Query 028487
Match_columns 208
No_of_seqs 193 out of 567
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 12:16:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028487.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028487hhsearch_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 2.3E-05 4.9E-10 49.1 2.8 38 55-96 2-39 (39)
2 PF00643 zf-B_box: B-box zinc 97.6 4.2E-05 9E-10 49.2 2.8 40 53-96 3-42 (42)
3 cd00021 BBOX B-Box-type zinc f 97.6 3.9E-05 8.4E-10 48.0 2.2 39 3-47 1-39 (39)
4 smart00336 BBOX B-Box-type zin 97.3 0.00024 5.2E-09 45.0 3.1 39 54-96 4-42 (42)
5 KOG4367 Predicted Zn-finger pr 97.3 8.3E-05 1.8E-09 70.8 1.1 83 4-86 164-257 (699)
6 PF00643 zf-B_box: B-box zinc 97.2 0.00032 7E-09 45.0 2.5 40 2-47 3-42 (42)
7 smart00336 BBOX B-Box-type zin 97.0 0.00049 1.1E-08 43.5 2.4 39 3-47 4-42 (42)
8 KOG2807 RNA polymerase II tran 74.8 1.7 3.8E-05 40.5 1.7 75 11-85 273-365 (378)
9 TIGR00622 ssl1 transcription f 70.9 4.3 9.3E-05 32.2 2.8 61 25-85 18-101 (112)
10 PF04438 zf-HIT: HIT zinc fing 61.7 3.9 8.5E-05 24.9 0.8 25 1-26 1-25 (30)
11 PF07975 C1_4: TFIIH C1-like d 60.6 3.9 8.5E-05 28.1 0.7 23 63-85 19-41 (51)
12 PF13248 zf-ribbon_3: zinc-rib 59.3 4.9 0.00011 23.4 0.9 25 1-31 1-25 (26)
13 KOG4367 Predicted Zn-finger pr 56.8 2.4 5.1E-05 41.2 -1.2 51 51-101 160-214 (699)
14 PF12773 DZR: Double zinc ribb 55.0 15 0.00032 23.9 2.7 39 19-71 9-49 (50)
15 PF07975 C1_4: TFIIH C1-like d 53.6 7.7 0.00017 26.6 1.2 23 13-35 20-42 (51)
16 KOG0129 Predicted RNA-binding 53.4 4.9 0.00011 39.4 0.3 43 3-48 456-505 (520)
17 PRK14559 putative protein seri 53.0 8.6 0.00019 38.7 1.9 23 3-31 2-24 (645)
18 cd02335 ZZ_ADA2 Zinc finger, Z 52.2 19 0.00042 23.8 3.0 30 55-84 2-35 (49)
19 KOG0129 Predicted RNA-binding 51.7 5.1 0.00011 39.2 0.1 49 42-90 443-499 (520)
20 PF10235 Cript: Microtubule-as 49.7 12 0.00025 28.7 1.8 48 34-83 27-79 (90)
21 COG5151 SSL1 RNA polymerase II 49.0 5.2 0.00011 37.4 -0.3 79 7-85 299-408 (421)
22 cd02342 ZZ_UBA_plant Zinc fing 41.9 20 0.00044 23.9 1.8 30 3-32 1-34 (43)
23 PF13842 Tnp_zf-ribbon_2: DDE_ 41.8 23 0.00049 21.8 1.9 23 56-78 3-29 (32)
24 KOG1280 Uncharacterized conser 40.7 12 0.00026 35.3 0.7 37 38-83 2-42 (381)
25 KOG1428 Inhibitor of type V ad 39.9 9.5 0.00021 42.5 -0.0 45 51-96 3320-3367(3738)
26 cd02341 ZZ_ZZZ3 Zinc finger, Z 38.5 38 0.00082 22.7 2.7 28 55-82 2-35 (48)
27 cd02249 ZZ Zinc finger, ZZ typ 34.3 56 0.0012 21.2 3.0 30 55-84 2-34 (46)
28 KOG4582 Uncharacterized conser 32.9 31 0.00066 31.1 2.1 30 3-32 153-186 (278)
29 KOG1428 Inhibitor of type V ad 32.9 15 0.00033 41.1 0.1 47 3-51 3323-3371(3738)
30 cd02334 ZZ_dystrophin Zinc fin 31.9 50 0.0011 22.2 2.5 30 55-84 2-35 (49)
31 cd02339 ZZ_Mind_bomb Zinc fing 31.4 49 0.0011 21.9 2.4 28 55-82 2-33 (45)
32 cd02344 ZZ_HERC2 Zinc finger, 30.6 54 0.0012 21.8 2.5 28 55-82 2-33 (45)
33 cd02338 ZZ_PCMF_like Zinc fing 28.9 97 0.0021 20.5 3.5 30 55-84 2-35 (49)
34 PF04216 FdhE: Protein involve 28.1 49 0.0011 29.5 2.6 90 2-121 172-273 (290)
35 cd02340 ZZ_NBR1_like Zinc fing 27.5 45 0.00097 21.7 1.6 28 55-82 2-32 (43)
36 PRK14873 primosome assembly pr 26.2 40 0.00087 34.0 1.8 20 12-31 381-401 (665)
37 PF03107 C1_2: C1 domain; Int 26.2 36 0.00077 20.3 0.9 26 4-34 2-27 (30)
38 PF13920 zf-C3HC4_3: Zinc fing 24.3 58 0.0013 21.1 1.8 32 3-34 3-35 (50)
39 KOG4317 Predicted Zn-finger pr 24.0 44 0.00096 31.3 1.5 33 50-82 4-37 (383)
40 PRK14714 DNA polymerase II lar 23.9 55 0.0012 35.8 2.3 48 2-63 667-719 (1337)
