Query 030621
Match_columns 174
No_of_seqs 122 out of 167
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 16:31:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04640 PLATZ: PLATZ transcri 100.0 2.5E-41 5.5E-46 243.2 5.8 72 100-171 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.7 0.00039 8.4E-09 43.6 0.2 37 59-99 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 95.4 0.01 2.2E-07 36.0 1.7 36 59-98 2-38 (39)
4 smart00336 BBOX B-Box-type zin 94.5 0.029 6.2E-07 34.4 2.0 35 59-97 5-40 (42)
5 PF12855 Ecl1: Life-span regul 91.7 0.038 8.2E-07 36.5 -0.6 26 148-173 6-34 (43)
6 PF03884 DUF329: Domain of unk 87.7 0.073 1.6E-06 37.1 -1.8 26 148-173 2-32 (57)
7 PRK01343 zinc-binding protein; 81.9 0.59 1.3E-05 32.7 0.7 26 148-173 9-35 (57)
8 PF10013 DUF2256: Uncharacteri 77.7 0.75 1.6E-05 30.5 0.1 23 148-170 8-39 (42)
9 PF13240 zinc_ribbon_2: zinc-r 71.5 1.9 4E-05 24.7 0.7 16 151-166 2-17 (23)
10 PF09889 DUF2116: Uncharacteri 71.4 1.3 2.9E-05 31.0 0.1 23 149-171 4-26 (59)
11 PRK00418 DNA gyrase inhibitor; 71.2 1.4 3.1E-05 31.2 0.2 26 148-173 6-36 (62)
12 COG3024 Uncharacterized protei 65.6 2.4 5.2E-05 30.5 0.4 25 149-173 8-37 (65)
13 PF02207 zf-UBR: Putative zinc 64.3 3.3 7.1E-05 29.0 0.9 34 69-102 10-48 (71)
14 PF06467 zf-FCS: MYM-type Zinc 63.1 2 4.3E-05 26.7 -0.4 25 147-171 5-41 (43)
15 cd02340 ZZ_NBR1_like Zinc fing 61.3 5.1 0.00011 25.9 1.3 27 73-99 15-43 (43)
16 PF13248 zf-ribbon_3: zinc-rib 61.1 4.6 0.0001 23.4 1.0 19 148-166 2-20 (26)
17 KOG4367 Predicted Zn-finger pr 60.3 2.7 5.9E-05 40.5 -0.1 36 57-96 223-260 (699)
18 COG4338 Uncharacterized protei 55.2 1.1 2.4E-05 30.9 -2.7 24 147-170 11-43 (54)
19 KOG2177 Predicted E3 ubiquitin 49.4 9.6 0.00021 29.8 1.3 38 59-101 88-127 (386)
20 smart00396 ZnF_UBR1 Putative z 42.0 28 0.00061 24.5 2.7 30 67-96 8-42 (71)
21 KOG0006 E3 ubiquitin-protein l 41.4 15 0.00032 34.3 1.4 28 52-79 190-228 (446)
22 PF04438 zf-HIT: HIT zinc fing 41.0 8.8 0.00019 23.2 -0.0 21 150-170 4-29 (30)
23 cd02341 ZZ_ZZZ3 Zinc finger, Z 40.7 17 0.00036 24.2 1.2 27 73-99 16-48 (48)
24 COG4068 Uncharacterized protei 36.0 12 0.00026 26.8 -0.0 23 148-170 8-30 (64)
25 PF01412 ArfGap: Putative GTPa 31.2 8.2 0.00018 29.3 -1.6 50 69-119 10-72 (116)
26 PF04570 DUF581: Protein of un 29.8 17 0.00037 25.4 -0.1 25 147-171 15-48 (58)
27 TIGR00412 redox_disulf_2 small 27.5 92 0.002 21.3 3.3 32 107-139 33-66 (76)
28 PF08002 DUF1697: Protein of u 27.0 33 0.00072 26.9 1.1 30 105-135 16-48 (137)
29 PF12773 DZR: Double zinc ribb 25.6 31 0.00067 21.9 0.6 13 147-159 11-23 (50)
30 KOG2807 RNA polymerase II tran 24.7 30 0.00065 32.2 0.5 19 70-88 351-374 (378)
31 KOG3200 Uncharacterized conser 24.1 26 0.00056 30.3 -0.0 33 21-53 43-75 (224)
