Query 021533
Match_columns 311
No_of_seqs 176 out of 577
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:44:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021533.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021533hhsearch_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 3.8E-05 8.2E-10 51.2 2.4 38 57-100 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.5 9E-05 2E-09 49.3 2.6 39 3-47 1-39 (39)
3 KOG4367 Predicted Zn-finger pr 97.4 4.7E-05 1E-09 77.2 0.6 87 3-89 163-257 (699)
4 PF00643 zf-B_box: B-box zinc 97.2 0.00018 4E-09 49.2 2.0 40 55-100 3-42 (42)
5 smart00336 BBOX B-Box-type zin 96.9 0.00084 1.8E-08 45.2 2.8 39 56-100 4-42 (42)
6 smart00336 BBOX B-Box-type zin 96.8 0.0011 2.3E-08 44.7 2.7 39 3-47 4-42 (42)
7 PF00643 zf-B_box: B-box zinc 96.8 0.0013 2.9E-08 44.9 3.1 39 3-47 4-42 (42)
8 PF13248 zf-ribbon_3: zinc-rib 65.2 5 0.00011 25.3 1.8 26 1-32 1-26 (26)
9 cd02335 ZZ_ADA2 Zinc finger, Z 60.4 7.9 0.00017 27.8 2.3 41 57-97 2-46 (49)
10 PF14776 UNC-79: Cation-channe 56.4 6.2 0.00013 41.5 1.6 64 22-88 227-303 (525)
11 PF01329 Pterin_4a: Pterin 4 a 54.2 7.5 0.00016 31.3 1.5 17 184-200 8-24 (95)
12 KOG2807 RNA polymerase II tran 52.4 5.3 0.00011 40.1 0.4 77 11-87 273-365 (378)
13 TIGR00622 ssl1 transcription f 52.3 9.4 0.0002 32.6 1.8 64 24-87 17-101 (112)
14 PRK00823 phhB pterin-4-alpha-c 51.0 8.4 0.00018 31.2 1.3 17 184-200 9-25 (97)
15 KOG0129 Predicted RNA-binding 47.2 8.3 0.00018 40.5 0.8 45 3-50 456-507 (520)
16 PF09416 UPF1_Zn_bind: RNA hel 47.0 16 0.00036 32.7 2.6 79 4-82 2-94 (152)
17 KOG4367 Predicted Zn-finger pr 45.0 7.3 0.00016 40.7 0.1 56 51-106 158-215 (699)
18 KOG0129 Predicted RNA-binding 43.7 8.3 0.00018 40.5 0.2 55 42-100 443-504 (520)
19 PRK00415 rps27e 30S ribosomal 42.1 13 0.00029 28.5 1.1 32 1-33 10-41 (59)
20 PF12773 DZR: Double zinc ribb 39.1 37 0.0008 23.7 2.9 16 18-33 8-23 (50)
21 PRK14559 putative protein seri 38.3 23 0.00049 38.2 2.5 25 1-32 1-25 (645)
22 PF04438 zf-HIT: HIT zinc fing 38.3 12 0.00026 24.7 0.3 25 1-26 1-25 (30)
23 PF07649 C1_3: C1-like domain; 36.8 13 0.00027 24.0 0.2 26 4-34 2-27 (30)
24 cd02342 ZZ_UBA_plant Zinc fing 36.0 30 0.00064 25.1 2.0 31 3-33 1-35 (43)
25 KOG2177 Predicted E3 ubiquitin 36.0 22 0.00047 30.7 1.6 30 56-86 87-117 (386)
26 TIGR00595 priA primosomal prot 33.0 53 0.0011 34.0 4.1 19 181-199 269-288 (505)
27 KOG1280 Uncharacterized conser 32.9 28 0.00061 35.2 2.0 48 38-96 2-53 (381)
28 PF07975 C1_4: TFIIH C1-like d 30.5 29 0.00063 25.8 1.3 23 13-35 20-42 (51)
29 PF03107 C1_2: C1 domain; Int 30.4 25 0.00053 22.8 0.8 26 4-34 2-27 (30)
