Query 031017
Match_columns 167
No_of_seqs 169 out of 557
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:00:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031017.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031017hhsearch_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 97.8 2.1E-05 4.6E-10 47.5 2.5 38 4-47 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.6 6.2E-05 1.3E-09 45.5 2.5 38 56-99 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.3 0.00023 4.9E-09 44.1 3.0 40 2-47 3-42 (42)
4 smart00336 BBOX B-Box-type zin 97.2 0.0003 6.6E-09 42.9 2.6 39 3-47 4-42 (42)
5 PF00643 zf-B_box: B-box zinc 97.2 0.00019 4.2E-09 44.4 1.3 40 54-99 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.9 0.00081 1.8E-08 41.0 2.5 39 55-99 4-42 (42)
7 KOG4367 Predicted Zn-finger pr 96.6 0.00054 1.2E-08 63.3 0.4 82 3-84 163-253 (699)
8 PF13248 zf-ribbon_3: zinc-rib 80.8 1.2 2.5E-05 25.2 1.5 25 1-31 1-25 (26)
9 KOG0129 Predicted RNA-binding 75.5 1.1 2.3E-05 42.3 0.4 55 42-99 443-504 (520)
10 PF12773 DZR: Double zinc ribb 67.5 6.1 0.00013 24.9 2.5 15 19-33 9-23 (50)
11 PF14776 UNC-79: Cation-channe 65.2 5.2 0.00011 37.9 2.6 66 22-88 227-304 (525)
12 KOG2807 RNA polymerase II tran 64.1 2.7 5.8E-05 37.9 0.5 76 11-86 273-365 (378)
13 PRK14559 putative protein seri 55.2 7.1 0.00015 37.8 1.7 25 1-32 1-25 (645)
14 PF04438 zf-HIT: HIT zinc fing 53.7 5.5 0.00012 23.4 0.4 25 1-26 1-25 (30)
15 cd02342 ZZ_UBA_plant Zinc fing 51.5 13 0.00028 24.0 1.9 30 3-32 1-34 (43)
16 PF09416 UPF1_Zn_bind: RNA hel 50.6 4.7 0.0001 32.4 -0.3 78 4-81 2-94 (152)
17 PF07975 C1_4: TFIIH C1-like d 49.4 11 0.00023 25.1 1.3 23 13-35 20-42 (51)
18 KOG4367 Predicted Zn-finger pr 45.3 7.7 0.00017 36.6 0.2 59 54-112 162-228 (699)
19 PRK00415 rps27e 30S ribosomal 44.9 12 0.00026 25.7 1.1 31 1-32 10-40 (59)
20 PF07649 C1_3: C1-like domain; 42.5 9.4 0.0002 21.9 0.3 26 4-34 2-27 (30)
21 TIGR00622 ssl1 transcription f 38.6 20 0.00043 27.5 1.5 62 25-86 18-101 (112)
22 PF03107 C1_2: C1 domain; Int 36.7 17 0.00037 20.9 0.7 26 4-34 2-27 (30)
23 PF13240 zinc_ribbon_2: zinc-r 36.2 25 0.00053 19.4 1.3 21 57-83 2-22 (23)
24 KOG0129 Predicted RNA-binding 36.0 14 0.00029 35.1 0.3 42 3-47 456-504 (520)
25 KOG3576 Ovo and related transc 32.4 6.8 0.00015 33.6 -2.0 57 3-63 118-182 (267)
26 PF08274 PhnA_Zn_Ribbon: PhnA 32.1 21 0.00046 21.1 0.6 25 54-81 2-26 (30)
27 KOG4582 Uncharacterized conser 31.8 33 0.0007 29.8 2.0 41 3-43 153-199 (278)
28 cd02335 ZZ_ADA2 Zinc finger, Z 30.8 64 0.0014 20.5 2.8 30 56-85 2-35 (49)
29 PF01667 Ribosomal_S27e: Ribos 26.0 22 0.00047 23.9 -0.0 31 1-32 6-36 (55)
30 TIGR02098 MJ0042_CXXC MJ0042 f 25.7 55 0.0012 19.3 1.7 10 1-10 1-10 (38)
31 KOG1428 Inhibitor of type V ad 25.4 16 0.00036 39.5 -1.1 57 53-111 3321-3383(3738)
32 smart00109 C1 Protein kinase C 25.1 32 0.00069 20.6 0.6 28 3-34 12-39 (49)
33 PF00569 ZZ: Zinc finger, ZZ t 25.0 53 0.0012 20.6 1.6 31 1-31 3-37 (46)
34 KOG1891 Proline binding protei 25.0 41 0.00088 29.2 1.4 20 133-152 77-105 (271)
35 PLN00209 ribosomal protein S27 24.0 38 0.00083 24.9 0.9 31 1-32 35-65 (86)
36 PTZ00083 40S ribosomal protein 22.9 41 0.0009 24.6 0.9 31 1-32 34-64 (85)
37 PF14951 DUF4503: Domain of un 21.6 62 0.0013 29.7 1.9 43 3-48 275-318 (389)