32 KOG4582 Uncharacterized conser 23.9 54 0.0012 28.9 2.0 56 43-101 132-199 (278)
33 PF06906 DUF1272: Protein of u 23.6 57 0.0012 23.0 1.6 22 150-171 7-31 (57)
34 cd02344 ZZ_HERC2 Zinc finger, 23.5 48 0.001 21.9 1.2 26 73-98 16-44 (45)
35 KOG3362 Predicted BBOX Zn-fing 21.4 58 0.0013 27.1 1.5 49 12-69 6-54 (156)
36 cd02337 ZZ_CBP Zinc finger, ZZ 20.8 32 0.00069 22.0 -0.1 29 71-99 12-41 (41)
37 smart00105 ArfGap Putative GTP 20.4 20 0.00043 27.1 -1.3 43 71-114 2-57 (112)
38 PF08459 UvrC_HhH_N: UvrC Heli 20.1 18 0.0004 29.4 -1.6 26 116-141 16-41 (155)
No 1
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=100.00 E-value=2.5e-41 Score=243.18 Aligned_cols=72 Identities=67% Similarity=1.158 Sum_probs=71.1
Q ss_pred EeccccceeeecchhhhhcccceeeEEecCcEEEEeeCCCCCCCCCCCCccccccccccCCCCeeeeccccc
Q 030621 100 RRSSYHDVIRVSEIQKYLDITGVQTYIINSARIVFLNERPQPRPGKGVTNTCLVCERSLLDSFTFCSLGCKV 171 (174)
Q Consensus 100 RRssYhdVVRv~DIqkl~D~S~IQtYvINsakVVFLn~RPq~r~~kg~~~~C~~C~R~L~d~~rFCSL~CKv 171 (174)
|||||||||||+||||+||||+||||+|||+||||||+|||+++++++++.|++|+|+|+|+|+||||+|||
T Consensus 1 Rr~sY~dVVrv~di~kl~D~s~IQtY~iNs~kVVfLn~Rpq~~~~~~~~~~C~~C~R~L~d~~~fCSl~CKv 72 (72)
T PF04640_consen 1 RRYSYHDVVRVSDIQKLLDCSGIQTYVINSAKVVFLNPRPQSRPSKGSGNICETCHRSLQDPYRFCSLSCKV 72 (72)
T ss_pred CcccccceEEHHHhHhhccccccEEEEeCCceEEEEccCCcCCCCCCCCCccCCCCCCCCCCCeEEeeeEEC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999997
No 2
>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=96.74 E-value=0.00039 Score=43.64 Aligned_cols=37 Identities=32% Similarity=0.820 Sum_probs=29.5
Q ss_pred cccccccCCCCCcceecccCCCCcCCccccc-CCCCCceeEE
Q 030621 59 QCKLHADAHKSECNMYCLDCMNGALCSLCLS-LHRDHRAIQI 99 (174)
Q Consensus 59 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~HrvlQI 99 (174)
.|..|.. .+..+||.+|. .++|..|.. .|++|.++.|
T Consensus 5 ~C~~H~~---~~~~~~C~~C~-~~~C~~C~~~~H~~H~~~~i 42 (42)
T PF00643_consen 5 KCPEHPE---EPLSLFCEDCN-EPLCSECTVSGHKGHKIVPI 42 (42)
T ss_dssp B-SSTTT---SBEEEEETTTT-EEEEHHHHHTSTTTSEEEEC
T ss_pred cCccCCc---cceEEEecCCC-CccCccCCCCCCCCCEEeEC
Confidence 5888864 34889999998 899999987 4999987754
No 3
>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=95.37 E-value=0.01 Score=35.99 Aligned_cols=36 Identities=25% Similarity=0.588 Sum_probs=27.7
Q ss_pred cccccccCCCCCcceecccCCCCcCCccccc-CCCCCceeE
Q 030621 59 QCKLHADAHKSECNMYCLDCMNGALCSLCLS-LHRDHRAIQ 98 (174)
Q Consensus 59 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~HrvlQ 98 (174)
.|+.|.. +...+||.+|. ..+|..|.. .|++|.++-
T Consensus 2 ~C~~H~~---~~~~~fC~~~~-~~iC~~C~~~~H~~H~~~~ 38 (39)
T cd00021 2 LCDEHGE---EPLSLFCETDR-ALLCVDCDLSVHSGHRRVP 38 (39)
T ss_pred CCCccCC---cceEEEeCccC-hhhhhhcChhhcCCCCEee
