Query 033000
Match_columns 129
No_of_seqs 150 out of 780
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 08:33:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033000.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033000hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4198 RNA-binding Ran Zn-fin 99.7 1.9E-18 4.2E-23 134.4 6.3 121 4-129 5-165 (280)
2 KOG4198 RNA-binding Ran Zn-fin 99.7 2.2E-17 4.8E-22 128.6 6.0 122 3-128 60-267 (280)
3 PF00641 zf-RanBP: Zn-finger i 99.0 1.4E-10 3E-15 62.0 2.0 30 4-33 1-30 (30)
4 KOG1995 Conserved Zn-finger pr 99.0 3.5E-10 7.7E-15 90.3 3.7 122 3-129 67-244 (351)
5 PF00641 zf-RanBP: Zn-finger i 98.8 2.2E-09 4.8E-14 57.3 2.0 30 48-79 1-30 (30)
6 smart00547 ZnF_RBZ Zinc finger 98.6 2.8E-08 6.1E-13 51.1 1.3 26 6-31 1-26 (26)
7 smart00547 ZnF_RBZ Zinc finger 98.4 2E-07 4.3E-12 47.9 1.4 25 50-76 1-25 (26)
8 KOG1995 Conserved Zn-finger pr 97.7 9.1E-05 2E-09 59.6 6.3 33 47-80 214-246 (351)
9 PF12773 DZR: Double zinc ribb 97.0 0.00076 1.6E-08 39.4 2.9 50 10-74 1-50 (50)
10 PRK14559 putative protein seri 95.9 0.0067 1.5E-07 52.9 3.3 50 9-78 3-52 (645)
11 PF12773 DZR: Double zinc ribb 94.6 0.038 8.2E-07 32.0 2.6 50 54-125 1-50 (50)
12 KOG4477 RING1 interactor RYBP 93.8 0.028 6E-07 42.0 1.0 29 5-33 22-50 (228)
13 PF13248 zf-ribbon_3: zinc-rib 92.2 0.067 1.5E-06 27.2 0.8 23 8-30 3-25 (26)
14 PF13240 zinc_ribbon_2: zinc-r 92.1 0.081 1.8E-06 26.2 1.0 22 9-30 1-22 (23)
15 PF13248 zf-ribbon_3: zinc-rib 91.4 0.13 2.7E-06 26.1 1.3 23 52-76 3-25 (26)
16 KOG4477 RING1 interactor RYBP 91.0 0.097 2.1E-06 39.1 0.8 34 44-79 17-50 (228)
17 PF13240 zinc_ribbon_2: zinc-r 89.4 0.22 4.9E-06 24.6 1.2 22 53-76 1-22 (23)
18 PRK14559 putative protein seri 87.4 0.53 1.2E-05 41.3 3.0 48 53-127 3-50 (645)
19 cd00350 rubredoxin_like Rubred 86.0 0.7 1.5E-05 24.6 1.9 25 51-77 1-27 (33)
20 PRK04136 rpl40e 50S ribosomal 84.1 0.53 1.2E-05 27.5 0.9 24 6-29 13-36 (48)
21 cd00729 rubredoxin_SM Rubredox 83.3 1.1 2.3E-05 24.2 1.9 26 51-78 2-29 (34)
22 PRK14714 DNA polymerase II lar 82.1 2.1 4.5E-05 40.4 4.3 52 8-80 668-722 (1337)
23 COG1552 RPL40A Ribosomal prote 76.0 0.54 1.2E-05 27.6 -0.8 22 9-30 16-37 (50)
24 KOG4345 NF-kappa B regulator A 75.0 0.29 6.2E-06 43.1 -3.1 75 1-77 1-115 (774)
25 PRK04136 rpl40e 50S ribosomal 68.3 2.9 6.2E-05 24.5 1.0 25 50-76 13-37 (48)
26 PF00301 Rubredoxin: Rubredoxi 63.6 3.4 7.4E-05 24.0 0.7 13 4-16 31-43 (47)
27 PF10571 UPF0547: Uncharacteri 63.5 4.2 9.2E-05 20.6 1.0 21 9-29 2-22 (26)
28 PF12172 DUF35_N: Rubredoxin-l 62.8 4.3 9.2E-05 21.9 1.0 22 53-76 13-34 (37)
29 PRK14714 DNA polymerase II lar 61.0 9.7 0.00021 36.1 3.4 50 50-127 666-718 (1337)
30 COG1592 Rubrerythrin [Energy p 59.5 5.9 0.00013 29.1 1.5 26 51-78 134-160 (166)
31 COG1773 Rubredoxin [Energy pro 57.5 17 0.00036 21.9 3.0 16 44-61 29-44 (55)
32 PRK13130 H/ACA RNA-protein com 45.5 36 0.00079 20.4 3.1 23 53-79 7-29 (56)
33 PF14803 Nudix_N_2: Nudix N-te 44.0 16 0.00034 19.7 1.3 32 69-115 2-33 (34)
34 COG3478 Predicted nucleic-acid 43.4 12 0.00026 23.4 0.8 16 6-21 3-18 (68)
35 cd00730 rubredoxin Rubredoxin; 43.4 23 0.00049 20.7 2.0 12 99-112 31-42 (50)
36 cd04718 BAH_plant_2 BAH, or Br 42.0 14 0.0003 26.6 1.1 16 4-19 15-30 (148)
37 COG1066 Sms Predicted ATP-depe 39.1 24 0.00052 29.9 2.2 31 1-31 1-31 (456)
38 PRK11823 DNA repair protein Ra 37.7 28 0.00061 29.1 2.4 32 1-32 1-32 (446)
39 PF11023 DUF2614: Protein of u 34.2 25 0.00055 24.2 1.4 32 2-33 64-97 (114)
40 PF01020 Ribosomal_L40e: Ribos 33.4 28 0.00062 20.6 1.3 22 8-29 18-41 (52)
41 PRK04023 DNA polymerase II lar 32.9 59 0.0013 30.5 3.8 52 6-80 625-676 (1121)
42 COG1545 Predicted nucleic-acid 32.6 33 0.00071 24.2 1.8 23 53-77 31-53 (140)
43 PF04810 zf-Sec23_Sec24: Sec23 32.2 23 0.00049 19.5 0.7 15 6-20 23-37 (40)
44 TIGR02098 MJ0042_CXXC MJ0042 f 31.5 25 0.00054 18.7 0.8 11 9-19 4-14 (38)
45 PRK05452 anaerobic nitric oxid 28.1 82 0.0018 26.7 3.7 16 44-61 451-466 (479)
46 PHA00626 hypothetical protein 28.0 47 0.001 20.1 1.6 11 9-19 2-12 (59)
47 COG1545 Predicted nucleic-acid 27.7 41 0.00089 23.7 1.6 23 9-31 31-53 (140)
48 PF08271 TF_Zn_Ribbon: TFIIB z 27.1 41 0.00089 18.5 1.2 12 100-113 17-28 (43)
49 PF09862 DUF2089: Protein of u 26.8 33 0.00072 23.6 1.0 22 10-31 1-22 (113)
50 TIGR00416 sms DNA repair prote 25.8 56 0.0012 27.5 2.3 32 1-32 1-32 (454)
51 TIGR00595 priA primosomal prot 24.9 62 0.0014 27.6 2.5 24 51-77 240-263 (505)
52 PF14952 zf-tcix: Putative tre 23.9 40 0.00087 19.3 0.8 16 9-24 13-28 (44)
53 PRK00420 hypothetical protein; 23.8 46 0.00099 22.8 1.2 21 9-29 25-48 (112)
54 PRK00398 rpoP DNA-directed RNA 23.6 57 0.0012 18.2 1.4 8 69-76 23-30 (46)
55 KOG1512 PHD Zn-finger protein 23.4 37 0.00079 27.4 0.7 41 7-55 308-357 (381)
56 COG1645 Uncharacterized Zn-fin 22.8 45 0.00098 23.6 1.0 10 68-77 29-38 (131)
