Query psy15724
Match_columns 360
No_of_seqs 154 out of 450
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 19:48:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15724.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15724hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2858|consensus 99.9 2.6E-25 5.5E-30 217.1 1.2 233 37-273 14-280 (390)
2 KOG2858|consensus 99.6 1.4E-16 3E-21 156.3 1.0 195 41-264 186-390 (390)
3 KOG2857|consensus 98.9 6.9E-10 1.5E-14 97.3 1.5 43 40-82 5-47 (157)
4 PF04438 zf-HIT: HIT zinc fing 98.8 7.1E-10 1.5E-14 73.6 -1.0 29 40-69 2-30 (30)
5 KOG4317|consensus 98.6 4E-08 8.7E-13 96.1 3.4 70 40-113 7-78 (383)
6 KOG3362|consensus 97.5 2.3E-05 5.1E-10 69.3 0.7 38 38-77 116-153 (156)
7 PF01753 zf-MYND: MYND finger; 92.7 0.03 6.4E-07 38.3 -0.2 29 43-72 1-30 (37)
8 PF13824 zf-Mss51: Zinc-finger 91.9 0.1 2.2E-06 39.5 1.7 24 42-65 1-28 (55)
9 PF07754 DUF1610: Domain of un 85.2 0.51 1.1E-05 30.0 1.3 18 43-60 1-24 (24)
10 KOG0551|consensus 78.8 2.7 5.9E-05 42.7 4.4 97 166-274 273-373 (390)
11 KOG1710|consensus 77.8 0.53 1.1E-05 46.9 -0.9 32 40-71 319-351 (396)
12 PRK13130 H/ACA RNA-protein com 75.4 1.5 3.3E-05 33.3 1.2 26 38-63 3-28 (56)
13 PRK14890 putative Zn-ribbon RN 73.4 1.3 2.7E-05 34.1 0.3 21 40-60 36-56 (59)
14 PLN03158 methionine aminopepti 71.4 1.5 3.2E-05 45.2 0.4 33 37-70 6-46 (396)
15 COG2888 Predicted Zn-ribbon RN 68.6 1.7 3.8E-05 33.5 0.2 22 39-60 37-58 (61)
16 TIGR00622 ssl1 transcription f 67.0 2.7 6E-05 36.2 1.1 43 53-110 2-44 (112)
17 PF13842 Tnp_zf-ribbon_2: DDE_ 65.4 4.3 9.3E-05 27.2 1.6 25 42-66 2-30 (32)
18 PHA00626 hypothetical protein 63.6 3.8 8.3E-05 31.3 1.1 40 40-90 11-50 (59)
19 cd00350 rubredoxin_like Rubred 54.9 7.1 0.00015 26.1 1.2 20 42-61 3-26 (33)
20 PF04640 PLATZ: PLATZ transcri 54.4 9 0.0002 30.5 1.9 26 36-67 45-70 (72)
21 KOG2807|consensus 51.5 7.9 0.00017 39.2 1.4 60 38-113 261-322 (378)
22 cd00729 rubredoxin_SM Rubredox 46.0 12 0.00026 25.3 1.2 20 42-61 4-27 (34)
23 smart00154 ZnF_AN1 AN1-like Zi 43.7 15 0.00033 25.6 1.5 23 43-65 1-25 (39)
24 COG5195 Uncharacterized conser 41.7 17 0.00038 31.0 1.8 30 36-66 62-91 (118)
25 PF09862 DUF2089: Protein of u 40.2 15 0.00033 31.7 1.3 20 43-62 1-22 (113)
26 PF12387 Peptidase_C74: Pestiv 35.9 17 0.00036 33.8 0.9 28 40-67 162-190 (200)
27 COG5151 SSL1 RNA polymerase II 35.6 16 0.00036 36.8 0.9 60 40-115 295-356 (421)
28 PF08265 YL1_C: YL1 nuclear pr 35.4 22 0.00049 23.7 1.2 27 42-69 2-28 (30)
29 TIGR00354 polC DNA polymerase, 33.0 21 0.00045 40.9 1.2 25 38-62 623-647 (1095)
30 PLN00206 DEAD-box ATP-dependen 33.0 15 0.00033 38.6 0.2 35 40-75 28-62 (518)
31 PRK00420 hypothetical protein; 32.9 29 0.00063 29.9 1.8 30 40-72 23-57 (112)
32 PF00643 zf-B_box: B-box zinc 32.9 19 0.00042 24.5 0.6 35 39-73 2-36 (42)
33 COG2260 Predicted Zn-ribbon RN 32.5 24 0.00052 27.2 1.1 11 82-92 31-41 (59)
34 PRK03824 hypA hydrogenase nick 31.8 20 0.00044 31.4 0.7 10 52-61 107-116 (135)
35 PF01428 zf-AN1: AN1-like Zinc 31.6 24 0.00051 24.9 0.9 33 46-81 6-39 (43)
36 PF07282 OrfB_Zn_ribbon: Putat 31.1 29 0.00063 26.2 1.4 21 41-61 29-55 (69)
37 PRK14714 DNA polymerase II lar 31.0 26 0.00057 41.2 1.6 22 41-62 668-689 (1337)
38 PRK14714 DNA polymerase II lar 31.0 27 0.00059 41.1 1.7 21 41-61 680-701 (1337)
39 KOG1356|consensus 30.9 22 0.00047 40.1 0.9 34 38-72 227-262 (889)
40 PF10122 Mu-like_Com: Mu-like 30.9 18 0.00039 27.1 0.2 23 39-61 3-33 (51)
41 smart00290 ZnF_UBP Ubiquitin C 30.1 34 0.00073 24.2 1.5 24 42-65 1-24 (50)
42 PRK12380 hydrogenase nickel in 30.0 22 0.00048 30.2 0.7 25 37-61 67-95 (113)
43 PRK00762 hypA hydrogenase nick 29.7 26 0.00056 30.3 1.0 24 37-61 67-101 (124)
44 PF07150 DUF1390: Protein of u 29.7 27 0.00059 33.6 1.3 40 51-92 6-47 (229)
45 KOG4850|consensus 29.2 24 0.00052 32.4 0.8 35 37-72 132-169 (190)
46 KOG4217|consensus 28.4 34 0.00074 36.4 1.8 24 37-63 266-289 (605)
47 COG1592 Rubrerythrin [Energy p 28.3 34 0.00074 31.4 1.6 22 40-61 134-158 (166)
48 COG4049 Uncharacterized protei 28.1 23 0.00049 27.3 0.3 13 49-61 14-26 (65)
49 PRK04023 DNA polymerase II lar 27.5 50 0.0011 38.2 3.0 25 37-61 623-647 (1121)
50 PF13894 zf-C2H2_4: C2H2-type 27.4 13 0.00027 21.5 -0.9 20 53-72 1-20 (24)
51 PRK00564 hypA hydrogenase nick 27.0 34 0.00075 29.2 1.3 25 37-61 68-97 (117)
52 PF00096 zf-C2H2: Zinc finger, 26.9 21 0.00046 21.0 -0.0 10 53-62 1-10 (23)
53 PRK01343 zinc-binding protein; 26.8 39 0.00085 25.8 1.4 29 38-71 7-35 (57)
54 TIGR00627 tfb4 transcription f 26.5 39 0.00084 33.4 1.7 29 37-66 239-269 (279)
55 PF14206 Cys_rich_CPCC: Cystei 26.4 29 0.00062 28.1 0.7 13 52-64 1-13 (78)
56 PHA00616 hypothetical protein 26.1 12 0.00025 27.2 -1.4 21 52-72 1-21 (44)
57 PF09855 DUF2082: Nucleic-acid 25.2 31 0.00068 26.8 0.7 11 53-63 1-11 (64)
58 PF14949 ARF7EP_C: ARF7 effect 25.2 37 0.0008 28.9 1.2 32 38-70 58-92 (103)
59 PF03884 DUF329: Domain of unk 24.9 21 0.00046 27.2 -0.3 9 61-69 22-30 (57)
60 COG4640 Predicted membrane pro 24.9 38 0.00083 35.3 1.4 26 40-65 1-28 (465)
61 PF13465 zf-H2C2_2: Zinc-finge 24.8 22 0.00048 22.3 -0.2 13 49-61 11-23 (26)
62 COG1571 Predicted DNA-binding 23.9 40 0.00086 35.3 1.3 23 40-62 350-377 (421)
63 PF07649 C1_3: C1-like domain; 23.3 38 0.00083 21.8 0.7 20 42-61 2-24 (30)
64 PF08271 TF_Zn_Ribbon: TFIIB z 22.9 40 0.00087 23.5 0.8 10 53-62 1-10 (43)
65 TIGR00100 hypA hydrogenase nic 22.3 43 0.00094 28.5 1.0 26 37-62 67-96 (115)
66 cd01121 Sms Sms (bacterial rad 22.2 50 0.0011 33.7 1.7 20 42-61 2-23 (372)
67 PF07975 C1_4: TFIIH C1-like d 22.1 36 0.00078 25.4 0.4 29 50-79 19-48 (51)
68 COG0675 Transposase and inacti 22.0 48 0.001 31.4 1.4 20 41-60 310-330 (364)
69 PRK12496 hypothetical protein; 21.8 40 0.00088 30.5 0.8 7 55-61 146-152 (164)
70 PRK03976 rpl37ae 50S ribosomal 21.0 47 0.001 27.6 1.0 13 50-62 34-46 (90)
71 smart00531 TFIIE Transcription 21.0 47 0.001 29.3 1.0 14 50-63 97-110 (147)
72 PRK14704 anaerobic ribonucleos 20.9 54 0.0012 35.9 1.7 24 37-60 556-580 (618)
73 PRK03681 hypA hydrogenase nick 20.9 43 0.00094 28.5 0.8 26 37-62 67-97 (114)
74 COG1997 RPL43A Ribosomal prote 20.7 47 0.001 27.6 0.9 13 50-62 33-45 (89)
75 PF01780 Ribosomal_L37ae: Ribo 20.5 43 0.00092 27.9 0.6 13 50-62 33-45 (90)