30 PF07975 C1_4: TFIIH C1-like d 30.3 19 0.0004 26.8 0.2 23 65-87 19-41 (51)
31 COG5151 SSL1 RNA polymerase II 28.2 11 0.00024 37.8 -1.6 76 12-87 306-408 (421)
32 cd02338 ZZ_PCMF_like Zinc fing 24.4 73 0.0016 22.9 2.4 40 57-96 2-45 (49)
33 PLN00209 ribosomal protein S27 23.5 38 0.00082 27.9 0.9 31 1-32 35-65 (86)
34 KOG0954 PHD finger protein [Ge 23.2 35 0.00075 37.8 0.7 50 3-64 272-321 (893)
35 PTZ00083 40S ribosomal protein 22.9 40 0.00086 27.7 0.9 31 1-32 34-64 (85)
36 PF01667 Ribosomal_S27e: Ribos 22.7 27 0.00058 26.4 -0.1 31 1-32 6-36 (55)
37 KOG4582 Uncharacterized conser 21.7 64 0.0014 31.1 2.2 38 3-40 153-196 (278)
38 cd02341 ZZ_ZZZ3 Zinc finger, Z 21.5 73 0.0016 23.1 1.9 28 58-85 3-36 (48)
39 smart00249 PHD PHD zinc finger 21.1 93 0.002 20.1 2.3 27 4-35 1-27 (47)
40 PF13831 PHD_2: PHD-finger; PD 20.5 20 0.00043 24.5 -1.1 34 21-62 3-36 (36)
41 KOG3576 Ovo and related transc 20.4 19 0.00041 34.4 -1.6 56 3-63 118-181 (267)
42 cd02249 ZZ Zinc finger, ZZ typ 20.2 92 0.002 21.8 2.2 29 58-86 3-34 (46)
43 PF10235 Cript: Microtubule-as 20.1 60 0.0013 26.8 1.4 51 30-85 24-79 (90)
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=97.62 E-value=3.8e-05 Score=51.18 Aligned_cols=38 Identities=47% Similarity=0.987 Sum_probs=33.8
Q ss_pred ccccccccceEEeecCCccccccccCcCccCCCcccCCccceee
Q 021533 57 ICDVCQERRAFLFCQQDRAILCRDCDIPIHTANEHTQKHNRFLL 100 (311)
Q Consensus 57 LCD~CqsapA~vfC~aDsA~LC~~CD~~iHsAN~la~rH~Rvpl 100 (311)
+|+.|+.+++.+||..|.+.+|..|+...|. .|.+++|
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 6999999899999999999999999988763 7888775
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=97.46 E-value=9e-05 Score=49.33 Aligned_cols=39 Identities=41% Similarity=0.761 Sum_probs=34.0
Q ss_pred CCCcccCCCCcEEEeccCccccchhhccccccCccccCCceeecc
Q 021533 3 IQCDVCNKSEASVFCTADEAALCDTCDHRVHHANKLASKHHRFSL 47 (311)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~rH~Rvpl 47 (311)
..|+.++.+++.+||..|++.+|..|+...|. .|.|++|
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 36999998899999999999999999988775 7888764
No 3
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.38 E-value=4.7e-05 Score=77.21 Aligned_cols=87 Identities=22% Similarity=0.492 Sum_probs=74.5
Q ss_pred CCCcccCCCC--cEEEeccCccccchhhccccccCccccCCceeecccC------CCCCCCCccccccccceEEeecCCc
Q 021533 3 IQCDVCNKSE--ASVFCTADEAALCDTCDHRVHHANKLASKHHRFSLLH------PSSKHFPICDVCQERRAFLFCQQDR 74 (311)
Q Consensus 3 ~~Cd~C~~a~--A~vyC~aD~A~LC~~CD~~vHsAN~La~rH~Rvpl~~------ps~k~~~LCD~CqsapA~vfC~aDs 74 (311)
-.|.+|++++ |.|+|..+..++|.-|..+.|-+-..+.||.-+|-.+ -+++....|..|+...-.+||.+|.