41 PF08274 PhnA_Zn_Ribbon: PhnA 23.5 48 0.001 20.3 1.1 25 53-80 2-26 (30)
42 TIGR00622 ssl1 transcription f 22.0 49 0.0011 26.2 1.2 21 14-34 81-101 (112)
43 PF07649 C1_3: C1-like domain; 21.7 48 0.001 19.5 0.9 24 55-78 2-28 (30)
44 PF11781 RRN7: RNA polymerase 21.1 65 0.0014 20.3 1.4 24 4-30 10-33 (36)
45 PF15616 TerY-C: TerY-C metal 20.6 79 0.0017 25.7 2.2 26 52-78 76-101 (131)
46 PF14776 UNC-79: Cation-channe 20.2 82 0.0018 31.2 2.6 66 22-88 227-305 (525)
47 TIGR02098 MJ0042_CXXC MJ0042 f 20.2 75 0.0016 19.4 1.6 10 1-10 1-10 (38)
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=97.77 E-value=2.3e-05 Score=49.11 Aligned_cols=38 Identities=39% Similarity=0.834 Sum_probs=33.2
Q ss_pred CCCCCCCCCeeEEecCCCccccccccccccCCCCCCccceEe
Q 028487 55 RCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 96 (208)
Q Consensus 55 lCd~C~~~pA~~yC~~d~a~LC~~CD~~~Hsan~~~H~R~~l 96 (208)
+|+.|+.+++.+||..|...+|..|+...| +.|.++||
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 699999889999999999999999998866 47877764
No 2
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=97.65 E-value=4.2e-05 Score=49.16 Aligned_cols=40 Identities=28% Similarity=0.622 Sum_probs=33.8
Q ss_pred CCCCCCCCCCCeeEEecCCCccccccccccccCCCCCCccceEe
Q 028487 53 VPRCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 96 (208)
Q Consensus 53 ~plCd~C~~~pA~~yC~~d~a~LC~~CD~~~Hsan~~~H~R~~l 96 (208)
...|+.|+..++.+||..|..++|..|....|.+ |..++|
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 4689999998899999999999999999998844 777654
No 3
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.61 E-value=3.9e-05 Score=48.05 Aligned_cols=39 Identities=46% Similarity=0.785 Sum_probs=33.7
Q ss_pred CcccccCCCceeEEecccccccchhhccccccCcccccccccccc
Q 028487 3 TLCDVCESAAAILFCAADEAALCRSCDEKVHMCNKLASRHVRVGL 47 (208)
Q Consensus 3 ~~Cd~C~~~~A~vyC~~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl 47 (208)
..|+.++++++.+||.+|.+.+|..|+...|. .|.++||
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 36889988899999999999999999987775 5888774
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.31 E-value=0.00024 Score=45.00 Aligned_cols=39 Identities=46% Similarity=0.883 Sum_probs=33.3
Q ss_pred CCCCCCCCCCeeEEecCCCccccccccccccCCCCCCccceEe
Q 028487 54 PRCDICENAPAFFYCEIDGSSLCLQCDMTVHVGGKRTHGRYLL 96 (208)
Q Consensus 54 plCd~C~~~pA~~yC~~d~a~LC~~CD~~~Hsan~~~H~R~~l 96 (208)
..|+.|+..++.+||..|...+|..|....| +.|.+++|
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 4799999899999999999999999998766 56766553
No 5
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=97.29 E-value=8.3e-05 Score=70.79 Aligned_cols=83 Identities=27% Similarity=0.490 Sum_probs=72.4
Q ss_pred cccccCCCc--eeEEecccccccchhhccccccCccccccccccccCC--------CCCCCCCCCCCCCCeeEEecCCCc
Q 028487 4 LCDVCESAA--AILFCAADEAALCRSCDEKVHMCNKLASRHVRVGLAN--------PSDVPRCDICENAPAFFYCEIDGS 73 (208)
Q Consensus 4 ~Cd~C~~~~--A~vyC~~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl~~--------~~~~plCd~C~~~pA~~yC~~d~a 73 (208)
.|..|++++ |.|+|..|..++|.-|..+.|-+...+.+|.-+|-++ +..+-.|.-|+.+.-..||..|.+
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck~ 243 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCKM 243 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecCC
Confidence 589999965 9999999999999999999999888899998777554 247788999999999999999999
Q ss_pred ccccccccc-ccCC
Q 028487 74 SLCLQCDMT-VHVG 86 (208)
Q Consensus 74 ~LC~~CD~~-~Hsa 86 (208)
++|..|... .|+.