76 PF01155 HypA: Hydrogenase exp 20.2 33 0.00071 29.1 -0.1 26 37-62 67-96 (113)
No 1
>KOG2858|consensus
Probab=99.90 E-value=2.6e-25 Score=217.10 Aligned_cols=233 Identities=16% Similarity=0.137 Sum_probs=139.4
Q ss_pred cCCccCcccCCCCCCcccCCCCCCccccccccccccccccccCCCCcccccc-CCCcc------hhhhhhhhhhHHHHHh
Q psy15724 37 VSRLGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIP-LQKFS------NLELQNDFNLLEEVSN 109 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp-~~~~~------~~~l~~DYnFLe~i~R 109 (360)
.....+|.||+.+++||+||||.++||||.|+++||...+|+|.|||..||| +++++ ++.|++|||||-+++|
T Consensus 14 ~~~~vlCgVClknE~KYkCPRCl~rtCsLeCskkHK~~dnCsG~rqp~t~Vp~l~q~d~~K~~~~q~v~~d~n~l~gvkr 93 (390)
T KOG2858|consen 14 GLHSVLCGVCLKNEPKYKCPRCLARTCSLECSKKHKIGDNCSGSRQPPTEVPMLDQPDTEKRLAGQWVEQDVNDLPGVKR 93 (390)
T ss_pred ccchhhhhhcccCcccccCcchhhhheeccccccccccCCCcCCcCCcccccccccCCchhhhhhHHHHHHhhhhhcccc
Confidence 4567789999999999999999999999999999999999999999999999 45553 4689999999999999
Q ss_pred h-hhhccCCCcc-----ccccCCCCCCchhHHHHHHHHHcCcEEE---EcCchhhhccccCcee--ccceEEEEEEEEEE
Q psy15724 110 S-LFKYKRDPVK-----NSVSMYNKLPHPLHILRKYAYMRKTQVK---FLPKLFTQHKINTSCV--YKNNLYWRVEWVFV 178 (360)
Q Consensus 110 ~-ve~~krd~~~-----r~~~~~~~lp~~~~~Lr~~a~~RgI~L~---~lP~gMsRrk~NtT~~--K~~~i~WtVEWiF~ 178 (360)
. +...+.|... +..... .....++....|.+|+.. |+|+|+...+.|.+.+ +.+.|.|+|+|-|.
T Consensus 94 e~v~~qk~D~~~~~ke~kv~~Pe----v~r~~~k~~~eRy~in~~~~rfi~~g~k~e~ln~~~~~~~sd~ikW~i~~dlk 169 (390)
T KOG2858|consen 94 ENVVKQKTDSSLVVKEAKVGEPE----VKREKVKGEVERYSINKQEERFIGQGIKEELLNGECVKEESDFIKWEIVDDLK 169 (390)
T ss_pred cccccccccccccccccccCCcc----cccccccchhhhhhhhhhhhhhcccchhhhhcchhhhhhhccchheeeeeeee
Confidence 7 6666666322 111110 111112222233333333 5566666666666666 56666666666665
Q ss_pred CC-------ceeEeecccccccchhhHhhhccCCCc---hhhhhhcCCccchhhhhcCCCceEEeeec--cC----Ccce
Q psy15724 179 SG-------NLKHVDEKLIDSTRLCIPLTAHLDQPD---LAFYKAADQPDLAFYKAAGINGLLILMKV--ER----SSKF 242 (360)
Q Consensus 179 ~~-------~~~~v~~rv~E~~tL~~iL~k~l~~~~---~dp~~~~~~~kLk~y~~~~i~~l~vlmK~--E~----~~~y 242 (360)
-. ++.-.....+|+....++......... .-+.......+|..+...++++.+|++.. +. ...+
T Consensus 170 v~s~~~il~p~~~k~~~~~eTi~te~~k~~~pr~k~y~clV~e~~k~v~ql~c~~~Rgidd~qf~e~~~s~~~R~~g~I~ 249 (390)
T KOG2858|consen 170 VKSEPPILHPVGCKRKSRCETIGTEEAKYRCPRCKRYSCLVPEVKKHVAQLTCNGVRGIDDQQFTEMNLSDVARTAGHIS 249 (390)
T ss_pred eeccCCCcCchhhhccccccchhhhhccccccchhhhceeccchhhhhhhhcccccccchHHHHHHHhccchhhhcceee
Confidence 10 111111233444433333332222210 00000012223443333466666666652 11 2223
Q ss_pred EEccCCCcHHHhhcCCEEEECcEEEEEecCC
Q psy15724 243 YILDHTLSIAENLKNKCIIEFPIFYVIFNYE 273 (360)
Q Consensus 243 ~~LD~~kTL~enLrgKtVIEFPTI~V~l~~~ 273 (360)
-..-+..++...+++-++++-|++.|.++..
T Consensus 250 ~k~~lk~~~s~~~~nf~k~~~~~k~vfl~~~ 280 (390)
T KOG2858|consen 250 RKAFLKRPISNKYMNFMKNRARRKGVFLKLL 280 (390)
T ss_pred hhcccccchhhhhhhhhheeccccchhHHHh
Confidence 3344556777777777777777777776655
No 2
>KOG2858|consensus
Probab=99.60 E-value=1.4e-16 Score=156.26 Aligned_cols=195 Identities=26% Similarity=0.441 Sum_probs=156.9
Q ss_pred cCcccCCCCCCcccCCCCCCccccccccccccccccccCCCCccccccCCCcchhhhhhhhhh----HHHHHhhhhhccC
Q psy15724 41 GDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQKFSNLELQNDFNL----LEEVSNSLFKYKR 116 (360)
Q Consensus 41 ~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~~~~~~~l~~DYnF----Le~i~R~ve~~kr 116 (360)
+.|+.|....++|+||+|....|.+.|+++|+.+..|.+.| ++ +|.+| |++.+|..+...+
T Consensus 186 ~~~eTi~te~~k~~~pr~k~y~clV~e~~k~v~ql~c~~~R----gi-----------dd~qf~e~~~s~~~R~~g~I~~ 250 (390)
T KOG2858|consen 186 SRCETIGTEEAKYRCPRCKRYSCLVPEVKKHVAQLTCNGVR----GI-----------DDQQFTEMNLSDVARTAGHISR 250 (390)
T ss_pred ccccchhhhhccccccchhhhceeccchhhhhhhhcccccc----cc-----------hHHHHHHHhccchhhhcceeeh
Confidence 88999999999999999999999999999999999999998 33 23333 4556677666666
Q ss_pred CCccccccCCCCCCchhHHHHHHHHHcCcEEEEcCchhhhccccCcee--ccceEEEEEEEEEECCceeEeecccccccc
Q psy15724 117 DPVKNSVSMYNKLPHPLHILRKYAYMRKTQVKFLPKLFTQHKINTSCV--YKNNLYWRVEWVFVSGNLKHVDEKLIDSTR 194 (360)
Q Consensus 117 d~~~r~~~~~~~lp~~~~~Lr~~a~~RgI~L~~lP~gMsRrk~NtT~~--K~~~i~WtVEWiF~~~~~~~v~~rv~E~~t 194 (360)
++..+....+ .....++..+.+.||.|.+++.++..+.+|+|++ ++..|.|+++--|+.+...+...+++...+
T Consensus 251 k~~lk~~~s~----~~~nf~k~~~~~k~vfl~~~q~~~~e~lenst~~~~~~q~f~~~~~~d~pes~~~~~~nr~p~ekt 326 (390)
T KOG2858|consen 251 KAFLKRPISN----KYMNFMKNRARRKGVFLKLLQNGFTERLENSTFFDKKKQQFCWHVKLDFPESQAEYIENRVPDEKT 326 (390)
T ss_pred hcccccchhh----hhhhhhheeccccchhHHHhhhhhhhhhccccccccCCceeeeeeeccCccchhhhhcccCCCccc
Confidence 6655433332 2355667788999999999999999999999999 678999999999998888888899999999
Q ss_pred hhhHhhhccCCCchhhhhhcCCccchhhhhcCCCceEEeeeccC----CcceEEccCCCcHHHhhcCCEEEECc
Q psy15724 195 LCIPLTAHLDQPDLAFYKAADQPDLAFYKAAGINGLLILMKVER----SSKFYILDHTLSIAENLKNKCIIEFP 264 (360)
Q Consensus 195 L~~iL~k~l~~~~~dp~~~~~~~kLk~y~~~~i~~l~vlmK~E~----~~~y~~LD~~kTL~enLrgKtVIEFP 264 (360)
...+...++++.+.++ ..+.+++ .+..+.++.+. ..+||.|||-+++..+|+|+.++|||
T Consensus 327 ~N~~k~p~~D~e~~d~---~~r~r~~-------t~~~~~rk~~y~s~~~~~~ysldPy~p~l~~~~n~l~~ey~ 390 (390)
T KOG2858|consen 327 INEIKKPYIDPEKSDP---VIRQRLK-------TGVQILRKIEYMSQNLVRYYSLDPYKPLLDNLRNKLIIEYP 390 (390)
T ss_pred cccccCCCCCcccccc---hhhccCC-------CCchhhhccchhhhccccccccCCccchhhcccccccccCC
Confidence 9888777888877665 3333332 34445555544 56789999999999999999999998
No 3
>KOG2857|consensus
Probab=98.86 E-value=6.9e-10 Score=97.31 Aligned_cols=43 Identities=35% Similarity=0.925 Sum_probs=38.2
Q ss_pred ccCcccCCCCCCcccCCCCCCccccccccccccccccccCCCC
Q psy15724 40 LGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELECDGIRN 82 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd 82 (360)
+..|.+|.+.+.||+||+|.++||||.|+|.||..-.|-..-+
T Consensus 5 t~tC~ic~e~~~KYKCpkC~vPYCSl~CfKiHk~tPq~~~ve~ 47 (157)
T KOG2857|consen 5 TTTCVICLESEIKYKCPKCSVPYCSLPCFKIHKSTPQCETVED 47 (157)
T ss_pred eeeehhhhcchhhccCCCCCCccccchhhhhccCCccccccCC
Confidence 6789999999999999999999999999999998667766543
No 4
>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=98.77 E-value=7.1e-10 Score=73.58 Aligned_cols=29 Identities=45% Similarity=1.107 Sum_probs=23.4
Q ss_pred ccCcccCCCCCCcccCCCCCCccccccccc
