~e~e~ekl 274 (274)
T KOG4017|consen 217 KKFEKKIKELRRKTRTSMYKRS--SEEKHVHEFGPET-GIEEDGYRITCCTCGLEEEQEKL 274 (274)
T ss_pred HHHHHHHHHHHHHHHhhhhhhc--cccccceecCCCC-CCCCCcceeEeecccchhhhhcC
Confidence 9999999999999999999987 3589999999998 89999999999999999999997
No 2
>TIGR00598 rad14 DNA repair protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=2.1e-70 Score=483.88 Aligned_cols=172 Identities=58% Similarity=1.008 Sum_probs=167.7
Q ss_pred cccccccCCchhHHhhcCccccccccCCCcccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHH
Q psy5133 135 CVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSL 214 (313)
Q Consensus 135 C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~ 214 (313)
|.+||+.||||+|+++|+++||++|++..++|+|||+|+||+||||+|+||++++|+|+||.|+|||+++|++|+|||++
T Consensus 1 C~eCg~~~~D~~l~~~F~~~vC~~C~~~~ek~~liTkTeak~dYlL~d~dL~~~e~~L~~i~k~NPh~~~~~~MkLYlr~ 80 (172)
T TIGR00598 1 CEECGKIFMDSYLFDHFDCAVCDNCRDKDDKYKLLTKTEAKEEYLLKDCDLDKREPLLRRIVKKNPHNPRWGDMKLYLKL 80 (172)
T ss_pred CccccchhhhHHHHHHCCChhhhhhhccccccccccHHHHHHHhcCChhhhhcchhhchhcccCCCCCCCcccceeehHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhhccccCCCCCCcccccCCccccCCCCceeee
Q psy5133 215 QVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIKALRMAVRSSLFNKISTSPSSHSHQFGMEVHNEEDDTYTRK 294 (313)
Q Consensus 215 QVe~~A~~~WGS~E~Le~E~erRe~~r~~~K~Kkf~kklkeLRk~tR~s~~~k~~~~~~~H~H~fg~e~~~~e~~~y~k~ 294 (313)
|||++|++||||+|+|++|+++|+++++++|+|||+++|++||++||+++|++. +.+..|+|+||++++|+++|+|+|+
T Consensus 81 qVe~~A~~~wGS~E~L~~E~e~Re~~k~~~kekkf~kklkelR~~~R~~~y~~~-~~~~~H~H~f~~~~~~~e~~~~~k~ 159 (172)
T TIGR00598 81 QVEKRALEVWGSEEALDEEKERREESKEEMKEKKFEKKLKELRRAVRSSEYTNK-KEGRVHEHEFGPETNGVEEDTYRRT 159 (172)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc-cCCCcccccCCcccccccCCceeee
Confidence 999999999999999999999999999999999999999999999999999754 2478999999999999999999999
Q ss_pred cCCCCCeeeeeeh
Q psy5133 295 CSTCDFEETFEKI 307 (313)
Q Consensus 295 C~~CG~ev~yEkm 307 (313)
|++|||+|+||+|
T Consensus 160 C~~Cg~e~~~e~m 172 (172)
T TIGR00598 160 CTTCGLEETYEKM 172 (172)
T ss_pred cCCCCceEEEEeC
Confidence 9999999999998
No 3
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.5e-61 Score=438.07 Aligned_cols=214 Identities=37% Similarity=0.621 Sum_probs=190.8
Q ss_pred cceeeeecccceeecCCcccccCCChh------------------hhhccCCCCC--CCCcCCCcccccccccCCchhHH
Q psy5133 89 RSIINAVGSKLFTDTGGGFLLDYDDKY------------------EEKYIKQPAP--LLLESEQPTCVECKKKFPQSFLY 148 (313)
Q Consensus 89 ~~~~k~y~~sk~~Dt~GGFl~ee~~~~------------------~~~~~~ep~p--i~~~~~~~~C~eC~~~~~Ds~l~ 148 (313)
+.||+ ||||+|-|++||||++++.-+ +.+.+.+.+| +++... |+|.+|.++.+|..|.