Confidence 4777753 24589999998 899999975 688887654
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.51 E-value=0.029 Score=34.44 Aligned_cols=35 Identities=31% Similarity=0.836 Sum_probs=27.5
Q ss_pred cccccccCCCCCcceecccCCCCcCCccccc-CCCCCcee
Q 030621 59 QCKLHADAHKSECNMYCLDCMNGALCSLCLS-LHRDHRAI 97 (174)
Q Consensus 59 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hrvl 97 (174)
.|..|.+ ....+||.+|. ..+|..|.. .|++|+++
T Consensus 5 ~C~~h~~---~~~~~~C~~c~-~~iC~~C~~~~H~~H~~~ 40 (42)
T smart00336 5 KCDSHGD---EPAEFFCEECG-ALLCRTCDEAEHRGHTVV 40 (42)
T ss_pred cCCCCCC---CceEEECCCCC-cccccccChhhcCCCcee
Confidence 4777763 24579999998 899999986 58888765
No 5
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=91.72 E-value=0.038 Score=36.49 Aligned_cols=26 Identities=27% Similarity=0.875 Sum_probs=22.9
Q ss_pred Ccccccccccc---CCCCeeeeccccccC
Q 030621 148 TNTCLVCERSL---LDSFTFCSLGCKVNQ 173 (174)
Q Consensus 148 ~~~C~~C~R~L---~d~~rFCSL~CKv~~ 173 (174)
.+.|.+|+|.+ .+...|||-.|++.+
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D 34 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKD 34 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHh
Confidence 46799999999 668999999999875
No 6
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=87.66 E-value=0.073 Score=37.11 Aligned_cols=26 Identities=35% Similarity=0.756 Sum_probs=16.0
Q ss_pred CccccccccccCC----CCe-eeeccccccC
Q 030621 148 TNTCLVCERSLLD----SFT-FCSLGCKVNQ 173 (174)
Q Consensus 148 ~~~C~~C~R~L~d----~~r-FCSL~CKv~~ 173 (174)
+..|-+|++...- +|+ |||-.||+.+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iD 32 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCKLID 32 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHHHHH
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhcccC
Confidence 3469999998875 665 9999999753
No 7
>PRK01343 zinc-binding protein; Provisional
Probab=81.95 E-value=0.59 Score=32.72 Aligned_cols=26 Identities=27% Similarity=0.667 Sum_probs=21.2
Q ss_pred CccccccccccCCC-CeeeeccccccC
Q 030621 148 TNTCLVCERSLLDS-FTFCSLGCKVNQ 173 (174)
Q Consensus 148 ~~~C~~C~R~L~d~-~rFCSL~CKv~~ 173 (174)
...|-+|++..... .-|||-.||..+
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iD 35 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDID 35 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhh
Confidence 45699999987764 589999999865
No 8
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=77.66 E-value=0.75 Score=30.50 Aligned_cols=23 Identities=35% Similarity=0.925 Sum_probs=19.6
Q ss_pred CccccccccccC---------CCCeeeecccc
Q 030621 148 TNTCLVCERSLL---------DSFTFCSLGCK 170 (174)
Q Consensus 148 ~~~C~~C~R~L~---------d~~rFCSL~CK 170 (174)
..+|.+|+|... |..+|||-.|.
