Query 031858
Match_columns 151
No_of_seqs 189 out of 771
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:20:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031858.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031858hhsearch_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 99.8 9.8E-19 2.1E-23 142.8 7.9 142 1-146 3-167 (280)
2 KOG4198 RNA-binding Ran Zn-fin 99.7 5.6E-18 1.2E-22 138.3 7.7 142 2-147 60-271 (280)
3 KOG1995 Conserved Zn-finger pr 99.2 1.7E-11 3.6E-16 102.6 4.7 139 3-147 68-247 (351)
4 PF00641 zf-RanBP: Zn-finger i 98.9 7.2E-10 1.6E-14 61.9 2.1 29 3-31 1-29 (30)
5 PF00641 zf-RanBP: Zn-finger i 98.7 6E-09 1.3E-13 58.1 1.9 30 114-145 1-30 (30)
6 smart00547 ZnF_RBZ Zinc finger 98.4 1.2E-07 2.6E-12 51.0 1.4 25 5-29 1-25 (26)
7 smart00547 ZnF_RBZ Zinc finger 98.3 2.6E-07 5.7E-12 49.6 1.2 26 116-143 1-26 (26)
8 KOG1995 Conserved Zn-finger pr 98.3 2.8E-06 6E-11 71.5 7.3 35 53-88 212-246 (351)
9 PF12773 DZR: Double zinc ribb 95.4 0.019 4E-07 34.9 3.0 50 9-82 1-50 (50)
10 PF12773 DZR: Double zinc ribb 92.6 0.14 3E-06 31.0 2.7 48 66-140 3-50 (50)
11 KOG4477 RING1 interactor RYBP 92.4 0.054 1.2E-06 42.4 0.9 29 4-32 22-50 (228)
12 PRK14559 putative protein seri 91.5 0.18 4E-06 46.3 3.4 50 8-86 3-52 (645)
13 PF13248 zf-ribbon_3: zinc-rib 89.6 0.17 3.7E-06 26.9 0.9 23 7-29 3-25 (26)
14 KOG4477 RING1 interactor RYBP 88.7 0.24 5.1E-06 38.9 1.5 34 111-146 18-51 (228)
15 PF13240 zinc_ribbon_2: zinc-r 88.5 0.25 5.4E-06 25.7 1.0 21 9-29 2-22 (23)
16 PRK14559 putative protein seri 85.0 0.89 1.9E-05 41.9 3.3 50 61-144 3-52 (645)
17 cd00729 rubredoxin_SM Rubredox 84.3 0.81 1.7E-05 25.9 1.8 25 6-30 2-28 (34)
18 cd00350 rubredoxin_like Rubred 84.0 0.84 1.8E-05 25.5 1.7 26 6-31 1-28 (33)
19 KOG4345 NF-kappa B regulator A 82.8 0.39 8.4E-06 44.3 0.0 139 1-145 1-211 (774)
20 PRK04136 rpl40e 50S ribosomal 75.4 1.5 3.2E-05 27.0 0.9 23 6-28 14-36 (48)
21 PRK14714 DNA polymerase II lar 66.2 6.7 0.00014 38.9 3.5 52 7-88 668-722 (1337)
22 PF10571 UPF0547: Uncharacteri 60.9 4.9 0.00011 21.4 1.0 21 8-28 2-22 (26)
23 COG1552 RPL40A Ribosomal prote 59.9 1.7 3.7E-05 26.8 -1.0 21 8-28 16-36 (50)
24 PRK04136 rpl40e 50S ribosomal 57.9 5.9 0.00013 24.3 1.1 24 58-83 13-36 (48)
25 PRK14714 DNA polymerase II lar 42.3 32 0.00069 34.4 3.9 54 58-146 666-722 (1337)
26 PF12172 DUF35_N: Rubredoxin-l 39.6 14 0.00031 20.7 0.7 22 61-84 13-34 (37)
27 cd04718 BAH_plant_2 BAH, or Br 38.1 14 0.00031 27.9 0.7 17 4-20 16-32 (148)
28 PF00301 Rubredoxin: Rubredoxi 35.1 19 0.00042 21.8 0.8 17 51-69 26-42 (47)
29 PRK13130 H/ACA RNA-protein com 33.9 57 0.0012 20.6 2.8 26 61-90 7-32 (56)
30 PF09862 DUF2089: Protein of u 28.7 28 0.0006 25.1 0.9 21 9-29 1-21 (113)
31 COG1592 Rubrerythrin [Energy p 27.4 36 0.00077 26.2 1.3 26 59-86 134-160 (166)
32 TIGR02098 MJ0042_CXXC MJ0042 f 25.8 32 0.0007 19.2 0.6 21 8-28 4-33 (38)
33 COG1066 Sms Predicted ATP-depe 24.7 55 0.0012 29.1 2.1 30 1-30 1-31 (456)
34 PRK00415 rps27e 30S ribosomal 23.8 48 0.001 21.2 1.2 25 6-30 11-40 (59)
35 cd00730 rubredoxin Rubredoxin; 23.7 47 0.001 20.4 1.1 17 51-69 26-42 (50)
36 PRK00398 rpoP DNA-directed RNA 22.9 56 0.0012 19.1 1.3 25 7-31 4-32 (46)
37 COG3478 Predicted nucleic-acid 22.0 50 0.0011 21.6 1.1 14 58-73 3-16 (68)
38 PRK04023 DNA polymerase II lar 21.7 1.2E+02 0.0026 30.0 3.8 27 59-89 651-677 (1121)
39 PF01020 Ribosomal_L40e: Ribos 20.9 68 0.0015 20.0 1.4 22 7-28 18-41 (52)
40 PF03604 DNA_RNApol_7kD: DNA d 20.8 88 0.0019 17.3 1.8 20 8-27 2-24 (32)
41 PF14446 Prok-RING_1: Prokaryo 20.2 50 0.0011 20.7 0.7 24 8-31 7-32 (54)
42 PRK00420 hypothetical protein; 20.1 59 0.0013 23.4 1.2 24 8-31 25-51 (112)
No 1
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=99.77 E-value=9.8e-19 Score=142.75 Aligned_cols=142 Identities=39% Similarity=0.686 Sum_probs=98.5
Q ss_pred CCCCC-CeEeCCCCcccccccccccccCCCCCCCCC--CCCCCCCCCCCcCcCCCCCCCCCCcccCCCCCCCcccccccc
Q 031858 1 MNRPG-DWNCRSCQHLNFQRRDSCQRCGDPRSSGDF--CGFGGRGGGSSFGFGTGSDVRPGDWYCSAGNCGAHNFASRSS 77 (151)
Q Consensus 1 ~~k~g-dW~C~~C~~~N~~~~~~C~~C~~pkp~~~~--~~~~g~~~~~~~g~~~~~~~~~gdW~C~~~~C~~~N~a~r~~ 77 (151)
|.++| ||.|..|..+||..+..|-+|..+++.... -++++....-.+.+.....+++|||+|+ .|+++||++|+.