T Consensus 244 pvc~~clee~khs~ 257 (699)
T KOG4367|consen 244 PVCYQCLEEGKHSS 257 (699)
T ss_pred hHHHHHHHhhcccc
Confidence 999999887 4543
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=97.16 E-value=0.00032 Score=44.97 Aligned_cols=40 Identities=25% Similarity=0.453 Sum_probs=33.9
Q ss_pred CCcccccCCCceeEEecccccccchhhccccccCcccccccccccc
Q 028487 2 RTLCDVCESAAAILFCAADEAALCRSCDEKVHMCNKLASRHVRVGL 47 (208)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl 47 (208)
...|+.+.+.++.+||..|...+|..|....|.. |..++|
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 777664
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.03 E-value=0.00049 Score=43.52 Aligned_cols=39 Identities=41% Similarity=0.686 Sum_probs=33.0
Q ss_pred CcccccCCCceeEEecccccccchhhccccccCcccccccccccc
Q 028487 3 TLCDVCESAAAILFCAADEAALCRSCDEKVHMCNKLASRHVRVGL 47 (208)
Q Consensus 3 ~~Cd~C~~~~A~vyC~~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl 47 (208)
..|..+.+.++.+||..|.+.+|..|....| +.|.+++|
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 5789999889999999999999999997766 45777654
No 8
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=74.82 E-value=1.7 Score=40.49 Aligned_cols=75 Identities=24% Similarity=0.469 Sum_probs=54.0
Q ss_pred CceeEEecccccccc------hhhccccccCccccc-cccccccCC--------CCCCCCCCCCCCC---CeeEEecCCC
Q 028487 11 AAAILFCAADEAALC------RSCDEKVHMCNKLAS-RHVRVGLAN--------PSDVPRCDICENA---PAFFYCEIDG 72 (208)
Q Consensus 11 ~~A~vyC~~D~A~LC------~~CD~~vH~aN~l~~-rH~Rvpl~~--------~~~~plCd~C~~~---pA~~yC~~d~ 72 (208)
.-+.++|..|.|..| .-|+..+=++.-|++ -|.-.||.. ......|-.|... .-.|.|..|.
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 458899999999875 467777666555554 455566653 1234458889543 3679999999
Q ss_pred ccccccccccccC
Q 028487 73 SSLCLQCDMTVHV 85 (208)
Q Consensus 73 a~LC~~CD~~~Hs 85 (208)
..+|.+||.-+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999999884
No 9
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=70.87 E-value=4.3 Score=32.22 Aligned_cols=61 Identities=23% Similarity=0.484 Sum_probs=40.7
Q ss_pred chhhccccccCccccc-cccccccCC--------CCCCCCCCCCCCC--------------CeeEEecCCCccccccccc
Q 028487 25 CRSCDEKVHMCNKLAS-RHVRVGLAN--------PSDVPRCDICENA--------------PAFFYCEIDGSSLCLQCDM 81 (208)
Q Consensus 25 C~~CD~~vH~aN~l~~-rH~Rvpl~~--------~~~~plCd~C~~~--------------pA~~yC~~d~a~LC~~CD~ 81 (208)
|..|+..+=++.-|+| =|--+||.. ......|-.|... ...+.|..|....|.+||+
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 5677776655555554 355455542 2222358888763 2357899999999999999
Q ss_pred cccC
Q 028487 82 TVHV 85 (208)
Q Consensus 82 ~~Hs 85 (208)
-+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 9885
No 10
>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=61.72 E-value=3.9 Score=24.93 Aligned_cols=25 Identities=36% Similarity=0.681 Sum_probs=18.2
Q ss_pred CCCcccccCCCceeEEecccccccch
Q 028487 1 MRTLCDVCESAAAILFCAADEAALCR 26 (208)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~~D~A~LC~ 26 (208)
++.+|.+|+. .|...|..+.+.+|.
