Query psy14516
Match_columns 76
No_of_seqs 103 out of 471
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 21:53:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14516.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14516hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02148 zf-UBP: Zn-finger in 99.2 9E-12 1.9E-16 73.0 1.3 32 45-76 1-33 (63)
2 KOG0804|consensus 99.1 2.3E-11 5E-16 94.3 0.9 36 41-76 227-262 (493)
3 smart00290 ZnF_UBP Ubiquitin C 99.0 1.3E-10 2.9E-15 64.5 1.8 33 44-76 1-33 (50)
4 COG5207 UBP14 Isopeptidase T [ 99.0 2E-10 4.3E-15 91.2 2.4 64 13-76 143-212 (749)
5 KOG0944|consensus 98.9 9.8E-10 2.1E-14 88.6 2.6 62 15-76 149-219 (763)
6 cd02669 Peptidase_C19M A subfa 97.8 1E-05 2.2E-10 61.7 2.5 37 40-76 14-50 (440)
7 KOG1873|consensus 96.9 0.00041 8.8E-09 57.4 1.4 52 25-76 45-116 (877)
8 PRK14890 putative Zn-ribbon RN 85.2 0.29 6.2E-06 28.8 0.1 24 41-64 35-58 (59)
9 COG2888 Predicted Zn-ribbon RN 82.5 0.4 8.8E-06 28.4 0.0 24 41-64 37-60 (61)
10 cd00350 rubredoxin_like Rubred 80.3 0.8 1.7E-05 23.3 0.7 20 43-62 2-25 (33)
11 cd00729 rubredoxin_SM Rubredox 78.7 1.3 2.7E-05 22.9 1.1 14 54-67 2-15 (34)
12 PF14803 Nudix_N_2: Nudix N-te 73.6 2.9 6.4E-05 21.7 1.7 14 51-64 19-32 (34)
13 PF00643 zf-B_box: B-box zinc 68.5 3.4 7.5E-05 21.3 1.3 26 42-67 3-28 (42)
14 COG5207 UBP14 Isopeptidase T [ 65.6 1.7 3.8E-05 35.6 -0.4 50 24-73 2-57 (749)
15 PF07754 DUF1610: Domain of un 62.6 6 0.00013 19.2 1.4 12 50-61 12-23 (24)
16 PF01927 Mut7-C: Mut7-C RNAse 62.3 6.3 0.00014 26.0 1.9 13 52-64 122-134 (147)
17 PRK11788 tetratricopeptide rep 59.8 6 0.00013 28.3 1.6 26 40-65 352-379 (389)
18 PF04810 zf-Sec23_Sec24: Sec23 59.5 8.7 0.00019 20.2 1.8 13 51-63 21-33 (40)
19 PF13923 zf-C3HC4_2: Zinc fing 58.1 7.7 0.00017 19.8 1.4 22 46-67 2-24 (39)
20 COG1773 Rubredoxin [Energy pro 57.5 5.7 0.00012 23.0 0.9 12 51-62 33-44 (55)
21 smart00661 RPOL9 RNA polymeras 57.4 10 0.00022 20.2 1.9 12 53-64 19-30 (52)
22 PF08274 PhnA_Zn_Ribbon: PhnA 57.3 6.4 0.00014 20.0 1.0 20 44-63 4-28 (30)
23 smart00154 ZnF_AN1 AN1-like Zi 56.9 10 0.00022 20.0 1.8 28 45-72 1-32 (39)
24 COG1997 RPL43A Ribosomal prote 55.8 9.5 0.00021 24.1 1.8 27 41-67 34-66 (89)
25 COG5574 PEX10 RING-finger-cont 54.3 9.8 0.00021 28.4 1.9 26 41-66 214-239 (271)
26 PF01412 ArfGap: Putative GTPa 54.2 11 0.00024 23.9 1.9 28 40-67 11-38 (116)
27 PRK10220 hypothetical protein; 53.8 9.9 0.00021 24.9 1.7 20 45-64 6-30 (111)
28 TIGR00686 phnA alkylphosphonat 52.3 9.3 0.0002 25.0 1.4 20 45-64 5-29 (109)
29 PF09538 FYDLN_acid: Protein o 50.1 15 0.00033 23.6 2.1 26 39-64 6-36 (108)
30 PHA02942 putative transposase; 49.4 14 0.0003 28.3 2.1 24 41-64 324-352 (383)
31 PF10571 UPF0547: Uncharacteri 49.1 8.5 0.00018 18.8 0.7 19 45-63 3-23 (26)
32 COG0777 AccD Acetyl-CoA carbox 47.6 6.4 0.00014 29.7 0.1 24 40-63 26-56 (294)
33 COG0675 Transposase and inacti 45.6 18 0.00038 25.3 2.1 25 41-65 308-333 (364)
34 KOG2026|consensus 45.6 16 0.00036 28.9 2.0 37 40-76 27-63 (442)
35 PF08271 TF_Zn_Ribbon: TFIIB z 45.5 22 0.00047 18.7 2.0 16 52-67 17-32 (43)
36 cd01121 Sms Sms (bacterial rad 45.3 12 0.00027 28.4 1.3 21 44-64 2-24 (372)
37 KOG0317|consensus 44.9 9.9 0.00021 28.7 0.7 27 40-66 237-263 (293)
38 smart00105 ArfGap Putative GTP 43.7 13 0.00029 23.4 1.1 26 42-67 3-28 (112)
39 PF07282 OrfB_Zn_ribbon: Putat 43.5 20 0.00044 20.2 1.8 23 41-63 27-55 (69)
40 PF00096 zf-C2H2: Zinc finger, 43.4 3.3 7.2E-05 18.6 -1.3 20 55-74 1-21 (23)
41 PRK11823 DNA repair protein Ra 43.3 13 0.00027 28.9 1.1 25 41-65 6-32 (446)
42 PF13719 zinc_ribbon_5: zinc-r 42.3 7.6 0.00017 20.1 -0.2 29 22-50 2-33 (37)
43 PF15227 zf-C3HC4_4: zinc fing 41.9 21 0.00046 18.8 1.6 23 45-67 1-23 (42)
44 COG1592 Rubrerythrin [Energy p 40.7 13 0.00029 25.7 0.8 13 54-66 134-146 (166)
45 TIGR02605 CxxC_CxxC_SSSS putat 40.7 13 0.00027 20.1 0.6 6 57-62 29-34 (52)
46 TIGR00416 sms DNA repair prote 40.3 14 0.00031 28.7 1.0 25 41-65 6-32 (454)
47 PF13920 zf-C3HC4_3: Zinc fing 39.5 25 0.00053 18.7 1.6 25 43-67 3-28 (50)
48 PF05715 zf-piccolo: Piccolo Z 38.1 26 0.00056 20.7 1.6 21 42-62 30-57 (61)
49 COG1656 Uncharacterized conser 37.8 20 0.00044 24.9 1.3 14 51-64 127-140 (165)
50 PRK14704 anaerobic ribonucleos 37.8 20 0.00043 29.4 1.5 23 41-63 558-581 (618)
51 PF06221 zf-C2HC5: Putative zi 36.0 12 0.00027 21.6 0.0 14 56-69 20-33 (57)
52 COG1066 Sms Predicted ATP-depe 35.9 19 0.00041 28.8 1.1 22 41-62 6-29 (456)
53 PF05191 ADK_lid: Adenylate ki 35.0 24 0.00051 18.4 1.0 10 55-64 2-11 (36)
54 PF08792 A2L_zn_ribbon: A2L zi 34.6 39 0.00085 17.2 1.8 22 43-64 4-31 (33)
55 PF11781 RRN7: RNA polymerase 34.4 33 0.00072 17.8 1.6 22 42-63 8-34 (36)
56 smart00547 ZnF_RBZ Zinc finger 33.6 24 0.00052 16.3 0.9 6 43-48 3-8 (26)
57 TIGR02487 NrdD anaerobic ribon 33.5 26 0.00056 28.3 1.5 26 41-66 523-550 (579)
58 PRK14873 primosome assembly pr 33.4 28 0.0006 28.7 1.7 23 41-63 409-431 (665)
59 PRK09263 anaerobic ribonucleos 33.0 26 0.00056 29.2 1.4 22 41-62 640-667 (711)
60 cd00730 rubredoxin Rubredoxin; 32.6 19 0.00042 20.1 0.5 12 55-66 2-13 (50)
61 PRK08270 anaerobic ribonucleos 32.4 27 0.00058 28.8 1.4 23 41-63 625-648 (656)
62 PF01780 Ribosomal_L37ae: Ribo 32.4 27 0.0006 22.0 1.2 27 41-67 34-66 (90)
63 PF15616 TerY-C: TerY-C metal 32.3 38 0.00082 22.6 1.9 22 43-65 78-99 (131)
64 PRK00762 hypA hydrogenase nick 32.1 17 0.00038 23.5 0.3 22 40-62 68-100 (124)
65 TIGR00515 accD acetyl-CoA carb 32.1 12 0.00027 27.7 -0.5 23 41-63 25-54 (285)
66 PF12523 DUF3725: Protein of u 31.4 25 0.00054 21.4 0.9 12 52-63 57-68 (74)
67 CHL00174 accD acetyl-CoA carbo 31.1 13 0.00027 28.0 -0.6 22 41-62 37-65 (296)
68 COG2051 RPS27A Ribosomal prote 30.6 49 0.0011 19.9 2.0 27 41-67 18-51 (67)
69 PRK05654 acetyl-CoA carboxylas 30.2 14 0.00031 27.4 -0.4 23 41-63 26-55 (292)
70 PF07649 C1_3: C1-like domain; 30.0 26 0.00056 17.0 0.6 20 44-63 2-24 (30)
71 PRK07218 replication factor A; 29.7 26 0.00057 27.4 1.0 23 41-63 296-318 (423)
72 PF00641 zf-RanBP: Zn-finger i 29.7 37 0.00081 16.4 1.2 14 53-66 3-16 (30)
73 PRK14559 putative protein seri 29.7 46 0.00099 27.5 2.3 36 22-63 1-36 (645)
74 PRK08271 anaerobic ribonucleos 29.4 33 0.00072 28.2 1.5 25 41-65 565-591 (623)
75 PF04438 zf-HIT: HIT zinc fing 29.3 26 0.00057 17.5 0.6 23 43-66 3-25 (30)
76 PF14835 zf-RING_6: zf-RING of 29.2 32 0.00069 20.5 1.1 26 42-67 7-33 (65)
77 PRK12380 hydrogenase nickel in 28.9 21 0.00046 22.7 0.3 24 40-63 68-95 (113)
78 smart00184 RING Ring finger. E 28.6 32 0.0007 15.9 0.9 21 46-66 2-22 (39)
79 PF13894 zf-C2H2_4: C2H2-type 28.4 35 0.00076 14.5 0.9 13 55-67 1-13 (24)
80 PF00097 zf-C3HC4: Zinc finger 28.2 53 0.0011 16.4 1.7 23 45-67 1-24 (41)
81 cd01675 RNR_III Class III ribo 27.2 33 0.00071 27.5 1.1 25 41-65 517-543 (555)
82 PF07295 DUF1451: Protein of u 26.8 37 0.00079 22.9 1.1 28 41-68 111-144 (146)
83 PF08882 Acetone_carb_G: Aceto 26.6 42 0.00091 22.0 1.4 17 52-68 13-37 (112)