T Consensus 3 ~~r~g~~~~~~~~~~~~~~~~~~c~~c~~~~~~i~~~~~~~~tid~~~~~~~~~~~~~~pgdw~c~--~c~~~n~arr~~ 80 (280)
T KOG4198|consen 3 MFRKGVDSLKRLCLHVNFDERDSCGRCSLSRAYIQPDDDEARTIDVMRLLLTNSKDPPRPGDWNCP--LCGFHNSARRLL 80 (280)
T ss_pred cccccCCcccchhhhhccccccccccccCCcccccccccccCccchhhhcccccCCCCCCcccccC--ccchhhHHHhhh
Confidence 66788 999999999999999999999999943100 0122211111112334567899999999 699999999999
Q ss_pred ccccCCCCCCCCCCC---CC--CCCCC-----------CccCC--CCC--CCCCCCCCCceEEeCCCCCccccccccccc
Q 031858 78 CFKCGAFKDDVAGGG---FD--CDMPR-----------SRGSS--FGG--GNRSGWKSGDWICTRSGCNEHNFASRMECF 137 (151)
Q Consensus 78 C~~C~~~~~~~~~~~---~~--~~~~~-----------~~~~g--~~~--~~~~~~~~gdW~C~~~~C~~~Nfa~r~~C~ 137 (151)
|++|+.++++..... .. ..... +...+ ++. .....+++|||+|+ .|++|||+++.+|+
T Consensus 81 c~~c~~s~~~~~~~~~~~~~g~~~~~~~~r~~~~~~~~~~~~g~~~~~n~~~~r~~~~GDW~Cp--~C~fhNfarn~~C~ 158 (280)
T KOG4198|consen 81 CFRCGFSKVPLDSALTAPNSGSRSLQTGPRYFKGDWLCPRCPGLGFSRNNKPKRPWRSGDWECP--GCNFHNFARNSECF 158 (280)
T ss_pred cceecccCCCccccccCCCCcccccccccccccCCCCCCCCCCCcccccccccCCccccCcccC--CCCceeccccchhh
Confidence 999999887554310 00 00000 00000 000 01125799999999 99999999999999
Q ss_pred CCCCCCCCC
Q 031858 138 RCNAPRDFG 146 (151)
Q Consensus 138 ~C~~pk~~~ 146 (151)
+|+++++..
T Consensus 159 rC~~~r~~~ 167 (280)
T KOG4198|consen 159 RCGAKRPLA 167 (280)
T ss_pred hcCCcCccc
Confidence 999999974
No 2
>KOG4198 consensus RNA-binding Ran Zn-finger protein and related proteins [General function prediction only]
Probab=99.73 E-value=5.6e-18 Score=138.32 Aligned_cols=142 Identities=37% Similarity=0.770 Sum_probs=97.2
Q ss_pred CCCCCeEeCCCCcccccccccccccCCCCCCCCCC------C----------C-CCCCCCCCcCcC------CCCCCCCC
Q 031858 2 NRPGDWNCRSCQHLNFQRRDSCQRCGDPRSSGDFC------G----------F-GGRGGGSSFGFG------TGSDVRPG 58 (151)
Q Consensus 2 ~k~gdW~C~~C~~~N~~~~~~C~~C~~pkp~~~~~------~----------~-~g~~~~~~~g~~------~~~~~~~g 58 (151)
.++|||.|+.|+++||++|+.|++|+.+++..+.+ + + ++.......|.+ ...+.++|
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 47899999999999999999999999988754221 0 0 000001111111 01257999
Q ss_pred CcccCCCCCCCccccccccccccCCCCCCCCC----------CCCCCCCCCC-----------------------cc---
Q 031858 59 DWYCSAGNCGAHNFASRSSCFKCGAFKDDVAG----------GGFDCDMPRS-----------------------RG--- 102 (151)
Q Consensus 59 dW~C~~~~C~~~N~a~r~~C~~C~~~~~~~~~----------~~~~~~~~~~-----------------------~~--- 102 (151)
||+|+ .|++|||+++.+|++|+++++.... +.+.+..... .+
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 9999999999999999999986441 1111000000 00
Q ss_pred C-CCC----------CCCCCCCCCCceEEeCCCCCcccccccccccCCCCCCCCCC
Q 031858 103 S-SFG----------GGNRSGWKSGDWICTRSGCNEHNFASRMECFRCNAPRDFGN 147 (151)
Q Consensus 103 ~-g~~----------~~~~~~~~~gdW~C~~~~C~~~Nfa~r~~C~~C~~pk~~~~ 147 (151)
. .|. .......+.|||.|. .|.++||.+|.+|.+|..+++.-.