57 PF10058 DUF2296: Predicted in 21.7 52 0.0011 19.5 1.0 33 21-63 22-54 (54)
58 PF09297 zf-NADH-PPase: NADH p 20.9 67 0.0015 16.5 1.3 10 22-31 4-13 (32)
59 PF03604 DNA_RNApol_7kD: DNA d 20.4 98 0.0021 16.3 1.8 7 58-64 5-11 (32)
60 PRK14873 primosome assembly pr 20.3 80 0.0017 28.1 2.3 25 50-78 409-433 (665)
No 1
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=99.75 E-value=1.9e-18 Score=134.45 Aligned_cols=121 Identities=34% Similarity=0.722 Sum_probs=93.4
Q ss_pred CCC-CeEcCccCccccccccccccCCCCCCCCCCCc------------ccccCCccccCCCcccCCCCCCCeecCCCcCc
Q 033000 4 PGG-DWMCAACQHQNFKKREACQRCGYPKYGGPDVS------------TYLCNRTEVLAGDWYCTAMNCGAHNYASRPNC 70 (129)
Q Consensus 4 ~~g-dW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~------------~~~~~~~~~~~gdW~C~~~~C~~~N~~~~~~C 70 (129)
++| ||.|..|.++||..+..|.+|..+++. .++. .+.+....+++|||.|+ .|+++||++|..|
T Consensus 5 r~g~~~~~~~~~~~~~~~~~~c~~c~~~~~~-i~~~~~~~~tid~~~~~~~~~~~~~~pgdw~c~--~c~~~n~arr~~c 81 (280)
T KOG4198|consen 5 RKGVDSLKRLCLHVNFDERDSCGRCSLSRAY-IQPDDDEARTIDVMRLLLTNSKDPPRPGDWNCP--LCGFHNSARRLLC 81 (280)
T ss_pred cccCCcccchhhhhccccccccccccCCccc-ccccccccCccchhhhcccccCCCCCCcccccC--ccchhhHHHhhhc
Confidence 345 999999999999999999999999943 1111 11235788999999999 8999999999999
Q ss_pred cccCCCCCCcccccc-c-----------ccCCC------CCCC---------CCCccCceeecCCCCCceeccCCccccC
Q 033000 71 YRCGAAKTDYACANM-M-----------AYGTD------GSVP---------PGWKSGDWICNRMGCGVHNYASRMVCYK 123 (129)
Q Consensus 71 ~~C~~~~~~~~~~~~-~-----------~~g~~------~~~~---------~~~~~gdW~C~~~~C~~~N~a~r~~C~~ 123 (129)
++|+.++++...... + .+... ..+. ..+++|||+|+ .|+||||+++..|++
T Consensus 82 ~~c~~s~~~~~~~~~~~~~g~~~~~~~~r~~~~~~~~~~~~g~~~~~n~~~~r~~~~GDW~Cp--~C~fhNfarn~~C~r 159 (280)
T KOG4198|consen 82 FRCGFSKVPLDSALTAPNSGSRSLQTGPRYFKGDWLCPRCPGLGFSRNNKPKRPWRSGDWECP--GCNFHNFARNSECFR 159 (280)
T ss_pred ceecccCCCccccccCCCCcccccccccccccCCCCCCCCCCCcccccccccCCccccCcccC--CCCceeccccchhhh
Confidence 999999877655310 0 11100 0000 13789999999 799999999999999
Q ss_pred CCCCCC
Q 033000 124 CKTPRE 129 (129)
Q Consensus 124 C~~pk~ 129 (129)
|+++++
T Consensus 160 C~~~r~ 165 (280)
T KOG4198|consen 160 CGAKRP 165 (280)
T ss_pred cCCcCc
Confidence 999875
No 2
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=99.70 E-value=2.2e-17 Score=128.55 Aligned_cols=122 Identities=35% Similarity=0.772 Sum_probs=89.8
Q ss_pred CCCCCeEcCccCccccccccccccCCCCCCCCCC----Cccc--------cc---------------CC-----ccccCC
Q 033000 3 LPGGDWMCAACQHQNFKKREACQRCGYPKYGGPD----VSTY--------LC---------------NR-----TEVLAG 50 (129)
Q Consensus 3 ~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~----~~~~--------~~---------------~~-----~~~~~g 50 (129)
.++|||.|+.|+++||++|..|++|+.+++.-.. +... .+ .+ .+.++|
T Consensus 60 ~~pgdw~c~~c~~~n~arr~~c~~c~~s~~~~~~~~~~~~~g~~~~~~~~r~~~~~~~~~~~~g~~~~~n~~~~r~~~~G 139 (280)
T KOG4198|consen 60 PRPGDWNCPLCGFHNSARRLLCFRCGFSKVPLDSALTAPNSGSRSLQTGPRYFKGDWLCPRCPGLGFSRNNKPKRPWRSG 139 (280)
T ss_pred CCCcccccCccchhhHHHhhhcceecccCCCccccccCCCCcccccccccccccCCCCCCCCCCCcccccccccCCcccc
Confidence 4689999999999999999999999998864211 1100 00 11 147899
Q ss_pred CcccCCCCCCCeecCCCcCccccCCCCCCccc-------cc---------cc-------------ccCC---------C-
Q 033000 51 DWYCTAMNCGAHNYASRPNCYRCGAAKTDYAC-------AN---------MM-------------AYGT---------D- 91 (129)
Q Consensus 51 dW~C~~~~C~~~N~~~~~~C~~C~~~~~~~~~-------~~---------~~-------------~~g~---------~- 91 (129)
||+|+ .|++|||+++..|++|+++++..+. .. .. .++. .
T Consensus 140 DW~Cp--~C~fhNfarn~~C~rC~~~r~~~a~~~~~~s~~~~~~~~s~~~~~~~~t~~~~~~r~~~~~~~~~~~~d~~~~ 217 (280)
T KOG4198|consen 140 DWECP--GCNFHNFARNSECFRCGAKRPLAALLGNQASEATEHDWLSKVADSSSSTRFESLLRCNARGEMSESRVDGADV 217 (280)
T ss_pred CcccC--CCCceeccccchhhhcCCcCcccccccccccccccccccccccccccceecccchhhcccCcccccccccccc
Confidence 99999 9999999999999999999987441 00 00 0000 0
Q ss_pred ---------------CCCCCCCccCceeecCCCCCceeccCCccccCCCCCC
Q 033000 92 ---------------GSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCKTPR 128 (129)
Q Consensus 92 ---------------~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~pk 128 (129)
..+....+.+||.|+ .|.++||.++.+|.+|..++
T Consensus 218 ~~~~~~~~e~~~~~~sr~s~~~~dgdw~~~--s~~~~~~r~r~a~~~c~~~~ 267 (280)
T KOG4198|consen 218 KGNFSSDDESRLEPLSRGSKSSRDGDWMCE--SCKAENFRRRNACLKCISPR 267 (280)
T ss_pred cccccccccccccccccCcccccCCCcccc--cccchhhhhhhhhhccccCc
Confidence 011123678999999 79999999999999998775
No 3
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=99.02 E-value=1.4e-10 Score=61.95 Aligned_cols=30 Identities=40% Similarity=0.991 Sum_probs=24.8
Q ss_pred CCCCeEcCccCccccccccccccCCCCCCC
Q 033000 4 PGGDWMCAACQHQNFKKREACQRCGYPKYG 33 (129)
Q Consensus 4 ~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~ 33 (129)
|+|+|.|+.|+++|++.+..|.+|+++||.