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 3699999876 9999999999999999999999888888998776432 2345566799999999999999999
Q ss_pred cccccccCcCccCCC
Q 021533 75 AILCRDCDIPIHTAN 89 (311)
Q Consensus 75 A~LC~~CD~~iHsAN 89 (311)
+++|..|...+.|+|
T Consensus 243 ~pvc~~clee~khs~ 257 (699)
T KOG4367|consen 243 MPVCYQCLEEGKHSS 257 (699)
T ss_pred ChHHHHHHHhhcccc
Confidence 999999998877666
No 4
>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=97.23 E-value=0.00018 Score=49.19 Aligned_cols=40 Identities=28% Similarity=0.566 Sum_probs=34.2
Q ss_pred CCccccccccceEEeecCCccccccccCcCccCCCcccCCccceee
Q 021533 55 FPICDVCQERRAFLFCQQDRAILCRDCDIPIHTANEHTQKHNRFLL 100 (311)
Q Consensus 55 ~~LCD~CqsapA~vfC~aDsA~LC~~CD~~iHsAN~la~rH~Rvpl 100 (311)
...|+.|....+.+||..|...||..|....|.. |..++|
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 3689999999999999999999999999988754 887775
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.90 E-value=0.00084 Score=45.21 Aligned_cols=39 Identities=41% Similarity=0.806 Sum_probs=33.6
Q ss_pred CccccccccceEEeecCCccccccccCcCccCCCcccCCccceee
Q 021533 56 PICDVCQERRAFLFCQQDRAILCRDCDIPIHTANEHTQKHNRFLL 100 (311)
Q Consensus 56 ~LCD~CqsapA~vfC~aDsA~LC~~CD~~iHsAN~la~rH~Rvpl 100 (311)
..|+.|+..++.+||..|.+.||..|....| +.|.+++|
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 5799999899999999999999999998754 57777664
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.81 E-value=0.0011 Score=44.69 Aligned_cols=39 Identities=36% Similarity=0.632 Sum_probs=33.3
Q ss_pred CCCcccCCCCcEEEeccCccccchhhccccccCccccCCceeecc
Q 021533 3 IQCDVCNKSEASVFCTADEAALCDTCDHRVHHANKLASKHHRFSL 47 (311)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~rH~Rvpl 47 (311)
..|..++..++.+||..|++.+|..|....| +.|.+++|
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 56777653
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=96.78 E-value=0.0013 Score=44.88 Aligned_cols=39 Identities=23% Similarity=0.530 Sum_probs=33.8
Q ss_pred CCCcccCCCCcEEEeccCccccchhhccccccCccccCCceeecc
Q 021533 3 IQCDVCNKSEASVFCTADEAALCDTCDHRVHHANKLASKHHRFSL 47 (311)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~rH~Rvpl 47 (311)
..|+.|.+.++.+||..++..+|..|....|.. |..++|
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 579999998899999999999999999999874 877754
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=65.20 E-value=5 Score=25.35 Aligned_cols=26 Identities=23% Similarity=0.709 Sum_probs=19.4
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhcccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRV 32 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (311)
|...|-.|+... .+++.+|..|..++
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 788899998732 56788888887653
No 9
>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=60.43 E-value=7.9 Score=27.75 Aligned_cols=41 Identities=24% Similarity=0.434 Sum_probs=29.9
Q ss_pred ccccccccceE---EeecCC-ccccccccCcCccCCCcccCCccc
Q 021533 57 ICDVCQERRAF---LFCQQD-RAILCRDCDIPIHTANEHTQKHNR 97 (311)
Q Consensus 57 LCD~CqsapA~---vfC~aD-sA~LC~~CD~~iHsAN~la~rH~R 97 (311)
.|+.|...... +.|..| .--||..|-..+...+.+...|.=
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~~ 46 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHNY 46 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCCe
Confidence 47777766554 678887 568999999987766666666653
No 10
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=56.40 E-value=6.2 Score=41.46 Aligned_cols=64 Identities=22% Similarity=0.537 Sum_probs=45.7
Q ss_pred cccchhhccccccCccccCCceeecccCCCCCCCCccc--ccc--ccceEEeecCC---------ccccccccCcCccCC
Q 021533 22 AALCDTCDHRVHHANKLASKHHRFSLLHPSSKHFPICD--VCQ--ERRAFLFCQQD---------RAILCRDCDIPIHTA 88 (311)
Q Consensus 22 A~LC~~CD~~vHsAN~La~rH~Rvpl~~ps~k~~~LCD--~Cq--sapA~vfC~aD---------sA~LC~~CD~~iHsA 88 (311)
.+||..|...||+.-+.. .++.+.+|.+.....|+ .|. .+.|.+.|... .+.+|..|....|+.