38 KOG1428 Inhibitor of type V ad 21.6 39 0.00085 36.9 0.7 45 3-49 3323-3369(3738)
39 KOG2177 Predicted E3 ubiquitin 21.2 71 0.0015 25.0 2.0 39 56-101 88-127 (386)
40 PF10235 Cript: Microtubule-as 20.7 64 0.0014 23.8 1.5 49 30-82 24-77 (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=97.76 E-value=2.1e-05 Score=47.52 Aligned_cols=38 Identities=39% Similarity=0.853 Sum_probs=33.6
Q ss_pred cccccCCCCeEEEecccccccchhhchhcccCcccccCceecee
Q 031017 4 QCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (167)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (167)
.|+.++++++.+||..|+..+|..|+...|. .|.|+||
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 6899998899999999999999999987773 8888875
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=97.56 E-value=6.2e-05 Score=45.46 Aligned_cols=38 Identities=42% Similarity=0.831 Sum_probs=33.4
Q ss_pred CCcccccCceEEEecCCccccccccCCCCCCCCCCCCCCcceee
Q 031017 56 PCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (167)
Q Consensus 56 ~Cd~C~~~pA~v~C~~d~a~LC~~CD~~iH~an~ls~~HqRv~l 99 (167)
.|+.|+++++.+||..|...+|..|+...| +.|++++|
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 499999989999999999999999998776 47888764
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=97.32 E-value=0.00023 Score=44.08 Aligned_cols=40 Identities=23% Similarity=0.571 Sum_probs=34.0
Q ss_pred CccccccCCCCeEEEecccccccchhhchhcccCcccccCceecee
Q 031017 2 KIQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (167)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (167)
...|+.+++.++.+||..+...+|..|....|.. |..++|
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 3579999998899999999999999999998854 887765
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.20 E-value=0.0003 Score=42.94 Aligned_cols=39 Identities=36% Similarity=0.642 Sum_probs=33.5
Q ss_pred ccccccCCCCeEEEecccccccchhhchhcccCcccccCceecee
Q 031017 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (167)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (167)
..|..+++.++.+||..|++.+|..|....| +.|.+++|
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 5689998889999999999999999997766 57877664
No 5
>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=97.15 E-value=0.00019 Score=44.41 Aligned_cols=40 Identities=23% Similarity=0.494 Sum_probs=33.5
Q ss_pred CCCCcccccCceEEEecCCccccccccCCCCCCCCCCCCCCcceee
Q 031017 54 LPPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (167)
Q Consensus 54 ~~~Cd~C~~~pA~v~C~~d~a~LC~~CD~~iH~an~ls~~HqRv~l 99 (167)
...|+.|++.++.+||.++...+|..|....|. +|+.++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~------~H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHK------GHKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTT------TSEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCC------CCEEeEC
Confidence 345999999999999999999999999988884 3877764
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.90 E-value=0.00081 Score=41.01 Aligned_cols=39 Identities=41% Similarity=0.782 Sum_probs=33.0
Q ss_pred CCCcccccCceEEEecCCccccccccCCCCCCCCCCCCCCcceee
Q 031017 55 PPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (167)
Q Consensus 55 ~~Cd~C~~~pA~v~C~~d~a~LC~~CD~~iH~an~ls~~HqRv~l 99 (167)