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR 39 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCWDEVKYCSDRCR 39 (42)
T ss_pred CCcCcccCCcchHHHHHHHhchhhccHHHHhc
Confidence 457999999996 47899999996
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=71.49 E-value=1.9 Score=24.73 Aligned_cols=16 Identities=31% Similarity=0.816 Sum_probs=14.3
Q ss_pred ccccccccCCCCeeee
Q 030621 151 CLVCERSLLDSFTFCS 166 (174)
Q Consensus 151 C~~C~R~L~d~~rFCS 166 (174)
|..|+..+.+...||+
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 7889999999999986
No 10
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=71.42 E-value=1.3 Score=30.99 Aligned_cols=23 Identities=30% Similarity=0.788 Sum_probs=20.7
Q ss_pred ccccccccccCCCCeeeeccccc
Q 030621 149 NTCLVCERSLLDSFTFCSLGCKV 171 (174)
Q Consensus 149 ~~C~~C~R~L~d~~rFCSL~CKv 171 (174)
..|..||..+..+-.|||-.|+-
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~ 26 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCRE 26 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHH
Confidence 46999999999989999999974
No 11
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=71.21 E-value=1.4 Score=31.22 Aligned_cols=26 Identities=31% Similarity=0.731 Sum_probs=20.5
Q ss_pred CccccccccccC---C-CC-eeeeccccccC
Q 030621 148 TNTCLVCERSLL---D-SF-TFCSLGCKVNQ 173 (174)
Q Consensus 148 ~~~C~~C~R~L~---d-~~-rFCSL~CKv~~ 173 (174)
.-.|-+|++... + +| -|||-.||+.+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ID 36 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLID 36 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhh
Confidence 456999999874 3 45 79999999864
No 12
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.57 E-value=2.4 Score=30.50 Aligned_cols=25 Identities=28% Similarity=0.651 Sum_probs=20.1
Q ss_pred ccccccccccCC----C-CeeeeccccccC
Q 030621 149 NTCLVCERSLLD----S-FTFCSLGCKVNQ 173 (174)
Q Consensus 149 ~~C~~C~R~L~d----~-~rFCSL~CKv~~ 173 (174)
-.|-+|++...- + +-|||-.||+-+
T Consensus 8 v~CP~Cgkpv~w~~~s~frPFCSkRCklID 37 (65)
T COG3024 8 VPCPTCGKPVVWGEESPFRPFCSKRCKLID 37 (65)
T ss_pred ccCCCCCCcccccccCCcCcchhHhhhhcc
Confidence 459999998864 4 479999999864
No 13
>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=64.31 E-value=3.3 Score=29.01 Aligned_cols=34 Identities=29% Similarity=0.642 Sum_probs=24.2
Q ss_pred CCcceecccCCC---CcCCccc-cc-CCCCCceeEEEec
Q 030621 69 SECNMYCLDCMN---GALCSLC-LS-LHRDHRAIQIRRS 102 (174)
Q Consensus 69 nE~N~FCldC~~---~~~C~~C-l~-~H~~HrvlQIRRs 102 (174)
++--..|++|.. .++|..| .. .|.+|++..++-.
T Consensus 10 ~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 10 GQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp T-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 366788999973 5799999 54 7999998866654
No 14
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 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. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=63.07 E-value=2 Score=26.69 Aligned_cols=25 Identities=28% Similarity=0.673 Sum_probs=15.8
Q ss_pred CCccccccccccCC-C-----------Ceeeeccccc
Q 030621 147 VTNTCLVCERSLLD-S-----------FTFCSLGCKV 171 (174)
Q Consensus 147 ~~~~C~~C~R~L~d-~-----------~rFCSL~CKv 171 (174)
....|..|++.+.. + ..|||.+|.-
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~~ 41 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCLS 41 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHHh
Confidence 45689999987743 2 3899999953
No 15
>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=61.32 E-value=5.1 Score=25.90 Aligned_cols=27 Identities=33% Similarity=0.781 Sum_probs=20.8
Q ss_pred eecccCCCCcCCccccc--CCCCCceeEE
Q 030621 73 MYCLDCMNGALCSLCLS--LHRDHRAIQI 99 (174)
Q Consensus 73 ~FCldC~~~~~C~~Cl~--~H~~HrvlQI 99 (174)
