Query 028326
Match_columns 210
No_of_seqs 179 out of 563
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:45:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028326.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028326hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4367 Predicted Zn-finger pr 98.0 1.7E-06 3.6E-11 81.7 1.1 85 3-87 163-256 (699)
2 cd00021 BBOX B-Box-type zinc f 97.9 9.2E-06 2E-10 50.9 2.5 38 56-99 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.8 1.2E-05 2.7E-10 51.6 2.2 40 54-99 3-42 (42)
4 cd00021 BBOX B-Box-type zinc f 97.7 2.1E-05 4.6E-10 49.2 2.3 38 4-47 2-39 (39)
5 smart00336 BBOX B-Box-type zin 97.4 0.00014 3E-09 46.0 2.7 39 55-99 4-42 (42)
6 PF00643 zf-B_box: B-box zinc 97.4 0.00015 3.2E-09 46.5 2.8 40 2-47 3-42 (42)
7 smart00336 BBOX B-Box-type zin 97.2 0.00026 5.5E-09 44.8 2.5 39 3-47 4-42 (42)
8 KOG2807 RNA polymerase II tran 75.1 1.2 2.6E-05 41.3 0.7 76 11-86 273-365 (378)
9 PF13248 zf-ribbon_3: zinc-rib 71.7 2.8 6.1E-05 24.3 1.5 25 1-31 1-25 (26)
10 cd02335 ZZ_ADA2 Zinc finger, Z 69.8 5.8 0.00013 26.3 2.9 40 56-95 2-45 (49)
11 TIGR00622 ssl1 transcription f 69.0 2.9 6.4E-05 33.0 1.5 62 25-86 18-101 (112)
12 COG5151 SSL1 RNA polymerase II 68.8 1.8 4E-05 40.1 0.4 76 11-86 305-408 (421)
13 cd02342 ZZ_UBA_plant Zinc fing 65.7 5.8 0.00012 26.3 2.2 31 3-33 1-35 (43)
14 PF09416 UPF1_Zn_bind: RNA hel 64.8 3.2 7E-05 34.4 1.1 78 4-81 2-94 (152)
15 PF04438 zf-HIT: HIT zinc fing 62.3 3.4 7.4E-05 25.0 0.6 25 1-26 1-25 (30)
16 PF10235 Cript: Microtubule-as 59.2 6.7 0.00014 29.9 1.8 48 34-84 27-79 (90)
17 PF07975 C1_4: TFIIH C1-like d 59.1 3.8 8.2E-05 28.0 0.4 24 64-87 19-42 (51)
18 KOG2177 Predicted E3 ubiquitin 56.9 18 0.0004 29.7 4.3 31 56-87 88-119 (386)
19 PF07975 C1_4: TFIIH C1-like d 54.7 8.4 0.00018 26.3 1.5 23 13-35 20-42 (51)
20 KOG0129 Predicted RNA-binding 53.1 4.6 9.9E-05 39.4 0.1 47 42-88 443-496 (520)
21 KOG4367 Predicted Zn-finger pr 52.5 5 0.00011 38.9 0.2 50 54-103 162-213 (699)
22 PRK14559 putative protein seri 50.6 8.2 0.00018 38.7 1.4 25 1-32 1-25 (645)
23 PF13920 zf-C3HC4_3: Zinc fing 48.5 28 0.00061 22.5 3.3 32 3-34 3-35 (50)
24 KOG0129 Predicted RNA-binding 48.2 11 0.00024 36.8 1.8 43 3-48 456-505 (520)
25 PF12773 DZR: Double zinc ribb 43.5 26 0.00057 22.6 2.6 16 18-33 8-23 (50)
26 PF07649 C1_3: C1-like domain; 43.3 8.5 0.00018 22.8 0.1 26 4-34 2-27 (30)
27 PF08274 PhnA_Zn_Ribbon: PhnA 43.2 13 0.00027 22.7 0.9 25 54-81 2-26 (30)
28 KOG1428 Inhibitor of type V ad 42.6 13 0.00028 41.3 1.4 44 3-48 3323-3368(3738)
29 PRK00415 rps27e 30S ribosomal 42.0 11 0.00024 26.5 0.6 31 1-32 10-40 (59)
30 cd02341 ZZ_ZZZ3 Zinc finger, Z 40.4 28 0.00061 23.2 2.3 29 56-84 2-36 (48)
31 KOG1280 Uncharacterized conser 39.8 18 0.00039 33.9 1.8 37 38-84 2-42 (381)
32 PF00569 ZZ: Zinc finger, ZZ t 37.1 28 0.00061 22.6 1.9 30 2-31 4-37 (46)
33 TIGR02098 MJ0042_CXXC MJ0042 f 36.9 29 0.00063 21.2 1.9 10 1-10 1-10 (38)
34 cd02334 ZZ_dystrophin Zinc fin 36.6 38 0.00082 22.7 2.5 39 56-94 2-44 (49)
35 KOG1428 Inhibitor of type V ad 34.6 12 0.00025 41.7 -0.4 48 51-100 3319-3368(3738)
36 KOG0954 PHD finger protein [Ge 33.7 25 0.00054 36.2 1.8 30 3-35 272-301 (893)
37 KOG4582 Uncharacterized conser 33.1 29 0.00062 31.2 1.9 34 3-36 153-191 (278)
38 PF13842 Tnp_zf-ribbon_2: DDE_ 32.6 36 0.00077 20.8 1.7 15 65-79 15-29 (32)
39 cd02249 ZZ Zinc finger, ZZ typ 32.0 51 0.0011 21.2 2.5 29 57-85 3-34 (46)
40 cd02344 ZZ_HERC2 Zinc finger, 28.6 59 0.0013 21.5 2.4 29 3-31 1-33 (45)
41 PF03107 C1_2: C1 domain; Int 27.8 22 0.00047 21.1 0.2 26 4-34 2-27 (30)
42 PLN02436 cellulose synthase A 27.8 43 0.00093 35.8 2.4 29 54-82 36-71 (1094)
43 cd02338 ZZ_PCMF_like Zinc fing 27.2 80 0.0017 20.8 2.9 32 56-87 2-37 (49)
44 PRK14714 DNA polymerase II lar 26.5 43 0.00092 36.4 2.1 21 4-24 669-689 (1337)
45 PF14446 Prok-RING_1: Prokaryo 26.1 29 0.00063 24.0 0.5 30 1-34 4-33 (54)
46 PRK14873 primosome assembly pr 25.9 34 0.00074 34.5 1.3 19 13-31 382-401 (665)
47 PF14776 UNC-79: Cation-channe 25.4 40 0.00087 33.2 1.6 65 22-87 227-303 (525)
48 cd02340 ZZ_NBR1_like Zinc fing 25.2 74 0.0016 20.5 2.4 28 3-30 1-31 (43)
49 PLN02400 cellulose synthase 24.5 54 0.0012 35.1 2.4 29 54-82 36-71 (1085)
50 PLN02189 cellulose synthase 24.4 55 0.0012 34.9 2.4 29 54-82 34-69 (1040)
51 COG1198 PriA Primosomal protei 24.4 58 0.0013 33.4 2.6 44 3-68 436-489 (730)
52 PRK14890 putative Zn-ribbon RN 23.6 34 0.00074 24.1 0.5 7 3-9 8-14 (59)
53 PF07191 zinc-ribbons_6: zinc- 23.2 42 0.0009 24.4 0.9 24 3-30 2-25 (70)
54 PF04216 FdhE: Protein involve 22.7 54 0.0012 29.2 1.8 65 2-84 172-248 (290)
55 cd02339 ZZ_Mind_bomb Zinc fing 22.6 85 0.0019 20.6 2.3 28 3-30 1-32 (45)
56 PF14951 DUF4503: Domain of un 22.4 66 0.0014 30.5 2.3 42 3-47 275-317 (389)