Q psy15724 40 LGDCEVCAIEPAKYTCPKCELKTCCLNCVN 69 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k 69 (360)
..+|.||+. .++|+||+|+.++|||+|+|
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CSl~C~k 30 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCSLACYK 30 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESSHHHHH
T ss_pred cCCCccCcC-CCEEECCCcCCceeCcEeEC
Confidence 357999998 99999999999999999986
No 5
>KOG4317|consensus
Probab=98.55 E-value=4e-08 Score=96.06 Aligned_cols=70 Identities=27% Similarity=0.637 Sum_probs=47.5
Q ss_pred ccCcccCCCCCCcccCCCCCCccccccccccccccccccCCCCccccccCCCcch--hhhhhhhhhHHHHHhhhhh
Q psy15724 40 LGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQKFSN--LELQNDFNLLEEVSNSLFK 113 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~~~~~--~~l~~DYnFLe~i~R~ve~ 113 (360)
-..|.||++..+.||||||..+||||.||+.||. +|+...-+-.- ..++.. ++...--+.+|...|..+.
T Consensus 7 ~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~~--~CsE~FyrdqV--~~eL~~~r~d~s~k~km~e~lkr~~q~ 78 (383)
T KOG4317|consen 7 FLACGICGVQKREYTCPRCNLLYCSLKCYRNHKH--SCSEKFYRDQV--KQELSGKRADISQKRKMGEELKRKMQK 78 (383)
T ss_pred eeeccccccccccccCCCCCccceeeeeecCCCc--cchHHHHHHHH--HHHhhhccccccchhHHHHHHHHHHhh
Confidence 4579999999999999999999999999999995 59976422111 011111 2233334556666666554
No 6
>KOG3362|consensus
Probab=97.55 E-value=2.3e-05 Score=69.32 Aligned_cols=38 Identities=32% Similarity=0.822 Sum_probs=33.0
Q ss_pred CCccCcccCCCCCCcccCCCCCCccccccccccccccccc
Q psy15724 38 SRLGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELEC 77 (360)
Q Consensus 38 ~~~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C 77 (360)
.....|.||| ..++|.|-+||.+|||+.|.+.|.. +-|
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne-TRC 153 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE-TRC 153 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc-ccc
Confidence 4456899999 5899999999999999999999974 555
No 7
>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=92.72 E-value=0.03 Score=38.27 Aligned_cols=29 Identities=28% Similarity=0.765 Sum_probs=23.5
Q ss_pred cccCCCCCCcccCCCC-CCcccccccccccc
Q psy15724 43 CEVCAIEPAKYTCPKC-ELKTCCLNCVNIHK 72 (360)
Q Consensus 43 C~vC~~~~~kY~CP~C-~~~tCSl~C~k~Hk 72 (360)
|.+|+....+ +|++| .+.|||.+|-+.|-
T Consensus 1 C~~C~~~~~~-~C~~C~~~~YCs~~Cq~~~w 30 (37)
T PF01753_consen 1 CAVCGKPALK-RCSRCKSVYYCSEECQRADW 30 (37)
T ss_dssp -TTTSSCSSE-EETTTSSSEESSHHHHHHHH
T ss_pred CcCCCCCcCC-cCCCCCCEEecCHHHHHHHH
Confidence 7789986666 99999 78899999987764
No 8
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=91.85 E-value=0.1 Score=39.51 Aligned_cols=24 Identities=33% Similarity=0.944 Sum_probs=18.7
Q ss_pred CcccCCC---CCCcccCCCCCCcc-ccc
Q psy15724 42 DCEVCAI---EPAKYTCPKCELKT-CCL 65 (360)
Q Consensus 42 ~C~vC~~---~~~kY~CP~C~~~t-CSl 65 (360)
+|.+|.. ....|.||.||++| ||-
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipthcS~ 28 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPTHCSE 28 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcCccCH
Confidence 4777876 35799999999987 554
No 9
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=85.18 E-value=0.51 Score=30.01 Aligned_cols=18 Identities=28% Similarity=1.071 Sum_probs=14.0
Q ss_pred cccC------CCCCCcccCCCCCC
Q psy15724 43 CEVC------AIEPAKYTCPKCEL 60 (360)
Q Consensus 43 C~vC------~~~~~kY~CP~C~~ 60 (360)
|..| .+....|.||.|+.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 6667 55577999999983
No 10
>KOG0551|consensus
Probab=78.82 E-value=2.7 Score=42.72 Aligned_cols=97 Identities=15% Similarity=0.241 Sum_probs=68.3
Q ss_pred cceEEEEEEEEEE-CCceeEeecccccccchhhHhhhccCCCchhhhhhcCCccchhhhhcCCCceEEeeeccCCcceEE
Q psy15724 166 KNNLYWRVEWVFV-SGNLKHVDEKLIDSTRLCIPLTAHLDQPDLAFYKAADQPDLAFYKAAGINGLLILMKVERSSKFYI 244 (360)
Q Consensus 166 ~~~i~WtVEWiF~-~~~~~~v~~rv~E~~tL~~iL~k~l~~~~~dp~~~~~~~kLk~y~~~~i~~l~vlmK~E~~~~y~~ 244 (360)
..+++|-+=+.+| ..+.-|+ ..++|.+|..++|.-+|..+..- +.-+.| .+.+|.|||..+... +++
T Consensus 273 ~s~LiwP~l~~YPe~~qsDFv-~e~~E~tT~~elL~~vl~~p~~w-------D~~~~y---~p~nv~Vf~e~~~~g-L~k 340 (390)
T KOG0551|consen 273 QSRLIWPALFLYPEYAQSDFV-SEVSELTTVIELLKTVLGEPAPW-------DLEQKY---NPDNVLVFMETEAGG-LIK 340 (390)
T ss_pred cceeehhHHHhccchhhcchh-hhccccccHHHHHHHHhCCCCCC-------CHHhcc---CccceeEEEeccccc-eee
Confidence 4678999988888 2333333 48999999999999988765311 111122 458999999887755 999
Q ss_pred ccCCCcHHHhhcCCEEE---ECcEEEEEecCCC
Q psy15724 245 LDHTLSIAENLKNKCII---EFPIFYVIFNYEK 274 (360)
Q Consensus 245 LD~~kTL~enLrgKtVI---EFPTI~V~l~~~~ 274 (360)
+....||.++|+..-|- ==|.|||+.++.+
T Consensus 341 V~~~~~~~~iL~~~~~~l~~g~~~i~Vv~k~~a 373 (390)
T KOG0551|consen 341 VGKKSTLLDILKHPGVFLKDGALKIYVVPKVSA 373 (390)
T ss_pred ccccchHHHHHcCCCeeecCCceEEEEecCccc
Confidence 99999999999965522 1356677665543
No 11
>KOG1710|consensus
Probab=77.84 E-value=0.53 Score=46.94 Aligned_cols=32 Identities=28% Similarity=0.695 Sum_probs=29.1
Q ss_pred ccCcccCCCCCCcccCCCCC-Cccccccccccc
Q psy15724 40 LGDCEVCAIEPAKYTCPKCE-LKTCCLNCVNIH 71 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~-~~tCSl~C~k~H 71 (360)
-..|.+|+...++=||..|. +-||+-.|-|.|
T Consensus 319 ~~fCstCG~~ga~KrCs~CKav~YCdqeCQk~h 351 (396)
T KOG1710|consen 319 CQFCSTCGHPGAKKRCSQCKAVAYCDQECQKFH 351 (396)
T ss_pred cccccccCCCCccchhhhhHHHHHHHHHHHHhh
Confidence 45799999999999999999 899999998765
No 12
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=75.41 E-value=1.5 Score=33.30 Aligned_cols=26 Identities=35% Similarity=0.696 Sum_probs=20.9
Q ss_pred CCccCcccCCCCCCcccCCCCCCccc
Q psy15724 38 SRLGDCEVCAIEPAKYTCPKCELKTC 63 (360)
Q Consensus 38 ~~~~~C~vC~~~~~kY~CP~C~~~tC 63 (360)
.++..|..|+.-.-+-.||.||..|-
T Consensus 3 s~mr~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 3 SKIRKCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred ccceECCCCCCEEccccCcCCCCCCC
Confidence 56778999998777888999987753
No 13
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=73.39 E-value=1.3 Score=34.09 Aligned_cols=21 Identities=43% Similarity=1.065 Sum_probs=16.3
Q ss_pred ccCcccCCCCCCcccCCCCCC
Q psy15724 40 LGDCEVCAIEPAKYTCPKCEL 60 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~ 60 (360)
..+|.-|.+....|+||.|+.