84 PF01428 zf-AN1: AN1-like Zinc 26.3 36 0.00078 17.9 0.9 19 54-72 13-33 (43)
85 cd02341 ZZ_ZZZ3 Zinc finger, Z 26.1 46 0.00099 18.3 1.3 11 51-61 12-22 (48)
86 TIGR00100 hypA hydrogenase nic 26.1 34 0.00074 21.8 0.9 24 40-63 68-95 (115)
87 COG2023 RPR2 RNase P subunit R 25.4 39 0.00084 21.9 1.0 12 53-64 81-92 (105)
88 PRK00398 rpoP DNA-directed RNA 24.8 57 0.0012 17.2 1.5 20 43-62 4-29 (46)
89 PF00569 ZZ: Zinc finger, ZZ t 24.8 60 0.0013 17.3 1.6 19 43-61 5-26 (46)
90 TIGR02300 FYDLN_acid conserved 24.5 58 0.0012 21.9 1.7 25 40-64 7-36 (129)
91 PRK00564 hypA hydrogenase nick 24.2 35 0.00077 21.8 0.7 24 40-63 69-97 (117)
92 PF09986 DUF2225: Uncharacteri 24.1 35 0.00077 23.9 0.7 15 53-67 47-61 (214)
93 smart00834 CxxC_CXXC_SSSS Puta 23.6 42 0.00092 16.8 0.8 7 56-62 28-34 (41)
94 PRK00415 rps27e 30S ribosomal 23.4 54 0.0012 19.1 1.3 27 41-67 10-43 (59)
95 smart00064 FYVE Protein presen 23.3 53 0.0011 18.3 1.2 26 42-67 10-39 (68)
96 PRK03681 hypA hydrogenase nick 23.1 39 0.00084 21.6 0.7 24 40-63 68-96 (114)
97 TIGR00595 priA primosomal prot 22.9 58 0.0013 25.7 1.8 23 41-63 239-262 (505)
98 PRK11032 hypothetical protein; 22.8 46 0.00099 22.9 1.0 28 41-68 123-156 (160)
99 COG5347 GTPase-activating prot 22.8 51 0.0011 25.0 1.4 28 40-67 18-45 (319)
100 PHA00616 hypothetical protein 22.4 9.1 0.0002 21.1 -2.0 19 56-74 3-22 (44)
101 PRK05452 anaerobic nitric oxid 22.4 49 0.0011 25.9 1.3 10 53-62 457-466 (479)
102 PF13717 zinc_ribbon_4: zinc-r 22.3 27 0.00058 18.0 -0.2 28 23-50 3-33 (36)
103 PHA00626 hypothetical protein 21.9 72 0.0016 18.7 1.6 25 42-66 11-35 (59)
104 smart00504 Ubox Modified RING 21.5 43 0.00093 18.1 0.6 23 45-67 4-26 (63)
105 PF09723 Zn-ribbon_8: Zinc rib 21.5 44 0.00095 17.6 0.6 9 54-62 26-34 (42)
106 PRK08579 anaerobic ribonucleos 21.4 56 0.0012 26.9 1.4 26 40-65 566-593 (625)
107 cd02344 ZZ_HERC2 Zinc finger, 21.1 93 0.002 16.9 1.9 11 51-61 12-22 (45)
108 PLN03119 putative ADP-ribosyla 21.0 80 0.0017 26.4 2.2 28 40-67 21-48 (648)
109 PRK00432 30S ribosomal protein 20.5 81 0.0018 17.4 1.6 21 44-64 22-47 (50)
110 PF13248 zf-ribbon_3: zinc-rib 20.3 63 0.0014 15.2 1.0 7 56-62 18-24 (26)
111 cd00065 FYVE FYVE domain; Zinc 20.2 55 0.0012 17.5 0.8 11 57-67 21-31 (57)
112 TIGR02827 RNR_anaer_Bdell anae 20.0 53 0.0012 26.9 1.1 25 41-65 531-557 (586)
No 1
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=99.16 E-value=9e-12 Score=72.97 Aligned_cols=32 Identities=41% Similarity=0.978 Sum_probs=28.0
Q ss_pred cCcCCCC-CCeeeecccCceeecCCCcchhccC
Q psy14516 45 CVDCASV-AENWVCLICYQVRCGRYIEEHSNEF 76 (76)
Q Consensus 45 C~~C~~~-~~~W~CL~Cg~v~CgR~~~~Ha~~H 76 (76)
|++|+.. .++|+||+||+++|||+.++||++|
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H 33 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKH 33 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHH
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHh
Confidence 7788877 8999999999999999999999887
No 2
>KOG0804|consensus
Probab=99.09 E-value=2.3e-11 Score=94.31 Aligned_cols=36 Identities=39% Similarity=1.001 Sum_probs=33.8
Q ss_pred CccccCcCCCCCCeeeecccCceeecCCCcchhccC
Q psy14516 41 VKAPCVDCASVAENWVCLICYQVRCGRYIEEHSNEF 76 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v~CgR~~~~Ha~~H 76 (76)
....|.+|+...++|+||+||+||||||..|||++|
T Consensus 227 e~~~c~~c~~~~~LwicliCg~vgcgrY~eghA~rH 262 (493)
T KOG0804|consen 227 ESSLCLACGCTEDLWICLICGNVGCGRYKEGHARRH 262 (493)
T ss_pred hhhhhhhhcccccEEEEEEccceecccccchhHHHH
Confidence 367799999999999999999999999999999998
No 3
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=99.01 E-value=1.3e-10 Score=64.53 Aligned_cols=33 Identities=42% Similarity=0.983 Sum_probs=30.7
Q ss_pred ccCcCCCCCCeeeecccCceeecCCCcchhccC
Q psy14516 44 PCVDCASVAENWVCLICYQVRCGRYIEEHSNEF 76 (76)
Q Consensus 44 ~C~~C~~~~~~W~CL~Cg~v~CgR~~~~Ha~~H 76 (76)
+|.+|....++|+||+|++++|+|+.++|+.+|
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~~~~~h~~~H 33 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGRYQLGHALEH 33 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCCCCCcHHHHH
Confidence 589999999999999999999999989999876
No 4
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=2e-10 Score=91.16 Aligned_cols=64 Identities=27% Similarity=0.444 Sum_probs=49.9
Q ss_pred ccceEeeeeCCCCCCccCcccCCCC-CCCCccccCcCCCCCCeeeecccCceeecCC-----CcchhccC
Q psy14516 13 NEEMFLVTPLADCPHTPLVAPVPQS-GVDVKAPCVDCASVAENWVCLICYQVRCGRY-----IEEHSNEF 76 (76)
Q Consensus 13 ~~~~fav~p~~~CpHl~~l~~~~~~-~~~~~~~C~~C~~~~~~W~CL~Cg~v~CgR~-----~~~Ha~~H 76 (76)
.+.-.|+..+.+|+|.-.+.+-... ..-....|+.|+...++|+||+||.+||||- +||||+.|
T Consensus 143 d~~~~w~~E~~tC~H~~n~~~~s~~~~ni~~~~Cs~CDl~~nLW~Cl~CG~vgCGR~QyG~~GngHAlsH 212 (749)
T COG5207 143 DERVLWRDEEVTCVHGCNEGPSSIEMGNIGGLKCSLCDLKTNLWVCLSCGYVGCGRMQYGAEGNGHALSH 212 (749)
T ss_pred hhhhhhhhhcccccccCCCCCCcccccccCCceeccccchhceEEEEecCcccccceeecCCCCcchhhh
Confidence 4456789999999998765431111 1125678999999999999999999999994 69999887
No 5
>KOG0944|consensus
Probab=98.87 E-value=9.8e-10 Score=88.59 Aligned_cols=62 Identities=18% Similarity=0.378 Sum_probs=46.7
Q ss_pred ceEeeeeCCCCCCcc-CcccCCCC-CC-CCccccCcCCCCCCeeeecccCceeecCC------CcchhccC
Q psy14516 15 EMFLVTPLADCPHTP-LVAPVPQS-GV-DVKAPCVDCASVAENWVCLICYQVRCGRY------IEEHSNEF 76 (76)
Q Consensus 15 ~~fav~p~~~CpHl~-~l~~~~~~-~~-~~~~~C~~C~~~~~~W~CL~Cg~v~CgR~------~~~Ha~~H 76 (76)
..-|+.++.++++.. .+.+++.. .+ ...++|+.|+...++|+||+||.|+|||. +|+||+.|
T Consensus 149 ~~aWd~Evr~v~k~~~nl~q~dng~~~~~~gwkCs~CDL~~NLWlcLtcG~v~CGR~qfg~~GgNgHA~~H 219 (763)
T KOG0944|consen 149 VNAWDNEVRTVSKHANNLSQIDNGKRIPPSGWKCSKCDLTENLWLCLTCGSVGCGRKQFGGSGGNGHALSH 219 (763)
T ss_pred hhhhhhheeeccCCCCChhhcccCcccCCCcceecccCcccceEEEeccCceeecceeecCCCCCcchHHh
Confidence 345667775555544 36554432 23 46799999999999999999999999995 49999987
No 6
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=97.84 E-value=1e-05 Score=61.72 Aligned_cols=37 Identities=24% Similarity=0.389 Sum_probs=34.2
Q ss_pred CCccccCcCCCCCCeeeecccCceeecCCCcchhccC
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCGRYIEEHSNEF 76 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~CgR~~~~Ha~~H 76 (76)
+....|+.|+...++|+||+||.+++||..++||..|
T Consensus 14 d~e~~C~~~~~~~n~~~CL~cg~~~~g~~~~~ha~~H 50 (440)
T cd02669 14 DFEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTH 50 (440)
T ss_pred cccccccccCCCCcEEEEcccCCeecCCCCCcHHHHH
Confidence 5677899999999999999999999999999999877
No 7
>KOG1873|consensus
Probab=96.90 E-value=0.00041 Score=57.41 Aligned_cols=52 Identities=25% Similarity=0.526 Sum_probs=38.0
Q ss_pred CCCccC-ccc--CCCCCC-CCccccCcCCC---------------CCCeeeecccCceeecC-CCcchhccC
Q psy14516 25 CPHTPL-VAP--VPQSGV-DVKAPCVDCAS---------------VAENWVCLICYQVRCGR-YIEEHSNEF 76 (76)
Q Consensus 25 CpHl~~-l~~--~~~~~~-~~~~~C~~C~~---------------~~~~W~CL~Cg~v~CgR-~~~~Ha~~H 76 (76)
