Query 029499
Match_columns 192
No_of_seqs 177 out of 497
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 13:53:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029499.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029499hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3183 Predicted Zn-finger pr 100.0 3E-43 6.4E-48 301.7 2.8 177 5-184 1-185 (250)
2 PF01428 zf-AN1: AN1-like Zinc 99.3 1.3E-12 2.9E-17 85.4 2.5 41 15-55 1-41 (43)
3 PF01428 zf-AN1: AN1-like Zinc 99.2 6E-12 1.3E-16 82.2 2.1 41 102-144 1-41 (43)
4 smart00154 ZnF_AN1 AN1-like Zi 99.2 1.4E-11 3E-16 79.4 2.5 34 19-52 3-37 (39)
5 smart00154 ZnF_AN1 AN1-like Zi 98.9 1E-09 2.2E-14 70.7 2.4 37 102-141 1-37 (39)
6 KOG3183 Predicted Zn-finger pr 98.1 1.2E-06 2.6E-11 76.3 1.9 75 100-177 9-87 (250)
7 COG3582 Predicted nucleic acid 97.7 3.7E-05 8E-10 63.7 3.8 113 19-144 5-138 (162)
8 KOG3173 Predicted Zn-finger pr 96.9 0.00049 1.1E-08 57.1 1.9 41 97-141 103-143 (167)
9 COG3582 Predicted nucleic acid 95.1 0.01 2.2E-07 49.3 1.4 37 19-55 102-138 (162)
10 KOG3173 Predicted Zn-finger pr 94.2 0.024 5.2E-07 47.1 1.6 38 14-53 107-144 (167)
11 PF04236 Transp_Tc5_C: Tc5 tra 91.6 0.14 3E-06 36.3 2.1 39 9-49 24-63 (63)
12 PF04236 Transp_Tc5_C: Tc5 tra 84.2 0.66 1.4E-05 32.9 1.7 36 99-138 27-63 (63)
13 PF05605 zf-Di19: Drought indu 78.6 0.33 7.2E-06 32.5 -1.5 34 28-68 3-40 (54)
14 smart00734 ZnF_Rad18 Rad18-lik 77.8 1 2.3E-05 26.4 0.7 20 60-88 2-21 (26)
15 PF13465 zf-H2C2_2: Zinc-finge 77.3 0.9 1.9E-05 26.2 0.3 12 26-37 13-24 (26)
16 PF01485 IBR: IBR domain; Int 77.3 1.9 4.2E-05 28.5 2.0 34 101-134 20-58 (64)
17 PF13912 zf-C2H2_6: C2H2-type 74.7 1.1 2.5E-05 25.3 0.3 11 27-37 1-11 (27)
18 smart00647 IBR In Between Ring 74.7 2.2 4.7E-05 28.3 1.7 35 100-134 19-58 (64)
19 PF07975 C1_4: TFIIH C1-like d 65.6 2.5 5.4E-05 28.8 0.4 27 25-51 19-48 (51)
20 KOG1813 Predicted E3 ubiquitin 65.5 3.1 6.8E-05 37.9 1.2 45 22-71 236-287 (313)
21 KOG2462 C2H2-type Zn-finger pr 62.1 6.8 0.00015 35.3 2.7 58 26-91 186-267 (279)
22 PLN03086 PRLI-interacting fact 58.9 5.6 0.00012 39.0 1.7 11 116-126 541-551 (567)
23 PF00096 zf-C2H2: Zinc finger, 53.4 5 0.00011 21.6 0.2 11 61-71 2-12 (23)
24 PF10571 UPF0547: Uncharacteri 52.5 9.8 0.00021 22.3 1.4 23 101-126 2-24 (26)
25 PHA00616 hypothetical protein 52.2 4.7 0.0001 26.8 -0.0 11 27-37 1-11 (44)
26 PF02928 zf-C5HC2: C5HC2 zinc 51.1 8.1 0.00018 26.0 1.0 24 107-132 4-29 (54)
27 PHA02768 hypothetical protein; 48.5 7.8 0.00017 26.9 0.6 13 25-37 3-15 (55)
28 PF13894 zf-C2H2_4: C2H2-type 46.9 8.1 0.00018 20.2 0.4 11 61-71 2-12 (24)
29 PF12773 DZR: Double zinc ribb 43.0 22 0.00048 22.8 2.1 12 59-70 12-23 (50)
30 TIGR02098 MJ0042_CXXC MJ0042 f 40.1 14 0.00031 22.5 0.9 34 28-70 3-36 (38)
31 KOG2807 RNA polymerase II tran 40.0 36 0.00078 31.7 3.7 73 59-140 290-372 (378)
32 PF14634 zf-RING_5: zinc-RING 39.3 11 0.00024 23.9 0.2 31 27-67 14-44 (44)
33 PRK04023 DNA polymerase II lar 37.4 50 0.0011 35.0 4.6 74 3-86 617-690 (1121)
34 PRK00398 rpoP DNA-directed RNA 37.3 24 0.00051 22.7 1.6 32 26-71 2-33 (46)
35 PF01844 HNH: HNH endonuclease 35.8 8.9 0.00019 23.9 -0.6 38 30-69 1-44 (47)
36 KOG1812 Predicted E3 ubiquitin 35.1 16 0.00034 34.0 0.6 30 14-43 235-274 (384)
37 KOG1729 FYVE finger containing 31.2 20 0.00044 32.3 0.7 59 7-70 162-225 (288)
38 PF06524 NOA36: NOA36 protein; 30.1 24 0.00053 32.0 0.9 39 28-71 183-221 (314)
39 TIGR00599 rad18 DNA repair pro 30.0 24 0.00053 33.2 1.0 25 59-93 181-205 (397)
40 smart00355 ZnF_C2H2 zinc finge 29.9 23 0.0005 18.4 0.5 10 61-70 2-11 (26)
41 PF09237 GAGA: GAGA factor; I 29.5 37 0.00081 23.5 1.6 26 55-88 20-45 (54)
42 TIGR00622 ssl1 transcription f 28.6 31 0.00066 27.2 1.2 15 27-41 81-95 (112)
43 PF13913 zf-C2HC_2: zinc-finge 27.3 29 0.00064 19.8 0.7 10 117-126 3-12 (25)
44 KOG2462 C2H2-type Zn-finger pr 26.9 29 0.00062 31.4 0.8 25 27-51 215-248 (279)
45 PRK14890 putative Zn-ribbon RN 26.8 28 0.00061 24.5 0.6 15 107-124 42-56 (59)
46 PF14169 YdjO: Cold-inducible 26.3 37 0.00081 23.9 1.2 15 57-71 37-51 (59)
47 PF01363 FYVE: FYVE zinc finge 26.3 9 0.0002 26.2 -2.0 55 12-68 9-66 (69)
48 cd00065 FYVE FYVE domain; Zinc 26.0 42 0.00091 21.8 1.3 29 14-44 4-35 (57)
49 PF04423 Rad50_zn_hook: Rad50 26.0 25 0.00055 23.3 0.2 11 61-71 22-32 (54)
50 smart00451 ZnF_U1 U1-like zinc 24.9 30 0.00066 20.2 0.4 10 61-70 5-14 (35)
51 PF12171 zf-C2H2_jaz: Zinc-fin 24.8 39 0.00084 19.1 0.9 21 61-89 3-23 (27)
52 KOG4739 Uncharacterized protei 24.4 33 0.00072 30.2 0.8 34 26-71 16-49 (233)
53 PHA02565 49 recombination endo 24.3 51 0.0011 27.4 1.8 39 29-71 22-67 (157)
54 PF05290 Baculo_IE-1: Baculovi 23.8 47 0.001 27.2 1.4 45 26-71 79-133 (140)
55 KOG1701 Focal adhesion adaptor 23.4 30 0.00065 33.2 0.3 46 22-81 369-414 (468)
56 PHA00626 hypothetical protein 22.5 55 0.0012 23.1 1.4 12 115-126 22-33 (59)
57 COG2888 Predicted Zn-ribbon RN 22.5 35 0.00075 24.2 0.4 15 107-124 44-58 (61)
58 PLN03086 PRLI-interacting fact 21.7 1.1E+02 0.0025 30.2 3.9 58 55-126 403-463 (567)
59 PHA00732 hypothetical protein 21.3 42 0.0009 24.5 0.6 12 27-38 1-12 (79)
60 PF04438 zf-HIT: HIT zinc fing 21.3 50 0.0011 19.9 0.9 19 19-39 7-25 (30)
61 PF12230 PRP21_like_P: Pre-mRN 20.7 33 0.00072 29.1 0.0 30 57-95 166-195 (229)
62 smart00064 FYVE Protein presen 20.1 74 0.0016 21.5 1.7 29 12-43 10-42 (68)
63 PF12874 zf-met: Zinc-finger o 20.0 39 0.00085 18.3 0.2 20 61-88 2-21 (25)
No 1
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3e-43 Score=301.70 Aligned_cols=177 Identities=43% Similarity=0.804 Sum_probs=155.2
Q ss_pred ccCCCccCcCCCcCCCCCcccccccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcccccCCCCCCChhHHHH
