Query 032350
Match_columns 142
No_of_seqs 173 out of 776
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 12:57:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032350.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032350hhsearch_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 3.7E-18 8E-23 137.2 6.2 121 17-142 5-165 (280)
2 KOG4198 RNA-binding Ran Zn-fin 99.7 1.9E-17 4.2E-22 133.1 6.7 123 15-141 59-267 (280)
3 PF00641 zf-RanBP: Zn-finger i 98.9 5.5E-10 1.2E-14 61.5 1.8 30 17-46 1-30 (30)
4 KOG1995 Conserved Zn-finger pr 98.8 2.1E-09 4.5E-14 88.8 3.7 126 11-142 62-244 (351)
5 PF00641 zf-RanBP: Zn-finger i 98.8 6.2E-09 1.3E-13 57.2 2.5 29 112-142 1-29 (30)
6 smart00547 ZnF_RBZ Zinc finger 98.5 6.3E-08 1.4E-12 51.3 1.3 26 19-44 1-26 (26)
7 smart00547 ZnF_RBZ Zinc finger 98.3 3.2E-07 7E-12 48.6 1.5 25 63-89 1-25 (26)
8 KOG1995 Conserved Zn-finger pr 97.6 7.1E-05 1.5E-09 62.2 4.5 34 59-93 213-246 (351)
9 PF12773 DZR: Double zinc ribb 96.9 0.0012 2.6E-08 39.7 3.0 50 23-87 1-50 (50)
10 PRK14559 putative protein seri 95.1 0.021 4.5E-07 51.5 3.3 50 22-91 3-52 (645)
11 PF12773 DZR: Double zinc ribb 94.3 0.05 1.1E-06 32.5 2.7 50 67-138 1-50 (50)
12 KOG4477 RING1 interactor RYBP 92.6 0.052 1.1E-06 41.9 0.9 29 18-46 22-50 (228)
13 KOG4477 RING1 interactor RYBP 91.1 0.1 2.2E-06 40.3 1.1 31 109-141 18-48 (228)
14 PF13248 zf-ribbon_3: zinc-rib 90.9 0.11 2.4E-06 27.2 0.9 23 21-43 3-25 (26)
15 PF13248 zf-ribbon_3: zinc-rib 90.9 0.15 3.2E-06 26.7 1.3 23 65-89 3-25 (26)
16 PF13240 zinc_ribbon_2: zinc-r 90.0 0.17 3.6E-06 25.9 1.0 22 22-43 1-22 (23)
17 PF13240 zinc_ribbon_2: zinc-r 88.8 0.26 5.6E-06 25.2 1.2 22 66-89 1-22 (23)
18 PRK14559 putative protein seri 86.4 0.66 1.4E-05 42.0 3.1 48 66-140 3-50 (645)
19 KOG4345 NF-kappa B regulator A 86.2 0.092 2E-06 47.5 -2.4 123 16-142 3-210 (774)
20 cd00350 rubredoxin_like Rubred 84.1 0.95 2.1E-05 24.9 1.9 26 64-91 1-28 (33)
21 PRK14714 DNA polymerase II lar 82.4 1.5 3.2E-05 42.6 3.6 54 19-93 666-722 (1337)
22 PRK04136 rpl40e 50S ribosomal 80.9 0.81 1.8E-05 27.7 0.9 24 19-42 13-36 (48)
23 cd00729 rubredoxin_SM Rubredox 79.3 1.7 3.8E-05 24.1 1.9 26 64-91 2-29 (34)
24 PRK04136 rpl40e 50S ribosomal 68.9 3.1 6.6E-05 25.2 1.2 25 63-89 13-37 (48)
25 COG1552 RPL40A Ribosomal prote 68.6 1.1 2.4E-05 27.2 -0.7 22 22-43 16-37 (50)
26 COG1773 Rubredoxin [Energy pro 65.9 9.1 0.0002 23.8 3.0 16 57-74 29-44 (55)
27 COG1592 Rubrerythrin [Energy p 65.5 3.9 8.5E-05 31.0 1.6 26 20-45 134-160 (166)
28 PF00301 Rubredoxin: Rubredoxi 65.1 8.2 0.00018 23.1 2.6 16 57-74 27-42 (47)
29 cd00730 rubredoxin Rubredoxin; 63.9 8.4 0.00018 23.3 2.5 16 57-74 27-42 (50)
30 PF10571 UPF0547: Uncharacteri 60.9 4.8 0.0001 21.1 0.9 21 22-42 2-22 (26)
31 PF12172 DUF35_N: Rubredoxin-l 59.5 5 0.00011 22.3 0.9 22 66-89 13-34 (37)
32 PRK14714 DNA polymerase II lar 58.5 12 0.00025 36.7 3.6 50 63-140 666-718 (1337)
33 COG1592 Rubrerythrin [Energy p 56.9 7.1 0.00015 29.6 1.6 27 64-92 134-161 (166)
34 cd04718 BAH_plant_2 BAH, or Br 54.3 8.9 0.00019 28.6 1.7 20 13-32 11-30 (148)
35 COG1545 Predicted nucleic-acid 45.9 8.8 0.00019 28.0 0.6 37 3-44 17-53 (140)
36 PF14803 Nudix_N_2: Nudix N-te 44.9 14 0.0003 20.6 1.1 32 82-128 2-33 (34)
37 PF10058 DUF2296: Predicted in 38.1 20 0.00044 22.0 1.3 13 18-30 42-54 (54)
38 PRK13130 H/ACA RNA-protein com 37.2 35 0.00077 21.2 2.3 25 66-94 7-31 (56)
39 PF04810 zf-Sec23_Sec24: Sec23 33.5 34 0.00075 19.4 1.7 15 113-129 22-36 (40)
40 PRK04023 DNA polymerase II lar 32.9 59 0.0013 31.5 3.9 61 11-94 617-677 (1121)
41 PF11023 DUF2614: Protein of u 32.2 25 0.00053 25.1 1.1 29 17-45 66-96 (114)
42 smart00778 Prim_Zn_Ribbon Zinc 32.2 38 0.00082 19.2 1.7 10 19-28 24-33 (37)
43 COG3478 Predicted nucleic-acid 31.9 25 0.00055 22.6 1.0 15 63-79 3-17 (68)
44 PRK05452 anaerobic nitric oxid 31.3 60 0.0013 28.3 3.6 44 18-74 423-466 (479)
45 PHA00626 hypothetical protein 30.7 39 0.00084 21.2 1.6 11 63-75 22-32 (59)
46 COG1545 Predicted nucleic-acid 30.1 37 0.00081 24.7 1.8 23 66-90 31-53 (140)
47 PRK11788 tetratricopeptide rep 29.4 39 0.00085 27.2 2.0 28 18-45 352-379 (389)
48 PF08271 TF_Zn_Ribbon: TFIIB z 28.9 34 0.00074 19.5 1.2 12 113-126 17-28 (43)
49 PF12523 DUF3725: Protein of u 28.2 30 0.00065 22.5 0.9 27 6-32 45-71 (74)
50 TIGR02098 MJ0042_CXXC MJ0042 f 28.1 29 0.00062 19.1 0.7 8 66-75 27-34 (38)
51 PRK00398 rpoP DNA-directed RNA 26.3 47 0.001 19.2 1.4 9 81-89 22-30 (46)
52 PF09862 DUF2089: Protein of u 25.7 34 0.00074 24.3 0.9 22 23-44 1-22 (113)
53 TIGR00595 priA primosomal prot 25.4 57 0.0012 28.7 2.4 24 64-90 240-263 (505)
54 PF03604 DNA_RNApol_7kD: DNA d 21.0 91 0.002 17.0 1.8 6 71-76 5-10 (32)
55 PRK15103 paraquat-inducible me 20.8 82 0.0018 27.1 2.4 34 10-43 210-244 (419)
