Query 023869
Match_columns 276
No_of_seqs 172 out of 558
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 07:14:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.6 4.2E-05 9.1E-10 50.1 2.5 38 57-100 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.4 9.5E-05 2.1E-09 48.4 2.4 38 4-47 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.4 0.00011 2.4E-09 49.4 2.1 40 55-100 3-42 (42)
4 KOG4367 Predicted Zn-finger pr 97.2 9E-05 1.9E-09 74.1 0.7 88 3-90 163-258 (699)
5 smart00336 BBOX B-Box-type zin 96.9 0.0009 1.9E-08 44.3 2.9 40 55-100 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.8 0.0011 2.3E-08 43.9 2.5 39 3-47 4-42 (42)
7 PF00643 zf-B_box: B-box zinc 96.7 0.0014 3E-08 44.0 2.8 39 3-47 4-42 (42)
8 cd02335 ZZ_ADA2 Zinc finger, Z 74.3 3.6 7.7E-05 29.0 2.8 40 57-96 2-45 (49)
9 PF13248 zf-ribbon_3: zinc-rib 73.7 2.5 5.4E-05 26.2 1.7 26 1-32 1-26 (26)
10 PF14776 UNC-79: Cation-channe 61.1 5.3 0.00011 41.3 2.0 64 22-88 227-303 (525)
11 PF09416 UPF1_Zn_bind: RNA hel 54.5 6.6 0.00014 34.6 1.3 106 4-110 2-123 (152)
12 TIGR00622 ssl1 transcription f 53.6 9.5 0.00021 32.0 2.0 65 24-88 17-102 (112)
13 PRK14559 putative protein seri 50.1 12 0.00026 39.5 2.6 25 1-32 1-25 (645)
14 KOG2807 RNA polymerase II tran 49.6 6.3 0.00014 38.9 0.4 78 11-88 273-366 (378)
15 cd02338 ZZ_PCMF_like Zinc fing 47.1 19 0.00041 25.4 2.4 40 57-96 2-45 (49)
16 PRK00415 rps27e 30S ribosomal 45.5 11 0.00024 28.4 1.0 31 1-32 10-40 (59)
17 KOG4367 Predicted Zn-finger pr 45.2 6.5 0.00014 40.4 -0.3 52 53-104 160-213 (699)
18 KOG0129 Predicted RNA-binding 43.6 13 0.00027 38.5 1.5 47 3-52 456-509 (520)
19 PF04438 zf-HIT: HIT zinc fing 41.4 12 0.00026 24.3 0.6 23 56-79 3-25 (30)
20 PF01329 Pterin_4a: Pterin 4 a 39.9 16 0.00034 28.9 1.2 16 170-186 9-24 (95)
21 PF07649 C1_3: C1-like domain; 39.1 11 0.00023 23.8 0.2 26 4-34 2-27 (30)
22 cd02334 ZZ_dystrophin Zinc fin 38.3 30 0.00065 24.8 2.4 39 57-95 2-44 (49)
23 KOG2177 Predicted E3 ubiquitin 38.0 12 0.00027 31.7 0.4 42 56-103 87-128 (386)
24 cd02249 ZZ Zinc finger, ZZ typ 36.3 39 0.00085 23.2 2.6 30 57-86 2-34 (46)
25 PRK00823 phhB pterin-4-alpha-c 35.9 19 0.00041 28.6 1.1 18 169-187 9-26 (97)
26 PF12773 DZR: Double zinc ribb 35.6 40 0.00088 23.1 2.6 16 18-33 8-23 (50)
27 PF10235 Cript: Microtubule-as 35.4 24 0.00052 28.6 1.6 51 30-85 24-79 (90)
28 cd02341 ZZ_ZZZ3 Zinc finger, Z 34.4 36 0.00079 24.2 2.3 29 57-85 2-36 (48)
29 PF06785 UPF0242: Uncharacteri 33.8 11 0.00024 37.3 -0.6 20 172-191 313-332 (401)
30 PF07975 C1_4: TFIIH C1-like d 33.1 25 0.00054 25.7 1.3 23 13-35 20-42 (51)
31 KOG1280 Uncharacterized conser 30.5 39 0.00084 33.7 2.4 47 38-95 2-52 (381)
32 PF03107 C1_2: C1 domain; Int 29.8 23 0.00051 22.5 0.6 26 4-34 2-27 (30)
33 COG5151 SSL1 RNA polymerase II 28.2 14 0.00031 36.5 -0.9 76 12-87 306-408 (421)
34 KOG0129 Predicted RNA-binding 26.9 21 0.00046 37.0 -0.0 37 54-90 454-497 (520)
35 KOG3576 Ovo and related transc 25.0 11 0.00025 35.2 -2.1 56 3-63 118-181 (267)
36 PLN00209 ribosomal protein S27 24.8 34 0.00074 27.6 0.8 31 1-32 35-65 (86)
37 PF01667 Ribosomal_S27e: Ribos 24.8 24 0.00051 26.2 -0.1 31 1-32 6-36 (55)