Q 029499 5 TEAFPDLGSHCQHQDCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIETTGEFGEGEKTMLE 84 (192)
Q Consensus 5 ~~ef~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~~~~~g~~~n~~v~ 84 (192)
||||||||+||++++|+|||||||+|+.|+..||+|||+|++|.||.....+++|++||+|+++|+.. .++.++.+|+
T Consensus 1 ~~efpDlGkHCs~~~CkqlDFLPf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~--~de~~~~~v~ 78 (250)
T KOG3183|consen 1 TMEFPDLGKHCSVPYCKQLDFLPFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTK--KDEAPDKVVE 78 (250)
T ss_pred CCcccccccccCcchhhhccccceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCC--CCcchhhhhc
Confidence 69999999999999999999999999999999999999999999999999999999999999999985 8999999999
Q ss_pred hhcccCCCCcC------CCCCCCCCcCcccccccccCcccccccCccccccCcCCCCCCCC-CCCCCCccccccccccCC
Q 029499 85 KHKKSGDCDPR------KQKKPSCPVKRCKEKLTFSNTATCKTCNLKVCLKHRFPADHSCK-KDSLLGKNAAADAAVGKG 157 (192)
Q Consensus 85 ~Hi~s~~C~p~------kk~~~~Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~-~~~~~~~~~~~~~a~~~~ 157 (192)
.|+ +++|++- +..+++|+..+|++.+.++|.|+|.+|+.+||++||++.||.|. .+...+..++........
T Consensus 79 ~h~-~~dC~~~~~~~~~k~~t~kc~~~~c~k~~~~~~~~~c~~c~~~~c~khr~~~dhsc~~~~~~~k~~a~~~~~~~~q 157 (250)
T KOG3183|consen 79 PHI-SNDCDRHPEQKKRKVFTNKCPVPRCKKTLTLANKITCSKCGRNFCLKHRHPLDHSCNKQLGNLKKKAGGDKIGPMQ 157 (250)
T ss_pred hhh-ccccccCchhhhcccccccCCchhhHHHHHHHHhhhhHhhcchhhhhccCCCCchhhhhccCcccccccccccccc
Confidence 996 6899872 22457899999999998888999999999999999999999999 454555555555544578
Q ss_pred chHHHHHHHHhhhc-CCcccCCCCCCCC
Q 029499 158 RWNDKFLFALASRN-GKECSKCDRGSSS 184 (192)
Q Consensus 158 ~~~~~f~s~l~~r~-~~~~~~~~~~~~~ 184 (192)
+|...+..+.+++. ++.|...+|++..
T Consensus 158 ~~~~~~~~~~~s~~~~~~~t~~~~~~~k 185 (250)
T KOG3183|consen 158 NRIYIWTYLSSSSETAKECTRMARYIGK 185 (250)
T ss_pred ceeeeeEeecCcccccccccccchhhcc
Confidence 88888888888886 6899888875443
No 2
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.29 E-value=1.3e-12 Score=85.35 Aligned_cols=41 Identities=46% Similarity=1.052 Sum_probs=31.7
Q ss_pred CCcCCCCCcccccccCCcccccccCCCCcCCCcCCCCCccC
Q 029499 15 CQHQDCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSDIK 55 (192)
Q Consensus 15 C~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~ 55 (192)
|++++|+++|||||+|++|++.||.+||.+++|+|+....+
T Consensus 1 C~~~~C~~~~~~~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDFLPFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCTSHEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccCCCeECCCCCcccCccccCccccCCcchhhc
Confidence 78889999999999999999999999999999999987654
No 3
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=99.20 E-value=6e-12 Score=82.24 Aligned_cols=41 Identities=41% Similarity=0.853 Sum_probs=30.3
Q ss_pred CCcCcccccccccCcccccccCccccccCcCCCCCCCCCCCCC
Q 029499 102 CPVKRCKEKLTFSNTATCKTCNLKVCLKHRFPADHSCKKDSLL 144 (192)
Q Consensus 102 Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~~~~~~ 144 (192)
|++.+|++++++ ++.|+.|++.||++||+|++|.|..+...
T Consensus 1 C~~~~C~~~~~~--~~~C~~C~~~FC~~Hr~~e~H~C~~~~~~ 41 (43)
T PF01428_consen 1 CSFPGCKKKDFL--PFKCKHCGKSFCLKHRLPEDHNCSKLQKK 41 (43)
T ss_dssp -SSTTT--BCTS--HEE-TTTS-EE-TTTHSTTTCT-SSTTSC
T ss_pred CccCcCcCccCC--CeECCCCCcccCccccCccccCCcchhhc
Confidence 788999999875 99999999999999999999999987543
No 4
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=99.17 E-value=1.4e-11 Score=79.40 Aligned_cols=34 Identities=41% Similarity=0.829 Sum_probs=32.6
Q ss_pred CCCCcccc-cccCCcccccccCCCCcCCCcCCCCC
Q 029499 19 DCHQLDFL-PFKCDGCHKVFCFEHRSFKSHECPKS 52 (192)
Q Consensus 19 ~C~qlDFL-Pf~C~~C~~~FC~eHr~~~~H~C~~~ 52 (192)
.|+++||| ||+|++|+++||.+||.+++|+|+..
T Consensus 3 ~C~~~~~l~~f~C~~C~~~FC~~HR~~e~H~C~~~ 37 (39)
T smart00154 3 FCRKKVGLTGFKCRHCGNLFCGEHRLPEDHDCPGD 37 (39)
T ss_pred ccCCcccccCeECCccCCccccccCCccccCCccc
Confidence 69999999 99999999999999999999999875
No 5
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=98.88 E-value=1e-09 Score=70.72 Aligned_cols=37 Identities=35% Similarity=0.946 Sum_probs=32.0
Q ss_pred CCcCcccccccccCcccccccCccccccCcCCCCCCCCCC
Q 029499 102 CPVKRCKEKLTFSNTATCKTCNLKVCLKHRFPADHSCKKD 141 (192)
Q Consensus 102 Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~~~ 141 (192)
|.+ |+++++++ +++|+.|++.||++||++++|.|..+
T Consensus 1 C~~--C~~~~~l~-~f~C~~C~~~FC~~HR~~e~H~C~~~ 37 (39)
T smart00154 1 CHF--CRKKVGLT-GFKCRHCGNLFCGEHRLPEDHDCPGD 37 (39)
T ss_pred Ccc--cCCccccc-CeECCccCCccccccCCccccCCccc
Confidence 445 88887664 89999999999999999999999865
No 6
>KOG3183 consensus Predicted Zn-finger protein [General function prediction only]
Probab=98.10 E-value=1.2e-06 Score=76.32 Aligned_cols=75 Identities=20% Similarity=0.363 Sum_probs=57.6
Q ss_pred CCCCcCcccccccccCcccccccCccccccCcCCCCCCCCCCCCCCccc----cccccccCCchHHHHHHHHhhhcCCcc
Q 029499 100 PSCPVKRCKEKLTFSNTATCKTCNLKVCLKHRFPADHSCKKDSLLGKNA----AADAAVGKGRWNDKFLFALASRNGKEC 175 (192)
Q Consensus 100 ~~Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~~~~~~~~~~----~~~~a~~~~~~~~~f~s~l~~r~~~~~ 175 (192)
.+|+...|++++++ ||+|..|++.||+.||.-++|+|.....-..+. .-..++...+.+++++.+.+. ..++|
T Consensus 9 kHCs~~~CkqlDFL--Pf~Cd~C~~~FC~eHrsye~H~Cp~~~~~~~~v~icp~cs~pv~~~~de~~~~~v~~h-~~~dC 85 (250)
T KOG3183|consen 9 KHCSVPYCKQLDFL--PFKCDGCSGIFCLEHRSYESHHCPKGLRIDVQVPICPLCSKPVPTKKDEAPDKVVEPH-ISNDC 85 (250)
T ss_pred cccCcchhhhcccc--ceeeCCccchhhhccchHhhcCCCcccccceeecccCCCCCCCCCCCCcchhhhhchh-hcccc
Confidence 47998899999998 999999999999999999999999874322111 011112344778999999999 58899
Q ss_pred cC
Q 029499 176 SK 177 (192)
Q Consensus 176 ~~ 177 (192)
-.