T Consensus 1 k~g~W~C~~C~~~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 1 KEGDWKCPSCTFMNPASRSKCVACGAPRPG 30 (30)
T ss_dssp -SSSEEETTTTEEEESSSSB-TTT--BTTB
T ss_pred CCcCccCCCCcCCchHHhhhhhCcCCCCcC
Confidence 579999999999999999999999999984
No 4
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=98.98 E-value=3.5e-10 Score=90.29 Aligned_cols=122 Identities=24% Similarity=0.379 Sum_probs=83.4
Q ss_pred CCCCCeEcC--ccCccccccccccccCCCCCCCCC-CCccc-------ccCCccccCCCcccCCCCCCCeecCCCcCccc
Q 033000 3 LPGGDWMCA--ACQHQNFKKREACQRCGYPKYGGP-DVSTY-------LCNRTEVLAGDWYCTAMNCGAHNYASRPNCYR 72 (129)
Q Consensus 3 ~~~gdW~C~--~C~~~Nf~~r~~C~~C~~prp~~~-~~~~~-------~~~~~~~~~gdW~C~~~~C~~~N~~~~~~C~~ 72 (129)
.+.++|+|+ .|.+.||.++.+|..|+..|.... .+.-+ .-+...+...||.|. .|.+++|+.+.+|.
T Consensus 67 ~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dkeT~~~KGeatvS~~D~~~a--kaai~~~agkdf~g- 143 (351)
T KOG1995|consen 67 ETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKETGAPKGEATVSYEDPPAA--KAAIEWFAGKDFCG- 143 (351)
T ss_pred ccceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhccccccccCcCCceeeeecChhhh--hhhhhhhccccccC-
Confidence 346799998 899999999999999999998741 11110 113445556788888 88888888888887
Q ss_pred cCCCCCCccc--c-c------------ccccC-------------CC------------------CCCCCCCccCceeec
Q 033000 73 CGAAKTDYAC--A-N------------MMAYG-------------TD------------------GSVPPGWKSGDWICN 106 (129)
Q Consensus 73 C~~~~~~~~~--~-~------------~~~~g-------------~~------------------~~~~~~~~~gdW~C~ 106 (129)
.+++..... + + ..+|+ .. .........+||.|+
T Consensus 144 -n~ikvs~a~~r~~ve~~rg~~~~~~g~g~fg~~~~grg~~~G~gg~~~~~~~~~rGg~~~~g~~g~~~~~~~d~Dw~c~ 222 (351)
T KOG1995|consen 144 -NTIKVSLAERRTGVESVRGGYPNDGGAGEFGRLRGGRGGPGGPGGGDGEAGKGDRGGVPDGGESGGGNVQDEDGDWDCP 222 (351)
T ss_pred -CCchhhhhhhccCcccccccccCcCCCCCccccccCCCCCCCCCCccccccccccCCcCCCcccCCccccccccccccc
Confidence 554432111 0 0 00000 00 000123567899999
Q ss_pred CCCCCceeccCCccccCCCCCCC
Q 033000 107 RMGCGVHNYASRMVCYKCKTPRE 129 (129)
Q Consensus 107 ~~~C~~~N~a~r~~C~~C~~pk~ 129 (129)
+.|.++||+++..|++|+++|+
T Consensus 223 -~~c~N~nfa~r~~cnrck~~Kp 244 (351)
T KOG1995|consen 223 -PSCGNRNFAWREECNRCKAPKP 244 (351)
T ss_pred -ccccccccccccccccccCCCc
Confidence 7899999999999999999985
No 5
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=98.82 E-value=2.2e-09 Score=57.26 Aligned_cols=30 Identities=43% Similarity=0.947 Sum_probs=24.4
Q ss_pred cCCCcccCCCCCCCeecCCCcCccccCCCCCC
Q 033000 48 LAGDWYCTAMNCGAHNYASRPNCYRCGAAKTD 79 (129)
Q Consensus 48 ~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~~~ 79 (129)
++|+|.|+ .|+++|++++..|.+|+++||.
T Consensus 1 k~g~W~C~--~C~~~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 1 KEGDWKCP--SCTFMNPASRSKCVACGAPRPG 30 (30)
T ss_dssp -SSSEEET--TTTEEEESSSSB-TTT--BTTB
T ss_pred CCcCccCC--CCcCCchHHhhhhhCcCCCCcC
Confidence 46899999 9999999999999999999973
No 6
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=98.55 E-value=2.8e-08 Score=51.11 Aligned_cols=26 Identities=50% Similarity=1.198 Sum_probs=24.5
Q ss_pred CCeEcCccCccccccccccccCCCCC
Q 033000 6 GDWMCAACQHQNFKKREACQRCGYPK 31 (129)
Q Consensus 6 gdW~C~~C~~~Nf~~r~~C~~C~~pr 31 (129)
|||+|+.|+++|++.+..|.+|++|.
T Consensus 1 g~W~C~~C~~~N~~~~~~C~~C~~p~ 26 (26)
T smart00547 1 GDWECPACTFLNFASRSKCFACGAPX 26 (26)
T ss_pred CcccCCCCCCcChhhhccccccCCcC
Confidence 79999999999999999999999873
No 7
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=98.35 E-value=2e-07 Score=47.89 Aligned_cols=25 Identities=52% Similarity=1.285 Sum_probs=23.9
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCC
Q 033000 50 GDWYCTAMNCGAHNYASRPNCYRCGAA 76 (129)
Q Consensus 50 gdW~C~~~~C~~~N~~~~~~C~~C~~~ 76 (129)
|+|+|+ .|+++|++.+..|..|++|
T Consensus 1 g~W~C~--~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 1 GDWECP--ACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CcccCC--CCCCcChhhhccccccCCc
Confidence 699999 9999999999999999986
No 8
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=97.72 E-value=9.1e-05 Score=59.65 Aligned_cols=33 Identities=42% Similarity=0.912 Sum_probs=30.3
Q ss_pred ccCCCcccCCCCCCCeecCCCcCccccCCCCCCc
Q 033000 47 VLAGDWYCTAMNCGAHNYASRPNCYRCGAAKTDY 80 (129)
Q Consensus 47 ~~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~~~~ 80 (129)
..++||.|+ ..|.++||+.+..|++|.++||..