57 smart00291 ZnF_ZZ Zinc-binding 22.2 1E+02 0.0022 19.7 2.6 30 1-30 3-35 (44)
58 PRK14714 DNA polymerase II lar 22.1 54 0.0012 35.7 1.9 31 55-85 668-703 (1337)
59 PF01667 Ribosomal_S27e: Ribos 21.3 25 0.00054 24.4 -0.5 29 1-30 6-34 (55)
60 KOG4317 Predicted Zn-finger pr 20.4 50 0.0011 30.8 1.1 33 50-82 3-36 (383)
61 PLN00209 ribosomal protein S27 20.0 38 0.00082 25.6 0.2 30 1-31 35-64 (86)
No 1
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=98.01 E-value=1.7e-06 Score=81.69 Aligned_cols=85 Identities=24% Similarity=0.508 Sum_probs=73.6
Q ss_pred ccccccCCCC--ceEEccCCCcccchhhhhhhhhccccccCcccccCCC-------CCCCCCCCCcccCccceEEecCcc
Q 028326 3 IQCNVCEAAE--AKVLCCADEAALCWECDDKVHAANKLASKHQRVPLSS-------SSTQMPKCDICQETSGFFFCLQDR 73 (210)
Q Consensus 3 ~~Cd~C~~a~--A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~~-------~~~~~~~Cd~C~~~~A~~fC~~D~ 73 (210)
..|..|++++ |.|+|..|+.+.|.-|..+.|-+...+.||.-+|-.+ .+.+...|..|+-+.-.+||.+|+
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 3699999765 9999999999999999999999988889999888755 245667899999999999999999
Q ss_pred ccccccccccccCC
Q 028326 74 ALLCRKCDVAIHTA 87 (210)
Q Consensus 74 a~LC~~Cd~~~H~a 87 (210)
+++|..|...+..+
T Consensus 243 ~pvc~~clee~khs 256 (699)
T KOG4367|consen 243 MPVCYQCLEEGKHS 256 (699)
T ss_pred ChHHHHHHHhhccc
Confidence 99999998864333
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=97.89 E-value=9.2e-06 Score=50.86 Aligned_cols=38 Identities=45% Similarity=0.855 Sum_probs=34.0
Q ss_pred CCCcccCccceEEecCccccccccccccccCCCCCCCCCcceee
Q 028326 56 KCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (210)
Q Consensus 56 ~Cd~C~~~~A~~fC~~D~a~LC~~Cd~~~H~aN~~~~~H~R~~l 99 (210)
.|+.|+.+++.+||..|...+|..|+...|+ .|+++||
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 4999998899999999999999999988874 8888775
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=97.81 E-value=1.2e-05 Score=51.56 Aligned_cols=40 Identities=30% Similarity=0.549 Sum_probs=34.4
Q ss_pred CCCCCcccCccceEEecCccccccccccccccCCCCCCCCCcceee
Q 028326 54 MPKCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (210)
Q Consensus 54 ~~~Cd~C~~~~A~~fC~~D~a~LC~~Cd~~~H~aN~~~~~H~R~~l 99 (210)
...|+.|+...+.+||..|+.+||..|....|.. |+..+|
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 4569999999999999999999999999999854 887765
No 4
>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=97.73 E-value=2.1e-05 Score=49.18 Aligned_cols=38 Identities=39% Similarity=0.791 Sum_probs=33.7
Q ss_pred cccccCCCCceEEccCCCcccchhhhhhhhhccccccCcccccC
Q 028326 4 QCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (210)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (210)
.|+.++++++.+||..|...+|..|+...|. .|.++||
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 6889988899999999999999999987764 7888875
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.39 E-value=0.00014 Score=46.04 Aligned_cols=39 Identities=49% Similarity=0.870 Sum_probs=33.6
Q ss_pred CCCCcccCccceEEecCccccccccccccccCCCCCCCCCcceee
Q 028326 55 PKCDICQETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLL 99 (210)
Q Consensus 55 ~~Cd~C~~~~A~~fC~~D~a~LC~~Cd~~~H~aN~~~~~H~R~~l 99 (210)
..|+.|+.+++.+||..|...||..|....| +.|++++|
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 3499999899999999999999999998766 57877764
No 6
>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=97.39 E-value=0.00015 Score=46.48 Aligned_cols=40 Identities=25% Similarity=0.507 Sum_probs=34.3
Q ss_pred CccccccCCCCceEEccCCCcccchhhhhhhhhccccccCcccccC
Q 028326 2 RIQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (210)
Q Consensus 2 k~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (210)
...|..+.+.++.+||..|...+|..|....|.. |..+||
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 3579999998899999999999999999998864 888775
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.23 E-value=0.00026 Score=44.80 Aligned_cols=39 Identities=31% Similarity=0.550 Sum_probs=33.5
Q ss_pred ccccccCCCCceEEccCCCcccchhhhhhhhhccccccCcccccC
Q 028326 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPL 47 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (210)
..|..++..++.+||..|.+.+|..|....| +.|.+++|
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 5688998889999999999999999997766 57877765
No 8
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=75.13 E-value=1.2 Score=41.33 Aligned_cols=76 Identities=28% Similarity=0.505 Sum_probs=53.8
Q ss_pred CCceEEccCCCccc------chhhhhhhhhcccccc-CcccccCCC---CC--C--CCCCCCcccC---ccceEEecCcc
Q 028326 11 AEAKVLCCADEAAL------CWECDDKVHAANKLAS-KHQRVPLSS---SS--T--QMPKCDICQE---TSGFFFCLQDR 73 (210)
Q Consensus 11 a~A~vyC~aD~A~L------C~~CD~~vH~aN~la~-rH~RvpL~~---~~--~--~~~~Cd~C~~---~~A~~fC~~D~ 73 (210)
..+-++|..|.|.. |.-|+..+=++.-|++ =|.-.||.. .+ . ....|-.|+. ....+.|..|+