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 3568999999 999999999999886
No 11
>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=60.58 E-value=3.9 Score=28.08 Aligned_cols=23 Identities=22% Similarity=0.680 Sum_probs=15.4
Q ss_pred CeeEEecCCCccccccccccccC
Q 028487 63 PAFFYCEIDGSSLCLQCDMTVHV 85 (208)
Q Consensus 63 pA~~yC~~d~a~LC~~CD~~~Hs 85 (208)
...+.|..|....|.+||+-+|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTT
T ss_pred CCeEECCCCCCccccCcChhhhc
Confidence 46789999999999999999884
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.34 E-value=4.9 Score=23.42 Aligned_cols=25 Identities=28% Similarity=0.769 Sum_probs=17.5
Q ss_pred CCCcccccCCCceeEEecccccccchhhccc
Q 028487 1 MRTLCDVCESAAAILFCAADEAALCRSCDEK 31 (208)
Q Consensus 1 m~~~Cd~C~~~~A~vyC~~D~A~LC~~CD~~ 31 (208)
|...|-.|+... .+++.+|..|..+
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 778899998731 4567777777654
No 13
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=56.82 E-value=2.4 Score=41.23 Aligned_cols=51 Identities=27% Similarity=0.490 Sum_probs=39.3
Q ss_pred CCCCCCCCCCCCC--eeEEecCCCccccccccccccCCC-C-CCccceEecccee
Q 028487 51 SDVPRCDICENAP--AFFYCEIDGSSLCLQCDMTVHVGG-K-RTHGRYLLLRQRV 101 (208)
Q Consensus 51 ~~~plCd~C~~~p--A~~yC~~d~a~LC~~CD~~~Hsan-~-~~H~R~~l~~~~v 101 (208)
...-.|..|+.++ |.++|+.|.+..|.-|....|-+- + .+|..+|-...||
T Consensus 160 ~aa~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grv 214 (699)
T KOG4367|consen 160 AAALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRV 214 (699)
T ss_pred HHhhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCce
Confidence 3455788888776 899999999999999999988654 3 5777766554444
No 14
>PF12773 DZR: Double zinc ribbon
Probab=54.97 E-value=15 Score=23.94 Aligned_cols=39 Identities=18% Similarity=0.429 Sum_probs=21.8
Q ss_pred ccccccchhhccccccCccccccccccccCCCCCCCCCCCCCCCC--eeEEecCC
Q 028487 19 ADEAALCRSCDEKVHMCNKLASRHVRVGLANPSDVPRCDICENAP--AFFYCEID 71 (208)
Q Consensus 19 ~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl~~~~~~plCd~C~~~p--A~~yC~~d 71 (208)
.+.+.+|..|...+- ........|..|+... ...||..|
T Consensus 9 ~~~~~fC~~CG~~l~--------------~~~~~~~~C~~Cg~~~~~~~~fC~~C 49 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP--------------PPDQSKKICPNCGAENPPNAKFCPNC 49 (50)
T ss_pred CccccCChhhcCChh--------------hccCCCCCCcCCcCCCcCCcCccCcc
Confidence 456778888875554 1112334688887643 34455444
No 15
>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=53.57 E-value=7.7 Score=26.63 Aligned_cols=23 Identities=22% Similarity=0.479 Sum_probs=16.1
Q ss_pred eeEEecccccccchhhccccccC
Q 028487 13 AILFCAADEAALCRSCDEKVHMC 35 (208)
Q Consensus 13 A~vyC~~D~A~LC~~CD~~vH~a 35 (208)
..+.|..+...+|..||.-||..
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 67899999999999999999974
No 16
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=53.38 E-value=4.9 Score=39.37 Aligned_cols=43 Identities=33% Similarity=0.553 Sum_probs=34.4
Q ss_pred CcccccCC-----CceeEEecc--cccccchhhccccccCccccccccccccC
Q 028487 3 TLCDVCES-----AAAILFCAA--DEAALCRSCDEKVHMCNKLASRHVRVGLA 48 (208)
Q Consensus 3 ~~Cd~C~~-----~~A~vyC~~--D~A~LC~~CD~~vH~aN~l~~rH~Rvpl~ 48 (208)
..||.|++ ..|-+||++ |--++|..|=+.+|+. ..++.=.||.
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 57999999 889999987 7899999999999986 3344444544
No 17
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.99 E-value=8.6 Score=38.69 Aligned_cols=23 Identities=17% Similarity=0.726 Sum_probs=13.8
Q ss_pred CcccccCCCceeEEecccccccchhhccc
Q 028487 3 TLCDVCESAAAILFCAADEAALCRSCDEK 31 (208)
Q Consensus 3 ~~Cd~C~~~~A~vyC~~D~A~LC~~CD~~ 31 (208)
..|-.|+.. ..+.+.+|..|...
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCC
Confidence 368889874 23455566666543
No 18
>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=52.19 E-value=19 Score=23.82 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=24.4
Q ss_pred CCCCCCCCCee---EEecCC-Ccccccccccccc
Q 028487 55 RCDICENAPAF---FYCEID-GSSLCLQCDMTVH 84 (208)
Q Consensus 55 lCd~C~~~pA~---~yC~~d-~a~LC~~CD~~~H 84 (208)
.|+.|...+.. +.|..| .--||..|-..-.
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 58999877644 889999 8899999998743
No 19
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=51.70 E-value=5.1 Score=39.21 Aligned_cols=49 Identities=27% Similarity=0.437 Sum_probs=41.1
Q ss_pred ccccccCCC-CCCCCCCCCCC-----CCeeEEec--CCCccccccccccccCCCCCC
Q 028487 42 HVRVGLANP-SDVPRCDICEN-----APAFFYCE--IDGSSLCLQCDMTVHVGGKRT 90 (208)
Q Consensus 42 H~Rvpl~~~-~~~plCd~C~~-----~pA~~yC~--~d~a~LC~~CD~~~Hsan~~~ 90 (208)
++||-|..- .+-.+|++|+. ..|-|||. +|---.|..|-..+|+.-.+.