T Consensus 36 I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred EeechhHHhcCCceECCCCCC
Confidence 455777777778899998875
No 14
>PLN03158 methionine aminopeptidase; Provisional
Probab=71.43 E-value=1.5 Score=45.17 Aligned_cols=33 Identities=30% Similarity=0.755 Sum_probs=26.0
Q ss_pred cCCccCcccCCCCCCcccCCCCCC--------cccccccccc
Q psy15724 37 VSRLGDCEVCAIEPAKYTCPKCEL--------KTCCLNCVNI 70 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~kY~CP~C~~--------~tCSl~C~k~ 70 (360)
...+..|.-|++ ++.-+||.|.. .+||-.|+|.
T Consensus 6 ~~~~~~c~~c~~-~a~l~Cp~C~k~~~~~~~s~fCsq~CFk~ 46 (396)
T PLN03158 6 TTSPLACARCSK-PAHLQCPKCLELKLPREGASFCSQDCFKA 46 (396)
T ss_pred CCCcccccCCCC-cccccCccchhcCCCCCCceeECHHHHHH
Confidence 345667999996 68899999965 4699999863
No 15
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=68.57 E-value=1.7 Score=33.46 Aligned_cols=22 Identities=32% Similarity=0.830 Sum_probs=16.9
Q ss_pred CccCcccCCCCCCcccCCCCCC
Q psy15724 39 RLGDCEVCAIEPAKYTCPKCEL 60 (360)
Q Consensus 39 ~~~~C~vC~~~~~kY~CP~C~~ 60 (360)
-..+|.-|.+....|+||.|+.
T Consensus 37 ~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 37 EIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred eeehhhhHHHcCCceECCCcCc
Confidence 3456777778788999999985
No 16
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=66.98 E-value=2.7 Score=36.16 Aligned_cols=43 Identities=28% Similarity=0.535 Sum_probs=26.7
Q ss_pred ccCCCCCCccccccccccccccccccCCCCccccccCCCcchhhhhhhhhhHHHHHhh
Q psy15724 53 YTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQKFSNLELQNDFNLLEEVSNS 110 (360)
Q Consensus 53 Y~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~~~~~~~l~~DYnFLe~i~R~ 110 (360)
|.||+|+.+.|+|+ ..|.-= .+.=....+|-|-|..|--+.-.
T Consensus 2 Y~CPrC~skvC~LP--------~~CpiC-------gLtLVss~HLARSyHHLfPl~~f 44 (112)
T TIGR00622 2 YFCPQCRAKVCELP--------VECPIC-------GLTLILSTHLARSYHHLFPLKAF 44 (112)
T ss_pred ccCCCCCCCccCCC--------CcCCcC-------CCEEeccchHHHhhhccCCCccc
Confidence 99999999999996 223100 01111345788888876555433
No 17
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=65.44 E-value=4.3 Score=27.25 Aligned_cols=25 Identities=32% Similarity=0.990 Sum_probs=20.1
Q ss_pred CcccCCCC----CCcccCCCCCCcccccc
Q psy15724 42 DCEVCAIE----PAKYTCPKCELKTCCLN 66 (360)
Q Consensus 42 ~C~vC~~~----~~kY~CP~C~~~tCSl~ 66 (360)
.|.+|..+ ..+|.|..|++..|--.
T Consensus 2 rC~vC~~~k~rk~T~~~C~~C~v~lC~~~ 30 (32)
T PF13842_consen 2 RCKVCSKKKRRKDTRYMCSKCDVPLCVEP 30 (32)
T ss_pred CCeECCcCCccceeEEEccCCCCcccCCC
Confidence 58888864 37899999999888655
No 18
>PHA00626 hypothetical protein
Probab=63.55 E-value=3.8 Score=31.32 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=29.0
Q ss_pred ccCcccCCCCCCcccCCCCCCccccccccccccccccccCCCCccccccCC
Q psy15724 40 LGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQ 90 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~ 90 (360)
..+|.+|......|.||.|+..+= | +--|.|.+..||.+.
T Consensus 11 Ivrcg~cr~~snrYkCkdCGY~ft--------~---~~~~~~~~~~~~~~~ 50 (59)
T PHA00626 11 IAKEKTMRGWSDDYVCCDCGYNDS--------K---DAFGERGKNEFVRIN 50 (59)
T ss_pred eeeeceecccCcceEcCCCCCeec--------h---hhhhhccccceEEec
Confidence 346888887778999999997651 1 234677777888764
No 19
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=54.91 E-value=7.1 Score=26.09 Aligned_cols=20 Identities=35% Similarity=0.863 Sum_probs=14.4
Q ss_pred CcccCCCC----CCcccCCCCCCc
Q psy15724 42 DCEVCAIE----PAKYTCPKCELK 61 (360)
Q Consensus 42 ~C~vC~~~----~~kY~CP~C~~~ 61 (360)
.|.+|+-. ...++||.|+..
T Consensus 3 ~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECCCcCCCcCcCCCCc
Confidence 57888742 367899999864
No 20
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=54.43 E-value=9 Score=30.53 Aligned_cols=26 Identities=27% Similarity=0.575 Sum_probs=18.6
Q ss_pred ccCCccCcccCCCCCCcccCCCCCCccccccc
Q psy15724 36 KVSRLGDCEVCAIEPAKYTCPKCELKTCCLNC 67 (360)
Q Consensus 36 ~~~~~~~C~vC~~~~~kY~CP~C~~~tCSl~C 67 (360)
.+.....|.+|+..-. =| .++|||.|
T Consensus 45 ~~~~~~~C~~C~R~L~---d~---~~fCSl~C 70 (72)
T PF04640_consen 45 SKGSGNICETCHRSLQ---DP---YRFCSLSC 70 (72)
T ss_pred CCCCCCccCCCCCCCC---CC---CeEEeeeE
Confidence 3456788999987543 12 68999999
No 21
>KOG2807|consensus
Probab=51.51 E-value=7.9 Score=39.19 Aligned_cols=60 Identities=23% Similarity=0.469 Sum_probs=39.2
Q ss_pred CCccCcccCCCC--CCcccCCCCCCccccccccccccccccccCCCCccccccCCCcchhhhhhhhhhHHHHHhhhhh
Q psy15724 38 SRLGDCEVCAIE--PAKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQKFSNLELQNDFNLLEEVSNSLFK 113 (360)
Q Consensus 38 ~~~~~C~vC~~~--~~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~~~~~~~l~~DYnFLe~i~R~ve~ 113 (360)
..+.+|. |+.. .+-|-||+|..+.|||+=.= ..|+ ...| ..-+|-|-|++|-=+.-..+.
T Consensus 261 ~~ps~C~-CH~~~~~~Gy~CP~CkakvCsLP~eC-----piC~-----ltLV-----ss~hLARSyhhL~PL~~F~Ei 322 (378)
T KOG2807|consen 261 DTPSFCA-CHSELSGGGYFCPQCKAKVCSLPIEC-----PICS-----LTLV-----SSPHLARSYHHLFPLKPFVEI 322 (378)
T ss_pred cCcchhe-eccccccCceeCCcccCeeecCCccC-----Cccc-----eeEe-----cchHHHHHHHhhcCCcchhhc
Confidence 3456787 8852 34799999999999995110 1233 1122 346899999999877655554
No 22
>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=45.98 E-value=12 Score=25.32 Aligned_cols=20 Identities=35% Similarity=0.745 Sum_probs=14.1
Q ss_pred CcccCCCC----CCcccCCCCCCc
Q psy15724 42 DCEVCAIE----PAKYTCPKCELK 61 (360)
Q Consensus 42 ~C~vC~~~----~~kY~CP~C~~~ 61 (360)
.|.+|+-. .+..+||.|+..