T Consensus 55 kdyie-ydfs~ie~~~ggyl~~~~kv~d~~e~~p~e~ef~~~eq~eRk~~~e~ap~~l~i~~a-pkC~eC~~IelD~~l~ 132 (292)
T COG5145 55 KDYIE-YDFSKIEDTKGGYLLEEKKVEDLMENAPQEGEFFAEEQDERKEVREDAPILLPIALA-PKCKECLQIELDDELE 132 (292)
T ss_pred hhhhh-hhhHhhhccCCcccCchhhHHHHhhcCchhcchhhhhHHHHHHHhhcCCCCCChhhC-ccceeeeeeecchHHH
Confidence 57888 999999999999999863311 1234667777 455554 9999999999999999
Q ss_pred hhcCccccccccCC-CcccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHHHHHHHHHHHhCCH
Q psy5133 149 DKFGHSVCDSCRDG-ESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSE 227 (313)
Q Consensus 149 ~~F~~~VC~~Cr~~-~~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~QVe~~A~~~WGS~ 227 (313)
.+|+++||.+|+.. |+||+|||||+||.||||||++|.+ +.+|++|.|+|||.++|+.|+||||+|||++|+.+|||+
T Consensus 133 d~F~~~VC~~Cr~~~pdky~llTKTeCk~dYlLTdpEL~d-qelf~rL~kpNPH~gtws~M~Lylr~eVE~FA~kKWGs~ 211 (292)
T COG5145 133 DTFGISVCRSCRHSMPDKYKLLTKTECKSDYLLTDPELKD-QELFRRLQKPNPHKGTWSKMHLYLREEVEQFAIKKWGSL 211 (292)
T ss_pred hhhcchhHHhhhhhcchhhhhhhhhhhhhhhhcCChhhcc-hHHHHHhcCCCCCccchHHHHHHHHHHHHHHHHHhcccH
Confidence 99999999999999 9999999999999999999999986 669999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhhhcccc-CCCCCCcccccCCccccC-CCCceeeecCCCCCeeeee
Q psy5133 228 EELEQERERRAEKASNSKLKQYNKKIKALRMAVRSSLFNKI-STSPSSHSHQFGMEVHNE-EDDTYTRKCSTCDFEETFE 305 (313)
Q Consensus 228 E~Le~E~erRe~~r~~~K~Kkf~kklkeLRk~tR~s~~~k~-~~~~~~H~H~fg~e~~~~-e~~~y~k~C~~CG~ev~yE 305 (313)
|+|++||++|+..+..+|+|||.++|++||++||++.|++. ++....|||.|+.++..+ +.|....+| +||++|+-+
T Consensus 212 E~ld~e~qrRe~~k~~rkekK~ekkikelR~kTrt~~ysrm~vRek~kHvH~f~e~vdg~~e~g~~iqRC-~CGlevEq~ 290 (292)
T COG5145 212 EELDREKQRREKMKDDRKEKKLEKKIKELRRKTRTSNYSRMDVREKEKHVHVFDEFVDGPNEPGVIIQRC-SCGLEVEQE 290 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccchhhhhhhcceeeccccccCCCCCCeEEEec-ccccchhhc
Confidence 99999999999999999999999999999999999999986 555667999999887443 447778999 999999865
Q ss_pred e
Q psy5133 306 K 306 (313)
Q Consensus 306 k 306 (313)
.
T Consensus 291 e 291 (292)
T COG5145 291 E 291 (292)
T ss_pred c
Confidence 4
No 4
>PF05181 XPA_C: XPA protein C-terminus; InterPro: IPR022656 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 describes the uncharacterised C-terminal in the XPA protein; PDB: 1D4U_A 1XPA_A.
Probab=99.92 E-value=1.5e-26 Score=169.12 Aligned_cols=52 Identities=62% Similarity=1.092 Sum_probs=40.7
Q ss_pred cccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHHHH
Q psy5133 164 SKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQV 216 (313)
Q Consensus 164 ~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~QV 216 (313)
+||+||||||||+||||+|+||++++ +|+||.|+|||+++|++|+||||+||
T Consensus 1 ek~~LiTkTeak~dYlL~d~dL~~~~-~L~~i~k~NPH~~~w~~MkLyLr~QV 52 (52)
T PF05181_consen 1 EKYSLITKTEAKEDYLLTDCDLDDRE-LLPFIEKPNPHNSTWGDMKLYLRCQV 52 (52)
T ss_dssp SSS--EEHHHHCCCTT--SSTTTTSS-S--EEESS-SSSS-TTS-EEE-HHHH
T ss_pred CcccceehhhhhhhhccCcccccccc-cccccccCCCCCCCccCeeEEEeecC
Confidence 58999999999999999999999988 89999999999999999999999998
No 5
>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=99.12 E-value=6.7e-12 Score=84.99 Aligned_cols=30 Identities=50% Similarity=1.085 Sum_probs=20.6
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
+.|.+||++|+||||+++|++.||++||++
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CRD~ 33 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCRDK 33 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-ST
T ss_pred chHhHhCCHHHHHHHHHhCCccccccccCC
Confidence 569999999999999999999999999985
No 6
>KOG2802|consensus
Probab=98.98 E-value=4.4e-10 Score=110.78 Aligned_cols=92 Identities=30% Similarity=0.532 Sum_probs=76.3
Q ss_pred ccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhh
Q psy5133 165 KHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNS 244 (313)
Q Consensus 165 k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~QVe~~A~~~WGS~E~Le~E~erRe~~r~~~ 244 (313)
.-++||+..|..+|+|++.||.+ ||.+.+..||..+ ++|.+||+.+|+..|+++|||.|+|++|+ |++...-+.
T Consensus 109 e~n~i~~v~aiaeF~lk~s~led----l~K~r~~s~~~~~-ssh~~yl~sdv~~kal~v~gs~eaL~rer-rplve~yr~ 182 (503)
T KOG2802|consen 109 ENNFITGVRAIAEFCLKSSDLED----LPKIRRRSPHEDT-SSHTVYLRSDVEAKALEVWGSPEALARER-RPLVEEYRE 182 (503)
T ss_pred hhcccchhHHHHHhhccccchhh----cccccccCcccCC-CCceEEeehhhhhhhheeecCHHHHhhhh-hhHHHHHHH
Confidence 34569999999999999999996 9999999999999 99999999999999999999999999998 555553333
Q ss_pred HHHHHHHHHHHHHHHHHh
Q psy5133 245 KLKQYNKKIKALRMAVRS 262 (313)
Q Consensus 245 K~Kkf~kklkeLRk~tR~ 262 (313)
..-.+++.+.++|..+-.