|.|+.. +.. +.+... ..+..|.+|.. ...+|+||.||+.+||| ....||++|
T Consensus 45 C~Hi~Kav~l~~lk~~iks~~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~halkH 116 (877)
T KOG1873|consen 45 CQHIKKAVDLSHLKRAIKSLLWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQHALKH 116 (877)
T ss_pred cchHHhhhcHHHHHHHHHHHHHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccchhhhh
Confidence 999987 332 111111 25677998873 34699999999999999 789999887
No 8
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.20 E-value=0.29 Score=28.84 Aligned_cols=24 Identities=17% Similarity=0.443 Sum_probs=21.0
Q ss_pred CccccCcCCCCCCeeeecccCcee
Q psy14516 41 VKAPCVDCASVAENWVCLICYQVR 64 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v~ 64 (76)
..++|..|....+...|..||..|
T Consensus 35 ~I~RC~~CRk~~~~Y~CP~CGF~G 58 (59)
T PRK14890 35 IIYRCEKCRKQSNPYTCPKCGFEG 58 (59)
T ss_pred eEeechhHHhcCCceECCCCCCcC
Confidence 367899999999999999999875
No 9
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=82.51 E-value=0.4 Score=28.37 Aligned_cols=24 Identities=17% Similarity=0.411 Sum_probs=21.3
Q ss_pred CccccCcCCCCCCeeeecccCcee
Q psy14516 41 VKAPCVDCASVAENWVCLICYQVR 64 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v~ 64 (76)
...+|+.|...++...|..||..|
T Consensus 37 ~I~Rc~~CRk~g~~Y~Cp~CGF~G 60 (61)
T COG2888 37 EIYRCAKCRKLGNPYRCPKCGFEG 60 (61)
T ss_pred eeehhhhHHHcCCceECCCcCccC
Confidence 578899999999999999999875
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=80.33 E-value=0.8 Score=23.32 Aligned_cols=20 Identities=30% Similarity=0.871 Sum_probs=12.8
Q ss_pred cccCcCCCC----CCeeeecccCc
Q psy14516 43 APCVDCASV----AENWVCLICYQ 62 (76)
Q Consensus 43 ~~C~~C~~~----~~~W~CL~Cg~ 62 (76)
+.|..|+-. ...|.|..||.
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCCCC
Confidence 356666633 35778888775
No 11
>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=78.67 E-value=1.3 Score=22.92 Aligned_cols=14 Identities=36% Similarity=0.980 Sum_probs=10.8
Q ss_pred eeeecccCceeecC
Q psy14516 54 NWVCLICYQVRCGR 67 (76)
Q Consensus 54 ~W~CL~Cg~v~CgR 67 (76)
.|+|..||++.=|+
T Consensus 2 ~~~C~~CG~i~~g~ 15 (34)
T cd00729 2 VWVCPVCGYIHEGE 15 (34)
T ss_pred eEECCCCCCEeECC
Confidence 58899999886554
No 12
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=73.58 E-value=2.9 Score=21.74 Aligned_cols=14 Identities=29% Similarity=0.479 Sum_probs=10.0
Q ss_pred CCCeeeecccCcee
Q psy14516 51 VAENWVCLICYQVR 64 (76)
Q Consensus 51 ~~~~W~CL~Cg~v~ 64 (76)
.++-++|..||.|+
T Consensus 19 ~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 19 DRERLVCPACGFIH 32 (34)
T ss_dssp SS-EEEETTTTEEE
T ss_pred CccceECCCCCCEE
Confidence 45678888888875
No 13
>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=68.46 E-value=3.4 Score=21.29 Aligned_cols=26 Identities=15% Similarity=0.429 Sum_probs=20.3
Q ss_pred ccccCcCCCCCCeeeecccCceeecC
Q psy14516 42 KAPCVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 42 ~~~C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
...|..+....-.+.|.+|+...|..
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~ 28 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSE 28 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHH
T ss_pred CccCccCCccceEEEecCCCCccCcc
Confidence 45688888777788899999999886
No 14
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=65.62 E-value=1.7 Score=35.65 Aligned_cols=50 Identities=24% Similarity=0.480 Sum_probs=33.3
Q ss_pred CCCCccCccc-CCCC-CCCCccccCcCCCCC----CeeeecccCceeecCCCcchh
Q psy14516 24 DCPHTPLVAP-VPQS-GVDVKAPCVDCASVA----ENWVCLICYQVRCGRYIEEHS 73 (76)
Q Consensus 24 ~CpHl~~l~~-~~~~-~~~~~~~C~~C~~~~----~~W~CL~Cg~v~CgR~~~~Ha 73 (76)
.|||...... +|.. .+-....|.-|..+. .+-+||.|+..+|+|.+--|.
T Consensus 2 S~~H~e~ae~vlpn~~av~~reeC~yCf~S~~~e~si~vClnCfqs~C~~h~~~H~ 57 (749)
T COG5207 2 SFSHSEMAEMVLPNLPAVRFREECCYCFRSIGDEHSISVCLNCFQSFCEKHRGIHL 57 (749)
T ss_pred CCchhhhhhhcCCCCchhhhhhhhheeeccCCCCcceehHHHHhHhhhhhccceee
Confidence 6888876432 2211 111345588888653 367899999999999877765
No 15
>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=62.60 E-value=6 Score=19.22 Aligned_cols=12 Identities=25% Similarity=0.390 Sum_probs=6.8
Q ss_pred CCCCeeeecccC
Q psy14516 50 SVAENWVCLICY 61 (76)
Q Consensus 50 ~~~~~W~CL~Cg 61 (76)
.......|..||
T Consensus 12 ~~~v~f~CPnCG 23 (24)
T PF07754_consen 12 EQAVPFPCPNCG 23 (24)
T ss_pred ccCceEeCCCCC
Confidence 334455666666
No 16
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=62.28 E-value=6.3 Score=25.99 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=10.7
Q ss_pred CCeeeecccCcee
Q psy14516 52 AENWVCLICYQVR 64 (76)
Q Consensus 52 ~~~W~CL~Cg~v~ 64 (76)
.+-|.|..||.+.
T Consensus 122 ~~f~~C~~C~kiy 134 (147)
T PF01927_consen 122 DEFWRCPGCGKIY 134 (147)
T ss_pred CeEEECCCCCCEe
Confidence 4589999999874
No 17
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=59.79 E-value=6 Score=28.34 Aligned_cols=26 Identities=19% Similarity=0.445 Sum_probs=21.3
Q ss_pred CCccccCcCCCCCCeee--ecccCceee
Q psy14516 40 DVKAPCVDCASVAENWV--CLICYQVRC 65 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~--CL~Cg~v~C 65 (76)
+..+.|+.|+.....|. |..||..+-
T Consensus 352 ~p~~~c~~cg~~~~~~~~~c~~c~~~~~ 379 (389)
T PRK11788 352 KPRYRCRNCGFTARTLYWHCPSCKAWET 379 (389)
T ss_pred CCCEECCCCCCCCccceeECcCCCCccC
Confidence 46678999999988775 999998764
No 18
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=59.48 E-value=8.7 Score=20.21 Aligned_cols=13 Identities=23% Similarity=0.807 Sum_probs=8.3
Q ss_pred CCCeeeecccCce
Q psy14516 51 VAENWVCLICYQV 63 (76)
Q Consensus 51 ~~~~W~CL~Cg~v 63 (76)
....|+|..|+..
T Consensus 21 ~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 21 GGKTWICNFCGTK 33 (40)
T ss_dssp TTTEEEETTT--E
T ss_pred CCCEEECcCCCCc
Confidence 4568999988864
No 19
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=58.09 E-value=7.7 Score=19.78 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=15.8
Q ss_pred CcCCCC-CCeeeecccCceeecC
Q psy14516 46 VDCASV-AENWVCLICYQVRCGR 67 (76)
Q Consensus 46 ~~C~~~-~~~W~CL~Cg~v~CgR 67 (76)
..|... .+.++-+.||++.|.+
T Consensus 2 ~iC~~~~~~~~~~~~CGH~fC~~ 24 (39)
T PF13923_consen 2 PICLDELRDPVVVTPCGHSFCKE 24 (39)
T ss_dssp TTTTSB-SSEEEECTTSEEEEHH
T ss_pred CCCCCcccCcCEECCCCCchhHH
Confidence 344433 5567899999999975
No 20
>COG1773 Rubredoxin [Energy production and conversion]
Probab=57.50 E-value=5.7 Score=22.97 Aligned_cols=12 Identities=33% Similarity=1.030 Sum_probs=8.3
Q ss_pred CCCeeeecccCc
Q psy14516 51 VAENWVCLICYQ 62 (76)
Q Consensus 51 ~~~~W~CL~Cg~ 62 (76)
..+.|+|..||.
T Consensus 33 lPd~w~CP~Cg~ 44 (55)
T COG1773 33 LPDDWVCPECGV 44 (55)
T ss_pred CCCccCCCCCCC
Confidence 456777777774
No 21
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=57.43 E-value=10 Score=20.24 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=9.0
Q ss_pred CeeeecccCcee
Q psy14516 53 ENWVCLICYQVR 64 (76)
Q Consensus 53 ~~W~CL~Cg~v~ 64 (76)
+.|+|..||+..