38 KOG0954 PHD finger protein [Ge 24.0 37 0.0008 37.0 1.1 50 3-64 272-321 (893)
39 PTZ00083 40S ribosomal protein 23.7 37 0.00081 27.4 0.8 31 1-32 34-64 (85)
40 cd02344 ZZ_HERC2 Zinc finger, 23.3 71 0.0015 22.6 2.1 30 57-86 2-35 (45)
41 cd02343 ZZ_EF Zinc finger, ZZ 23.1 48 0.0011 23.9 1.3 38 58-95 3-43 (48)
42 smart00249 PHD PHD zinc finger 22.9 73 0.0016 20.2 2.0 27 4-35 1-27 (47)
43 PF13831 PHD_2: PHD-finger; PD 21.9 19 0.00041 24.1 -1.0 34 21-62 3-36 (36)
44 cd02345 ZZ_dah Zinc finger, ZZ 21.8 81 0.0018 22.3 2.2 39 57-95 2-44 (49)
45 KOG4317 Predicted Zn-finger pr 21.6 53 0.0011 32.6 1.6 34 54-87 6-40 (383)
46 smart00109 C1 Protein kinase C 21.3 38 0.00083 22.2 0.4 29 3-35 12-40 (49)
47 KOG4582 Uncharacterized conser 21.1 70 0.0015 30.3 2.3 38 3-40 153-196 (278)
48 PF13842 Tnp_zf-ribbon_2: DDE_ 21.1 74 0.0016 20.8 1.7 15 66-80 15-29 (32)
49 cd02339 ZZ_Mind_bomb Zinc fing 20.7 91 0.002 21.9 2.2 28 57-84 2-33 (45)
50 PF00569 ZZ: Zinc finger, ZZ t 20.6 82 0.0018 21.8 2.0 30 2-31 4-37 (46)
No 1
>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=97.61 E-value=4.2e-05 Score=50.11 Aligned_cols=38 Identities=47% Similarity=0.966 Sum_probs=33.7
Q ss_pred ccccccCcceeEeccccccccccccccCcccCCCccCCcceeee
Q 023869 57 LCDICQERRALLFCQEDRAILCRECDIPIHKASEYTKKHNRFLL 100 (276)
Q Consensus 57 LCDvCqs~pA~vfC~~D~A~LC~~CD~~~HsAN~la~rH~RvpL 100 (276)
+|+.|+.+++.+||..|.+.+|..|+..+| +.|.+++|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H------~~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhc------CCCCEeeC
Confidence 699999999999999999999999998875 37888775
No 2
>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=97.44 E-value=9.5e-05 Score=48.41 Aligned_cols=38 Identities=47% Similarity=0.865 Sum_probs=33.6
Q ss_pred cccccCCCCceEEeccCccccchhhhhccccCccccCCcccccc
Q 023869 4 WCDVCDKEEASVFCSADEAALCVACDRRVHHANKLASKHPRFNL 47 (276)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHsAN~La~rH~RvpL 47 (276)
.|+.++++++.+||..|.+.+|..|+...|. .|.++||
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 6999998899999999999999999988774 7888764
No 3
>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=97.37 E-value=0.00011 Score=49.42 Aligned_cols=40 Identities=33% Similarity=0.647 Sum_probs=34.2
Q ss_pred CCccccccCcceeEeccccccccccccccCcccCCCccCCcceeee
Q 023869 55 SPLCDICQERRALLFCQEDRAILCRECDIPIHKASEYTKKHNRFLL 100 (276)
Q Consensus 55 ~pLCDvCqs~pA~vfC~~D~A~LC~~CD~~~HsAN~la~rH~RvpL 100 (276)
...|+.|+..++.+||..|...||..|....|.. |..++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 4699999999999999999999999999998643 887765
No 4
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.24 E-value=9e-05 Score=74.12 Aligned_cols=88 Identities=22% Similarity=0.439 Sum_probs=75.4
Q ss_pred ccccccCCC--CceEEeccCccccchhhhhccccCccccCCcccccccC------CCCCCCCccccccCcceeEeccccc
Q 023869 3 IWCDVCDKE--EASVFCSADEAALCVACDRRVHHANKLASKHPRFNLVS------PSYKESPLCDICQERRALLFCQEDR 74 (276)
Q Consensus 3 ~~Cd~C~~a--~A~vyC~aD~A~LC~~CD~~VHsAN~La~rH~RvpL~~------p~~k~~pLCDvCqs~pA~vfC~~D~ 74 (276)
.+|.+|+++ .|.|+|..+..++|.-|..+.|-+-..+.||.-+|-.+ -+++....|..|+.+.-.+||.+|.
