Query 033229
Match_columns 124
No_of_seqs 136 out of 227
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 11:22:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033229.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033229hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4137 Uncharacterized conser 100.0 3.9E-39 8.4E-44 230.8 7.8 102 16-124 1-102 (102)
2 COG5195 Uncharacterized conser 100.0 4.3E-36 9.3E-41 218.6 5.8 99 18-124 20-118 (118)
3 PF08265 YL1_C: YL1 nuclear pr 99.6 1.1E-16 2.3E-21 93.3 2.1 30 73-102 1-30 (30)
4 KOG3362 Predicted BBOX Zn-fing 99.5 1.3E-14 2.9E-19 111.0 1.7 68 32-101 80-147 (156)
5 KOG2897 DNA-binding protein YL 98.4 1.1E-07 2.4E-12 81.9 2.9 46 71-119 292-337 (390)
6 PF04438 zf-HIT: HIT zinc fing 98.4 7.4E-08 1.6E-12 55.8 1.1 30 71-100 1-30 (30)
7 KOG4317 Predicted Zn-finger pr 96.8 0.00033 7.2E-09 60.1 0.2 48 72-119 7-61 (383)
8 PF13824 zf-Mss51: Zinc-finger 94.3 0.027 5.9E-07 36.9 1.7 25 74-98 1-29 (55)
9 KOG2857 Predicted MYND Zn-fing 89.6 0.19 4.1E-06 39.1 1.5 34 72-105 5-39 (157)
10 cd00350 rubredoxin_like Rubred 78.6 1.3 2.7E-05 25.5 1.2 19 74-92 3-26 (33)
11 cd00730 rubredoxin Rubredoxin; 62.8 5.7 0.00012 25.2 1.7 15 78-92 29-43 (50)
12 cd00729 rubredoxin_SM Rubredox 62.1 5 0.00011 23.3 1.2 19 74-92 4-27 (34)
13 PHA00616 hypothetical protein 50.8 7 0.00015 24.5 0.6 19 83-101 1-19 (44)
14 KOG2858 Uncharacterized conser 50.1 5.9 0.00013 34.8 0.3 28 73-100 18-46 (390)
15 PRK00432 30S ribosomal protein 46.8 9.9 0.00021 24.0 0.9 37 57-94 6-48 (50)
16 PF09538 FYDLN_acid: Protein o 45.3 10 0.00022 27.5 0.9 14 82-95 8-21 (108)
17 PRK08271 anaerobic ribonucleos 43.0 21 0.00045 33.1 2.6 54 36-102 541-597 (623)
18 PF13894 zf-C2H2_4: C2H2-type 41.2 18 0.00039 17.6 1.2 18 84-101 1-18 (24)
19 PHA02757 hypothetical protein; 40.0 14 0.0003 25.5 0.8 17 65-81 7-23 (75)
20 PF03884 DUF329: Domain of unk 38.4 21 0.00046 23.4 1.4 28 73-100 3-30 (57)
21 PF00096 zf-C2H2: Zinc finger, 38.2 15 0.00032 18.4 0.6 18 84-101 1-18 (23)
22 PRK14704 anaerobic ribonucleos 38.1 27 0.00058 32.3 2.6 57 35-102 533-592 (618)
23 KOG0129 Predicted RNA-binding 37.8 19 0.0004 33.0 1.5 38 71-108 454-498 (520)
24 PRK07111 anaerobic ribonucleos 36.7 15 0.00032 34.5 0.7 54 36-102 655-710 (735)
25 PLN03158 methionine aminopepti 36.1 27 0.00059 30.4 2.2 32 70-101 7-46 (396)
26 COG1592 Rubrerythrin [Energy p 35.5 22 0.00048 27.8 1.4 22 72-93 134-159 (166)
27 TIGR02300 FYDLN_acid conserved 33.4 21 0.00045 27.2 0.9 14 82-95 8-21 (129)
28 PF00301 Rubredoxin: Rubredoxi 32.7 24 0.00052 22.1 1.0 16 77-92 28-43 (47)
29 COG4640 Predicted membrane pro 31.4 26 0.00057 31.5 1.4 27 72-98 1-30 (465)
30 TIGR02487 NrdD anaerobic ribon 31.0 25 0.00054 31.9 1.2 53 36-101 499-554 (579)
31 TIGR02827 RNR_anaer_Bdell anae 30.4 29 0.00063 31.9 1.5 53 36-101 507-562 (586)
32 PRK08270 anaerobic ribonucleos 30.0 17 0.00037 33.7 -0.0 52 36-100 600-653 (656)
33 PRK00418 DNA gyrase inhibitor; 29.5 62 0.0013 21.6 2.6 31 70-100 4-34 (62)
34 PRK04179 rpl37e 50S ribosomal 28.9 26 0.00056 23.6 0.7 19 65-83 25-44 (62)
35 KOG1710 MYND Zn-finger and ank 28.8 17 0.00038 31.7 -0.2 32 70-101 317-350 (396)
36 PRK00420 hypothetical protein; 28.6 31 0.00068 25.4 1.2 23 73-95 24-52 (112)
37 PF01753 zf-MYND: MYND finger; 28.3 43 0.00092 19.1 1.5 27 75-101 1-28 (37)
38 PRK08579 anaerobic ribonucleos 27.6 48 0.001 30.7 2.4 54 36-102 543-599 (625)
39 KOG2934 Uncharacterized conser 27.4 35 0.00076 27.6 1.3 39 78-116 93-132 (204)
40 COG0675 Transposase and inacti 27.0 37 0.0008 26.4 1.4 26 69-94 306-333 (364)
41 cd02341 ZZ_ZZZ3 Zinc finger, Z 26.0 22 0.00047 22.3 -0.1 20 75-99 3-22 (48)
42 COG3024 Uncharacterized protei 25.8 49 0.0011 22.5 1.6 28 73-100 8-35 (65)
43 TIGR01159 DRP1 density-regulat 25.3 26 0.00056 27.5 0.2 38 73-114 5-43 (173)
44 cd00241 CDH_cytochrome Cellobi 25.0 28 0.00061 27.4 0.4 14 81-94 2-15 (184)
45 KOG3556 Familial cylindromatos 24.6 37 0.0008 31.8 1.1 18 72-89 558-575 (724)
46 TIGR00373 conserved hypothetic 23.7 38 0.00083 25.6 0.9 19 82-100 108-126 (158)
47 PLN00206 DEAD-box ATP-dependen 23.2 71 0.0015 28.1 2.5 31 72-102 28-58 (518)
48 PRK09263 anaerobic ribonucleos 22.9 49 0.0011 31.0 1.6 45 36-92 617-668 (711)
49 KOG1159 NADP-dependent flavopr 22.6 54 0.0012 30.4 1.7 70 34-109 336-414 (574)
50 PF01907 Ribosomal_L37e: Ribos 22.4 27 0.00058 23.0 -0.2 17 67-83 25-41 (55)
51 PRK03824 hypA hydrogenase nick 21.9 48 0.001 24.6 1.1 14 69-82 67-80 (135)