T Consensus 86 ~~ 87 (250)
T KOG3183|consen 86 DR 87 (250)
T ss_pred cc
Confidence 44
No 7
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=97.70 E-value=3.7e-05 Score=63.67 Aligned_cols=113 Identities=19% Similarity=0.286 Sum_probs=66.1
Q ss_pred CCCCcccccccCCcccccccCCCCcCCCcCCCCCc----------cCCcccccc-cccCcccccCCCCCCChhHHHHhhc
Q 029499 19 DCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSD----------IKSRKVIVC-EVCSVSIETTGEFGEGEKTMLEKHK 87 (192)
Q Consensus 19 ~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~----------~~~~~v~~C-PlC~~~v~~~~~~g~~~n~~v~~Hi 87 (192)
.+....=||++|+.+.++|+.+|+..-.|.++-.. ....++..| |+=...|.. ++.+-
T Consensus 5 s~~~~~~lP~r~~~~~kv~s~~~~~~~~~~f~~~i~~~~r~~i~k~~~~~~~~~~p~i~~~~~~-----------~~~~~ 73 (162)
T COG3582 5 SRVSETRLPSRGNITAKVSSTDNSLTLFSPFKLFIQLCDRKKIKKPDPGQAMKCLPLISSAVSN-----------PSNTD 73 (162)
T ss_pred ccceeccCCccccceeeeccCccccccccccchhhhhhhhhccccCCCcchhhhcceEEEEeec-----------ccccc
Confidence 34455669999999999999999998889888641 011122211 110000100 00110
Q ss_pred c---cCCCC---cCCCCCC---CCCcCcc-cccccccCcccccccCccccccCcCCCCCCCCCCCCC
Q 029499 88 K---SGDCD---PRKQKKP---SCPVKRC-KEKLTFSNTATCKTCNLKVCLKHRFPADHSCKKDSLL 144 (192)
Q Consensus 88 ~---s~~C~---p~kk~~~---~Cs~~~C-k~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~~~~~~ 144 (192)
. +..=. +....+. .|....| .+...+ +..|++|+..||..||+++.|+|..+...
T Consensus 74 ~~k~s~~~~~~~~~~~~~~~t~~~a~~~~~g~~s~l--~~~c~~c~g~fc~~h~lp~nhdc~~L~s~ 138 (162)
T COG3582 74 TPKRSTRVPLNGPFDSGKGITDRCATPQCTGKGSTL--AGKCNYCTGYFCAEHRLPENHDCNGLGSL 138 (162)
T ss_pred CcccccccccccccccccccceeeecceeccCCccc--cccccCCCCcceeceecccccccccHHHh
Confidence 0 00000 0111222 4555444 344555 78999999999999999999999987543
No 8
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=96.90 E-value=0.00049 Score=57.09 Aligned_cols=41 Identities=34% Similarity=0.845 Sum_probs=33.6
Q ss_pred CCCCCCCcCcccccccccCcccccccCccccccCcCCCCCCCCCC
Q 029499 97 QKKPSCPVKRCKEKLTFSNTATCKTCNLKVCLKHRFPADHSCKKD 141 (192)
Q Consensus 97 k~~~~Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p~dH~C~~~ 141 (192)
+++.+|-. |++.+.+. .+.| .|+..||..|||++.|+|.-.
T Consensus 103 ~~~~rC~~--C~kk~glt-gf~C-rCG~~fC~~HRy~e~H~C~fD 143 (167)
T KOG3173|consen 103 KKKKRCFK--CRKKVGLT-GFKC-RCGNTFCGTHRYPEQHDCSFD 143 (167)
T ss_pred ccchhhhh--hhhhhccc-cccc-ccCCcccccccCCcccccccc
Confidence 44567888 88766654 5899 999999999999999999743
No 9
>COG3582 Predicted nucleic acid binding protein containing the AN1-type Zn-finger [General function prediction only]
Probab=95.07 E-value=0.01 Score=49.27 Aligned_cols=37 Identities=30% Similarity=0.454 Sum_probs=34.1
Q ss_pred CCCCcccccccCCcccccccCCCCcCCCcCCCCCccC
Q 029499 19 DCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSDIK 55 (192)
Q Consensus 19 ~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~ 55 (192)
.|+.---||++|++|+.+||.+|+.++.|.|..+.++
T Consensus 102 ~~g~~s~l~~~c~~c~g~fc~~h~lp~nhdc~~L~s~ 138 (162)
T COG3582 102 CTGKGSTLAGKCNYCTGYFCAEHRLPENHDCNGLGSL 138 (162)
T ss_pred eccCCccccccccCCCCcceeceecccccccccHHHh
Confidence 6777889999999999999999999999999998764
No 10
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=94.24 E-value=0.024 Score=47.08 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=30.2
Q ss_pred CCCcCCCCCcccccccCCcccccccCCCCcCCCcCCCCCc
Q 029499 14 HCQHQDCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSD 53 (192)
Q Consensus 14 hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~ 53 (192)
+|..-. .++..+.|.|. |+.+||..||.++.|.|.-..