T Consensus 218 ~~~~~~~~e~~~~~~sr~s~~~~dgdw~~~--s~~~~~~r~r~a~~~c~~~~~~~~ 271 (280)
T KOG4198|consen 218 KGNFSSDDESRLEPLSRGSKSSRDGDWMCE--SCKAENFRRRNACLKCISPRGSFD 271 (280)
T ss_pred cccccccccccccccccCcccccCCCcccc--cccchhhhhhhhhhccccCccccc
Confidence 0 010 123456789999999 899999999999999998887543
No 3
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=99.19 E-value=1.7e-11 Score=102.57 Aligned_cols=139 Identities=24% Similarity=0.329 Sum_probs=85.4
Q ss_pred CCCCeEeC--CCCcccccccccccccCCCCCCCCCCCCCCCCCCCCcCcCCCCCCCCCCcccCCCCCCCccccccccccc
Q 031858 3 RPGDWNCR--SCQHLNFQRRDSCQRCGDPRSSGDFCGFGGRGGGSSFGFGTGSDVRPGDWYCSAGNCGAHNFASRSSCFK 80 (151)
Q Consensus 3 k~gdW~C~--~C~~~N~~~~~~C~~C~~pkp~~~~~~~~g~~~~~~~g~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~ 80 (151)
..++|+|+ +|.+.||.+.++|..|+..|.+..+..+....-. .........+...||.|. .|.+.+|+.+..|.
T Consensus 68 ti~v~g~~d~~~~~~~~~~f~qcg~ikrnK~t~kPki~~y~dke-T~~~KGeatvS~~D~~~a--kaai~~~agkdf~g- 143 (351)
T KOG1995|consen 68 TIFVWGCPDSVCENDNADFFLQCGVIKRNKRTGKPKIKIYTDKE-TGAPKGEATVSYEDPPAA--KAAIEWFAGKDFCG- 143 (351)
T ss_pred cceeeccCccchHHHHHHHHhhcceeccCCCCCCcchhcccccc-ccCcCCceeeeecChhhh--hhhhhhhccccccC-
Confidence 35799998 8999999999999999999987533211110000 000001133455678887 77888887777776
Q ss_pred cCCCCCCCCC--C-------CCC----CCC-C---------CCccCCCC----------------CCCCCCCCCCceEEe
Q 031858 81 CGAFKDDVAG--G-------GFD----CDM-P---------RSRGSSFG----------------GGNRSGWKSGDWICT 121 (151)
Q Consensus 81 C~~~~~~~~~--~-------~~~----~~~-~---------~~~~~g~~----------------~~~~~~~~~gdW~C~ 121 (151)
++++-.... + ++. +.. . ...+.+++ ++..+..+.+||.|+
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 333321100 0 010 000 0 00000011 122345788999999
Q ss_pred CCCCCcccccccccccCCCCCCCCCC
Q 031858 122 RSGCNEHNFASRMECFRCNAPRDFGN 147 (151)
Q Consensus 122 ~~~C~~~Nfa~r~~C~~C~~pk~~~~ 147 (151)
|.|.+.||++|..|++|+++||...
T Consensus 223 -~~c~N~nfa~r~~cnrck~~Kp~~~ 247 (351)
T KOG1995|consen 223 -PSCGNRNFAWREECNRCKAPKPERS 247 (351)
T ss_pred -ccccccccccccccccccCCCcccc
Confidence 8999999999999999999998653
No 4
>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=98.91 E-value=7.2e-10 Score=61.91 Aligned_cols=29 Identities=45% Similarity=1.151 Sum_probs=24.4
Q ss_pred CCCCeEeCCCCcccccccccccccCCCCC
Q 031858 3 RPGDWNCRSCQHLNFQRRDSCQRCGDPRS 31 (151)
Q Consensus 3 k~gdW~C~~C~~~N~~~~~~C~~C~~pkp 31 (151)
|+|+|.|+.|.++|++++..|.+|+++||
T Consensus 1 k~g~W~C~~C~~~N~~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 1 KEGDWKCPSCTFMNPASRSKCVACGAPRP 29 (30)
T ss_dssp -SSSEEETTTTEEEESSSSB-TTT--BTT
T ss_pred CCcCccCCCCcCCchHHhhhhhCcCCCCc
Confidence 68999999999999999999999999997
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=98.72 E-value=6e-09 Score=58.14 Aligned_cols=30 Identities=50% Similarity=0.959 Sum_probs=24.5
Q ss_pred CCCceEEeCCCCCcccccccccccCCCCCCCC
Q 031858 114 KSGDWICTRSGCNEHNFASRMECFRCNAPRDF 145 (151)
Q Consensus 114 ~~gdW~C~~~~C~~~Nfa~r~~C~~C~~pk~~ 145 (151)
++|+|.|+ .|.++|++++..|++|+++||.
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 8999999999999999999984
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=98.40 E-value=1.2e-07 Score=51.01 Aligned_cols=25 Identities=52% Similarity=1.370 Sum_probs=24.1
Q ss_pred CCeEeCCCCcccccccccccccCCC
Q 031858 5 GDWNCRSCQHLNFQRRDSCQRCGDP 29 (151)
Q Consensus 5 gdW~C~~C~~~N~~~~~~C~~C~~p 29 (151)
|||.|+.|.++|++++..|..|++|
T Consensus 1 g~W~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 1 GDWECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred CcccCCCCCCcChhhhccccccCCc
Confidence 7999999999999999999999987
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=98.30 E-value=2.6e-07 Score=49.63 Aligned_cols=26 Identities=58% Similarity=1.287 Sum_probs=24.3
Q ss_pred CceEEeCCCCCcccccccccccCCCCCC
Q 031858 116 GDWICTRSGCNEHNFASRMECFRCNAPR 143 (151)
Q Consensus 116 gdW~C~~~~C~~~Nfa~r~~C~~C~~pk 143 (151)
|||+|+ .|+++||+.+..|++|++|.