T Consensus 183 ~l~~~~R~~~~~R~e~~n 200 (503)
T KOG2802|consen 183 RLFRNQRILREYRDELGN 200 (503)
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 334445666677777654
No 7
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=82.16 E-value=0.62 Score=34.30 Aligned_cols=17 Identities=41% Similarity=0.978 Sum_probs=14.6
Q ss_pred CCCCceeeecCCCCCeee
Q psy5133 286 EEDDTYTRKCSTCDFEET 303 (313)
Q Consensus 286 ~e~~~y~k~C~~CG~ev~ 303 (313)
.++|+|+++| .||+.|+
T Consensus 33 V~edtfkRtC-kCGfnie 49 (49)
T PF12677_consen 33 VEEDTFKRTC-KCGFNIE 49 (49)
T ss_pred Eeccceeeee-ccccccC
Confidence 4789999999 8999874
No 8
>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=71.24 E-value=1.2 Score=37.10 Aligned_cols=29 Identities=21% Similarity=0.625 Sum_probs=19.4
Q ss_pred CcccccccccCCchhHHhhcCccccccccC
Q psy5133 132 QPTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 132 ~~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
+..|.+||.... .|..-+||+-||..|..
T Consensus 13 N~~CaDCg~~~p-~w~s~~~GiflC~~Cag 41 (116)
T PF01412_consen 13 NKVCADCGAPNP-TWASLNYGIFLCLECAG 41 (116)
T ss_dssp CTB-TTT-SBS---EEETTTTEEE-HHHHH
T ss_pred cCcCCCCCCCCC-CEEEeecChhhhHHHHH
Confidence 466999998877 44556799999999986
No 9
>PF11261 IRF-2BP1_2: Interferon regulatory factor 2-binding protein zinc finger; InterPro: IPR022750 IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger and C-terminal RING finger domains []. This entry represents the N-terminal zinc finger domain of IRF-2BP1 and IRF-2BP2.
Probab=68.45 E-value=2.8 Score=31.37 Aligned_cols=31 Identities=23% Similarity=0.408 Sum_probs=28.1
Q ss_pred ccccccccCCchhHHhhcCccccccccCCCc
Q psy5133 134 TCVECKKKFPQSFLYDKFGHSVCDSCRDGES 164 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~ 164 (313)
.|..|.-+-+-|-+...|.-.||+.|-+-+|
T Consensus 5 ~CyLCdlPr~PWami~df~EpVCRgCvNyEG 35 (54)
T PF11261_consen 5 QCYLCDLPRMPWAMIWDFSEPVCRGCVNYEG 35 (54)
T ss_pred eEEeccCCCCchHHHhhccchhhhhhcCccc
Confidence 5999999999999999999999999987643
No 10
>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=54.65 E-value=4 Score=33.85 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=22.7
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
..|.+||..... |..-+||+-||..|.-.
T Consensus 4 ~~CaDC~~~~p~-w~s~~~GifvC~~Csgi 32 (112)
T smart00105 4 KKCFDCGAPNPT-WASVNLGVFLCIECSGI 32 (112)
T ss_pred CcccCCCCCCCC-cEEeccceeEhHHhHHH
Confidence 569999995533 44669999999999763
No 11
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=50.71 E-value=28 Score=33.20 Aligned_cols=91 Identities=15% Similarity=0.271 Sum_probs=46.7
Q ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH-HhhhccccCCC-CCCcccccCCccccCCCCcee
Q psy5133 215 QVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIKALRMAV-RSSLFNKISTS-PSSHSHQFGMEVHNEEDDTYT 292 (313)
Q Consensus 215 QVe~~A~~~WGS~E~Le~E~erRe~~r~~~K~Kkf~kklkeLRk~t-R~s~~~k~~~~-~~~H~H~fg~e~~~~e~~~y~ 292 (313)
||-=--+.-|.+.--.-+|..++.....+.++.+...+|.+|=++. ....|.-..+. ...+.-+-+.. +..++...
T Consensus 7 eILPqRIQEw~~~p~~A~E~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~~~~~~~~--e~~D~~~~ 84 (236)
T PF12269_consen 7 EILPQRIQEWQLSPCVAEEQNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQDEEQNDD--ESEDDDLS 84 (236)
T ss_pred HHChHHHHHhcCCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccccccc--ccccccee
Confidence 4444455566655555556666666666677777777777765532 23333322110 11111111211 11222344
Q ss_pred eecCCCCCeeeeeeh
Q psy5133 293 RKCSTCDFEETFEKI 307 (313)
Q Consensus 293 k~C~~CG~ev~yEkm 307 (313)
-.|++||++|.--+.