T Consensus 443 ~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~~r~ 499 (520)
T KOG0129|consen 443 DKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGPGRE 499 (520)
T ss_pred ceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCCchh
Confidence 568888744 48899999998 77999996 588899999999999887654
No 20
>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=49.69 E-value=12 Score=28.69 Aligned_cols=48 Identities=25% Similarity=0.481 Sum_probs=35.8
Q ss_pred cCccccccccccccCCCCCCCCCCCCCCCCee---EEecCC--Cccccccccccc
Q 028487 34 MCNKLASRHVRVGLANPSDVPRCDICENAPAF---FYCEID--GSSLCLQCDMTV 83 (208)
Q Consensus 34 ~aN~l~~rH~Rvpl~~~~~~plCd~C~~~pA~---~yC~~d--~a~LC~~CD~~~ 83 (208)
.-|+|++.-.+-|+.. .+..|.+|+..... .||..| ..-+|.-|-..+
T Consensus 27 ~eNKlLs~~~~nPy~~--~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 27 GENKLLSKKKKNPYAP--YSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred cceeeecccccCcccc--cCccccccccccccCCCccChhhhcccCcccccCCee
Confidence 4588888777766542 36689999977544 899999 567999998764
No 21
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=49.01 E-value=5.2 Score=37.37 Aligned_cols=79 Identities=24% Similarity=0.525 Sum_probs=53.6
Q ss_pred ccCC--CceeEEecccccccc------hhhccccccCcccc-ccccccccCCC--------CCCCCCCCCCCC-------
Q 028487 7 VCES--AAAILFCAADEAALC------RSCDEKVHMCNKLA-SRHVRVGLANP--------SDVPRCDICENA------- 62 (208)
Q Consensus 7 ~C~~--~~A~vyC~~D~A~LC------~~CD~~vH~aN~l~-~rH~Rvpl~~~--------~~~plCd~C~~~------- 62 (208)
+|.. .-+.++|..|.+..| .-|+..+=...-|+ +-|.-.||..- ....-|-.|+..
T Consensus 299 aCHs~~~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~ 378 (421)
T COG5151 299 ACHSEVKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVS 378 (421)
T ss_pred eeeeeeccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCC
Confidence 5555 447899999988765 56776543333333 34666666531 234457778762
Q ss_pred -------CeeEEecCCCccccccccccccC
Q 028487 63 -------PAFFYCEIDGSSLCLQCDMTVHV 85 (208)
Q Consensus 63 -------pA~~yC~~d~a~LC~~CD~~~Hs 85 (208)
...|.|+.|...+|.+||.-+|.
T Consensus 379 ~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 379 PFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cccccccccceechhhhhhhhhhhHHHHHH
Confidence 35789999999999999998884
No 22
>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=41.92 E-value=20 Score=23.86 Aligned_cols=30 Identities=23% Similarity=0.451 Sum_probs=22.7
Q ss_pred CcccccCCCc---eeEEecccccc-cchhhcccc
Q 028487 3 TLCDVCESAA---AILFCAADEAA-LCRSCDEKV 32 (208)
Q Consensus 3 ~~Cd~C~~~~---A~vyC~~D~A~-LC~~CD~~v 32 (208)
+.||.|+..| ..+.|..+.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 3699999855 67888887665 999996554
No 23
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=41.79 E-value=23 Score=21.78 Aligned_cols=23 Identities=22% Similarity=0.778 Sum_probs=17.0
Q ss_pred CCCCCCC----CeeEEecCCCcccccc
Q 028487 56 CDICENA----PAFFYCEIDGSSLCLQ 78 (208)
Q Consensus 56 Cd~C~~~----pA~~yC~~d~a~LC~~ 78 (208)
|.+|... ...|+|..|.+.||..
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CeECCcCCccceeEEEccCCCCcccCC
Confidence 5555543 2789999999999975
No 24
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=40.68 E-value=12 Score=35.28 Aligned_cols=37 Identities=32% Similarity=0.476 Sum_probs=29.8
Q ss_pred ccccccccccCCCCCCCCCCCCCCCCeeEEecCC----Cccccccccccc
Q 028487 38 LASRHVRVGLANPSDVPRCDICENAPAFFYCEID----GSSLCLQCDMTV 83 (208)
Q Consensus 38 l~~rH~Rvpl~~~~~~plCd~C~~~pA~~yC~~d----~a~LC~~CD~~~ 83 (208)
++++|++| .||-|....-.++|..| .--||.+|...-
T Consensus 2 ~~~rHe~v---------~CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~ 42 (381)
T KOG1280|consen 2 LTSRHEGV---------SCDGCGKTAFTFRRYKCLRCSDYDLCFSCYENG 42 (381)
T ss_pred CCCCcCCc---------eeccccccceeeeeeEeeeecchhHHHHHhhcC
Confidence 57899999 49999998887777666 557999998763
No 25
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=39.89 E-value=9.5 Score=42.46 Aligned_cols=45 Identities=31% Similarity=0.777 Sum_probs=36.0
Q ss_pred CCCCCCCCCCC--CCeeEEecCCCccccccccccccCCCC-CCccceEe
Q 028487 51 SDVPRCDICEN--APAFFYCEIDGSSLCLQCDMTVHVGGK-RTHGRYLL 96 (208)
Q Consensus 51 ~~~plCd~C~~--~pA~~yC~~d~a~LC~~CD~~~Hsan~-~~H~R~~l 96 (208)
.+.|+||.|.. ..|.++|..|. .||.+||.-.|-.-. +.|+|.-+
T Consensus 3320 kQ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHrrtktH~~q~f 3367 (3738)
T KOG1428|consen 3320 KQMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHRRTKTHQRQVF 3367 (3738)
T ss_pred hcCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHhhccchhhhhh
Confidence 47889999975 35899999999 999999998665443 78998543
No 26
>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=38.45 E-value=38 Score=22.73 Aligned_cols=28 Identities=29% Similarity=0.733 Sum_probs=22.4
Q ss_pred CCCCCCCCC---eeEEecCCC---cccccccccc
Q 028487 55 RCDICENAP---AFFYCEIDG---SSLCLQCDMT 82 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d~---a~LC~~CD~~ 82 (208)
.|+.|+..| ..|.|..|. --||..|-..