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 45788899998886 4577766666555554 677788854 11 1 2334888832 23458899999
Q ss_pred ccccccccccccC
Q 028326 74 ALLCRKCDVAIHT 86 (210)
Q Consensus 74 a~LC~~Cd~~~H~ 86 (210)
...|.+||+-+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999999985
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=71.72 E-value=2.8 Score=24.30 Aligned_cols=25 Identities=32% Similarity=0.680 Sum_probs=17.3
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDK 31 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~ 31 (210)
|...|-.|++.. .+++.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 788899999631 4557777777643
No 10
>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=69.76 E-value=5.8 Score=26.29 Aligned_cols=40 Identities=23% Similarity=0.344 Sum_probs=29.0
Q ss_pred CCCcccCccce---EEecCc-cccccccccccccCCCCCCCCCc
Q 028326 56 KCDICQETSGF---FFCLQD-RALLCRKCDVAIHTANSYVSAHQ 95 (210)
Q Consensus 56 ~Cd~C~~~~A~---~fC~~D-~a~LC~~Cd~~~H~aN~~~~~H~ 95 (210)
.|+.|...... +.|.+| ..-||..|-......+.....|.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 48888776554 789998 67999999987765554444554
No 11
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=68.99 E-value=2.9 Score=33.00 Aligned_cols=62 Identities=27% Similarity=0.491 Sum_probs=41.2
Q ss_pred chhhhhhhhhcccccc-CcccccCCC---C----CCCCCCCCcccCc--------------cceEEecCccccccccccc
Q 028326 25 CWECDDKVHAANKLAS-KHQRVPLSS---S----STQMPKCDICQET--------------SGFFFCLQDRALLCRKCDV 82 (210)
Q Consensus 25 C~~CD~~vH~aN~la~-rH~RvpL~~---~----~~~~~~Cd~C~~~--------------~A~~fC~~D~a~LC~~Cd~ 82 (210)
|.-|+..+=++.-|++ =|.-.||.. . ......|-.|+.. ...+.|..|....|.+||+
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 5667766655554554 466666643 1 1112358888763 2347799999999999999
Q ss_pred cccC
Q 028326 83 AIHT 86 (210)
Q Consensus 83 ~~H~ 86 (210)
-+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 9996
No 12
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=68.84 E-value=1.8 Score=40.06 Aligned_cols=76 Identities=28% Similarity=0.519 Sum_probs=53.8
Q ss_pred CCceEEccCCCccc------chhhhhhhhhccccc-cCcccccCCCC---C----CCCCCCCcccC--------------
Q 028326 11 AEAKVLCCADEAAL------CWECDDKVHAANKLA-SKHQRVPLSSS---S----TQMPKCDICQE-------------- 62 (210)
Q Consensus 11 a~A~vyC~aD~A~L------C~~CD~~vH~aN~la-~rH~RvpL~~~---~----~~~~~Cd~C~~-------------- 62 (210)
..+.++|..|.+.. |.-|+..+=...-|+ +-|.-.||..- + .....|-.||.
T Consensus 305 ~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ 384 (421)
T COG5151 305 KGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVSPFDEST 384 (421)
T ss_pred ccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCCcccccc
Confidence 35778899988876 567886654433343 46788888651 1 23345877876
Q ss_pred ccceEEecCccccccccccccccC
Q 028326 63 TSGFFFCLQDRALLCRKCDVAIHT 86 (210)
Q Consensus 63 ~~A~~fC~~D~a~LC~~Cd~~~H~ 86 (210)
....+.|..|.--.|.+||+-+|.
T Consensus 385 ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 385 SSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cccceechhhhhhhhhhhHHHHHH
Confidence 245688999999999999999985
No 13
>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=65.70 E-value=5.8 Score=26.28 Aligned_cols=31 Identities=26% Similarity=0.482 Sum_probs=23.8
Q ss_pred ccccccCCCC---ceEEccCCCcc-cchhhhhhhh
Q 028326 3 IQCNVCEAAE---AKVLCCADEAA-LCWECDDKVH 33 (210)
Q Consensus 3 ~~Cd~C~~a~---A~vyC~aD~A~-LC~~CD~~vH 33 (210)
+.||.|+..| ..+.|..+.-+ ||..|=.+.-
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 5799999754 77889888666 9999965543
No 14
>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=64.84 E-value=3.2 Score=34.41 Aligned_cols=78 Identities=27% Similarity=0.565 Sum_probs=41.7
Q ss_pred cccccC--CCCceEEccCCCcccchhhhh--hhhhccc-cccCcccccCCCCC---CCCCCCCcccCccceEE----ecC
Q 028326 4 QCNVCE--AAEAKVLCCADEAALCWECDD--KVHAANK-LASKHQRVPLSSSS---TQMPKCDICQETSGFFF----CLQ 71 (210)
Q Consensus 4 ~Cd~C~--~a~A~vyC~aD~A~LC~~CD~--~vH~aN~-la~rH~RvpL~~~~---~~~~~Cd~C~~~~A~~f----C~~ 71 (210)
.|.+|+ ....+|.|..+.-.+|-.=+. .-|=-+- +.+||.-|.|.+-. -....|-.|+....+.. ...
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 699999 677999999999999986543 2233333 44688888886532 23567999999887633 344
Q ss_pred cc--cccccc-cc
Q 028326 72 DR--ALLCRK-CD 81 (210)
Q Consensus 72 D~--a~LC~~-Cd 81 (210)
+. ++||+. |.
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 55 689988 75
No 15
>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=62.30 E-value=3.4 Score=25.04 Aligned_cols=25 Identities=36% Similarity=0.539 Sum_probs=18.1
Q ss_pred CCccccccCCCCceEEccCCCcccch
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCW 26 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~ 26 (210)
+..+|.+|+. ++...|..+...+|.