T Consensus 107 rC~~C~-kk~gltgf~Cr-CG~~fC~~HRy~e~H~C~fDy 144 (167)
T KOG3173|consen 107 RCFKCR-KKVGLTGFKCR-CGNTFCGTHRYPEQHDCSFDY 144 (167)
T ss_pred hhhhhh-hhhcccccccc-cCCcccccccCCccccccccH
Confidence 355222 45677899996 999999999999999998544
No 11
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=91.60 E-value=0.14 Score=36.34 Aligned_cols=39 Identities=28% Similarity=0.823 Sum_probs=33.1
Q ss_pred CccCcCCCcCCCCCcccccccCCcccccccCCCCcC-CCcCC
Q 029499 9 PDLGSHCQHQDCHQLDFLPFKCDGCHKVFCFEHRSF-KSHEC 49 (192)
Q Consensus 9 ~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~-~~H~C 49 (192)
.+....|..+.|+.+-| ++|.+|++.+|-+|+.. +-|.|
T Consensus 24 ~~~~~~C~~~gC~~~s~--I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 24 KNVAGDCDITGCNNTSF--IRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred CCCcCcCCCCCCCCcCE--EEccccCCcccccceeeeeeEcC
Confidence 35567899999999988 48999999999999986 67776
No 12
>PF04236 Transp_Tc5_C: Tc5 transposase C-terminal domain; InterPro: IPR007350 This domain corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA-binding. It is found in association with the DDE superfamily (IPR004875 from INTERPRO) and the Tc5 transposase family (IPR004906 from INTERPRO). More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.23 E-value=0.66 Score=32.87 Aligned_cols=36 Identities=22% Similarity=0.646 Sum_probs=29.8
Q ss_pred CCCCCcCcccccccccCcccccccCccccccCcCC-CCCCC
Q 029499 99 KPSCPVKRCKEKLTFSNTATCKTCNLKVCLKHRFP-ADHSC 138 (192)
Q Consensus 99 ~~~Cs~~~Ck~~~~~~n~~~C~~C~~~FClkHR~p-~dH~C 138 (192)
+..|...+|.+..+ +.|.+|++.+|.+|=+- +-|.|
T Consensus 27 ~~~C~~~gC~~~s~----I~C~~Ckk~~Cf~Hfiv~~~H~C 63 (63)
T PF04236_consen 27 AGDCDITGCNNTSF----IRCAYCKKSLCFNHFIVSEYHLC 63 (63)
T ss_pred cCcCCCCCCCCcCE----EEccccCCcccccceeeeeeEcC
Confidence 45799999999864 58999999999999984 55665
No 13
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=78.55 E-value=0.33 Score=32.51 Aligned_cols=34 Identities=38% Similarity=0.745 Sum_probs=19.6
Q ss_pred ccCCcccccccC----CCCcCCCcCCCCCccCCcccccccccCcc
Q 029499 28 FKCDGCHKVFCF----EHRSFKSHECPKSDIKSRKVIVCEVCSVS 68 (192)
Q Consensus 28 f~C~~C~~~FC~----eHr~~~~H~C~~~~~~~~~v~~CPlC~~~ 68 (192)
|+|++|++.|=. +|.. +.|. .+...++||+|...
T Consensus 3 f~CP~C~~~~~~~~L~~H~~-~~H~------~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCE-DEHR------SESKNVVCPICSSR 40 (54)
T ss_pred cCCCCCCCccCHHHHHHHHH-hHCc------CCCCCccCCCchhh
Confidence 789999884321 1211 1121 23446899999974
No 14
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=77.85 E-value=1 Score=26.37 Aligned_cols=20 Identities=20% Similarity=0.615 Sum_probs=15.5
Q ss_pred ccccccCcccccCCCCCCChhHHHHhhcc
Q 029499 60 IVCEVCSVSIETTGEFGEGEKTMLEKHKK 88 (192)
Q Consensus 60 ~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~ 88 (192)
+.||+|++.|.. ..+++|++
T Consensus 2 v~CPiC~~~v~~---------~~in~HLD 21 (26)
T smart00734 2 VQCPVCFREVPE---------NLINSHLD 21 (26)
T ss_pred CcCCCCcCcccH---------HHHHHHHH
Confidence 469999998843 35788987
No 15
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=77.33 E-value=0.9 Score=26.21 Aligned_cols=12 Identities=50% Similarity=1.107 Sum_probs=10.5
Q ss_pred ccccCCcccccc
Q 029499 26 LPFKCDGCHKVF 37 (192)
Q Consensus 26 LPf~C~~C~~~F 37 (192)
-||+|+.|++.|
T Consensus 13 k~~~C~~C~k~F 24 (26)
T PF13465_consen 13 KPYKCPYCGKSF 24 (26)
T ss_dssp SSEEESSSSEEE
T ss_pred CCCCCCCCcCee
Confidence 489999999987
No 16
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=77.26 E-value=1.9 Score=28.49 Aligned_cols=34 Identities=29% Similarity=0.659 Sum_probs=22.0
Q ss_pred CCCcCccccccccc---Cc--ccccccCccccccCcCCC
Q 029499 101 SCPVKRCKEKLTFS---NT--ATCKTCNLKVCLKHRFPA 134 (192)
Q Consensus 101 ~Cs~~~Ck~~~~~~---n~--~~C~~C~~~FClkHR~p~ 134 (192)
.|+..+|...+... +. +.|+.|+..||...+.+-
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~~ 58 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEPW 58 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSES
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCccc
Confidence 78888898653321 23 899999999999998654
No 17
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=74.72 E-value=1.1 Score=25.30 Aligned_cols=11 Identities=64% Similarity=1.558 Sum_probs=6.4
Q ss_pred cccCCcccccc
Q 029499 27 PFKCDGCHKVF 37 (192)
Q Consensus 27 Pf~C~~C~~~F 37 (192)
||+|+.|++.|
T Consensus 1 ~~~C~~C~~~F 11 (27)
T PF13912_consen 1 PFECDECGKTF 11 (27)
T ss_dssp SEEETTTTEEE
T ss_pred CCCCCccCCcc
Confidence 45566666555
No 18
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=74.65 E-value=2.2 Score=28.32 Aligned_cols=35 Identities=26% Similarity=0.771 Sum_probs=26.2
Q ss_pred CCCCcCcccccccc-----cCcccccccCccccccCcCCC
Q 029499 100 PSCPVKRCKEKLTF-----SNTATCKTCNLKVCLKHRFPA 134 (192)
Q Consensus 100 ~~Cs~~~Ck~~~~~-----~n~~~C~~C~~~FClkHR~p~ 134 (192)
..|+..+|...+.. ...+.|+.|+..||...+.+-
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~~ 58 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVPW 58 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCcC
Confidence 46888889754322 236789999999999998763
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=65.59 E-value=2.5 Score=28.84 Aligned_cols=27 Identities=26% Similarity=0.739 Sum_probs=14.0
Q ss_pred cccccCCcccccccCCC---CcCCCcCCCC
Q 029499 25 FLPFKCDGCHKVFCFEH---RSFKSHECPK 51 (192)
Q Consensus 25 FLPf~C~~C~~~FC~eH---r~~~~H~C~~ 51 (192)
-..|+|+.|++.||.|= ....-|+||.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiHE~LH~CPG 48 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIHETLHNCPG 48 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTTTTS-SSST
T ss_pred CCeEECCCCCCccccCcChhhhccccCCcC
Confidence 46799999999999874 2335666664
No 20
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.47 E-value=3.1 Score=37.89 Aligned_cols=45 Identities=33% Similarity=0.580 Sum_probs=30.2
Q ss_pred CcccccccCCcccccc-------cCCCCcCCCcCCCCCccCCcccccccccCccccc
Q 029499 22 QLDFLPFKCDGCHKVF-------CFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 22 qlDFLPf~C~~C~~~F-------C~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~ 71 (192)
-++-|||.|..|.+.| |..++-. .|..... .+-..|.+|++.+..
T Consensus 236 D~~~~Pf~c~icr~~f~~pVvt~c~h~fc~---~ca~~~~--qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 236 DIELLPFKCFICRKYFYRPVVTKCGHYFCE---VCALKPY--QKGEKCYVCSQQTHG 287 (313)
T ss_pred CcccCCccccccccccccchhhcCCceeeh---hhhcccc--ccCCcceeccccccc
Confidence 3677999999999998 5555421 1332222 235889999998864
No 21
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=62.12 E-value=6.8 Score=35.29 Aligned_cols=58 Identities=33% Similarity=0.557 Sum_probs=39.4
Q ss_pred ccccCCccccccc---------CCCCcCCCcCCCCCc---------------cCCcccccccccCcccccCCCCCCChhH
Q 029499 26 LPFKCDGCHKVFC---------FEHRSFKSHECPKSD---------------IKSRKVIVCEVCSVSIETTGEFGEGEKT 81 (192)
Q Consensus 26 LPf~C~~C~~~FC---------~eHr~~~~H~C~~~~---------------~~~~~v~~CPlC~~~v~~~~~~g~~~n~ 81 (192)
||++|..|+|.|= .-|.-.+.+.|+-=. ..+++-..|+.|.+.+.+ -.