56 PF01020 Ribosomal_L40e: Ribos 20.5 75 0.0016 19.5 1.5 26 63-90 16-43 (52)
57 PRK11823 DNA repair protein Ra 20.3 82 0.0018 27.2 2.4 28 18-45 5-32 (446)
58 PRK11788 tetratricopeptide rep 20.3 64 0.0014 26.0 1.6 30 60-91 350-379 (389)
No 1
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=99.73 E-value=3.7e-18 Score=137.25 Aligned_cols=121 Identities=34% Similarity=0.727 Sum_probs=93.6
Q ss_pred CCC-CeeccccCccccccccccccCCCCCCCCCCCc------------ccccccccccCCCcccCCCCCCCeecCCCcCc
Q 032350 17 PGG-DWMCAACQHQNFKKREACQRCGYPKYGGPDVS------------TYLCNRTEVLAGDWYCTAMNCGAHNYASRPNC 83 (142)
Q Consensus 17 ~~g-dW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~------------~~~~~~~~~~~gdW~C~~~~C~~~N~~~r~~C 83 (142)
+.| ||.|..|...||..+..|.+|..+++. ..+. .+.+....+++|||.|+ .|+++||++|..|
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 344 999999999999999999999999944 2111 11235678999999999 8999999999999
Q ss_pred cccCCCCCCccccc-ccccC-----------C------CCCCC---------CCCCCCCeeecCCCCCceeccCCccccC
Q 032350 84 YRCGAAKTDYACAN-MMAYG-----------T------DGSVP---------PGWKSGDWICNRMGCGVHNYASRMVCYK 136 (142)
Q Consensus 84 ~~C~~~~~~~~~~~-~~g~g-----------~------~~~~~---------~~~~~gdW~C~~~~C~~~N~a~r~~C~~ 136 (142)
.+|+.++++..+.+ ++..| . ...+. ..+++|||+|+ .|+||||+++.+|++
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 99999988766531 11111 0 00000 13789999999 899999999999999
Q ss_pred CCCCCC
Q 032350 137 CKTPRE 142 (142)
Q Consensus 137 C~~~k~ 142 (142)
|+++++
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=1.9e-17 Score=133.11 Aligned_cols=123 Identities=35% Similarity=0.754 Sum_probs=90.9
Q ss_pred CCCCCCeeccccCccccccccccccCCCCCCCCCC----Cccc--------cc-----------c----c-----ccccC
Q 032350 15 SLPGGDWMCAACQHQNFKKREACQRCGYPKYGGPD----VSTY--------LC-----------N----R-----TEVLA 62 (142)
Q Consensus 15 ~~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~----~~~~--------~~-----------~----~-----~~~~~ 62 (142)
..++|||.|+.|+++||++|+.|++|+.+++.-.. +.++ ++ + + .+.++
T Consensus 59 ~~~pgdw~c~~c~~~n~arr~~c~~c~~s~~~~~~~~~~~~~g~~~~~~~~r~~~~~~~~~~~~g~~~~~n~~~~r~~~~ 138 (280)
T KOG4198|consen 59 PPRPGDWNCPLCGFHNSARRLLCFRCGFSKVPLDSALTAPNSGSRSLQTGPRYFKGDWLCPRCPGLGFSRNNKPKRPWRS 138 (280)
T ss_pred CCCCcccccCccchhhHHHhhhcceecccCCCccccccCCCCcccccccccccccCCCCCCCCCCCcccccccccCCccc
Confidence 56799999999999999999999999998864221 1110 00 0 1 14689
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCCCCCccc-------c----c-----cc-------------ccCC---------C
Q 032350 63 GDWYCTAMNCGAHNYASRPNCYRCGAAKTDYAC-------A----N-----MM-------------AYGT---------D 104 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~r~~C~~C~~~~~~~~~-------~----~-----~~-------------g~g~---------~ 104 (142)
|||+|+ .|++|||+++..|.+|+++++.... . + .. .++. .
T Consensus 139 GDW~Cp--~C~fhNfarn~~C~rC~~~r~~~a~~~~~~s~~~~~~~~s~~~~~~~~t~~~~~~r~~~~~~~~~~~~d~~~ 216 (280)
T KOG4198|consen 139 GDWECP--GCNFHNFARNSECFRCGAKRPLAALLGNQASEATEHDWLSKVADSSSSTRFESLLRCNARGEMSESRVDGAD 216 (280)
T ss_pred cCcccC--CCCceeccccchhhhcCCcCcccccccccccccccccccccccccccceecccchhhcccCccccccccccc
Confidence 999999 9999999999999999999987441 0 0 00 0000 0
Q ss_pred ----------------CCCCCCCCCCCeeecCCCCCceeccCCccccCCCCCC
Q 032350 105 ----------------GSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCKTPR 141 (142)
Q Consensus 105 ----------------~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~k 141 (142)
..+....+.+||.|+ .|.++||.++.+|..|..++
T Consensus 217 ~~~~~~~~~e~~~~~~sr~s~~~~dgdw~~~--s~~~~~~r~r~a~~~c~~~~ 267 (280)
T KOG4198|consen 217 VKGNFSSDDESRLEPLSRGSKSSRDGDWMCE--SCKAENFRRRNACLKCISPR 267 (280)
T ss_pred ccccccccccccccccccCcccccCCCcccc--cccchhhhhhhhhhccccCc
Confidence 001123678999999 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=98.92 E-value=5.5e-10 Score=61.51 Aligned_cols=30 Identities=40% Similarity=0.991 Sum_probs=24.7
Q ss_pred CCCCeeccccCccccccccccccCCCCCCC
Q 032350 17 PGGDWMCAACQHQNFKKREACQRCGYPKYG 46 (142)
Q Consensus 17 ~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~ 46 (142)
++|+|.|+.|+++|++.+..|.+|+++||+
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 478999999999999999999999999984
No 4
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=98.84 E-value=2.1e-09 Score=88.76 Aligned_cols=126 Identities=24% Similarity=0.328 Sum_probs=85.1
Q ss_pred CCCCCCCCCCeecc--ccCccccccccccccCCCCCCCCCCCc--------ccc-cccccccCCCcccCCCCCCCeecCC
Q 032350 11 DKKMSLPGGDWMCA--ACQHQNFKKREACQRCGYPKYGGPDVS--------TYL-CNRTEVLAGDWYCTAMNCGAHNYAS 79 (142)
Q Consensus 11 ~~~~~~~~gdW~C~--~C~~~Nf~~r~~C~~C~~prp~~~~~~--------~~~-~~~~~~~~gdW~C~~~~C~~~N~~~ 79 (142)
.+....+.++|.|+ .|.+.||.+..+|..|+.+|.... +- +.. -+...+..-||.|. .|.++||+.