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 479999999999854433 34567777777777777 454 45788888332 257999999887754
No 11
>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=54.25 E-value=7.5 Score=31.33 Aligned_cols=17 Identities=41% Similarity=0.911 Sum_probs=14.9
Q ss_pred ccHHHHHhhCCCccccc
Q 021533 184 SSISEYLEMLPGWHVED 200 (311)
Q Consensus 184 ssiseyl~~~pgw~ved 200 (311)
--|.++|..||||++++
T Consensus 8 ~ei~~~L~~l~~W~~~~ 24 (95)
T PF01329_consen 8 EEIAEALAELPGWKLDG 24 (95)
T ss_dssp HHHHHHHHTSTTSEEET
T ss_pred HHHHHhhhcCcCCEECC
Confidence 45889998899999997
No 12
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=52.37 E-value=5.3 Score=40.06 Aligned_cols=77 Identities=30% Similarity=0.615 Sum_probs=53.8
Q ss_pred CCcEEEeccCccccc------hhhccccccCccccC-CceeecccC----CCC--CCCCcccccccc---ceEEeecCCc
Q 021533 11 SEASVFCTADEAALC------DTCDHRVHHANKLAS-KHHRFSLLH----PSS--KHFPICDVCQER---RAFLFCQQDR 74 (311)
Q Consensus 11 a~A~vyC~aD~A~LC------~~CD~~vHsAN~La~-rH~Rvpl~~----ps~--k~~~LCD~Cqsa---pA~vfC~aDs 74 (311)
..+.++|..+.|..| .-|+..+=++.-|++ =|.-+||.. |.. .-+..|-.|+.. ...+.|..|.
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 457889999998876 467777666655554 466677742 111 122349999432 4567999999
Q ss_pred cccccccCcCccC
Q 021533 75 AILCRDCDIPIHT 87 (311)
Q Consensus 75 A~LC~~CD~~iHs 87 (311)
-.+|.+||.-+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999999885
No 13
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.28 E-value=9.4 Score=32.62 Aligned_cols=64 Identities=27% Similarity=0.498 Sum_probs=43.2
Q ss_pred cchhhccccccCccccCC-ceeecccCC--C----CCCCCcccccccc--------------ceEEeecCCccccccccC
Q 021533 24 LCDTCDHRVHHANKLASK-HHRFSLLHP--S----SKHFPICDVCQER--------------RAFLFCQQDRAILCRDCD 82 (311)
Q Consensus 24 LC~~CD~~vHsAN~La~r-H~Rvpl~~p--s----~k~~~LCD~Cqsa--------------pA~vfC~aDsA~LC~~CD 82 (311)
-|..|+..+=++.-|++. |.-+||..= . ......|-.|+.. ...+.|..|.-.+|.+||
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 366777777666666663 555665321 1 1123459999873 224679999999999999
Q ss_pred cCccC
Q 021533 83 IPIHT 87 (311)
Q Consensus 83 ~~iHs 87 (311)
.-+|.
T Consensus 97 ~fiHe 101 (112)
T TIGR00622 97 VFVHE 101 (112)
T ss_pred hhhhh
Confidence 99985
No 14
>PRK00823 phhB pterin-4-alpha-carbinolamine dehydratase; Validated
Probab=51.05 E-value=8.4 Score=31.19 Aligned_cols=17 Identities=41% Similarity=0.856 Sum_probs=14.7
Q ss_pred ccHHHHHhhCCCccccc
Q 021533 184 SSISEYLEMLPGWHVED 200 (311)
Q Consensus 184 ssiseyl~~~pgw~ved 200 (311)
.-|.++|..||||++++
T Consensus 9 ~ei~~~l~~l~gW~~~~ 25 (97)
T PRK00823 9 EEIAELLPQLPGWTLVG 25 (97)
T ss_pred HHHHHHhhcCCCCeEeC
Confidence 56889998899999965
No 15
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=47.19 E-value=8.3 Score=40.46 Aligned_cols=45 Identities=27% Similarity=0.623 Sum_probs=36.9
Q ss_pred CCCcccCC-----CCcEEEecc--CccccchhhccccccCccccCCceeecccCC
Q 021533 3 IQCDVCNK-----SEASVFCTA--DEAALCDTCDHRVHHANKLASKHHRFSLLHP 50 (311)
Q Consensus 3 ~~Cd~C~~-----a~A~vyC~a--D~A~LC~~CD~~vHsAN~La~rH~Rvpl~~p 50 (311)
..||.|+. ..|-+||++ +--++|..|=+.+|+. ..+|.-.||..+
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlvr~ 507 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLVRP 507 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCceecc
Confidence 47999998 889999998 6799999999999996 556666666544
No 16
>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=47.04 E-value=16 Score=32.69 Aligned_cols=79 Identities=28% Similarity=0.569 Sum_probs=41.5
Q ss_pred CCcccC--CCCcEEEeccCccccchhhccc--cccCcc-ccCCceeecccCCCC--CCCCccccccccceEE----eecC
Q 021533 4 QCDVCN--KSEASVFCTADEAALCDTCDHR--VHHANK-LASKHHRFSLLHPSS--KHFPICDVCQERRAFL----FCQQ 72 (311)
Q Consensus 4 ~Cd~C~--~a~A~vyC~aD~A~LC~~CD~~--vHsAN~-La~rH~Rvpl~~ps~--k~~~LCD~CqsapA~v----fC~a 72 (311)
.|.+|+ ....++.|..+.-.+|..=+.. -|=-+- ..+||.-|.|+.-++ ....-|-.|+.+...+ -..+
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 599998 7778999999999999865432 122222 456888888865433 4556799999876543 4455
Q ss_pred Cc--cccccc-cC
Q 021533 73 DR--AILCRD-CD 82 (311)
Q Consensus 73 Ds--A~LC~~-CD 82 (311)
|. +.||+. |.