T Consensus 186 l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl--------~S 257 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFAL--------KS 257 (279)
T ss_pred CCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHH--------HH
Confidence 7888888888885 345556677775311 245567888888888864 23
Q ss_pred HHHhhcccCC
Q 029499 82 MLEKHKKSGD 91 (192)
Q Consensus 82 ~v~~Hi~s~~ 91 (192)
.|++|.++++
T Consensus 258 yLnKH~ES~C 267 (279)
T KOG2462|consen 258 YLNKHSESAC 267 (279)
T ss_pred HHHHhhhhcc
Confidence 5788887653
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=58.89 E-value=5.6 Score=39.05 Aligned_cols=11 Identities=45% Similarity=0.960 Sum_probs=7.3
Q ss_pred cccccccCccc
Q 029499 116 TATCKTCNLKV 126 (192)
Q Consensus 116 ~~~C~~C~~~F 126 (192)
++.|..|++.|
T Consensus 541 t~~C~~Cgk~V 551 (567)
T PLN03086 541 TAPCDSCGRSV 551 (567)
T ss_pred ceEccccCCee
Confidence 45677777655
No 23
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=53.37 E-value=5 Score=21.65 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=7.1
Q ss_pred cccccCccccc
Q 029499 61 VCEVCSVSIET 71 (192)
Q Consensus 61 ~CPlC~~~v~~ 71 (192)
+||.|++....
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 47777776653
No 24
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=52.53 E-value=9.8 Score=22.34 Aligned_cols=23 Identities=22% Similarity=0.729 Sum_probs=16.3
Q ss_pred CCCcCcccccccccCcccccccCccc
Q 029499 101 SCPVKRCKEKLTFSNTATCKTCNLKV 126 (192)
Q Consensus 101 ~Cs~~~Ck~~~~~~n~~~C~~C~~~F 126 (192)
.|+. |.+.+.. +...|+.||..|
T Consensus 2 ~CP~--C~~~V~~-~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPE--CGAEVPE-SAKFCPHCGYDF 24 (26)
T ss_pred cCCC--CcCCchh-hcCcCCCCCCCC
Confidence 3555 8876654 367899999876
No 25
>PHA00616 hypothetical protein
Probab=52.19 E-value=4.7 Score=26.76 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=6.0
Q ss_pred cccCCcccccc
Q 029499 27 PFKCDGCHKVF 37 (192)
Q Consensus 27 Pf~C~~C~~~F 37 (192)
||+|..|++.|
T Consensus 1 pYqC~~CG~~F 11 (44)
T PHA00616 1 MYQCLRCGGIF 11 (44)
T ss_pred CCccchhhHHH
Confidence 45555555555
No 26
>PF02928 zf-C5HC2: C5HC2 zinc finger; InterPro: IPR004198 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 a predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji [], and may have a DNA binding function. The mouse jumonji protein is required for neural tube formation, and is essential for normal heart development. It also plays a role in the down-regulation of cell proliferation signalling. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005634 nucleus
Probab=51.07 E-value=8.1 Score=26.00 Aligned_cols=24 Identities=42% Similarity=0.858 Sum_probs=19.3
Q ss_pred ccccccccCccccccc--CccccccCcC
Q 029499 107 CKEKLTFSNTATCKTC--NLKVCLKHRF 132 (192)
Q Consensus 107 Ck~~~~~~n~~~C~~C--~~~FClkHR~ 132 (192)
||....++ -+.|+ | ++.+||.|-.
T Consensus 4 Ck~~~yLS-~v~C~-C~~~~~~CL~H~~ 29 (54)
T PF02928_consen 4 CKAYCYLS-AVTCS-CKPDKVVCLRHAK 29 (54)
T ss_pred cCCchhhc-ccccC-CCCCcEEccccch
Confidence 88876654 78898 6 8999999966
No 27
>PHA02768 hypothetical protein; Provisional
Probab=48.46 E-value=7.8 Score=26.86 Aligned_cols=13 Identities=23% Similarity=0.935 Sum_probs=9.4
Q ss_pred cccccCCcccccc
Q 029499 25 FLPFKCDGCHKVF 37 (192)
Q Consensus 25 FLPf~C~~C~~~F 37 (192)
.|-|+|+.|++.|
T Consensus 3 ~~~y~C~~CGK~F 15 (55)
T PHA02768 3 LLGYECPICGEIY 15 (55)
T ss_pred ccccCcchhCCee
Confidence 4667777777776
No 28
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=46.87 E-value=8.1 Score=20.24 Aligned_cols=11 Identities=27% Similarity=0.845 Sum_probs=5.9
Q ss_pred cccccCccccc
Q 029499 61 VCEVCSVSIET 71 (192)
Q Consensus 61 ~CPlC~~~v~~ 71 (192)
.|++|+.....
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 47777776654
No 29
>PF12773 DZR: Double zinc ribbon
Probab=43.01 E-value=22 Score=22.82 Aligned_cols=12 Identities=17% Similarity=0.603 Sum_probs=6.5
Q ss_pred cccccccCcccc
Q 029499 59 VIVCEVCSVSIE 70 (192)
Q Consensus 59 v~~CPlC~~~v~ 70 (192)
+..||.|...|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 555555555444
No 30
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=40.15 E-value=14 Score=22.53 Aligned_cols=34 Identities=15% Similarity=0.405 Sum_probs=20.0
Q ss_pred ccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcccc
Q 029499 28 FKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIE 70 (192)
Q Consensus 28 f~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~ 70 (192)
++|++|+..|=.+-... .. +...+.||.|+..+.
T Consensus 3 ~~CP~C~~~~~v~~~~~--------~~-~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQL--------GA-NGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHc--------CC-CCCEEECCCCCCEEE
Confidence 67888877765443211 11 123577888887664
No 31
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=40.04 E-value=36 Score=31.74 Aligned_cols=73 Identities=22% Similarity=0.456 Sum_probs=41.1
Q ss_pred cccccccCcccccCCCCCCChhHHHHhhcccCCCCc-----C--CCCCCCCCcCcccccccccCcccccccCccccccC-
Q 029499 59 VIVCEVCSVSIETTGEFGEGEKTMLEKHKKSGDCDP-----R--KQKKPSCPVKRCKEKLTFSNTATCKTCNLKVCLKH- 130 (192)
Q Consensus 59 v~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~s~~C~p-----~--kk~~~~Cs~~~Ck~~~~~~n~~~C~~C~~~FClkH- 130 (192)
-..||+|+-.+... ++.+=+-|..- --+| . ..+...|.. |...+.....+.|+.|+..||+.=
T Consensus 290 P~eCpiC~ltLVss------~hLARSyhhL~-PL~~F~Eip~~~~~~~~~Cf~--C~~~~~~~~~y~C~~Ck~~FCldCD 360 (378)
T KOG2807|consen 290 PIECPICSLTLVSS------PHLARSYHHLF-PLKPFVEIPETEYNGSRFCFA--CQGELLSSGRYRCESCKNVFCLDCD 360 (378)
T ss_pred CccCCccceeEecc------hHHHHHHHhhc-CCcchhhccccccCCCcceee--eccccCCCCcEEchhccceeeccch
Confidence 46799998776542 44443333320 0111 1 123456877 854433334789999999999852
Q ss_pred --cCCCCCCCCC
Q 029499 131 --RFPADHSCKK 140 (192)
Q Consensus 131 --R~p~dH~C~~ 140 (192)
=|..=|.|.+
T Consensus 361 v~iHesLh~Cpg 372 (378)
T KOG2807|consen 361 VFIHESLHNCPG 372 (378)
T ss_pred HHHHhhhhcCCC
Confidence 2344466654
No 32
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=39.27 E-value=11 Score=23.88 Aligned_cols=31 Identities=19% Similarity=0.475 Sum_probs=21.1
Q ss_pred cccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCc
Q 029499 27 PFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSV 67 (192)
Q Consensus 27 Pf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~ 67 (192)
++.=-.|+-+||.+...... .....||+|++
T Consensus 14 ~~~l~~CgH~~C~~C~~~~~----------~~~~~CP~C~k 44 (44)
T PF14634_consen 14 RPRLTSCGHIFCEKCLKKLK----------GKSVKCPICRK 44 (44)
T ss_pred CeEEcccCCHHHHHHHHhhc----------CCCCCCcCCCC
Confidence 34445688899988875433 24568999975
No 33
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.41 E-value=50 Score=35.01 Aligned_cols=74 Identities=18% Similarity=0.287 Sum_probs=48.3
Q ss_pred CCccCCCccCcCCCcCCCCCcccccccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcccccCCCCCCChhHH
Q 029499 3 GGTEAFPDLGSHCQHQDCHQLDFLPFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIETTGEFGEGEKTM 82 (192)
Q Consensus 3 ~g~~ef~diG~hC~~~~C~qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~~~~~g~~~n~~ 82 (192)
+|+.+.+--...|. .|+..- .-|+|+.|+.. ......|+.=... .....||-|+..+........+....