T Consensus 4 ~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECCcCCCcCcCCCCc
Confidence 58888743 256789999864
No 23
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=43.73 E-value=15 Score=25.62 Aligned_cols=23 Identities=22% Similarity=0.668 Sum_probs=19.3
Q ss_pred cccCCCCCC--cccCCCCCCccccc
Q psy15724 43 CEVCAIEPA--KYTCPKCELKTCCL 65 (360)
Q Consensus 43 C~vC~~~~~--kY~CP~C~~~tCSl 65 (360)
|.+|++... .++|..|+..+|+.
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCcccccCeECCccCCccccc
Confidence 678887666 69999999999984
No 24
>COG5195 Uncharacterized conserved protein [Function unknown]
Probab=41.73 E-value=17 Score=31.04 Aligned_cols=30 Identities=33% Similarity=0.665 Sum_probs=25.0
Q ss_pred ccCCccCcccCCCCCCcccCCCCCCcccccc
Q psy15724 36 KVSRLGDCEVCAIEPAKYTCPKCELKTCCLN 66 (360)
Q Consensus 36 ~~~~~~~C~vC~~~~~kY~CP~C~~~tCSl~ 66 (360)
.+.+|..|+|=+- .+.|+||.=+++|=..+
T Consensus 62 v~P~~KyCDvTGL-~a~Yt~P~t~lrYhn~e 91 (118)
T COG5195 62 VKPRMKYCDVTGL-PAPYTCPNTGLRYHNSE 91 (118)
T ss_pred cccccccccccCC-cccccCCCcCceeccHH
Confidence 4778999999997 79999999999884433
No 25
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=40.19 E-value=15 Score=31.69 Aligned_cols=20 Identities=35% Similarity=0.921 Sum_probs=15.2
Q ss_pred cccCCCCCC--cccCCCCCCcc
Q psy15724 43 CEVCAIEPA--KYTCPKCELKT 62 (360)
Q Consensus 43 C~vC~~~~~--kY~CP~C~~~t 62 (360)
|.||+..-. +++||.|++..
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 888986544 89999988653
No 26
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=35.92 E-value=17 Score=33.85 Aligned_cols=28 Identities=29% Similarity=0.509 Sum_probs=20.6
Q ss_pred ccCcccCCCCCC-cccCCCCCCccccccc
Q psy15724 40 LGDCEVCAIEPA-KYTCPKCELKTCCLNC 67 (360)
Q Consensus 40 ~~~C~vC~~~~~-kY~CP~C~~~tCSl~C 67 (360)
-.+|.||..... .=+||+|+..-=+..|
T Consensus 162 cilCtvCe~r~w~g~~CPKCGr~G~pi~C 190 (200)
T PF12387_consen 162 CILCTVCEGREWKGGNCPKCGRHGKPITC 190 (200)
T ss_pred eEEEeeeecCccCCCCCCcccCCCCCeec
Confidence 346999987666 5679999987655555
No 27
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=35.56 E-value=16 Score=36.85 Aligned_cols=60 Identities=25% Similarity=0.440 Sum_probs=41.4
Q ss_pred ccCcccCCCCC--CcccCCCCCCccccccccccccccccccCCCCccccccCCCcchhhhhhhhhhHHHHHhhhhhcc
Q psy15724 40 LGDCEVCAIEP--AKYTCPKCELKTCCLNCVNIHKRELECDGIRNKVKFIPLQKFSNLELQNDFNLLEEVSNSLFKYK 115 (360)
Q Consensus 40 ~~~C~vC~~~~--~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd~t~fVp~~~~~~~~l~~DYnFLe~i~R~ve~~k 115 (360)
..+|. |+... +-|-||+|..+-|||+=+= ..|+-. .| -..+|.|.|++|--..-.+|...
T Consensus 295 Ps~Ca-CHs~~~~gGy~CP~CktkVCsLPi~C-----P~Csl~-----Li-----lsthLarSyhhL~PLk~f~E~p~ 356 (421)
T COG5151 295 PSVCA-CHSEVKGGGYECPVCKTKVCSLPISC-----PICSLQ-----LI-----LSTHLARSYHHLYPLKPFVEKPE 356 (421)
T ss_pred cccee-eeeeeccCceeCCcccceeecCCccC-----cchhHH-----HH-----HHHHHHHHHHhhccCcccccccC
Confidence 56788 88643 4799999999999995211 224311 11 34689999999988877776544
No 28
>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=35.40 E-value=22 Score=23.67 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=22.8
Q ss_pred CcccCCCCCCcccCCCCCCccccccccc
Q psy15724 42 DCEVCAIEPAKYTCPKCELKTCCLNCVN 69 (360)
Q Consensus 42 ~C~vC~~~~~kY~CP~C~~~tCSl~C~k 69 (360)
.|.|=+. +++|+.|+=+.++.++.-++
T Consensus 2 ~C~iTgl-pA~Y~DP~T~l~Y~n~~ayk 28 (30)
T PF08265_consen 2 YCDITGL-PARYRDPKTGLPYANSEAYK 28 (30)
T ss_pred cccccCC-CccccCCCCCCcccCHHHhh
Confidence 5888776 89999999999998887665
No 29
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=33.01 E-value=21 Score=40.93 Aligned_cols=25 Identities=28% Similarity=0.578 Sum_probs=20.6
Q ss_pred CCccCcccCCCCCCcccCCCCCCcc
Q psy15724 38 SRLGDCEVCAIEPAKYTCPKCELKT 62 (360)
Q Consensus 38 ~~~~~C~vC~~~~~kY~CP~C~~~t 62 (360)
..+..|.-|+.-..+.+||.|+.+|
T Consensus 623 v~~RKCPkCG~yTlk~rCP~CG~~T 647 (1095)
T TIGR00354 623 IAIRKCPQCGKESFWLKCPVCGELT 647 (1095)
T ss_pred EEEEECCCCCcccccccCCCCCCcc
Confidence 3456799999988899999999886
No 30
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=32.98 E-value=15 Score=38.62 Aligned_cols=35 Identities=26% Similarity=0.607 Sum_probs=30.4
Q ss_pred ccCcccCCCCCCcccCCCCCCccccccccccccccc
Q psy15724 40 LGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKREL 75 (360)
Q Consensus 40 ~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~~~ 75 (360)
...|.+|+. -.-|=|-.=.-..|||+|...|-...
T Consensus 28 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (518)
T PLN00206 28 EPKCVVCGR-YGEYICDETDDDICSLECKQALLRRV 62 (518)
T ss_pred CceEEEecC-ccceeccCCCCccccHHHHHHHHHHH
Confidence 345999997 78999999999999999999997544
No 31
>PRK00420 hypothetical protein; Validated
Probab=32.93 E-value=29 Score=29.90 Aligned_cols=30 Identities=17% Similarity=0.389 Sum_probs=21.1
Q ss_pred ccCcccCCC-----CCCcccCCCCCCcccccccccccc
Q psy15724 40 LGDCEVCAI-----EPAKYTCPKCELKTCCLNCVNIHK 72 (360)
Q Consensus 40 ~~~C~vC~~-----~~~kY~CP~C~~~tCSl~C~k~Hk 72 (360)
...|.+|+. +..+.-||.|+. .+.|...++
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~---~~~v~~~ee 57 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGK---VYIVKSDEE 57 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCC---eeeeccHHH
Confidence 357999996 455678999998 556655553
No 32
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=32.88 E-value=19 Score=24.52 Aligned_cols=35 Identities=26% Similarity=0.426 Sum_probs=25.9
Q ss_pred CccCcccCCCCCCcccCCCCCCccccccccccccc
Q psy15724 39 RLGDCEVCAIEPAKYTCPKCELKTCCLNCVNIHKR 73 (360)
Q Consensus 39 ~~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~Hk~ 73 (360)
++..|..|......|-|..|....|+.=-...|+.
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~ 36 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG 36 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC
Confidence 46789999987799999999999987533333653
No 33
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=32.47 E-value=24 Score=27.20 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=5.8
Q ss_pred CccccccCCCc
Q psy15724 82 NKVKFIPLQKF 92 (360)
Q Consensus 82 d~t~fVp~~~~ 92 (360)
.|..|-|-..|
T Consensus 31 ~PprFSPeD~y 41 (59)
T COG2260 31 HPPRFSPEDKY 41 (59)
T ss_pred CCCCCCccchH
Confidence 45566555444
No 34
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.77 E-value=20 Score=31.43 Aligned_cols=10 Identities=40% Similarity=1.012 Sum_probs=7.6
Q ss_pred cccCCCCCCc
Q psy15724 52 KYTCPKCELK 61 (360)
Q Consensus 52 kY~CP~C~~~ 61 (360)
.++||.|+..