52 PRK00762 hypA hydrogenase nick 20.4 50 0.0011 24.1 0.9 23 69-92 67-101 (124)
53 cd02334 ZZ_dystrophin Zinc fin 20.2 31 0.00066 21.7 -0.2 20 75-99 3-22 (49)
No 1
>KOG4137 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=3.9e-39 Score=230.77 Aligned_cols=102 Identities=42% Similarity=0.719 Sum_probs=95.1
Q ss_pred CCCCchhhhhcCCCCCCCCcccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCcccCCCCCCCCccC
Q 033229 16 MSFKRIQMYEKYPKGQSRGRHWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAPYYDPRTNLRYAN 95 (124)
Q Consensus 16 ~~FK~~~~~~~~~~~~~k~r~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~Y~dP~tglrY~~ 95 (124)
.+||++ ..+.+.|+.||++|++..|..+.+.+..++|++|+||||++|+++|||||||||.|+||.|||||||
T Consensus 1 ~~fk~p-------~~kk~t~~~kn~rq~~~~e~~q~l~~~k~tYfsi~appSv~PakKycDvTGLpapYtdP~t~Lry~n 73 (102)
T KOG4137|consen 1 MKFQKP-------WYKKSTRRGKNMRQKILKELLQRLIEKKHTYFSIEAPPSVKPAKKYCDVTGLPAPYTDPNTGLRYHN 73 (102)
T ss_pred CCccCc-------cccCCcccCccHHHHHhhhhhhhcccccCceEEecCCCccccchhhccccCCcccccCCCccceecc
Confidence 367775 3345679999999999999998888889999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCChHHHHHHHHhhccccccC
Q 033229 96 AEVFKLVRSLPNEYVQRYLALRNAAVVLK 124 (124)
Q Consensus 96 ~~~y~~ir~l~~~~~q~YL~lR~a~~~lk 124 (124)
+++|+.|++||+|+||+||.|||++++||
T Consensus 74 aeiY~~i~empsd~vq~ylklRg~~~~l~ 102 (102)
T KOG4137|consen 74 AEIYKLICEMPSDRVQEYLKLRGFGKVLK 102 (102)
T ss_pred HHHHHHHHHCCchHhhhHHhhhccccccC
Confidence 99999999999999999999999999996
No 2
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=4.3e-36 Score=218.56 Aligned_cols=99 Identities=40% Similarity=0.741 Sum_probs=90.7
Q ss_pred CCchhhhhcCCCCCCCCcccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCcccCCCCCCCCccCHH
Q 033229 18 FKRIQMYEKYPKGQSRGRHWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAPYYDPRTNLRYANAE 97 (124)
Q Consensus 18 FK~~~~~~~~~~~~~k~r~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~Y~dP~tglrY~~~~ 97 (124)
||++++ +.+.|++|+++|||..+..++.+. ..+|++|+||||++|+++|||||||+|.||||.|||||||++
T Consensus 20 fk~~~Y-------k~~~rr~ktlrQli~~~~i~ne~s-k~~Y~sieappSv~P~~KyCDvTGL~a~Yt~P~t~lrYhn~e 91 (118)
T COG5195 20 FKKSTY-------KGKNRRFKTLRQLIPRLTIENESS-KHRYLSIEAPPSVKPRMKYCDVTGLPAPYTCPNTGLRYHNSE 91 (118)
T ss_pred ccCccc-------cCcccchhhHHHHccccccccccc-cceeEeecCCCccccccccccccCCcccccCCCcCceeccHH
Confidence 888654 346799999999999987666444 579999999999999999999999999999999999999999
Q ss_pred HHHHhhcCChHHHHHHHHhhccccccC
Q 033229 98 VFKLVRSLPNEYVQRYLALRNAAVVLK 124 (124)
Q Consensus 98 ~y~~ir~l~~~~~q~YL~lR~a~~~lk 124 (124)
+|+.|++||+|++|+||+||++++|||
T Consensus 92 iY~lI~elpsg~dQeylkLR~~~~vLk 118 (118)
T COG5195 92 IYKLICELPSGRDQEYLKLREFGKVLK 118 (118)
T ss_pred HHHHhhcCCCchhHHHHHhhhcCcccC
Confidence 999999999999999999999999997
No 3
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=99.63 E-value=1.1e-16 Score=93.28 Aligned_cols=30 Identities=53% Similarity=1.047 Sum_probs=28.8
Q ss_pred ccccccCCCcccCCCCCCCCccCHHHHHHh
Q 033229 73 RICDITGFEAPYYDPRTNLRYANAEVFKLV 102 (124)
Q Consensus 73 kyCdITGl~A~Y~dP~tglrY~~~~~y~~i 102 (124)
|+|||||+||+|+||+|||||+|.++|++|
T Consensus 1 k~C~iTglpA~Y~DP~T~l~Y~n~~ayk~i 30 (30)
T PF08265_consen 1 KYCDITGLPARYRDPKTGLPYANSEAYKII 30 (30)
T ss_pred CcccccCCCccccCCCCCCcccCHHHhhcC
Confidence 689999999999999999999999999976
No 4
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=99.47 E-value=1.3e-14 Score=110.95 Aligned_cols=68 Identities=22% Similarity=0.480 Sum_probs=60.7
Q ss_pred CCCcccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCcccCCCCCCCCccCHHHHHH
Q 033229 32 SRGRHWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAPYYDPRTNLRYANAEVFKL 101 (124)
Q Consensus 32 ~k~r~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~Y~dP~tglrY~~~~~y~~ 101 (124)
.+.+++|||+++|++... ++. ..++|.++.||||.+|.++||.|||++++|.|-.||.+||++.|+++
T Consensus 80 ~~~~~RKnf~~~Ldea~~-~~~-k~~~Y~~~~a~p~~KP~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~~ 147 (156)
T KOG3362|consen 80 FKLRFRKNFQALLDEALL-NLM-KNPNYHTAYAKPSFKPLRKFCAVCGYDSKYSCVNCGTKYCSVRCLKT 147 (156)
T ss_pred hhhhHHHHHHHHHHccch-hhh-hccchhhcccCCCCCCcchhhhhcCCCchhHHHhcCCceeechhhhh
Confidence 467899999999987654 222 56899999999999999999999999999999999999999999986
No 5
>KOG2897 consensus DNA-binding protein YL1 and related proteins [General function prediction only]
Probab=98.44 E-value=1.1e-07 Score=81.89 Aligned_cols=46 Identities=37% Similarity=0.675 Sum_probs=38.9
Q ss_pred CcccccccCCCcccCCCCCCCCccCHHHHHHhhcCChHHHHHHHHhhcc