T Consensus 214 ~~d~Dw~c~-~~c~N~nfa~r~~cnrck~~Kp~~ 246 (351)
T KOG1995|consen 214 DEDGDWDCP-PSCGNRNFAWREECNRCKAPKPER 246 (351)
T ss_pred ccccccccc-ccccccccccccccccccCCCccc
Confidence 566899999 899999999999999999999865
No 9
>PF12773 DZR: Double zinc ribbon
Probab=97.01 E-value=0.00076 Score=39.39 Aligned_cols=50 Identities=32% Similarity=0.672 Sum_probs=42.8
Q ss_pred cCccCccccccccccccCCCCCCCCCCCcccccCCccccCCCcccCCCCCCCeecCCCcCccccC
Q 033000 10 CAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCG 74 (129)
Q Consensus 10 C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~~~~C~~C~ 74 (129)
|+.|+..|......|..|+++-+.. ....++|+ .|+..|......|..||
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~~~-------------~~~~~~C~--~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLPPP-------------DQSKKICP--NCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCCccccCChhhcCChhhc-------------cCCCCCCc--CCcCCCcCCcCccCccc
Confidence 7899999999999999999986611 12368999 99999999999999986
No 10
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=95.95 E-value=0.0067 Score=52.92 Aligned_cols=50 Identities=30% Similarity=0.737 Sum_probs=43.7
Q ss_pred EcCccCccccccccccccCCCCCCCCCCCcccccCCccccCCCcccCCCCCCCeecCCCcCccccCCCCC
Q 033000 9 MCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKT 78 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~~ 78 (129)
.|+.|++.|.....+|.+|+++-... .|+ .|+..+......|..||++-.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~------------------~Cp--~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHK------------------PCP--QCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCC------------------cCC--CCCCCCCcccccccccCCccc
Confidence 69999999999999999998874310 599 999999999999999998853
No 11
>PF12773 DZR: Double zinc ribbon
Probab=94.59 E-value=0.038 Score=32.01 Aligned_cols=50 Identities=28% Similarity=0.670 Sum_probs=40.6
Q ss_pred cCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCccCceeecCCCCCceeccCCccccCCC
Q 033000 54 CTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCK 125 (129)
Q Consensus 54 C~~~~C~~~N~~~~~~C~~C~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~ 125 (129)
|+ .|+..|-.....|..||++-+.. ....+.|+ .|+..|......|..|+
T Consensus 1 Cp--~Cg~~~~~~~~fC~~CG~~l~~~------------------~~~~~~C~--~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 1 CP--HCGTPNPDDAKFCPHCGTPLPPP------------------DQSKKICP--NCGAENPPNAKFCPNCG 50 (50)
T ss_pred CC--CcCCcCCccccCChhhcCChhhc------------------cCCCCCCc--CCcCCCcCCcCccCccc
Confidence 66 89999999999999999886511 13458899 69999999999998885
No 12
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=93.75 E-value=0.028 Score=42.00 Aligned_cols=29 Identities=28% Similarity=0.628 Sum_probs=26.2
Q ss_pred CCCeEcCccCccccccccccccCCCCCCC
Q 033000 5 GGDWMCAACQHQNFKKREACQRCGYPKYG 33 (129)
Q Consensus 5 ~gdW~C~~C~~~Nf~~r~~C~~C~~prp~ 33 (129)
.|-|.|..|+|.|-+-..+|+.|+.-+..
T Consensus 22 eg~WdCsvCTFrNsAeAfkC~vCdvRKGT 50 (228)
T KOG4477|consen 22 EGKWDCSVCTFRNSAEAFKCFVCDVRKGT 50 (228)
T ss_pred cCceeeeeeeecchhhhhheeeecccccc
Confidence 47899999999999999999999987654
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.17 E-value=0.067 Score=27.15 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=20.5
Q ss_pred eEcCccCccccccccccccCCCC
Q 033000 8 WMCAACQHQNFKKREACQRCGYP 30 (129)
Q Consensus 8 W~C~~C~~~Nf~~r~~C~~C~~p 30 (129)
..|+.|+..+......|..|+++
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 47999999999999999999875
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=92.05 E-value=0.081 Score=26.23 Aligned_cols=22 Identities=27% Similarity=0.768 Sum_probs=19.5
Q ss_pred EcCccCccccccccccccCCCC
Q 033000 9 MCAACQHQNFKKREACQRCGYP 30 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C~~C~~p 30 (129)
.|+.|+..+......|..|+++
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 3889999999999999999875
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=91.42 E-value=0.13 Score=26.11 Aligned_cols=23 Identities=39% Similarity=0.871 Sum_probs=20.1
Q ss_pred cccCCCCCCCeecCCCcCccccCCC
Q 033000 52 WYCTAMNCGAHNYASRPNCYRCGAA 76 (129)
Q Consensus 52 W~C~~~~C~~~N~~~~~~C~~C~~~ 76 (129)
..|+ .|+..+......|..||++
T Consensus 3 ~~Cp--~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCcccccChhhCCC
Confidence 5788 9999999999999999875
No 16
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=90.96 E-value=0.097 Score=39.14 Aligned_cols=34 Identities=26% Similarity=0.623 Sum_probs=28.8
Q ss_pred CccccCCCcccCCCCCCCeecCCCcCccccCCCCCC
Q 033000 44 RTEVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKTD 79 (129)
Q Consensus 44 ~~~~~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~~~ 79 (129)
.....+|.|.|. .|.|+|-+.+-.|+.|+..+..
T Consensus 17 kp~~Deg~WdCs--vCTFrNsAeAfkC~vCdvRKGT 50 (228)
T KOG4477|consen 17 KPNDDEGKWDCS--VCTFRNSAEAFKCFVCDVRKGT 50 (228)
T ss_pred CCccccCceeee--eeeecchhhhhheeeecccccc
Confidence 445567899999 9999999999999999877644
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.42 E-value=0.22 Score=24.60 Aligned_cols=22 Identities=41% Similarity=0.942 Sum_probs=18.5
Q ss_pred ccCCCCCCCeecCCCcCccccCCC
Q 033000 53 YCTAMNCGAHNYASRPNCYRCGAA 76 (129)
Q Consensus 53 ~C~~~~C~~~N~~~~~~C~~C~~~ 76 (129)
.|+ .|+..+......|..||++
T Consensus 1 ~Cp--~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCcCcchhhhCCc
Confidence 377 8999998888899999875
No 18
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=87.39 E-value=0.53 Score=41.32 Aligned_cols=48 Identities=27% Similarity=0.641 Sum_probs=38.8
Q ss_pred ccCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCccCceeecCCCCCceeccCCccccCCCCC
Q 033000 53 YCTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCKTP 127 (129)
Q Consensus 53 ~C~~~~C~~~N~~~~~~C~~C~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~p 127 (129)
.|+ .|+..|-.....|.+||++-.. + .|+ .|+..|-.....|..|+++
T Consensus 3 ~Cp--~Cg~~n~~~akFC~~CG~~l~~-------------------~----~Cp--~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 3 ICP--QCQFENPNNNRFCQKCGTSLTH-------------------K----PCP--QCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred cCC--CCCCcCCCCCccccccCCCCCC-------------------C----cCC--CCCCCCCcccccccccCCc
Confidence 588 9999999999999999876321 0 388 6999999888899999875
No 19
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=85.96 E-value=0.7 Score=24.62 Aligned_cols=25 Identities=32% Similarity=0.606 Sum_probs=17.7
Q ss_pred CcccCCCCCCCeecCC--CcCccccCCCC
Q 033000 51 DWYCTAMNCGAHNYAS--RPNCYRCGAAK 77 (129)
Q Consensus 51 dW~C~~~~C~~~N~~~--~~~C~~C~~~~ 77 (129)
.|+|. .|+++-... -..|+.|++++
T Consensus 1 ~~~C~--~CGy~y~~~~~~~~CP~Cg~~~ 27 (33)
T cd00350 1 KYVCP--VCGYIYDGEEAPWVCPVCGAPK 27 (33)
T ss_pred CEECC--CCCCEECCCcCCCcCcCCCCcH
Confidence 38888 888885554 44688887765
No 20
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=84.12 E-value=0.53 Score=27.54 Aligned_cols=24 Identities=29% Similarity=0.871 Sum_probs=22.0
Q ss_pred CCeEcCccCccccccccccccCCC
Q 033000 6 GDWMCAACQHQNFKKREACQRCGY 29 (129)
Q Consensus 6 gdW~C~~C~~~Nf~~r~~C~~C~~ 29 (129)
..++|-.|+..|....+.|.+|+.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 457999999999999999999986
No 21
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=83.27 E-value=1.1 Score=24.17 Aligned_cols=26 Identities=35% Similarity=0.792 Sum_probs=20.2
Q ss_pred CcccCCCCCCCeecCC--CcCccccCCCCC
Q 033000 51 DWYCTAMNCGAHNYAS--RPNCYRCGAAKT 78 (129)
Q Consensus 51 dW~C~~~~C~~~N~~~--~~~C~~C~~~~~ 78 (129)
-|.|. .||++-... -..|+.|++++.