T Consensus 617 ~g~~eVEVg~RfCp--sCG~~t-~~frCP~CG~~------Te~i~fCP~CG~~-~~~y~CPKCG~El~~~s~~~i~l~~~ 686 (1121)
T PRK04023 617 KGTIEVEIGRRKCP--SCGKET-FYRRCPFCGTH------TEPVYRCPRCGIE-VEEDECEKCGREPTPYSKRKIDLKEL 686 (1121)
T ss_pred CCceeecccCccCC--CCCCcC-CcccCCCCCCC------CCcceeCccccCc-CCCCcCCCCCCCCCccceEEecHHHH
Confidence 46777777778898 999985 55899999875 3344555544322 22356999998886544455566655
Q ss_pred HHhh
Q 029499 83 LEKH 86 (192)
Q Consensus 83 v~~H 86 (192)
+.+=
T Consensus 687 ~~~A 690 (1121)
T PRK04023 687 YDRA 690 (1121)
T ss_pred HHHH
Confidence 5443
No 34
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.32 E-value=24 Score=22.68 Aligned_cols=32 Identities=19% Similarity=0.464 Sum_probs=20.9
Q ss_pred ccccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCccccc
Q 029499 26 LPFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 26 LPf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~ 71 (192)
+.|+|..|+..|=.+-. .....||.|+.++..
T Consensus 2 ~~y~C~~CG~~~~~~~~--------------~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 2 AEYKCARCGREVELDEY--------------GTGVRCPYCGYRILF 33 (46)
T ss_pred CEEECCCCCCEEEECCC--------------CCceECCCCCCeEEE
Confidence 46788888775533211 125789999988875
No 35
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=35.83 E-value=8.9 Score=23.91 Aligned_cols=38 Identities=18% Similarity=0.316 Sum_probs=18.9
Q ss_pred CCccccccc------CCCCcCCCcCCCCCccCCcccccccccCccc
Q 029499 30 CDGCHKVFC------FEHRSFKSHECPKSDIKSRKVIVCEVCSVSI 69 (192)
Q Consensus 30 C~~C~~~FC------~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v 69 (192)
|..|++.|. .+|+.+..+ ...+..+.-+++|+.|++.+
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~--gg~~~~~Nl~~lC~~Ch~~k 44 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSK--GGKNDLENLILLCPSCHRKK 44 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTT--T---STTTEEEEEHHHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhc--CCCCCHHHHHHHhHHHHHHh
Confidence 456666654 457766655 34444556788888887643
No 36
>KOG1812 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.12 E-value=16 Score=34.00 Aligned_cols=30 Identities=27% Similarity=0.642 Sum_probs=23.2
Q ss_pred CCCcCCCCCcccccc----------cCCcccccccCCCCc
Q 029499 14 HCQHQDCHQLDFLPF----------KCDGCHKVFCFEHRS 43 (192)
Q Consensus 14 hC~~~~C~qlDFLPf----------~C~~C~~~FC~eHr~ 43 (192)
.|.++.|-.+-|... .|..|+..||.+=..
T Consensus 235 ycp~~~C~~l~~~~el~~~~~~~~~~C~~C~~~fCv~C~~ 274 (384)
T KOG1812|consen 235 YCPYPRCSSLMSKTELSSEVKSKRRPCVKCHELFCVKCKV 274 (384)
T ss_pred cCCCCCchHhhhhhhhccchhhcccccccCCCceeecCCC
Confidence 677788877766544 789999999988665
No 37
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=31.21 E-value=20 Score=32.30 Aligned_cols=59 Identities=24% Similarity=0.576 Sum_probs=38.4
Q ss_pred CCCc-cCcCCCcCCCCCcccccc----cCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcccc
Q 029499 7 AFPD-LGSHCQHQDCHQLDFLPF----KCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIE 70 (192)
Q Consensus 7 ef~d-iG~hC~~~~C~qlDFLPf----~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~ 70 (192)
.+|| .-.+|.+.+| ..|-.+ .|..||.+||. |.......=+.. .+..+.+|+.|-..+.
T Consensus 162 W~PD~ea~~C~~C~~--~~Ftl~~RRHHCR~CG~ivC~-~Cs~n~~~l~~~--~~k~~rvC~~CF~el~ 225 (288)
T KOG1729|consen 162 WLPDSEATECMVCGC--TEFTLSERRHHCRNCGDIVCA-PCSRNRFLLPNL--STKPIRVCDICFEELE 225 (288)
T ss_pred ccCcccceecccCCC--ccccHHHHHHHHHhcchHhhh-hhhcCccccccc--CCCCceecHHHHHHHh
Confidence 4677 7889995555 466655 49999999999 765444222222 2233449999976554
No 38
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=30.11 E-value=24 Score=31.95 Aligned_cols=39 Identities=26% Similarity=0.573 Sum_probs=24.4
Q ss_pred ccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCccccc
Q 029499 28 FKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 28 f~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~ 71 (192)
+.|=.|+--||.+|...+... + ....++.||.|+-.+..
T Consensus 183 ~sCLRCK~cfCddHvrrKg~k---y--~k~k~~PCPKCg~et~e 221 (314)
T PF06524_consen 183 YSCLRCKICFCDDHVRRKGFK---Y--EKGKPIPCPKCGYETQE 221 (314)
T ss_pred hhhhheeeeehhhhhhhcccc---c--ccCCCCCCCCCCCcccc
Confidence 344445556999997654311 2 12378899999876654
No 39
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.95 E-value=24 Score=33.21 Aligned_cols=25 Identities=24% Similarity=0.716 Sum_probs=19.3
Q ss_pred cccccccCcccccCCCCCCChhHHHHhhcccCCCC
Q 029499 59 VIVCEVCSVSIETTGEFGEGEKTMLEKHKKSGDCD 93 (192)
Q Consensus 59 v~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~s~~C~ 93 (192)
.+.||+|++.|+.. .|+.|+++ +|.
T Consensus 181 ~v~CPiC~~~~~~~---------~i~~Hld~-~Cl 205 (397)
T TIGR00599 181 LVQCPICQQRMPEK---------AVERHLDS-ECL 205 (397)
T ss_pred cccCCCcccccCHH---------HHHHHHhc-cCC
Confidence 46799999988853 58899985 354
No 40
>smart00355 ZnF_C2H2 zinc finger.
Probab=29.85 E-value=23 Score=18.43 Aligned_cols=10 Identities=20% Similarity=0.617 Sum_probs=5.1
Q ss_pred cccccCcccc
Q 029499 61 VCEVCSVSIE 70 (192)
Q Consensus 61 ~CPlC~~~v~ 70 (192)
.|+.|.+...