Q 033229 71 CKRICDITGFEAPYYDPRTNLRYANAEVFKLVRSLPNEYVQRYLALRNA 119 (124)
Q Consensus 71 ~kkyCdITGl~A~Y~dP~tglrY~~~~~y~~ir~l~~~~~q~YL~lR~a 119 (124)
.+-.|.|||.||+|.||.|||+|+++.+|++||. ..-+.|+.+||-
T Consensus 292 ~~~~C~iTg~PA~Y~DPVT~lPy~ta~AFKviRe---~y~~~~~~~~~~ 337 (390)
T KOG2897|consen 292 ERVVCVITGRPARYLDPVTGLPYSTAQAFKVIRE---RYKKHLRSIRGN 337 (390)
T ss_pred ccccccccCCcccccCcccCCcchhHHHHHHHHH---HHHHHhhhcccc
Confidence 5669999999999999999999999999999995 345566666653
No 6
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=98.43 E-value=7.4e-08 Score=55.83 Aligned_cols=30 Identities=30% Similarity=0.659 Sum_probs=23.9
Q ss_pred CcccccccCCCcccCCCCCCCCccCHHHHH
Q 033229 71 CKRICDITGFEAPYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 71 ~kkyCdITGl~A~Y~dP~tglrY~~~~~y~ 100 (124)
++++|.|+|.+|+|+||+++++|++.++|+
T Consensus 1 ~~~~C~vC~~~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 1 PRKLCSVCGNPAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp --EEETSSSSEESEE-TTT--EESSHHHHH
T ss_pred CcCCCccCcCCCEEECCCcCCceeCcEeEC
Confidence 467999999999999999999999999985
No 7
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.79 E-value=0.00033 Score=60.11 Aligned_cols=48 Identities=23% Similarity=0.376 Sum_probs=35.2
Q ss_pred cccccccCC-CcccCCCCCCCCccCHHHHHHhhc------CChHHHHHHHHhhcc
Q 033229 72 KRICDITGF-EAPYYDPRTNLRYANAEVFKLVRS------LPNEYVQRYLALRNA 119 (124)
Q Consensus 72 kkyCdITGl-~A~Y~dP~tglrY~~~~~y~~ir~------l~~~~~q~YL~lR~a 119 (124)
.-+|.|||. ++.||||+|.++||+..||+.=.. +-..|.|+.=.+|+.
T Consensus 7 ~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~~~CsE~FyrdqV~~eL~~~r~d 61 (383)
T KOG4317|consen 7 FLACGICGVQKREYTCPRCNLLYCSLKCYRNHKHSCSEKFYRDQVKQELSGKRAD 61 (383)
T ss_pred eeeccccccccccccCCCCCccceeeeeecCCCccchHHHHHHHHHHHhhhcccc
Confidence 458999996 789999999999999999986443 223344555555554
No 8
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=94.30 E-value=0.027 Score=36.93 Aligned_cols=25 Identities=12% Similarity=0.242 Sum_probs=21.8
Q ss_pred cccccCC----CcccCCCCCCCCccCHHH
Q 033229 74 ICDITGF----EAPYYDPRTNLRYANAEV 98 (124)
Q Consensus 74 yCdITGl----~A~Y~dP~tglrY~~~~~ 98 (124)
+|.+|+- .-+|.||.||++++.++.
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~e 29 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSEE 29 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCHH
Confidence 5999999 999999999999876654
No 9
>KOG2857 consensus Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription]
Probab=89.64 E-value=0.19 Score=39.09 Aligned_cols=34 Identities=26% Similarity=0.408 Sum_probs=28.6
Q ss_pred cccccccCC-CcccCCCCCCCCccCHHHHHHhhcC
Q 033229 72 KRICDITGF-EAPYYDPRTNLRYANAEVFKLVRSL 105 (124)
Q Consensus 72 kkyCdITGl-~A~Y~dP~tglrY~~~~~y~~ir~l 105 (124)
...|.||-- +.+|+||.|..+||+.-||++=+.-
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~t 39 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVPYCSLPCFKIHKST 39 (157)
T ss_pred eeeehhhhcchhhccCCCCCCccccchhhhhccCC
Confidence 346888865 5699999999999999999987763
No 10
>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=78.58 E-value=1.3 Score=25.51 Aligned_cols=19 Identities=26% Similarity=0.679 Sum_probs=15.6
Q ss_pred cccccCCC-----cccCCCCCCCC
Q 033229 74 ICDITGFE-----APYYDPRTNLR 92 (124)
Q Consensus 74 yCdITGl~-----A~Y~dP~tglr 92 (124)
.|.+||+. +.++||.||.+
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCc
Confidence 58888887 78899999874
No 11
>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=62.83 E-value=5.7 Score=25.21 Aligned_cols=15 Identities=7% Similarity=0.082 Sum_probs=11.6
Q ss_pred cCCCcccCCCCCCCC
Q 033229 78 TGFEAPYYDPRTNLR 92 (124)
Q Consensus 78 TGl~A~Y~dP~tglr 92 (124)
.-||..|+||.||..
T Consensus 29 ~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 29 EDLPDDWVCPVCGAG 43 (50)
T ss_pred hHCCCCCCCCCCCCc
Confidence 447888999998864
No 12
>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=62.08 E-value=5 Score=23.34 Aligned_cols=19 Identities=26% Similarity=0.536 Sum_probs=12.8
Q ss_pred cccccCCC-----cccCCCCCCCC
Q 033229 74 ICDITGFE-----APYYDPRTNLR 92 (124)
Q Consensus 74 yCdITGl~-----A~Y~dP~tglr 92 (124)
.|.+||+. ++..||.||.+
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCc
Confidence 47777776 45677777753
No 13
>PHA00616 hypothetical protein
Probab=50.81 E-value=7 Score=24.48 Aligned_cols=19 Identities=11% Similarity=-0.078 Sum_probs=16.7
Q ss_pred ccCCCCCCCCccCHHHHHH
Q 033229 83 PYYDPRTNLRYANAEVFKL 101 (124)
Q Consensus 83 ~Y~dP~tglrY~~~~~y~~ 101 (124)
+|.||+||..|.+...+..