T Consensus 2 ~~~C~--~CG~i~~g~~~p~~CP~Cg~~~~ 29 (34)
T cd00729 2 VWVCP--VCGYIHEGEEAPEKCPICGAPKE 29 (34)
T ss_pred eEECC--CCCCEeECCcCCCcCcCCCCchH
Confidence 49999 999985543 468999998753
No 22
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.05 E-value=2.1 Score=40.35 Aligned_cols=52 Identities=29% Similarity=0.749 Sum_probs=39.9
Q ss_pred eEcCccCccccccccccccCCCCCCCCCCCcccccCCccccCCCcccCCCCCCCeecCC---CcCccccCCCCCCc
Q 033000 8 WMCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYAS---RPNCYRCGAAKTDY 80 (129)
Q Consensus 8 W~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~---~~~C~~C~~~~~~~ 80 (129)
=.|+.|+...+. ..|..|+++... .+.|+ .|+...-.. +..|..|+.+-...
T Consensus 668 rkCPkCG~~t~~--~fCP~CGs~te~-----------------vy~CP--sCGaev~~des~a~~CP~CGtplv~~ 722 (1337)
T PRK14714 668 RRCPSCGTETYE--NRCPDCGTHTEP-----------------VYVCP--DCGAEVPPDESGRVECPRCDVELTPY 722 (1337)
T ss_pred EECCCCCCcccc--ccCcccCCcCCC-----------------ceeCc--cCCCccCCCccccccCCCCCCccccc
Confidence 689999998876 499999988421 45899 999965443 67899999886543
No 23
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=75.99 E-value=0.54 Score=27.65 Aligned_cols=22 Identities=32% Similarity=0.988 Sum_probs=19.7
Q ss_pred EcCccCccccccccccccCCCC
Q 033000 9 MCAACQHQNFKKREACQRCGYP 30 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C~~C~~p 30 (129)
+|-.|+..|....++|.+|+.-
T Consensus 16 IC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 16 ICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHhcCCCCcchhHHhhccCC
Confidence 6888999999999999999764
No 24
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=75.05 E-value=0.29 Score=43.11 Aligned_cols=75 Identities=12% Similarity=0.188 Sum_probs=55.8
Q ss_pred CCCCCCCeEcCccCccccccccccccCCCCCCCCCCCc----------------cc-------------cc---------
Q 033000 1 MSLPGGDWMCAACQHQNFKKREACQRCGYPKYGGPDVS----------------TY-------------LC--------- 42 (129)
Q Consensus 1 ~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~----------------~~-------------~~--------- 42 (129)
|....-.|.|..|.+.|+.....|..|.+.++..+... ++ .+
T Consensus 1 ~~~~~~~W~~~~~~~~~lp~al~lS~~~~s~~~~~~l~eDifk~~n~~~~~~~sd~~~~r~v~~~~~~p~f~~s~~~r~~ 80 (774)
T KOG4345|consen 1 MPTSAEKWACELCDYMTLPMALVLSDFRRSTGAEPGLAEDIFKGKNWDIHAALSDYEQLRQVHEMNLTPSFCESGQPREI 80 (774)
T ss_pred CcchhHHHHHHhhccccCchhhHHHHHHhccCCCCCcchhhccCCCccceeecccHHHHHhhhccCCCCcccccCCcccc
Confidence 55556689999999999999999999999988543211 00 00
Q ss_pred -CCc-cccCCCcccCCCCCCCeecCCCcCccccCCCC
Q 033000 43 -NRT-EVLAGDWYCTAMNCGAHNYASRPNCYRCGAAK 77 (129)
Q Consensus 43 -~~~-~~~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~ 77 (129)
.++ .-..-.|.|+ .|...|+++...|.+|-..+
T Consensus 81 ~~~s~~~~~~k~~~~--~~~~lnw~re~R~~~~ls~~ 115 (774)
T KOG4345|consen 81 IHKSLIDRNIKWPRP--SLQRLNWPREKRLSRGLSHA 115 (774)
T ss_pred cccccccccccCCch--HhhhhhHHHHHHHHHHhhcc
Confidence 121 2223579999 99999999999999996554
No 25
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=68.30 E-value=2.9 Score=24.47 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=22.6
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCC
Q 033000 50 GDWYCTAMNCGAHNYASRPNCYRCGAA 76 (129)
Q Consensus 50 gdW~C~~~~C~~~N~~~~~~C~~C~~~ 76 (129)
..++|- .|+..|-..++.|.+||..
T Consensus 13 ~k~ICr--kC~ARnp~~A~~CRKCg~~ 37 (48)
T PRK04136 13 NKKICM--RCNARNPWRATKCRKCGYK 37 (48)
T ss_pred cccchh--cccCCCCccccccccCCCC
Confidence 468999 9999999999999999963
No 26
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=63.56 E-value=3.4 Score=23.97 Aligned_cols=13 Identities=31% Similarity=0.976 Sum_probs=7.8
Q ss_pred CCCCeEcCccCcc
Q 033000 4 PGGDWMCAACQHQ 16 (129)
Q Consensus 4 ~~gdW~C~~C~~~ 16 (129)
.+.+|.|+.|+..
T Consensus 31 Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 31 LPDDWVCPVCGAP 43 (47)
T ss_dssp S-TT-B-TTTSSB
T ss_pred CCCCCcCcCCCCc
Confidence 4789999999764
No 27
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=63.55 E-value=4.2 Score=20.59 Aligned_cols=21 Identities=29% Similarity=0.857 Sum_probs=15.9
Q ss_pred EcCccCccccccccccccCCC
Q 033000 9 MCAACQHQNFKKREACQRCGY 29 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C~~C~~ 29 (129)
.||.|..........|..|+-
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 478888777777778877764
No 28
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=62.81 E-value=4.3 Score=21.86 Aligned_cols=22 Identities=36% Similarity=1.085 Sum_probs=13.5
Q ss_pred ccCCCCCCCeecCCCcCccccCCC
Q 033000 53 YCTAMNCGAHNYASRPNCYRCGAA 76 (129)
Q Consensus 53 ~C~~~~C~~~N~~~~~~C~~C~~~ 76 (129)
.|. .|+.+-|.-+..|..|+..