T Consensus 85 ~~Cv~Cg~~i~~~~a 99 (236)
T PF12269_consen 85 IYCVTCGHEIPSKKA 99 (236)
T ss_pred eeeeeCCCcCCHHHH
Confidence 569999999875443
No 12
>PRK11032 hypothetical protein; Provisional
Probab=50.27 E-value=25 Score=31.65 Aligned_cols=105 Identities=12% Similarity=0.088 Sum_probs=53.7
Q ss_pred cccccCCCCcCCCCccccceeccCCCCCCCCCcchhhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhHHHHHHHHHHH
Q psy5133 176 NEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIKA 255 (313)
Q Consensus 176 ~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYlr~QVe~~A~~~WGS~E~Le~E~erRe~~r~~~K~Kkf~kklke 255 (313)
.+|+.--.||...| +....-||+.+++++|-..--|.+.|..=.- ...-+...=.-|.+
T Consensus 34 ~~~~~~~~elT~dE---------------l~lv~~ylkRDL~ef~~~~~~~~~~~~~s~~------~~~i~~slw~~L~~ 92 (160)
T PRK11032 34 RKRVDAAGELTRDE---------------VDLITRAVRRDLEEFARSYEESKEEFSDSVF------MRVIKESLWQELAD 92 (160)
T ss_pred HHHHHHHHhcCHHH---------------HHHHHHHHHHHHHHHHHHHHhccccccccHH------HHHHHHHHHHHHHH
Confidence 45666666666433 4667889999999998843232222222000 11111222333444
Q ss_pred HHHHHHhhhccccCCCCCCcccccC-CccccCCCCceeeecCCCCCeeeeeeh
Q psy5133 256 LRMAVRSSLFNKISTSPSSHSHQFG-MEVHNEEDDTYTRKCSTCDFEETFEKI 307 (313)
Q Consensus 256 LRk~tR~s~~~k~~~~~~~H~H~fg-~e~~~~e~~~y~k~C~~CG~ev~yEkm 307 (313)
+=-+|+.+ |... .++-.|.=.|- .|+ -+...-+|..||++++|.+-
T Consensus 93 ItDrTqvE-w~el-~~dl~h~g~Y~sGEv----vg~G~LvC~~Cg~~~~~~~p 139 (160)
T PRK11032 93 ITDKTQLE-WREV-FQDLNHHGVYHSGEV----VGLGNLVCEKCHHHLAFYTP 139 (160)
T ss_pred HHHHhHHH-HHHH-HHHhhhcCeeeccee----eecceEEecCCCCEEEecCC
Confidence 44455432 1111 01223322221 122 26677899999999999753
No 13
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=50.00 E-value=39 Score=29.83 Aligned_cols=19 Identities=21% Similarity=0.352 Sum_probs=15.1
Q ss_pred CceeeecCCCCCeeeeeeh
Q psy5133 289 DTYTRKCSTCDFEETFEKI 307 (313)
Q Consensus 289 ~~y~k~C~~CG~ev~yEkm 307 (313)
+..+-+|..||+++.|..-
T Consensus 109 g~G~l~C~~Cg~~~~~~~~ 127 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTHP 127 (146)
T ss_pred cCceEecccCCCEEEecCC
Confidence 4555689999999999753
No 14
>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=49.11 E-value=5.7 Score=26.58 Aligned_cols=27 Identities=26% Similarity=0.757 Sum_probs=22.0
Q ss_pred cccccccCCchhHHhhcCccccccccC
Q psy5133 135 CVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 135 C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
|.+||..+++.-|.-.=+..+|..|..
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS-HHHHH
T ss_pred ccccCChHHHHHHHhCCCcEECHHHhC
Confidence 999999999999887778899999865
No 15
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=47.05 E-value=9.8 Score=36.94 Aligned_cols=46 Identities=22% Similarity=0.468 Sum_probs=30.7
Q ss_pred cccccccccCCchhHHhhcCccccccccCCCcccccccccccccccccCCCCc
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDL 185 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~dYlL~d~DL 185 (313)
.+|..|+..+--.-|.++| .||..| +.|--||..|=. +.|+-+..+
T Consensus 27 ~~c~~c~~~~~~~~l~~~~--~vc~~c----~~h~rl~areRi-~~L~D~gsF 72 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNL--EVCPKC----DHHMRMDARERI-ESLLDEGSF 72 (285)
T ss_pred eECCCCcchhhHHHHHhhC--CCCCCC----CCcCcCCHHHHH-HHceeCCee
Confidence 5699999998777788877 799999 445445554432 344444434
No 16
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=45.92 E-value=6.7 Score=38.77 Aligned_cols=31 Identities=16% Similarity=0.455 Sum_probs=25.9
Q ss_pred CCcccccccccCCchhHHhhcCccccccccCC
Q psy5133 131 EQPTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 131 ~~~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
.+.+|.+||..- =.|-..+||+-.|-.|--.
T Consensus 19 ~Nk~CaDCga~~-P~W~S~nlGvfiCi~Cagv 49 (319)
T COG5347 19 SNKKCADCGAPN-PTWASVNLGVFLCIDCAGV 49 (319)
T ss_pred ccCccccCCCCC-CceEecccCeEEEeecchh
Confidence 447799999998 4445899999999999875
No 17
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=42.00 E-value=12 Score=34.32 Aligned_cols=33 Identities=21% Similarity=0.490 Sum_probs=24.8
Q ss_pred ccccccccCCch----hHHhhcCccccccccCCCcccc
Q psy5133 134 TCVECKKKFPQS----FLYDKFGHSVCDSCRDGESKHC 167 (313)
Q Consensus 134 ~C~eC~~~~~Ds----~l~~~F~~~VC~~Cr~~~~k~~ 167 (313)
+|.|||.+ .++ |=.++..+..|.+|..--+||=
T Consensus 2 iCIeCg~~-v~~Ly~~Ys~~~irLt~C~~C~~vaDkYi 38 (208)
T PF04161_consen 2 ICIECGHP-VKSLYRQYSPGNIRLTKCPNCGKVADKYI 38 (208)
T ss_pred EeccCCCc-chhhhhccCCCcEEEeeccccCCccccee
Confidence 49999998 332 2246788899999998866775
No 18
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=40.58 E-value=14 Score=34.63 Aligned_cols=30 Identities=23% Similarity=0.536 Sum_probs=25.7
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
.+|..||..|+.....-.=|-.||..|-.+
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccccchhhhcCCceeccccccc
Confidence 569999999998887777788999999763
No 19
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.36 E-value=20 Score=27.00 Aligned_cols=27 Identities=33% Similarity=0.584 Sum_probs=19.5
Q ss_pred CCcccccccccCCchhHHhhcCccccccccCC
Q psy5133 131 EQPTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 131 ~~~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
...+|..||+.|.|. =++.||..|...