T Consensus 1 pYqC~~CG~~F~~~s~l~~ 19 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIE 19 (44)
T ss_pred CCccchhhHHHhhHHHHHH
Confidence 5999999999999988764
No 14
>KOG2858 consensus Uncharacterized conserved protein [General function prediction only]
Probab=50.11 E-value=5.9 Score=34.84 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=24.4
Q ss_pred ccccccCCCc-ccCCCCCCCCccCHHHHH
Q 033229 73 RICDITGFEA-PYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 73 kyCdITGl~A-~Y~dP~tglrY~~~~~y~ 100 (124)
..|-||+-.+ +|.||+|-.|+|+.+|=+
T Consensus 18 vlCgVClknE~KYkCPRCl~rtCsLeCsk 46 (390)
T KOG2858|consen 18 VLCGVCLKNEPKYKCPRCLARTCSLECSK 46 (390)
T ss_pred hhhhhcccCcccccCcchhhhheeccccc
Confidence 4899999876 799999999999988743
No 15
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.85 E-value=9.9 Score=24.00 Aligned_cols=37 Identities=8% Similarity=0.160 Sum_probs=26.4
Q ss_pred CCceeeeCCCCCCCCcccccccCC------CcccCCCCCCCCcc
Q 033229 57 PNYVNIESPPSMHPCKRICDITGF------EAPYYDPRTNLRYA 94 (124)
Q Consensus 57 ptY~si~appS~~P~kkyCdITGl------~A~Y~dP~tglrY~ 94 (124)
-.|..|+.- .+.+.+++|+-||- ..++.|..||..|.
T Consensus 6 ~~~y~v~~~-~v~~~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 6 REYYEVDGG-KVKRKNKFCPRCGSGFMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred eeeEEECCC-EEEEccCcCcCCCcchheccCCcEECCCcCCEEe
Confidence 356777655 56777889999984 23788888887664
No 16
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=45.33 E-value=10 Score=27.54 Aligned_cols=14 Identities=7% Similarity=0.169 Sum_probs=8.5
Q ss_pred cccCCCCCCCCccC
Q 033229 82 APYYDPRTNLRYAN 95 (124)
Q Consensus 82 A~Y~dP~tglrY~~ 95 (124)
.+-+||.||.||++
T Consensus 8 tKR~Cp~CG~kFYD 21 (108)
T PF09538_consen 8 TKRTCPSCGAKFYD 21 (108)
T ss_pred CcccCCCCcchhcc
Confidence 34566666666665
No 17
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=42.97 E-value=21 Score=33.08 Aligned_cols=54 Identities=15% Similarity=0.153 Sum_probs=36.8
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCC---cccCCCCCCCCccCHHHHHHh
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFE---APYYDPRTNLRYANAEVFKLV 102 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~---A~Y~dP~tglrY~~~~~y~~i 102 (124)
-++.+++|+..... ....|++|.-| -.+|..||+. -.++||.||- .+.+++..|
T Consensus 541 n~eal~~lv~~~~~-----~~i~Yf~in~~------~~iC~~CG~~~~g~~~~CP~CGs--~~~ev~~RV 597 (623)
T PRK08271 541 SEEGYRKLLNIAAK-----TGCNYFAFNVK------ITICNDCHHIDKRTGKRCPICGS--ENIDYYTRV 597 (623)
T ss_pred CHHHHHHHHHHHHH-----cCCceEEeCCC------CccCCCCCCcCCCCCcCCcCCCC--cchhHHHHH
Confidence 56677777754321 24678888744 4588889985 4789999997 355666654
No 18
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=41.19 E-value=18 Score=17.57 Aligned_cols=18 Identities=6% Similarity=0.176 Sum_probs=12.2
Q ss_pred cCCCCCCCCccCHHHHHH
Q 033229 84 YYDPRTNLRYANAEVFKL 101 (124)
Q Consensus 84 Y~dP~tglrY~~~~~y~~ 101 (124)
|.|+.|+..|.+...+..
T Consensus 1 ~~C~~C~~~~~~~~~l~~ 18 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQ 18 (24)
T ss_dssp EE-SSTS-EESSHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHH
Confidence 678888888888877653
No 19
>PHA02757 hypothetical protein; Provisional
Probab=40.02 E-value=14 Score=25.52 Aligned_cols=17 Identities=29% Similarity=0.387 Sum_probs=13.6
Q ss_pred CCCCCCCcccccccCCC
Q 033229 65 PPSMHPCKRICDITGFE 81 (124)
Q Consensus 65 ppS~~P~kkyCdITGl~ 81 (124)
.-|.+|+|.+|.||--+
T Consensus 7 kGSskPprnvCViTPsg 23 (75)
T PHA02757 7 KGSSKPPRNVCVITPSG 23 (75)
T ss_pred cCCCCCCCCEEEEeCCC
Confidence 35788999999999544
No 20
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=38.37 E-value=21 Score=23.38 Aligned_cols=28 Identities=11% Similarity=0.113 Sum_probs=18.2
Q ss_pred ccccccCCCcccCCCCCCCCccCHHHHH
Q 033229 73 RICDITGFEAPYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 73 kyCdITGl~A~Y~dP~tglrY~~~~~y~ 100 (124)
.-|.+||-+..+..-..--+||+.+|-.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk~ 30 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCKL 30 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHHH
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhcc
Confidence 4599999999998777777899999864
No 21
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=38.24 E-value=15 Score=18.44 Aligned_cols=18 Identities=17% Similarity=0.242 Sum_probs=14.8
Q ss_pred cCCCCCCCCccCHHHHHH
Q 033229 84 YYDPRTNLRYANAEVFKL 101 (124)
Q Consensus 84 Y~dP~tglrY~~~~~y~~ 101 (124)
|+|+.|+-.|.+...+..