T Consensus 19 ~~~vC~~Cg~~~ 30 (52)
T smart00661 19 RRFVCRKCGYEE 30 (52)
T ss_pred CEEECCcCCCeE
Confidence 478888888754
No 22
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=57.34 E-value=6.4 Score=19.99 Aligned_cols=20 Identities=35% Similarity=0.559 Sum_probs=11.3
Q ss_pred ccCcCCC-----CCCeeeecccCce
Q psy14516 44 PCVDCAS-----VAENWVCLICYQV 63 (76)
Q Consensus 44 ~C~~C~~-----~~~~W~CL~Cg~v 63 (76)
.|..|.. .+.+++|.+|++.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCcceeccCCEEeCCccccc
Confidence 3555553 4678899999864
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=56.90 E-value=10 Score=20.04 Aligned_cols=28 Identities=29% Similarity=0.650 Sum_probs=18.4
Q ss_pred cCcCCCCCCe--eeecccCceeecC--CCcch
Q psy14516 45 CVDCASVAEN--WVCLICYQVRCGR--YIEEH 72 (76)
Q Consensus 45 C~~C~~~~~~--W~CL~Cg~v~CgR--~~~~H 72 (76)
|..|.....+ -.|-.|+.+.|++ +...|
T Consensus 1 C~~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H 32 (39)
T smart00154 1 CHFCRKKVGLTGFKCRHCGNLFCGEHRLPEDH 32 (39)
T ss_pred CcccCCcccccCeECCccCCccccccCCcccc
Confidence 4455554443 5589999999995 45555
No 24
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=55.76 E-value=9.5 Score=24.11 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=21.4
Q ss_pred CccccCcCCC------CCCeeeecccCceeecC
Q psy14516 41 VKAPCVDCAS------VAENWVCLICYQVRCGR 67 (76)
Q Consensus 41 ~~~~C~~C~~------~~~~W~CL~Cg~v~CgR 67 (76)
....|.+|.. ....|.|-.||..+-|-
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGg 66 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGG 66 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeeccc
Confidence 4556888884 46799999999998875
No 25
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.29 E-value=9.8 Score=28.42 Aligned_cols=26 Identities=23% Similarity=0.407 Sum_probs=23.9
Q ss_pred CccccCcCCCCCCeeeecccCceeec
Q psy14516 41 VKAPCVDCASVAENWVCLICYQVRCG 66 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v~Cg 66 (76)
...+|.-|...-+.-.|..||+++|-
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgHlFC~ 239 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGHLFCL 239 (271)
T ss_pred cccceeeeecccCCcccccccchhhH
Confidence 57789999999999999999999984
No 26
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=54.23 E-value=11 Score=23.92 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=18.2
Q ss_pred CCccccCcCCCCCCeeeecccCceeecC
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
+....|.+|+...-.|+++.=|...|.+
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~ 38 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLE 38 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHH
Confidence 3667899999999999988877777654
No 27
>PRK10220 hypothetical protein; Provisional
Probab=53.76 E-value=9.9 Score=24.93 Aligned_cols=20 Identities=20% Similarity=0.602 Sum_probs=14.1
Q ss_pred cCcCC-----CCCCeeeecccCcee
Q psy14516 45 CVDCA-----SVAENWVCLICYQVR 64 (76)
Q Consensus 45 C~~C~-----~~~~~W~CL~Cg~v~ 64 (76)
|..|. ..+++|+|..|++.-
T Consensus 6 CP~C~seytY~d~~~~vCpeC~hEW 30 (111)
T PRK10220 6 CPKCNSEYTYEDNGMYICPECAHEW 30 (111)
T ss_pred CCCCCCcceEcCCCeEECCcccCcC
Confidence 55555 246789999998754
No 28
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=52.29 E-value=9.3 Score=24.98 Aligned_cols=20 Identities=25% Similarity=0.632 Sum_probs=14.3
Q ss_pred cCcCCC-----CCCeeeecccCcee
Q psy14516 45 CVDCAS-----VAENWVCLICYQVR 64 (76)
Q Consensus 45 C~~C~~-----~~~~W~CL~Cg~v~ 64 (76)
|..|.. .+++|+|..|++.-
T Consensus 5 CP~C~seytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 5 CPKCNSEYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred CCcCCCcceEecCCeeECccccccc
Confidence 555552 46789999998754
No 29
>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=50.13 E-value=15 Score=23.61 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=18.2
Q ss_pred CCCccccCcCC-----CCCCeeeecccCcee
Q psy14516 39 VDVKAPCVDCA-----SVAENWVCLICYQVR 64 (76)
Q Consensus 39 ~~~~~~C~~C~-----~~~~~W~CL~Cg~v~ 64 (76)
+..+..|.+|+ ..++.=+|..||.+.
T Consensus 6 lGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 34556688887 346777799998764
No 30
>PHA02942 putative transposase; Provisional
Probab=49.44 E-value=14 Score=28.29 Aligned_cols=24 Identities=17% Similarity=0.436 Sum_probs=18.8
Q ss_pred CccccCcCCCC-----CCeeeecccCcee
Q psy14516 41 VKAPCVDCASV-----AENWVCLICYQVR 64 (76)
Q Consensus 41 ~~~~C~~C~~~-----~~~W~CL~Cg~v~ 64 (76)
.+..|..|+.. ...|.|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 45669999953 4589999999875
No 31
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=49.12 E-value=8.5 Score=18.79 Aligned_cols=19 Identities=21% Similarity=0.527 Sum_probs=10.0
Q ss_pred cCcCCCC--CCeeeecccCce
Q psy14516 45 CVDCASV--AENWVCLICYQV 63 (76)
Q Consensus 45 C~~C~~~--~~~W~CL~Cg~v 63 (76)
|.+|+.. ...-.|..||++
T Consensus 3 CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 3 CPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CCCCcCCchhhcCcCCCCCCC
Confidence 4555532 334457777765
No 32
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=47.56 E-value=6.4 Score=29.68 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=19.2
Q ss_pred CCccccCcCCC-------CCCeeeecccCce
Q psy14516 40 DVKAPCVDCAS-------VAENWVCLICYQV 63 (76)
Q Consensus 40 ~~~~~C~~C~~-------~~~~W~CL~Cg~v 63 (76)
+.+..|.+|.. ..++|+|+.|++-
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h 56 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHH 56 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCcc
Confidence 46788999983 5789999999863
No 33
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.64 E-value=18 Score=25.25 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=19.3
Q ss_pred CccccCcCCCC-CCeeeecccCceee
Q psy14516 41 VKAPCVDCASV-AENWVCLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~~-~~~W~CL~Cg~v~C 65 (76)
.+..|..|+.. ...|.|..||.+.=
T Consensus 308 tS~~C~~cg~~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 308 TSKTCPCCGHLSGRLFKCPRCGFVHD 333 (364)
T ss_pred CcccccccCCccceeEECCCCCCeeh
Confidence 45678888864 57899999998753
No 34
>KOG2026|consensus
Probab=45.57 E-value=16 Score=28.89 Aligned_cols=37 Identities=27% Similarity=0.486 Sum_probs=32.5
Q ss_pred CCccccCcCCCCCCeeeecccCceeecCCCcchhccC
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCGRYIEEHSNEF 76 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~CgR~~~~Ha~~H 76 (76)
+....|..-...-+...||.||.-.=||..+.||..|
T Consensus 27 d~ek~c~vslsnLnvyAclvcg~y~qgr~~kS~A~~h 63 (442)
T KOG2026|consen 27 DFEKPCSVSLSNLNVYACLVCGKYFQGRGEKSHAYTH 63 (442)
T ss_pred cCCCCCcccccccceeeeeeeCchhhCcCccccchhc
Confidence 4667798888889999999999999999999999876
No 35
>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=45.51 E-value=22 Score=18.70 Aligned_cols=16 Identities=25% Similarity=0.256 Sum_probs=9.0
Q ss_pred CCeeeecccCceeecC
Q psy14516 52 AENWVCLICYQVRCGR 67 (76)
Q Consensus 52 ~~~W~CL~Cg~v~CgR 67 (76)
+...+|..||.|.=.+
T Consensus 17 ~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 17 RGELVCPNCGLVLEEN 32 (43)
T ss_dssp TTEEEETTT-BBEE-T
T ss_pred CCeEECCCCCCEeecc
Confidence 3456788888775433
No 36
>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=45.34 E-value=12 Score=28.42 Aligned_cols=21 Identities=29% Similarity=0.884 Sum_probs=16.4
Q ss_pred ccCcCCCCCCeee--ecccCcee
Q psy14516 44 PCVDCASVAENWV--CLICYQVR 64 (76)
Q Consensus 44 ~C~~C~~~~~~W~--CL~Cg~v~ 64 (76)
.|++|+.....|. |..|+.=+
T Consensus 2 ~c~~cg~~~~~~~g~cp~c~~w~ 24 (372)
T cd01121 2 VCSECGYVSPKWLGKCPECGEWN 24 (372)
T ss_pred CCCCCCCCCCCccEECcCCCCce
Confidence 6999998777665 99998644
No 37
>KOG0317|consensus
Probab=44.89 E-value=9.9 Score=28.69 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=24.2
Q ss_pred CCccccCcCCCCCCeeeecccCceeec
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCG 66 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~Cg 66 (76)
..+..|+-|...+.+--|.-||+++|=
T Consensus 237 ~a~~kC~LCLe~~~~pSaTpCGHiFCW 263 (293)
T KOG0317|consen 237 EATRKCSLCLENRSNPSATPCGHIFCW 263 (293)
T ss_pred CCCCceEEEecCCCCCCcCcCcchHHH
Confidence 356789999999999999999999984
No 38
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=43.67 E-value=13 Score=23.43 Aligned_cols=26 Identities=19% Similarity=0.498 Sum_probs=22.5
Q ss_pred ccccCcCCCCCCeeeecccCceeecC
Q psy14516 42 KAPCVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 42 ~~~C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
...|.+|+...-.|+++.=|...|.+
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~ 28 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIE 28 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHH
Confidence 46799999999999999988888874
No 39
>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=43.47 E-value=20 Score=20.23 Aligned_cols=23 Identities=17% Similarity=0.463 Sum_probs=16.3
Q ss_pred CccccCcCCC------CCCeeeecccCce
Q psy14516 41 VKAPCVDCAS------VAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~------~~~~W~CL~Cg~v 63 (76)
.+..|..|+. ....|.|..||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 4555777773 4557889999987
No 40
>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=43.41 E-value=3.3 Score=18.57 Aligned_cols=20 Identities=20% Similarity=0.517 Sum_probs=11.2
Q ss_pred eeecccCceeecCC-Ccchhc
Q psy14516 55 WVCLICYQVRCGRY-IEEHSN 74 (76)
Q Consensus 55 W~CL~Cg~v~CgR~-~~~Ha~ 74 (76)
+.|..|+...=.++ -..|++
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~ 21 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMR 21 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHh
Confidence 46777777665542 344443
No 41
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.26 E-value=13 Score=28.91 Aligned_cols=25 Identities=20% Similarity=0.639 Sum_probs=19.2
Q ss_pred CccccCcCCCCCCeee--ecccCceee
Q psy14516 41 VKAPCVDCASVAENWV--CLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~--CL~Cg~v~C 65 (76)
....|++|+.....|. |..|+.=+.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (446)
T PRK11823 6 TAYVCQECGAESPKWLGRCPECGAWNT 32 (446)
T ss_pred CeEECCcCCCCCcccCeeCcCCCCccc
Confidence 4578999998877665 999986543
No 42
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=42.27 E-value=7.6 Score=20.13 Aligned_cols=29 Identities=24% Similarity=0.583 Sum_probs=18.2
Q ss_pred CCCCCCccCcccCCCCCC---CCccccCcCCC
Q psy14516 22 LADCPHTPLVAPVPQSGV---DVKAPCVDCAS 50 (76)
Q Consensus 22 ~~~CpHl~~l~~~~~~~~---~~~~~C~~C~~ 50 (76)
+..||+....-.++.+.+ ....+|..|..
