Query psy6684
Match_columns 77
No_of_seqs 80 out of 82
Neff 3.6
Searched_HMMs 46136
Date Sat Aug 17 00:25:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6684.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6684hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1777|consensus 99.9 2.3E-27 5E-32 193.4 5.3 72 6-77 525-596 (625)
2 KOG0943|consensus 99.5 1.1E-14 2.3E-19 129.7 1.7 54 22-76 1238-1291(3015)
3 PF02207 zf-UBR: Putative zinc 99.4 2E-13 4.3E-18 84.5 2.5 47 25-76 1-48 (71)
4 smart00396 ZnF_UBR1 Putative z 99.0 3.4E-10 7.4E-15 70.7 3.2 47 25-76 1-48 (71)
5 KOG1776|consensus 98.3 2.8E-08 6.1E-13 85.8 -3.2 52 23-75 763-815 (1110)
6 KOG2752|consensus 97.7 2E-05 4.4E-10 62.6 1.9 48 23-73 39-87 (345)
7 PF00643 zf-B_box: B-box zinc 96.1 0.005 1.1E-07 33.7 2.3 28 41-72 14-41 (42)
8 smart00336 BBOX B-Box-type zin 93.9 0.044 9.5E-07 29.2 1.7 28 40-71 13-40 (42)
9 cd00021 BBOX B-Box-type zinc f 93.2 0.065 1.4E-06 28.2 1.7 29 40-72 10-38 (39)
10 smart00290 ZnF_UBP Ubiquitin C 62.8 4.1 8.9E-05 22.6 0.9 19 44-62 1-19 (50)
11 PF07649 C1_3: C1-like domain; 57.7 6.5 0.00014 20.3 1.1 18 40-61 13-30 (30)
12 PF01422 zf-NF-X1: NF-X1 type 56.6 3.2 7E-05 21.0 -0.2 9 59-67 5-13 (20)
13 TIGR00269 conserved hypothetic 53.9 6.1 0.00013 25.6 0.7 20 42-61 80-99 (104)
14 PF10186 Atg14: UV radiation r 45.3 13 0.00028 26.6 1.3 20 44-63 1-20 (302)
15 smart00659 RPOLCX RNA polymera 44.7 26 0.00056 20.1 2.3 28 42-75 2-34 (44)
16 PF08271 TF_Zn_Ribbon: TFIIB z 42.4 11 0.00023 20.9 0.4 19 43-61 1-26 (43)
17 PF14976 FAM72: FAM72 protein 40.0 25 0.00054 25.6 2.1 31 44-74 73-106 (150)
18 PF01412 ArfGap: Putative GTPa 37.7 15 0.00034 24.0 0.7 23 44-67 15-45 (116)
19 PRK09853 putative selenate red 37.6 16 0.00034 33.1 0.9 32 35-71 878-909 (1019)
20 PF07911 DUF1677: Protein of u 35.9 22 0.00048 23.8 1.2 21 43-63 5-40 (91)
21 PF02148 zf-UBP: Zn-finger in 35.7 15 0.00032 21.7 0.3 10 41-50 10-19 (63)
22 COG1439 Predicted nucleic acid 32.6 37 0.00079 25.1 2.1 30 41-76 138-169 (177)
23 PF03604 DNA_RNApol_7kD: DNA d 31.7 26 0.00057 19.0 0.9 26 43-74 1-31 (32)
24 cd00729 rubredoxin_SM Rubredox 30.4 25 0.00053 19.0 0.7 19 42-60 2-24 (34)
25 smart00438 ZnF_NFX Repressor o 29.5 16 0.00034 19.4 -0.2 9 59-67 5-13 (26)
26 cd00350 rubredoxin_like Rubred 27.6 29 0.00064 18.3 0.7 18 43-60 2-23 (33)
27 PF06689 zf-C4_ClpX: ClpX C4-t 27.2 43 0.00093 18.7 1.3 13 53-65 23-35 (41)
28 cd02340 ZZ_NBR1_like Zinc fing 26.5 54 0.0012 18.4 1.6 29 38-69 10-39 (43)
29 cd06219 DHOD_e_trans_like1 FAD 25.3 18 0.00038 25.9 -0.6 15 54-68 218-240 (248)
30 TIGR03315 Se_ygfK putative sel 24.0 38 0.00082 30.6 1.0 28 35-67 873-900 (1012)
31 PF02132 RecR: RecR protein; 23.8 28 0.0006 19.3 0.1 23 40-62 15-37 (41)
32 PF12346 HJURP_mid: Holliday j 23.5 21 0.00046 25.0 -0.5 12 31-43 13-24 (116)
33 PF01363 FYVE: FYVE zinc finge 22.9 37 0.0008 19.8 0.5 18 40-61 23-40 (69)
34 COG2956 Predicted N-acetylgluc 21.9 44 0.00095 27.6 0.9 24 38-61 350-375 (389)
35 cd06008 NF-X1-zinc-finger Pres 21.6 28 0.0006 20.0 -0.2 10 58-67 14-23 (49)
36 PF01096 TFIIS_C: Transcriptio 20.7 83 0.0018 17.2 1.7 16 35-50 21-36 (39)
37 cd00974 DSRD Desulforedoxin (D 20.6 58 0.0013 17.1 1.0 13 40-52 2-14 (34)
38 PF12838 Fer4_7: 4Fe-4S diclus 20.2 55 0.0012 18.0 0.9 11 57-67 41-51 (52)
No 1
>KOG1777|consensus
Probab=99.94 E-value=2.3e-27 Score=193.43 Aligned_cols=72 Identities=64% Similarity=1.203 Sum_probs=70.4