T Consensus 1 y~C~~C~~~f~~~~~l~~ 18 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKR 18 (23)
T ss_dssp EEETTTTEEESSHHHHHH
T ss_pred CCCCCCCCccCCHHHHHH
Confidence 678999999998887764
No 22
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=38.12 E-value=27 Score=32.26 Aligned_cols=57 Identities=26% Similarity=0.289 Sum_probs=36.9
Q ss_pred cccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCcc--cCCCCCCCCc-cCHHHHHHh
Q 033229 35 RHWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAP--YYDPRTNLRY-ANAEVFKLV 102 (124)
Q Consensus 35 r~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~--Y~dP~tglrY-~~~~~y~~i 102 (124)
.-++.+++|+.-... ...-|++|.-| -.+|..||+.+- ++||.||-+= ++.+++..|
T Consensus 533 ~n~~Al~~lvk~~~~-----~~i~Y~sin~~------~~~C~~CGy~g~~~~~CP~CG~~d~~~~~v~~Ri 592 (618)
T PRK14704 533 HNKKALKQIVQAMAE-----HGVGYGSINHP------VDRCKCCSYHGVIGNECPSCGNEDEANIERIRRI 592 (618)
T ss_pred CCHHHHHHHHHHHHh-----cCCceEEeCCC------CeecCCCCCCCCcCccCcCCCCCCcchhHHHHHH
Confidence 356777777755221 24678887754 457888887655 7999999731 236666654
No 23
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=37.82 E-value=19 Score=33.00 Aligned_cols=38 Identities=24% Similarity=0.413 Sum_probs=32.2
Q ss_pred CcccccccCC------CcccCCC-CCCCCccCHHHHHHhhcCChH
Q 033229 71 CKRICDITGF------EAPYYDP-RTNLRYANAEVFKLVRSLPNE 108 (124)
Q Consensus 71 ~kkyCdITGl------~A~Y~dP-~tglrY~~~~~y~~ir~l~~~ 108 (124)
.-..||+||- .|+|.|. .|.+.|++-.|+..|-+.+..
T Consensus 454 eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~~r 498 (520)
T KOG0129|consen 454 EDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGPGR 498 (520)
T ss_pred cccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCCch
Confidence 3468999975 9999998 589999999999999877653
No 24
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=36.65 E-value=15 Score=34.54 Aligned_cols=54 Identities=15% Similarity=0.242 Sum_probs=34.2
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCc--ccCCCCCCCCccCHHHHHHh
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEA--PYYDPRTNLRYANAEVFKLV 102 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A--~Y~dP~tglrY~~~~~y~~i 102 (124)
-++.+++|+.-... ...-|++|.- +-.+|..||+.+ .+.||.||- .+.+++..|
T Consensus 655 n~eal~~lvk~~~~-----~~i~Y~sin~------~~~~C~~CG~~~~~~~~CP~CG~--~~~~~~~Ri 710 (735)
T PRK07111 655 NVEAFEIIVKAMKN-----TNIGYGSINH------PVDRCPVCGYLGVIEDKCPKCGS--TNIQRIRRI 710 (735)
T ss_pred CHHHHHHHHHHHHh-----CCCceEEeCC------CCeecCCCCCCCCcCccCcCCCC--ccceeeehh
Confidence 45667777754221 1356888764 455788888744 389999997 355555543
No 25
>PLN03158 methionine aminopeptidase; Provisional
Probab=36.10 E-value=27 Score=30.35 Aligned_cols=32 Identities=16% Similarity=0.259 Sum_probs=26.1
Q ss_pred CCcccccccCCCcccCCCCC--------CCCccCHHHHHH
Q 033229 70 PCKRICDITGFEAPYYDPRT--------NLRYANAEVFKL 101 (124)
Q Consensus 70 P~kkyCdITGl~A~Y~dP~t--------glrY~~~~~y~~ 101 (124)
|...-|.=||-+|.-.||.| +.-|||.+||+.
T Consensus 7 ~~~~~c~~c~~~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~ 46 (396)
T PLN03158 7 TSPLACARCSKPAHLQCPKCLELKLPREGASFCSQDCFKA 46 (396)
T ss_pred CCcccccCCCCcccccCccchhcCCCCCCceeECHHHHHH
Confidence 44556988999999999984 457999999974
No 26
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=35.54 E-value=22 Score=27.81 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=17.1
Q ss_pred cccccccCCC----cccCCCCCCCCc
Q 033229 72 KRICDITGFE----APYYDPRTNLRY 93 (124)
Q Consensus 72 kkyCdITGl~----A~Y~dP~tglrY 93 (124)
--.|.+||+. ++-.||.||.+.
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k 159 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPK 159 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChH
Confidence 4469999874 788999999764
No 27
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=33.44 E-value=21 Score=27.17 Aligned_cols=14 Identities=14% Similarity=0.259 Sum_probs=7.9
Q ss_pred cccCCCCCCCCccC
Q 033229 82 APYYDPRTNLRYAN 95 (124)
Q Consensus 82 A~Y~dP~tglrY~~ 95 (124)
.+.+||.||.||++
T Consensus 8 tKr~Cp~cg~kFYD 21 (129)
T TIGR02300 8 TKRICPNTGSKFYD 21 (129)
T ss_pred ccccCCCcCccccc
Confidence 34556666666654
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=32.69 E-value=24 Score=22.12 Aligned_cols=16 Identities=6% Similarity=0.100 Sum_probs=10.1
Q ss_pred ccCCCcccCCCCCCCC
Q 033229 77 ITGFEAPYYDPRTNLR 92 (124)
Q Consensus 77 ITGl~A~Y~dP~tglr 92 (124)
+..||..|+||.|+..
T Consensus 28 F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 28 FEDLPDDWVCPVCGAP 43 (47)
T ss_dssp GGGS-TT-B-TTTSSB
T ss_pred HHHCCCCCcCcCCCCc
Confidence 4567899999999875
No 29
>COG4640 Predicted membrane protein [Function unknown]
Probab=31.37 E-value=26 Score=31.47 Aligned_cols=27 Identities=11% Similarity=0.253 Sum_probs=23.2
Q ss_pred cccccccC---CCcccCCCCCCCCccCHHH
Q 033229 72 KRICDITG---FEAPYYDPRTNLRYANAEV 98 (124)
Q Consensus 72 kkyCdITG---l~A~Y~dP~tglrY~~~~~ 98 (124)
++||.-|| ....+.||+||..+.+-..
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t~~~s 30 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFTSRQS 30 (465)
T ss_pred CCcccccccccccccccccccCCcCCchhh
Confidence 47999999 7788899999999988654
No 30
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=31.03 E-value=25 Score=31.93 Aligned_cols=53 Identities=21% Similarity=0.316 Sum_probs=35.2
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCccc---CCCCCCCCccCHHHHHH
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAPY---YDPRTNLRYANAEVFKL 101 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~Y---~dP~tglrY~~~~~y~~ 101 (124)
-+..+++|+..... . ...|++|.-| -.+|.-||+.+.. +||.||-+ +.+++..