T Consensus 62 ~~s~~~ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~k-Pki~~y~dkeT~~~KGeatvS~~D~~~a--kaai~~~ag 138 (351)
T KOG1995|consen 62 DKSDNETIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGK-PKIKIYTDKETGAPKGEATVSYEDPPAA--KAAIEWFAG 138 (351)
T ss_pred cccccccceeeccCccchHHHHHHHHhhcceeccCCCCCC-cchhccccccccCcCCceeeeecChhhh--hhhhhhhcc
Confidence 36667778999998 799999999999999999998742 11 100 12334556688888 888888887
Q ss_pred CcCccccCCCCCCcccc---c------------ccccC-------------CCCC------------------CCCCCCC
Q 032350 80 RPNCYRCGAAKTDYACA---N------------MMAYG-------------TDGS------------------VPPGWKS 113 (142)
Q Consensus 80 r~~C~~C~~~~~~~~~~---~------------~~g~g-------------~~~~------------------~~~~~~~ 113 (142)
+..|. .+++...+.. + ..+|+ .... .......
T Consensus 139 kdf~g--n~ikvs~a~~r~~ve~~rg~~~~~~g~g~fg~~~~grg~~~G~gg~~~~~~~~~rGg~~~~g~~g~~~~~~~d 216 (351)
T KOG1995|consen 139 KDFCG--NTIKVSLAERRTGVESVRGGYPNDGGAGEFGRLRGGRGGPGGPGGGDGEAGKGDRGGVPDGGESGGGNVQDED 216 (351)
T ss_pred ccccC--CCchhhhhhhccCcccccccccCcCCCCCccccccCCCCCCCCCCccccccccccCCcCCCcccCCccccccc
Confidence 77776 3333211100 0 00000 0000 0112467
Q ss_pred CCeeecCCCCCceeccCCccccCCCCCCC
Q 032350 114 GDWICNRMGCGVHNYASRMVCYKCKTPRE 142 (142)
Q Consensus 114 gdW~C~~~~C~~~N~a~r~~C~~C~~~k~ 142 (142)
+||.|+ +.|.+.||+++..|++|+++|+
T Consensus 217 ~Dw~c~-~~c~N~nfa~r~~cnrck~~Kp 244 (351)
T KOG1995|consen 217 GDWDCP-PSCGNRNFAWREECNRCKAPKP 244 (351)
T ss_pred cccccc-ccccccccccccccccccCCCc
Confidence 899999 7999999999999999999985
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=98.75 E-value=6.2e-09 Score=57.24 Aligned_cols=29 Identities=48% Similarity=0.996 Sum_probs=23.6
Q ss_pred CCCCeeecCCCCCceeccCCccccCCCCCCC
Q 032350 112 KSGDWICNRMGCGVHNYASRMVCYKCKTPRE 142 (142)
Q Consensus 112 ~~gdW~C~~~~C~~~N~a~r~~C~~C~~~k~ 142 (142)
++|+|.|+ .|+++|++++..|++|+++||
T Consensus 1 k~g~W~C~--~C~~~N~~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 1 KEGDWKCP--SCTFMNPASRSKCVACGAPRP 29 (30)
T ss_dssp -SSSEEET--TTTEEEESSSSB-TTT--BTT
T ss_pred CCcCccCC--CCcCCchHHhhhhhCcCCCCc
Confidence 36899999 799999999999999999986
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=98.46 E-value=6.3e-08 Score=51.35 Aligned_cols=26 Identities=50% Similarity=1.198 Sum_probs=24.5
Q ss_pred CCeeccccCccccccccccccCCCCC
Q 032350 19 GDWMCAACQHQNFKKREACQRCGYPK 44 (142)
Q Consensus 19 gdW~C~~C~~~Nf~~r~~C~~C~~pr 44 (142)
|||.|+.|+++|++.+..|.+|++|.
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=98.29 E-value=3.2e-07 Score=48.57 Aligned_cols=25 Identities=52% Similarity=1.285 Sum_probs=23.9
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCC
Q 032350 63 GDWYCTAMNCGAHNYASRPNCYRCGAA 89 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~r~~C~~C~~~ 89 (142)
|||+|+ .|+++|++.+..|..|++|
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=97.62 E-value=7.1e-05 Score=62.20 Aligned_cols=34 Identities=41% Similarity=0.902 Sum_probs=31.2
Q ss_pred cccCCCcccCCCCCCCeecCCCcCccccCCCCCCc
Q 032350 59 EVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKTDY 93 (142)
Q Consensus 59 ~~~~gdW~C~~~~C~~~N~~~r~~C~~C~~~~~~~ 93 (142)
...++||.|+ ..|.++||+.+..|++|.++||..
T Consensus 213 ~~~d~Dw~c~-~~c~N~nfa~r~~cnrck~~Kp~~ 246 (351)
T KOG1995|consen 213 QDEDGDWDCP-PSCGNRNFAWREECNRCKAPKPER 246 (351)
T ss_pred cccccccccc-ccccccccccccccccccCCCccc
Confidence 4578899999 999999999999999999999865
No 9
>PF12773 DZR: Double zinc ribbon
Probab=96.86 E-value=0.0012 Score=39.73 Aligned_cols=50 Identities=32% Similarity=0.671 Sum_probs=42.8
Q ss_pred ccccCccccccccccccCCCCCCCCCCCcccccccccccCCCcccCCCCCCCeecCCCcCccccC
Q 032350 23 CAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCG 87 (142)
Q Consensus 23 C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~r~~C~~C~ 87 (142)
|+.|+..|-.....|..|+++-+. .....++|+ .|+..|...+..|..||
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~~-------------~~~~~~~C~--~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLPP-------------PDQSKKICP--NCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCCccccCChhhcCChhh-------------ccCCCCCCc--CCcCCCcCCcCccCccc
Confidence 789999999999999999998661 112368999 99999999999999996
No 10
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=95.05 E-value=0.021 Score=51.52 Aligned_cols=50 Identities=30% Similarity=0.731 Sum_probs=43.4
Q ss_pred eccccCccccccccccccCCCCCCCCCCCcccccccccccCCCcccCCCCCCCeecCCCcCccccCCCCC
Q 032350 22 MCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKT 91 (142)
Q Consensus 22 ~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~r~~C~~C~~~~~ 91 (142)
.|+.|++.|-.....|.+|+++-.. + .|+ .||..+-.....|..||++-.