T Consensus 1 g~W~C~--~C~~~N~~~~~~C~~C~~p~ 26 (26)
T smart00547 1 GDWECP--ACTFLNFASRSKCFACGAPX 26 (26)
T ss_pred CcccCC--CCCCcChhhhccccccCCcC
Confidence 689999 89999999999999999873
No 8
>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]
Probab=98.27 E-value=2.8e-06 Score=71.54 Aligned_cols=35 Identities=40% Similarity=0.831 Sum_probs=31.9
Q ss_pred CCCCCCCcccCCCCCCCccccccccccccCCCCCCC
Q 031858 53 SDVRPGDWYCSAGNCGAHNFASRSSCFKCGAFKDDV 88 (151)
Q Consensus 53 ~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~~~~~ 88 (151)
.+.+++||.|+ +.|.++||++|.+|++|+++||..
T Consensus 212 ~~~~d~Dw~c~-~~c~N~nfa~r~~cnrck~~Kp~~ 246 (351)
T KOG1995|consen 212 VQDEDGDWDCP-PSCGNRNFAWREECNRCKAPKPER 246 (351)
T ss_pred ccccccccccc-ccccccccccccccccccCCCccc
Confidence 34688999999 999999999999999999999865
No 9
>PF12773 DZR: Double zinc ribbon
Probab=95.43 E-value=0.019 Score=34.93 Aligned_cols=50 Identities=32% Similarity=0.718 Sum_probs=41.6
Q ss_pred eCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCcCcCCCCCCCCCCcccCCCCCCCccccccccccccC
Q 031858 9 CRSCQHLNFQRRDSCQRCGDPRSSGDFCGFGGRGGGSSFGFGTGSDVRPGDWYCSAGNCGAHNFASRSSCFKCG 82 (151)
Q Consensus 9 C~~C~~~N~~~~~~C~~C~~pkp~~~~~~~~g~~~~~~~g~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~ 82 (151)
|+.|+..|-.....|..|+++-+. .....+.|+ .|+..|......|..|+
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 789999999999999999987651 112367898 99999999999999885
No 10
>PF12773 DZR: Double zinc ribbon
Probab=92.59 E-value=0.14 Score=31.00 Aligned_cols=48 Identities=25% Similarity=0.523 Sum_probs=39.3
Q ss_pred CCCCccccccccccccCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCceEEeCCCCCcccccccccccCCC
Q 031858 66 NCGAHNFASRSSCFKCGAFKDDVAGGGFDCDMPRSRGSSFGGGNRSGWKSGDWICTRSGCNEHNFASRMECFRCN 140 (151)
Q Consensus 66 ~C~~~N~a~r~~C~~C~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~Nfa~r~~C~~C~ 140 (151)
.|+..+-.....|..|+++.+.. ....+.|+ .|+..|......|..|+
T Consensus 3 ~Cg~~~~~~~~fC~~CG~~l~~~-------------------------~~~~~~C~--~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 3 HCGTPNPDDAKFCPHCGTPLPPP-------------------------DQSKKICP--NCGAENPPNAKFCPNCG 50 (50)
T ss_pred CcCCcCCccccCChhhcCChhhc-------------------------cCCCCCCc--CCcCCCcCCcCccCccc
Confidence 89999999999999999887511 12346899 89999999999999885
No 11
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=92.44 E-value=0.054 Score=42.42 Aligned_cols=29 Identities=24% Similarity=0.667 Sum_probs=25.7
Q ss_pred CCCeEeCCCCcccccccccccccCCCCCC
Q 031858 4 PGDWNCRSCQHLNFQRRDSCQRCGDPRSS 32 (151)
Q Consensus 4 ~gdW~C~~C~~~N~~~~~~C~~C~~pkp~ 32 (151)
.|-|+|..|.|+|-+-..+|+.|..-|..
T Consensus 22 eg~WdCsvCTFrNsAeAfkC~vCdvRKGT 50 (228)
T KOG4477|consen 22 EGKWDCSVCTFRNSAEAFKCFVCDVRKGT 50 (228)
T ss_pred cCceeeeeeeecchhhhhheeeecccccc
Confidence 46899999999999999999999986643
No 12
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=91.53 E-value=0.18 Score=46.26 Aligned_cols=50 Identities=30% Similarity=0.697 Sum_probs=42.8
Q ss_pred EeCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCcCcCCCCCCCCCCcccCCCCCCCccccccccccccCCCCC
Q 031858 8 NCRSCQHLNFQRRDSCQRCGDPRSSGDFCGFGGRGGGSSFGFGTGSDVRPGDWYCSAGNCGAHNFASRSSCFKCGAFKD 86 (151)
Q Consensus 8 ~C~~C~~~N~~~~~~C~~C~~pkp~~~~~~~~g~~~~~~~g~~~~~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~~~ 86 (151)
.||.|+..|-....+|.+|+++-.. + .|+ .|+..+-.....|..|+++-.