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 65 578877 75
No 17
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=44.96 E-value=7.3 Score=40.65 Aligned_cols=56 Identities=21% Similarity=0.427 Sum_probs=45.8
Q ss_pred CCCCCCcccccccc--ceEEeecCCccccccccCcCccCCCcccCCccceeecCcccC
Q 021533 51 SSKHFPICDVCQER--RAFLFCQQDRAILCRDCDIPIHTANEHTQKHNRFLLTGVKLS 106 (311)
Q Consensus 51 s~k~~~LCD~Cqsa--pA~vfC~aDsA~LC~~CD~~iHsAN~la~rH~Rvpl~~~~~~ 106 (311)
+..+...|..|+.. .|.++|.+|.++.|..|....|-+-+..++|..+|-....++
T Consensus 158 s~~aa~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs 215 (699)
T KOG4367|consen 158 SKAAALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVS 215 (699)
T ss_pred hhHHhhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCcee
Confidence 34455668888765 688999999999999999999999999999999887665543
No 18
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=43.69 E-value=8.3 Score=40.46 Aligned_cols=55 Identities=22% Similarity=0.390 Sum_probs=38.9
Q ss_pred ceeecccCCCCCCCCccccccc-----cceEEee--cCCccccccccCcCccCCCcccCCccceee
Q 021533 42 HHRFSLLHPSSKHFPICDVCQE-----RRAFLFC--QQDRAILCRDCDIPIHTANEHTQKHNRFLL 100 (311)
Q Consensus 42 H~Rvpl~~ps~k~~~LCD~Cqs-----apA~vfC--~aDsA~LC~~CD~~iHsAN~la~rH~Rvpl 100 (311)
++||-|..- -.+..+||.|+. +.|-+|| ..|-...|..|-..+|+- +.++...||
T Consensus 443 ~KRVEIkPY-v~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPl 504 (520)
T KOG0129|consen 443 DKRVEIKPY-VMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPL 504 (520)
T ss_pred ceeeeecce-eccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCce
Confidence 457654321 124579999999 8899999 567789999999999975 344444444
No 19
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=42.15 E-value=13 Score=28.48 Aligned_cols=32 Identities=28% Similarity=0.678 Sum_probs=27.9
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhccccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRVH 33 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH 33 (311)
|++.|..|+. .-+||=++..+..|..|...+=
T Consensus 10 ~~VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 10 LKVKCPDCGN-EQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EEEECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence 7889999994 8899999999999999987653
No 20
>PF12773 DZR: Double zinc ribbon
Probab=39.09 E-value=37 Score=23.70 Aligned_cols=16 Identities=25% Similarity=0.704 Sum_probs=10.7
Q ss_pred ccCccccchhhccccc
Q 021533 18 TADEAALCDTCDHRVH 33 (311)
Q Consensus 18 ~aD~A~LC~~CD~~vH 33 (311)
..+++.+|..|...+-
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 3456777887776665
No 21
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.30 E-value=23 Score=38.18 Aligned_cols=25 Identities=20% Similarity=0.655 Sum_probs=17.8
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhcccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRV 32 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (311)
|+ .|-.|+.. ..+.|.+|..|...+
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 58999875 346778888886654
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=38.25 E-value=12 Score=24.71 Aligned_cols=25 Identities=28% Similarity=0.576 Sum_probs=17.8
Q ss_pred CCCCCcccCCCCcEEEeccCccccch
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCD 26 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~ 26 (311)
+..+|.+|+. .+...|....+.+|.
T Consensus 1 ~~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 1 PRKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp --EEETSSSS-EESEE-TTT--EESS
T ss_pred CcCCCccCcC-CCEEECCCcCCceeC
Confidence 3568999998 999999999998886
No 23
>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=36.77 E-value=13 Score=23.95 Aligned_cols=26 Identities=31% Similarity=0.714 Sum_probs=8.9
Q ss_pred CCcccCCCCcEEEeccCccccchhhcccccc
Q 021533 4 QCDVCNKSEASVFCTADEAALCDTCDHRVHH 34 (311)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHs 34 (311)
.|++|++.... +..+.|..||-.+|.