..|+.|+..++.+||..|...+|..|....| ++|.+++|
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 3499999899999999999999999997766 57877654
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.64 E-value=0.00054 Score=63.33 Aligned_cols=82 Identities=27% Similarity=0.560 Sum_probs=69.7
Q ss_pred ccccccCCCC--eEEEecccccccchhhchhcccCcccccCceeceecc-------cCCCCCCCcccccCceEEEecCCc
Q 031017 3 IQCDVCEKAP--ATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQC-------LSNKLPPCDICQEKAAFIFCVEDR 73 (167)
Q Consensus 3 ~~Cd~C~~~~--A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~~-------~~~~~~~Cd~C~~~pA~v~C~~d~ 73 (167)
..|..|++++ |+|+|..+..+.|.-|..+.|-+...+.||.-+|-++ .+++...|..|+.+.-..||..+.
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 3699999975 9999999999999999999999888889998776544 334677899999999889999998
Q ss_pred cccccccCCCC
Q 031017 74 ALFCKDCDEPI 84 (167)
Q Consensus 74 a~LC~~CD~~i 84 (167)
...|..|-...
T Consensus 243 ~pvc~~clee~ 253 (699)
T KOG4367|consen 243 MPVCYQCLEEG 253 (699)
T ss_pred ChHHHHHHHhh
Confidence 88888887553
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=80.80 E-value=1.2 Score=25.21 Aligned_cols=25 Identities=24% Similarity=0.706 Sum_probs=18.4
Q ss_pred CCccccccCCCCeEEEecccccccchhhchh
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~ 31 (167)
|...|-.|+... .+++.+|..|..+
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 788899999732 5567888888754
No 9
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=75.46 E-value=1.1 Score=42.31 Aligned_cols=55 Identities=22% Similarity=0.373 Sum_probs=39.4
Q ss_pred ceeceecccCCCCCCCccccc-----CceEEEec--CCccccccccCCCCCCCCCCCCCCcceee
Q 031017 42 HQRLLLQCLSNKLPPCDICQE-----KAAFIFCV--EDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (167)
Q Consensus 42 H~RvpL~~~~~~~~~Cd~C~~-----~pA~v~C~--~d~a~LC~~CD~~iH~an~ls~~HqRv~l 99 (167)
++||-+.+---.-..|+.|+. +.|-+||. .|..++|..|-..+|+- .+++...||
T Consensus 443 ~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPl 504 (520)
T KOG0129|consen 443 DKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPL 504 (520)
T ss_pred ceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCce
Confidence 447766433334567999999 88999995 56789999999999964 344444454
No 10
>PF12773 DZR: Double zinc ribbon
Probab=67.51 E-value=6.1 Score=24.85 Aligned_cols=15 Identities=27% Similarity=0.798 Sum_probs=9.5
Q ss_pred ccccccchhhchhcc
Q 031017 19 ADEAALCAKCDVEVH 33 (167)
Q Consensus 19 aD~A~LC~~CD~~vH 33 (167)
.+++.+|..|...+-
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 455777777775444
No 11
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=65.23 E-value=5.2 Score=37.90 Aligned_cols=66 Identities=21% Similarity=0.395 Sum_probs=42.4
Q ss_pred cccchhhchhcccCcccccC-ceeceecccCCC--CCCCcccccCceEEEecCC---------ccccccccCCCCCCCC
Q 031017 22 AALCAKCDVEVHAANKLASK-HQRLLLQCLSNK--LPPCDICQEKAAFIFCVED---------RALFCKDCDEPIHSPG 88 (167)
Q Consensus 22 A~LC~~CD~~vH~aN~la~r-H~RvpL~~~~~~--~~~Cd~C~~~pA~v~C~~d---------~a~LC~~CD~~iH~an 88 (167)
.+||.+|...+|+.-+.... +.-.|+.+.+.. ...|..- ++.|.+.|... -..||..|+...|+.-
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n~ 304 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNR 304 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhcccc