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 357999887544554322 35677888764
No 43
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=41.87 E-value=21 Score=18.81 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=14.8
Q ss_pred cCcCCCCCCeeeecccCceeecC
Q psy14516 45 CVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 45 C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
|..|...-..-+=|.||++.|-+
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~ 23 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRS 23 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHH
T ss_pred CCccchhhCCccccCCcCHHHHH
Confidence 44566655666678899999964
No 44
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=40.74 E-value=13 Score=25.71 Aligned_cols=13 Identities=38% Similarity=0.966 Sum_probs=11.3
Q ss_pred eeeecccCceeec
Q psy14516 54 NWVCLICYQVRCG 66 (76)
Q Consensus 54 ~W~CL~Cg~v~Cg 66 (76)
.|+|..||++.=|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 8999999998755
No 45
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=40.72 E-value=13 Score=20.07 Aligned_cols=6 Identities=33% Similarity=0.722 Sum_probs=3.1
Q ss_pred ecccCc
Q psy14516 57 CLICYQ 62 (76)
Q Consensus 57 CL~Cg~ 62 (76)
|..||.
T Consensus 29 CP~Cg~ 34 (52)
T TIGR02605 29 CPECGG 34 (52)
T ss_pred CCCCCC
Confidence 555554
No 46
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=40.27 E-value=14 Score=28.72 Aligned_cols=25 Identities=24% Similarity=0.634 Sum_probs=18.7
Q ss_pred CccccCcCCCCCCeee--ecccCceee
Q psy14516 41 VKAPCVDCASVAENWV--CLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~--CL~Cg~v~C 65 (76)
....|+.|+.....|. |..|+.=+.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t 32 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQGKCPACHAWNT 32 (454)
T ss_pred CeEECCcCCCCCccccEECcCCCCccc
Confidence 4577999998777655 999986443
No 47
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=39.45 E-value=25 Score=18.72 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=20.1
Q ss_pred cccCcCCCCCCeeeecccCce-eecC
Q psy14516 43 APCVDCASVAENWVCLICYQV-RCGR 67 (76)
Q Consensus 43 ~~C~~C~~~~~~W~CL~Cg~v-~CgR 67 (76)
..|..|.......+-+-||+. .|..
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~~ 28 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCEE 28 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEHH
T ss_pred CCCccCCccCCceEEeCCCChHHHHH
Confidence 468899998888999999999 7763
No 48
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=38.05 E-value=26 Score=20.70 Aligned_cols=21 Identities=29% Similarity=0.868 Sum_probs=14.3
Q ss_pred ccccCcCC-------CCCCeeeecccCc
Q psy14516 42 KAPCVDCA-------SVAENWVCLICYQ 62 (76)
Q Consensus 42 ~~~C~~C~-------~~~~~W~CL~Cg~ 62 (76)
...|.-|+ ....-|+||.|..
T Consensus 30 ~~VCnlCGFNP~Phl~E~~eWLCLnCQ~ 57 (61)
T PF05715_consen 30 SQVCNLCGFNPTPHLTEVKEWLCLNCQM 57 (61)
T ss_pred hhhhcccCCCCCccccccceeeeecchh
Confidence 44566666 3357899999964
No 49
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=37.82 E-value=20 Score=24.93 Aligned_cols=14 Identities=21% Similarity=0.451 Sum_probs=10.5
Q ss_pred CCCeeeecccCcee
Q psy14516 51 VAENWVCLICYQVR 64 (76)
Q Consensus 51 ~~~~W~CL~Cg~v~ 64 (76)
..+-|.|..||.+.
T Consensus 127 ~~~f~~C~~CgkiY 140 (165)
T COG1656 127 YEEFYRCPKCGKIY 140 (165)
T ss_pred ccceeECCCCcccc
Confidence 45678899888764
No 50
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.78 E-value=20 Score=29.36 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=19.3
Q ss_pred CccccCcCCCCCCe-eeecccCce
Q psy14516 41 VKAPCVDCASVAEN-WVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~~~~~-W~CL~Cg~v 63 (76)
..+.|.+|+-.++. |.|..||+-
T Consensus 558 ~~~~C~~CGy~g~~~~~CP~CG~~ 581 (618)
T PRK14704 558 PVDRCKCCSYHGVIGNECPSCGNE 581 (618)
T ss_pred CCeecCCCCCCCCcCccCcCCCCC
Confidence 67789999987676 999999964
No 51
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=36.05 E-value=12 Score=21.61 Aligned_cols=14 Identities=29% Similarity=0.600 Sum_probs=11.2
Q ss_pred eecccCceeecCCC
Q psy14516 56 VCLICYQVRCGRYI 69 (76)
Q Consensus 56 ~CL~Cg~v~CgR~~ 69 (76)
-||.||.|-|..-.
T Consensus 20 NCl~CGkIiC~~Eg 33 (57)
T PF06221_consen 20 NCLNCGKIICEQEG 33 (57)
T ss_pred cccccChhhccccc
Confidence 49999999997643
No 52
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=35.93 E-value=19 Score=28.77 Aligned_cols=22 Identities=27% Similarity=0.830 Sum_probs=18.8
Q ss_pred CccccCcCCCCCCeee--ecccCc
Q psy14516 41 VKAPCVDCASVAENWV--CLICYQ 62 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~--CL~Cg~ 62 (76)
....|++|+....-|. |..||.
T Consensus 6 t~f~C~~CG~~s~KW~GkCp~Cg~ 29 (456)
T COG1066 6 TAFVCQECGYVSPKWLGKCPACGA 29 (456)
T ss_pred cEEEcccCCCCCccccccCCCCCC
Confidence 3467999999999998 999984
No 53
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=35.03 E-value=24 Score=18.37 Aligned_cols=10 Identities=20% Similarity=0.630 Sum_probs=7.9
Q ss_pred eeecccCcee
Q psy14516 55 WVCLICYQVR 64 (76)
Q Consensus 55 W~CL~Cg~v~ 64 (76)
|+|..||.+.
T Consensus 2 r~C~~Cg~~Y 11 (36)
T PF05191_consen 2 RICPKCGRIY 11 (36)
T ss_dssp EEETTTTEEE
T ss_pred cCcCCCCCcc
Confidence 7888888764
No 54
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=34.59 E-value=39 Score=17.23 Aligned_cols=22 Identities=23% Similarity=0.593 Sum_probs=13.5
Q ss_pred cccCcCCCC------CCeeeecccCcee
Q psy14516 43 APCVDCASV------AENWVCLICYQVR 64 (76)
Q Consensus 43 ~~C~~C~~~------~~~W~CL~Cg~v~ 64 (76)
..|..|+.. .+..+|..||.+.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 456777643 3445688887653
No 55
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=34.41 E-value=33 Score=17.78 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=13.8
Q ss_pred ccccCcCCCC-----CCeeeecccCce
Q psy14516 42 KAPCVDCASV-----AENWVCLICYQV 63 (76)
Q Consensus 42 ~~~C~~C~~~-----~~~W~CL~Cg~v 63 (76)
..+|..|... ...+.|-.||++
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhCceE
Confidence 3458888753 345567777765
No 56
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=33.60 E-value=24 Score=16.32 Aligned_cols=6 Identities=33% Similarity=0.933 Sum_probs=2.7
Q ss_pred cccCcC
Q psy14516 43 APCVDC 48 (76)
Q Consensus 43 ~~C~~C 48 (76)
+.|..|
T Consensus 3 W~C~~C 8 (26)
T smart00547 3 WECPAC 8 (26)
T ss_pred ccCCCC
Confidence 344444
No 57
>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=33.51 E-value=26 Score=28.27 Aligned_cols=26 Identities=23% Similarity=0.348 Sum_probs=20.3
Q ss_pred CccccCcCCCCCCe--eeecccCceeec
Q psy14516 41 VKAPCVDCASVAEN--WVCLICYQVRCG 66 (76)
Q Consensus 41 ~~~~C~~C~~~~~~--W~CL~Cg~v~Cg 66 (76)
..+.|.+|+-..+. |.|..||+-.+.
T Consensus 523 ~~~~C~~CG~~g~~~~~~CP~Cgs~~~~ 550 (579)
T TIGR02487 523 PVDVCEDCGYTGEGLNDKCPKCGSHDIE 550 (579)
T ss_pred CCccCCCCCCCCCCCCCcCcCCCCccce
Confidence 56789999987665 899999975444
No 58
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.37 E-value=28 Score=28.69 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=19.4
Q ss_pred CccccCcCCCCCCeeeecccCce
Q psy14516 41 VKAPCVDCASVAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v 63 (76)
....|.-|+.....|.|..||..