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~--------------~----~Cp--~CG~~~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTH--------------K----PCP--QCGTEVPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCC--------------C----cCC--CCCCCCCcccccccccCCccc
Confidence 5999999999999999999886421 0 599 999999999999999998854
No 11
>PF12773 DZR: Double zinc ribbon
Probab=94.30 E-value=0.05 Score=32.51 Aligned_cols=50 Identities=28% Similarity=0.658 Sum_probs=41.0
Q ss_pred cCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCCCCCeeecCCCCCceeccCCccccCCC
Q 032350 67 CTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCK 138 (142)
Q Consensus 67 C~~~~C~~~N~~~r~~C~~C~~~~~~~~~~~~~g~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~ 138 (142)
|+ .|+..|-.....|..||++-+. .....+.|+ .|+..|......|..|+
T Consensus 1 Cp--~Cg~~~~~~~~fC~~CG~~l~~------------------~~~~~~~C~--~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 1 CP--HCGTPNPDDAKFCPHCGTPLPP------------------PDQSKKICP--NCGAENPPNAKFCPNCG 50 (50)
T ss_pred CC--CcCCcCCccccCChhhcCChhh------------------ccCCCCCCc--CCcCCCcCCcCccCccc
Confidence 67 8999999999999999988551 113468899 69999999999998885
No 12
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=92.55 E-value=0.052 Score=41.88 Aligned_cols=29 Identities=28% Similarity=0.628 Sum_probs=26.4
Q ss_pred CCCeeccccCccccccccccccCCCCCCC
Q 032350 18 GGDWMCAACQHQNFKKREACQRCGYPKYG 46 (142)
Q Consensus 18 ~gdW~C~~C~~~Nf~~r~~C~~C~~prp~ 46 (142)
.|.|.|..|.|.|-+-.-.|+.|+..+..
T Consensus 22 eg~WdCsvCTFrNsAeAfkC~vCdvRKGT 50 (228)
T KOG4477|consen 22 EGKWDCSVCTFRNSAEAFKCFVCDVRKGT 50 (228)
T ss_pred cCceeeeeeeecchhhhhheeeecccccc
Confidence 47899999999999999999999987754
No 13
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=91.11 E-value=0.1 Score=40.32 Aligned_cols=31 Identities=29% Similarity=0.792 Sum_probs=26.3
Q ss_pred CCCCCCCeeecCCCCCceeccCCccccCCCCCC
Q 032350 109 PGWKSGDWICNRMGCGVHNYASRMVCYKCKTPR 141 (142)
Q Consensus 109 ~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~k 141 (142)
+....|-|+|. .|+|.|-|-.-.|++|...+
T Consensus 18 p~~Deg~WdCs--vCTFrNsAeAfkC~vCdvRK 48 (228)
T KOG4477|consen 18 PNDDEGKWDCS--VCTFRNSAEAFKCFVCDVRK 48 (228)
T ss_pred CccccCceeee--eeeecchhhhhheeeecccc
Confidence 34557889999 79999999999999998654
No 14
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.92 E-value=0.11 Score=27.20 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=20.2
Q ss_pred eeccccCccccccccccccCCCC
Q 032350 21 WMCAACQHQNFKKREACQRCGYP 43 (142)
Q Consensus 21 W~C~~C~~~Nf~~r~~C~~C~~p 43 (142)
..|+.|+..+......|..|+++
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 46999999999999999999875
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.91 E-value=0.15 Score=26.71 Aligned_cols=23 Identities=39% Similarity=0.871 Sum_probs=20.2
Q ss_pred cccCCCCCCCeecCCCcCccccCCC
Q 032350 65 WYCTAMNCGAHNYASRPNCYRCGAA 89 (142)
Q Consensus 65 W~C~~~~C~~~N~~~r~~C~~C~~~ 89 (142)
..|+ .|+..+......|..||++
T Consensus 3 ~~Cp--~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCP--NCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCc--ccCCcCCcccccChhhCCC
Confidence 5789 9999999999999999975
No 16
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=89.97 E-value=0.17 Score=25.92 Aligned_cols=22 Identities=27% Similarity=0.768 Sum_probs=19.1
Q ss_pred eccccCccccccccccccCCCC
Q 032350 22 MCAACQHQNFKKREACQRCGYP 43 (142)
Q Consensus 22 ~C~~C~~~Nf~~r~~C~~C~~p 43 (142)
.|+.|+..+......|..|+++
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 3889999999999999999875
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.84 E-value=0.26 Score=25.20 Aligned_cols=22 Identities=41% Similarity=0.942 Sum_probs=18.7
Q ss_pred ccCCCCCCCeecCCCcCccccCCC
Q 032350 66 YCTAMNCGAHNYASRPNCYRCGAA 89 (142)
Q Consensus 66 ~C~~~~C~~~N~~~r~~C~~C~~~ 89 (142)
.|+ .||..+-.....|..||++
T Consensus 1 ~Cp--~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCP--NCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCc--ccCCCCCCcCcchhhhCCc
Confidence 378 8999999999999999875
No 18
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=86.45 E-value=0.66 Score=42.02 Aligned_cols=48 Identities=27% Similarity=0.641 Sum_probs=39.5
Q ss_pred ccCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCCCCCeeecCCCCCceeccCCccccCCCCC
Q 032350 66 YCTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYASRMVCYKCKTP 140 (142)
Q Consensus 66 ~C~~~~C~~~N~~~r~~C~~C~~~~~~~~~~~~~g~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~ 140 (142)
+|+ .|+..|-..+..|..||++-.. + .|+ .|+..|-.....|..|+++
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 689 9999999999999999876321 0 388 6999999999999999875
No 19
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=86.17 E-value=0.092 Score=47.53 Aligned_cols=123 Identities=12% Similarity=0.119 Sum_probs=80.4
Q ss_pred CCCCCeeccccCccccccccccccCCCCCCCCC----CC---c---------cc-------------cc----------c
Q 032350 16 LPGGDWMCAACQHQNFKKREACQRCGYPKYGGP----DV---S---------TY-------------LC----------N 56 (142)
Q Consensus 16 ~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~----~~---~---------~~-------------~~----------~ 56 (142)
.....|.|..|.+.|+....+|..|.+.++..+ |+ + ++ .+ .
T Consensus 3 ~~~~~W~~~~~~~~~lp~al~lS~~~~s~~~~~~l~eDifk~~n~~~~~~~sd~~~~r~v~~~~~~p~f~~s~~~r~~~~ 82 (774)
T KOG4345|consen 3 TSAEKWACELCDYMTLPMALVLSDFRRSTGAEPGLAEDIFKGKNWDIHAALSDYEQLRQVHEMNLTPSFCESGQPREIIH 82 (774)
T ss_pred chhHHHHHHhhccccCchhhHHHHHHhccCCCCCcchhhccCCCccceeecccHHHHHhhhccCCCCcccccCCcccccc
Confidence 345689999999999999999999999887542 11 0 00 00 1
Q ss_pred cc-cccCCCcccCCCCCCCeecCCCcCccccCCCCCCccc-c--cc--cccCCC----------------CCCCCC---C
Q 032350 57 RT-EVLAGDWYCTAMNCGAHNYASRPNCYRCGAAKTDYAC-A--NM--MAYGTD----------------GSVPPG---W 111 (142)
Q Consensus 57 ~~-~~~~gdW~C~~~~C~~~N~~~r~~C~~C~~~~~~~~~-~--~~--~g~g~~----------------~~~~~~---~ 111 (142)
+. ....-.|.|+ .|...|+++...|.+|-.-+.+... + .. .++-.+ .....+ +
T Consensus 83 ~s~~~~~~k~~~~--~~~~lnw~re~R~~~~ls~~gd~~~~~~q~pq~s~~~qs~~VaL~~~l~~~l~~~dt~~~N~l~w 160 (774)
T KOG4345|consen 83 KSLIDRNIKWPRP--SLQRLNWPREKRLSRGLSHAGDMPILAFQLPQLSVYEQSTPVALEKALFRLLPLADTGDGNCLMW 160 (774)
T ss_pred cccccccccCCch--HhhhhhHHHHHHHHHHhhccCCCccchhccchhhccccccchhhhhhhhhcccccccCCccchhh
Confidence 21 3345689999 9999999999999998554421110 0 00 111000 000001 0
Q ss_pred C---------------------CCCeeecCCCCCceeccCCccccCCCCCCC
Q 032350 112 K---------------------SGDWICNRMGCGVHNYASRMVCYKCKTPRE 142 (142)
Q Consensus 112 ~---------------------~gdW~C~~~~C~~~N~a~r~~C~~C~~~k~ 142 (142)
. ..+|+|. .|++.|+++-..|.+|+++++
T Consensus 161 ~~h~lvlqk~l~t~l~~~~~rw~~eW~~l--ik~ass~pr~~r~~~~~~~~~ 210 (774)
T KOG4345|consen 161 GFHDLVLQKALYTGLCYGTERWNDEWTEL--IKLASSEPRMHRSGNGGTGGG 210 (774)
T ss_pred hhhhHHHHHHHHHhhchhhHHHHHHHHHH--HHhhcccchhhhcccCCCCCC
Confidence 0 1349999 799999999999999987753
No 20
>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=84.05 E-value=0.95 Score=24.90 Aligned_cols=26 Identities=31% Similarity=0.583 Sum_probs=17.7
Q ss_pred CcccCCCCCCCeecCC--CcCccccCCCCC
Q 032350 64 DWYCTAMNCGAHNYAS--RPNCYRCGAAKT 91 (142)
Q Consensus 64 dW~C~~~~C~~~N~~~--r~~C~~C~~~~~ 91 (142)
.|+|. .||++-... --.|+.|++++.