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 999999999998885
No 16
>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=59.20 E-value=6.7 Score=29.86 Aligned_cols=48 Identities=29% Similarity=0.547 Sum_probs=35.8
Q ss_pred hccccccCcccccCCCCCCCCCCCCcccCccce---EEecCccc--cccccccccc
Q 028326 34 AANKLASKHQRVPLSSSSTQMPKCDICQETSGF---FFCLQDRA--LLCRKCDVAI 84 (210)
Q Consensus 34 ~aN~la~rH~RvpL~~~~~~~~~Cd~C~~~~A~---~fC~~D~a--~LC~~Cd~~~ 84 (210)
.-|+|+++-.+-|+. ..+..|.+|...... .||..|+. .+|.-|...+
T Consensus 27 ~eNKlLs~~~~nPy~---~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 27 GENKLLSKKKKNPYA---PYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred cceeeecccccCccc---ccCccccccccccccCCCccChhhhcccCcccccCCee
Confidence 458898888776663 336679999776544 89999974 7899997754
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=59.09 E-value=3.8 Score=27.98 Aligned_cols=24 Identities=33% Similarity=0.676 Sum_probs=15.7
Q ss_pred cceEEecCccccccccccccccCC
Q 028326 64 SGFFFCLQDRALLCRKCDVAIHTA 87 (210)
Q Consensus 64 ~A~~fC~~D~a~LC~~Cd~~~H~a 87 (210)
...+.|..|+...|.+||+-+|..
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTT
T ss_pred CCeEECCCCCCccccCcChhhhcc
Confidence 466889999999999999999963
No 18
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.87 E-value=18 Score=29.73 Aligned_cols=31 Identities=32% Similarity=0.617 Sum_probs=25.4
Q ss_pred CCCcccCccceEEecCcccccccccc-ccccCC
Q 028326 56 KCDICQETSGFFFCLQDRALLCRKCD-VAIHTA 87 (210)
Q Consensus 56 ~Cd~C~~~~A~~fC~~D~a~LC~~Cd-~~~H~a 87 (210)
.|..|+.. ..+||..|...+|..|. ...|..
T Consensus 88 ~c~~~~~~-~~~~c~~~~~~~c~~c~~~~~h~~ 119 (386)
T KOG2177|consen 88 LCEKHGEE-LKLFCEEDEKLLCVLCRESGEHRG 119 (386)
T ss_pred hhhhcCCc-ceEEecccccccCCCCCCcccccC
Confidence 68888776 78999999999999999 455543
No 19
>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=54.73 E-value=8.4 Score=26.30 Aligned_cols=23 Identities=22% Similarity=0.573 Sum_probs=15.8
Q ss_pred ceEEccCCCcccchhhhhhhhhc
Q 028326 13 AKVLCCADEAALCWECDDKVHAA 35 (210)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vH~a 35 (210)
.++.|..+...+|.+||.-||..
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 57889999999999999999973
No 20
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=53.13 E-value=4.6 Score=39.40 Aligned_cols=47 Identities=26% Similarity=0.487 Sum_probs=38.4
Q ss_pred cccccCCCCCCCCCCCCcccC-----ccceEEec--CccccccccccccccCCC
Q 028326 42 HQRVPLSSSSTQMPKCDICQE-----TSGFFFCL--QDRALLCRKCDVAIHTAN 88 (210)
Q Consensus 42 H~RvpL~~~~~~~~~Cd~C~~-----~~A~~fC~--~D~a~LC~~Cd~~~H~aN 88 (210)
++||-|.+---+-..|+.|+. +.|-|||. .|....|..|-..+|+--
T Consensus 443 ~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~ 496 (520)
T KOG0129|consen 443 DKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP 496 (520)
T ss_pred ceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC
Confidence 458877554456678999998 88999995 699999999999999754
No 21
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=52.51 E-value=5 Score=38.91 Aligned_cols=50 Identities=18% Similarity=0.460 Sum_probs=39.8
Q ss_pred CCCCCcccCc--cceEEecCccccccccccccccCCCCCCCCCcceeeeCcc
Q 028326 54 MPKCDICQET--SGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLLTGVK 103 (210)
Q Consensus 54 ~~~Cd~C~~~--~A~~fC~~D~a~LC~~Cd~~~H~aN~~~~~H~R~~l~~~~ 103 (210)
..+|..|+.. .|.++|.+|.+..|.-|...-|-.-...++|+.+|-+.-+
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~gr 213 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGR 213 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCc
Confidence 3467777654 5679999999999999999999888888899877654333
No 22
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.63 E-value=8.2 Score=38.75 Aligned_cols=25 Identities=20% Similarity=0.619 Sum_probs=16.2
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDKV 32 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (210)
|+ .|-.|+.. ..+.+.+|..|...+
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 53 69999864 235667777776443
No 23
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=48.47 E-value=28 Score=22.51 Aligned_cols=32 Identities=19% Similarity=0.468 Sum_probs=25.6
Q ss_pred ccccccCCCCceEEccCCCcc-cchhhhhhhhh
Q 028326 3 IQCNVCEAAEAKVLCCADEAA-LCWECDDKVHA 34 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~-LC~~CD~~vH~ 34 (210)
..|..|...++.+.-.-+.-. +|..|-.+...
T Consensus 3 ~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 3 EECPICFENPRDVVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp SB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHH
T ss_pred CCCccCCccCCceEEeCCCChHHHHHHhHHhcc
Confidence 468899988888888888877 99999877765
No 24
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=48.20 E-value=11 Score=36.85 Aligned_cols=43 Identities=23% Similarity=0.471 Sum_probs=34.2
Q ss_pred ccccccCC-----CCceEEccC--CCcccchhhhhhhhhccccccCcccccCC
Q 028326 3 IQCNVCEA-----AEAKVLCCA--DEAALCWECDDKVHAANKLASKHQRVPLS 48 (210)
Q Consensus 3 ~~Cd~C~~-----a~A~vyC~a--D~A~LC~~CD~~vH~aN~la~rH~RvpL~ 48 (210)
..||.|+. ..|-+||++ |--|+|..|=+.+|+. ..++.-.||.