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~ 35 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVK 35 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhC
Confidence 488888766 457888886 7899999886
No 27
>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=34.30 E-value=56 Score=21.15 Aligned_cols=30 Identities=23% Similarity=0.479 Sum_probs=23.1
Q ss_pred CCCCCCCCC--eeEEecCCC-cccccccccccc
Q 028487 55 RCDICENAP--AFFYCEIDG-SSLCLQCDMTVH 84 (208)
Q Consensus 55 lCd~C~~~p--A~~yC~~d~-a~LC~~CD~~~H 84 (208)
.|+.|+... ..|.|..|. -.||..|-...+
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 478887632 678898885 889999998755
No 28
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=32.93 E-value=31 Score=31.09 Aligned_cols=30 Identities=27% Similarity=0.585 Sum_probs=25.3
Q ss_pred CcccccCCCc---eeEEecccccc-cchhhcccc
Q 028487 3 TLCDVCESAA---AILFCAADEAA-LCRSCDEKV 32 (208)
Q Consensus 3 ~~Cd~C~~~~---A~vyC~~D~A~-LC~~CD~~v 32 (208)
..||.|..++ ..+-|..|..+ ||.+|.+..
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 5799999844 88999999655 999999985
No 29
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=32.91 E-value=15 Score=41.05 Aligned_cols=47 Identities=28% Similarity=0.593 Sum_probs=36.2
Q ss_pred CcccccCC--CceeEEecccccccchhhccccccCccccccccccccCCCC
Q 028487 3 TLCDVCES--AAAILFCAADEAALCRSCDEKVHMCNKLASRHVRVGLANPS 51 (208)
Q Consensus 3 ~~Cd~C~~--~~A~vyC~~D~A~LC~~CD~~vH~aN~l~~rH~Rvpl~~~~ 51 (208)
++||.-.. ..|+++|..|. +||..||.-+|-.- -.+.|+|--+.+..
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~eee 3371 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFKEEE 3371 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhhhhh
Confidence 46776654 67999999998 99999999877543 36789997776653
No 30
>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=31.91 E-value=50 Score=22.22 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=23.4
Q ss_pred CCCCCCCCC---eeEEecCC-Ccccccccccccc
Q 028487 55 RCDICENAP---AFFYCEID-GSSLCLQCDMTVH 84 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d-~a~LC~~CD~~~H 84 (208)
.|+.|+..+ ..+.|..| .--||..|-+.-.
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~ 35 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGR 35 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCC
Confidence 589998766 45778877 6789999998743
No 31
>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=31.42 E-value=49 Score=21.86 Aligned_cols=28 Identities=25% Similarity=0.556 Sum_probs=22.8
Q ss_pred CCCCCCCCC---eeEEecCC-Ccccccccccc
Q 028487 55 RCDICENAP---AFFYCEID-GSSLCLQCDMT 82 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d-~a~LC~~CD~~ 82 (208)
.|+.|+..+ ..+.|..| .--||..|-..
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 589998655 57889988 68899999874
No 32
>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=30.64 E-value=54 Score=21.80 Aligned_cols=28 Identities=32% Similarity=0.631 Sum_probs=22.8
Q ss_pred CCCCCCCCC---eeEEecCC-Ccccccccccc
Q 028487 55 RCDICENAP---AFFYCEID-GSSLCLQCDMT 82 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d-~a~LC~~CD~~ 82 (208)
.|+.|+..| ..|.|..| .--||..|-..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 589998776 45888888 47899999986
No 33
>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=28.94 E-value=97 Score=20.52 Aligned_cols=30 Identities=27% Similarity=0.531 Sum_probs=22.9
Q ss_pred CCCCCCCCC---eeEEecCC-Ccccccccccccc
Q 028487 55 RCDICENAP---AFFYCEID-GSSLCLQCDMTVH 84 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d-~a~LC~~CD~~~H 84 (208)
.|+.|+..+ ..|.|..| .-.||..|-....
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~~ 35 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSGV 35 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCCC
Confidence 588998655 34788887 6689999988743
No 34
>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=28.09 E-value=49 Score=29.45 Aligned_cols=90 Identities=22% Similarity=0.364 Sum_probs=42.7
Q ss_pred CCcccccCCCceeEEeccc-----ccccchhhccccccCccccccccccccCCCCCCCCCCCCCCCCeeEEe----cC--
Q 028487 2 RTLCDVCESAAAILFCAAD-----EAALCRSCDEKVHMCNKLASRHVRVGLANPSDVPRCDICENAPAFFYC----EI-- 70 (208)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~~D-----~A~LC~~CD~~vH~aN~l~~rH~Rvpl~~~~~~plCd~C~~~pA~~yC----~~-- 70 (208)
+..|-+|++.|..-+=... +-..|.-|+..-| ..|+ .|+.|+.....-+- ..