Q ss_pred cccccccCCchhHHhhhhCCcceEEeecCcccceeceEEeecCCCCCCeeeehhhHHhhcCCCceEEeeeCC
Q psy6684 6 GKKELYLKENWDVQRAVTSGQCLYKISSYTSFPMHDFYRCQTCHTTDRNAICVNCIKSCHAGHDVAFIRHDR 77 (77)
Q Consensus 6 ~k~~~~~~n~d~~e~al~~~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~y~r~sR 77 (77)
-+.|.||+|+|.||+|++.++|+|++|++++|||++||+|.|||++|+|+||.+|++.||+||+|+|+|+||
T Consensus 525 ~~~N~iydN~D~vekAik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~CH~GH~Vefir~Dr 596 (625)
T KOG1777|consen 525 ERGNQIYDNLDHVEKAIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKRCHEGHDVEFIRHDR 596 (625)
T ss_pred ccccccccchHHHHHHhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHHhcCCCceEEEeece
Confidence 467999999999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG0943|consensus
Probab=99.47 E-value=1.1e-14 Score=129.70 Aligned_cols=54 Identities=24% Similarity=0.628 Sum_probs=50.8
Q ss_pred hhCCcceEEeecCcccceeceEEeecCCCCCCeeeehhhHHhhcCCCceEEeeeC
Q psy6684 22 VTSGQCLYKISSYTSFPMHDFYRCQTCHTTDRNAICVNCIKSCHAGHDVAFIRHD 76 (77)
Q Consensus 22 l~~~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~y~r~s 76 (77)
..+.+|+|+|+ +.++++||.|.|.||++.++..||+.||.+||+|||..+.|.|
T Consensus 1238 C~NDtCSFTWT-GadHINQDIfECkTCGL~~SLCCCsECAltCHk~HDCkLKRTS 1291 (3015)
T KOG0943|consen 1238 CCNDTCSFTWT-GADHINQDIFECKTCGLLESLCCCSECALTCHKGHDCKLKRTS 1291 (3015)
T ss_pred EecCccceeec-chhhccchhhhhcccccchhhhhhHHHHHHhccCCccceeccC
Confidence 56799999996 5689999999999999999999999999999999999999987
No 3
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=99.38 E-value=2e-13 Score=84.50 Aligned_cols=47 Identities=40% Similarity=0.912 Sum_probs=35.5
Q ss_pred CcceEEeecCcccceeceEEeecCCCCCCeeeehhh-HHhhcCCCceEEeeeC
Q psy6684 25 GQCLYKISSYTSFPMHDFYRCQTCHTTDRNAICVNC-IKSCHAGHDVAFIRHD 76 (77)
Q Consensus 25 ~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d~~giC~~C-a~~CH~GHdv~y~r~s 76 (77)
++|+++++.+ |.+|+|.||.+.++.+||..| ++.||+||++++.+.+
T Consensus 1 ~~C~~~~~~~-----q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 1 KKCTYVWTSG-----QIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp -SS--B--TT------EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CcCCCCCcCC-----CEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 3688886433 999999999999999999999 9999999999999876
No 4
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=98.99 E-value=3.4e-10 Score=70.73 Aligned_cols=47 Identities=32% Similarity=0.846 Sum_probs=39.9
Q ss_pred CcceEEeecCcccceeceEEeecCCCCCCeeeehhhHH-hhcCCCceEEeeeC
Q psy6684 25 GQCLYKISSYTSFPMHDFYRCQTCHTTDRNAICVNCIK-SCHAGHDVAFIRHD 76 (77)
Q Consensus 25 ~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d~~giC~~Ca~-~CH~GHdv~y~r~s 76 (77)
.+|+++++.+ ++ .|+|.||.+.+..+||..|++ .||+||++++.+.+
T Consensus 1 ~~C~~~~~~~-~~----~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~~~~~~~ 48 (71)
T smart00396 1 DVCTYKFTGG-EV----IYRCKTCGLDPTCVLCSDCFRSNCHKGHDYSLKTSR 48 (71)
T ss_pred CCCCCccCCC-CE----EEECcCCCCCCCEeEChHHCCCCCCCCCCEEEEEec
Confidence 3689997433 33 399999999999999999999 99999999988765
No 5
>KOG1776|consensus
Probab=98.33 E-value=2.8e-08 Score=85.75 Aligned_cols=52 Identities=4% Similarity=-0.162 Sum_probs=47.5
Q ss_pred hCCcceEEeecCcccceeceEEeecCCCCCCe-eeehhhHHhhcCCCceEEeee
Q psy6684 23 TSGQCLYKISSYTSFPMHDFYRCQTCHTTDRN-AICVNCIKSCHAGHDVAFIRH 75 (77)
Q Consensus 23 ~~~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d~~-giC~~Ca~~CH~GHdv~y~r~ 75 (77)
....||++ +++.-++.|+||.|+||+|..+. |.|++|+++||.||++.|+..