Confidence 46999999999985544333 444455544431 3334443 45788887432 4589999999999643
No 12
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=64.06 E-value=2.7 Score=37.94 Aligned_cols=76 Identities=25% Similarity=0.480 Sum_probs=52.4
Q ss_pred CCeEEEeccccccc------chhhchhcccCccccc-Cceeceec---ccCC----CCCCCcccccC---ceEEEecCCc
Q 031017 11 APATVICCADEAAL------CAKCDVEVHAANKLAS-KHQRLLLQ---CLSN----KLPPCDICQEK---AAFIFCVEDR 73 (167)
Q Consensus 11 ~~A~vyC~aD~A~L------C~~CD~~vH~aN~la~-rH~RvpL~---~~~~----~~~~Cd~C~~~---pA~v~C~~d~ 73 (167)
.-+.++|..+.|.. |.-|+...=++--|++ =|.-.||. +++. .+..|-.|++. ...+.|..+.
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 34778898888876 4567766555444544 56667774 3332 24449999443 3456799999
Q ss_pred cccccccCCCCCC
Q 031017 74 ALFCKDCDEPIHS 86 (167)
Q Consensus 74 a~LC~~CD~~iH~ 86 (167)
..||.+||.=+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999998884
No 13
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=55.18 E-value=7.1 Score=37.82 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=16.4
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (167)
|+ .|-.|+.. -.+.+++|..|...+
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 54 69999875 245667777776443
No 14
>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=53.66 E-value=5.5 Score=23.44 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=17.4
Q ss_pred CCccccccCCCCeEEEecccccccch
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCA 26 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~ 26 (167)
+..+|.+|+. .+...|......+|.
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 999999999888875
No 15
>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=51.53 E-value=13 Score=23.95 Aligned_cols=30 Identities=33% Similarity=0.588 Sum_probs=21.6
Q ss_pred ccccccCCCC---eEEEecccccc-cchhhchhc
Q 031017 3 IQCDVCEKAP---ATVICCADEAA-LCAKCDVEV 32 (167)
Q Consensus 3 ~~Cd~C~~~~---A~vyC~aD~A~-LC~~CD~~v 32 (167)
+.||.|+..| ..+.|..+.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 4799999865 55678766554 899986544
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=50.60 E-value=4.7 Score=32.44 Aligned_cols=78 Identities=23% Similarity=0.563 Sum_probs=39.5
Q ss_pred cccccC--CCCeEEEecccccccchhhch--hcccCcc-cccCceeceecc---cCCCCCCCcccccCceEEE----ecC
Q 031017 4 QCDVCE--KAPATVICCADEAALCAKCDV--EVHAANK-LASKHQRLLLQC---LSNKLPPCDICQEKAAFIF----CVE 71 (167)
Q Consensus 4 ~Cd~C~--~~~A~vyC~aD~A~LC~~CD~--~vH~aN~-la~rH~RvpL~~---~~~~~~~Cd~C~~~pA~v~----C~~ 71 (167)
.|.+|| ....++.|..+.-.||..=+. .-|--+- ..+||.-|-|-+ ++-....|..|+....+.. ...
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 589999 566888999999999985443 2232232 345888777743 2234566999999966544 344
Q ss_pred Cc--cccccc-cC
Q 031017 72 DR--ALFCKD-CD 81 (167)
Q Consensus 72 d~--a~LC~~-CD 81 (167)
|. .+||+. |-
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 43 688877 75
No 17
>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=49.37 E-value=11 Score=25.05 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.8
Q ss_pred eEEEecccccccchhhchhcccC
Q 031017 13 ATVICCADEAALCAKCDVEVHAA 35 (167)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vH~a 35 (167)
..+.|..+...+|.+||.-+|..