T Consensus 13 rC~--~Cg~~~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 13 RCR--DCGRVQFPPRPVCPHCGSD 34 (37)
T ss_dssp E-T--TT--EEES--SEETTTT--
T ss_pred EcC--CCCCEecCCCcCCCCcCcc
Confidence 488 9999999999999999854
No 29
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.98 E-value=9.7 Score=36.14 Aligned_cols=50 Identities=28% Similarity=0.836 Sum_probs=36.3
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCccCceeecCCCCCceeccC---CccccCCCC
Q 033000 50 GDWYCTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYAS---RMVCYKCKT 126 (129)
Q Consensus 50 gdW~C~~~~C~~~N~~~~~~C~~C~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~---r~~C~~C~~ 126 (129)
+.-.|+ .|+...+.. .|..||++... .+.|+ .|+...-.. +..|..|+.
T Consensus 666 ~~rkCP--kCG~~t~~~--fCP~CGs~te~----------------------vy~CP--sCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 666 GRRRCP--SCGTETYEN--RCPDCGTHTEP----------------------VYVCP--DCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred EEEECC--CCCCccccc--cCcccCCcCCC----------------------ceeCc--cCCCccCCCccccccCCCCCC
Confidence 458899 999988764 99999987421 25788 588864333 567888886
Q ss_pred C
Q 033000 127 P 127 (129)
Q Consensus 127 p 127 (129)
+
T Consensus 718 p 718 (1337)
T PRK14714 718 E 718 (1337)
T ss_pred c
Confidence 5
No 30
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=59.48 E-value=5.9 Score=29.09 Aligned_cols=26 Identities=35% Similarity=0.790 Sum_probs=21.5
Q ss_pred CcccCCCCCCCeecC-CCcCccccCCCCC
Q 033000 51 DWYCTAMNCGAHNYA-SRPNCYRCGAAKT 78 (129)
Q Consensus 51 dW~C~~~~C~~~N~~-~~~~C~~C~~~~~ 78 (129)
-|+|+ .||++-.. .-..|+.|++|+.
T Consensus 134 ~~vC~--vCGy~~~ge~P~~CPiCga~k~ 160 (166)
T COG1592 134 VWVCP--VCGYTHEGEAPEVCPICGAPKE 160 (166)
T ss_pred EEEcC--CCCCcccCCCCCcCCCCCChHH
Confidence 69999 99998776 4566999999874
No 31
>COG1773 Rubredoxin [Energy production and conversion]
Probab=57.46 E-value=17 Score=21.90 Aligned_cols=16 Identities=44% Similarity=1.051 Sum_probs=12.8
Q ss_pred CccccCCCcccCCCCCCC
Q 033000 44 RTEVLAGDWYCTAMNCGA 61 (129)
Q Consensus 44 ~~~~~~gdW~C~~~~C~~ 61 (129)
+++.-+.+|.|+ .|+.
T Consensus 29 ~fedlPd~w~CP--~Cg~ 44 (55)
T COG1773 29 PFEDLPDDWVCP--ECGV 44 (55)
T ss_pred chhhCCCccCCC--CCCC
Confidence 567778999999 7765
No 32
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=45.45 E-value=36 Score=20.44 Aligned_cols=23 Identities=26% Similarity=0.771 Sum_probs=18.9
Q ss_pred ccCCCCCCCeecCCCcCccccCCCCCC
Q 033000 53 YCTAMNCGAHNYASRPNCYRCGAAKTD 79 (129)
Q Consensus 53 ~C~~~~C~~~N~~~~~~C~~C~~~~~~ 79 (129)
.|+ .|+...+ ...|..||.+-..
T Consensus 7 ~C~--~CgvYTL--k~~CP~CG~~t~~ 29 (56)
T PRK13130 7 KCP--KCGVYTL--KEICPVCGGKTKN 29 (56)
T ss_pred ECC--CCCCEEc--cccCcCCCCCCCC
Confidence 588 9999888 8899999987543
No 33
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=44.04 E-value=16 Score=19.70 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=15.2
Q ss_pred CccccCCCCCCcccccccccCCCCCCCCCCccCceeecCCCCCceec
Q 033000 69 NCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNY 115 (129)
Q Consensus 69 ~C~~C~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~N~ 115 (129)
.|..||.+-....+ .+.....+.|+ +|+++.|
T Consensus 2 fC~~CG~~l~~~ip-------------~gd~r~R~vC~--~Cg~IhY 33 (34)
T PF14803_consen 2 FCPQCGGPLERRIP-------------EGDDRERLVCP--ACGFIHY 33 (34)
T ss_dssp B-TTT--B-EEE---------------TT-SS-EEEET--TTTEEE-
T ss_pred ccccccChhhhhcC-------------CCCCccceECC--CCCCEEe
Confidence 58888877432211 12234669999 7998865
No 34
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=43.42 E-value=12 Score=23.36 Aligned_cols=16 Identities=19% Similarity=0.821 Sum_probs=12.5
Q ss_pred CCeEcCccCccccccc
Q 033000 6 GDWMCAACQHQNFKKR 21 (129)
Q Consensus 6 gdW~C~~C~~~Nf~~r 21 (129)
+-|.|+.|+..||.-.
T Consensus 3 ~~~kCpKCgn~~~~ek 18 (68)
T COG3478 3 NAFKCPKCGNTNYEEK 18 (68)
T ss_pred ccccCCCcCCcchhhc
Confidence 4577999999998643
No 35
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=43.37 E-value=23 Score=20.74 Aligned_cols=12 Identities=42% Similarity=1.273 Sum_probs=7.6
Q ss_pred ccCceeecCCCCCc
Q 033000 99 KSGDWICNRMGCGV 112 (129)
Q Consensus 99 ~~gdW~C~~~~C~~ 112 (129)
-+.+|.|+ .|+.
T Consensus 31 Lp~~w~CP--~C~a 42 (50)
T cd00730 31 LPDDWVCP--VCGA 42 (50)
T ss_pred CCCCCCCC--CCCC
Confidence 35677777 5754
No 36
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=42.05 E-value=14 Score=26.64 Aligned_cols=16 Identities=38% Similarity=1.126 Sum_probs=12.4
Q ss_pred CCCCeEcCccCccccc
Q 033000 4 PGGDWMCAACQHQNFK 19 (129)
Q Consensus 4 ~~gdW~C~~C~~~Nf~ 19 (129)
-+|||.|+.|....-.
T Consensus 15 P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 15 PEGDWICPFCEVEKSG 30 (148)
T ss_pred CCCCcCCCCCcCCCCC
Confidence 3599999999876544
No 37
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=39.07 E-value=24 Score=29.85 Aligned_cols=31 Identities=23% Similarity=0.424 Sum_probs=27.5
Q ss_pred CCCCCCCeEcCccCccccccccccccCCCCC
Q 033000 1 MSLPGGDWMCAACQHQNFKKREACQRCGYPK 31 (129)
Q Consensus 1 ~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~pr 31 (129)
|.+++-.|.|..|++.-..+.-+|..|++=+
T Consensus 1 MaK~~t~f~C~~CG~~s~KW~GkCp~Cg~Wn 31 (456)
T COG1066 1 MAKKKTAFVCQECGYVSPKWLGKCPACGAWN 31 (456)
T ss_pred CCCcccEEEcccCCCCCccccccCCCCCCcc
Confidence 6677789999999999999999999999744
No 38
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.69 E-value=28 Score=29.14 Aligned_cols=32 Identities=22% Similarity=0.452 Sum_probs=27.1
Q ss_pred CCCCCCCeEcCccCccccccccccccCCCCCC
Q 033000 1 MSLPGGDWMCAACQHQNFKKREACQRCGYPKY 32 (129)
Q Consensus 1 ~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp 32 (129)
|.+++-.+.|..|++.-...--+|..|++-..