T Consensus 763 ~v~~~T~K-kk~q~~m~n~~~q~~k~~M~~~~gG~~kV~s~t~H~~~~i~~S~~ 815 (1110)
T KOG1776|consen 763 LVRDETEK-KKKQMAMLNREKQLTKMRMKVGTGGQIKVSSRTLHNEPSIDDSDS 815 (1110)
T ss_pred HHHHHHHh-hhhhHHHHHHHhhhhhheeeeccCceEEEeeecccCCCCccccCC
Confidence 34789999 67889999999999999999999 999999999999999999853
No 6
>KOG2752|consensus
Probab=97.68 E-value=2e-05 Score=62.58 Aligned_cols=48 Identities=25% Similarity=0.654 Sum_probs=39.9
Q ss_pred hCCcceEEeecCcccceeceEEeecCCCCC-CeeeehhhHHhhcCCCceEEe
Q psy6684 23 TSGQCLYKISSYTSFPMHDFYRCQTCHTTD-RNAICVNCIKSCHAGHDVAFI 73 (77)
Q Consensus 23 ~~~~Ctf~~st~~~f~~Q~~Y~C~TC~~~d-~~giC~~Ca~~CH~GHdv~y~ 73 (77)
+...|||.. + .-+.|-.|.|.||-... .+|||..|+..||.||+++=.
T Consensus 39 ~~~~CTy~~-G--y~~rQ~l~sClTC~P~~~~agvC~~C~~~CH~~H~lveL 87 (345)
T KOG2752|consen 39 NPDVCTYAK-G--YKKRQALFSCLTCTPAPEMAGVCYACSLSCHDGHELVEL 87 (345)
T ss_pred CCccccccc-C--cccccceeEeecccCChhhceeEEEeeeeecCCceeeec
Confidence 457899993 3 33469999999999987 569999999999999998744
No 7
>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=96.15 E-value=0.005 Score=33.67 Aligned_cols=28 Identities=29% Similarity=0.688 Sum_probs=25.3
Q ss_pred ceEEeecCCCCCCeeeehhhHHhhcCCCceEE
Q psy6684 41 DFYRCQTCHTTDRNAICVNCIKSCHAGHDVAF 72 (77)
Q Consensus 41 ~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~y 72 (77)
--|.|.+|+. .+|..|+..=|+||++.-
T Consensus 14 ~~~~C~~C~~----~~C~~C~~~~H~~H~~~~ 41 (42)
T PF00643_consen 14 LSLFCEDCNE----PLCSECTVSGHKGHKIVP 41 (42)
T ss_dssp EEEEETTTTE----EEEHHHHHTSTTTSEEEE
T ss_pred eEEEecCCCC----ccCccCCCCCCCCCEEeE
Confidence 6789999998 899999999999999863
No 8
>smart00336 BBOX B-Box-type zinc finger.
Probab=93.87 E-value=0.044 Score=29.23 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=24.2
Q ss_pred eceEEeecCCCCCCeeeehhhHHhhcCCCceE
Q psy6684 40 HDFYRCQTCHTTDRNAICVNCIKSCHAGHDVA 71 (77)
Q Consensus 40 Q~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~ 71 (77)
.-+|.|.+|.. .||..|...=|+||.+.