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck 242 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCK 242 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecC
Confidence 369999987 69999999999999999999999988888998776422 2345667899999999999999999
Q ss_pred cccccccccCcccCCC
Q 023869 75 AILCRECDIPIHKASE 90 (276)
Q Consensus 75 A~LC~~CD~~~HsAN~ 90 (276)
+++|..|-..+.|+|-
T Consensus 243 ~pvc~~clee~khs~h 258 (699)
T KOG4367|consen 243 MPVCYQCLEEGKHSSH 258 (699)
T ss_pred ChHHHHHHHhhcccch
Confidence 9999999998877763
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.90 E-value=0.0009 Score=44.30 Aligned_cols=40 Identities=43% Similarity=0.816 Sum_probs=33.9
Q ss_pred CCccccccCcceeEeccccccccccccccCcccCCCccCCcceeee
Q 023869 55 SPLCDICQERRALLFCQEDRAILCRECDIPIHKASEYTKKHNRFLL 100 (276)
Q Consensus 55 ~pLCDvCqs~pA~vfC~~D~A~LC~~CD~~~HsAN~la~rH~RvpL 100 (276)
...|+.|+.+++.+||..|...+|..|....| +.|.+++|
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 36899999999999999999999999998744 57777664
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.78 E-value=0.0011 Score=43.92 Aligned_cols=39 Identities=36% Similarity=0.584 Sum_probs=33.3
Q ss_pred ccccccCCCCceEEeccCccccchhhhhccccCccccCCcccccc
Q 023869 3 IWCDVCDKEEASVFCSADEAALCVACDRRVHHANKLASKHPRFNL 47 (276)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHsAN~La~rH~RvpL 47 (276)
..|..++..++.+||..|++.+|..|....| +.|.+++|
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 5799999889999999999999999998866 47777653
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=96.72 E-value=0.0014 Score=44.03 Aligned_cols=39 Identities=26% Similarity=0.487 Sum_probs=33.3
Q ss_pred ccccccCCCCceEEeccCccccchhhhhccccCccccCCcccccc
Q 023869 3 IWCDVCDKEEASVFCSADEAALCVACDRRVHHANKLASKHPRFNL 47 (276)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHsAN~La~rH~RvpL 47 (276)
..|+.|.+..+.+||..++..+|..|....|.. |..++|
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred ccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 579999998899999999999999999999864 777653
No 8
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=74.33 E-value=3.6 Score=29.02 Aligned_cols=40 Identities=28% Similarity=0.439 Sum_probs=31.6
Q ss_pred ccccccCccee---Eecccc-ccccccccccCcccCCCccCCcc
Q 023869 57 LCDICQERRAL---LFCQED-RAILCRECDIPIHKASEYTKKHN 96 (276)
Q Consensus 57 LCDvCqs~pA~---vfC~~D-~A~LC~~CD~~~HsAN~la~rH~ 96 (276)
.|+.|...... +.|..| .-.||..|-..+...+.+...|.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 58888876665 789988 57899999998877766666665
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.71 E-value=2.5 Score=26.23 Aligned_cols=26 Identities=27% Similarity=0.806 Sum_probs=20.1
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|...|-.|+... .+++.+|..|..++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCCC
Confidence 788999999732 56788898887653
No 10
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=61.12 E-value=5.3 Score=41.27 Aligned_cols=64 Identities=23% Similarity=0.542 Sum_probs=47.2
Q ss_pred cccchhhhhccccCccccCCcccccccCCCCCCCCccc--ccc--CcceeEecc--cc-------ccccccccccCcccC
Q 023869 22 AALCVACDRRVHHANKLASKHPRFNLVSPSYKESPLCD--ICQ--ERRALLFCQ--ED-------RAILCRECDIPIHKA 88 (276)
Q Consensus 22 A~LC~~CD~~VHsAN~La~rH~RvpL~~p~~k~~pLCD--vCq--s~pA~vfC~--~D-------~A~LC~~CD~~~HsA 88 (276)
.+||.+|...+|+..+.. .++.+.+|.......|+ .|. .+.|.+.|. +| -+-+|.+|....|+.
T Consensus 227 LylC~~Ca~~i~~e~~~~---~~~~il~P~~~vS~~CenK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n 303 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQ---MFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNN 303 (525)
T ss_pred eeeHHHHHHHHhcccchh---hhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhccc
Confidence 469999999999864432 44577888887777887 454 567888883 33 267999999987754
No 11
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=54.54 E-value=6.6 Score=34.57 Aligned_cols=106 Identities=21% Similarity=0.338 Sum_probs=50.7
Q ss_pred cccccC--CCCceEEeccCccccchhhhh--ccccCcccc-CCcccccccCCCC--CCCCccccccCcceeE----eccc
Q 023869 4 WCDVCD--KEEASVFCSADEAALCVACDR--RVHHANKLA-SKHPRFNLVSPSY--KESPLCDICQERRALL----FCQE 72 (276)
Q Consensus 4 ~Cd~C~--~a~A~vyC~aD~A~LC~~CD~--~VHsAN~La-~rH~RvpL~~p~~--k~~pLCDvCqs~pA~v----fC~~ 72 (276)
.|.+|+ ....++.|....-.+|..=+. .-|--|-|. .||.-|.|+.-++ ....-|-.|+.+..+. -...
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~NvF~LGFipak~ 81 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKS 81 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT----TTTEEEEEETT
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCCceeeEEEEEecc
Confidence 599999 778899999999999996443 333333333 3888877743222 4467899999987654 3455
Q ss_pred cc--cccccc-cccCc--ccCCCccCCcceeeecCccccCCcc
Q 023869 73 DR--AILCRE-CDIPI--HKASEYTKKHNRFLLTGVKLTASAS 110 (276)
Q Consensus 73 D~--A~LC~~-CD~~~--HsAN~la~rH~RvpL~g~~~s~~~~ 110 (276)
|. +.||+. |-... +..|- ....=.-.|++-.+-+|-+
T Consensus 82 d~vvvllCR~pC~~~~~~kd~~w-D~~~W~PLI~dr~fl~wlv 123 (152)
T PF09416_consen 82 DSVVVLLCRQPCANQPSLKDMNW-DTSQWQPLIEDRQFLPWLV 123 (152)
T ss_dssp SCEEEEEETTTTTSTTTCTTTTS--GGG-EESEETTCE-TTTS
T ss_pred CCeEEEEeCCchhccchhccccC-CHhhCccccccccchHhhc
Confidence 65 689977 75321 11121 1112223355666666655
No 12
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.56 E-value=9.5 Score=32.03 Aligned_cols=65 Identities=26% Similarity=0.532 Sum_probs=44.0
Q ss_pred cchhhhhccccCccccC-CcccccccCC------CCCCCCccccccCc--------------ceeEeccccccccccccc
Q 023869 24 LCVACDRRVHHANKLAS-KHPRFNLVSP------SYKESPLCDICQER--------------RALLFCQEDRAILCRECD 82 (276)
Q Consensus 24 LC~~CD~~VHsAN~La~-rH~RvpL~~p------~~k~~pLCDvCqs~--------------pA~vfC~~D~A~LC~~CD 82 (276)
-|.-|+..+=++.-|++ =|.-+||..= .......|-.|+.. ...+.|..|.-.+|.+||
T Consensus 17 ~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD 96 (112)
T TIGR00622 17 ECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCD 96 (112)
T ss_pred cCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccc
Confidence 36678877777766776 3555666310 01122459999873 234679999999999999
Q ss_pred cCcccC
Q 023869 83 IPIHKA 88 (276)
Q Consensus 83 ~~~HsA 88 (276)
+-+|..