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 58889875432 345678888888884
No 24
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=36.01 E-value=30 Score=25.09 Aligned_cols=31 Identities=32% Similarity=0.574 Sum_probs=21.3
Q ss_pred CCCcccCCCC---cEEEeccCcc-ccchhhccccc
Q 021533 3 IQCDVCNKSE---ASVFCTADEA-ALCDTCDHRVH 33 (311)
Q Consensus 3 ~~Cd~C~~a~---A~vyC~aD~A-~LC~~CD~~vH 33 (311)
+.||.|+..| ..+.|..+.- -||..|=.+.-
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 4799999765 5566777654 48888865543
No 25
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.99 E-value=22 Score=30.75 Aligned_cols=30 Identities=33% Similarity=0.733 Sum_probs=24.9
Q ss_pred CccccccccceEEeecCCccccccccC-cCcc
Q 021533 56 PICDVCQERRAFLFCQQDRAILCRDCD-IPIH 86 (311)
Q Consensus 56 ~LCD~CqsapA~vfC~aDsA~LC~~CD-~~iH 86 (311)
.+|..|+.. ..+||..|...+|..|. ...|
T Consensus 87 ~~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h 117 (386)
T KOG2177|consen 87 ELCEKHGEE-LKLFCEEDEKLLCVLCRESGEH 117 (386)
T ss_pred hhhhhcCCc-ceEEecccccccCCCCCCcccc
Confidence 378888876 88999999999999999 4444
No 26
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=33.01 E-value=53 Score=33.99 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=14.8
Q ss_pred cccccHHHHH-hhCCCcccc
Q 021533 181 VSASSISEYL-EMLPGWHVE 199 (311)
Q Consensus 181 ~~~ssiseyl-~~~pgw~ve 199 (311)
.+|--|.|+| +.+||.+|.
T Consensus 269 ~Gte~~~e~l~~~fp~~~v~ 288 (505)
T TIGR00595 269 YGTEQVEEELAKLFPGARIA 288 (505)
T ss_pred ccHHHHHHHHHhhCCCCcEE
Confidence 3447889999 788998875
No 27
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=32.93 E-value=28 Score=35.24 Aligned_cols=48 Identities=25% Similarity=0.326 Sum_probs=34.2
Q ss_pred ccCCceeecccCCCCCCCCccccccccceEEeecCC---cc-ccccccCcCccCCCcccCCcc
Q 021533 38 LASKHHRFSLLHPSSKHFPICDVCQERRAFLFCQQD---RA-ILCRDCDIPIHTANEHTQKHN 96 (311)
Q Consensus 38 La~rH~Rvpl~~ps~k~~~LCD~CqsapA~vfC~aD---sA-~LC~~CD~~iHsAN~la~rH~ 96 (311)
+.++|++| -||.|....-.++|..| .- -||.+|...+-...-+.-.|-
T Consensus 2 ~~~rHe~v-----------~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~~tt~~H~~dHP 53 (381)
T KOG1280|consen 2 LTSRHEGV-----------SCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENGATTPIHDEDHP 53 (381)
T ss_pred CCCCcCCc-----------eeccccccceeeeeeEeeeecchhHHHHHhhcCCCCcccCCCCc
Confidence 57899998 59999998887766444 32 699999887644433444553
No 28
>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=30.49 E-value=29 Score=25.78 Aligned_cols=23 Identities=22% Similarity=0.515 Sum_probs=15.6
Q ss_pred cEEEeccCccccchhhccccccC
Q 021533 13 ASVFCTADEAALCDTCDHRVHHA 35 (311)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vHsA 35 (311)
..+-|......+|.+||.-||..
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 45679999999999999999974
No 29
>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=30.35 E-value=25 Score=22.79 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=19.1
Q ss_pred CCcccCCCCcEEEeccCccccchhhcccccc
Q 021533 4 QCDVCNKSEASVFCTADEAALCDTCDHRVHH 34 (311)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHs 34 (311)
.|++|++.....+ .+-|..|+..+|.