.-|+.|.+--+|..|-. .|..|+.++|
T Consensus 15 y~C~~C~d~dLC~~C~~~~~H~~H~f~~~ 43 (43)
T cd02340 15 YKCLVCPDYDLCESCEAKGVHPEHAMLKI 43 (43)
T ss_pred EECCCCCCccchHHhhCcCCCCCCCEEeC
Confidence 66888877889999965 5777877653
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=61.08 E-value=4.6 Score=23.36 Aligned_cols=19 Identities=21% Similarity=0.494 Sum_probs=15.6
Q ss_pred CccccccccccCCCCeeee
Q 030621 148 TNTCLVCERSLLDSFTFCS 166 (174)
Q Consensus 148 ~~~C~~C~R~L~d~~rFCS 166 (174)
...|..|+..+.+..+||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred cCCCcccCCcCCcccccCh
Confidence 3468899998888899996
No 17
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=60.29 E-value=2.7 Score=40.49 Aligned_cols=36 Identities=31% Similarity=0.728 Sum_probs=28.1
Q ss_pred cccccccccCCCCCcceecccCCCCcCCccccc--CCCCCce
Q 030621 57 FVQCKLHADAHKSECNMYCLDCMNGALCSLCLS--LHRDHRA 96 (174)
Q Consensus 57 F~~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~--~H~~Hrv 96 (174)
-..|..|+.. ...|||+.|. -++|..|+. .|..|.|
T Consensus 223 ~~~ct~h~~e---~~smyc~~ck-~pvc~~clee~khs~hev 260 (699)
T KOG4367|consen 223 VSTCTDHELE---NHSMYCVQCK-MPVCYQCLEEGKHSSHEV 260 (699)
T ss_pred hhhccCCCCC---CceEEEEecC-ChHHHHHHHhhcccchhh
Confidence 4578888753 2569999998 899999997 5777764
No 18
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.17 E-value=1.1 Score=30.93 Aligned_cols=24 Identities=33% Similarity=0.881 Sum_probs=20.4
Q ss_pred CCccccccccccC---------CCCeeeecccc
Q 030621 147 VTNTCLVCERSLL---------DSFTFCSLGCK 170 (174)
Q Consensus 147 ~~~~C~~C~R~L~---------d~~rFCSL~CK 170 (174)
...+|++|+|.+. |...|||-.|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999985 56899999997
No 19
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.39 E-value=9.6 Score=29.76 Aligned_cols=38 Identities=29% Similarity=0.691 Sum_probs=30.1
Q ss_pred cccccccCCCCCcceecccCCCCcCCcccc-c-CCCCCceeEEEe
Q 030621 59 QCKLHADAHKSECNMYCLDCMNGALCSLCL-S-LHRDHRAIQIRR 101 (174)
Q Consensus 59 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl-~-~H~~HrvlQIRR 101 (174)
.|..|... ..+||..|. ..+|..|. . .|.+|+++-+..
T Consensus 88 ~c~~~~~~----~~~~c~~~~-~~~c~~c~~~~~h~~h~~~~~~~ 127 (386)
T KOG2177|consen 88 LCEKHGEE----LKLFCEEDE-KLLCVLCRESGEHRGHPVLPLEE 127 (386)
T ss_pred hhhhcCCc----ceEEecccc-cccCCCCCCcccccCCccccHHH
Confidence 78888653 679999998 78999996 3 799999776553
No 20
>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=41.95 E-value=28 Score=24.54 Aligned_cols=30 Identities=30% Similarity=0.535 Sum_probs=22.5
Q ss_pred CCCCcceecccCCC---CcCCccccc--CCCCCce
Q 030621 67 HKSECNMYCLDCMN---GALCSLCLS--LHRDHRA 96 (174)
Q Consensus 67 ~knE~N~FCldC~~---~~~C~~Cl~--~H~~Hrv 96 (174)
.++|--..|++|.. ..+|..|-. .|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 45677788999973 358888865 6999983
No 21
>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]
Probab=41.36 E-value=15 Score=34.31 Aligned_cols=28 Identities=29% Similarity=0.755 Sum_probs=23.5
Q ss_pred hcchhcccccccccCC-----------CCCcceecccCC
Q 030621 52 LQTSFFVQCKLHADAH-----------KSECNMYCLDCM 79 (174)
Q Consensus 52 L~~~FF~~C~~H~~~~-----------knE~N~FCldC~ 79 (174)
|..+||=.|.+|+++. .|-+|+-|+.|.
T Consensus 190 ~fAEFfFKC~ah~~~~k~~aa~lhli~~N~~ni~C~~Ct 228 (446)
T KOG0006|consen 190 LFAEFFFKCGAHPTSDKETAAALHLIATNSRNITCITCT 228 (446)
T ss_pred chHhheehhccCCCccccchhHHHHhhcccccceeEEec
Confidence 6678999999999873 368999999997
No 22
>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=40.97 E-value=8.8 Score=23.25 Aligned_cols=21 Identities=33% Similarity=0.746 Sum_probs=12.5
Q ss_pred cccccccccC-----CCCeeeecccc
Q 030621 150 TCLVCERSLL-----DSFTFCSLGCK 170 (174)
Q Consensus 150 ~C~~C~R~L~-----d~~rFCSL~CK 170 (174)
.|.+|+..-. -..+||||.|.