T Consensus 13 ~~~~~C~~c~~----~iC~~C~~~~H~~H~~~ 40 (42)
T smart00336 13 PAEFFCEECGA----LLCRTCDEAEHRGHTVV 40 (42)
T ss_pred ceEEECCCCCc----ccccccChhhcCCCcee
Confidence 34788999987 89999998899999885
No 9
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=93.22 E-value=0.065 Score=28.21 Aligned_cols=29 Identities=31% Similarity=0.493 Sum_probs=23.8
Q ss_pred eceEEeecCCCCCCeeeehhhHHhhcCCCceEE
Q psy6684 40 HDFYRCQTCHTTDRNAICVNCIKSCHAGHDVAF 72 (77)
Q Consensus 40 Q~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~y 72 (77)
.-.+.|.+|.. .+|..|...=|+||.+..
T Consensus 10 ~~~~fC~~~~~----~iC~~C~~~~H~~H~~~~ 38 (39)
T cd00021 10 PLSLFCETDRA----LLCVDCDLSVHSGHRRVP 38 (39)
T ss_pred ceEEEeCccCh----hhhhhcChhhcCCCCEee
Confidence 34788999887 899999866699999864
No 10
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=62.81 E-value=4.1 Score=22.57 Aligned_cols=19 Identities=32% Similarity=0.875 Sum_probs=12.8
Q ss_pred EeecCCCCCCeeeehhhHH
Q psy6684 44 RCQTCHTTDRNAICVNCIK 62 (77)
Q Consensus 44 ~C~TC~~~d~~giC~~Ca~ 62 (77)
+|.+|+.....++|-.|-.
T Consensus 1 ~C~~C~~~~~l~~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQ 19 (50)
T ss_pred CcccCCCcCCeEEecCCCC
Confidence 4667777666777777654
No 11
>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=57.71 E-value=6.5 Score=20.29 Aligned_cols=18 Identities=33% Similarity=0.835 Sum_probs=7.9
Q ss_pred eceEEeecCCCCCCeeeehhhH
Q psy6684 40 HDFYRCQTCHTTDRNAICVNCI 61 (77)
Q Consensus 40 Q~~Y~C~TC~~~d~~giC~~Ca 61 (77)
+.+|+|..|+. .+-..||
T Consensus 13 ~~~Y~C~~Cdf----~lH~~Ca 30 (30)
T PF07649_consen 13 GWFYRCSECDF----DLHEECA 30 (30)
T ss_dssp --EEE-TTT---------HHHH
T ss_pred CceEECccCCC----ccChhcC
Confidence 57899999988 4555554
No 12
>PF01422 zf-NF-X1: NF-X1 type zinc finger; InterPro: IPR000967 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 domain presumed to be a zinc binding domain. The following pattern describes the zinc finger: C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C where X can be any amino acid, and numbers in brackets indicate the number of residues. The two position can be either His or Cys. This domain is found in the human transcriptional repressor NK-X1, a repressor of HLA-DRA transcription; the Drosophila shuttle craft protein, which plays an essential role during the late stages of embryonic neurogenesis; and a yeast hypothetical protein YNL023C. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=56.64 E-value=3.2 Score=20.96 Aligned_cols=9 Identities=44% Similarity=1.254 Sum_probs=7.7
Q ss_pred hhHHhhcCC
Q psy6684 59 NCIKSCHAG 67 (77)
Q Consensus 59 ~Ca~~CH~G 67 (77)
.|.++||.|
T Consensus 5 ~C~~~CH~G 13 (20)
T PF01422_consen 5 TCQQLCHPG 13 (20)
T ss_pred ccCCcccCC
Confidence 588899998
No 13
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=53.89 E-value=6.1 Score=25.64 Aligned_cols=20 Identities=30% Similarity=0.841 Sum_probs=17.8
Q ss_pred eEEeecCCCCCCeeeehhhH
Q psy6684 42 FYRCQTCHTTDRNAICVNCI 61 (77)
Q Consensus 42 ~Y~C~TC~~~d~~giC~~Ca 61 (77)
.-+|.-||..-+..||+.|.
T Consensus 80 ~~~C~~CG~pss~~iC~~C~ 99 (104)
T TIGR00269 80 LRRCERCGEPTSGRICKACK 99 (104)
T ss_pred CCcCCcCcCcCCccccHhhh
Confidence 44799999999999999995
No 14
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=45.30 E-value=13 Score=26.55 Aligned_cols=20 Identities=35% Similarity=1.084 Sum_probs=17.8
Q ss_pred EeecCCCCCCeeeehhhHHh
Q psy6684 44 RCQTCHTTDRNAICVNCIKS 63 (77)
Q Consensus 44 ~C~TC~~~d~~giC~~Ca~~ 63 (77)
+|..|+.....-.|..|++.