T Consensus 499 n~eal~~lv~~a~~----~-~i~Y~~~n~~------~~~C~~CG~~g~~~~~~CP~Cgs~--~~~~~~R 554 (579)
T TIGR02487 499 DPEALKDITKKAMK----N-GIGYFGINPP------VDVCEDCGYTGEGLNDKCPKCGSH--DIEVISR 554 (579)
T ss_pred CHHHHHHHHHHHHh----c-CCceEEeccC------CccCCCCCCCCCCCCCcCcCCCCc--cceehhh
Confidence 46677777755432 1 2678888755 4578888887764 79999975 3555544
No 31
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=30.40 E-value=29 Score=31.93 Aligned_cols=53 Identities=13% Similarity=0.056 Sum_probs=34.3
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCcc---cCCCCCCCCccCHHHHHH
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEAP---YYDPRTNLRYANAEVFKL 101 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A~---Y~dP~tglrY~~~~~y~~ 101 (124)
-.+.+++|+..... ...-|++|.-+ -.+|..||+... ++||.||-. +.+++..
T Consensus 507 n~ea~~~lv~~~~~-----~~i~Y~tin~~------~siC~~CGy~~g~~~~~CP~CGs~--~~ev~sR 562 (586)
T TIGR02827 507 SEDGYRKLLRVAAD-----TGCNYFCFNIK------ITICNDCHHIDKRTLHRCPVCGSA--NIDYGTR 562 (586)
T ss_pred CHHHHHHHHHHHHh-----cCCceEEeCCC------CeecCCCCCcCCCcCCcCcCCCCc--cceEEEe
Confidence 45667777654321 14678888744 457889998543 899999963 4444443
No 32
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.96 E-value=17 Score=33.66 Aligned_cols=52 Identities=19% Similarity=0.317 Sum_probs=32.8
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCc--ccCCCCCCCCccCHHHHH
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEA--PYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A--~Y~dP~tglrY~~~~~y~ 100 (124)
-++.++.|+..-.. .....|++|.-|.+ +|..||+.. .+.||.||-. .++|.
T Consensus 600 n~~a~~~lv~~~~~----~~~i~Y~~in~~~~------~C~~CG~~~g~~~~CP~CG~~---~~v~s 653 (656)
T PRK08270 600 DAEACKKLVKKALE----NYRLPYITITPTFS------ICPKHGYLSGEHEFCPKCGEE---TEVYS 653 (656)
T ss_pred CHHHHHHHHHHHHH----hCCCceEEeCCCCc------ccCCCCCcCCCCCCCcCCcCc---cceEE
Confidence 46777777754321 12367898885554 677777643 4899999944 55544
No 33
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=29.49 E-value=62 Score=21.61 Aligned_cols=31 Identities=6% Similarity=0.025 Sum_probs=23.1
Q ss_pred CCcccccccCCCcccCCCCCCCCccCHHHHH
Q 033229 70 PCKRICDITGFEAPYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 70 P~kkyCdITGl~A~Y~dP~tglrY~~~~~y~ 100 (124)
+...-|.|||-+..|..-.---+||+.+|-.
T Consensus 4 ~~~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ 34 (62)
T PRK00418 4 TITVNCPTCGKPVEWGEISPFRPFCSKRCQL 34 (62)
T ss_pred CccccCCCCCCcccccCCCCcCCcccHHHHh
Confidence 3455799999999886544455899988853
No 34
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=28.93 E-value=26 Score=23.57 Aligned_cols=19 Identities=26% Similarity=0.471 Sum_probs=14.4
Q ss_pred CCCCCCCcccccccCC-Ccc
Q 033229 65 PPSMHPCKRICDITGF-EAP 83 (124)
Q Consensus 65 ppS~~P~kkyCdITGl-~A~ 83 (124)
.-|.--++++|.-||+ |+.
T Consensus 25 ~~syh~qK~~CasCGygps~ 44 (62)
T PRK04179 25 RHSYNVRKKYCAACGFGRSK 44 (62)
T ss_pred cccccccccchhhcCCCccc
Confidence 3455578999999999 764
No 35
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=28.81 E-value=17 Score=31.72 Aligned_cols=32 Identities=16% Similarity=0.277 Sum_probs=26.3
Q ss_pred CCcccccccCCCc-ccCCCCCC-CCccCHHHHHH
Q 033229 70 PCKRICDITGFEA-PYYDPRTN-LRYANAEVFKL 101 (124)
Q Consensus 70 P~kkyCdITGl~A-~Y~dP~tg-lrY~~~~~y~~ 101 (124)
-.-.||..||-|+ +=+|.+|+ +-||+.+|-+.
T Consensus 317 ~d~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~ 350 (396)
T KOG1710|consen 317 ADCQFCSTCGHPGAKKRCSQCKAVAYCDQECQKF 350 (396)
T ss_pred EecccccccCCCCccchhhhhHHHHHHHHHHHHh
Confidence 3457999999985 56799999 99999998653
No 36
>PRK00420 hypothetical protein; Validated
Probab=28.59 E-value=31 Score=25.36 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=15.9
Q ss_pred ccccccCCC------cccCCCCCCCCccC
Q 033229 73 RICDITGFE------APYYDPRTNLRYAN 95 (124)
Q Consensus 73 kyCdITGl~------A~Y~dP~tglrY~~ 95 (124)
..|++||.| +...||.||-.+--
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCeeee
Confidence 468888864 55678888876653
No 37
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=28.34 E-value=43 Score=19.09 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=18.2
Q ss_pred ccccCCCcccCCCCC-CCCccCHHHHHH
Q 033229 75 CDITGFEAPYYDPRT-NLRYANAEVFKL 101 (124)
Q Consensus 75 CdITGl~A~Y~dP~t-glrY~~~~~y~~ 101 (124)
|+++|-++.-.++.+ ...|++.++.+.