T Consensus 409 ~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCCcCccCCCCcCC
Confidence 45779999988789999999875
No 59
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.99 E-value=26 Score=29.15 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=18.3
Q ss_pred CccccCcCCCCCCe------eeecccCc
Q psy14516 41 VKAPCVDCASVAEN------WVCLICYQ 62 (76)
Q Consensus 41 ~~~~C~~C~~~~~~------W~CL~Cg~ 62 (76)
..+.|.+|+-.++. |.|..||+
T Consensus 640 ~~~~C~~CG~~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 640 PIDECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CCcccCCCCCCccccCCCCCCcCcCCCC
Confidence 56889999986555 99999996
No 60
>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=32.60 E-value=19 Score=20.10 Aligned_cols=12 Identities=25% Similarity=0.495 Sum_probs=9.1
Q ss_pred eeecccCceeec
Q psy14516 55 WVCLICYQVRCG 66 (76)
Q Consensus 55 W~CL~Cg~v~Cg 66 (76)
|+|..||.|.=.
T Consensus 2 y~C~~CgyiYd~ 13 (50)
T cd00730 2 YECRICGYIYDP 13 (50)
T ss_pred cCCCCCCeEECC
Confidence 788888887643
No 61
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.39 E-value=27 Score=28.77 Aligned_cols=23 Identities=17% Similarity=0.251 Sum_probs=19.4
Q ss_pred CccccCcCCC-CCCeeeecccCce
Q psy14516 41 VKAPCVDCAS-VAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~-~~~~W~CL~Cg~v 63 (76)
..+.|.+|+- .+..|.|+.||.-
T Consensus 625 ~~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 625 TFSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred CCcccCCCCCcCCCCCCCcCCcCc
Confidence 5678999996 6789999999954
No 62
>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=32.35 E-value=27 Score=21.97 Aligned_cols=27 Identities=26% Similarity=0.564 Sum_probs=20.1
Q ss_pred CccccCcCCC------CCCeeeecccCceeecC
Q psy14516 41 VKAPCVDCAS------VAENWVCLICYQVRCGR 67 (76)
Q Consensus 41 ~~~~C~~C~~------~~~~W~CL~Cg~v~CgR 67 (76)
....|..|+. ....|-|-.|+....|-
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp S-BEESSSSSSEEEEEETTEEEETTTTEEEE-B
T ss_pred CCCcCCCCCCceeEEeeeEEeecCCCCCEEeCC
Confidence 4566888884 45689999999999885
No 63
>PF15616 TerY-C: TerY-C metal binding domain
Probab=32.29 E-value=38 Score=22.63 Aligned_cols=22 Identities=27% Similarity=0.619 Sum_probs=19.2
Q ss_pred cccCcCCCCCCeeeecccCceee
Q psy14516 43 APCVDCASVAENWVCLICYQVRC 65 (76)
Q Consensus 43 ~~C~~C~~~~~~W~CL~Cg~v~C 65 (76)
.-|.-|+.....=+| .||++.|
T Consensus 78 PgCP~CGn~~~fa~C-~CGkl~C 99 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCGKLFC 99 (131)
T ss_pred CCCCCCcChhcEEEe-cCCCEEE
Confidence 559999998888888 8999999
No 64
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.13 E-value=17 Score=23.52 Aligned_cols=22 Identities=27% Similarity=0.650 Sum_probs=15.9
Q ss_pred CCccccCcCCCC-----CC------eeeecccCc
Q psy14516 40 DVKAPCVDCASV-----AE------NWVCLICYQ 62 (76)
Q Consensus 40 ~~~~~C~~C~~~-----~~------~W~CL~Cg~ 62 (76)
+...+| +|+.. .. .+.|+.||.
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 467889 99966 22 167999994
No 65
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=32.11 E-value=12 Score=27.70 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=18.2
Q ss_pred CccccCcCCC-------CCCeeeecccCce
Q psy14516 41 VKAPCVDCAS-------VAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~-------~~~~W~CL~Cg~v 63 (76)
.+.+|..|.. .++.++|..||+-
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 5888999984 3567899999873
No 66
>PF12523 DUF3725: Protein of unknown function (DUF3725); InterPro: IPR022199 This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with PF01577 from PFAM. There is a conserved FLE sequence motif.
Probab=31.38 E-value=25 Score=21.40 Aligned_cols=12 Identities=33% Similarity=0.866 Sum_probs=8.6
Q ss_pred CCeeeecccCce
Q psy14516 52 AENWVCLICYQV 63 (76)
Q Consensus 52 ~~~W~CL~Cg~v 63 (76)
.++|.|..|++.
T Consensus 57 ~Elw~Ch~C~~t 68 (74)
T PF12523_consen 57 SELWECHSCDNT 68 (74)
T ss_pred cceEEeecCCCc
Confidence 567888777764
No 67
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.10 E-value=13 Score=27.99 Aligned_cols=22 Identities=18% Similarity=0.459 Sum_probs=18.1
Q ss_pred CccccCcCCC-------CCCeeeecccCc
Q psy14516 41 VKAPCVDCAS-------VAENWVCLICYQ 62 (76)
Q Consensus 41 ~~~~C~~C~~-------~~~~W~CL~Cg~ 62 (76)
.+.+|..|.. .++.++|..||+
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGY 65 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCC
Confidence 5888999984 366789999987
No 68
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=30.56 E-value=49 Score=19.88 Aligned_cols=27 Identities=26% Similarity=0.632 Sum_probs=18.5
Q ss_pred CccccCcCCC-------CCCeeeecccCceeecC
Q psy14516 41 VKAPCVDCAS-------VAENWVCLICYQVRCGR 67 (76)
Q Consensus 41 ~~~~C~~C~~-------~~~~W~CL~Cg~v~CgR 67 (76)
..-+|.+|+. ....-.|+.||.+.+--
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 3456888884 23344599999988754
No 69
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=30.21 E-value=14 Score=27.44 Aligned_cols=23 Identities=26% Similarity=0.475 Sum_probs=18.2
Q ss_pred CccccCcCCC-------CCCeeeecccCce
Q psy14516 41 VKAPCVDCAS-------VAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~-------~~~~W~CL~Cg~v 63 (76)
.+.+|..|.. .++.++|..||+-
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 5888999984 3567899999874
No 70
>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=29.98 E-value=26 Score=17.01 Aligned_cols=20 Identities=20% Similarity=0.534 Sum_probs=6.8
Q ss_pred ccCcCCCCCCe---eeecccCce
Q psy14516 44 PCVDCASVAEN---WVCLICYQV 63 (76)
Q Consensus 44 ~C~~C~~~~~~---W~CL~Cg~v 63 (76)
.|..|+..... ..|.+|..+
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 47777766553 348888654
No 71
>PRK07218 replication factor A; Provisional
Probab=29.74 E-value=26 Score=27.44 Aligned_cols=23 Identities=22% Similarity=0.407 Sum_probs=20.5
Q ss_pred CccccCcCCCCCCeeeecccCce
Q psy14516 41 VKAPCVDCASVAENWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~~~~~W~CL~Cg~v 63 (76)
...+|..|...-..|.|..||.+
T Consensus 296 li~rCP~C~r~v~~~~C~~hG~v 318 (423)
T PRK07218 296 LIERCPECGRVIQKGQCRSHGAV 318 (423)
T ss_pred ceecCcCccccccCCcCCCCCCc
Confidence 45789999999999999999987
No 72
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=29.66 E-value=37 Score=16.35 Aligned_cols=14 Identities=21% Similarity=0.657 Sum_probs=7.7
Q ss_pred CeeeecccCceeec
Q psy14516 53 ENWVCLICYQVRCG 66 (76)
Q Consensus 53 ~~W~CL~Cg~v~Cg 66 (76)
..|.|..|+.+.-.
T Consensus 3 g~W~C~~C~~~N~~ 16 (30)
T PF00641_consen 3 GDWKCPSCTFMNPA 16 (30)
T ss_dssp SSEEETTTTEEEES
T ss_pred cCccCCCCcCCchH
Confidence 35666666655433
No 73
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.66 E-value=46 Score=27.50 Aligned_cols=36 Identities=19% Similarity=0.466 Sum_probs=18.9
Q ss_pred CCCCCCccCcccCCCCCCCCccccCcCCCCCCeeeecccCce
Q psy14516 22 LADCPHTPLVAPVPQSGVDVKAPCVDCASVAENWVCLICYQV 63 (76)
Q Consensus 22 ~~~CpHl~~l~~~~~~~~~~~~~C~~C~~~~~~W~CL~Cg~v 63 (76)
|+.||+.....+ . ....|..|+..-..-.|..||..
T Consensus 1 M~~Cp~Cg~~n~--~----~akFC~~CG~~l~~~~Cp~CG~~ 36 (645)
T PRK14559 1 MLICPQCQFENP--N----NNRFCQKCGTSLTHKPCPQCGTE 36 (645)
T ss_pred CCcCCCCCCcCC--C----CCccccccCCCCCCCcCCCCCCC
Confidence 467888876442 1 22235555554433345555554
No 74
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=29.35 E-value=33 Score=28.20 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=20.4
Q ss_pred CccccCcCCC--CCCeeeecccCceee
Q psy14516 41 VKAPCVDCAS--VAENWVCLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~--~~~~W~CL~Cg~v~C 65 (76)
..+.|.+|+- .++.|.|+.||+..+
T Consensus 565 ~~~iC~~CG~~~~g~~~~CP~CGs~~~ 591 (623)
T PRK08271 565 KITICNDCHHIDKRTGKRCPICGSENI 591 (623)
T ss_pred CCccCCCCCCcCCCCCcCCcCCCCcch
Confidence 6788999997 567999999997543
No 75
>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=29.31 E-value=26 Score=17.50 Aligned_cols=23 Identities=22% Similarity=0.626 Sum_probs=15.3
Q ss_pred cccCcCCCCCCeeeecccCceeec
Q psy14516 43 APCVDCASVAENWVCLICYQVRCG 66 (76)
Q Consensus 43 ~~C~~C~~~~~~W~CL~Cg~v~Cg 66 (76)
..|..|+. .....|..|+.-.|+
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-EESEE-TTT--EESS
T ss_pred CCCccCcC-CCEEECCCcCCceeC
Confidence 35788888 777789999888776
No 76
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=29.16 E-value=32 Score=20.52 Aligned_cols=26 Identities=27% Similarity=0.606 Sum_probs=10.6
Q ss_pred ccccCcCCCCCCeeeecc-cCceeecC
Q psy14516 42 KAPCVDCASVAENWVCLI-CYQVRCGR 67 (76)
Q Consensus 42 ~~~C~~C~~~~~~W~CL~-Cg~v~CgR 67 (76)
..+|+.|...-+.-+||. |.+++|+-
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~ 33 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSS 33 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TT
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHH
Confidence 456788887777777754 88888764
No 77
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=28.85 E-value=21 Score=22.75 Aligned_cols=24 Identities=29% Similarity=0.544 Sum_probs=17.0
Q ss_pred CCccccCcCCCCC----CeeeecccCce
Q psy14516 40 DVKAPCVDCASVA----ENWVCLICYQV 63 (76)
Q Consensus 40 ~~~~~C~~C~~~~----~~W~CL~Cg~v 63 (76)
+...+|.+|+..- ..+.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 4678899998532 34669999853
No 78
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=28.57 E-value=32 Score=15.86 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=11.5
Q ss_pred CcCCCCCCeeeecccCceeec
Q psy14516 46 VDCASVAENWVCLICYQVRCG 66 (76)
Q Consensus 46 ~~C~~~~~~W~CL~Cg~v~Cg 66 (76)
..|......-+-+.||++.|.