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 6999988665554 6778888777774
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=30.26 E-value=19 Score=26.82 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=14.4
Q ss_pred ceEEeecCCccccccccCcCccC
Q 021533 65 RAFLFCQQDRAILCRDCDIPIHT 87 (311)
Q Consensus 65 pA~vfC~aDsA~LC~~CD~~iHs 87 (311)
...+.|..|...+|.+||.-+|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 35677888888999999999985
No 31
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=28.17 E-value=11 Score=37.79 Aligned_cols=76 Identities=28% Similarity=0.517 Sum_probs=51.2
Q ss_pred CcEEEeccCccccc------hhhccccccCcccc-CCceeecccCCCCC------CCCcccccccc--------------
Q 021533 12 EASVFCTADEAALC------DTCDHRVHHANKLA-SKHHRFSLLHPSSK------HFPICDVCQER-------------- 64 (311)
Q Consensus 12 ~A~vyC~aD~A~LC------~~CD~~vHsAN~La-~rH~Rvpl~~ps~k------~~~LCD~Cqsa-------------- 64 (311)
.+.++|..+.+..| .-|+..+=...-|+ +-|.-+||..=..+ ...-|-.||..
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 46778888887765 46776643333333 35777787532111 12359999872
Q ss_pred ceEEeecCCccccccccCcCccC
Q 021533 65 RAFLFCQQDRAILCRDCDIPIHT 87 (311)
Q Consensus 65 pA~vfC~aDsA~LC~~CD~~iHs 87 (311)
...+.|..|..-+|..||.-+|.
T Consensus 386 s~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 386 SGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred ccceechhhhhhhhhhhHHHHHH
Confidence 45678999999999999998874
No 32
>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=24.36 E-value=73 Score=22.87 Aligned_cols=40 Identities=28% Similarity=0.356 Sum_probs=24.4
Q ss_pred ccccccccceE---EeecCCc-cccccccCcCccCCCcccCCcc
Q 021533 57 ICDVCQERRAF---LFCQQDR-AILCRDCDIPIHTANEHTQKHN 96 (311)
Q Consensus 57 LCD~CqsapA~---vfC~aDs-A~LC~~CD~~iHsAN~la~rH~ 96 (311)
.|+.|...+.. +.|..|. --||..|-........+...|.
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 47777744333 5666664 4799999887655444444443
No 33
>PLN00209 ribosomal protein S27; Provisional
Probab=23.51 E-value=38 Score=27.89 Aligned_cols=31 Identities=23% Similarity=0.712 Sum_probs=26.5
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhcccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRV 32 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (311)
|++.|-.|+. .-+||=++-...+|..|...+
T Consensus 35 m~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 35 MDVKCQGCFN-ITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred EEEECCCCCC-eeEEEecCceEEEccccCCEe
Confidence 7789999995 789999999999999997654
No 34
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=23.19 E-value=35 Score=37.78 Aligned_cols=50 Identities=30% Similarity=0.717 Sum_probs=32.9
Q ss_pred CCCcccCCCCcEEEeccCccccchhhccccccCccccCCceeecccCCCCCCCCcccccccc
Q 021533 3 IQCDVCNKSEASVFCTADEAALCDTCDHRVHHANKLASKHHRFSLLHPSSKHFPICDVCQER 64 (311)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~rH~Rvpl~~ps~k~~~LCD~Cqsa 64 (311)
.+||+|...-.- .+++..+|+.|..-||.+ .+-|.. .|.-.|||..|..-
T Consensus 272 viCDvCrspD~e---~~neMVfCd~Cn~cVHqa--------CyGIle-~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 272 VICDVCRSPDSE---EANEMVFCDKCNICVHQA--------CYGILE-VPEGPWLCRTCALG 321 (893)
T ss_pred ceeceecCCCcc---ccceeEEeccchhHHHHh--------hhceee-cCCCCeeehhcccc
Confidence 579999864322 256778899999999986 333332 23345888888753
No 35
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.90 E-value=40 Score=27.72 Aligned_cols=31 Identities=29% Similarity=0.789 Sum_probs=26.5
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhcccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRV 32 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (311)
|++.|-.|+. .-+||=++-...+|..|...+
T Consensus 34 m~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCSQ-ITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCCC-eeEEEecCceEEEccccCCEe
Confidence 7788999994 889999999999999997654
No 36
>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=22.70 E-value=27 Score=26.40 Aligned_cols=31 Identities=26% Similarity=0.620 Sum_probs=20.8
Q ss_pred CCCCCcccCCCCcEEEeccCccccchhhcccc
Q 021533 1 MKIQCDVCNKSEASVFCTADEAALCDTCDHRV 32 (311)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (311)
|++.|..|+. .-+||=++-...+|..|...+
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 7788999984 778888888888898886554
No 37
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=21.65 E-value=64 Score=31.10 Aligned_cols=38 Identities=34% Similarity=0.707 Sum_probs=28.5
Q ss_pred CCCcccCCC---CcEEEeccCc-cccchhhcccc-ccCc-cccC
Q 021533 3 IQCDVCNKS---EASVFCTADE-AALCDTCDHRV-HHAN-KLAS 40 (311)
Q Consensus 3 ~~Cd~C~~a---~A~vyC~aD~-A~LC~~CD~~v-HsAN-~La~ 40 (311)
..||.|.+. -..+.|.-+. =-||.+|-+.. |+++ ++++
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 579999984 3788899986 45999999995 5544 3443
No 38
>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=21.50 E-value=73 Score=23.13 Aligned_cols=28 Identities=29% Similarity=0.602 Sum_probs=18.3
Q ss_pred cccccccce---EEeecCCc---cccccccCcCc
Q 021533 58 CDVCQERRA---FLFCQQDR---AILCRDCDIPI 85 (311)
Q Consensus 58 CD~CqsapA---~vfC~aDs---A~LC~~CD~~i 85 (311)
|+.|+..+. .+.|..|. --||..|-...