T Consensus 107 ~~~CP~Cgs~ 116 (135)
T PRK03824 107 FLKCPKCGSR 116 (135)
T ss_pred CcCCcCCCCC
Confidence 4679999864
No 35
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=31.55 E-value=24 Score=24.86 Aligned_cols=33 Identities=15% Similarity=0.519 Sum_probs=17.1
Q ss_pred CCCCCC-cccCCCCCCccccccccccccccccccCCC
Q psy15724 46 CAIEPA-KYTCPKCELKTCCLNCVNIHKRELECDGIR 81 (360)
Q Consensus 46 C~~~~~-kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~r 81 (360)
|..... .++|+.|+..+|+.- ++..+.+|.+..
T Consensus 6 C~~~~~~~~~C~~C~~~FC~~H---r~~e~H~C~~~~ 39 (43)
T PF01428_consen 6 CKKKDFLPFKCKHCGKSFCLKH---RLPEDHNCSKLQ 39 (43)
T ss_dssp T--BCTSHEE-TTTS-EE-TTT---HSTTTCT-SSTT
T ss_pred CcCccCCCeECCCCCcccCccc---cCccccCCcchh
Confidence 665444 899999999999742 223445666553
No 36
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=31.12 E-value=29 Score=26.24 Aligned_cols=21 Identities=29% Similarity=0.898 Sum_probs=14.0
Q ss_pred cCcccCCCCCC------cccCCCCCCc
Q psy15724 41 GDCEVCAIEPA------KYTCPKCELK 61 (360)
Q Consensus 41 ~~C~vC~~~~~------kY~CP~C~~~ 61 (360)
..|..|+.... .|+||.|+..
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCE
Confidence 35778875433 4888888753
No 37
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.04 E-value=26 Score=41.22 Aligned_cols=22 Identities=32% Similarity=0.807 Sum_probs=16.2
Q ss_pred cCcccCCCCCCcccCCCCCCcc
Q psy15724 41 GDCEVCAIEPAKYTCPKCELKT 62 (360)
Q Consensus 41 ~~C~vC~~~~~kY~CP~C~~~t 62 (360)
..|.-|+.......||.|+.++
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred EECCCCCCccccccCcccCCcC
Confidence 5688888766666888888776
No 38
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=31.02 E-value=27 Score=41.10 Aligned_cols=21 Identities=29% Similarity=0.901 Sum_probs=17.0
Q ss_pred cCcccCCCCC-CcccCCCCCCc
Q psy15724 41 GDCEVCAIEP-AKYTCPKCELK 61 (360)
Q Consensus 41 ~~C~vC~~~~-~kY~CP~C~~~ 61 (360)
..|..|+... ..|.||.|+..
T Consensus 680 ~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 680 NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred ccCcccCCcCCCceeCccCCCc
Confidence 4899999753 48999999985
No 39
>KOG1356|consensus
Probab=30.92 E-value=22 Score=40.09 Aligned_cols=34 Identities=24% Similarity=0.705 Sum_probs=27.6
Q ss_pred CCccCcccCCCCCCc--ccCCCCCCcccccccccccc
Q psy15724 38 SRLGDCEVCAIEPAK--YTCPKCELKTCCLNCVNIHK 72 (360)
Q Consensus 38 ~~~~~C~vC~~~~~k--Y~CP~C~~~tCSl~C~k~Hk 72 (360)
.-...|.+|.....+ .+||+|+..+| +.|++.-+
T Consensus 227 g~~~mC~~C~~tlfn~hw~C~~C~~~~C-l~C~r~~~ 262 (889)
T KOG1356|consen 227 GIREMCDRCETTLFNIHWRCPRCGFGVC-LDCYRKWY 262 (889)
T ss_pred CcchhhhhhcccccceeEEccccCCeee-ecchhhcc
Confidence 334569999998875 79999999965 89998774
No 40
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=30.86 E-value=18 Score=27.11 Aligned_cols=23 Identities=26% Similarity=0.608 Sum_probs=14.9
Q ss_pred CccCcccCCCCCC--------cccCCCCCCc
Q psy15724 39 RLGDCEVCAIEPA--------KYTCPKCELK 61 (360)
Q Consensus 39 ~~~~C~vC~~~~~--------kY~CP~C~~~ 61 (360)
+...|..|+.--+ .-+||||+.-
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 4456888874333 3479999863
No 41
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=30.11 E-value=34 Score=24.17 Aligned_cols=24 Identities=25% Similarity=0.643 Sum_probs=20.4
Q ss_pred CcccCCCCCCcccCCCCCCccccc
Q psy15724 42 DCEVCAIEPAKYTCPKCELKTCCL 65 (360)
Q Consensus 42 ~C~vC~~~~~kY~CP~C~~~tCSl 65 (360)
.|..|+.....|-|..|+.-.|..
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCC
Confidence 489999888899999999888843
No 42
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=30.03 E-value=22 Score=30.21 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=17.8
Q ss_pred cCCccCcccCCCCC----CcccCCCCCCc
Q psy15724 37 VSRLGDCEVCAIEP----AKYTCPKCELK 61 (360)
Q Consensus 37 ~~~~~~C~vC~~~~----~kY~CP~C~~~ 61 (360)
......|..|+... ..|.||.|+..
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 44556799998533 45779999965
No 43
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.74 E-value=26 Score=30.32 Aligned_cols=24 Identities=33% Similarity=0.679 Sum_probs=16.2
Q ss_pred cCCccCcccCCCC-----C------CcccCCCCCCc
Q psy15724 37 VSRLGDCEVCAIE-----P------AKYTCPKCELK 61 (360)
Q Consensus 37 ~~~~~~C~vC~~~-----~------~kY~CP~C~~~ 61 (360)
......| -|+.. . +.+.||.|+-.
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 4445679 89965 1 23789999853
No 44
>PF07150 DUF1390: Protein of unknown function (DUF1390); InterPro: IPR009820 This entry is represented by Paramecium bursaria Chlorella virus 1, A79R; it is a family of uncharacterised viral proteins.
Probab=29.70 E-value=27 Score=33.65 Aligned_cols=40 Identities=25% Similarity=0.500 Sum_probs=29.9
Q ss_pred CcccCCCCCCccccccccccccccccccCCCC--ccccccCCCc
Q psy15724 51 AKYTCPKCELKTCCLNCVNIHKRELECDGIRN--KVKFIPLQKF 92 (360)
Q Consensus 51 ~kY~CP~C~~~tCSl~C~k~Hk~~~~C~g~rd--~t~fVp~~~~ 92 (360)
.-|.| +||-.|=+..+..+||+- .|.+.-- ...||..+++
T Consensus 6 ~lY~C-~CGYkT~~~gnAsKHkKt-sC~hem~~~~~~FVl~ed~ 47 (229)
T PF07150_consen 6 TLYTC-GCGYKTTNKGNASKHKKT-SCGHEMKSETKEFVLKEDY 47 (229)
T ss_pred EEEEe-cCCceecCCccccccCCC-cCCCeeeeeeeceeehhhh
Confidence 46999 899999999999999986 9987631 2255544333
No 45
>KOG4850|consensus
Probab=29.17 E-value=24 Score=32.43 Aligned_cols=35 Identities=23% Similarity=0.708 Sum_probs=26.4
Q ss_pred cCCccCcccCCCCC---CcccCCCCCCcccccccccccc
Q psy15724 37 VSRLGDCEVCAIEP---AKYTCPKCELKTCCLNCVNIHK 72 (360)
Q Consensus 37 ~~~~~~C~vC~~~~---~kY~CP~C~~~tCSl~C~k~Hk 72 (360)
...+-+|. |...+ -.|-||.|+.--|-..|-..-|
T Consensus 132 ~~G~DlCD-Cl~~eCdGC~Y~C~~CGSTkCG~~CR~nRK 169 (190)
T KOG4850|consen 132 TLGFDLCD-CLVVECDGCHYPCKQCGSTKCGIGCRQNRK 169 (190)
T ss_pred eccccHHh-hhccccccceeccccccccccccccccchH
Confidence 45566777 65544 3899999999999999976555
No 46
>KOG4217|consensus
Probab=28.39 E-value=34 Score=36.44 Aligned_cols=24 Identities=38% Similarity=0.819 Sum_probs=16.7
Q ss_pred cCCccCcccCCCCCCcccCCCCCCccc
Q psy15724 37 VSRLGDCEVCAIEPAKYTCPKCELKTC 63 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~kY~CP~C~~~tC 63 (360)
-...++|.||+.+.+ |--=|+|||
T Consensus 266 ~~~e~~CAVCgDnAa---CqHYGvRTC 289 (605)
T KOG4217|consen 266 LSAEGLCAVCGDNAA---CQHYGVRTC 289 (605)
T ss_pred CCccceeeecCChHH---hhhcCcccc
Confidence 445789999998754 555566666
No 47
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=28.27 E-value=34 Score=31.43 Aligned_cols=22 Identities=32% Similarity=0.641 Sum_probs=16.7
Q ss_pred ccCcccCC---CCCCcccCCCCCCc
Q psy15724 40 LGDCEVCA---IEPAKYTCPKCELK 61 (360)
Q Consensus 40 ~~~C~vC~---~~~~kY~CP~C~~~ 61 (360)
.-.|.||+ ..++.=.||-|+.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 45688887 34778899999865
No 48
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=28.09 E-value=23 Score=27.30 Aligned_cols=13 Identities=23% Similarity=0.738 Sum_probs=10.4
Q ss_pred CCCcccCCCCCCc
Q psy15724 49 EPAKYTCPKCELK 61 (360)
Q Consensus 49 ~~~kY~CP~C~~~ 61 (360)
.+...+||+|+.-
T Consensus 14 GE~~lrCPRC~~~ 26 (65)
T COG4049 14 GEEFLRCPRCGMV 26 (65)
T ss_pred CceeeeCCchhHH
Confidence 4678999999864
No 49
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.53 E-value=50 Score=38.24 Aligned_cols=25 Identities=24% Similarity=0.475 Sum_probs=19.8
Q ss_pred cCCccCcccCCCCCCcccCCCCCCc
Q psy15724 37 VSRLGDCEVCAIEPAKYTCPKCELK 61 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~kY~CP~C~~~ 61 (360)
......|.-|+......+||.|+..