T Consensus 4 ~~~~C~~Cg~~~~~~-----dDiVvCp~Cgap 30 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDG-----DDIVVCPECGAP 30 (54)
T ss_pred cCccChhhCCcccCC-----CCEEECCCCCCc
Confidence 346799999998432 157899999764
No 20
>KOG1701|consensus
Probab=34.63 E-value=12 Score=38.78 Aligned_cols=46 Identities=28% Similarity=0.537 Sum_probs=32.9
Q ss_pred cccccccccCCchhHH--------hhcCccccccccCC-CcccccccccccccccccCCC
Q psy5133 133 PTCVECKKKFPQSFLY--------DKFGHSVCDSCRDG-ESKHCLVTRTDAKNEYLLKDC 183 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~--------~~F~~~VC~~Cr~~-~~k~~LiTkTeak~dYlL~d~ 183 (313)
-+|.-||..++|..|. .-|-|.||..|-+. + +|-.-..+-|++.|-
T Consensus 335 ekC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgip-----Ftvd~~n~v~Cv~df 389 (468)
T KOG1701|consen 335 EKCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIP-----FTVDSQNNVYCVPDF 389 (468)
T ss_pred HHHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCcc-----ccccCCCceeeehhh
Confidence 4599999999999886 33566677777665 3 555566677887763
No 21
>PF08412 Ion_trans_N: Ion transport protein N-terminal; InterPro: IPR013621 This domain is found to the N terminus of IPR005821 from INTERPRO in voltage- and cyclic nucleotide-gated K/Na ion channels.
Probab=34.61 E-value=28 Score=27.73 Aligned_cols=25 Identities=32% Similarity=0.563 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHhCCHHHHHHHHHH
Q psy5133 212 LSLQVEQRAIEVWGSEEELEQERER 236 (313)
Q Consensus 212 lr~QVe~~A~~~WGS~E~Le~E~er 236 (313)
|.-++-..++.++||..+++.|.+|
T Consensus 6 ~~p~~nk~sl~~f~S~~ai~~E~~R 30 (77)
T PF08412_consen 6 LQPGDNKFSLRVFGSKKAIEKEKER 30 (77)
T ss_pred hccccCHHHHHHHccHHHHHHHHHH
Confidence 3456678899999999999998776
No 22
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=33.85 E-value=22 Score=29.52 Aligned_cols=26 Identities=19% Similarity=0.437 Sum_probs=20.3
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
..|.-||.. -.-.|||+..|..|+.=
T Consensus 19 ~~C~VCg~~----a~g~hyGv~sC~aCk~F 44 (101)
T cd07160 19 EVCSVCGDK----ASGFHYNVLSCEGCKGF 44 (101)
T ss_pred CCCeecCCc----CcceEECcceehhhhhh
Confidence 349999963 34569999999999863
No 23
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=33.40 E-value=17 Score=36.91 Aligned_cols=29 Identities=24% Similarity=0.551 Sum_probs=22.8
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
.+|.+||..--.| ..-+||+-||-.|--.
T Consensus 23 k~CaDCga~nPtW-ASvn~GIFLCl~CSGV 51 (395)
T PLN03114 23 KICFDCNAKNPTW-ASVTYGIFLCIDCSAV 51 (395)
T ss_pred CcCccCCCCCCCc-eeeccceeehhhhhHh
Confidence 5699999875433 4669999999999763
No 24
>PF11240 DUF3042: Protein of unknown function (DUF3042); InterPro: IPR021402 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=33.38 E-value=41 Score=25.36 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=15.9
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q psy5133 19 LSAMQKEQIERNRQRAIQIQ 38 (313)
Q Consensus 19 lT~eq~~rIE~NR~kAl~lr 38 (313)
.-+++-++||+||.||.-.|
T Consensus 33 Pie~ke~~~eenRkkA~RK~ 52 (54)
T PF11240_consen 33 PIEEKEAKIEENRKKAARKR 52 (54)
T ss_pred cHHHHHHHHHHHHHHHHhhc
Confidence 45678899999999997543
No 25
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=31.63 E-value=27 Score=16.96 Aligned_cols=8 Identities=50% Similarity=1.381 Sum_probs=6.5
Q ss_pred CCCCCCCC
Q psy5133 200 PHNKHWGD 207 (313)
Q Consensus 200 Ph~~~w~~ 207 (313)
||..+|+.
T Consensus 1 phgG~Wgq 8 (8)
T PF03991_consen 1 PHGGGWGQ 8 (8)
T ss_pred CCCCcCCC
Confidence 78899974
No 26
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=31.60 E-value=8.9 Score=33.59 Aligned_cols=27 Identities=33% Similarity=0.830 Sum_probs=20.6
Q ss_pred cccccccCCchhHHhhcCccccccccCC-Ccccc
Q psy5133 135 CVECKKKFPQSFLYDKFGHSVCDSCRDG-ESKHC 167 (313)
Q Consensus 135 C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~-~~k~~ 167 (313)
|..||+.|.-. +-.||.+|... +..|.