T Consensus 2 ~iC~~~~~~~~~~~C~H~~c~ 22 (39)
T smart00184 2 PICLEELKDPVVLPCGHTFCR 22 (39)
T ss_pred CcCccCCCCcEEecCCChHHH
Confidence 344444444455667776664
No 79
>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=28.43 E-value=35 Score=14.49 Aligned_cols=13 Identities=23% Similarity=0.539 Sum_probs=7.2
Q ss_pred eeecccCceeecC
Q psy14516 55 WVCLICYQVRCGR 67 (76)
Q Consensus 55 W~CL~Cg~v~CgR 67 (76)
|.|..|+...-.+
T Consensus 1 ~~C~~C~~~~~~~ 13 (24)
T PF13894_consen 1 FQCPICGKSFRSK 13 (24)
T ss_dssp EE-SSTS-EESSH
T ss_pred CCCcCCCCcCCcH
Confidence 6778887766544
No 80
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=28.20 E-value=53 Score=16.36 Aligned_cols=23 Identities=30% Similarity=0.452 Sum_probs=15.0
Q ss_pred cCcCCCCCCeee-ecccCceeecC
Q psy14516 45 CVDCASVAENWV-CLICYQVRCGR 67 (76)
Q Consensus 45 C~~C~~~~~~W~-CL~Cg~v~CgR 67 (76)
|..|...-.... =+.||+..|..
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~ 24 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRD 24 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHH
T ss_pred CCcCCccccCCCEEecCCCcchHH
Confidence 445555555555 78899988863
No 81
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=27.17 E-value=33 Score=27.52 Aligned_cols=25 Identities=24% Similarity=0.526 Sum_probs=19.5
Q ss_pred CccccCcCCCC--CCeeeecccCceee
Q psy14516 41 VKAPCVDCASV--AENWVCLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~~--~~~W~CL~Cg~v~C 65 (76)
....|.+|+.. +..|.|+.||+-..
T Consensus 517 p~~~C~~CG~~~~~~~~~CP~CGs~~~ 543 (555)
T cd01675 517 PIDICNDCGYIGEGEGFKCPKCGSEDV 543 (555)
T ss_pred CCccCCCCCCCCcCCCCCCcCCCCcCc
Confidence 33489999985 58999999997543
No 82
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=26.84 E-value=37 Score=22.91 Aligned_cols=28 Identities=18% Similarity=0.281 Sum_probs=21.1
Q ss_pred CccccCcCCC------CCCeeeecccCceeecCC
Q psy14516 41 VKAPCVDCAS------VAENWVCLICYQVRCGRY 68 (76)
Q Consensus 41 ~~~~C~~C~~------~~~~W~CL~Cg~v~CgR~ 68 (76)
....|..|+. ...+-.|..||.....|.
T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred ceEecccCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 5677888883 456777999998887764
No 83
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=26.62 E-value=42 Score=22.02 Aligned_cols=17 Identities=18% Similarity=0.473 Sum_probs=13.4
Q ss_pred CCeeeecc--------cCceeecCC
Q psy14516 52 AENWVCLI--------CYQVRCGRY 68 (76)
Q Consensus 52 ~~~W~CL~--------Cg~v~CgR~ 68 (76)
..+|+|-. ||+.+|+-.
T Consensus 13 ~~l~i~~~~~k~vkc~CGh~f~d~r 37 (112)
T PF08882_consen 13 PHLWIVQKKDKVVKCDCGHEFCDAR 37 (112)
T ss_pred CcEEEEEecCceeeccCCCeecChh
Confidence 46788877 999999843
No 84
>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=26.31 E-value=36 Score=17.93 Aligned_cols=19 Identities=26% Similarity=0.571 Sum_probs=10.9
Q ss_pred eeeecccCceeecC--CCcch
Q psy14516 54 NWVCLICYQVRCGR--YIEEH 72 (76)
Q Consensus 54 ~W~CL~Cg~v~CgR--~~~~H 72 (76)
.-.|-.|+...|.+ +...|
T Consensus 13 ~~~C~~C~~~FC~~Hr~~e~H 33 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHRLPEDH 33 (43)
T ss_dssp HEE-TTTS-EE-TTTHSTTTC
T ss_pred CeECCCCCcccCccccCcccc
Confidence 34599999999986 44444
No 85
>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=26.10 E-value=46 Score=18.32 Aligned_cols=11 Identities=18% Similarity=0.498 Sum_probs=6.1
Q ss_pred CCCeeeecccC
Q psy14516 51 VAENWVCLICY 61 (76)
Q Consensus 51 ~~~~W~CL~Cg 61 (76)
.+.-|-|+.|.
T Consensus 12 ~G~R~~C~~C~ 22 (48)
T cd02341 12 PGTRYHCSECD 22 (48)
T ss_pred ccceEECCCCC
Confidence 34455566665
No 86
>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=26.08 E-value=34 Score=21.81 Aligned_cols=24 Identities=25% Similarity=0.675 Sum_probs=17.2
Q ss_pred CCccccCcCCCC----CCeeeecccCce
Q psy14516 40 DVKAPCVDCASV----AENWVCLICYQV 63 (76)
Q Consensus 40 ~~~~~C~~C~~~----~~~W~CL~Cg~v 63 (76)
+....|..|+.. ...+.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 467789999853 235679999864
No 87
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=25.42 E-value=39 Score=21.91 Aligned_cols=12 Identities=33% Similarity=0.595 Sum_probs=10.0
Q ss_pred CeeeecccCcee
Q psy14516 53 ENWVCLICYQVR 64 (76)
Q Consensus 53 ~~W~CL~Cg~v~ 64 (76)
-.|.||.||.+-
T Consensus 81 v~vtC~~CG~~~ 92 (105)
T COG2023 81 VVVTCLECGTIR 92 (105)
T ss_pred EEEEecCCCcEE
Confidence 578899999873
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=24.80 E-value=57 Score=17.21 Aligned_cols=20 Identities=20% Similarity=0.482 Sum_probs=11.6
Q ss_pred cccCcCCCC------CCeeeecccCc
Q psy14516 43 APCVDCASV------AENWVCLICYQ 62 (76)
Q Consensus 43 ~~C~~C~~~------~~~W~CL~Cg~ 62 (76)
..|..|+.. ...+.|..||.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGY 29 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCC
Confidence 356666632 12566777775
No 89
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=24.76 E-value=60 Score=17.29 Aligned_cols=19 Identities=26% Similarity=0.898 Sum_probs=11.8
Q ss_pred cccCcCCC---CCCeeeecccC
Q psy14516 43 APCVDCAS---VAENWVCLICY 61 (76)
Q Consensus 43 ~~C~~C~~---~~~~W~CL~Cg 61 (76)
..|..|.. .+.-|-|+.|.
T Consensus 5 ~~C~~C~~~~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTDPIIGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SSSEESSEEEESSSS
T ss_pred eECcCCCCCcCcCCeEECCCCC
Confidence 45667765 46778888886
No 90
>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=24.51 E-value=58 Score=21.88 Aligned_cols=25 Identities=16% Similarity=0.006 Sum_probs=17.3
Q ss_pred CCccccCcCCC-----CCCeeeecccCcee
Q psy14516 40 DVKAPCVDCAS-----VAENWVCLICYQVR 64 (76)
Q Consensus 40 ~~~~~C~~C~~-----~~~~W~CL~Cg~v~ 64 (76)
..+..|.+|+. .++.-+|..||.+.
T Consensus 7 GtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 7 GTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred CccccCCCcCccccccCCCCccCCCcCCcc
Confidence 34556777773 46777888888774
No 91
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.18 E-value=35 Score=21.84 Aligned_cols=24 Identities=29% Similarity=0.639 Sum_probs=16.6
Q ss_pred CCccccCcCCCCC----Ceee-ecccCce
Q psy14516 40 DVKAPCVDCASVA----ENWV-CLICYQV 63 (76)
Q Consensus 40 ~~~~~C~~C~~~~----~~W~-CL~Cg~v 63 (76)
+....|.+|+... ..+. |+.||..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 4677899998542 2344 9999864
No 92
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=24.15 E-value=35 Score=23.94 Aligned_cols=15 Identities=33% Similarity=0.669 Sum_probs=12.4
Q ss_pred CeeeecccCceeecC
Q psy14516 53 ENWVCLICYQVRCGR 67 (76)
Q Consensus 53 ~~W~CL~Cg~v~CgR 67 (76)
+.|+|..||...-.+
T Consensus 47 ~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 47 EVWVCPHCGYAAFEE 61 (214)
T ss_pred eEEECCCCCCccccc
Confidence 689999999887665
No 93
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=23.62 E-value=42 Score=16.78 Aligned_cols=7 Identities=29% Similarity=0.619 Sum_probs=3.4
Q ss_pred eecccCc
Q psy14516 56 VCLICYQ 62 (76)
Q Consensus 56 ~CL~Cg~ 62 (76)
.|..||.