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlv 505 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLV 505 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCcee
Confidence 36899987 889999998 6799999999999985 3445555653
No 25
>PF12773 DZR: Double zinc ribbon
Probab=43.53 E-value=26 Score=22.63 Aligned_cols=16 Identities=25% Similarity=0.594 Sum_probs=10.6
Q ss_pred cCCCcccchhhhhhhh
Q 028326 18 CADEAALCWECDDKVH 33 (210)
Q Consensus 18 ~aD~A~LC~~CD~~vH 33 (210)
..+++.+|..|...+-
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 3456778888875554
No 26
>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=43.29 E-value=8.5 Score=22.76 Aligned_cols=26 Identities=27% Similarity=0.548 Sum_probs=8.3
Q ss_pred cccccCCCCceEEccCCCcccchhhhhhhhh
Q 028326 4 QCNVCEAAEAKVLCCADEAALCWECDDKVHA 34 (210)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~ 34 (210)
.|+.|+...-. ...+-|..||..+|.
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 58888864332 234567788877774
No 27
>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=43.19 E-value=13 Score=22.69 Aligned_cols=25 Identities=28% Similarity=0.886 Sum_probs=11.8
Q ss_pred CCCCCcccCccceEEecCcccccccccc
Q 028326 54 MPKCDICQETSGFFFCLQDRALLCRKCD 81 (210)
Q Consensus 54 ~~~Cd~C~~~~A~~fC~~D~a~LC~~Cd 81 (210)
.|+|+.|...-.+ ......+|..|.
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 4679999887655 455667888885
No 28
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=42.60 E-value=13 Score=41.33 Aligned_cols=44 Identities=27% Similarity=0.508 Sum_probs=33.0
Q ss_pred ccccccC--CCCceEEccCCCcccchhhhhhhhhccccccCcccccCC
Q 028326 3 IQCNVCE--AAEAKVLCCADEAALCWECDDKVHAANKLASKHQRVPLS 48 (210)
Q Consensus 3 ~~Cd~C~--~a~A~vyC~aD~A~LC~~CD~~vH~aN~la~rH~RvpL~ 48 (210)
++||.-. +..|.|+|..|. .||.+||+-.|-.. -.+.|+|--+.
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~ 3368 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFK 3368 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhh
Confidence 4687766 467999999999 99999998777532 24678876553
No 29
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=41.99 E-value=11 Score=26.52 Aligned_cols=31 Identities=23% Similarity=0.622 Sum_probs=25.9
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDKV 32 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~v 32 (210)
|++.|.-|+ +.-+||=.+.....|..|...+
T Consensus 10 ~~VkCp~C~-n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCG-NEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCC-CeEEEEecCCcEEECcccCCCc
Confidence 788999999 4778888888999999997544
No 30
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=40.36 E-value=28 Score=23.20 Aligned_cols=29 Identities=31% Similarity=0.556 Sum_probs=21.4
Q ss_pred CCCcccCccce---EEecCcc---ccccccccccc
Q 028326 56 KCDICQETSGF---FFCLQDR---ALLCRKCDVAI 84 (210)
Q Consensus 56 ~Cd~C~~~~A~---~fC~~D~---a~LC~~Cd~~~ 84 (210)
.|+.|+..+.. +.|..|. .-||..|-...
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 47888775443 6688777 89999997765
No 31
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=39.79 E-value=18 Score=33.94 Aligned_cols=37 Identities=32% Similarity=0.411 Sum_probs=29.2
Q ss_pred cccCcccccCCCCCCCCCCCCcccCccceEEecCcc----ccccccccccc
Q 028326 38 LASKHQRVPLSSSSTQMPKCDICQETSGFFFCLQDR----ALLCRKCDVAI 84 (210)
Q Consensus 38 la~rH~RvpL~~~~~~~~~Cd~C~~~~A~~fC~~D~----a~LC~~Cd~~~ 84 (210)
+.++|++|. |+.|....-.|+|..|- .-||..|...+
T Consensus 2 ~~~rHe~v~----------CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~ 42 (381)
T KOG1280|consen 2 LTSRHEGVS----------CDGCGKTAFTFRRYKCLRCSDYDLCFSCYENG 42 (381)
T ss_pred CCCCcCCce----------eccccccceeeeeeEeeeecchhHHHHHhhcC
Confidence 578999997 99999888777765543 37899998765
No 32
>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=37.14 E-value=28 Score=22.63 Aligned_cols=30 Identities=23% Similarity=0.520 Sum_probs=21.7
Q ss_pred CccccccCC---CCceEEccCCC-cccchhhhhh
Q 028326 2 RIQCNVCEA---AEAKVLCCADE-AALCWECDDK 31 (210)
Q Consensus 2 k~~Cd~C~~---a~A~vyC~aD~-A~LC~~CD~~ 31 (210)
...|+.|+. ....+.|..+. --||..|=..
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 578999997 35889999884 7799999765
No 33
>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=36.93 E-value=29 Score=21.23 Aligned_cols=10 Identities=60% Similarity=1.245 Sum_probs=7.8
Q ss_pred CCccccccCC
Q 028326 1 MRIQCNVCEA 10 (210)
Q Consensus 1 Mk~~Cd~C~~ 10 (210)
|++.|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 7778888875
No 34
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=36.63 E-value=38 Score=22.69 Aligned_cols=39 Identities=33% Similarity=0.576 Sum_probs=25.5
Q ss_pred CCCcccCccce---EEecCcc-ccccccccccccCCCCCCCCC
Q 028326 56 KCDICQETSGF---FFCLQDR-ALLCRKCDVAIHTANSYVSAH 94 (210)
Q Consensus 56 ~Cd~C~~~~A~---~fC~~D~-a~LC~~Cd~~~H~aN~~~~~H 94 (210)
.|+.|...+.. +.|..|. .-||..|-..+.........|
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~~~~H~~~H 44 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRTSKSHKNSH 44 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCcCCCCCCCC
Confidence 48888865443 6677665 589999988776554333333
No 35
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=34.63 E-value=12 Score=41.68 Aligned_cols=48 Identities=33% Similarity=0.596 Sum_probs=35.7
Q ss_pred CCCCCCCCccc--CccceEEecCccccccccccccccCCCCCCCCCcceeee
Q 028326 51 STQMPKCDICQ--ETSGFFFCLQDRALLCRKCDVAIHTANSYVSAHQRFLLT 100 (210)
Q Consensus 51 ~~~~~~Cd~C~--~~~A~~fC~~D~a~LC~~Cd~~~H~aN~~~~~H~R~~l~ 100 (210)
..+.|.|+.|- ...|.++|..|. -||.+|+.-.|-. .-.+.|+|.-+.