T Consensus 6 C~~CgklF~~~------~~~iCp~C~~~~e~~f~ 33 (137)
T TIGR03826 6 CPKCGRLFVKT------GRDVCPSCYEEEEREFE 33 (137)
T ss_pred ccccchhhhhc------CCccCHHHhHHHHHHHH
Confidence 99999988652 45689999987 54554
No 27
>KOG3134|consensus
Probab=30.34 E-value=11 Score=35.60 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=24.8
Q ss_pred ccccccccCCchhH---HhhcCccccccccCCCcccc
Q psy5133 134 TCVECKKKFPQSFL---YDKFGHSVCDSCRDGESKHC 167 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l---~~~F~~~VC~~Cr~~~~k~~ 167 (313)
+|.|||..-.-=|. ..++.+.-|++|.+.-+||-
T Consensus 2 ~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYi 38 (225)
T KOG3134|consen 2 RCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYI 38 (225)
T ss_pred cccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHe
Confidence 59999986433222 35688899999999866663
No 28
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=29.74 E-value=19 Score=25.25 Aligned_cols=27 Identities=22% Similarity=0.637 Sum_probs=21.2
Q ss_pred cccccccccCCchhHHhhcCccccccccC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
+.|-.||+. ..+.....+...|..|+.
T Consensus 19 ~~CP~Cg~~--~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST--KHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe--eeEEeCCCCeEECCCCCC
Confidence 559999988 555566688899999974
No 29
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.72 E-value=25 Score=34.51 Aligned_cols=60 Identities=20% Similarity=0.418 Sum_probs=36.6
Q ss_pred cccccccccCCchhHHhhcCccccccccCCCcccccccccccccccccCCCCcCCCCccccceeccCCCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHN 202 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~ 202 (313)
.+|..|+....-..|.+++ .||..| +.|--||.-| .-+.||-+..+.- .-.++.-.||.+
T Consensus 39 ~kc~~C~~~~~~~~l~~~~--~vcp~c----~~h~rltAre-RI~~L~D~gSF~E---~~~~~~~~dpl~ 98 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKM--NICEQC----GYHLKMSSSD-RIELLIDPGTWNP---MDEDMVSLDPIE 98 (296)
T ss_pred eECCCccchhhHHHHHHcC--CCCCCC----CCCcCCCHHH-HHHHHccCCccEE---cCCccCcCCCcc
Confidence 5699999998777777766 789999 4455555443 2345555544541 223333346665
No 30
>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=29.52 E-value=22 Score=20.74 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=11.9
Q ss_pred ccccccccCCchhHH
Q psy5133 134 TCVECKKKFPQSFLY 148 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l~ 148 (313)
.|..|++.|.+...+
T Consensus 2 ~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 2 KCPICGKSFSSKSNL 16 (23)
T ss_dssp EETTTTEEESSHHHH
T ss_pred CCCCCCCccCCHHHH
Confidence 499999999877644
No 31
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.24 E-value=47 Score=21.98 Aligned_cols=19 Identities=16% Similarity=0.436 Sum_probs=12.4
Q ss_pred ceeeecCCCCCeeeeeehh
Q psy5133 290 TYTRKCSTCDFEETFEKIF 308 (313)
Q Consensus 290 ~y~k~C~~CG~ev~yEkm~ 308 (313)
+|.=+|..||...+....+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKI 21 (41)
T ss_pred CEEEEcCCCCCEEEEEEec
Confidence 3556788888876655443
No 32
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=28.88 E-value=22 Score=23.57 Aligned_cols=25 Identities=24% Similarity=0.644 Sum_probs=10.8
Q ss_pred cccccccccCCchhHHhhcCccccccccC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
|+|..|++.+.- .-=.+.||..|..
T Consensus 3 p~Cp~C~se~~y----~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY----EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E----E-SSSEEETTTTE
T ss_pred CCCCCCCCccee----ccCCEEeCCcccc
Confidence 679999987632 1124678998854
No 33
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=28.30 E-value=28 Score=33.96 Aligned_cols=67 Identities=22% Similarity=0.458 Sum_probs=41.3
Q ss_pred cccccccccCCchhHHhhcCccccccccCCCcccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchh
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLY 211 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLY 211 (313)
.+|..|+..+--..|..++ .||..|- .|--||..| .-+.||-+..+. +.-.++.-.||.+ |.+-+.|
T Consensus 28 ~~c~~c~~~~~~~~l~~~~--~vc~~c~----~h~rl~are-Ri~~L~D~gsF~---E~~~~~~~~d~l~--f~~~~~Y 94 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANL--NVCPKCG----HHMRISARE-RLDLLLDEGSFV---ELDAELEPKDPLK--FRDSKKY 94 (292)
T ss_pred eECCCccchhhHHHHHhcC--CCCCCCC----CCeeCCHHH-HHHHHccCCccE---EecCccccCCccc--CCccccc
Confidence 5699999998777777764 7999994 344444433 335555554454 2444555556665 5554555
No 34
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.15 E-value=24 Score=24.70 Aligned_cols=28 Identities=18% Similarity=0.301 Sum_probs=17.3
Q ss_pred ccccccccCCchhHHhhcCccccccccCC
Q psy5133 134 TCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
-|.+||....-..+.. -...||..|--.