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 6999999999999999999876321 0 488 999999999999999998854
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.59 E-value=0.17 Score=26.91 Aligned_cols=23 Identities=22% Similarity=0.471 Sum_probs=20.7
Q ss_pred eEeCCCCcccccccccccccCCC
Q 031858 7 WNCRSCQHLNFQRRDSCQRCGDP 29 (151)
Q Consensus 7 W~C~~C~~~N~~~~~~C~~C~~p 29 (151)
..|+.|+..+......|..|+++
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCcccccChhhCCC
Confidence 57999999999999999999975
No 14
>KOG4477 consensus RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription]
Probab=88.75 E-value=0.24 Score=38.91 Aligned_cols=34 Identities=26% Similarity=0.671 Sum_probs=29.3
Q ss_pred CCCCCCceEEeCCCCCcccccccccccCCCCCCCCC
Q 031858 111 SGWKSGDWICTRSGCNEHNFASRMECFRCNAPRDFG 146 (151)
Q Consensus 111 ~~~~~gdW~C~~~~C~~~Nfa~r~~C~~C~~pk~~~ 146 (151)
.....|-|.|. .|.++|-|-...|+.|...+..+
T Consensus 18 p~~Deg~WdCs--vCTFrNsAeAfkC~vCdvRKGTS 51 (228)
T KOG4477|consen 18 PNDDEGKWDCS--VCTFRNSAEAFKCFVCDVRKGTS 51 (228)
T ss_pred CccccCceeee--eeeecchhhhhheeeeccccccc
Confidence 34567889999 89999999999999998887765
No 15
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=88.50 E-value=0.25 Score=25.68 Aligned_cols=21 Identities=29% Similarity=0.741 Sum_probs=19.3
Q ss_pred eCCCCcccccccccccccCCC
Q 031858 9 CRSCQHLNFQRRDSCQRCGDP 29 (151)
Q Consensus 9 C~~C~~~N~~~~~~C~~C~~p 29 (151)
|+.|+..+......|..|+++
T Consensus 2 Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCcchhhhCCc
Confidence 899999999999999999975
No 16
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=85.01 E-value=0.89 Score=41.88 Aligned_cols=50 Identities=26% Similarity=0.564 Sum_probs=41.8
Q ss_pred ccCCCCCCCccccccccccccCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCceEEeCCCCCcccccccccccCCC
Q 031858 61 YCSAGNCGAHNFASRSSCFKCGAFKDDVAGGGFDCDMPRSRGSSFGGGNRSGWKSGDWICTRSGCNEHNFASRMECFRCN 140 (151)
Q Consensus 61 ~C~~~~C~~~N~a~r~~C~~C~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~Nfa~r~~C~~C~ 140 (151)
.|+ .|+..|-.....|.+|+++-.. + .|+ .|+..|-.....|..|+
T Consensus 3 ~Cp--~Cg~~n~~~akFC~~CG~~l~~--------------------------~----~Cp--~CG~~~~~~~~fC~~CG 48 (645)
T PRK14559 3 ICP--QCQFENPNNNRFCQKCGTSLTH--------------------------K----PCP--QCGTEVPVDEAHCPNCG 48 (645)
T ss_pred cCC--CCCCcCCCCCccccccCCCCCC--------------------------C----cCC--CCCCCCCcccccccccC
Confidence 587 9999999999999999876420 1 599 89999999999999998
Q ss_pred CCCC
Q 031858 141 APRD 144 (151)
Q Consensus 141 ~pk~ 144 (151)
++-.
T Consensus 49 ~~~~ 52 (645)
T PRK14559 49 AETG 52 (645)
T ss_pred Cccc
Confidence 8754
No 17
>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=84.34 E-value=0.81 Score=25.91 Aligned_cols=25 Identities=28% Similarity=0.872 Sum_probs=20.2
Q ss_pred CeEeCCCCcccccc--cccccccCCCC
Q 031858 6 DWNCRSCQHLNFQR--RDSCQRCGDPR 30 (151)
Q Consensus 6 dW~C~~C~~~N~~~--~~~C~~C~~pk 30 (151)
.|.|..|+++-... ...|..|++++
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~~ 28 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAPK 28 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCch
Confidence 49999999985543 47899999876
No 18
>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=83.97 E-value=0.84 Score=25.52 Aligned_cols=26 Identities=23% Similarity=0.608 Sum_probs=20.1
Q ss_pred CeEeCCCCcccccc--cccccccCCCCC
Q 031858 6 DWNCRSCQHLNFQR--RDSCQRCGDPRS 31 (151)
Q Consensus 6 dW~C~~C~~~N~~~--~~~C~~C~~pkp 31 (151)
.|.|..|+++-... ...|..|++++.
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~~~ 28 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAPKD 28 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCcHH
Confidence 49999999985544 567999998763
No 19
>KOG4345 consensus NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms]
Probab=82.81 E-value=0.39 Score=44.31 Aligned_cols=139 Identities=14% Similarity=0.162 Sum_probs=84.3
Q ss_pred CCCCC-CeEeCCCCcccccccccccccCCCCCCC-----CCCCCCCCCC--------------------CCCc----CcC
Q 031858 1 MNRPG-DWNCRSCQHLNFQRRDSCQRCGDPRSSG-----DFCGFGGRGG--------------------GSSF----GFG 50 (151)
Q Consensus 1 ~~k~g-dW~C~~C~~~N~~~~~~C~~C~~pkp~~-----~~~~~~g~~~--------------------~~~~----g~~ 50 (151)
|+-.+ .|.|..|.+.|+....+|..|++.++.+ |+ |.+.++ ..++ .+.
T Consensus 1 ~~~~~~~W~~~~~~~~~lp~al~lS~~~~s~~~~~~l~eDi--fk~~n~~~~~~~sd~~~~r~v~~~~~~p~f~~s~~~r 78 (774)
T KOG4345|consen 1 MPTSAEKWACELCDYMTLPMALVLSDFRRSTGAEPGLAEDI--FKGKNWDIHAALSDYEQLRQVHEMNLTPSFCESGQPR 78 (774)
T ss_pred CcchhHHHHHHhhccccCchhhHHHHHHhccCCCCCcchhh--ccCCCccceeecccHHHHHhhhccCCCCcccccCCcc
Confidence 44444 6999999999999999999999988754 32 111110 0011 011
Q ss_pred ---CC-CCCCCCCcccCCCCCCCccccccccccccCCCCCCCCC--------CCCCCCCC--------CCcc-CCCCCCC
Q 031858 51 ---TG-SDVRPGDWYCSAGNCGAHNFASRSSCFKCGAFKDDVAG--------GGFDCDMP--------RSRG-SSFGGGN 109 (151)
Q Consensus 51 ---~~-~~~~~gdW~C~~~~C~~~N~a~r~~C~~C~~~~~~~~~--------~~~~~~~~--------~~~~-~g~~~~~ 109 (151)
.+ .......|.|+ .|...||++...|.+|-..+.+... ..+..++. +..+ ...+.++
T Consensus 79 ~~~~~s~~~~~~k~~~~--~~~~lnw~re~R~~~~ls~~gd~~~~~~q~pq~s~~~qs~~VaL~~~l~~~l~~~dt~~~N 156 (774)
T KOG4345|consen 79 EIIHKSLIDRNIKWPRP--SLQRLNWPREKRLSRGLSHAGDMPILAFQLPQLSVYEQSTPVALEKALFRLLPLADTGDGN 156 (774)
T ss_pred cccccccccccccCCch--HhhhhhHHHHHHHHHHhhccCCCccchhccchhhccccccchhhhhhhhhcccccccCCcc
Confidence 11 23456799999 9999999999999999665532211 00100000 0000 0000001
Q ss_pred --CCCC-------------------CCCceEEeCCCCCcccccccccccCCCCCCCC
Q 031858 110 --RSGW-------------------KSGDWICTRSGCNEHNFASRMECFRCNAPRDF 145 (151)
Q Consensus 110 --~~~~-------------------~~gdW~C~~~~C~~~Nfa~r~~C~~C~~pk~~ 145 (151)
.... =...|+|. .|.+.|+++-..|..|+++++.