T Consensus 1 ~~~C~--~CGy~y~~~~~~~~CP~Cg~~~~ 28 (33)
T cd00350 1 KYVCP--VCGYIYDGEEAPWVCPVCGAPKD 28 (33)
T ss_pred CEECC--CCCCEECCCcCCCcCcCCCCcHH
Confidence 38888 888885543 446777777653
No 21
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.45 E-value=1.5 Score=42.58 Aligned_cols=54 Identities=30% Similarity=0.760 Sum_probs=41.3
Q ss_pred CCeeccccCccccccccccccCCCCCCCCCCCcccccccccccCCCcccCCCCCCCeecCC---CcCccccCCCCCCc
Q 032350 19 GDWMCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYAS---RPNCYRCGAAKTDY 93 (142)
Q Consensus 19 gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~---r~~C~~C~~~~~~~ 93 (142)
+.=.|+.|+...+.. .|..|+++... .+.|+ .|+...-.. +..|..|+.+....
T Consensus 666 ~~rkCPkCG~~t~~~--fCP~CGs~te~-----------------vy~CP--sCGaev~~des~a~~CP~CGtplv~~ 722 (1337)
T PRK14714 666 GRRRCPSCGTETYEN--RCPDCGTHTEP-----------------VYVCP--DCGAEVPPDESGRVECPRCDVELTPY 722 (1337)
T ss_pred EEEECCCCCCccccc--cCcccCCcCCC-----------------ceeCc--cCCCccCCCccccccCCCCCCccccc
Confidence 447899999988764 99999987421 46899 999965443 67899999886543
No 22
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=80.92 E-value=0.81 Score=27.70 Aligned_cols=24 Identities=29% Similarity=0.871 Sum_probs=22.1
Q ss_pred CCeeccccCccccccccccccCCC
Q 032350 19 GDWMCAACQHQNFKKREACQRCGY 42 (142)
Q Consensus 19 gdW~C~~C~~~Nf~~r~~C~~C~~ 42 (142)
..++|-.|+..|....+.|.+|+.
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 467899999999999999999987
No 23
>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=79.32 E-value=1.7 Score=24.12 Aligned_cols=26 Identities=35% Similarity=0.792 Sum_probs=20.1
Q ss_pred CcccCCCCCCCeecCC--CcCccccCCCCC
Q 032350 64 DWYCTAMNCGAHNYAS--RPNCYRCGAAKT 91 (142)
Q Consensus 64 dW~C~~~~C~~~N~~~--r~~C~~C~~~~~ 91 (142)
-|.|. .||++=... -..|+.|++++.
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 358999998764
No 24
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=68.91 E-value=3.1 Score=25.21 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=22.7
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCC
Q 032350 63 GDWYCTAMNCGAHNYASRPNCYRCGAA 89 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~r~~C~~C~~~ 89 (142)
..++|- .|+..|-.+++.|.+||..
T Consensus 13 ~k~ICr--kC~ARnp~~A~~CRKCg~~ 37 (48)
T PRK04136 13 NKKICM--RCNARNPWRATKCRKCGYK 37 (48)
T ss_pred cccchh--cccCCCCccccccccCCCC
Confidence 578999 9999999999999999963
No 25
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=68.65 E-value=1.1 Score=27.22 Aligned_cols=22 Identities=32% Similarity=0.988 Sum_probs=20.0
Q ss_pred eccccCccccccccccccCCCC
Q 032350 22 MCAACQHQNFKKREACQRCGYP 43 (142)
Q Consensus 22 ~C~~C~~~Nf~~r~~C~~C~~p 43 (142)
+|-.|+..|....+.|.+|+.-
T Consensus 16 IC~rC~Arnp~~A~kCRkC~~k 37 (50)
T COG1552 16 ICRRCYARNPPRATKCRKCGYK 37 (50)
T ss_pred HHHHhcCCCCcchhHHhhccCC
Confidence 6889999999999999999774
No 26
>COG1773 Rubredoxin [Energy production and conversion]
Probab=65.90 E-value=9.1 Score=23.82 Aligned_cols=16 Identities=44% Similarity=1.051 Sum_probs=12.8
Q ss_pred cccccCCCcccCCCCCCC
Q 032350 57 RTEVLAGDWYCTAMNCGA 74 (142)
Q Consensus 57 ~~~~~~gdW~C~~~~C~~ 74 (142)
++..-+.+|.|+ .|+.
T Consensus 29 ~fedlPd~w~CP--~Cg~ 44 (55)
T COG1773 29 PFEDLPDDWVCP--ECGV 44 (55)
T ss_pred chhhCCCccCCC--CCCC
Confidence 467788999999 7765
No 27
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=65.53 E-value=3.9 Score=30.98 Aligned_cols=26 Identities=35% Similarity=0.828 Sum_probs=19.6
Q ss_pred CeeccccCccccc-cccccccCCCCCC
Q 032350 20 DWMCAACQHQNFK-KREACQRCGYPKY 45 (142)
Q Consensus 20 dW~C~~C~~~Nf~-~r~~C~~C~~prp 45 (142)
-|.|+.|++.-.. ....|.-|++|+.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k~ 160 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPKE 160 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChHH
Confidence 6999999887554 5567888887763
No 28
>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=65.14 E-value=8.2 Score=23.11 Aligned_cols=16 Identities=50% Similarity=1.034 Sum_probs=9.1
Q ss_pred cccccCCCcccCCCCCCC
Q 032350 57 RTEVLAGDWYCTAMNCGA 74 (142)
Q Consensus 57 ~~~~~~gdW~C~~~~C~~ 74 (142)
.+...+.||.|+ .|+.