T Consensus 1 ~C~iC~~~~~~~~C~~C~~~ 20 (302)
T PF10186_consen 1 QCPICHNSRRRFYCANCVNN 20 (302)
T ss_pred CCCCCCCCCCCeECHHHHHH
Confidence 59999988889999999974
No 15
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.67 E-value=26 Score=20.09 Aligned_cols=28 Identities=21% Similarity=0.693 Sum_probs=20.8
Q ss_pred eEEeecCCCCC-----CeeeehhhHHhhcCCCceEEeee
Q psy6684 42 FYRCQTCHTTD-----RNAICVNCIKSCHAGHDVAFIRH 75 (77)
Q Consensus 42 ~Y~C~TC~~~d-----~~giC~~Ca~~CH~GHdv~y~r~ 75 (77)
.|.|-.|+..- ..--|..| ||.|.|...
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~C------G~rIlyK~R 34 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCREC------GYRILYKKR 34 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCC------CceEEEEeC
Confidence 48999998743 23667777 999999764
No 16
>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=42.35 E-value=11 Score=20.88 Aligned_cols=19 Identities=26% Similarity=0.894 Sum_probs=9.4
Q ss_pred EEeecCCCCC-------CeeeehhhH
Q psy6684 43 YRCQTCHTTD-------RNAICVNCI 61 (77)
Q Consensus 43 Y~C~TC~~~d-------~~giC~~Ca 61 (77)
|.|..|+... +.-||..|-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG 26 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCG 26 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCC
Confidence 4455555532 345666663
No 17
>PF14976 FAM72: FAM72 protein
Probab=39.95 E-value=25 Score=25.59 Aligned_cols=31 Identities=29% Similarity=0.641 Sum_probs=26.2
Q ss_pred EeecCCCCCCe---eeehhhHHhhcCCCceEEee
Q psy6684 44 RCQTCHTTDRN---AICVNCIKSCHAGHDVAFIR 74 (77)
Q Consensus 44 ~C~TC~~~d~~---giC~~Ca~~CH~GHdv~y~r 74 (77)
.|+.|+.+-+- .-|+.|-..|-.||--+|-.
T Consensus 73 aC~~CGn~vGYhV~~PC~~Cl~scNNGH~wmFhs 106 (150)
T PF14976_consen 73 ACLGCGNIVGYHVVVPCSRCLSSCNNGHFWMFHS 106 (150)
T ss_pred eeecCCCeeeeEEEEEcchHhcCccCCceEEEec
Confidence 69999998876 55899999999999988753
No 18
>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=37.75 E-value=15 Score=24.05 Aligned_cols=23 Identities=22% Similarity=0.678 Sum_probs=14.9
Q ss_pred EeecCCCCC--------CeeeehhhHHhhcCC
Q psy6684 44 RCQTCHTTD--------RNAICVNCIKSCHAG 67 (77)
Q Consensus 44 ~C~TC~~~d--------~~giC~~Ca~~CH~G 67 (77)
.|-+|+..+ +.-+|..||.+ |+.
T Consensus 15 ~CaDCg~~~p~w~s~~~GiflC~~Cag~-HR~ 45 (116)
T PF01412_consen 15 VCADCGAPNPTWASLNYGIFLCLECAGI-HRS 45 (116)
T ss_dssp B-TTT-SBS--EEETTTTEEE-HHHHHH-HHH
T ss_pred cCCCCCCCCCCEEEeecChhhhHHHHHH-HHH
Confidence 477888766 45789999987 774
No 19
>PRK09853 putative selenate reductase subunit YgfK; Provisional
Probab=37.59 E-value=16 Score=33.07 Aligned_cols=32 Identities=25% Similarity=0.759 Sum_probs=26.0
Q ss_pred cccceeceEEeecCCCCCCeeeehhhHHhhcCCCceE
Q psy6684 35 TSFPMHDFYRCQTCHTTDRNAICVNCIKSCHAGHDVA 71 (77)
Q Consensus 35 ~~f~~Q~~Y~C~TC~~~d~~giC~~Ca~~CH~GHdv~ 71 (77)
..+..|+--+|..|+. +|..|..+|-.+=+++
T Consensus 878 ~~~~~~~~~rC~~C~~-----~C~~C~~vCP~~A~~~ 909 (1019)
T PRK09853 878 DAFVAQEAARCLECNY-----VCEKCVDVCPNRANVS 909 (1019)
T ss_pred cccccccccccCCccc-----ccchhhhhCCcccccc
Confidence 3456788899999997 9999999999765443
No 20
>PF07911 DUF1677: Protein of unknown function (DUF1677); InterPro: IPR012876 The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues.