T Consensus 4 ~C~vC~~~~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 4 LCSVCGNPAKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EETSSSSEESEE-TTT--EESSHHHH
T ss_pred CCccCcCCCEEECCCcCCceeCcEeE
Confidence 4677776211 13689999984
No 23
>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=40.75 E-value=17 Score=24.25 Aligned_cols=27 Identities=33% Similarity=0.751 Sum_probs=19.5
Q ss_pred eecccCC--CCcCCccccc---CCC-CCceeEE
Q 030621 73 MYCLDCM--NGALCSLCLS---LHR-DHRAIQI 99 (174)
Q Consensus 73 ~FCldC~--~~~~C~~Cl~---~H~-~HrvlQI 99 (174)
.-|++|. +--+|+.|.. .|. +|+++.|
T Consensus 16 ~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 16 YHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred EECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 6688888 7789999964 354 5776654
No 24
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=36.02 E-value=12 Score=26.81 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=20.5
Q ss_pred CccccccccccCCCCeeeecccc
Q 030621 148 TNTCLVCERSLLDSFTFCSLGCK 170 (174)
Q Consensus 148 ~~~C~~C~R~L~d~~rFCSL~CK 170 (174)
...|.+|+..+...-+|||-.|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 35799999999998999999996
No 25
>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=31.23 E-value=8.2 Score=29.26 Aligned_cols=50 Identities=26% Similarity=0.384 Sum_probs=29.2
Q ss_pred CCcceecccCCC-----------CcCCcccccCCCC--CceeEEEeccccceeeecchhhhhcc
Q 030621 69 SECNMYCLDCMN-----------GALCSLCLSLHRD--HRAIQIRRSSYHDVIRVSEIQKYLDI 119 (174)
Q Consensus 69 nE~N~FCldC~~-----------~~~C~~Cl~~H~~--HrvlQIRRssYhdVVRv~DIqkl~D~ 119 (174)
..-|..|.||.. .-+|..|...|+. .++-+| |+.-.|-...+||+.+...
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~V-kSi~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRV-KSITMDNWSPEEVQRMREG 72 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--E-EETTTS---HHHHHHHHHS
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhc-cccccCCCCHHHHHHHHHH
Confidence 356889999962 2389999877773 223333 6777888888888887655
No 26
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=29.76 E-value=17 Score=25.39 Aligned_cols=25 Identities=32% Similarity=0.869 Sum_probs=19.3
Q ss_pred CCccccccccccC---CC--C----eeeeccccc
Q 030621 147 VTNTCLVCERSLL---DS--F----TFCSLGCKV 171 (174)
Q Consensus 147 ~~~~C~~C~R~L~---d~--~----rFCSL~CKv 171 (174)
.-..|-.|.|.|. |- | -|||..|.-
T Consensus 15 FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~ 48 (58)
T PF04570_consen 15 FLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRS 48 (58)
T ss_pred HHHHHHccCCCCCCCCCeeeeccccccccHHHHH
Confidence 4568999999998 32 3 599999964
No 27
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=27.52 E-value=92 Score=21.34 Aligned_cols=32 Identities=9% Similarity=0.318 Sum_probs=22.3
Q ss_pred eeeecchhhh--hcccceeeEEecCcEEEEeeCCC
Q 030621 107 VIRVSEIQKY--LDITGVQTYIINSARIVFLNERP 139 (174)
Q Consensus 107 VVRv~DIqkl--~D~S~IQtYvINsakVVFLn~RP 139 (174)
+++++|+... +++.+|-|.++||..+ +....|
T Consensus 33 ~~~v~~~~~a~~~~v~~vPti~i~G~~~-~~G~~~ 66 (76)
T TIGR00412 33 FEKVTDMNEILEAGVTATPGVAVDGELV-IMGKIP 66 (76)
T ss_pred EEEeCCHHHHHHcCCCcCCEEEECCEEE-EEeccC
Confidence 5666655554 7899999999987655 554444
No 28
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=26.95 E-value=33 Score=26.89 Aligned_cols=30 Identities=37% Similarity=0.656 Sum_probs=20.1
Q ss_pred cceeeecchhhh---hcccceeeEEecCcEEEEe
Q 030621 105 HDVIRVSEIQKY---LDITGVQTYIINSARIVFL 135 (174)
Q Consensus 105 hdVVRv~DIqkl---~D~S~IQtYvINsakVVFL 135 (174)
++-|+..|+... +-..+|+||+ +|.-|||=
T Consensus 16 ~nki~MaeLr~~l~~~Gf~~V~Tyi-~SGNvvf~ 48 (137)
T PF08002_consen 16 KNKIKMAELREALEDLGFTNVRTYI-QSGNVVFE 48 (137)
T ss_dssp BS---HHHHHHHHHHCT-EEEEEET-TTTEEEEE
T ss_pred CCcccHHHHHHHHHHcCCCCceEEE-eeCCEEEe
Confidence 345666777665 5788999995 88899997
No 29
>PF12773 DZR: Double zinc ribbon
Probab=25.59 E-value=31 Score=21.94 Aligned_cols=13 Identities=23% Similarity=0.414 Sum_probs=9.3
Q ss_pred CCccccccccccC
Q 030621 147 VTNTCLVCERSLL 159 (174)
Q Consensus 147 ~~~~C~~C~R~L~ 159 (174)
....|..|+..|.