T Consensus 2 FCp~Cg~~l~~~~~~~-~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKE-KRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCC-CCEEECCcCCCe
Confidence 4999998753332222 136789999653
No 35
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=27.96 E-value=23 Score=37.94 Aligned_cols=28 Identities=21% Similarity=0.599 Sum_probs=23.0
Q ss_pred cccccccccCCchhHHhhcCccccccccC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
..|.+||... =.|..-+||+-||-.|.-
T Consensus 24 k~CADCgs~~-P~WASiNlGIFICi~CSG 51 (648)
T PLN03119 24 RRCINCNSLG-PQYVCTTFWTFVCMACSG 51 (648)
T ss_pred CccccCCCCC-CCceeeccceEEeccchh
Confidence 5699999865 344578999999999986
No 36
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=26.54 E-value=21 Score=26.30 Aligned_cols=29 Identities=31% Similarity=0.752 Sum_probs=20.5
Q ss_pred ccccccccCC------chhHHhhcC--ccccccccCC
Q psy5133 134 TCVECKKKFP------QSFLYDKFG--HSVCDSCRDG 162 (313)
Q Consensus 134 ~C~eC~~~~~------Ds~l~~~F~--~~VC~~Cr~~ 162 (313)
.|.+||..|+ ..|..+.|. -.-|..||.+
T Consensus 6 ~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 6 TCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQA 42 (49)
T ss_pred EcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHHH
Confidence 4999999874 344456673 4678888875
No 37
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=26.25 E-value=36 Score=22.12 Aligned_cols=16 Identities=25% Similarity=0.819 Sum_probs=10.6
Q ss_pred CCCceeeecCCCCCee
Q psy5133 287 EDDTYTRKCSTCDFEE 302 (313)
Q Consensus 287 e~~~y~k~C~~CG~ev 302 (313)
..+.|.+.|..||++.
T Consensus 16 ~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 16 APGGWARRCPSCGHEH 31 (32)
T ss_dssp -SSSS-EEESSSS-EE
T ss_pred CCCcCEeECCCCcCEe
Confidence 3456899999999874
No 38
>PRK06424 transcription factor; Provisional
Probab=25.57 E-value=15 Score=32.34 Aligned_cols=28 Identities=39% Similarity=0.631 Sum_probs=20.5
Q ss_pred cccccccCCchhHH--hhcCccccccccCC
Q psy5133 135 CVECKKKFPQSFLY--DKFGHSVCDSCRDG 162 (313)
Q Consensus 135 C~eC~~~~~Ds~l~--~~F~~~VC~~Cr~~ 162 (313)
|.-||+..-..+.- +---+.||+.|.+-
T Consensus 3 CE~CG~~~~~~~~v~ieg~~l~vC~~Ca~~ 32 (144)
T PRK06424 3 CEMCGKKVPQTTKVMIDGAILNVCDDCAKF 32 (144)
T ss_pred ccccCcccCCceEEEEcCeeeehhHHHHHc
Confidence 99999988766432 22347999999854
No 39
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=24.63 E-value=38 Score=29.72 Aligned_cols=38 Identities=18% Similarity=0.328 Sum_probs=23.0
Q ss_pred ccccccccCCchhHHhhcCccccccccCCCccccccccccccc
Q psy5133 134 TCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKN 176 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~ 176 (313)
+|..||+.|-|.-..=-=||++|. . .||.++.......
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CG---g--~kF~yv~~~~~~~ 40 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECG---G--NKFQYVPEEKDAE 40 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccC---C--cceEEcCCCcccc
Confidence 499999999877643222555554 3 3566555544443
No 40
>PRK12495 hypothetical protein; Provisional
Probab=23.83 E-value=36 Score=32.37 Aligned_cols=25 Identities=24% Similarity=0.643 Sum_probs=20.0
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
..|.+||.++. ..=|+.+|-.|...
T Consensus 43 ~hC~~CG~PIp-----a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIF-----RHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCccc-----CCCCeeECCCCCCc
Confidence 44999999876 44689999999764
No 41
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=23.52 E-value=97 Score=28.21 Aligned_cols=23 Identities=13% Similarity=0.229 Sum_probs=19.5
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHH
Q psy5133 18 SLSAMQKEQIERNRQRAIQIQQT 40 (313)
Q Consensus 18 ~lT~eq~~rIE~NR~kAl~lr~~ 40 (313)
-|||||++..+.|.++-....++
T Consensus 123 lLTPEQKaq~~~~~~~rm~~~~~ 145 (166)
T PRK10363 123 LLTPEQQAVLNEKHQQRMEQLRD 145 (166)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHH
Confidence 49999999999999888776654
No 42
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=22.89 E-value=96 Score=24.68 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=14.5
Q ss_pred HHHHHHHHhCCHHHHHHHHHHHHH---HHHhhHHHHHHHHHHHHHHHHHh
Q psy5133 216 VEQRAIEVWGSEEELEQERERRAE---KASNSKLKQYNKKIKALRMAVRS 262 (313)
Q Consensus 216 Ve~~A~~~WGS~E~Le~E~erRe~---~r~~~K~Kkf~kklkeLRk~tR~ 262 (313)
-.+.|.++||+ +.+.+..++... .....-.+.+..-+++|+..+..
T Consensus 2 y~~e~~e~yg~-~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~l~~~~~~ 50 (118)
T PF07739_consen 2 YEEEARERYGD-EAYAESEERLASLSKEEWQELQKEWDELFAELAALMEE 50 (118)
T ss_dssp T--HHHHH------------------------TTHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHCh-HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 35678999999 888876666511 12222234455555666665553
No 43
>PLN03131 hypothetical protein; Provisional
Probab=22.76 E-value=32 Score=37.27 Aligned_cols=29 Identities=21% Similarity=0.618 Sum_probs=23.2
Q ss_pred CcccccccccCCchhHHhhcCccccccccC
Q psy5133 132 QPTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 132 ~~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
+..|.+||..- -.|..-+||+-||-.|.-
T Consensus 23 Nk~CADCga~~-P~WASiNlGIFICi~CSG 51 (705)
T PLN03131 23 NRRCINCNSLG-PQFVCTNFWTFICMTCSG 51 (705)
T ss_pred CCccccCCCCC-CCeeEeccceEEchhchh
Confidence 35699999865 344578999999999986
No 44
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=22.07 E-value=74 Score=31.39 Aligned_cols=69 Identities=23% Similarity=0.440 Sum_probs=46.5
Q ss_pred cccccccccCCchhHHhhcCccccccccCCCcccccccccccccccccCCCCcCCCCccccceeccCCCCCCCCCcchhh
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYL 212 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~~~k~~LiTkTeak~dYlL~d~DL~~re~~L~~i~k~NPh~~~w~~MkLYl 212 (313)
-||..|+...--.-|..++ .||.+|.- |-=| .....-++||-...+. ++..-+.-.||-+ |.+=+-|.