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 56889999999999999999963
No 18
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=45.33 E-value=7.7 Score=36.62 Aligned_cols=59 Identities=25% Similarity=0.564 Sum_probs=45.3
Q ss_pred CCCCcccccC--ceEEEecCCccccccccCCCCCCCCCCCCCCcceeecceeeec--c----CCCCc
Q 031017 54 LPPCDICQEK--AAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLATGIRVAL--S----SSCSK 112 (167)
Q Consensus 54 ~~~Cd~C~~~--pA~v~C~~d~a~LC~~CD~~iH~an~ls~~HqRv~l~~irv~~--~----s~c~~ 112 (167)
...|..|... .|.++|..+-.++|.-|....|-+-...++|..++-..=||.- + +.|++
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~ 228 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTD 228 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccC
Confidence 3447777665 5889999999999999999999887777789888876446543 1 67755
No 19
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=44.94 E-value=12 Score=25.65 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=26.6
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (167)
|+..|..|+ +.-++|=.+.....|..|...+
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 678899999 6788999999999999998554
No 20
>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=42.53 E-value=9.4 Score=21.86 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=8.2
Q ss_pred cccccCCCCeEEEecccccccchhhchhccc
Q 031017 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (167)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (167)
.|+.|++.... +..+.|..||..+|.
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 234567888877774
No 21
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.60 E-value=20 Score=27.46 Aligned_cols=62 Identities=27% Similarity=0.527 Sum_probs=39.4
Q ss_pred chhhchhcccCccccc-Cceeceecc---cC----CCCCCCcccccCc--------------eEEEecCCccccccccCC
Q 031017 25 CAKCDVEVHAANKLAS-KHQRLLLQC---LS----NKLPPCDICQEKA--------------AFIFCVEDRALFCKDCDE 82 (167)
Q Consensus 25 C~~CD~~vH~aN~la~-rH~RvpL~~---~~----~~~~~Cd~C~~~p--------------A~v~C~~d~a~LC~~CD~ 82 (167)
|..|+..+=++.-|++ =|.-+||.. .+ .....|-.|+..- ..+.|..+...||.+||.
T Consensus 18 CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 18 CPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred CCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 5667655544444554 355555532 21 1233599998742 235699999999999999
Q ss_pred CCCC
Q 031017 83 PIHS 86 (167)
Q Consensus 83 ~iH~ 86 (167)
=+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 8885
No 22
>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=36.68 E-value=17 Score=20.91 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=18.2
Q ss_pred cccccCCCCeEEEecccccccchhhchhccc
Q 031017 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (167)
Q Consensus 4 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (167)
.|++|++.....+ .+-|..|+..+|.
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 5899988665554 5677777777664
No 23
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=36.22 E-value=25 Score=19.36 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=13.2
Q ss_pred CcccccCceEEEecCCccccccccCCC
Q 031017 57 CDICQEKAAFIFCVEDRALFCKDCDEP 83 (167)
Q Consensus 57 Cd~C~~~pA~v~C~~d~a~LC~~CD~~ 83 (167)
|+.|+.+. .+.+.||..|..+
T Consensus 2 Cp~CG~~~------~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEI------EDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCC------CCcCcchhhhCCc
Confidence 66666663 4467777777654
No 24
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=36.05 E-value=14 Score=35.11 Aligned_cols=42 Identities=21% Similarity=0.434 Sum_probs=32.7
Q ss_pred ccccccCC-----CCeEEEecc--cccccchhhchhcccCcccccCceecee
Q 031017 3 IQCDVCEK-----APATVICCA--DEAALCAKCDVEVHAANKLASKHQRLLL 47 (167)
Q Consensus 3 ~~Cd~C~~-----~~A~vyC~a--D~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (167)
..||.|+. ..|.+||++ +--++|..|=+.+|+. ..++.=.||
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPl 504 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPL 504 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCce
Confidence 46999998 889999995 5589999999999984 234444455
No 25
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=32.42 E-value=6.8 Score=33.57 Aligned_cols=57 Identities=23% Similarity=0.531 Sum_probs=40.3
Q ss_pred ccccccCCC-------CeEEEeccc-ccccchhhchhcccCcccccCceeceecccCCCCCCCcccccC
Q 031017 3 IQCDVCEKA-------PATVICCAD-EAALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEK 63 (167)
Q Consensus 3 ~~Cd~C~~~-------~A~vyC~aD-~A~LC~~CD~~vH~aN~la~rH~RvpL~~~~~~~~~Cd~C~~~ 63 (167)
..|++|++. .--+-|.+| ...||..|.+..|.+- -+.||.|..- +.....|..|...