T Consensus 3319 qkQ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLH-rrtktH~~q~f~ 3368 (3738)
T KOG1428|consen 3319 QKQMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLH-RRTKTHQRQVFK 3368 (3738)
T ss_pred hhcCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHH-hhccchhhhhhh
Confidence 35678999984 457889999999 7999999976522 224689986554
No 36
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=33.74 E-value=25 Score=36.19 Aligned_cols=30 Identities=33% Similarity=0.771 Sum_probs=22.1
Q ss_pred ccccccCCCCceEEccCCCcccchhhhhhhhhc
Q 028326 3 IQCNVCEAAEAKVLCCADEAALCWECDDKVHAA 35 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~a 35 (210)
++||+|.....- .+++..+|..|..-||.+
T Consensus 272 viCDvCrspD~e---~~neMVfCd~Cn~cVHqa 301 (893)
T KOG0954|consen 272 VICDVCRSPDSE---EANEMVFCDKCNICVHQA 301 (893)
T ss_pred ceeceecCCCcc---ccceeEEeccchhHHHHh
Confidence 579999864322 246778899999999986
No 37
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=33.08 E-value=29 Score=31.21 Aligned_cols=34 Identities=26% Similarity=0.592 Sum_probs=27.3
Q ss_pred ccccccCC---CCceEEccCCCcc-cchhhhhhh-hhcc
Q 028326 3 IQCNVCEA---AEAKVLCCADEAA-LCWECDDKV-HAAN 36 (210)
Q Consensus 3 ~~Cd~C~~---a~A~vyC~aD~A~-LC~~CD~~v-H~aN 36 (210)
+.||.|.+ .-.++-|.-|..| ||..|-+.. |.++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~ 191 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAA 191 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcc
Confidence 68999997 4589999999655 999999985 4443
No 38
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=32.55 E-value=36 Score=20.76 Aligned_cols=15 Identities=20% Similarity=0.496 Sum_probs=12.4
Q ss_pred ceEEecCcccccccc
Q 028326 65 GFFFCLQDRALLCRK 79 (210)
Q Consensus 65 A~~fC~~D~a~LC~~ 79 (210)
..|+|..|.+.||..
T Consensus 15 T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 15 TRYMCSKCDVPLCVE 29 (32)
T ss_pred eEEEccCCCCcccCC
Confidence 568899999988875
No 39
>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=32.01 E-value=51 Score=21.23 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=21.1
Q ss_pred CCcccCc--cceEEecCcc-cccccccccccc
Q 028326 57 CDICQET--SGFFFCLQDR-ALLCRKCDVAIH 85 (210)
Q Consensus 57 Cd~C~~~--~A~~fC~~D~-a~LC~~Cd~~~H 85 (210)
|+.|... ...+.|..|. .-||..|-...+
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 6777653 2457788887 789999987664
No 40
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=28.62 E-value=59 Score=21.47 Aligned_cols=29 Identities=17% Similarity=0.550 Sum_probs=22.4
Q ss_pred ccccccCCCC---ceEEccCCC-cccchhhhhh
Q 028326 3 IQCNVCEAAE---AKVLCCADE-AALCWECDDK 31 (210)
Q Consensus 3 ~~Cd~C~~a~---A~vyC~aD~-A~LC~~CD~~ 31 (210)
+.||.|+..| ..+.|..+. --||..|=..
T Consensus 1 V~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 1 VTCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 4799999643 778999985 6699999643
No 41
>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=27.83 E-value=22 Score=21.12 Aligned_cols=26 Identities=27% Similarity=0.494 Sum_probs=17.2
Q ss_pred cccccCCCCceEEccCCCcccchhhhhhhhh
Q 028326 4 QCNVCEAAEAKVLCCADEAALCWECDDKVHA 34 (210)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~ 34 (210)
.|++|++.....+ .+-|..|+..+|.
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 5899987554443 5667777766664
No 42
>PLN02436 cellulose synthase A
Probab=27.81 E-value=43 Score=35.77 Aligned_cols=29 Identities=28% Similarity=0.613 Sum_probs=24.3
Q ss_pred CCCCCcccCcc-------ceEEecCccccccccccc
Q 028326 54 MPKCDICQETS-------GFFFCLQDRALLCRKCDV 82 (210)
Q Consensus 54 ~~~Cd~C~~~~-------A~~fC~~D~a~LC~~Cd~ 82 (210)
...|.+|.+.. .++-|.+|.-++|+.|-.
T Consensus 36 ~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye 71 (1094)
T PLN02436 36 GQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE 71 (1094)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhh
Confidence 45899998774 667799999999999975
No 43
>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=27.24 E-value=80 Score=20.82 Aligned_cols=32 Identities=28% Similarity=0.434 Sum_probs=21.9
Q ss_pred CCCcccCccce---EEecCcc-ccccccccccccCC
Q 028326 56 KCDICQETSGF---FFCLQDR-ALLCRKCDVAIHTA 87 (210)
Q Consensus 56 ~Cd~C~~~~A~---~fC~~D~-a~LC~~Cd~~~H~a 87 (210)
.|+.|...+.. +.|..|. .-||..|-......
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~~~ 37 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGVTT 37 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCCcC
Confidence 48888754443 6687774 58999998766543
No 44
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.50 E-value=43 Score=36.44 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=11.8
Q ss_pred cccccCCCCceEEccCCCccc
Q 028326 4 QCNVCEAAEAKVLCCADEAAL 24 (210)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~L 24 (210)
.|..|+...-..+|..|.+.+
T Consensus 669 kCPkCG~~t~~~fCP~CGs~t 689 (1337)
T PRK14714 669 RCPSCGTETYENRCPDCGTHT 689 (1337)
T ss_pred ECCCCCCccccccCcccCCcC
Confidence 577777644444555555443
No 45
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=26.07 E-value=29 Score=24.02 Aligned_cols=30 Identities=27% Similarity=0.506 Sum_probs=20.8
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhhhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDKVHA 34 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vH~ 34 (210)
++.+|.+|++.- =..|+...|..|.+..|+
T Consensus 4 ~~~~C~~Cg~~~----~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 4 EGCKCPVCGKKF----KDGDDIVVCPECGAPYHR 33 (54)
T ss_pred cCccChhhCCcc----cCCCCEEECCCCCCcccH
Confidence 456899999632 235677777778777776
No 46
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.95 E-value=34 Score=34.47 Aligned_cols=19 Identities=21% Similarity=0.552 Sum_probs=13.8
Q ss_pred ceEEccCCC-cccchhhhhh
Q 028326 13 AKVLCCADE-AALCWECDDK 31 (210)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~ 31 (210)
..++|..|. ..-|..||..