T Consensus 27 ~F~~Lp~~w~CP--~C~a 42 (47)
T PF00301_consen 27 PFEDLPDDWVCP--VCGA 42 (47)
T ss_dssp -GGGS-TT-B-T--TTSS
T ss_pred CHHHCCCCCcCc--CCCC
Confidence 466778899999 7664
No 29
>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=63.92 E-value=8.4 Score=23.34 Aligned_cols=16 Identities=50% Similarity=1.034 Sum_probs=11.3
Q ss_pred cccccCCCcccCCCCCCC
Q 032350 57 RTEVLAGDWYCTAMNCGA 74 (142)
Q Consensus 57 ~~~~~~gdW~C~~~~C~~ 74 (142)
.+...+.+|.|+ .|+.
T Consensus 27 ~f~~Lp~~w~CP--~C~a 42 (50)
T cd00730 27 PFEDLPDDWVCP--VCGA 42 (50)
T ss_pred CHhHCCCCCCCC--CCCC
Confidence 355567899999 6653
No 30
>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=60.89 E-value=4.8 Score=21.11 Aligned_cols=21 Identities=29% Similarity=0.857 Sum_probs=15.7
Q ss_pred eccccCccccccccccccCCC
Q 032350 22 MCAACQHQNFKKREACQRCGY 42 (142)
Q Consensus 22 ~C~~C~~~Nf~~r~~C~~C~~ 42 (142)
.||.|+..-......|..|+-
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 477887777777777777764
No 31
>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=59.54 E-value=5 Score=22.30 Aligned_cols=22 Identities=36% Similarity=1.085 Sum_probs=13.6
Q ss_pred ccCCCCCCCeecCCCcCccccCCC
Q 032350 66 YCTAMNCGAHNYASRPNCYRCGAA 89 (142)
Q Consensus 66 ~C~~~~C~~~N~~~r~~C~~C~~~ 89 (142)
.|. .|+.+-|.-+..|..|++.
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 32
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=58.50 E-value=12 Score=36.74 Aligned_cols=50 Identities=28% Similarity=0.836 Sum_probs=36.0
Q ss_pred CCcccCCCCCCCeecCCCcCccccCCCCCCcccccccccCCCCCCCCCCCCCCeeecCCCCCceeccC---CccccCCCC
Q 032350 63 GDWYCTAMNCGAHNYASRPNCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNYAS---RMVCYKCKT 139 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~r~~C~~C~~~~~~~~~~~~~g~g~~~~~~~~~~~gdW~C~~~~C~~~N~a~---r~~C~~C~~ 139 (142)
+.-.|+ .||...+.. .|..||++... .+.|+ .|+...-.. +..|..|+.
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 347899 999988764 99999987421 34787 588765333 557888876
Q ss_pred C
Q 032350 140 P 140 (142)
Q Consensus 140 ~ 140 (142)
+
T Consensus 718 p 718 (1337)
T PRK14714 718 E 718 (1337)
T ss_pred c
Confidence 5
No 33
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=56.85 E-value=7.1 Score=29.58 Aligned_cols=27 Identities=33% Similarity=0.767 Sum_probs=21.5
Q ss_pred CcccCCCCCCCeecC-CCcCccccCCCCCC
Q 032350 64 DWYCTAMNCGAHNYA-SRPNCYRCGAAKTD 92 (142)
Q Consensus 64 dW~C~~~~C~~~N~~-~r~~C~~C~~~~~~ 92 (142)
-|+|+ .||+.-.. .-..|+.||+|+..
T Consensus 134 ~~vC~--vCGy~~~ge~P~~CPiCga~k~~ 161 (166)
T COG1592 134 VWVCP--VCGYTHEGEAPEVCPICGAPKEK 161 (166)
T ss_pred EEEcC--CCCCcccCCCCCcCCCCCChHHH
Confidence 69999 99998776 33469999998753
No 34
>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=54.30 E-value=8.9 Score=28.56 Aligned_cols=20 Identities=30% Similarity=0.876 Sum_probs=14.5
Q ss_pred CCCCCCCCeeccccCccccc
Q 032350 13 KMSLPGGDWMCAACQHQNFK 32 (142)
Q Consensus 13 ~~~~~~gdW~C~~C~~~Nf~ 32 (142)
-....+|||.|+.|....-.
T Consensus 11 l~~~P~g~W~Cp~C~~~~~~ 30 (148)
T cd04718 11 LKEVPEGDWICPFCEVEKSG 30 (148)
T ss_pred CCCCCCCCcCCCCCcCCCCC
Confidence 33556799999999876443
No 35
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=45.86 E-value=8.8 Score=27.99 Aligned_cols=37 Identities=27% Similarity=0.610 Sum_probs=27.6
Q ss_pred ccchhhhcCCCCCCCCCCeeccccCccccccccccccCCCCC
Q 032350 3 KFARVICQDKKMSLPGGDWMCAACQHQNFKKREACQRCGYPK 44 (142)
Q Consensus 3 ~~~~~~~~~~~~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~pr 44 (142)
.|...|.+.|-+-. .|.+|+..=|+.|..|..|+.+-
T Consensus 17 ~f~~~l~~~kl~g~-----kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 17 KFFKGLKEGKLLGT-----KCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred HHhhhhhhCcEEEE-----EcCCCCeEEcCCcccCCCCCCCC
Confidence 44444544443322 69999999999999999999983
No 36
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=44.88 E-value=14 Score=20.62 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=15.5
Q ss_pred CccccCCCCCCcccccccccCCCCCCCCCCCCCCeeecCCCCCceec
Q 032350 82 NCYRCGAAKTDYACANMMAYGTDGSVPPGWKSGDWICNRMGCGVHNY 128 (142)
Q Consensus 82 ~C~~C~~~~~~~~~~~~~g~g~~~~~~~~~~~gdW~C~~~~C~~~N~ 128 (142)
.|..||.+-....+ .......+.|+ .|+++.|
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 47888877432211 12335679999 7998865
No 37
>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=38.05 E-value=20 Score=21.97 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=8.3
Q ss_pred CCCeeccccCccc
Q 032350 18 GGDWMCAACQHQN 30 (142)
Q Consensus 18 ~gdW~C~~C~~~N 30 (142)
+-.|.|+.|++.|
T Consensus 42 ~i~y~C~~Cg~~N 54 (54)
T PF10058_consen 42 EIQYRCPYCGALN 54 (54)
T ss_pred ceEEEcCCCCCcC
Confidence 4467777776655
No 38
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=37.24 E-value=35 Score=21.18 Aligned_cols=25 Identities=24% Similarity=0.657 Sum_probs=20.1
Q ss_pred ccCCCCCCCeecCCCcCccccCCCCCCcc
Q 032350 66 YCTAMNCGAHNYASRPNCYRCGAAKTDYA 94 (142)
Q Consensus 66 ~C~~~~C~~~N~~~r~~C~~C~~~~~~~~ 94 (142)
.|+ .|+.... ...|..||.+-....
T Consensus 7 ~C~--~CgvYTL--k~~CP~CG~~t~~~~ 31 (56)
T PRK13130 7 KCP--KCGVYTL--KEICPVCGGKTKNPH 31 (56)
T ss_pred ECC--CCCCEEc--cccCcCCCCCCCCCC
Confidence 588 9999888 889999998865443
No 39
>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=33.48 E-value=34 Score=19.36 Aligned_cols=15 Identities=47% Similarity=1.017 Sum_probs=9.7
Q ss_pred CCCeeecCCCCCceecc
Q 032350 113 SGDWICNRMGCGVHNYA 129 (142)
Q Consensus 113 ~gdW~C~~~~C~~~N~a 129 (142)
...|.|. -|+..|..