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtf-dlkrh~rtht---gvrpykc~~c~ka 182 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTF-DLKRHTRTHT---GVRPYKCSLCEKA 182 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchh-hhhhhhcccc---CccccchhhhhHH
Confidence 468888875 234679888 6889999999998754 4589999753 2223447776554
No 26
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=32.09 E-value=21 Score=21.11 Aligned_cols=25 Identities=28% Similarity=0.925 Sum_probs=11.6
Q ss_pred CCCCcccccCceEEEecCCccccccccC
Q 031017 54 LPPCDICQEKAAFIFCVEDRALFCKDCD 81 (167)
Q Consensus 54 ~~~Cd~C~~~pA~v~C~~d~a~LC~~CD 81 (167)
+|.|+.|++.-.. .+...+.|..|.
T Consensus 2 ~p~Cp~C~se~~y---~D~~~~vCp~C~ 26 (30)
T PF08274_consen 2 LPKCPLCGSEYTY---EDGELLVCPECG 26 (30)
T ss_dssp S---TTT-----E---E-SSSEEETTTT
T ss_pred CCCCCCCCCccee---ccCCEEeCCccc
Confidence 5679999988655 455677888775
No 27
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=31.76 E-value=33 Score=29.77 Aligned_cols=41 Identities=32% Similarity=0.666 Sum_probs=29.7
Q ss_pred ccccccCCC---CeEEEeccccc-ccchhhchh--cccCcccccCce
Q 031017 3 IQCDVCEKA---PATVICCADEA-ALCAKCDVE--VHAANKLASKHQ 43 (167)
Q Consensus 3 ~~Cd~C~~~---~A~vyC~aD~A-~LC~~CD~~--vH~aN~la~rH~ 43 (167)
..||.|++. ...+-|.-+.. -||.+|.+. +|.+-++++-|.
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT 199 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceeeccc
Confidence 579999983 47789998865 499999988 454445555343
No 28
>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=30.82 E-value=64 Score=20.51 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=18.8
Q ss_pred CCcccccCceE---EEecCC-ccccccccCCCCC
Q 031017 56 PCDICQEKAAF---IFCVED-RALFCKDCDEPIH 85 (167)
Q Consensus 56 ~Cd~C~~~pA~---v~C~~d-~a~LC~~CD~~iH 85 (167)
.|+.|...... +.|..+ .--||..|-....