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~--------~~R~---------~Cp~Cg~~~~~~l~~~~~e~~~ 234 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWR--------FVRI---------KCPYCGNTDHEKLEYFTVEGEP 234 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE----------TT---------S-TTT---SS-EEE--------
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeee--------ecCC---------CCcCCCCCCCcceeeEecCCCC
Confidence 3579999998755555544 5678999985444 5566 59999976533221 11
Q ss_pred -CCccccccccccccCCCCCCccceEeccceecCCCCCcchhhHhhhhccCc
Q 028487 71 -DGSSLCLQCDMTVHVGGKRTHGRYLLLRQRVEFPGDKAGRLEELALQSLDQ 121 (208)
Q Consensus 71 -d~a~LC~~CD~~~Hsan~~~H~R~~l~~~~v~~~~~cP~~~e~~~~~~~d~ 121 (208)
-.+-+|..|...+-... +...+ . -....++..+.+||.
T Consensus 235 ~~rve~C~~C~~YlK~vd-~~~~~-----------~-~~~~~dDl~tl~LD~ 273 (290)
T PF04216_consen 235 AYRVEVCESCGSYLKTVD-REKDP-----------E-LDPVADDLATLHLDL 273 (290)
T ss_dssp SEEEEEETTTTEEEEEEE-TTT-T-----------T---HHHHHHTTHHHHH
T ss_pred cEEEEECCcccchHHHHh-hhhCc-----------c-cchhhHHhhhhhHHH
Confidence 26778999987643333 11111 1 112467777777764
No 35
>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=27.50 E-value=45 Score=21.68 Aligned_cols=28 Identities=25% Similarity=0.647 Sum_probs=22.3
Q ss_pred CCCCCCCCC--eeEEecCC-Ccccccccccc
Q 028487 55 RCDICENAP--AFFYCEID-GSSLCLQCDMT 82 (208)
Q Consensus 55 lCd~C~~~p--A~~yC~~d-~a~LC~~CD~~ 82 (208)
.|+.|+... ..|.|..| .--||..|-..
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 588888732 67889998 68999999876
No 36
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.22 E-value=40 Score=34.03 Aligned_cols=20 Identities=35% Similarity=0.624 Sum_probs=15.5
Q ss_pred ceeEEecccc-cccchhhccc
Q 028487 12 AAILFCAADE-AALCRSCDEK 31 (208)
Q Consensus 12 ~A~vyC~~D~-A~LC~~CD~~ 31 (208)
...++|..|+ ..-|..||..
T Consensus 381 ap~l~C~~Cg~~~~C~~C~~~ 401 (665)
T PRK14873 381 VPSLACARCRTPARCRHCTGP 401 (665)
T ss_pred CCeeEhhhCcCeeECCCCCCc
Confidence 3567899985 7889999854
No 37
>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=26.16 E-value=36 Score=20.29 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=16.8
Q ss_pred cccccCCCceeEEecccccccchhhcccccc
Q 028487 4 LCDVCESAAAILFCAADEAALCRSCDEKVHM 34 (208)
Q Consensus 4 ~Cd~C~~~~A~vyC~~D~A~LC~~CD~~vH~ 34 (208)
.|++|+.....++ .+-|..|+..+|.
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 5899988655443 5666666666663
No 38
>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=24.29 E-value=58 Score=21.07 Aligned_cols=32 Identities=16% Similarity=0.397 Sum_probs=23.9
Q ss_pred CcccccCCCceeEEecccccc-cchhhcccccc
Q 028487 3 TLCDVCESAAAILFCAADEAA-LCRSCDEKVHM 34 (208)
Q Consensus 3 ~~Cd~C~~~~A~vyC~~D~A~-LC~~CD~~vH~ 34 (208)
..|..|...++.+.-..++=. +|..|-.++..
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 468899998877777788766 99999765554
No 39
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=23.97 E-value=44 Score=31.32 Aligned_cols=33 Identities=21% Similarity=0.425 Sum_probs=27.8
Q ss_pred CCCCCCCCCCCCCCeeEEecCCCccccc-ccccc
Q 028487 50 PSDVPRCDICENAPAFFYCEIDGSSLCL-QCDMT 82 (208)
Q Consensus 50 ~~~~plCd~C~~~pA~~yC~~d~a~LC~-~CD~~ 82 (208)
.+.+..|.+|...++.|.|.-|+...|. .|...