T Consensus 22 ~~~w~C~--~C~~~N~l 36 (40)
T PF04810_consen 22 GKTWICN--FCGTKNPL 36 (40)
T ss_dssp TTEEEET--TT--EEE-
T ss_pred CCEEECc--CCCCcCCC
Confidence 3579999 79998854
No 40
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.93 E-value=59 Score=31.47 Aligned_cols=61 Identities=23% Similarity=0.578 Sum_probs=44.0
Q ss_pred CCCCCCCCCCeeccccCccccccccccccCCCCCCCCCCCcccccccccccCCCcccCCCCCCCeecCCCcCccccCCCC
Q 032350 11 DKKMSLPGGDWMCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGAHNYASRPNCYRCGAAK 90 (142)
Q Consensus 11 ~~~~~~~~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~~N~~~r~~C~~C~~~~ 90 (142)
.+.++...+.=.|+.|+..- ....|..|++.-. .-|.|+ .|+-..-. ..|.+|+...
T Consensus 617 ~g~~eVEVg~RfCpsCG~~t--~~frCP~CG~~Te-----------------~i~fCP--~CG~~~~~--y~CPKCG~El 673 (1121)
T PRK04023 617 KGTIEVEIGRRKCPSCGKET--FYRRCPFCGTHTE-----------------PVYRCP--RCGIEVEE--DECEKCGREP 673 (1121)
T ss_pred CCceeecccCccCCCCCCcC--CcccCCCCCCCCC-----------------cceeCc--cccCcCCC--CcCCCCCCCC
Confidence 45555666777899999885 4468999998721 258999 99776443 5699999887
Q ss_pred CCcc
Q 032350 91 TDYA 94 (142)
Q Consensus 91 ~~~~ 94 (142)
....
T Consensus 674 ~~~s 677 (1121)
T PRK04023 674 TPYS 677 (1121)
T ss_pred Cccc
Confidence 6543
No 41
>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=32.16 E-value=25 Score=25.08 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=23.1
Q ss_pred CCCCeeccccCccc--cccccccccCCCCCC
Q 032350 17 PGGDWMCAACQHQN--FKKREACQRCGYPKY 45 (142)
Q Consensus 17 ~~gdW~C~~C~~~N--f~~r~~C~~C~~prp 45 (142)
+.-.=.||.|+-.- ..+...|..|++|--
T Consensus 66 kav~V~CP~C~K~TKmLGr~D~CM~C~~pLT 96 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVDACMHCKEPLT 96 (114)
T ss_pred cceeeECCCCCChHhhhchhhccCcCCCcCc
Confidence 34455799998877 778889999999854
No 42
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=32.15 E-value=38 Score=19.21 Aligned_cols=10 Identities=40% Similarity=1.491 Sum_probs=8.3
Q ss_pred CCeeccccCc
Q 032350 19 GDWMCAACQH 28 (142)
Q Consensus 19 gdW~C~~C~~ 28 (142)
|.|.|..|+.
T Consensus 24 G~~~C~~Cg~ 33 (37)
T smart00778 24 GTWFCSVCGA 33 (37)
T ss_pred cCEEeCCCCC
Confidence 8899988864
No 43
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.86 E-value=25 Score=22.65 Aligned_cols=15 Identities=33% Similarity=0.961 Sum_probs=11.1
Q ss_pred CCcccCCCCCCCeecCC
Q 032350 63 GDWYCTAMNCGAHNYAS 79 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~ 79 (142)
+-|.|+ .|+++||.-
T Consensus 3 ~~~kCp--KCgn~~~~e 17 (68)
T COG3478 3 NAFKCP--KCGNTNYEE 17 (68)
T ss_pred ccccCC--CcCCcchhh
Confidence 457788 888888843
No 44
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=31.26 E-value=60 Score=28.29 Aligned_cols=44 Identities=18% Similarity=0.394 Sum_probs=23.7
Q ss_pred CCCeeccccCccccccccccccCCCCCCCCCCCcccccccccccCCCcccCCCCCCC
Q 032350 18 GGDWMCAACQHQNFKKREACQRCGYPKYGGPDVSTYLCNRTEVLAGDWYCTAMNCGA 74 (142)
Q Consensus 18 ~gdW~C~~C~~~Nf~~r~~C~~C~~prp~~~~~~~~~~~~~~~~~gdW~C~~~~C~~ 74 (142)
...|.|..|++.=-... +-|..+- .++ -.+..-+.||.|| .|+.
T Consensus 423 ~~~~~c~~c~~~yd~~~------g~~~~~~-~~g----t~~~~lp~~~~cp--~c~~ 466 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAK------GEPMQDV-APG----TPWSEVPDNFLCP--ECSL 466 (479)
T ss_pred CCeEEECCCCeEECCCC------CCcccCC-CCC----CChhhCCCCCcCc--CCCC
Confidence 45788888886633211 1111110 111 2466678899999 5553
No 45
>PHA00626 hypothetical protein
Probab=30.72 E-value=39 Score=21.22 Aligned_cols=11 Identities=36% Similarity=1.153 Sum_probs=7.4
Q ss_pred CCcccCCCCCCCe
Q 032350 63 GDWYCTAMNCGAH 75 (142)
Q Consensus 63 gdW~C~~~~C~~~ 75 (142)
+.+.|+ .|++.
T Consensus 22 nrYkCk--dCGY~ 32 (59)
T PHA00626 22 DDYVCC--DCGYN 32 (59)
T ss_pred cceEcC--CCCCe
Confidence 467777 77764
No 46
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.06 E-value=37 Score=24.66 Aligned_cols=23 Identities=30% Similarity=0.930 Sum_probs=21.4
Q ss_pred ccCCCCCCCeecCCCcCccccCCCC
Q 032350 66 YCTAMNCGAHNYASRPNCYRCGAAK 90 (142)
Q Consensus 66 ~C~~~~C~~~N~~~r~~C~~C~~~~ 90 (142)
.|. .||..=|+-+..|..|+++-
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 47
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=29.36 E-value=39 Score=27.25 Aligned_cols=28 Identities=14% Similarity=0.259 Sum_probs=24.5
Q ss_pred CCCeeccccCccccccccccccCCCCCC
Q 032350 18 GGDWMCAACQHQNFKKREACQRCGYPKY 45 (142)
Q Consensus 18 ~gdW~C~~C~~~Nf~~r~~C~~C~~prp 45 (142)
.-+|.|.+|++.--...-.|..|++.-.
T Consensus 352 ~p~~~c~~cg~~~~~~~~~c~~c~~~~~ 379 (389)
T PRK11788 352 KPRYRCRNCGFTARTLYWHCPSCKAWET 379 (389)
T ss_pred CCCEECCCCCCCCccceeECcCCCCccC
Confidence 5679999999999999999999998643
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=28.90 E-value=34 Score=19.49 Aligned_cols=12 Identities=33% Similarity=1.121 Sum_probs=6.9
Q ss_pred CCCeeecCCCCCce
Q 032350 113 SGDWICNRMGCGVH 126 (142)
Q Consensus 113 ~gdW~C~~~~C~~~ 126 (142)
.|+..|+ .|+.+
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 4667777 47654
No 49
>PF12523 DUF3725: Protein of unknown function (DUF3725); InterPro: IPR022199 This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with PF01577 from PFAM. There is a conserved FLE sequence motif.