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~ 35 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGA 35 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcC
Confidence 37777766543 556665 3468888876443
No 29
>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=26.04 E-value=22 Score=23.94 Aligned_cols=31 Identities=26% Similarity=0.549 Sum_probs=19.9
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (167)
|+..|..|+ +.-++|=.+-...+|..|...+
T Consensus 6 m~VkCp~C~-~~q~vFSha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 6 MDVKCPGCY-NIQTVFSHAQTVVKCVVCGTVL 36 (55)
T ss_dssp EEEE-TTT--SEEEEETT-SS-EE-SSSTSEE
T ss_pred EEEECCCCC-CeeEEEecCCeEEEcccCCCEe
Confidence 677888898 5777788888888888887443
No 30
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=25.70 E-value=55 Score=19.31 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=7.6
Q ss_pred CCccccccCC
Q 031017 1 MKIQCDVCEK 10 (167)
Q Consensus 1 m~~~Cd~C~~ 10 (167)
|+..|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 7777888875
No 31
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=25.42 E-value=16 Score=39.51 Aligned_cols=57 Identities=33% Similarity=0.638 Sum_probs=43.2
Q ss_pred CCCCCcccccC--ceEEEecCCccccccccCCCCCCCCCCCCCCcceeec----ceeeeccCCCC
Q 031017 53 KLPPCDICQEK--AAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLAT----GIRVALSSSCS 111 (167)
Q Consensus 53 ~~~~Cd~C~~~--pA~v~C~~d~a~LC~~CD~~iH~an~ls~~HqRv~l~----~irv~~~s~c~ 111 (167)
+.|.|+.|.+. .|.++|..+. .||.+||.-.|-. ...++|+|.-+. .|.|-+..+|.
T Consensus 3321 Q~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f~eeeea~kvdlHeGC~ 3383 (3738)
T KOG1428|consen 3321 QMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVFKEEEEAIKVDLHEGCG 3383 (3738)
T ss_pred cCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhhhhhhhhcccchhhcch
Confidence 47889998664 6788998887 8999999765532 234789996553 48888889994
No 32
>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=25.07 E-value=32 Score=20.61 Aligned_cols=28 Identities=29% Similarity=0.615 Sum_probs=20.5
Q ss_pred ccccccCCCCeEEEecccccccchhhchhccc
Q 031017 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (167)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~vH~ 34 (167)
..|+.|++.-..+. .+.-|..|+..+|.
T Consensus 12 ~~C~~C~~~i~~~~----~~~~C~~C~~~~H~ 39 (49)
T smart00109 12 TKCCVCRKSIWGSF----QGLRCSWCKVKCHK 39 (49)
T ss_pred CCccccccccCcCC----CCcCCCCCCchHHH
Confidence 45888887654433 57889999999985
No 33
>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=25.02 E-value=53 Score=20.59 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=20.9
Q ss_pred CCccccccCCC---CeEEEecccc-cccchhhchh
Q 031017 1 MKIQCDVCEKA---PATVICCADE-AALCAKCDVE 31 (167)
Q Consensus 1 m~~~Cd~C~~~---~A~vyC~aD~-A~LC~~CD~~ 31 (167)
+...|+.|+.. ...+.|.... --||..|=..
T Consensus 3 ~~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 3 HGYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SSCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CCeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 35789999983 4677888764 7799999765
No 34
>KOG1891 consensus Proline binding protein WW45 [General function prediction only]
Probab=24.95 E-value=41 Score=29.16 Aligned_cols=20 Identities=30% Similarity=0.426 Sum_probs=14.0
Q ss_pred CCCCCCCC---------CCCCchhhhccc
Q 031017 133 MPTQQSSG---------ISSPWAVDDFLQ 152 (167)
Q Consensus 133 ~~~~~~~~---------~~~~~~~~~~~~ 152 (167)
++-|+++| +|.+||||--++
T Consensus 77 ~slq~~~s~~~~sedlPLPpgWav~~T~~ 105 (271)
T KOG1891|consen 77 MSLQQYRSSCDCSEDLPLPPGWAVEFTTE 105 (271)
T ss_pred hhhhhccccCCCcccCCCCCCcceeeEec
Confidence 45666665 778999986554
No 35
>PLN00209 ribosomal protein S27; Provisional
Probab=23.96 E-value=38 Score=24.86 Aligned_cols=31 Identities=23% Similarity=0.622 Sum_probs=25.2
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (167)
|++.|..|+ +.-+||=.+-...+|..|...+
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 677899998 5778888888999999997443
No 36
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.94 E-value=41 Score=24.62 Aligned_cols=31 Identities=29% Similarity=0.698 Sum_probs=25.2
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 031017 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (167)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~v 32 (167)
|++.|..|+ +.-+||=.+-...+|..|...+
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 677899998 5778888888999999997443
No 37
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=21.59 E-value=62 Score=29.71 Aligned_cols=43 Identities=23% Similarity=0.400 Sum_probs=32.3
Q ss_pred ccccccCCCCeEEEeccc-ccccchhhchhcccCcccccCceeceec
Q 031017 3 IQCDVCEKAPATVICCAD-EAALCAKCDVEVHAANKLASKHQRLLLQ 48 (167)
Q Consensus 3 ~~Cd~C~~~~A~vyC~aD-~A~LC~~CD~~vH~aN~la~rH~RvpL~ 48 (167)
+.|+-||... .-....| .++.|..|+.-+- +++.++|--|-|.