T Consensus 28 ~CP~Cg~ 34 (41)
T smart00834 28 TCPECGG 34 (41)
T ss_pred CCCCCCC
Confidence 3555554
No 94
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=23.35 E-value=54 Score=19.15 Aligned_cols=27 Identities=30% Similarity=0.650 Sum_probs=17.8
Q ss_pred CccccCcCCCC------CCee-eecccCceeecC
Q psy14516 41 VKAPCVDCASV------AENW-VCLICYQVRCGR 67 (76)
Q Consensus 41 ~~~~C~~C~~~------~~~W-~CL~Cg~v~CgR 67 (76)
..-+|.+|... ...+ .|..||.+.+--
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~P 43 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEP 43 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccC
Confidence 34568888843 2333 499999888754
No 95
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.11 E-value=39 Score=21.55 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=17.1
Q ss_pred CCccccCcCCCCC----C-eeeecccCce
Q psy14516 40 DVKAPCVDCASVA----E-NWVCLICYQV 63 (76)
Q Consensus 40 ~~~~~C~~C~~~~----~-~W~CL~Cg~v 63 (76)
+....|.+|+..- . .+.|+.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 4678899998542 2 2669999964
No 97
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.95 E-value=58 Score=25.69 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=18.5
Q ss_pred CccccCcCCCCCC-eeeecccCce
Q psy14516 41 VKAPCVDCASVAE-NWVCLICYQV 63 (76)
Q Consensus 41 ~~~~C~~C~~~~~-~W~CL~Cg~v 63 (76)
....|.-|+.... .|.|..||..
T Consensus 239 ~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 239 GKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CeEEcCCCcCcCCCCCCCCCCCCC
Confidence 4677999997765 8999999874
No 98
>PRK11032 hypothetical protein; Provisional
Probab=22.81 E-value=46 Score=22.90 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=21.6
Q ss_pred CccccCcCC------CCCCeeeecccCceeecCC
Q psy14516 41 VKAPCVDCA------SVAENWVCLICYQVRCGRY 68 (76)
Q Consensus 41 ~~~~C~~C~------~~~~~W~CL~Cg~v~CgR~ 68 (76)
....|..|+ ....+-.|..||+....|-
T Consensus 123 G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~ 156 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRR 156 (160)
T ss_pred ceEEecCCCCEEEecCCCcCCCCCCCCCCeeeeC
Confidence 567788888 3566777999999888774
No 99
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=22.78 E-value=51 Score=24.97 Aligned_cols=28 Identities=18% Similarity=0.449 Sum_probs=19.8
Q ss_pred CCccccCcCCCCCCeeeecccCceeecC
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
.....|.+|+...-.|.--.=|.+.|.|
T Consensus 18 ~~Nk~CaDCga~~P~W~S~nlGvfiCi~ 45 (319)
T COG5347 18 SSNKKCADCGAPNPTWASVNLGVFLCID 45 (319)
T ss_pred cccCccccCCCCCCceEecccCeEEEee
Confidence 4677899999999999844444444443
No 100
>PHA00616 hypothetical protein
Probab=22.40 E-value=9.1 Score=21.12 Aligned_cols=19 Identities=26% Similarity=0.356 Sum_probs=11.4
Q ss_pred eecccCceeecCC-Ccchhc
Q psy14516 56 VCLICYQVRCGRY-IEEHSN 74 (76)
Q Consensus 56 ~CL~Cg~v~CgR~-~~~Ha~ 74 (76)
-|+.||.+..-.+ -..|.+
T Consensus 3 qC~~CG~~F~~~s~l~~H~r 22 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHLL 22 (44)
T ss_pred ccchhhHHHhhHHHHHHHHH
Confidence 4888888776543 244443
No 101
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=22.35 E-value=49 Score=25.90 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=7.7
Q ss_pred CeeeecccCc
Q psy14516 53 ENWVCLICYQ 62 (76)
Q Consensus 53 ~~W~CL~Cg~ 62 (76)
+.|.|..||.
T Consensus 457 ~~~~cp~c~~ 466 (479)
T PRK05452 457 DNFLCPECSL 466 (479)
T ss_pred CCCcCcCCCC
Confidence 4688888875
No 102
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=22.26 E-value=27 Score=18.00 Aligned_cols=28 Identities=18% Similarity=0.501 Sum_probs=16.8
Q ss_pred CCCCCccCcccCCCCCC---CCccccCcCCC
Q psy14516 23 ADCPHTPLVAPVPQSGV---DVKAPCVDCAS 50 (76)
Q Consensus 23 ~~CpHl~~l~~~~~~~~---~~~~~C~~C~~ 50 (76)
..||+....-.++...+ ....+|..|+.
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 46888887544444322 24667887764
No 103
>PHA00626 hypothetical protein
Probab=21.93 E-value=72 Score=18.69 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=20.2
Q ss_pred ccccCcCCCCCCeeeecccCceeec
Q psy14516 42 KAPCVDCASVAENWVCLICYQVRCG 66 (76)
Q Consensus 42 ~~~C~~C~~~~~~W~CL~Cg~v~Cg 66 (76)
..+|..|...++...|..||+..--
T Consensus 11 Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 11 IAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred eeeeceecccCcceEcCCCCCeech
Confidence 3468888888999999999987654
No 104
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=21.47 E-value=43 Score=18.09 Aligned_cols=23 Identities=26% Similarity=0.111 Sum_probs=12.1
Q ss_pred cCcCCCCCCeeeecccCceeecC
Q psy14516 45 CVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 45 C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
|.-|+..-+.-+.+.||++.|.+
T Consensus 4 Cpi~~~~~~~Pv~~~~G~v~~~~ 26 (63)
T smart00504 4 CPISLEVMKDPVILPSGQTYERR 26 (63)
T ss_pred CcCCCCcCCCCEECCCCCEEeHH
Confidence 44444443444556666666654
No 105
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.46 E-value=44 Score=17.56 Aligned_cols=9 Identities=22% Similarity=0.331 Sum_probs=4.6
Q ss_pred eeeecccCc
Q psy14516 54 NWVCLICYQ 62 (76)
Q Consensus 54 ~W~CL~Cg~ 62 (76)
...|..||.
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 344555554
No 106
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.43 E-value=56 Score=26.87 Aligned_cols=26 Identities=15% Similarity=0.268 Sum_probs=20.9
Q ss_pred CCccccCcCCC--CCCeeeecccCceee
Q psy14516 40 DVKAPCVDCAS--VAENWVCLICYQVRC 65 (76)
Q Consensus 40 ~~~~~C~~C~~--~~~~W~CL~Cg~v~C 65 (76)
.....|.+|+. ....+.|..||.-.+
T Consensus 566 p~~~~C~~CG~~~~g~~~~CP~CGs~~~ 593 (625)
T PRK08579 566 PAITVCNKCGRSTTGLYTRCPRCGSEDV 593 (625)
T ss_pred CCCccCCCCCCccCCCCCcCcCCCCchh
Confidence 36788999996 588999999997543
No 107
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=21.05 E-value=93 Score=16.94 Aligned_cols=11 Identities=18% Similarity=0.461 Sum_probs=6.4
Q ss_pred CCCeeeecccC
Q psy14516 51 VAENWVCLICY 61 (76)
Q Consensus 51 ~~~~W~CL~Cg 61 (76)
.+.-|-|+.|.
T Consensus 12 ~G~RykC~~C~ 22 (45)
T cd02344 12 NGPRFKCRNCD 22 (45)
T ss_pred ccCeEECCCCC
Confidence 34556666665
No 108
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=21.04 E-value=80 Score=26.35 Aligned_cols=28 Identities=21% Similarity=0.660 Sum_probs=24.2
Q ss_pred CCccccCcCCCCCCeeeecccCceeecC
Q psy14516 40 DVKAPCVDCASVAENWVCLICYQVRCGR 67 (76)
Q Consensus 40 ~~~~~C~~C~~~~~~W~CL~Cg~v~CgR 67 (76)
+....|.+|+...-.|+|+.-|..-|-+
T Consensus 21 PgNk~CADCgs~~P~WASiNlGIFICi~ 48 (648)
T PLN03119 21 PPNRRCINCNSLGPQYVCTTFWTFVCMA 48 (648)
T ss_pred cCCCccccCCCCCCCceeeccceEEecc
Confidence 4677899999999999999888888875
No 109
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.54 E-value=81 Score=17.41 Aligned_cols=21 Identities=29% Similarity=0.683 Sum_probs=13.8
Q ss_pred ccCcCCC-----CCCeeeecccCcee
Q psy14516 44 PCVDCAS-----VAENWVCLICYQVR 64 (76)
Q Consensus 44 ~C~~C~~-----~~~~W~CL~Cg~v~ 64 (76)
.|..|+. ..+.|.|-.||...
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEE
Confidence 4666654 45677788887654
No 110
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.32 E-value=63 Score=15.24 Aligned_cols=7 Identities=29% Similarity=0.657 Sum_probs=3.4
Q ss_pred eecccCc
Q psy14516 56 VCLICYQ 62 (76)
Q Consensus 56 ~CL~Cg~ 62 (76)
.|..||.
T Consensus 18 fC~~CG~ 24 (26)
T PF13248_consen 18 FCPNCGA 24 (26)
T ss_pred cChhhCC
Confidence 3555553
No 111
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=20.15 E-value=55 Score=17.51 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=7.4
Q ss_pred ecccCceeecC
Q psy14516 57 CLICYQVRCGR 67 (76)
Q Consensus 57 CL~Cg~v~CgR 67 (76)
|-.||.+.|+.
T Consensus 21 Cr~Cg~~~C~~ 31 (57)
T cd00065 21 CRNCGRIFCSK 31 (57)
T ss_pred cCcCcCCcChH
Confidence 66777776664
No 112
>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=20.04 E-value=53 Score=26.85 Aligned_cols=25 Identities=20% Similarity=0.518 Sum_probs=19.2
Q ss_pred CccccCcCCCC-CCe-eeecccCceee
Q psy14516 41 VKAPCVDCASV-AEN-WVCLICYQVRC 65 (76)
Q Consensus 41 ~~~~C~~C~~~-~~~-W~CL~Cg~v~C 65 (76)
..+.|.+|+-. ++. |.|+.||+..+
T Consensus 531 ~~siC~~CGy~~g~~~~~CP~CGs~~~ 557 (586)
T TIGR02827 531 KITICNDCHHIDKRTLHRCPVCGSANI 557 (586)
T ss_pred CCeecCCCCCcCCCcCCcCcCCCCccc
Confidence 67889999984 544 99999996443
Done!