T Consensus 4 ts~~~~C~ic~vq~~~YtCPRCn~~YCsl~CYr~ 37 (383)
T KOG4317|consen 4 TSSFLACGICGVQKREYTCPRCNLLYCSLKCYRN 37 (383)
T ss_pred CCceeeccccccccccccCCCCCccceeeeeecC
Confidence 3567789999999999999999999995 56554
No 40
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.89 E-value=55 Score=35.75 Aligned_cols=48 Identities=19% Similarity=0.416 Sum_probs=0.0
Q ss_pred CCcccccCCCceeEEeccccccc-----chhhccccccCccccccccccccCCCCCCCCCCCCCCCC
Q 028487 2 RTLCDVCESAAAILFCAADEAAL-----CRSCDEKVHMCNKLASRHVRVGLANPSDVPRCDICENAP 63 (208)
Q Consensus 2 ~~~Cd~C~~~~A~vyC~~D~A~L-----C~~CD~~vH~aN~l~~rH~Rvpl~~~~~~plCd~C~~~p 63 (208)
...|..|+...-..+|..|++.+ |..|...+.. .+.. ...|+.|....
T Consensus 667 ~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~-------------des~-a~~CP~CGtpl 719 (1337)
T PRK14714 667 RRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPP-------------DESG-RVECPRCDVEL 719 (1337)
T ss_pred EEECCCCCCccccccCcccCCcCCCceeCccCCCccCC-------------Cccc-cccCCCCCCcc
No 41
>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=23.49 E-value=48 Score=20.31 Aligned_cols=25 Identities=24% Similarity=0.788 Sum_probs=10.2
Q ss_pred CCCCCCCCCCCeeEEecCCCcccccccc
Q 028487 53 VPRCDICENAPAFFYCEIDGSSLCLQCD 80 (208)
Q Consensus 53 ~plCd~C~~~pA~~yC~~d~a~LC~~CD 80 (208)
.|.|+.|...-.. ......+|..|.
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 4689999765443 344566666664
No 42
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.05 E-value=49 Score=26.25 Aligned_cols=21 Identities=33% Similarity=0.634 Sum_probs=19.3
Q ss_pred eEEecccccccchhhcccccc
Q 028487 14 ILFCAADEAALCRSCDEKVHM 34 (208)
Q Consensus 14 ~vyC~~D~A~LC~~CD~~vH~ 34 (208)
.+.|..+.-.+|..||.-+|.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 577999999999999999996
No 43
>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=21.68 E-value=48 Score=19.53 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=7.4
Q ss_pred CCCCCCCCC---eeEEecCCCcccccc
Q 028487 55 RCDICENAP---AFFYCEIDGSSLCLQ 78 (208)
Q Consensus 55 lCd~C~~~p---A~~yC~~d~a~LC~~ 78 (208)
.|+.|+... ..++|..|.-.|...
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~ 28 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEE 28 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HH
T ss_pred cCCcCCCcCCCCceEECccCCCccChh
Confidence 478887654 355565555444433
No 44
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.14 E-value=65 Score=20.31 Aligned_cols=24 Identities=33% Similarity=0.739 Sum_probs=19.7
Q ss_pred cccccCCCceeEEecccccccchhhcc
Q 028487 4 LCDVCESAAAILFCAADEAALCRSCDE 30 (208)
Q Consensus 4 ~Cd~C~~~~A~vyC~~D~A~LC~~CD~ 30 (208)
.|+.|++. +|=..|.-+.|.+|..
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCce
Confidence 49999875 8888899999998864
No 45
>PF15616 TerY-C: TerY-C metal binding domain
Probab=20.55 E-value=79 Score=25.70 Aligned_cols=26 Identities=35% Similarity=0.746 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCCeeEEecCCCcccccc
Q 028487 52 DVPRCDICENAPAFFYCEIDGSSLCLQ 78 (208)
Q Consensus 52 ~~plCd~C~~~pA~~yC~~d~a~LC~~ 78 (208)
..|-|+.|....++..| .|.-.+|.+
T Consensus 76 g~PgCP~CGn~~~fa~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 76 GAPGCPHCGNQYAFAVC-GCGKLFCID 101 (131)
T ss_pred CCCCCCCCcChhcEEEe-cCCCEEEeC
Confidence 45899999999999999 688777744
No 46
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=20.23 E-value=82 Score=31.19 Aligned_cols=66 Identities=20% Similarity=0.336 Sum_probs=40.2
Q ss_pred cccchhhccccccCcccccc-ccccccCCC---CCCCCCCCCCCCCeeEEec--CC-------CccccccccccccCCCC
Q 028487 22 AALCRSCDEKVHMCNKLASR-HVRVGLANP---SDVPRCDICENAPAFFYCE--ID-------GSSLCLQCDMTVHVGGK 88 (208)
Q Consensus 22 A~LC~~CD~~vH~aN~l~~r-H~Rvpl~~~---~~~plCd~C~~~pA~~yC~--~d-------~a~LC~~CD~~~Hsan~ 88 (208)
.+||..|...+|+.-+.... +.-.|+.+. .+-+-|..- +..|.+.|- +| .+-+|..|....|....
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n~~ 305 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNRR 305 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhccccc
Confidence 46999999999985443322 223333321 233333333 345888874 33 45799999999996653
No 47
>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=20.22 E-value=75 Score=19.43 Aligned_cols=10 Identities=40% Similarity=0.986 Sum_probs=5.5
Q ss_pred CCCcccccCC
Q 028487 1 MRTLCDVCES 10 (208)
Q Consensus 1 m~~~Cd~C~~ 10 (208)
|...|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 5555555554
Done!