T Consensus 623 EVg~RfCpsCG~~t~~frCP~CG~~ 647 (1121)
T PRK04023 623 EIGRRKCPSCGKETFYRRCPFCGTH 647 (1121)
T ss_pred cccCccCCCCCCcCCcccCCCCCCC
Confidence 4556679899988788899999864
No 50
>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=27.42 E-value=13 Score=21.53 Aligned_cols=20 Identities=20% Similarity=0.452 Sum_probs=11.8
Q ss_pred ccCCCCCCcccccccccccc
Q psy15724 53 YTCPKCELKTCCLNCVNIHK 72 (360)
Q Consensus 53 Y~CP~C~~~tCSl~C~k~Hk 72 (360)
|.||.|+..+=+..-.+.|.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~ 20 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHM 20 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHH
Confidence 67888887776665555553
No 51
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.04 E-value=34 Score=29.23 Aligned_cols=25 Identities=28% Similarity=0.541 Sum_probs=16.9
Q ss_pred cCCccCcccCCCCC----Ccc-cCCCCCCc
Q psy15724 37 VSRLGDCEVCAIEP----AKY-TCPKCELK 61 (360)
Q Consensus 37 ~~~~~~C~vC~~~~----~kY-~CP~C~~~ 61 (360)
......|..|+... ..| +||+|+.+
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 44556799998643 234 49999865
No 52
>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=26.91 E-value=21 Score=21.04 Aligned_cols=10 Identities=40% Similarity=1.045 Sum_probs=6.9
Q ss_pred ccCCCCCCcc
Q psy15724 53 YTCPKCELKT 62 (360)
Q Consensus 53 Y~CP~C~~~t 62 (360)
|+||.|+..+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 6777777654
No 53
>PRK01343 zinc-binding protein; Provisional
Probab=26.83 E-value=39 Score=25.84 Aligned_cols=29 Identities=17% Similarity=0.414 Sum_probs=18.6
Q ss_pred CCccCcccCCCCCCcccCCCCCCccccccccccc
Q psy15724 38 SRLGDCEVCAIEPAKYTCPKCELKTCCLNCVNIH 71 (360)
Q Consensus 38 ~~~~~C~vC~~~~~kY~CP~C~~~tCSl~C~k~H 71 (360)
.....|.+|++... .. ..++||-.|-..-
T Consensus 7 ~p~~~CP~C~k~~~-~~----~rPFCS~RC~~iD 35 (57)
T PRK01343 7 RPTRPCPECGKPST-RE----AYPFCSERCRDID 35 (57)
T ss_pred CCCCcCCCCCCcCc-CC----CCcccCHHHhhhh
Confidence 34567999987432 11 3588998886543
No 54
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.49 E-value=39 Score=33.40 Aligned_cols=29 Identities=21% Similarity=0.519 Sum_probs=22.6
Q ss_pred cCCccCcccCCCCCCc--ccCCCCCCcccccc
Q psy15724 37 VSRLGDCEVCAIEPAK--YTCPKCELKTCCLN 66 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~k--Y~CP~C~~~tCSl~ 66 (360)
..-...|. |+.+... |-||.|...+|++.
T Consensus 239 vd~ra~Cf-Ch~k~v~~GyvCs~Clsi~C~~p 269 (279)
T TIGR00627 239 VDYRASCF-CHHQLVSIGFVCSVCLSVLCQYT 269 (279)
T ss_pred CCCcceee-ecCccccceEECCCccCCcCCCC
Confidence 33445787 8877665 99999999999874
No 55
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=26.36 E-value=29 Score=28.11 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=11.0
Q ss_pred cccCCCCCCcccc
Q psy15724 52 KYTCPKCELKTCC 64 (360)
Q Consensus 52 kY~CP~C~~~tCS 64 (360)
||+||-|+.+|=.
T Consensus 1 K~~CPCCg~~Tl~ 13 (78)
T PF14206_consen 1 KYPCPCCGYYTLE 13 (78)
T ss_pred CccCCCCCcEEec
Confidence 7999999998843
No 56
>PHA00616 hypothetical protein
Probab=26.15 E-value=12 Score=27.22 Aligned_cols=21 Identities=24% Similarity=0.205 Sum_probs=15.2
Q ss_pred cccCCCCCCcccccccccccc
Q psy15724 52 KYTCPKCELKTCCLNCVNIHK 72 (360)
Q Consensus 52 kY~CP~C~~~tCSl~C~k~Hk 72 (360)
.|+||+|+....-..=...|-
T Consensus 1 pYqC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 1 MYQCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred CCccchhhHHHhhHHHHHHHH
Confidence 389999998887665555553
No 57
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=25.18 E-value=31 Score=26.80 Aligned_cols=11 Identities=45% Similarity=1.165 Sum_probs=7.7
Q ss_pred ccCCCCCCccc
Q psy15724 53 YTCPKCELKTC 63 (360)
Q Consensus 53 Y~CP~C~~~tC 63 (360)
|+||+|+-..+
T Consensus 1 y~C~KCg~~~~ 11 (64)
T PF09855_consen 1 YKCPKCGNEEY 11 (64)
T ss_pred CCCCCCCCcce
Confidence 77888876543
No 58
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=25.15 E-value=37 Score=28.87 Aligned_cols=32 Identities=31% Similarity=0.762 Sum_probs=23.3
Q ss_pred CCccCcccCCCCC---CcccCCCCCCcccccccccc
Q psy15724 38 SRLGDCEVCAIEP---AKYTCPKCELKTCCLNCVNI 70 (360)
Q Consensus 38 ~~~~~C~vC~~~~---~kY~CP~C~~~tCSl~C~k~ 70 (360)
...-+|+ |.... -.|-||+|+.+-|...|-..
T Consensus 58 ~~~DlCD-CL~~~C~GC~~PC~~C~S~KCG~~CR~n 92 (103)
T PF14949_consen 58 NGKDLCD-CLDEDCPGCHYPCPKCGSRKCGPECRCN 92 (103)
T ss_pred CCCcccc-ccCCCCCCccccCCCCCCCccChhhCcC
Confidence 3345677 65433 27999999999999999543
No 59
>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=24.94 E-value=21 Score=27.19 Aligned_cols=9 Identities=22% Similarity=0.486 Sum_probs=5.9
Q ss_pred ccccccccc
Q psy15724 61 KTCCLNCVN 69 (360)
Q Consensus 61 ~tCSl~C~k 69 (360)
++||-.|-.
T Consensus 22 PFCS~RCk~ 30 (57)
T PF03884_consen 22 PFCSERCKL 30 (57)
T ss_dssp SSSSHHHHH
T ss_pred CcccHhhcc
Confidence 458877754
No 60
>COG4640 Predicted membrane protein [Function unknown]
Probab=24.89 E-value=38 Score=35.28 Aligned_cols=26 Identities=19% Similarity=0.453 Sum_probs=19.6
Q ss_pred ccCcccCC--CCCCcccCCCCCCccccc
Q psy15724 40 LGDCEVCA--IEPAKYTCPKCELKTCCL 65 (360)
Q Consensus 40 ~~~C~vC~--~~~~kY~CP~C~~~tCSl 65 (360)
|..|..|+ .++.-|.||.||.+.=+-
T Consensus 1 M~fC~kcG~qk~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQKAEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccccccccccccccCCcCCch
Confidence 67899999 344567799999876543
No 61
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.76 E-value=22 Score=22.26 Aligned_cols=13 Identities=31% Similarity=0.802 Sum_probs=9.6
Q ss_pred CCCcccCCCCCCc
Q psy15724 49 EPAKYTCPKCELK 61 (360)
Q Consensus 49 ~~~kY~CP~C~~~ 61 (360)
++-.|.||.|+..
T Consensus 11 ~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 11 GEKPYKCPYCGKS 23 (26)
T ss_dssp SSSSEEESSSSEE
T ss_pred CCCCCCCCCCcCe
Confidence 4567999988764
No 62
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.89 E-value=40 Score=35.30 Aligned_cols=23 Identities=22% Similarity=0.592 Sum_probs=15.9
Q ss_pred ccCcccCCCC---CC--cccCCCCCCcc
Q psy15724 40 LGDCEVCAIE---PA--KYTCPKCELKT 62 (360)
Q Consensus 40 ~~~C~vC~~~---~~--kY~CP~C~~~t 62 (360)
..+|..|+.. .. =||||+|+.+.