T Consensus 97 ~fiHe~ 102 (112)
T TIGR00622 97 VFVHES 102 (112)
T ss_pred hhhhhh
Confidence 998853
No 13
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.11 E-value=12 Score=39.54 Aligned_cols=25 Identities=24% Similarity=0.672 Sum_probs=18.6
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|+ .|-.|+.. ..+.|++|..|...+
T Consensus 1 M~-~Cp~Cg~~------n~~~akFC~~CG~~l 25 (645)
T PRK14559 1 ML-ICPQCQFE------NPNNNRFCQKCGTSL 25 (645)
T ss_pred CC-cCCCCCCc------CCCCCccccccCCCC
Confidence 64 69999876 356788899997655
No 14
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=49.61 E-value=6.3 Score=38.90 Aligned_cols=78 Identities=27% Similarity=0.578 Sum_probs=54.3
Q ss_pred CCceEEeccCccccc------hhhhhccccCccccC-CcccccccC----CCC--CCCCccccccC---cceeEeccccc
Q 023869 11 EEASVFCSADEAALC------VACDRRVHHANKLAS-KHPRFNLVS----PSY--KESPLCDICQE---RRALLFCQEDR 74 (276)
Q Consensus 11 a~A~vyC~aD~A~LC------~~CD~~VHsAN~La~-rH~RvpL~~----p~~--k~~pLCDvCqs---~pA~vfC~~D~ 74 (276)
.-+.++|..+.|..| .-|+..+=++.-|++ -|.-+||.. |-. ..+..|-.|+. ....+.|..|.
T Consensus 273 ~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck 352 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCK 352 (378)
T ss_pred ccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhcc
Confidence 357788999888875 467877766666666 466677731 111 12344999942 23567899999
Q ss_pred cccccccccCcccC
Q 023869 75 AILCRECDIPIHKA 88 (276)
Q Consensus 75 A~LC~~CD~~~HsA 88 (276)
-.+|.+||.-+|..
T Consensus 353 ~~FCldCDv~iHes 366 (378)
T KOG2807|consen 353 NVFCLDCDVFIHES 366 (378)
T ss_pred ceeeccchHHHHhh
Confidence 99999999998854
No 15
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=47.10 E-value=19 Score=25.44 Aligned_cols=40 Identities=20% Similarity=0.228 Sum_probs=27.1
Q ss_pred ccccccCccee---Eeccccc-cccccccccCcccCCCccCCcc
Q 023869 57 LCDICQERRAL---LFCQEDR-AILCRECDIPIHKASEYTKKHN 96 (276)
Q Consensus 57 LCDvCqs~pA~---vfC~~D~-A~LC~~CD~~~HsAN~la~rH~ 96 (276)
.|+.|...+.. +.|..|. -.||.+|-..+.....+...|.
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~~~H~~~H~ 45 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTTERHLFDHP 45 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcCCCCCCCCC
Confidence 57888854443 6788875 6899999887765544444553
No 16
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=45.51 E-value=11 Score=28.43 Aligned_cols=31 Identities=29% Similarity=0.740 Sum_probs=27.1
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|++.|.-|+ +.-+||=++..+..|..|...+
T Consensus 10 ~~VkCp~C~-n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCG-NEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCC-CeEEEEecCCcEEECcccCCCc
Confidence 788999999 5788999999999999997655
No 17
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=45.19 E-value=6.5 Score=40.37 Aligned_cols=52 Identities=17% Similarity=0.431 Sum_probs=41.8
Q ss_pred CCCCccccccCc--ceeEeccccccccccccccCcccCCCccCCcceeeecCcc
Q 023869 53 KESPLCDICQER--RALLFCQEDRAILCRECDIPIHKASEYTKKHNRFLLTGVK 104 (276)
Q Consensus 53 k~~pLCDvCqs~--pA~vfC~~D~A~LC~~CD~~~HsAN~la~rH~RvpL~g~~ 104 (276)
.....|..|+.. .|.++|.+|.++.|.-|....|-..+..++|..+|-..-+
T Consensus 160 ~aa~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~gr 213 (699)
T KOG4367|consen 160 AAALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGR 213 (699)
T ss_pred HHhhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCc
Confidence 345677777754 5889999999999999999999999988999877644333
No 18
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=43.60 E-value=13 Score=38.52 Aligned_cols=47 Identities=26% Similarity=0.518 Sum_probs=38.1
Q ss_pred ccccccCC-----CCceEEec--cCccccchhhhhccccCccccCCcccccccCCCC
Q 023869 3 IWCDVCDK-----EEASVFCS--ADEAALCVACDRRVHHANKLASKHPRFNLVSPSY 52 (276)
Q Consensus 3 ~~Cd~C~~-----a~A~vyC~--aD~A~LC~~CD~~VHsAN~La~rH~RvpL~~p~~ 52 (276)
..||.|+. ..|-+||+ .+--++|..|=+.+|+. ..++.-.||..+..