T Consensus 2 ~C~~C~~~f~ 11 (26)
T smart00355 2 RCPECGKVFK 11 (26)
T ss_pred CCCCCcchhC
Confidence 3555655443
No 41
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=29.55 E-value=37 Score=23.50 Aligned_cols=26 Identities=23% Similarity=0.562 Sum_probs=14.5
Q ss_pred CCcccccccccCcccccCCCCCCChhHHHHhhcc
Q 029499 55 KSRKVIVCEVCSVSIETTGEFGEGEKTMLEKHKK 88 (192)
Q Consensus 55 ~~~~v~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~ 88 (192)
.+.+-++||+|...|... .-|.+|++
T Consensus 20 ~S~~PatCP~C~a~~~~s--------rnLrRHle 45 (54)
T PF09237_consen 20 QSEQPATCPICGAVIRQS--------RNLRRHLE 45 (54)
T ss_dssp TTS--EE-TTT--EESSH--------HHHHHHHH
T ss_pred ccCCCCCCCcchhhccch--------hhHHHHHH
Confidence 455789999999988753 34677764
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=28.59 E-value=31 Score=27.18 Aligned_cols=15 Identities=33% Similarity=1.037 Sum_probs=13.2
Q ss_pred cccCCcccccccCCC
Q 029499 27 PFKCDGCHKVFCFEH 41 (192)
Q Consensus 27 Pf~C~~C~~~FC~eH 41 (192)
.|+|..|++.||.|=
T Consensus 81 ~y~C~~C~~~FC~dC 95 (112)
T TIGR00622 81 RYVCAVCKNVFCVDC 95 (112)
T ss_pred ceeCCCCCCcccccc
Confidence 588999999999775
No 43
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=27.31 E-value=29 Score=19.83 Aligned_cols=10 Identities=30% Similarity=0.783 Sum_probs=8.8
Q ss_pred ccccccCccc
Q 029499 117 ATCKTCNLKV 126 (192)
Q Consensus 117 ~~C~~C~~~F 126 (192)
+.|+.|++.|
T Consensus 3 ~~C~~CgR~F 12 (25)
T PF13913_consen 3 VPCPICGRKF 12 (25)
T ss_pred CcCCCCCCEE
Confidence 5799999998
No 44
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=26.92 E-value=29 Score=31.40 Aligned_cols=25 Identities=44% Similarity=1.085 Sum_probs=21.1
Q ss_pred cccCCccccccc---------CCCCcCCCcCCCC
Q 029499 27 PFKCDGCHKVFC---------FEHRSFKSHECPK 51 (192)
Q Consensus 27 Pf~C~~C~~~FC---------~eHr~~~~H~C~~ 51 (192)
||.|.+|++.|= .-|-..+.|.|..
T Consensus 215 PF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~ 248 (279)
T KOG2462|consen 215 PFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPR 248 (279)
T ss_pred CccCCcccchhcchHHHHHHHHhhcCCccccCcc
Confidence 999999999994 4577888898875
No 45
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=26.76 E-value=28 Score=24.53 Aligned_cols=15 Identities=33% Similarity=0.975 Sum_probs=10.3
Q ss_pred ccccccccCcccccccCc
Q 029499 107 CKEKLTFSNTATCKTCNL 124 (192)
Q Consensus 107 Ck~~~~~~n~~~C~~C~~ 124 (192)
|++.. |+.+|+.|+-
T Consensus 42 CRk~~---~~Y~CP~CGF 56 (59)
T PRK14890 42 CRKQS---NPYTCPKCGF 56 (59)
T ss_pred HHhcC---CceECCCCCC
Confidence 66653 4778888874
No 46
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=26.30 E-value=37 Score=23.85 Aligned_cols=15 Identities=20% Similarity=0.587 Sum_probs=11.9
Q ss_pred cccccccccCccccc
Q 029499 57 RKVIVCEVCSVSIET 71 (192)
Q Consensus 57 ~~v~~CPlC~~~v~~ 71 (192)
...|+||||+.+...
T Consensus 37 ~~~p~CPlC~s~M~~ 51 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVS 51 (59)
T ss_pred CCCccCCCcCCcccc
Confidence 457999999987653
No 47
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=26.29 E-value=9 Score=26.23 Aligned_cols=55 Identities=24% Similarity=0.439 Sum_probs=21.4
Q ss_pred CcCCCcCCCCCcc-cc--cccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcc
Q 029499 12 GSHCQHQDCHQLD-FL--PFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVS 68 (192)
Q Consensus 12 G~hC~~~~C~qlD-FL--Pf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~ 68 (192)
...|. .|+..= || -..|..||.+||.++.......=.........+.+|..|...
T Consensus 9 ~~~C~--~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~ 66 (69)
T PF01363_consen 9 ASNCM--ICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSK 66 (69)
T ss_dssp -SB-T--TT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHH
T ss_pred CCcCc--CcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHH
Confidence 34555 455431 11 456889999999877643221100011223445666665443
No 48
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=26.02 E-value=42 Score=21.82 Aligned_cols=29 Identities=24% Similarity=0.762 Sum_probs=19.1
Q ss_pred CCCcCCCCC-cccc--cccCCcccccccCCCCcC
Q 029499 14 HCQHQDCHQ-LDFL--PFKCDGCHKVFCFEHRSF 44 (192)
Q Consensus 14 hC~~~~C~q-lDFL--Pf~C~~C~~~FC~eHr~~ 44 (192)
.|. .|++ +.++ -..|..|+++||.++...
T Consensus 4 ~C~--~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~ 35 (57)
T cd00065 4 SCM--GCGKPFTLTRRRHHCRNCGRIFCSKCSSN 35 (57)
T ss_pred cCc--ccCccccCCccccccCcCcCCcChHHcCC
Confidence 444 5543 4444 467889999998877643
No 49
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.97 E-value=25 Score=23.28 Aligned_cols=11 Identities=18% Similarity=0.863 Sum_probs=6.0
Q ss_pred cccccCccccc
Q 029499 61 VCEVCSVSIET 71 (192)
Q Consensus 61 ~CPlC~~~v~~ 71 (192)
.||+|.+++..
T Consensus 22 ~CPlC~r~l~~ 32 (54)
T PF04423_consen 22 CCPLCGRPLDE 32 (54)
T ss_dssp E-TTT--EE-H
T ss_pred cCCCCCCCCCH
Confidence 89999998864
No 50
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.87 E-value=30 Score=20.20 Aligned_cols=10 Identities=30% Similarity=1.052 Sum_probs=5.8
Q ss_pred cccccCcccc
Q 029499 61 VCEVCSVSIE 70 (192)
Q Consensus 61 ~CPlC~~~v~ 70 (192)
.|.+|++.+.
T Consensus 5 ~C~~C~~~~~ 14 (35)
T smart00451 5 YCKLCNVTFT 14 (35)
T ss_pred EccccCCccC
Confidence 3666666544
No 51
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=24.78 E-value=39 Score=19.10 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=13.9
Q ss_pred cccccCcccccCCCCCCChhHHHHhhccc
Q 029499 61 VCEVCSVSIETTGEFGEGEKTMLEKHKKS 89 (192)
Q Consensus 61 ~CPlC~~~v~~~~~~g~~~n~~v~~Hi~s 89 (192)
.|++|++.+.. ..+++.|+.+
T Consensus 3 ~C~~C~k~f~~--------~~~~~~H~~s 23 (27)
T PF12171_consen 3 YCDACDKYFSS--------ENQLKQHMKS 23 (27)
T ss_dssp BBTTTTBBBSS--------HHHHHCCTTS
T ss_pred CcccCCCCcCC--------HHHHHHHHcc
Confidence 47888876653 3467788753
No 52
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=24.44 E-value=33 Score=30.18 Aligned_cols=34 Identities=35% Similarity=0.585 Sum_probs=24.5
Q ss_pred ccccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCccccc
Q 029499 26 LPFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 26 LPf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~ 71 (192)
-||.=..|..+||..|..... ..+||+|.++|..
T Consensus 16 ~~f~LTaC~HvfC~~C~k~~~------------~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 16 DPFFLTACRHVFCEPCLKASS------------PDVCPLCKKSIRI 49 (233)
T ss_pred CceeeeechhhhhhhhcccCC------------ccccccccceeee
Confidence 355556788999999875321 1289999999864
No 53
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=24.34 E-value=51 Score=27.44 Aligned_cols=39 Identities=18% Similarity=0.487 Sum_probs=25.5
Q ss_pred cCCccccccc-------CCCCcCCCcCCCCCccCCcccccccccCccccc
Q 029499 29 KCDGCHKVFC-------FEHRSFKSHECPKSDIKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 29 ~C~~C~~~FC-------~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~ 71 (192)
.|..|+..+. .|| +|.|.......++-+.|+.||..+-.