T Consensus 157 ~l~w~~h~lvlqk~l~t~l~~~~~rw~~eW~~l--ik~ass~pr~~r~~~~~~~~~~ 211 (774)
T KOG4345|consen 157 CLMWGFHDLVLQKALYTGLCYGTERWNDEWTEL--IKLASSEPRMHRSGNGGTGGGV 211 (774)
T ss_pred chhhhhhhHHHHHHHHHhhchhhHHHHHHHHHH--HHhhcccchhhhcccCCCCCCc
Confidence 0000 12349999 8999999999999999888774
No 20
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=75.42 E-value=1.5 Score=26.98 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=21.5
Q ss_pred CeEeCCCCcccccccccccccCC
Q 031858 6 DWNCRSCQHLNFQRRDSCQRCGD 28 (151)
Q Consensus 6 dW~C~~C~~~N~~~~~~C~~C~~ 28 (151)
.++|-.|...|-.+.+.|.+|+.
T Consensus 14 k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 14 KKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred ccchhcccCCCCccccccccCCC
Confidence 57999999999999999999986
No 21
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=66.20 E-value=6.7 Score=38.89 Aligned_cols=52 Identities=25% Similarity=0.659 Sum_probs=37.0
Q ss_pred eEeCCCCcccccccccccccCCCCCCCCCCCCCCCCCCCCcCcCCCCCCCCCCcccCCCCCCCccccc---cccccccCC
Q 031858 7 WNCRSCQHLNFQRRDSCQRCGDPRSSGDFCGFGGRGGGSSFGFGTGSDVRPGDWYCSAGNCGAHNFAS---RSSCFKCGA 83 (151)
Q Consensus 7 W~C~~C~~~N~~~~~~C~~C~~pkp~~~~~~~~g~~~~~~~g~~~~~~~~~gdW~C~~~~C~~~N~a~---r~~C~~C~~ 83 (151)
=.||.|+...+.. .|..|+++... .+.|+ .|+...-.. ++.|..|+.
T Consensus 668 rkCPkCG~~t~~~--fCP~CGs~te~--------------------------vy~CP--sCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 668 RRCPSCGTETYEN--RCPDCGTHTEP--------------------------VYVCP--DCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred EECCCCCCccccc--cCcccCCcCCC--------------------------ceeCc--cCCCccCCCccccccCCCCCC
Confidence 5788898887753 88888876311 35788 898865333 678999998
Q ss_pred CCCCC
Q 031858 84 FKDDV 88 (151)
Q Consensus 84 ~~~~~ 88 (151)
+....
T Consensus 718 plv~~ 722 (1337)
T PRK14714 718 ELTPY 722 (1337)
T ss_pred ccccc
Confidence 86543
No 22
>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=60.91 E-value=4.9 Score=21.39 Aligned_cols=21 Identities=24% Similarity=0.604 Sum_probs=18.3
Q ss_pred EeCCCCcccccccccccccCC
Q 031858 8 NCRSCQHLNFQRRDSCQRCGD 28 (151)
Q Consensus 8 ~C~~C~~~N~~~~~~C~~C~~ 28 (151)
.||.|....-.+...|..|+-
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCC
Confidence 489999999999999999875
No 23
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=59.89 E-value=1.7 Score=26.82 Aligned_cols=21 Identities=38% Similarity=0.873 Sum_probs=19.0
Q ss_pred EeCCCCcccccccccccccCC
Q 031858 8 NCRSCQHLNFQRRDSCQRCGD 28 (151)
Q Consensus 8 ~C~~C~~~N~~~~~~C~~C~~ 28 (151)
+|-.|...|-...++|.+|+.
T Consensus 16 IC~rC~Arnp~~A~kCRkC~~ 36 (50)
T COG1552 16 ICRRCYARNPPRATKCRKCGY 36 (50)
T ss_pred HHHHhcCCCCcchhHHhhccC
Confidence 577899999999999999976
No 24
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=57.93 E-value=5.9 Score=24.34 Aligned_cols=24 Identities=33% Similarity=0.648 Sum_probs=22.1
Q ss_pred CCcccCCCCCCCccccccccccccCC
Q 031858 58 GDWYCSAGNCGAHNFASRSSCFKCGA 83 (151)
Q Consensus 58 gdW~C~~~~C~~~N~a~r~~C~~C~~ 83 (151)
..++|- .|+.+|-.+++.|.+|+.