Probab=35.90 E-value=22 Score=23.80 Aligned_cols=21 Identities=24% Similarity=0.686 Sum_probs=16.8
Q ss_pred EEeecCCCCC---------------CeeeehhhHHh
Q psy6684 43 YRCQTCHTTD---------------RNAICVNCIKS 63 (77)
Q Consensus 43 Y~C~TC~~~d---------------~~giC~~Ca~~ 63 (77)
=+|.-|++++ +.|||.-|+..
T Consensus 5 akCeCCG~~EECT~~YI~~VR~ry~GrWvCGLC~EA 40 (91)
T PF07911_consen 5 AKCECCGLTEECTPEYIARVRERYGGRWVCGLCSEA 40 (91)
T ss_pred eeecCCCCchhccHHHHHHHHHHhCCeehhhcCHHH
Confidence 3688899986 57999999863
No 21
>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=35.75 E-value=15 Score=21.73 Aligned_cols=10 Identities=30% Similarity=0.889 Sum_probs=4.6
Q ss_pred ceEEeecCCC
Q psy6684 41 DFYRCQTCHT 50 (77)
Q Consensus 41 ~~Y~C~TC~~ 50 (77)
+.|-|.+|+.
T Consensus 10 ~lw~CL~Cg~ 19 (63)
T PF02148_consen 10 NLWLCLTCGY 19 (63)
T ss_dssp SEEEETTTS-
T ss_pred ceEEeCCCCc
Confidence 4455555554
No 22
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=32.59 E-value=37 Score=25.10 Aligned_cols=30 Identities=23% Similarity=0.431 Sum_probs=23.8
Q ss_pred ceEEeecCCCCCC--eeeehhhHHhhcCCCceEEeeeC
Q psy6684 41 DFYRCQTCHTTDR--NAICVNCIKSCHAGHDVAFIRHD 76 (77)
Q Consensus 41 ~~Y~C~TC~~~d~--~giC~~Ca~~CH~GHdv~y~r~s 76 (77)
.-|+|+-|...-. ..+|..| ||.+.-.|.+
T Consensus 138 w~~rC~GC~~~f~~~~~~Cp~C------G~~~~~~~~~ 169 (177)
T COG1439 138 WRLRCHGCKRIFPEPKDFCPIC------GSPLKRKRVK 169 (177)
T ss_pred eeEEEecCceecCCCCCcCCCC------CCceEEeeec
Confidence 4589999998766 6999999 8887766544
No 23
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=31.74 E-value=26 Score=19.01 Aligned_cols=26 Identities=27% Similarity=0.765 Sum_probs=15.4
Q ss_pred EEeecCCCCCCe-----eeehhhHHhhcCCCceEEee
Q psy6684 43 YRCQTCHTTDRN-----AICVNCIKSCHAGHDVAFIR 74 (77)
Q Consensus 43 Y~C~TC~~~d~~-----giC~~Ca~~CH~GHdv~y~r 74 (77)
|.|-.|+...+. -.|..| ||.+.|.+
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~C------G~RIlyK~ 31 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPEC------GHRILYKK 31 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSS------S-SEEBE-
T ss_pred CCCCcCCCeeEcCCCCcEECCcC------CCeEEEec
Confidence 667777765332 457766 88888764
No 24
>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=30.35 E-value=25 Score=18.99 Aligned_cols=19 Identities=21% Similarity=0.702 Sum_probs=12.8
Q ss_pred eEEeecCCCC-CCe---eeehhh
Q psy6684 42 FYRCQTCHTT-DRN---AICVNC 60 (77)
Q Consensus 42 ~Y~C~TC~~~-d~~---giC~~C 60 (77)
.|+|..|+.+ ++. ..|..|
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~C 24 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPIC 24 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCC
Confidence 5888888887 322 466666
No 25
>smart00438 ZnF_NFX Repressor of transcription.