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlvr~~~ 509 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLVRPGK 509 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCceecccc
Confidence 47999998 88999997 45789999999999996 55676677766544
No 19
>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=41.38 E-value=12 Score=24.29 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=17.8
Q ss_pred CccccccCcceeEecccccccccc
Q 023869 56 PLCDICQERRALLFCQEDRAILCR 79 (276)
Q Consensus 56 pLCDvCqs~pA~vfC~~D~A~LC~ 79 (276)
.+|.+|+. .+...|..|.+.+|.
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-EESEE-TTT--EESS
T ss_pred CCCccCcC-CCEEECCCcCCceeC
Confidence 58999999 999999999998883
No 20
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=39.88 E-value=16 Score=28.92 Aligned_cols=16 Identities=50% Similarity=1.074 Sum_probs=13.6
Q ss_pred chhHHhhhcCCCccccc
Q 023869 170 SISEYLMETLPGWRVDD 186 (276)
Q Consensus 170 siseyl~~~~pgw~v~d 186 (276)
-|.++|. .||||++++
T Consensus 9 ei~~~L~-~l~~W~~~~ 24 (95)
T PF01329_consen 9 EIAEALA-ELPGWKLDG 24 (95)
T ss_dssp HHHHHHH-TSTTSEEET
T ss_pred HHHHhhh-cCcCCEECC
Confidence 4788996 779999998
No 21
>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=39.12 E-value=11 Score=23.82 Aligned_cols=26 Identities=31% Similarity=0.602 Sum_probs=8.9
Q ss_pred cccccCCCCceEEeccCccccchhhhhcccc
Q 023869 4 WCDVCDKEEASVFCSADEAALCVACDRRVHH 34 (276)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHs 34 (276)
.|+.|++.-.. +..+.|..||..+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 58888875432 345678899988884
No 22
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=38.32 E-value=30 Score=24.75 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=28.2
Q ss_pred ccccccCcc---eeEeccccc-cccccccccCcccCCCccCCc
Q 023869 57 LCDICQERR---ALLFCQEDR-AILCRECDIPIHKASEYTKKH 95 (276)
Q Consensus 57 LCDvCqs~p---A~vfC~~D~-A~LC~~CD~~~HsAN~la~rH 95 (276)
.|+.|+..+ ..+.|..|. --||..|-..+.+...+...|
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~H 44 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSH 44 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCC
Confidence 588888654 345677775 689999999887776665565
No 23
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.03 E-value=12 Score=31.69 Aligned_cols=42 Identities=31% Similarity=0.548 Sum_probs=30.2
Q ss_pred CccccccCcceeEeccccccccccccccCcccCCCccCCcceeeecCc
Q 023869 56 PLCDICQERRALLFCQEDRAILCRECDIPIHKASEYTKKHNRFLLTGV 103 (276)
Q Consensus 56 pLCDvCqs~pA~vfC~~D~A~LC~~CD~~~HsAN~la~rH~RvpL~g~ 103 (276)
.+|..|+.. ..+||..|...+|..|.... ....|.-.++..+
T Consensus 87 ~~c~~~~~~-~~~~c~~~~~~~c~~c~~~~-----~h~~h~~~~~~~~ 128 (386)
T KOG2177|consen 87 ELCEKHGEE-LKLFCEEDEKLLCVLCRESG-----EHRGHPVLPLEEA 128 (386)
T ss_pred hhhhhcCCc-ceEEecccccccCCCCCCcc-----cccCCccccHHHH
Confidence 378887777 88999999999999998322 2345555555544
No 24
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=36.32 E-value=39 Score=23.21 Aligned_cols=30 Identities=23% Similarity=0.386 Sum_probs=21.5
Q ss_pred ccccccCc--ceeEeccccc-cccccccccCcc
Q 023869 57 LCDICQER--RALLFCQEDR-AILCRECDIPIH 86 (276)
Q Consensus 57 LCDvCqs~--pA~vfC~~D~-A~LC~~CD~~~H 86 (276)
.|+.|+.. ...+.|..|. --||..|-..++
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 46777652 2455788886 789999988765
No 25
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=35.93 E-value=19 Score=28.60 Aligned_cols=18 Identities=39% Similarity=0.728 Sum_probs=14.1
Q ss_pred cchhHHhhhcCCCcccccc
Q 023869 169 SSISEYLMETLPGWRVDDF 187 (276)
Q Consensus 169 ssiseyl~~~~pgw~v~d~ 187 (276)
.-|.++| ..||||++++-
T Consensus 9 ~ei~~~l-~~l~gW~~~~~ 26 (97)
T PRK00823 9 EEIAELL-PQLPGWTLVGD 26 (97)
T ss_pred HHHHHHh-hcCCCCeEeCC
Confidence 4588888 57899999753
No 26
>PF12773 DZR: Double zinc ribbon
Probab=35.56 E-value=40 Score=23.05 Aligned_cols=16 Identities=25% Similarity=0.681 Sum_probs=11.4
Q ss_pred ccCccccchhhhhccc
Q 023869 18 SADEAALCVACDRRVH 33 (276)
Q Consensus 18 ~aD~A~LC~~CD~~VH 33 (276)
..+++.+|..|...+-
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 3566888888876665
No 27
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=35.39 E-value=24 Score=28.62 Aligned_cols=51 Identities=29% Similarity=0.514 Sum_probs=35.7
Q ss_pred hccccCccccCCcccccccCCCCCCCCccccccCcce---eEeccccc--cccccccccCc
Q 023869 30 RRVHHANKLASKHPRFNLVSPSYKESPLCDICQERRA---LLFCQEDR--AILCRECDIPI 85 (276)
Q Consensus 30 ~~VHsAN~La~rH~RvpL~~p~~k~~pLCDvCqs~pA---~vfC~~D~--A~LC~~CD~~~ 85 (276)
+.| +-|+|+.+-.+-|+ ...+..|.+|..... ..||+.|+ ..+|.-|-..+
T Consensus 24 r~i-~eNKlLs~~~~nPy----~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 24 RKI-GENKLLSKKKKNPY----APYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred ccc-cceeeecccccCcc----cccCccccccccccccCCCccChhhhcccCcccccCCee
Confidence 445 46899988777444 333568999987644 48999995 67888886544
No 28
>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=34.45 E-value=36 Score=24.25 Aligned_cols=29 Identities=28% Similarity=0.558 Sum_probs=20.4
Q ss_pred ccccccCcce---eEeccccc---cccccccccCc
Q 023869 57 LCDICQERRA---LLFCQEDR---AILCRECDIPI 85 (276)
Q Consensus 57 LCDvCqs~pA---~vfC~~D~---A~LC~~CD~~~ 85 (276)
.|+.|+..|. .+.|..|. --||..|-..+
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 4777776443 35677776 68999998766
No 29
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=33.79 E-value=11 Score=37.33 Aligned_cols=20 Identities=25% Similarity=0.453 Sum_probs=17.1
Q ss_pred hHHhhhcCCCccccccCCCC
Q 023869 172 SEYLMETLPGWRVDDFLDPP 191 (276)
Q Consensus 172 seyl~~~~pgw~v~d~l~~~ 191 (276)
..-|++|+-||.+||||.+.