T Consensus 3 Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 3 CDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 666665332 24666665 68999997765
No 39
>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=20.47 E-value=20 Score=24.48 Aligned_cols=34 Identities=24% Similarity=0.599 Sum_probs=13.2
Q ss_pred ccccchhhccccccCccccCCceeecccCCCCCCCCcccccc
Q 021533 21 EAALCDTCDHRVHHANKLASKHHRFSLLHPSSKHFPICDVCQ 62 (311)
Q Consensus 21 ~A~LC~~CD~~vHsAN~La~rH~Rvpl~~ps~k~~~LCD~Cq 62 (311)
.-..|..|+..||.. -+.+........++|+.|+
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 345688999999973 2223222223348888874
No 41
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=20.39 E-value=19 Score=34.39 Aligned_cols=56 Identities=23% Similarity=0.548 Sum_probs=39.8
Q ss_pred CCCcccCCCC-------cEEEeccC-ccccchhhccccccCccccCCceeecccCCCCCCCCccccccc
Q 021533 3 IQCDVCNKSE-------ASVFCTAD-EAALCDTCDHRVHHANKLASKHHRFSLLHPSSKHFPICDVCQE 63 (311)
Q Consensus 3 ~~Cd~C~~a~-------A~vyC~aD-~A~LC~~CD~~vHsAN~La~rH~Rvpl~~ps~k~~~LCD~Cqs 63 (311)
..|++|++.- --+-|.+| ..+||.-|....|.+ .-+.||.|.- -+-+ ...|..|..
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rth---tgvr-pykc~~c~k 181 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRTH---TGVR-PYKCSLCEK 181 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhccc---cCcc-ccchhhhhH
Confidence 4689998742 34669998 689999999999985 5688999962 1111 135777765
No 42
>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=20.24 E-value=92 Score=21.78 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=18.8
Q ss_pred ccccccc--ceEEeecCCc-cccccccCcCcc
Q 021533 58 CDVCQER--RAFLFCQQDR-AILCRDCDIPIH 86 (311)
Q Consensus 58 CD~Cqsa--pA~vfC~aDs-A~LC~~CD~~iH 86 (311)
|+.|... ...+.|..|. --||..|-...+
T Consensus 3 C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 3 CDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 5555542 2345666666 689999988665
No 43
>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=20.13 E-value=60 Score=26.84 Aligned_cols=51 Identities=24% Similarity=0.459 Sum_probs=34.4
Q ss_pred cccccCccccCCceeecccCCCCCCCCccccccccce---EEeecCCc--cccccccCcCc
Q 021533 30 HRVHHANKLASKHHRFSLLHPSSKHFPICDVCQERRA---FLFCQQDR--AILCRDCDIPI 85 (311)
Q Consensus 30 ~~vHsAN~La~rH~Rvpl~~ps~k~~~LCD~CqsapA---~vfC~aDs--A~LC~~CD~~i 85 (311)
+.| +-|+|+++-.+-|+.. .+..|..|..... ..||+.|+ .-+|.-|-..+
T Consensus 24 r~i-~eNKlLs~~~~nPy~~----~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 24 RKI-GENKLLSKKKKNPYAP----YSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred ccc-cceeeecccccCcccc----cCccccccccccccCCCccChhhhcccCcccccCCee
Confidence 345 4589998888855443 2457999987643 37888886 46787776543
Done!