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~ 401 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGP 401 (665)
T ss_pred CeeEhhhCcCeeECCCCCCc
Confidence 467888885 5669999843
No 47
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=25.37 E-value=40 Score=33.19 Aligned_cols=65 Identities=22% Similarity=0.437 Sum_probs=39.8
Q ss_pred cccchhhhhhhhhccccccC-cccccCCCCC--CCCCCCCcccCccceEEe--cCcc-------ccccccccccccCC
Q 028326 22 AALCWECDDKVHAANKLASK-HQRVPLSSSS--TQMPKCDICQETSGFFFC--LQDR-------ALLCRKCDVAIHTA 87 (210)
Q Consensus 22 A~LC~~CD~~vH~aN~la~r-H~RvpL~~~~--~~~~~Cd~C~~~~A~~fC--~~D~-------a~LC~~Cd~~~H~a 87 (210)
.+||.+|...+|+.-+.... +.-.|+.+.+ -+...|... ++.|.+.| .+|. +.+|..|....|+.
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 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNN 303 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhccc
Confidence 47999999999986544322 3333443322 123344443 45666766 3343 57999999998854
No 48
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=25.18 E-value=74 Score=20.51 Aligned_cols=28 Identities=21% Similarity=0.674 Sum_probs=21.8
Q ss_pred ccccccCC--CCceEEccCC-Ccccchhhhh
Q 028326 3 IQCNVCEA--AEAKVLCCAD-EAALCWECDD 30 (210)
Q Consensus 3 ~~Cd~C~~--a~A~vyC~aD-~A~LC~~CD~ 30 (210)
+.|+.|+. ....+.|..+ +--||..|=.
T Consensus 1 v~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~ 31 (43)
T cd02340 1 VICDGCQGPIVGVRYKCLVCPDYDLCESCEA 31 (43)
T ss_pred CCCCCCCCcCcCCeEECCCCCCccchHHhhC
Confidence 46899986 3478889998 5779999943
No 49
>PLN02400 cellulose synthase
Probab=24.50 E-value=54 Score=35.09 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=23.9
Q ss_pred CCCCCcccCc-------cceEEecCccccccccccc
Q 028326 54 MPKCDICQET-------SGFFFCLQDRALLCRKCDV 82 (210)
Q Consensus 54 ~~~Cd~C~~~-------~A~~fC~~D~a~LC~~Cd~ 82 (210)
...|.+|.+. ..++-|.+|.-++|+.|-.
T Consensus 36 gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE 71 (1085)
T PLN02400 36 GQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE 71 (1085)
T ss_pred CceeeecccccCcCCCCCEEEEEccCCCccccchhh
Confidence 4589999776 3567799999999999975
No 50
>PLN02189 cellulose synthase
Probab=24.40 E-value=55 Score=34.88 Aligned_cols=29 Identities=28% Similarity=0.576 Sum_probs=23.6
Q ss_pred CCCCCcccCcc-------ceEEecCccccccccccc
Q 028326 54 MPKCDICQETS-------GFFFCLQDRALLCRKCDV 82 (210)
Q Consensus 54 ~~~Cd~C~~~~-------A~~fC~~D~a~LC~~Cd~ 82 (210)
...|.+|.+.. .++-|.+|.-++|+.|-.
T Consensus 34 ~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye 69 (1040)
T PLN02189 34 GQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE 69 (1040)
T ss_pred CccccccccccCcCCCCCEEEeeccCCCccccchhh
Confidence 34799997763 467799999999999975
No 51
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.35 E-value=58 Score=33.36 Aligned_cols=44 Identities=23% Similarity=0.503 Sum_probs=0.0
Q ss_pred ccccccCCCCceEEccCCCccc----------chhhhhhhhhccccccCcccccCCCCCCCCCCCCcccCccceEE
Q 028326 3 IQCNVCEAAEAKVLCCADEAAL----------CWECDDKVHAANKLASKHQRVPLSSSSTQMPKCDICQETSGFFF 68 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~L----------C~~CD~~vH~aN~la~rH~RvpL~~~~~~~~~Cd~C~~~~A~~f 68 (210)
..|..|+. ++-|..|+..| |..|+ +++++|.. |+.|.+....++
T Consensus 436 l~C~~Cg~---v~~Cp~Cd~~lt~H~~~~~L~CH~Cg-----------~~~~~p~~--------Cp~Cgs~~L~~~ 489 (730)
T COG1198 436 LLCRDCGY---IAECPNCDSPLTLHKATGQLRCHYCG-----------YQEPIPQS--------CPECGSEHLRAV 489 (730)
T ss_pred eecccCCC---cccCCCCCcceEEecCCCeeEeCCCC-----------CCCCCCCC--------CCCCCCCeeEEe
No 52
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.62 E-value=34 Score=24.11 Aligned_cols=7 Identities=29% Similarity=0.980 Sum_probs=3.7
Q ss_pred ccccccC
Q 028326 3 IQCNVCE 9 (210)
Q Consensus 3 ~~Cd~C~ 9 (210)
+.|..|+
T Consensus 8 ~~CtSCg 14 (59)
T PRK14890 8 PKCTSCG 14 (59)
T ss_pred ccccCCC
Confidence 3455555
No 53
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=23.24 E-value=42 Score=24.44 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=10.0
Q ss_pred ccccccCCCCceEEccCCCcccchhhhh
Q 028326 3 IQCNVCEAAEAKVLCCADEAALCWECDD 30 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~ 30 (210)
..|..|...-.. ....+.|..|+.