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (446)
T PRK11823 1 MAKKKTAYVCQECGAESPKWLGRCPECGAWNT 32 (446)
T ss_pred CCCCCCeEECCcCCCCCcccCeeCcCCCCccc
Confidence 66777789999999999999999999987644
No 39
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=34.25 E-value=25 Score=24.21 Aligned_cols=32 Identities=25% Similarity=0.462 Sum_probs=24.5
Q ss_pred CCCCCCeEcCccCccc--cccccccccCCCCCCC
Q 033000 2 SLPGGDWMCAACQHQN--FKKREACQRCGYPKYG 33 (129)
Q Consensus 2 ~~~~gdW~C~~C~~~N--f~~r~~C~~C~~prp~ 33 (129)
|.+--+=+||.|.-.- ..+...|+.|++|-..
T Consensus 64 Stkav~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 64 STKAVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred cccceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 3344456899998776 7888999999998643
No 40
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=33.39 E-value=28 Score=20.65 Aligned_cols=22 Identities=23% Similarity=0.733 Sum_probs=14.7
Q ss_pred eEcCccCcccccccccccc--CCC
Q 033000 8 WMCAACQHQNFKKREACQR--CGY 29 (129)
Q Consensus 8 W~C~~C~~~Nf~~r~~C~~--C~~ 29 (129)
=+|-.|..+|....+.|.+ |+-
T Consensus 18 ~ICrkCyarl~~~A~nCRKkkCGh 41 (52)
T PF01020_consen 18 MICRKCYARLPPRATNCRKKKCGH 41 (52)
T ss_dssp EEETTT--EE-TTSSS-TSSSCTS
T ss_pred eecccccCcCCCCccceecccCCC
Confidence 4788999999999999997 753
No 41
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.86 E-value=59 Score=30.52 Aligned_cols=52 Identities=27% Similarity=0.679 Sum_probs=35.3
Q ss_pred CCeEcCccCccccccccccccCCCCCCCCCCCcccccCCccccCCCcccCCCCCCCeecCCCcCccccCCCCCCc
Q 033000 6 GDWMCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKTDY 80 (129)
Q Consensus 6 gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~~~~C~~C~~~~~~~ 80 (129)
+.=.|+.|+..- ....|..|++.-. .-+.|+ .|+...- ...|.+|+......
T Consensus 625 g~RfCpsCG~~t--~~frCP~CG~~Te-----------------~i~fCP--~CG~~~~--~y~CPKCG~El~~~ 676 (1121)
T PRK04023 625 GRRKCPSCGKET--FYRRCPFCGTHTE-----------------PVYRCP--RCGIEVE--EDECEKCGREPTPY 676 (1121)
T ss_pred cCccCCCCCCcC--CcccCCCCCCCCC-----------------cceeCc--cccCcCC--CCcCCCCCCCCCcc
Confidence 344688887774 4467888887621 257899 8977644 35699999886543
No 42
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=32.62 E-value=33 Score=24.21 Aligned_cols=23 Identities=30% Similarity=0.930 Sum_probs=21.3
Q ss_pred ccCCCCCCCeecCCCcCccccCCCC
Q 033000 53 YCTAMNCGAHNYASRPNCYRCGAAK 77 (129)
Q Consensus 53 ~C~~~~C~~~N~~~~~~C~~C~~~~ 77 (129)
.|. .||.+=|+-+..|..|+.+-
T Consensus 31 kC~--~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 31 KCK--KCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred EcC--CCCeEEcCCcccCCCCCCCC
Confidence 599 99999999999999999883
No 43
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=32.17 E-value=23 Score=19.47 Aligned_cols=15 Identities=27% Similarity=0.744 Sum_probs=9.7
Q ss_pred CCeEcCccCcccccc
Q 033000 6 GDWMCAACQHQNFKK 20 (129)
Q Consensus 6 gdW~C~~C~~~Nf~~ 20 (129)
..|+|+-|+..|...
T Consensus 23 ~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 23 KTWICNFCGTKNPLP 37 (40)
T ss_dssp TEEEETTT--EEE--
T ss_pred CEEECcCCCCcCCCC
Confidence 489999999988753
No 44
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.54 E-value=25 Score=18.69 Aligned_cols=11 Identities=18% Similarity=0.467 Sum_probs=5.7
Q ss_pred EcCccCccccc
Q 033000 9 MCAACQHQNFK 19 (129)
Q Consensus 9 ~C~~C~~~Nf~ 19 (129)
.|+.|+..+..
T Consensus 4 ~CP~C~~~~~v 14 (38)
T TIGR02098 4 QCPNCKTSFRV 14 (38)
T ss_pred ECCCCCCEEEe
Confidence 45555554443
No 45
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=28.11 E-value=82 Score=26.66 Aligned_cols=16 Identities=13% Similarity=0.524 Sum_probs=11.8
Q ss_pred CccccCCCcccCCCCCCC
Q 033000 44 RTEVLAGDWYCTAMNCGA 61 (129)
Q Consensus 44 ~~~~~~gdW~C~~~~C~~ 61 (129)
.+.-.+.||.|+ .|+.
T Consensus 451 ~~~~lp~~~~cp--~c~~ 466 (479)
T PRK05452 451 PWSEVPDNFLCP--ECSL 466 (479)
T ss_pred ChhhCCCCCcCc--CCCC
Confidence 466677899999 6654
No 46
>PHA00626 hypothetical protein
Probab=28.02 E-value=47 Score=20.13 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=6.5
Q ss_pred EcCccCccccc
Q 033000 9 MCAACQHQNFK 19 (129)
Q Consensus 9 ~C~~C~~~Nf~ 19 (129)
.||.|+..|.+
T Consensus 2 ~CP~CGS~~Iv 12 (59)
T PHA00626 2 SCPKCGSGNIA 12 (59)
T ss_pred CCCCCCCceee
Confidence 36666665554
No 47
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=27.68 E-value=41 Score=23.70 Aligned_cols=23 Identities=30% Similarity=0.805 Sum_probs=21.4
Q ss_pred EcCccCccccccccccccCCCCC
Q 033000 9 MCAACQHQNFKKREACQRCGYPK 31 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C~~C~~pr 31 (129)
.|..|+..=|..|..|..|+.+-
T Consensus 31 kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 31 KCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred EcCCCCeEEcCCcccCCCCCCCC
Confidence 69999999999999999999983
No 48
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=27.10 E-value=41 Score=18.52 Aligned_cols=12 Identities=33% Similarity=1.121 Sum_probs=7.1
Q ss_pred cCceeecCCCCCce
Q 033000 100 SGDWICNRMGCGVH 113 (129)
Q Consensus 100 ~gdW~C~~~~C~~~ 113 (129)
.|+..|. .||.+
T Consensus 17 ~g~~vC~--~CG~V 28 (43)
T PF08271_consen 17 RGELVCP--NCGLV 28 (43)
T ss_dssp TTEEEET--TT-BB
T ss_pred CCeEECC--CCCCE
Confidence 5667777 47654
No 49
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.80 E-value=33 Score=23.58 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=19.7
Q ss_pred cCccCccccccccccccCCCCC
Q 033000 10 CAACQHQNFKKREACQRCGYPK 31 (129)
Q Consensus 10 C~~C~~~Nf~~r~~C~~C~~pr 31 (129)
||.|+..=-+.+..|..|++.-
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 8999999999999999999853
No 50
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=25.77 E-value=56 Score=27.47 Aligned_cols=32 Identities=19% Similarity=0.411 Sum_probs=26.7
Q ss_pred CCCCCCCeEcCccCccccccccccccCCCCCC
Q 033000 1 MSLPGGDWMCAACQHQNFKKREACQRCGYPKY 32 (129)
Q Consensus 1 ~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp 32 (129)
|.++.-.+.|..|++.-...--+|..|++=..