T Consensus 275 PvCd~CGn~r-Le~~pe~rg~~~C~~Cs~~V~--sP~~r~~LeVfl~ 318 (389)
T PF14951_consen 275 PVCDRCGNGR-LEQSPEDRGAFSCGDCSRVVT--SPVLRMHLEVFLD 318 (389)
T ss_pred ccccccCCcc-ceeCccCCCceeccchhhhcc--CcceeeeEEEEEe
Confidence 5799999544 3344555 4688999998876 5789999998884
No 38
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=21.58 E-value=39 Score=36.90 Aligned_cols=45 Identities=27% Similarity=0.552 Sum_probs=33.0
Q ss_pred ccccccCC--CCeEEEecccccccchhhchhcccCcccccCceeceecc
Q 031017 3 IQCDVCEK--APATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQC 49 (167)
Q Consensus 3 ~~Cd~C~~--~~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~~ 49 (167)
++||+-.. ..|.++|..+. +||.+||+-.|-. +-.+.|+|--+.+
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f~e 3369 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVFKE 3369 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhhhh
Confidence 46776543 56888998888 9999999887753 2357888876643
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.20 E-value=71 Score=24.99 Aligned_cols=39 Identities=28% Similarity=0.527 Sum_probs=29.5
Q ss_pred CCcccccCceEEEecCCccccccccC-CCCCCCCCCCCCCcceeecc
Q 031017 56 PCDICQEKAAFIFCVEDRALFCKDCD-EPIHSPGSLSANHQRFLATG 101 (167)
Q Consensus 56 ~Cd~C~~~pA~v~C~~d~a~LC~~CD-~~iH~an~ls~~HqRv~l~~ 101 (167)
.|..|... ..+||..+...+|..|. ...| ..|.-.++..
T Consensus 88 ~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h------~~h~~~~~~~ 127 (386)
T KOG2177|consen 88 LCEKHGEE-LKLFCEEDEKLLCVLCRESGEH------RGHPVLPLEE 127 (386)
T ss_pred hhhhcCCc-ceEEecccccccCCCCCCcccc------cCCccccHHH
Confidence 68888777 78999999999999998 4455 3565556553
No 40
>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=20.71 E-value=64 Score=23.79 Aligned_cols=49 Identities=24% Similarity=0.457 Sum_probs=28.5
Q ss_pred hhcccCcccccCceeceecccCCCCCCCcccccCceE---EEecCCc--cccccccCC
Q 031017 30 VEVHAANKLASKHQRLLLQCLSNKLPPCDICQEKAAF---IFCVEDR--ALFCKDCDE 82 (167)
Q Consensus 30 ~~vH~aN~la~rH~RvpL~~~~~~~~~Cd~C~~~pA~---v~C~~d~--a~LC~~CD~ 82 (167)
+.| +-|+|+++-.+-|+. ..+..|.+|.....- -||..+. .-+|.-|..
T Consensus 24 r~i-~eNKlLs~~~~nPy~---~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGK 77 (90)
T PF10235_consen 24 RKI-GENKLLSKKKKNPYA---PYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGK 77 (90)
T ss_pred ccc-cceeeecccccCccc---ccCccccccccccccCCCccChhhhcccCcccccCC
Confidence 344 468888877775553 336679999887432 4444441 334444443
Done!