T Consensus 13 ~k~ICr--kC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICM--RCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchh--cccCCCCccccccccCCC
Confidence 578998 999999999999999986
No 25
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=42.34 E-value=32 Score=34.39 Aligned_cols=54 Identities=26% Similarity=0.733 Sum_probs=39.4
Q ss_pred CCcccCCCCCCCccccccccccccCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCceEEeCCCCCcccccc---cc
Q 031858 58 GDWYCSAGNCGAHNFASRSSCFKCGAFKDDVAGGGFDCDMPRSRGSSFGGGNRSGWKSGDWICTRSGCNEHNFAS---RM 134 (151)
Q Consensus 58 gdW~C~~~~C~~~N~a~r~~C~~C~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~gdW~C~~~~C~~~Nfa~---r~ 134 (151)
+.=.|+ .|+...+.. .|..|+++... .+.|+ .|+...-.. ++
T Consensus 666 ~~rkCP--kCG~~t~~~--fCP~CGs~te~-----------------------------vy~CP--sCGaev~~des~a~ 710 (1337)
T PRK14714 666 GRRRCP--SCGTETYEN--RCPDCGTHTEP-----------------------------VYVCP--DCGAEVPPDESGRV 710 (1337)
T ss_pred EEEECC--CCCCccccc--cCcccCCcCCC-----------------------------ceeCc--cCCCccCCCccccc
Confidence 457898 999988764 99999976421 25898 798865333 66
Q ss_pred cccCCCCCCCCC
Q 031858 135 ECFRCNAPRDFG 146 (151)
Q Consensus 135 ~C~~C~~pk~~~ 146 (151)
.|..|+.+.-..
T Consensus 711 ~CP~CGtplv~~ 722 (1337)
T PRK14714 711 ECPRCDVELTPY 722 (1337)
T ss_pred cCCCCCCccccc
Confidence 899998876543
No 26
>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=39.62 E-value=14 Score=20.68 Aligned_cols=22 Identities=36% Similarity=0.949 Sum_probs=13.4
Q ss_pred ccCCCCCCCccccccccccccCCC
Q 031858 61 YCSAGNCGAHNFASRSSCFKCGAF 84 (151)
Q Consensus 61 ~C~~~~C~~~N~a~r~~C~~C~~~ 84 (151)
.|. .|+.+-|.-|..|..|+..
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 377 8999999999999999754
No 27
>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=38.08 E-value=14 Score=27.88 Aligned_cols=17 Identities=29% Similarity=0.720 Sum_probs=13.0
Q ss_pred CCCeEeCCCCccccccc
Q 031858 4 PGDWNCRSCQHLNFQRR 20 (151)
Q Consensus 4 ~gdW~C~~C~~~N~~~~ 20 (151)
+|||.|+.|....-...
T Consensus 16 ~g~W~Cp~C~~~~~~~~ 32 (148)
T cd04718 16 EGDWICPFCEVEKSGQS 32 (148)
T ss_pred CCCcCCCCCcCCCCCCc
Confidence 58999999998654433
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=35.10 E-value=19 Score=21.82 Aligned_cols=17 Identities=47% Similarity=1.007 Sum_probs=9.6
Q ss_pred CCCCCCCCCcccCCCCCCC
Q 031858 51 TGSDVRPGDWYCSAGNCGA 69 (151)
Q Consensus 51 ~~~~~~~gdW~C~~~~C~~ 69 (151)
+.+...+.||.|+ .|+.
T Consensus 26 t~F~~Lp~~w~CP--~C~a 42 (47)
T PF00301_consen 26 TPFEDLPDDWVCP--VCGA 42 (47)
T ss_dssp --GGGS-TT-B-T--TTSS
T ss_pred CCHHHCCCCCcCc--CCCC
Confidence 4467778999999 7775
No 29
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=33.94 E-value=57 Score=20.59 Aligned_cols=26 Identities=23% Similarity=0.643 Sum_probs=20.6
Q ss_pred ccCCCCCCCccccccccccccCCCCCCCCC
Q 031858 61 YCSAGNCGAHNFASRSSCFKCGAFKDDVAG 90 (151)
Q Consensus 61 ~C~~~~C~~~N~a~r~~C~~C~~~~~~~~~ 90 (151)
.|+ .|++..+ ...|..|+.+....-+
T Consensus 7 ~C~--~CgvYTL--k~~CP~CG~~t~~~~P 32 (56)
T PRK13130 7 KCP--KCGVYTL--KEICPVCGGKTKNPHP 32 (56)
T ss_pred ECC--CCCCEEc--cccCcCCCCCCCCCCC
Confidence 477 8999998 8999999988655433
No 30
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.73 E-value=28 Score=25.14 Aligned_cols=21 Identities=29% Similarity=0.648 Sum_probs=19.4
Q ss_pred eCCCCcccccccccccccCCC
Q 031858 9 CRSCQHLNFQRRDSCQRCGDP 29 (151)
Q Consensus 9 C~~C~~~N~~~~~~C~~C~~p 29 (151)
||.|+..=-+++..|..|++.
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTE 21 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE
Confidence 899999999999999999984
No 31
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=27.38 E-value=36 Score=26.20 Aligned_cols=26 Identities=35% Similarity=0.781 Sum_probs=21.3
Q ss_pred CcccCCCCCCCcccc-ccccccccCCCCC
Q 031858 59 DWYCSAGNCGAHNFA-SRSSCFKCGAFKD 86 (151)
Q Consensus 59 dW~C~~~~C~~~N~a-~r~~C~~C~~~~~ 86 (151)
-|+|+ .||+.-.. .-..|+.|++|+.
T Consensus 134 ~~vC~--vCGy~~~ge~P~~CPiCga~k~ 160 (166)
T COG1592 134 VWVCP--VCGYTHEGEAPEVCPICGAPKE 160 (166)
T ss_pred EEEcC--CCCCcccCCCCCcCCCCCChHH
Confidence 79999 99998766 4457999999874
No 32
>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=25.80 E-value=32 Score=19.16 Aligned_cols=21 Identities=24% Similarity=0.656 Sum_probs=13.0
Q ss_pred EeCCCCccccccc---------ccccccCC
Q 031858 8 NCRSCQHLNFQRR---------DSCQRCGD 28 (151)
Q Consensus 8 ~C~~C~~~N~~~~---------~~C~~C~~ 28 (151)
.||.|+.++.... .+|..|++
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~ 33 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGH 33 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCC
Confidence 5777777655542 36666665
No 33
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=24.74 E-value=55 Score=29.06 Aligned_cols=30 Identities=20% Similarity=0.536 Sum_probs=25.8
Q ss_pred CCCC-CCeEeCCCCcccccccccccccCCCC
Q 031858 1 MNRP-GDWNCRSCQHLNFQRRDSCQRCGDPR 30 (151)
Q Consensus 1 ~~k~-gdW~C~~C~~~N~~~~~~C~~C~~pk 30 (151)
|.|. -.|.|..|++.---..-+|..|++=.