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccC
Confidence 3478888732 12 59999998876
No 63
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.35 E-value=38 Score=21.83 Aligned_cols=20 Identities=25% Similarity=0.855 Sum_probs=9.1
Q ss_pred CcccCCCCC---CcccCCCCCCc
Q psy15724 42 DCEVCAIEP---AKYTCPKCELK 61 (360)
Q Consensus 42 ~C~vC~~~~---~kY~CP~C~~~ 61 (360)
.|.+|+... ..|.|+.|..-
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFD 24 (30)
T ss_dssp --TTTS----S--EEE-TTT---
T ss_pred cCCcCCCcCCCCceEECccCCCc
Confidence 588898765 47999999753
No 64
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.92 E-value=40 Score=23.54 Aligned_cols=10 Identities=40% Similarity=1.049 Sum_probs=8.2
Q ss_pred ccCCCCCCcc
Q psy15724 53 YTCPKCELKT 62 (360)
Q Consensus 53 Y~CP~C~~~t 62 (360)
|+||.|+...
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 7899998876
No 65
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=22.33 E-value=43 Score=28.50 Aligned_cols=26 Identities=35% Similarity=0.649 Sum_probs=18.1
Q ss_pred cCCccCcccCCCCC----CcccCCCCCCcc
Q psy15724 37 VSRLGDCEVCAIEP----AKYTCPKCELKT 62 (360)
Q Consensus 37 ~~~~~~C~vC~~~~----~kY~CP~C~~~t 62 (360)
......|..|+... ..+.||.|+...
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEIDLYRCPKCHGIM 96 (115)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCcCCC
Confidence 34456799998643 356799999764
No 66
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=22.19 E-value=50 Score=33.69 Aligned_cols=20 Identities=30% Similarity=0.818 Sum_probs=16.5
Q ss_pred CcccCCCCCCcc--cCCCCCCc
Q psy15724 42 DCEVCAIEPAKY--TCPKCELK 61 (360)
Q Consensus 42 ~C~vC~~~~~kY--~CP~C~~~ 61 (360)
.|..|+...+|+ +||.|+.=
T Consensus 2 ~c~~cg~~~~~~~g~cp~c~~w 23 (372)
T cd01121 2 VCSECGYVSPKWLGKCPECGEW 23 (372)
T ss_pred CCCCCCCCCCCccEECcCCCCc
Confidence 599999888776 89999853
No 67
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=22.07 E-value=36 Score=25.41 Aligned_cols=29 Identities=41% Similarity=1.047 Sum_probs=14.3
Q ss_pred CCcccCCCCCCccccccc-cccccccccccC
Q psy15724 50 PAKYTCPKCELKTCCLNC-VNIHKRELECDG 79 (360)
Q Consensus 50 ~~kY~CP~C~~~tCSl~C-~k~Hk~~~~C~g 79 (360)
...|+||+|...+|- .| +..|-.-.+|-|
T Consensus 19 ~~~y~C~~C~~~FC~-dCD~fiHE~LH~CPG 48 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCI-DCDVFIHETLHNCPG 48 (51)
T ss_dssp -EEE--TTTT--B-H-HHHHTTTTTS-SSST
T ss_pred CCeEECCCCCCcccc-CcChhhhccccCCcC
Confidence 468999999999984 33 344665555554
No 68
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.96 E-value=48 Score=31.36 Aligned_cols=20 Identities=25% Similarity=0.904 Sum_probs=11.6
Q ss_pred cCcccCCCCC-CcccCCCCCC
Q psy15724 41 GDCEVCAIEP-AKYTCPKCEL 60 (360)
Q Consensus 41 ~~C~vC~~~~-~kY~CP~C~~ 60 (360)
..|..|+.-. ..|.||+|+.
T Consensus 310 ~~C~~cg~~~~r~~~C~~cg~ 330 (364)
T COG0675 310 KTCPCCGHLSGRLFKCPRCGF 330 (364)
T ss_pred ccccccCCccceeEECCCCCC
Confidence 3577777521 2467777763
No 69
>PRK12496 hypothetical protein; Provisional
Probab=21.83 E-value=40 Score=30.50 Aligned_cols=7 Identities=29% Similarity=0.804 Sum_probs=4.0
Q ss_pred CCCCCCc
Q psy15724 55 CPKCELK 61 (360)
Q Consensus 55 CP~C~~~ 61 (360)
||.||.+
T Consensus 146 C~~CG~~ 152 (164)
T PRK12496 146 CEICGSP 152 (164)
T ss_pred CCCCCCh
Confidence 6666544
No 70
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=21.02 E-value=47 Score=27.64 Aligned_cols=13 Identities=38% Similarity=0.715 Sum_probs=10.1
Q ss_pred CCcccCCCCCCcc
Q psy15724 50 PAKYTCPKCELKT 62 (360)
Q Consensus 50 ~~kY~CP~C~~~t 62 (360)
-++|+||.|+...
T Consensus 34 ~a~y~CpfCgk~~ 46 (90)
T PRK03976 34 RAKHVCPVCGRPK 46 (90)
T ss_pred hcCccCCCCCCCc
Confidence 4799999996543
No 71
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=20.96 E-value=47 Score=29.27 Aligned_cols=14 Identities=43% Similarity=0.930 Sum_probs=9.8
Q ss_pred CCcccCCCCCCccc
Q psy15724 50 PAKYTCPKCELKTC 63 (360)
Q Consensus 50 ~~kY~CP~C~~~tC 63 (360)
...|.||.|+.++=
T Consensus 97 ~~~Y~Cp~C~~~y~ 110 (147)
T smart00531 97 NAYYKCPNCQSKYT 110 (147)
T ss_pred CcEEECcCCCCEee
Confidence 45788888876653
No 72
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.94 E-value=54 Score=35.90 Aligned_cols=24 Identities=21% Similarity=0.625 Sum_probs=17.7
Q ss_pred cCCccCcccCCCC-CCcccCCCCCC
Q psy15724 37 VSRLGDCEVCAIE-PAKYTCPKCEL 60 (360)
Q Consensus 37 ~~~~~~C~vC~~~-~~kY~CP~C~~ 60 (360)
......|..|+-. +..++||.|+.
T Consensus 556 n~~~~~C~~CGy~g~~~~~CP~CG~ 580 (618)
T PRK14704 556 NHPVDRCKCCSYHGVIGNECPSCGN 580 (618)
T ss_pred CCCCeecCCCCCCCCcCccCcCCCC
Confidence 4456689999853 34589999986
No 73
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.89 E-value=43 Score=28.49 Aligned_cols=26 Identities=23% Similarity=0.424 Sum_probs=17.7
Q ss_pred cCCccCcccCCCCCC-----cccCCCCCCcc
Q psy15724 37 VSRLGDCEVCAIEPA-----KYTCPKCELKT 62 (360)
Q Consensus 37 ~~~~~~C~vC~~~~~-----kY~CP~C~~~t 62 (360)
......|.-|+.... .+.||.|+...
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 445567999986532 26699999653
No 74
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=20.70 E-value=47 Score=27.57 Aligned_cols=13 Identities=46% Similarity=0.754 Sum_probs=10.8
Q ss_pred CCcccCCCCCCcc
Q psy15724 50 PAKYTCPKCELKT 62 (360)
Q Consensus 50 ~~kY~CP~C~~~t 62 (360)
-++|.||.|+.++
T Consensus 33 ~~~~~Cp~C~~~~ 45 (89)
T COG1997 33 RAKHVCPFCGRTT 45 (89)
T ss_pred hcCCcCCCCCCcc
Confidence 4789999999875
No 75
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 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 ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=20.54 E-value=43 Score=27.90 Aligned_cols=13 Identities=54% Similarity=1.045 Sum_probs=9.7
Q ss_pred CCcccCCCCCCcc
Q psy15724 50 PAKYTCPKCELKT 62 (360)
Q Consensus 50 ~~kY~CP~C~~~t 62 (360)
-++|+||.|+...
T Consensus 33 ~~ky~Cp~Cgk~~ 45 (90)
T PF01780_consen 33 HAKYTCPFCGKTS 45 (90)
T ss_dssp HS-BEESSSSSSE
T ss_pred hCCCcCCCCCCce
Confidence 3689999999765
No 76
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=20.24 E-value=33 Score=29.08 Aligned_cols=26 Identities=27% Similarity=0.698 Sum_probs=15.3
Q ss_pred cCCccCcccCCCCC----CcccCCCCCCcc
Q psy15724 37 VSRLGDCEVCAIEP----AKYTCPKCELKT 62 (360)
Q Consensus 37 ~~~~~~C~vC~~~~----~kY~CP~C~~~t 62 (360)
......|..|+... ..|.||.|+...
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFDFSCPRCGSPD 96 (113)
T ss_dssp E--EEEETTTS-EEECHHCCHH-SSSSSS-
T ss_pred cCCcEECCCCCCEEecCCCCCCCcCCcCCC
Confidence 34456799999643 257899998753
Done!