T Consensus 11 ~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 11 DAKFCPHCGTPLP 23 (50)
T ss_pred cccCChhhcCChh
Confidence 3567778877777
No 30
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=24.68 E-value=30 Score=32.21 Aligned_cols=19 Identities=37% Similarity=0.742 Sum_probs=14.7
Q ss_pred CcceecccCC-----CCcCCcccc
Q 030621 70 ECNMYCLDCM-----NGALCSLCL 88 (174)
Q Consensus 70 E~N~FCldC~-----~~~~C~~Cl 88 (174)
=+|.||+||. ....|+.|-
T Consensus 351 Ck~~FCldCDv~iHesLh~CpgCe 374 (378)
T KOG2807|consen 351 CKNVFCLDCDVFIHESLHNCPGCE 374 (378)
T ss_pred ccceeeccchHHHHhhhhcCCCcC
Confidence 3789999995 345899986
No 31
>KOG3200 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.07 E-value=26 Score=30.30 Aligned_cols=33 Identities=27% Similarity=0.539 Sum_probs=19.3
Q ss_pred ccccccccCCCCCCchhhhhcCCCCCcHHHHhc
Q 030621 21 KPKNRRIMGGGGPEEEDEEMSNKWPPWLRPLLQ 53 (174)
Q Consensus 21 ~~~~~~~m~~~~~~~~~~e~~~~~P~WL~~LL~ 53 (174)
-++|||+-.-||-.-+.--..+..|+||+.+..
T Consensus 43 ~L~NRRLqNyGGvvh~~glipeelP~wLq~~v~ 75 (224)
T KOG3200|consen 43 VLANRRLQNYGGVVHKTGLIPEELPPWLQYYVD 75 (224)
T ss_pred HHHhhhhhhcCCccccCCcCccccCHHHHHHHH
Confidence 367999876333321110112348999999886
No 32
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=23.95 E-value=54 Score=28.89 Aligned_cols=56 Identities=20% Similarity=0.341 Sum_probs=36.0
Q ss_pred CCCCcHHHHhcc-hhc-----c---cccccccCCCCCcceecccCCCCcCCccccc---CCCCCceeEEEe
Q 030621 43 KWPPWLRPLLQT-SFF-----V---QCKLHADAHKSECNMYCLDCMNGALCSLCLS---LHRDHRAIQIRR 101 (174)
Q Consensus 43 ~~P~WL~~LL~~-~FF-----~---~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~---~H~~HrvlQIRR 101 (174)
..+.||++-+.+ -++ . .|..|+-.+ --.-|+.|.+--||..|-. .|..|..||+.+
T Consensus 132 ~~~~~~~~~~~~~H~~~~~~~v~CD~C~~~~IvG---~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 132 SLVITLNPVVGEMHPNISKLSVPCDNCGKPGIVG---ARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT 199 (278)
T ss_pred hhhhhcCCCccccCCCcccccccCCCccCCcccc---ceeeecCCCccchhHHhhcCCCCCcccceeeccc
Confidence 456677665552 233 2 444444321 1267999988889999954 455799999887
No 33
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=23.63 E-value=57 Score=22.98 Aligned_cols=22 Identities=32% Similarity=0.806 Sum_probs=18.0
Q ss_pred cccccccccCC-C--Ceeeeccccc
Q 030621 150 TCLVCERSLLD-S--FTFCSLGCKV 171 (174)
Q Consensus 150 ~C~~C~R~L~d-~--~rFCSL~CKv 171 (174)
.||.|++.|.- + .+-||..|-.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTF 31 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTF 31 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcc
Confidence 59999999975 3 7899998854
No 34
>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=23.53 E-value=48 Score=21.89 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=19.3
Q ss_pred eecccCCCCcCCccccc--CCC-CCceeE
Q 030621 73 MYCLDCMNGALCSLCLS--LHR-DHRAIQ 98 (174)
Q Consensus 73 ~FCldC~~~~~C~~Cl~--~H~-~HrvlQ 98 (174)
.-|+.|.+--+|..|-. .|. .|.-+.