Probab=28.20 E-value=30 Score=22.52 Aligned_cols=27 Identities=15% Similarity=0.465 Sum_probs=20.5
Q ss_pred hhhhcCCCCCCCCCCeeccccCccccc
Q 032350 6 RVICQDKKMSLPGGDWMCAACQHQNFK 32 (142)
Q Consensus 6 ~~~~~~~~~~~~~gdW~C~~C~~~Nf~ 32 (142)
..++++..-.....+|.|..|++.|-.
T Consensus 45 ktmvg~LgYdfe~Elw~Ch~C~~ts~k 71 (74)
T PF12523_consen 45 KTMVGRLGYDFESELWECHSCDNTSTK 71 (74)
T ss_pred HHHHHHhcCCCccceEEeecCCCchhh
Confidence 456667777777899999999887643
No 50
>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=28.06 E-value=29 Score=19.06 Aligned_cols=8 Identities=38% Similarity=1.028 Sum_probs=4.3
Q ss_pred ccCCCCCCCe
Q 032350 66 YCTAMNCGAH 75 (142)
Q Consensus 66 ~C~~~~C~~~ 75 (142)
.|+ .|+..
T Consensus 27 ~C~--~C~~~ 34 (38)
T TIGR02098 27 RCG--KCGHV 34 (38)
T ss_pred ECC--CCCCE
Confidence 455 55544
No 51
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=26.28 E-value=47 Score=19.16 Aligned_cols=9 Identities=33% Similarity=0.755 Sum_probs=4.1
Q ss_pred cCccccCCC
Q 032350 81 PNCYRCGAA 89 (142)
Q Consensus 81 ~~C~~C~~~ 89 (142)
..|+.||.+
T Consensus 22 ~~Cp~CG~~ 30 (46)
T PRK00398 22 VRCPYCGYR 30 (46)
T ss_pred eECCCCCCe
Confidence 344455443
No 52
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.66 E-value=34 Score=24.30 Aligned_cols=22 Identities=27% Similarity=0.673 Sum_probs=19.8
Q ss_pred ccccCccccccccccccCCCCC
Q 032350 23 CAACQHQNFKKREACQRCGYPK 44 (142)
Q Consensus 23 C~~C~~~Nf~~r~~C~~C~~pr 44 (142)
||.|+..=-+.+..|..|++.=
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 8999999999999999999854
No 53
>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=25.35 E-value=57 Score=28.65 Aligned_cols=24 Identities=25% Similarity=0.685 Sum_probs=13.5
Q ss_pred CcccCCCCCCCeecCCCcCccccCCCC
Q 032350 64 DWYCTAMNCGAHNYASRPNCYRCGAAK 90 (142)
Q Consensus 64 dW~C~~~~C~~~N~~~r~~C~~C~~~~ 90 (142)
.=.|. .||+. ..--..|+.|+...
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 22335677776653
No 54
>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=20.95 E-value=91 Score=17.01 Aligned_cols=6 Identities=50% Similarity=1.088 Sum_probs=2.5
Q ss_pred CCCCee
Q 032350 71 NCGAHN 76 (142)
Q Consensus 71 ~C~~~N 76 (142)
.|+..|
T Consensus 5 ~Cg~~~ 10 (32)
T PF03604_consen 5 ECGAEV 10 (32)
T ss_dssp SSSSSE
T ss_pred cCCCee
Confidence 444443
No 55
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.81 E-value=82 Score=27.15 Aligned_cols=34 Identities=15% Similarity=0.288 Sum_probs=0.0
Q ss_pred cCCCCCCCCCCee-ccccCccccccccccccCCCC
Q 032350 10 QDKKMSLPGGDWM-CAACQHQNFKKREACQRCGYP 43 (142)
Q Consensus 10 ~~~~~~~~~gdW~-C~~C~~~Nf~~r~~C~~C~~p 43 (142)
++........+.. |+.|+......+..|.||++.
T Consensus 210 ~~~~~~~~~~~l~~C~~Cd~l~~~~~a~CpRC~~~ 244 (419)
T PRK15103 210 LKPGVTGLRQGLRSCSCCTAILPADQPVCPRCHTK 244 (419)
T ss_pred ccccCCccccCCCcCCCCCCCCCCCCCCCCCCCCc
No 56
>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=20.52 E-value=75 Score=19.52 Aligned_cols=26 Identities=27% Similarity=0.646 Sum_probs=16.7
Q ss_pred CCcccCCCCCCCeecCCCcCccc--cCCCC
Q 032350 63 GDWYCTAMNCGAHNYASRPNCYR--CGAAK 90 (142)
Q Consensus 63 gdW~C~~~~C~~~N~~~r~~C~~--C~~~~ 90 (142)
+.-+|- .|..+|-.+++.|.+ ||...
T Consensus 16 ~k~ICr--kCyarl~~~A~nCRKkkCGhsn 43 (52)
T PF01020_consen 16 DKMICR--KCYARLPPRATNCRKKKCGHSN 43 (52)
T ss_dssp S-EEET--TT--EE-TTSSS-TSSSCTS-S
T ss_pred cceecc--cccCcCCCCccceecccCCCCc
Confidence 456888 999999999999998 87543
No 57
>PRK11823 DNA repair protein RadA; Provisional
Probab=20.32 E-value=82 Score=27.19 Aligned_cols=28 Identities=21% Similarity=0.484 Sum_probs=22.8
Q ss_pred CCCeeccccCccccccccccccCCCCCC
Q 032350 18 GGDWMCAACQHQNFKKREACQRCGYPKY 45 (142)
Q Consensus 18 ~gdW~C~~C~~~Nf~~r~~C~~C~~prp 45 (142)
.-.+.|..|++.-..+.-+|..|++-..
T Consensus 5 ~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (446)
T PRK11823 5 KTAYVCQECGAESPKWLGRCPECGAWNT 32 (446)
T ss_pred CCeEECCcCCCCCcccCeeCcCCCCccc
Confidence 4568999999998888888998887554
No 58
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.30 E-value=64 Score=26.02 Aligned_cols=30 Identities=27% Similarity=0.430 Sum_probs=25.0
Q ss_pred ccCCCcccCCCCCCCeecCCCcCccccCCCCC
Q 032350 60 VLAGDWYCTAMNCGAHNYASRPNCYRCGAAKT 91 (142)
Q Consensus 60 ~~~gdW~C~~~~C~~~N~~~r~~C~~C~~~~~ 91 (142)
...-+|.|. .||+.=-..--.|+.|++--.
T Consensus 350 ~~~p~~~c~--~cg~~~~~~~~~c~~c~~~~~ 379 (389)
T PRK11788 350 KRKPRYRCR--NCGFTARTLYWHCPSCKAWET 379 (389)
T ss_pred hCCCCEECC--CCCCCCccceeECcCCCCccC
Confidence 445579999 999999999999999987643
Done!