T Consensus 29 ~KCp~c~~~~y~~eL~~n~--~vcp~c~~----h~ri-~A~~Ri~~llD~gsf~---el~~~l~~~dPL~--F~d~k~Y~ 96 (294)
T COG0777 29 TKCPSCGEMLYRKELESNL--KVCPKCGH----HMRI-SARERLEALLDEGSFE---ELDSPLEPKDPLK--FPDSKKYK 96 (294)
T ss_pred eECCCccceeeHHHHHhhh--hcccccCc----cccc-CHHHHHHHhhCCCcce---ecccCCCcCCccc--CCcchhhH
Confidence 4699999998777777654 78999944 2223 3344556777666554 4667777888887 66666664
Q ss_pred H
Q psy5133 213 S 213 (313)
Q Consensus 213 r 213 (313)
.
T Consensus 97 ~ 97 (294)
T COG0777 97 D 97 (294)
T ss_pred H
Confidence 3
No 45
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.91 E-value=40 Score=28.39 Aligned_cols=26 Identities=35% Similarity=0.693 Sum_probs=20.5
Q ss_pred cccccccccCCchhHHhhcCccccccccCC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRDG 162 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~~ 162 (313)
..|..||..|-|- |. .-.||-.|-..
T Consensus 10 R~Cp~CG~kFYDL---nk-~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGAKFYDL---NK-DPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcchhccC---CC-CCccCCCCCCc
Confidence 3599999999773 33 67889999775
No 46
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.47 E-value=55 Score=29.77 Aligned_cols=33 Identities=18% Similarity=0.440 Sum_probs=23.7
Q ss_pred ccccccccCCc----h--------hHHhhcCccccccccCC--Cccc
Q psy5133 134 TCVECKKKFPQ----S--------FLYDKFGHSVCDSCRDG--ESKH 166 (313)
Q Consensus 134 ~C~eC~~~~~D----s--------~l~~~F~~~VC~~Cr~~--~~k~ 166 (313)
.|.+||..+.. - ...+.+...+|..|... +|-|
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsH 145 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSH 145 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccCchH
Confidence 49999987531 1 34667788999999886 5544
No 47
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.41 E-value=47 Score=24.20 Aligned_cols=25 Identities=20% Similarity=0.592 Sum_probs=18.6
Q ss_pred cccccccccCCchhHHhhcCccccccccC
Q psy5133 133 PTCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 133 ~~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
+-|..||+. +|..+.+-.+|.+|--
T Consensus 21 ~fCP~Cg~~----~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 21 KFCPRCGSG----FMAEHLDRWHCGKCGY 45 (50)
T ss_pred CcCcCCCcc----hheccCCcEECCCcCC
Confidence 459999974 4556668889999954
No 48
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=20.27 E-value=69 Score=28.56 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=20.0
Q ss_pred CCCcCCCcccccccccC--CchhHHhhcCccc
Q psy5133 126 LLLESEQPTCVECKKKF--PQSFLYDKFGHSV 155 (313)
Q Consensus 126 i~~~~~~~~C~eC~~~~--~Ds~l~~~F~~~V 155 (313)
+-+|+- .|.|||+.| +-..|..+||+..
T Consensus 72 VtpD~I--icLEDGkkfKSLKRHL~t~~gmTP 101 (148)
T COG4957 72 VTPDYI--ICLEDGKKFKSLKRHLTTHYGLTP 101 (148)
T ss_pred cCCCeE--EEeccCcchHHHHHHHhcccCCCH
Confidence 444564 499999999 4566888887643
No 49
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=20.16 E-value=36 Score=31.05 Aligned_cols=28 Identities=29% Similarity=0.653 Sum_probs=22.1
Q ss_pred ccccccccCCchhHHhhcCccccccccC
Q psy5133 134 TCVECKKKFPQSFLYDKFGHSVCDSCRD 161 (313)
Q Consensus 134 ~C~eC~~~~~Ds~l~~~F~~~VC~~Cr~ 161 (313)
.|..||+.....++.-.-|-.||..|.+
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred hHhcCCCCCCceEEecccCCcccccccC
Confidence 4999998865566666668899999984
No 50
>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=20.12 E-value=33 Score=29.94 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=13.7
Q ss_pred CCCcCCCcccccccccC--CchhHHhhcCcc
Q psy5133 126 LLLESEQPTCVECKKKF--PQSFLYDKFGHS 154 (313)
Q Consensus 126 i~~~~~~~~C~eC~~~~--~Ds~l~~~F~~~ 154 (313)
|-.++ ..|.+||+.| +-..|..++|+.
T Consensus 68 I~~d~--i~clecGk~~k~LkrHL~~~~glt 96 (132)
T PF05443_consen 68 ITPDY--IICLECGKKFKTLKRHLRTHHGLT 96 (132)
T ss_dssp B-SS---EE-TBT--EESBHHHHHHHTT-S-
T ss_pred cccCe--eEEccCCcccchHHHHHHHccCCC
Confidence 44444 4599999987 356677777754
Done!