T Consensus 16 ykC~~C~dyDLC~~Cf~~~~H~~~H~F~r 44 (45)
T cd02344 16 FKCRNCDDFDFCENCFKTRKHNTRHTFGR 44 (45)
T ss_pred EECCCCCCccchHHhhCCCCcCCCCceee
Confidence 67999998889999976 453 565443
No 35
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=21.43 E-value=58 Score=27.05 Aligned_cols=49 Identities=22% Similarity=0.184 Sum_probs=29.0
Q ss_pred hhcccccccccccccccCCCCCCchhhhhcCCCCCcHHHHhcchhcccccccccCCCC
Q 030621 12 QELLTVREFKPKNRRIMGGGGPEEEDEEMSNKWPPWLRPLLQTSFFVQCKLHADAHKS 69 (174)
Q Consensus 12 ~~~~~~~~~~~~~~~~m~~~~~~~~~~e~~~~~P~WL~~LL~~~FF~~C~~H~~~~kn 69 (174)
++....|++.++-||.|.- .. ..-+.-+=|++|....|-+. -|.+.-++
T Consensus 6 e~r~s~r~~~~~~rRvlD~-----~a--r~rr~~r~l~~Le~Dn~~dd--pha~l~~~ 54 (156)
T KOG3362|consen 6 EERASQRIKDQEQRRVLDL-----NA--RQRRDNRNLEALEQDNFHDD--PHASLVKP 54 (156)
T ss_pred HHHHHHHHhhhhhccccch-----HH--HHhhhhhhhHHHhhhccCCC--cccccccc
Confidence 3445678888999999841 11 11223456888888776553 45544444
No 36
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=20.75 E-value=32 Score=22.05 Aligned_cols=29 Identities=21% Similarity=0.515 Sum_probs=21.3
Q ss_pred cceecccCCCCcCCccccc-CCCCCceeEE
Q 030621 71 CNMYCLDCMNGALCSLCLS-LHRDHRAIQI 99 (174)
Q Consensus 71 ~N~FCldC~~~~~C~~Cl~-~H~~HrvlQI 99 (174)
.-+-|..|.+--+|..|.. ..+.|...||
T Consensus 12 ~r~~C~~C~dfDLC~~C~~~~~H~H~~~~~ 41 (41)
T cd02337 12 TRWHCTVCEDYDLCITCYNTKNHPHKMEKL 41 (41)
T ss_pred CceECCCCcchhhHHHHhCCCCCCcccccC
Confidence 4477999987789999986 3446776664
No 37
>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=20.40 E-value=20 Score=27.08 Aligned_cols=43 Identities=30% Similarity=0.457 Sum_probs=26.1
Q ss_pred cceecccCCC-----------CcCCcccccCCCCC--ceeEEEeccccceeeecchh
Q 030621 71 CNMYCLDCMN-----------GALCSLCLSLHRDH--RAIQIRRSSYHDVIRVSEIQ 114 (174)
Q Consensus 71 ~N~FCldC~~-----------~~~C~~Cl~~H~~H--rvlQIRRssYhdVVRv~DIq 114 (174)
-|..|.||.. .-+|..|...|+.. ++-. .|+.-.|...-++|+
T Consensus 2 ~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~-VkSl~md~w~~~~i~ 57 (112)
T smart00105 2 GNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISK-VRSLTLDTWTEEELR 57 (112)
T ss_pred CCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCe-eeecccCCCCHHHHH
Confidence 3788999962 13788888777753 2222 445555655555554
No 38
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=20.15 E-value=18 Score=29.43 Aligned_cols=26 Identities=27% Similarity=0.393 Sum_probs=22.4
Q ss_pred hhcccceeeEEecCcEEEEeeCCCCC
Q 030621 116 YLDITGVQTYIINSARIVFLNERPQP 141 (174)
Q Consensus 116 l~D~S~IQtYvINsakVVFLn~RPq~ 141 (174)
.||+|.+|.--.-++-|||.+.+|.+
T Consensus 16 ~fDiSh~~G~~~Vgs~Vvf~~G~~~k 41 (155)
T PF08459_consen 16 CFDISHIQGSDTVGSMVVFENGKPDK 41 (155)
T ss_dssp EEEEEECTTTCEEEEEEEEETTEE-G
T ss_pred EEECcccCCcccEEEEEEEECCccCh
Confidence 48999999888889999999988764
Done!