T Consensus 2 ~~CP~C~~~L~~----~~~~~~C~~C~~ 25 (70)
T PF07191_consen 2 NTCPKCQQELEW----QGGHYHCEACQK 25 (70)
T ss_dssp -B-SSS-SBEEE----ETTEEEETTT--
T ss_pred CcCCCCCCccEE----eCCEEECccccc
Confidence 356666643221 125666777765
No 54
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.73 E-value=54 Score=29.18 Aligned_cols=65 Identities=23% Similarity=0.413 Sum_probs=28.7
Q ss_pred CccccccCCCCceEEccCCC-----cccchhhhhhhhhccccccCcccccCCCCCCCCCCCCcccCccceEEe-------
Q 028326 2 RIQCNVCEAAEAKVLCCADE-----AALCWECDDKVHAANKLASKHQRVPLSSSSTQMPKCDICQETSGFFFC------- 69 (210)
Q Consensus 2 k~~Cd~C~~a~A~vyC~aD~-----A~LC~~CD~~vH~aN~la~rH~RvpL~~~~~~~~~Cd~C~~~~A~~fC------- 69 (210)
+..|-+|+..|..-+=...+ -..|.-|...=| +.|+ +|+.|.+....-+-
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~--------~~R~----------~Cp~Cg~~~~~~l~~~~~e~~ 233 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR--------FVRI----------KCPYCGNTDHEKLEYFTVEGE 233 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE----------TT----------S-TTT---SS-EEE-------
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee--------ecCC----------CCcCCCCCCCcceeeEecCCC
Confidence 35799999877555555542 234889975443 2333 29999776555222
Q ss_pred cCccccccccccccc
Q 028326 70 LQDRALLCRKCDVAI 84 (210)
Q Consensus 70 ~~D~a~LC~~Cd~~~ 84 (210)
..-++-+|..|.--+
T Consensus 234 ~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 234 PAYRVEVCESCGSYL 248 (290)
T ss_dssp -SEEEEEETTTTEEE
T ss_pred CcEEEEECCcccchH
Confidence 124567888886543
No 55
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=22.61 E-value=85 Score=20.55 Aligned_cols=28 Identities=25% Similarity=0.616 Sum_probs=22.4
Q ss_pred ccccccCCC---CceEEccCC-Ccccchhhhh
Q 028326 3 IQCNVCEAA---EAKVLCCAD-EAALCWECDD 30 (210)
Q Consensus 3 ~~Cd~C~~a---~A~vyC~aD-~A~LC~~CD~ 30 (210)
+.|+.|++. ...+.|..+ +--||..|-.
T Consensus 1 i~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~ 32 (45)
T cd02339 1 IICDTCRKQGIIGIRWKCAECPNYDLCTTCYH 32 (45)
T ss_pred CCCCCCCCCCcccCeEECCCCCCccchHHHhC
Confidence 479999953 578899998 5779999964
No 56
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=22.35 E-value=66 Score=30.45 Aligned_cols=42 Identities=24% Similarity=0.351 Sum_probs=32.2
Q ss_pred ccccccCCCCceEEccCC-CcccchhhhhhhhhccccccCcccccC
Q 028326 3 IQCNVCEAAEAKVLCCAD-EAALCWECDDKVHAANKLASKHQRVPL 47 (210)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD-~A~LC~~CD~~vH~aN~la~rH~RvpL 47 (210)
+.|+-|+...= -....| .++.|.+|++-|- .++.++|.-|-|
T Consensus 275 PvCd~CGn~rL-e~~pe~rg~~~C~~Cs~~V~--sP~~r~~LeVfl 317 (389)
T PF14951_consen 275 PVCDRCGNGRL-EQSPEDRGAFSCGDCSRVVT--SPVLRMHLEVFL 317 (389)
T ss_pred ccccccCCccc-eeCccCCCceeccchhhhcc--CcceeeeEEEEE
Confidence 57999995443 344445 5788999998887 478999999988
No 57
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=22.21 E-value=1e+02 Score=19.71 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=22.6
Q ss_pred CCccccccCC--CCceEEccCC-Ccccchhhhh
Q 028326 1 MRIQCNVCEA--AEAKVLCCAD-EAALCWECDD 30 (210)
Q Consensus 1 Mk~~Cd~C~~--a~A~vyC~aD-~A~LC~~CD~ 30 (210)
+.+.|+.|+. ....+.|..+ +--||..|=.
T Consensus 3 ~~~~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~ 35 (44)
T smart00291 3 HSYSCDTCGKPIVGVRYHCLVCPDYDLCQSCFA 35 (44)
T ss_pred CCcCCCCCCCCCcCCEEECCCCCCccchHHHHh
Confidence 3578999996 3467788877 5779999954
No 58
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.14 E-value=54 Score=35.70 Aligned_cols=31 Identities=16% Similarity=0.394 Sum_probs=19.7
Q ss_pred CCCCcccCccceEEecCccccc-----ccccccccc
Q 028326 55 PKCDICQETSGFFFCLQDRALL-----CRKCDVAIH 85 (210)
Q Consensus 55 ~~Cd~C~~~~A~~fC~~D~a~L-----C~~Cd~~~H 85 (210)
-+|+.|....-..||..|...+ |..|.....
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~ 703 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVP 703 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCCceeCccCCCccC
Confidence 3577777665556777776554 777766543
No 59
>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=21.27 E-value=25 Score=24.37 Aligned_cols=29 Identities=24% Similarity=0.526 Sum_probs=17.1
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDD 30 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~ 30 (210)
|++.|.-|+. .-+||=.+-...+|..|..
T Consensus 6 m~VkCp~C~~-~q~vFSha~t~V~C~~Cg~ 34 (55)
T PF01667_consen 6 MDVKCPGCYN-IQTVFSHAQTVVKCVVCGT 34 (55)
T ss_dssp EEEE-TTT-S-EEEEETT-SS-EE-SSSTS
T ss_pred EEEECCCCCC-eeEEEecCCeEEEcccCCC
Confidence 6788999984 5666777777777777763
No 60
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=20.37 E-value=50 Score=30.83 Aligned_cols=33 Identities=24% Similarity=0.572 Sum_probs=27.2
Q ss_pred CCCCCCCCCcccCccceEEecCccccccc-cccc
Q 028326 50 SSTQMPKCDICQETSGFFFCLQDRALLCR-KCDV 82 (210)
Q Consensus 50 ~~~~~~~Cd~C~~~~A~~fC~~D~a~LC~-~Cd~ 82 (210)
+...+..|.+|..++..+.|.-|+.+.|. .|..
T Consensus 3 pts~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr 36 (383)
T KOG4317|consen 3 PTSSFLACGICGVQKREYTCPRCNLLYCSLKCYR 36 (383)
T ss_pred CCCceeeccccccccccccCCCCCccceeeeeec
Confidence 34567789999999999999999999885 5554
No 61
>PLN00209 ribosomal protein S27; Provisional
Probab=20.04 E-value=38 Score=25.63 Aligned_cols=30 Identities=20% Similarity=0.548 Sum_probs=23.9
Q ss_pred CCccccccCCCCceEEccCCCcccchhhhhh
Q 028326 1 MRIQCNVCEAAEAKVLCCADEAALCWECDDK 31 (210)
Q Consensus 1 Mk~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~ 31 (210)
|++.|.-|+. .-+||=.+-...+|..|...
T Consensus 35 m~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCFN-ITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEEECCCCCC-eeEEEecCceEEEccccCCE
Confidence 7788999994 67788888888888888743
Done!