T Consensus 1 C~~C~~~~~~~C~~C~~~~YCs~~Cq~~ 28 (37)
T PF01753_consen 1 CAVCGKPALKRCSRCKSVYYCSEECQRA 28 (37)
T ss_dssp -TTTSSCSSEEETTTSSSEESSHHHHHH
T ss_pred CcCCCCCcCCcCCCCCCEEecCHHHHHH
Confidence 566677766688888 567777776553
No 38
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.64 E-value=48 Score=30.72 Aligned_cols=54 Identities=17% Similarity=0.217 Sum_probs=34.7
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCC---CcccCCCCCCCCccCHHHHHHh
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGF---EAPYYDPRTNLRYANAEVFKLV 102 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl---~A~Y~dP~tglrY~~~~~y~~i 102 (124)
-++.++.|+..-.. ...-|++|. |+-.+|..||. --.+.||.||-. +.+++..|
T Consensus 543 n~~al~~lv~~~~~-----~~i~Y~~in------p~~~~C~~CG~~~~g~~~~CP~CGs~--~~~v~~Rv 599 (625)
T PRK08579 543 DPEALAKLTKRIMN-----TKLVYWSYT------PAITVCNKCGRSTTGLYTRCPRCGSE--DVEVWSRI 599 (625)
T ss_pred CHHHHHHHHHHHHh-----cCCceEEeC------CCCccCCCCCCccCCCCCcCcCCCCc--hhHHHHHH
Confidence 35666666654311 236688876 45567888886 235789999984 56666654
No 39
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=27.42 E-value=35 Score=27.61 Aligned_cols=39 Identities=31% Similarity=0.554 Sum_probs=33.1
Q ss_pred cCCCcccCCCCCCCCccC-HHHHHHhhcCChHHHHHHHHh
Q 033229 78 TGFEAPYYDPRTNLRYAN-AEVFKLVRSLPNEYVQRYLAL 116 (124)
Q Consensus 78 TGl~A~Y~dP~tglrY~~-~~~y~~ir~l~~~~~q~YL~l 116 (124)
+|+.|-+-|-++-.--.. ..+|+.|.+||....-|||.|
T Consensus 93 ~gl~avw~dRrrd~~~l~L~~v~gfIlnlp~~~slG~L~L 132 (204)
T KOG2934|consen 93 CGLEAVWLDRRRDVTALALSVVFGFILNLPCKFSLGYLRL 132 (204)
T ss_pred cCceeeeccccCCcchhhhHHHHHHHHcCCchhccccccc
Confidence 999999999887765544 478999999999999999875
No 40
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.04 E-value=37 Score=26.39 Aligned_cols=26 Identities=15% Similarity=0.206 Sum_probs=20.1
Q ss_pred CCCcccccccCCC--cccCCCCCCCCcc
Q 033229 69 HPCKRICDITGFE--APYYDPRTNLRYA 94 (124)
Q Consensus 69 ~P~kkyCdITGl~--A~Y~dP~tglrY~ 94 (124)
.+.-+.|..||.. ..|.||.||...+
T Consensus 306 ~~tS~~C~~cg~~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 306 YYTSKTCPCCGHLSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCCcccccccCCccceeEECCCCCCeeh
Confidence 4556799999974 4589999998654
No 41
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.02 E-value=22 Score=22.27 Aligned_cols=20 Identities=35% Similarity=0.645 Sum_probs=15.6
Q ss_pred ccccCCCcccCCCCCCCCccCHHHH
Q 033229 75 CDITGFEAPYYDPRTNLRYANAEVF 99 (124)
Q Consensus 75 CdITGl~A~Y~dP~tglrY~~~~~y 99 (124)
||+||. +|-+|.||+...+.
T Consensus 3 Cd~C~~-----~pI~G~R~~C~~C~ 22 (48)
T cd02341 3 CDSCGI-----EPIPGTRYHCSECD 22 (48)
T ss_pred CCCCCC-----CccccceEECCCCC
Confidence 788885 68889999877664
No 42
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.80 E-value=49 Score=22.46 Aligned_cols=28 Identities=7% Similarity=0.042 Sum_probs=24.1
Q ss_pred ccccccCCCcccCCCCCCCCccCHHHHH
Q 033229 73 RICDITGFEAPYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 73 kyCdITGl~A~Y~dP~tglrY~~~~~y~ 100 (124)
.-|.+||-|.-+..-..--+||+.+|-.
T Consensus 8 v~CP~Cgkpv~w~~~s~frPFCSkRCkl 35 (65)
T COG3024 8 VPCPTCGKPVVWGEESPFRPFCSKRCKL 35 (65)
T ss_pred ccCCCCCCcccccccCCcCcchhHhhhh
Confidence 3599999999998888888999998853
No 43
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=25.28 E-value=26 Score=27.53 Aligned_cols=38 Identities=13% Similarity=0.217 Sum_probs=24.0
Q ss_pred ccccccCCCcccCCCCCCCCccCHHHHHHhh-cCChHHHHHHH
Q 033229 73 RICDITGFEAPYYDPRTNLRYANAEVFKLVR-SLPNEYVQRYL 114 (124)
Q Consensus 73 kyCdITGl~A~Y~dP~tglrY~~~~~y~~ir-~l~~~~~q~YL 114 (124)
.||.||+||.-|=.=- - .-..|-.++. +.|.-..+-|+
T Consensus 5 ~YCgvCs~P~EyCEf~--~--~~~kCk~WL~~n~p~l~~~l~~ 43 (173)
T TIGR01159 5 LYCGVCSLPPEYCEFS--G--DLKRCKVWLSENAPDLYAKLYG 43 (173)
T ss_pred EECCCCCCchHHhcCC--C--CHHHHHHHHHHhChHHHHHHhh
Confidence 5999999999985411 1 1156777765 56555544443
No 44
>cd00241 CDH_cytochrome Cellobiose dehydrogenase (CellobioseDH), cytochrome domain; This extracellular fungal oxidoreductase degrades both lignin and cellulose. It is a hemoflavoenzyme that is comprised of a b-type cytochrome domain linked to a large flavodehydrogenase domain. The 2 domains can be separated proteolytically. The cytochrome domain folds as a beta sandwich and complexes a heme molecule.
Probab=24.96 E-value=28 Score=27.41 Aligned_cols=14 Identities=36% Similarity=0.660 Sum_probs=12.1
Q ss_pred CcccCCCCCCCCcc
Q 033229 81 EAPYYDPRTNLRYA 94 (124)
Q Consensus 81 ~A~Y~dP~tglrY~ 94 (124)
++.|+||.||+-|.
T Consensus 2 ~~~y~D~~Tgi~f~ 15 (184)
T cd00241 2 AAPYTDSGTGFVFD 15 (184)
T ss_pred CcceEcCCCCeEEe
Confidence 57899999999884
No 45
>KOG3556 consensus Familial cylindromatosis protein [General function prediction only]
Probab=24.57 E-value=37 Score=31.81 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=15.8
Q ss_pred cccccccCCCcccCCCCC
Q 033229 72 KRICDITGFEAPYYDPRT 89 (124)
Q Consensus 72 kkyCdITGl~A~Y~dP~t 89 (124)
-+-|.|||+.|.|-|+-|
T Consensus 558 prQcsicg~la~yecr~c 575 (724)
T KOG3556|consen 558 PRQCSICGLLAPYECRYC 575 (724)
T ss_pred cceeeecccCCCCCCccC
Confidence 357999999999999876
No 46
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=23.70 E-value=38 Score=25.62 Aligned_cols=19 Identities=16% Similarity=0.308 Sum_probs=13.4
Q ss_pred cccCCCCCCCCccCHHHHH
Q 033229 82 APYYDPRTNLRYANAEVFK 100 (124)
Q Consensus 82 A~Y~dP~tglrY~~~~~y~ 100 (124)
.-|.||.|+.||.-.++..