T Consensus 313 AN~~fk~wtGy~~edFl~~~ 332 (401)
T PF06785_consen 313 ANSQFKTWTGYSSEDFLKDF 332 (401)
T ss_pred hHHHHHHHhccCHHHHHhcc
Confidence 34578999999999999887
No 30
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=33.15 E-value=25 Score=25.65 Aligned_cols=23 Identities=22% Similarity=0.615 Sum_probs=15.8
Q ss_pred ceEEeccCccccchhhhhccccC
Q 023869 13 ASVFCSADEAALCVACDRRVHHA 35 (276)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~VHsA 35 (276)
.++-|......+|.+||.-||..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 56889999999999999999974
No 31
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=30.45 E-value=39 Score=33.73 Aligned_cols=47 Identities=21% Similarity=0.242 Sum_probs=34.4
Q ss_pred ccCCcccccccCCCCCCCCccccccCcceeEeccc---cc-cccccccccCcccCCCccCCc
Q 023869 38 LASKHPRFNLVSPSYKESPLCDICQERRALLFCQE---DR-AILCRECDIPIHKASEYTKKH 95 (276)
Q Consensus 38 La~rH~RvpL~~p~~k~~pLCDvCqs~pA~vfC~~---D~-A~LC~~CD~~~HsAN~la~rH 95 (276)
+.++|++| -||.|....-.++|-. |. --||.+|...+-...-+...|
T Consensus 2 ~~~rHe~v-----------~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dH 52 (381)
T KOG1280|consen 2 LTSRHEGV-----------SCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDH 52 (381)
T ss_pred CCCCcCCc-----------eeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCC
Confidence 57899997 8999999888876644 43 479999988764444344455
No 32
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=29.80 E-value=23 Score=22.46 Aligned_cols=26 Identities=31% Similarity=0.850 Sum_probs=19.2
Q ss_pred cccccCCCCceEEeccCccccchhhhhcccc
Q 023869 4 WCDVCDKEEASVFCSADEAALCVACDRRVHH 34 (276)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHs 34 (276)
.|++|++.....+ .+-|..|+..+|.
T Consensus 2 ~C~~C~~~~~~~~-----~Y~C~~c~f~lh~ 27 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-----FYHCSECCFTLHV 27 (30)
T ss_pred CCCCCCCCcCCCE-----eEEeCCCCCeEcC
Confidence 5899987665554 6788888877774
No 33
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=28.19 E-value=14 Score=36.49 Aligned_cols=76 Identities=22% Similarity=0.464 Sum_probs=51.8
Q ss_pred CceEEeccCccccc------hhhhhccccCccccC-CcccccccCCCC------CCCCccccccCc--------------
Q 023869 12 EASVFCSADEAALC------VACDRRVHHANKLAS-KHPRFNLVSPSY------KESPLCDICQER-------------- 64 (276)
Q Consensus 12 ~A~vyC~aD~A~LC------~~CD~~VHsAN~La~-rH~RvpL~~p~~------k~~pLCDvCqs~-------------- 64 (276)
.+.++|..+.+..| .-|+..+=...-|++ -|.-+||..=.. ....-|-+||..
T Consensus 306 ~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~s 385 (421)
T COG5151 306 GGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDESTS 385 (421)
T ss_pred cCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCccccccc
Confidence 56778888877765 467765544444444 566677732111 223469999982
Q ss_pred ceeEeccccccccccccccCccc
Q 023869 65 RALLFCQEDRAILCRECDIPIHK 87 (276)
Q Consensus 65 pA~vfC~~D~A~LC~~CD~~~Hs 87 (276)
...+.|..|.--+|..||+-+|.
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHH
Confidence 56679999999999999998874
No 34
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=26.85 E-value=21 Score=36.96 Aligned_cols=37 Identities=32% Similarity=0.643 Sum_probs=31.7
Q ss_pred CCCccccccC-----cceeEecc--ccccccccccccCcccCCC
Q 023869 54 ESPLCDICQE-----RRALLFCQ--EDRAILCRECDIPIHKASE 90 (276)
Q Consensus 54 ~~pLCDvCqs-----~pA~vfC~--~D~A~LC~~CD~~~HsAN~ 90 (276)
+-.+||.|+. +.|-+||. .|.-..|..|-...|+--.