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 5555 68999999999999999999999744
No 34
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=23.79 E-value=48 Score=21.22 Aligned_cols=25 Identities=20% Similarity=0.486 Sum_probs=21.0
Q ss_pred CeEeCCCCccc-----ccccccccccCCCC
Q 031858 6 DWNCRSCQHLN-----FQRRDSCQRCGDPR 30 (151)
Q Consensus 6 dW~C~~C~~~N-----~~~~~~C~~C~~pk 30 (151)
+-.|+.|.+.+ -.+...|..|++.-
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 67899999988 77788899999855
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=23.70 E-value=47 Score=20.36 Aligned_cols=17 Identities=47% Similarity=1.007 Sum_probs=12.6
Q ss_pred CCCCCCCCCcccCCCCCCC
Q 031858 51 TGSDVRPGDWYCSAGNCGA 69 (151)
Q Consensus 51 ~~~~~~~gdW~C~~~~C~~ 69 (151)
+.+...+.+|.|+ .|+.
T Consensus 26 t~f~~Lp~~w~CP--~C~a 42 (50)
T cd00730 26 TPFEDLPDDWVCP--VCGA 42 (50)
T ss_pred CCHhHCCCCCCCC--CCCC
Confidence 3456677899999 7765
No 36
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.92 E-value=56 Score=19.14 Aligned_cols=25 Identities=20% Similarity=0.546 Sum_probs=16.2
Q ss_pred eEeCCCCccc----ccccccccccCCCCC
Q 031858 7 WNCRSCQHLN----FQRRDSCQRCGDPRS 31 (151)
Q Consensus 7 W~C~~C~~~N----~~~~~~C~~C~~pkp 31 (151)
-.|+.|+... ......|..|+.+-.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 3688888765 222567888887643
No 37
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.01 E-value=50 Score=21.61 Aligned_cols=14 Identities=29% Similarity=0.968 Sum_probs=9.9
Q ss_pred CCcccCCCCCCCcccc
Q 031858 58 GDWYCSAGNCGAHNFA 73 (151)
Q Consensus 58 gdW~C~~~~C~~~N~a 73 (151)
+.|.|+ .|+++||.
T Consensus 3 ~~~kCp--KCgn~~~~ 16 (68)
T COG3478 3 NAFKCP--KCGNTNYE 16 (68)
T ss_pred ccccCC--CcCCcchh
Confidence 356687 88888864
No 38
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.70 E-value=1.2e+02 Score=29.96 Aligned_cols=27 Identities=26% Similarity=0.586 Sum_probs=19.5
Q ss_pred CcccCCCCCCCccccccccccccCCCCCCCC
Q 031858 59 DWYCSAGNCGAHNFASRSSCFKCGAFKDDVA 89 (151)
Q Consensus 59 dW~C~~~~C~~~N~a~r~~C~~C~~~~~~~~ 89 (151)
-|.|+ .|+..-- ...|.+|+.......
T Consensus 651 i~fCP--~CG~~~~--~y~CPKCG~El~~~s 677 (1121)
T PRK04023 651 VYRCP--RCGIEVE--EDECEKCGREPTPYS 677 (1121)
T ss_pred ceeCc--cccCcCC--CCcCCCCCCCCCccc
Confidence 57888 8877643 366999998876544
No 39
>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=20.92 E-value=68 Score=20.00 Aligned_cols=22 Identities=32% Similarity=0.780 Sum_probs=15.2
Q ss_pred eEeCCCCcccccccccccc--cCC
Q 031858 7 WNCRSCQHLNFQRRDSCQR--CGD 28 (151)
Q Consensus 7 W~C~~C~~~N~~~~~~C~~--C~~ 28 (151)
=+|-.|..+|-.+.+.|.+ |+.
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 764
No 40
>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=20.75 E-value=88 Score=17.34 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=10.9
Q ss_pred EeCCCCcccccccc---cccccC
Q 031858 8 NCRSCQHLNFQRRD---SCQRCG 27 (151)
Q Consensus 8 ~C~~C~~~N~~~~~---~C~~C~ 27 (151)
+|..|+..|..... +|..|+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCcCCCeeEcCCCCcEECCcCC
Confidence 46667666654443 565554
No 41
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=20.21 E-value=50 Score=20.75 Aligned_cols=24 Identities=25% Similarity=0.563 Sum_probs=16.0
Q ss_pred EeCCCCccc--ccccccccccCCCCC
Q 031858 8 NCRSCQHLN--FQRRDSCQRCGDPRS 31 (151)
Q Consensus 8 ~C~~C~~~N--~~~~~~C~~C~~pkp 31 (151)
.|+.|+-.- -...+.|..|++|--
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCccc
Confidence 466666555 556677888888754
No 42
>PRK00420 hypothetical protein; Validated
Probab=20.12 E-value=59 Score=23.41 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=18.3
Q ss_pred EeCCCCccccc---ccccccccCCCCC
Q 031858 8 NCRSCQHLNFQ---RRDSCQRCGDPRS 31 (151)
Q Consensus 8 ~C~~C~~~N~~---~~~~C~~C~~pkp 31 (151)
.||.|+..-|. ....|..|+.+--
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCeee
Confidence 58889988774 6677889988543
Done!