Probab=29.52 E-value=16 Score=19.43 Aligned_cols=9 Identities=56% Similarity=1.328 Sum_probs=7.5
Q ss_pred hhHHhhcCC
Q psy6684 59 NCIKSCHAG 67 (77)
Q Consensus 59 ~Ca~~CH~G 67 (77)
.|.+.||.|
T Consensus 5 ~C~~~CH~G 13 (26)
T smart00438 5 KCQKLCHPG 13 (26)
T ss_pred cCCCCCCCC
Confidence 588899987
No 26
>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=27.62 E-value=29 Score=18.31 Aligned_cols=18 Identities=33% Similarity=0.859 Sum_probs=9.8
Q ss_pred EEeecCCCC-C---Ceeeehhh
Q psy6684 43 YRCQTCHTT-D---RNAICVNC 60 (77)
Q Consensus 43 Y~C~TC~~~-d---~~giC~~C 60 (77)
|.|..|+.+ + ..+.|-.|
T Consensus 2 ~~C~~CGy~y~~~~~~~~CP~C 23 (33)
T cd00350 2 YVCPVCGYIYDGEEAPWVCPVC 23 (33)
T ss_pred EECCCCCCEECCCcCCCcCcCC
Confidence 566666665 1 23555555
No 27
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=27.16 E-value=43 Score=18.65 Aligned_cols=13 Identities=23% Similarity=0.623 Sum_probs=10.8
Q ss_pred CeeeehhhHHhhc
Q psy6684 53 RNAICVNCIKSCH 65 (77)
Q Consensus 53 ~~giC~~Ca~~CH 65 (77)
+..||..|+..|+
T Consensus 23 ~~~IC~~Cv~~~~ 35 (41)
T PF06689_consen 23 GAYICDECVEQAY 35 (41)
T ss_dssp SEEEEHHHHHHHH
T ss_pred CcEECHHHHHHHH
Confidence 4689999999886
No 28
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=26.54 E-value=54 Score=18.43 Aligned_cols=29 Identities=24% Similarity=0.616 Sum_probs=20.4
Q ss_pred ceeceEEeecCCCCCCeeeehhhHHh-hcCCCc
Q psy6684 38 PMHDFYRCQTCHTTDRNAICVNCIKS-CHAGHD 69 (77)
Q Consensus 38 ~~Q~~Y~C~TC~~~d~~giC~~Ca~~-CH~GHd 69 (77)
+.-.+|+|.+|.- --.|..|... -|..|.
T Consensus 10 i~G~ry~C~~C~d---~dLC~~C~~~~~H~~H~ 39 (43)
T cd02340 10 IVGVRYKCLVCPD---YDLCESCEAKGVHPEHA 39 (43)
T ss_pred CcCCeEECCCCCC---ccchHHhhCcCCCCCCC
Confidence 4557899999973 5789999554 454444
No 29
>cd06219 DHOD_e_trans_like1 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD,
Probab=25.34 E-value=18 Score=25.87 Aligned_cols=15 Identities=27% Similarity=0.769 Sum_probs=11.1
Q ss_pred eeeehhhHH--------hhcCCC
Q psy6684 54 NAICVNCIK--------SCHAGH 68 (77)
Q Consensus 54 ~giC~~Ca~--------~CH~GH 68 (77)
.|+|..|+. +|+.|=
T Consensus 218 ~G~C~~C~~~~~~~~~~~C~~Gp 240 (248)
T cd06219 218 TGMCGACRVTVGGETKFACVDGP 240 (248)
T ss_pred cceeeeEEEEeCCCEEEEeCcCC
Confidence 499999954 677763
No 30
>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
Probab=23.98 E-value=38 Score=30.60 Aligned_cols=28 Identities=29% Similarity=0.883 Sum_probs=23.9
Q ss_pred cccceeceEEeecCCCCCCeeeehhhHHhhcCC
Q psy6684 35 TSFPMHDFYRCQTCHTTDRNAICVNCIKSCHAG 67 (77)
Q Consensus 35 ~~f~~Q~~Y~C~TC~~~d~~giC~~Ca~~CH~G 67 (77)
..++.|+--+|..|+. .|..|+.+|=.|
T Consensus 873 ~~~~~~~~~rC~~c~~-----~Cg~Cv~vCP~~ 900 (1012)
T TIGR03315 873 SCFPEQESQRCLECSY-----VCEKCVDVCPNR 900 (1012)
T ss_pred ccccccccccccCCCC-----CCCChhhhCChh
Confidence 3455788899999998 899999999887
No 31
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=23.82 E-value=28 Score=19.27 Aligned_cols=23 Identities=17% Similarity=0.502 Sum_probs=13.9
Q ss_pred eceEEeecCCCCCCeeeehhhHH
Q psy6684 40 HDFYRCQTCHTTDRNAICVNCIK 62 (77)
Q Consensus 40 Q~~Y~C~TC~~~d~~giC~~Ca~ 62 (77)
+..-.|..|+......+|..|..
T Consensus 15 ~~i~~C~~C~nlse~~~C~IC~d 37 (41)
T PF02132_consen 15 ENIKFCSICGNLSEEDPCEICSD 37 (41)
T ss_dssp HH-EE-SSS--EESSSS-HHHH-
T ss_pred HcCCccCCCCCcCCCCcCcCCCC
Confidence 45668999998888889999874
No 32
>PF12346 HJURP_mid: Holliday junction recognition protein-associated repeat; InterPro: IPR021052 Vertebral Holliday junction recognition proteins carry an SCM3 domain at their N terminus as do the eukaryotic fungi, but they also carry this central, conserved region. Further downstream there is also a repeated domain, also of unknown function. Investigation of Scm3 and associated proteins is likely to be directly relevant to understanding the mechanism of HJURP-mediated CENP-A chromatin assembly at human centromeres [, ].