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNT 32 (454)
T ss_pred CCCCCCeEECCcCCCCCccccEECcCCCCccc
Confidence 66666689999999999999999999988544
No 51
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.93 E-value=62 Score=27.56 Aligned_cols=24 Identities=25% Similarity=0.685 Sum_probs=13.4
Q ss_pred CcccCCCCCCCeecCCCcCccccCCCC
Q 033000 51 DWYCTAMNCGAHNYASRPNCYRCGAAK 77 (129)
Q Consensus 51 dW~C~~~~C~~~N~~~~~~C~~C~~~~ 77 (129)
.=.|. .|++. ..-...|+.|+...
T Consensus 240 ~l~Ch--~Cg~~-~~~~~~Cp~C~s~~ 263 (505)
T TIGR00595 240 KLRCH--YCGYQ-EPIPKTCPQCGSED 263 (505)
T ss_pred eEEcC--CCcCc-CCCCCCCCCCCCCe
Confidence 44566 66644 22335677776654
No 52
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.88 E-value=40 Score=19.31 Aligned_cols=16 Identities=25% Similarity=0.598 Sum_probs=10.2
Q ss_pred EcCccCcccccccccc
Q 033000 9 MCAACQHQNFKKREAC 24 (129)
Q Consensus 9 ~C~~C~~~Nf~~r~~C 24 (129)
.|+.|+..|=.+...|
T Consensus 13 kCp~CGt~NG~R~~~C 28 (44)
T PF14952_consen 13 KCPKCGTYNGTRGLSC 28 (44)
T ss_pred cCCcCcCccCcccccc
Confidence 5788888885444444
No 53
>PRK00420 hypothetical protein; Validated
Probab=23.75 E-value=46 Score=22.84 Aligned_cols=21 Identities=24% Similarity=0.543 Sum_probs=10.0
Q ss_pred EcCccCccccc---cccccccCCC
Q 033000 9 MCAACQHQNFK---KREACQRCGY 29 (129)
Q Consensus 9 ~C~~C~~~Nf~---~r~~C~~C~~ 29 (129)
.||.|++.-|. ....|..|+.
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCC
Confidence 35555554442 3444555544
No 54
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=23.64 E-value=57 Score=18.19 Aligned_cols=8 Identities=38% Similarity=0.924 Sum_probs=3.6
Q ss_pred CccccCCC
Q 033000 69 NCYRCGAA 76 (129)
Q Consensus 69 ~C~~C~~~ 76 (129)
.|+.||.+
T Consensus 23 ~Cp~CG~~ 30 (46)
T PRK00398 23 RCPYCGYR 30 (46)
T ss_pred ECCCCCCe
Confidence 34444433
No 55
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=23.44 E-value=37 Score=27.42 Aligned_cols=41 Identities=27% Similarity=0.711 Sum_probs=26.0
Q ss_pred CeEcCccCccccccccccccCCCCCCCCCC---------CcccccCCccccCCCcccC
Q 033000 7 DWMCAACQHQNFKKREACQRCGYPKYGGPD---------VSTYLCNRTEVLAGDWYCT 55 (129)
Q Consensus 7 dW~C~~C~~~Nf~~r~~C~~C~~prp~~~~---------~~~~~~~~~~~~~gdW~C~ 55 (129)
.|.|..| ..|..|+.|-..... .-++=-+-..+-.|.|+|+
T Consensus 308 ~W~C~~C--------~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVGL~~lP~G~WICD 357 (381)
T KOG1512|consen 308 FWKCSSC--------ELCRICLGPVIESEHLFCDVCDRGPHTLCVGLQDLPRGEWICD 357 (381)
T ss_pred chhhccc--------HhhhccCCcccchheeccccccCCCCccccccccccCccchhh
Confidence 5888888 578888888654310 0011114456667999997
No 56
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=22.78 E-value=45 Score=23.57 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=5.4
Q ss_pred cCccccCCCC
Q 033000 68 PNCYRCGAAK 77 (129)
Q Consensus 68 ~~C~~C~~~~ 77 (129)
.+|..||.|-
T Consensus 29 ~hCp~Cg~PL 38 (131)
T COG1645 29 KHCPKCGTPL 38 (131)
T ss_pred hhCcccCCcc
Confidence 3455566554
No 57
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.68 E-value=52 Score=19.47 Aligned_cols=33 Identities=27% Similarity=0.494 Sum_probs=19.1
Q ss_pred ccccccCCCCCCCCCCCcccccCCccccCCCcccCCCCCCCee
Q 033000 21 REACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHN 63 (129)
Q Consensus 21 r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N 63 (129)
..-|.+|...+...+ +.+...-.|.|+ .|++.|
T Consensus 22 aLIC~~C~~hNGla~--------~~~~~~i~y~C~--~Cg~~N 54 (54)
T PF10058_consen 22 ALICSKCFSHNGLAP--------KEEFEEIQYRCP--YCGALN 54 (54)
T ss_pred eEECcccchhhcccc--------cccCCceEEEcC--CCCCcC
Confidence 344666665544321 123334479999 998876
No 58
>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=20.91 E-value=67 Score=16.47 Aligned_cols=10 Identities=50% Similarity=1.228 Sum_probs=4.3
Q ss_pred cccccCCCCC
Q 033000 22 EACQRCGYPK 31 (129)
Q Consensus 22 ~~C~~C~~pr 31 (129)
..|.+|++|-
T Consensus 4 rfC~~CG~~t 13 (32)
T PF09297_consen 4 RFCGRCGAPT 13 (32)
T ss_dssp SB-TTT--BE
T ss_pred cccCcCCccc
Confidence 4677777763
No 59
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.41 E-value=98 Score=16.31 Aligned_cols=7 Identities=43% Similarity=0.805 Sum_probs=2.6
Q ss_pred CCCCeec
Q 033000 58 NCGAHNY 64 (129)
Q Consensus 58 ~C~~~N~ 64 (129)
.|+..|.
T Consensus 5 ~Cg~~~~ 11 (32)
T PF03604_consen 5 ECGAEVE 11 (32)
T ss_dssp SSSSSE-
T ss_pred cCCCeeE
Confidence 4444443
No 60
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.27 E-value=80 Score=28.08 Aligned_cols=25 Identities=32% Similarity=0.703 Sum_probs=17.7
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCCCC
Q 033000 50 GDWYCTAMNCGAHNYASRPNCYRCGAAKT 78 (129)
Q Consensus 50 gdW~C~~~~C~~~N~~~~~~C~~C~~~~~ 78 (129)
+.=.|. .|++.- ....|..|+....
T Consensus 409 ~~l~Ch--~CG~~~--~p~~Cp~Cgs~~l 433 (665)
T PRK14873 409 GTPRCR--WCGRAA--PDWRCPRCGSDRL 433 (665)
T ss_pred CeeECC--CCcCCC--cCccCCCCcCCcc
Confidence 456788 888852 4678889987653
Done!