T Consensus 454 eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~~ 497 (520)
T KOG0129|consen 454 EDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGPG 497 (520)
T ss_pred cccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCCc
Confidence 4579999999 88999995 6889999999999887644
No 35
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=25.01 E-value=11 Score=35.24 Aligned_cols=56 Identities=23% Similarity=0.533 Sum_probs=40.3
Q ss_pred ccccccCCCC-------ceEEeccC-ccccchhhhhccccCccccCCcccccccCCCCCCCCccccccC
Q 023869 3 IWCDVCDKEE-------ASVFCSAD-EAALCVACDRRVHHANKLASKHPRFNLVSPSYKESPLCDICQE 63 (276)
Q Consensus 3 ~~Cd~C~~a~-------A~vyC~aD-~A~LC~~CD~~VHsAN~La~rH~RvpL~~p~~k~~pLCDvCqs 63 (276)
..|++|++.- --+-|.+| ..+||..|....|.+ .=+.||.|. |. .-....|..|+.
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rt---ht-gvrpykc~~c~k 181 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRT---HT-GVRPYKCSLCEK 181 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhcc---cc-CccccchhhhhH
Confidence 3688998742 34779998 689999999999975 456899995 21 223457777765
No 36
>PLN00209 ribosomal protein S27; Provisional
Probab=24.83 E-value=34 Score=27.63 Aligned_cols=31 Identities=23% Similarity=0.606 Sum_probs=26.1
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|++.|..|+ +.-+||=++-...+|..|...+
T Consensus 35 m~VkCp~C~-n~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 35 MDVKCQGCF-NITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred EEEECCCCC-CeeEEEecCceEEEccccCCEe
Confidence 788999999 4778899999999999996544
No 37
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=24.77 E-value=24 Score=26.21 Aligned_cols=31 Identities=29% Similarity=0.622 Sum_probs=20.1
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|++.|.-|+. .-+||=++-...+|..|...+
T Consensus 6 m~VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 6 MDVKCPGCYN-IQTVFSHAQTVVKCVVCGTVL 36 (55)
T ss_dssp EEEE-TTT-S-EEEEETT-SS-EE-SSSTSEE
T ss_pred EEEECCCCCC-eeEEEecCCeEEEcccCCCEe
Confidence 7888999994 677788888888888886543
No 38
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=23.99 E-value=37 Score=36.99 Aligned_cols=50 Identities=28% Similarity=0.649 Sum_probs=32.4
Q ss_pred ccccccCCCCceEEeccCccccchhhhhccccCccccCCcccccccCCCCCCCCccccccCc
Q 023869 3 IWCDVCDKEEASVFCSADEAALCVACDRRVHHANKLASKHPRFNLVSPSYKESPLCDICQER 64 (276)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHsAN~La~rH~RvpL~~p~~k~~pLCDvCqs~ 64 (276)
++||+|...-.. .+++..+|+.|..-||.+= +-|..- +...|+|..|...
T Consensus 272 viCDvCrspD~e---~~neMVfCd~Cn~cVHqaC--------yGIle~-p~gpWlCr~Calg 321 (893)
T KOG0954|consen 272 VICDVCRSPDSE---EANEMVFCDKCNICVHQAC--------YGILEV-PEGPWLCRTCALG 321 (893)
T ss_pred ceeceecCCCcc---ccceeEEeccchhHHHHhh--------hceeec-CCCCeeehhcccc
Confidence 579999864322 2567788999999999862 222221 1246888887654
No 39
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=23.68 E-value=37 Score=27.36 Aligned_cols=31 Identities=29% Similarity=0.715 Sum_probs=26.0
Q ss_pred CCccccccCCCCceEEeccCccccchhhhhcc
Q 023869 1 MKIWCDVCDKEEASVFCSADEAALCVACDRRV 32 (276)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~V 32 (276)
|++.|.-|+ +.-+||=++-...+|..|...+
T Consensus 34 m~VkCp~C~-n~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCS-QITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCC-CeeEEEecCceEEEccccCCEe
Confidence 788999999 5778899999999999996544
No 40
>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=23.26 E-value=71 Score=22.60 Aligned_cols=30 Identities=23% Similarity=0.398 Sum_probs=22.2
Q ss_pred ccccccCccee---Eeccccc-cccccccccCcc
Q 023869 57 LCDICQERRAL---LFCQEDR-AILCRECDIPIH 86 (276)
Q Consensus 57 LCDvCqs~pA~---vfC~~D~-A~LC~~CD~~~H 86 (276)
.||.|+..|.. +.|..|. --||..|-....