Probab=23.47 E-value=21 Score=24.98 Aligned_cols=12 Identities=42% Similarity=0.609 Sum_probs=9.6
Q ss_pred eecCcccceeceE
Q psy6684 31 ISSYTSFPMHDFY 43 (77)
Q Consensus 31 ~st~~~f~~Q~~Y 43 (77)
|||++ |++|+|-
T Consensus 13 ISTKT-fI~qnW~ 24 (116)
T PF12346_consen 13 ISTKT-FIMQNWS 24 (116)
T ss_pred EechH-HHhhhhh
Confidence 46887 9999994
No 33
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=22.88 E-value=37 Score=19.76 Aligned_cols=18 Identities=22% Similarity=0.800 Sum_probs=11.7
Q ss_pred eceEEeecCCCCCCeeeehhhH
Q psy6684 40 HDFYRCQTCHTTDRNAICVNCI 61 (77)
Q Consensus 40 Q~~Y~C~TC~~~d~~giC~~Ca 61 (77)
..-++|+-||. .+|..|.
T Consensus 23 ~rrhhCr~CG~----~vC~~Cs 40 (69)
T PF01363_consen 23 RRRHHCRNCGR----VVCSSCS 40 (69)
T ss_dssp S-EEE-TTT------EEECCCS
T ss_pred eeeEccCCCCC----EECCchh
Confidence 56689999998 7888886
No 34
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=21.85 E-value=44 Score=27.59 Aligned_cols=24 Identities=33% Similarity=0.645 Sum_probs=18.6
Q ss_pred ceeceEEeecCCCCCCe--eeehhhH
Q psy6684 38 PMHDFYRCQTCHTTDRN--AICVNCI 61 (77)
Q Consensus 38 ~~Q~~Y~C~TC~~~d~~--giC~~Ca 61 (77)
..-.-|+|.-|+.+-.. |.|.+|-
T Consensus 350 ~~~~~YRC~~CGF~a~~l~W~CPsC~ 375 (389)
T COG2956 350 RRKPRYRCQNCGFTAHTLYWHCPSCR 375 (389)
T ss_pred hhcCCceecccCCcceeeeeeCCCcc
Confidence 34456999999988765 9999885
No 35
>cd06008 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms.
Probab=21.57 E-value=28 Score=20.00 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=8.4
Q ss_pred hhhHHhhcCC
Q psy6684 58 VNCIKSCHAG 67 (77)
Q Consensus 58 ~~Ca~~CH~G 67 (77)
-.|.+.||.|
T Consensus 14 H~C~~~CH~G 23 (49)
T cd06008 14 HKCEQLCHEG 23 (49)
T ss_pred CcCCCcCcCC
Confidence 4688999998
No 36
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=20.75 E-value=83 Score=17.22 Aligned_cols=16 Identities=38% Similarity=0.771 Sum_probs=13.3
Q ss_pred cccceeceEEeecCCC
Q psy6684 35 TSFPMHDFYRCQTCHT 50 (77)
Q Consensus 35 ~~f~~Q~~Y~C~TC~~ 50 (77)
.+-+|--||.|..|+-
T Consensus 21 aDE~~T~fy~C~~C~~ 36 (39)
T PF01096_consen 21 ADEPMTLFYVCCNCGH 36 (39)
T ss_dssp SSSSSEEEEEESSSTE
T ss_pred CCCCCeEEEEeCCCCC
Confidence 4567899999999985
No 37
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=20.65 E-value=58 Score=17.10 Aligned_cols=13 Identities=23% Similarity=0.797 Sum_probs=10.2
Q ss_pred eceEEeecCCCCC
Q psy6684 40 HDFYRCQTCHTTD 52 (77)
Q Consensus 40 Q~~Y~C~TC~~~d 52 (77)
..+|+|..|+..-
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4589999998753
No 38
>PF12838 Fer4_7: 4Fe-4S dicluster domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3CF4_A 1K0T_A 2VKR_C 1JB0_C 3PCQ_C.
Probab=20.24 E-value=55 Score=17.96 Aligned_cols=11 Identities=36% Similarity=1.220 Sum_probs=7.9
Q ss_pred ehhhHHhhcCC
Q psy6684 57 CVNCIKSCHAG 67 (77)
Q Consensus 57 C~~Ca~~CH~G 67 (77)
|..|+.+|..|
T Consensus 41 C~~C~~~CP~~ 51 (52)
T PF12838_consen 41 CGACVEVCPTG 51 (52)
T ss_dssp -SHHHHHTTTS
T ss_pred cChhhhhCcCc
Confidence 46799998765
Done!