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~ 126 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAME 126 (158)
T ss_pred CeEECCCCCcEeeHHHHHH
Confidence 4477888888877766654
No 47
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=23.18 E-value=71 Score=28.10 Aligned_cols=31 Identities=16% Similarity=0.174 Sum_probs=28.0
Q ss_pred cccccccCCCcccCCCCCCCCccCHHHHHHh
Q 033229 72 KRICDITGFEAPYYDPRTNLRYANAEVFKLV 102 (124)
Q Consensus 72 kkyCdITGl~A~Y~dP~tglrY~~~~~y~~i 102 (124)
--.|.+||--+-|.|-.|.-.-|+.||-..+
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 58 (518)
T PLN00206 28 EPKCVVCGRYGEYICDETDDDICSLECKQAL 58 (518)
T ss_pred CceEEEecCccceeccCCCCccccHHHHHHH
Confidence 3359999999999999999999999999864
No 48
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.91 E-value=49 Score=31.00 Aligned_cols=45 Identities=18% Similarity=0.327 Sum_probs=30.2
Q ss_pred ccccHHHHHHHhhhCCCCCCCCCceeeeCCCCCCCCcccccccCCCc-------ccCCCCCCCC
Q 033229 36 HWKHLKQILQAENYQNYPPDEPNYVNIESPPSMHPCKRICDITGFEA-------PYYDPRTNLR 92 (124)
Q Consensus 36 ~~K~lkQll~~e~~~~~~~~~ptY~si~appS~~P~kkyCdITGl~A-------~Y~dP~tglr 92 (124)
-++.+++|+..... ..-|++|.-| -.+|..||+.+ .+.||.||-+
T Consensus 617 n~~a~~~lv~~~~~------~i~Y~~in~~------~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 617 NLKALEAVWDYSYD------RVGYLGTNTP------IDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CHHHHHHHHHHHHH------CCCeEEeCCC------CcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 34666666654321 3779988744 45788999843 2699999963
No 49
>KOG1159 consensus NADP-dependent flavoprotein reductase [Energy production and conversion]
Probab=22.62 E-value=54 Score=30.38 Aligned_cols=70 Identities=20% Similarity=0.295 Sum_probs=53.2
Q ss_pred CcccccHHHHHHHhhhCC---------CCCCCCCceeeeCCCCCCCCcccccccCCCcccCCCCCCCCccCHHHHHHhhc
Q 033229 34 GRHWKHLKQILQAENYQN---------YPPDEPNYVNIESPPSMHPCKRICDITGFEAPYYDPRTNLRYANAEVFKLVRS 104 (124)
Q Consensus 34 ~r~~K~lkQll~~e~~~~---------~~~~~ptY~si~appS~~P~kkyCdITGl~A~Y~dP~tglrY~~~~~y~~ir~ 104 (124)
+|-++++-.+|++-+... .|.-.|.++||.+.|+..+-.-.-+|--+-..+.+|+-|| |=.+|.+
T Consensus 336 nRpRRtilEvLeDF~sv~lp~~yl~d~~P~IrPR~fSIas~~~~~~leL~VAiV~ykT~l~~pRrGl------CS~wl~s 409 (574)
T KOG1159|consen 336 NRPRRTILEVLEDFRSVKLPIDYLLDLLPVIRPRAFSIASSPGAHHLELLVAIVEYKTILKEPRRGL------CSNWLAS 409 (574)
T ss_pred cchhhhHHHHHHhchhccCCHHHHHHhccccccceeeeccCCCCCceeEEEEEEEEeeeccccccch------hHHHHhh
Confidence 477889999998887433 3444689999999999888665677888889999999987 4456666
Q ss_pred CChHH
Q 033229 105 LPNEY 109 (124)
Q Consensus 105 l~~~~ 109 (124)
|.++.
T Consensus 410 L~~g~ 414 (574)
T KOG1159|consen 410 LKPGD 414 (574)
T ss_pred cCCCC
Confidence 65543
No 50
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=22.36 E-value=27 Score=22.97 Aligned_cols=17 Identities=35% Similarity=0.610 Sum_probs=14.1
Q ss_pred CCCCCcccccccCCCcc
Q 033229 67 SMHPCKRICDITGFEAP 83 (124)
Q Consensus 67 S~~P~kkyCdITGl~A~ 83 (124)
|.-.+++.|.-||+|+.
T Consensus 25 syH~qK~~CasCGyp~~ 41 (55)
T PF01907_consen 25 SYHIQKKTCASCGYPAA 41 (55)
T ss_dssp EEETTTTEETTTBTTTS
T ss_pred eeecCCCcccccCCCcc
Confidence 44578999999999985
No 51
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.89 E-value=48 Score=24.55 Aligned_cols=14 Identities=21% Similarity=0.140 Sum_probs=10.1
Q ss_pred CCCcccccccCCCc
Q 033229 69 HPCKRICDITGFEA 82 (124)
Q Consensus 69 ~P~kkyCdITGl~A 82 (124)
.|.+-.|..||..-
T Consensus 67 ~p~~~~C~~CG~~~ 80 (135)
T PRK03824 67 EEAVLKCRNCGNEW 80 (135)
T ss_pred cceEEECCCCCCEE
Confidence 46778899999543
No 52
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.45 E-value=50 Score=24.07 Aligned_cols=23 Identities=22% Similarity=0.314 Sum_probs=17.0
Q ss_pred CCCcccccccCCC-----c-------ccCCCCCCCC
Q 033229 69 HPCKRICDITGFE-----A-------PYYDPRTNLR 92 (124)
Q Consensus 69 ~P~kkyCdITGl~-----A-------~Y~dP~tglr 92 (124)
.|.+-+| =||-. . .+.||.||-.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 4778899 89966 1 1679999854
No 53
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=20.25 E-value=31 Score=21.69 Aligned_cols=20 Identities=35% Similarity=0.602 Sum_probs=14.4
Q ss_pred ccccCCCcccCCCCCCCCccCHHHH
Q 033229 75 CDITGFEAPYYDPRTNLRYANAEVF 99 (124)
Q Consensus 75 CdITGl~A~Y~dP~tglrY~~~~~y 99 (124)
||+|+ .+|-+|+||....+.
T Consensus 3 Cd~C~-----~~pi~g~RykC~~C~ 22 (49)
T cd02334 3 CNICK-----EFPITGFRYRCLKCF 22 (49)
T ss_pred CCCCC-----CCCceeeeEECCCCC
Confidence 77777 477888888776553
Done!