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~~~ 35 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKTRK 35 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCCCC
Confidence 58888866544 6788876 689999988643
No 41
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.13 E-value=48 Score=23.90 Aligned_cols=38 Identities=26% Similarity=0.436 Sum_probs=23.6
Q ss_pred cccccCcc--eeEeccccc-cccccccccCcccCCCccCCc
Q 023869 58 CDICQERR--ALLFCQEDR-AILCRECDIPIHKASEYTKKH 95 (276)
Q Consensus 58 CDvCqs~p--A~vfC~~D~-A~LC~~CD~~~HsAN~la~rH 95 (276)
||.|+... ..+.|..|. --||.+|-..+..+..+...|
T Consensus 3 CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g~~~~~H~~~H 43 (48)
T cd02343 3 CDGCDEIAPWHRYRCLQCTDMDLCKTCFLGGVKPEGHEDDH 43 (48)
T ss_pred CCCCCCcCCCceEECCCCCCchhHHHHHhCCccCCCCCCCC
Confidence 55555322 233556554 579999998887776655555
No 42
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=21.88 E-value=19 Score=24.14 Aligned_cols=34 Identities=24% Similarity=0.573 Sum_probs=12.8
Q ss_pred ccccchhhhhccccCccccCCcccccccCCCCCCCCcccccc
Q 023869 21 EAALCVACDRRVHHANKLASKHPRFNLVSPSYKESPLCDICQ 62 (276)
Q Consensus 21 ~A~LC~~CD~~VHsAN~La~rH~RvpL~~p~~k~~pLCDvCq 62 (276)
.-..|..|+..||.. -+.+........++|+.|+
T Consensus 3 ~ll~C~~C~v~VH~~--------CYGv~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 3 PLLFCDNCNVAVHQS--------CYGVSEVPDGDDWLCDRCE 36 (36)
T ss_dssp EEEE-SSS--EEEHH--------HHT-SS--SS-----HHH-
T ss_pred ceEEeCCCCCcCChh--------hCCcccCCCCCcEECCcCC
Confidence 345688999999974 2222222223348888774
No 44
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=21.77 E-value=81 Score=22.26 Aligned_cols=39 Identities=23% Similarity=0.430 Sum_probs=24.3
Q ss_pred ccccccCcc---eeEeccccc-cccccccccCcccCCCccCCc
Q 023869 57 LCDICQERR---ALLFCQEDR-AILCRECDIPIHKASEYTKKH 95 (276)
Q Consensus 57 LCDvCqs~p---A~vfC~~D~-A~LC~~CD~~~HsAN~la~rH 95 (276)
.|+.|...+ ..+.|..|. -.||..|-..+.....+...|
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~~~~~~H~~~H 44 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKGRETKRHNSLH 44 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCCCcCCCCCCCC
Confidence 477777632 235777775 689999988765443333344
No 45
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.58 E-value=53 Score=32.56 Aligned_cols=34 Identities=18% Similarity=0.413 Sum_probs=29.6
Q ss_pred CCCccccccCcceeEeccccccccc-cccccCccc
Q 023869 54 ESPLCDICQERRALLFCQEDRAILC-RECDIPIHK 87 (276)
Q Consensus 54 ~~pLCDvCqs~pA~vfC~~D~A~LC-~~CD~~~Hs 87 (276)
.+..|.+|+.+++.+.|.-|+...| ..|...+.+
T Consensus 6 ~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~h~~ 40 (383)
T KOG4317|consen 6 SFLACGICGVQKREYTCPRCNLLYCSLKCYRNHKH 40 (383)
T ss_pred ceeeccccccccccccCCCCCccceeeeeecCCCc
Confidence 4689999999999999999999999 778776544
No 46
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.34 E-value=38 Score=22.21 Aligned_cols=29 Identities=28% Similarity=0.540 Sum_probs=21.2
Q ss_pred ccccccCCCCceEEeccCccccchhhhhccccC
Q 023869 3 IWCDVCDKEEASVFCSADEAALCVACDRRVHHA 35 (276)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~VHsA 35 (276)
..|+.|++.-..+. .+.-|..|+..+|..
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~~~~H~~ 40 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCKVKCHKK 40 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCCchHHHH
Confidence 36888987644333 578899999999963
No 47
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=21.11 E-value=70 Score=30.31 Aligned_cols=38 Identities=32% Similarity=0.605 Sum_probs=28.2
Q ss_pred ccccccCC---CCceEEeccCc-cccchhhhhcc-ccC-ccccC
Q 023869 3 IWCDVCDK---EEASVFCSADE-AALCVACDRRV-HHA-NKLAS 40 (276)
Q Consensus 3 ~~Cd~C~~---a~A~vyC~aD~-A~LC~~CD~~V-HsA-N~La~ 40 (276)
+.||.|++ .-..+-|.-+. =-||.+|-+.. |.+ .++++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceee
Confidence 58999998 36789998764 56999999985 444 34444
No 48
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.10 E-value=74 Score=20.77 Aligned_cols=15 Identities=27% Similarity=0.534 Sum_probs=11.8
Q ss_pred eeEeccccccccccc
Q 023869 66 ALLFCQEDRAILCRE 80 (276)
Q Consensus 66 A~vfC~~D~A~LC~~ 80 (276)
..++|..|.+.||..
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 677888888888865
No 49
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=20.70 E-value=91 Score=21.85 Aligned_cols=28 Identities=29% Similarity=0.622 Sum_probs=20.8
Q ss_pred ccccccCcc---eeEecccc-ccccccccccC
Q 023869 57 LCDICQERR---ALLFCQED-RAILCRECDIP 84 (276)
Q Consensus 57 LCDvCqs~p---A~vfC~~D-~A~LC~~CD~~ 84 (276)
.||.|+..+ ..+.|..| .--||..|-..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 588888643 35678888 47899999774
No 50
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=20.64 E-value=82 Score=21.76 Aligned_cols=30 Identities=23% Similarity=0.488 Sum_probs=20.8
Q ss_pred CccccccCC---CCceEEeccC-ccccchhhhhc
Q 023869 2 KIWCDVCDK---EEASVFCSAD-EAALCVACDRR 31 (276)
Q Consensus 2 ~~~Cd~C~~---a~A~vyC~aD-~A~LC~~CD~~ 31 (276)
...|+.|+. ....+.|... +-.||..|=..
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 568999998 3578888755 58899999766
Done!