T Consensus 22 ~CaiC~~~l~~~~~~~~vDH----DH~l~g~~TG~VRGLLC~~CN~~lG~ 67 (157)
T PHA02565 22 ICPLCKRELDGDVSKNHLDH----DHELNGPNAGRVRGLLCNLCNALEGQ 67 (157)
T ss_pred cCCCCCCccCCCccccccCC----CCCCCCcccccccccCchhhhhhhhh
Confidence 3555665544 444 56666555555789999999986643
No 54
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=23.76 E-value=47 Score=27.17 Aligned_cols=45 Identities=24% Similarity=0.415 Sum_probs=34.3
Q ss_pred ccccCCcccccccCCCCcCCCcCCCCCc----------cCCcccccccccCccccc
Q 029499 26 LPFKCDGCHKVFCFEHRSFKSHECPKSD----------IKSRKVIVCEVCSVSIET 71 (192)
Q Consensus 26 LPf~C~~C~~~FC~eHr~~~~H~C~~~~----------~~~~~v~~CPlC~~~v~~ 71 (192)
--|+|+.|+.+.=.+|+. +.-.|-++. .....-|+||.|..+...
T Consensus 79 ~lYeCnIC~etS~ee~FL-KPneCCgY~iCn~Cya~LWK~~~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 79 KLYECNICKETSAEERFL-KPNECCGYSICNACYANLWKFCNLYPVCPVCKTSFKS 133 (140)
T ss_pred CceeccCcccccchhhcC-CcccccchHHHHHHHHHHHHHcccCCCCCcccccccc
Confidence 358999999999999987 344576654 133568999999988765
No 55
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=23.37 E-value=30 Score=33.24 Aligned_cols=46 Identities=28% Similarity=0.496 Sum_probs=36.1
Q ss_pred CcccccccCCcccccccCCCCcCCCcCCCCCccCCcccccccccCcccccCCCCCCChhH
Q 029499 22 QLDFLPFKCDGCHKVFCFEHRSFKSHECPKSDIKSRKVIVCEVCSVSIETTGEFGEGEKT 81 (192)
Q Consensus 22 qlDFLPf~C~~C~~~FC~eHr~~~~H~C~~~~~~~~~v~~CPlC~~~v~~~~~~g~~~n~ 81 (192)
-||=.||+-+.=++++|.+-+. ++-+|.|-+|+++|-.. .|+++.+
T Consensus 369 ~ldgipFtvd~~n~v~Cv~dfh------------~kfAPrCs~C~~PI~P~--~G~~etv 414 (468)
T KOG1701|consen 369 CLDGIPFTVDSQNNVYCVPDFH------------KKFAPRCSVCGNPILPR--DGKDETV 414 (468)
T ss_pred ccCCccccccCCCceeeehhhh------------hhcCcchhhccCCccCC--CCCcceE
Confidence 3788999999989999987663 34689999999999763 6776544
No 56
>PHA00626 hypothetical protein
Probab=22.54 E-value=55 Score=23.06 Aligned_cols=12 Identities=17% Similarity=0.515 Sum_probs=9.1
Q ss_pred CcccccccCccc
Q 029499 115 NTATCKTCNLKV 126 (192)
Q Consensus 115 n~~~C~~C~~~F 126 (192)
|.+.|+.|+-.|
T Consensus 22 nrYkCkdCGY~f 33 (59)
T PHA00626 22 DDYVCCDCGYND 33 (59)
T ss_pred cceEcCCCCCee
Confidence 467899998766
No 57
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.54 E-value=35 Score=24.24 Aligned_cols=15 Identities=27% Similarity=0.784 Sum_probs=9.8
Q ss_pred ccccccccCcccccccCc
Q 029499 107 CKEKLTFSNTATCKTCNL 124 (192)
Q Consensus 107 Ck~~~~~~n~~~C~~C~~ 124 (192)
|++.- |+.+|+.|+-
T Consensus 44 CRk~g---~~Y~Cp~CGF 58 (61)
T COG2888 44 CRKLG---NPYRCPKCGF 58 (61)
T ss_pred HHHcC---CceECCCcCc
Confidence 55543 4778888873
No 58
>PLN03086 PRLI-interacting factor K; Provisional
Probab=21.65 E-value=1.1e+02 Score=30.18 Aligned_cols=58 Identities=21% Similarity=0.485 Sum_probs=37.4
Q ss_pred CCcccccccccCcccccCCCCCCChhHHHHhhcccCCCCcCCCCCCCCCcCccccccc---ccCcccccccCccc
Q 029499 55 KSRKVIVCEVCSVSIETTGEFGEGEKTMLEKHKKSGDCDPRKQKKPSCPVKRCKEKLT---FSNTATCKTCNLKV 126 (192)
Q Consensus 55 ~~~~v~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~s~~C~p~kk~~~~Cs~~~Ck~~~~---~~n~~~C~~C~~~F 126 (192)
.+...+.|+-|.+.|+.. .+..|.. .|.- ....|+..+|+.++. +-+..+|+.|++.|
T Consensus 403 ~~~~~V~C~NC~~~i~l~---------~l~lHe~--~C~r---~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f 463 (567)
T PLN03086 403 MDVDTVECRNCKHYIPSR---------SIALHEA--YCSR---HNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAF 463 (567)
T ss_pred CCCCeEECCCCCCccchh---------HHHHHHh--hCCC---cceeCCcccccceeeccccccCccCCCCCCcc
Confidence 344566899999988864 3557763 3542 234577667886432 22456899998877
No 59
>PHA00732 hypothetical protein
Probab=21.32 E-value=42 Score=24.46 Aligned_cols=12 Identities=33% Similarity=0.520 Sum_probs=10.1
Q ss_pred cccCCccccccc
Q 029499 27 PFKCDGCHKVFC 38 (192)
Q Consensus 27 Pf~C~~C~~~FC 38 (192)
||+|+.|++.|=
T Consensus 1 py~C~~Cgk~F~ 12 (79)
T PHA00732 1 MFKCPICGFTTV 12 (79)
T ss_pred CccCCCCCCccC
Confidence 788999998884
No 60
>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=21.29 E-value=50 Score=19.86 Aligned_cols=19 Identities=21% Similarity=0.726 Sum_probs=12.7
Q ss_pred CCCCcccccccCCcccccccC
Q 029499 19 DCHQLDFLPFKCDGCHKVFCF 39 (192)
Q Consensus 19 ~C~qlDFLPf~C~~C~~~FC~ 39 (192)
.|+. +-.|+|+.|+..||.
T Consensus 7 vC~~--~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 7 VCGN--PAKYRCPRCGARYCS 25 (30)
T ss_dssp SSSS--EESEE-TTT--EESS
T ss_pred cCcC--CCEEECCCcCCceeC
Confidence 5777 778899999888885
No 61
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=20.65 E-value=33 Score=29.10 Aligned_cols=30 Identities=27% Similarity=0.534 Sum_probs=0.0
Q ss_pred cccccccccCcccccCCCCCCChhHHHHhhcccCCCCcC
Q 029499 57 RKVIVCEVCSVSIETTGEFGEGEKTMLEKHKKSGDCDPR 95 (192)
Q Consensus 57 ~~v~~CPlC~~~v~~~~~~g~~~n~~v~~Hi~s~~C~p~ 95 (192)
...++||+|++.||.. -|++|++..--||.
T Consensus 166 ~~~~~cPitGe~IP~~---------e~~eHmRi~LlDP~ 195 (229)
T PF12230_consen 166 EKMIICPITGEMIPAD---------EMDEHMRIELLDPR 195 (229)
T ss_dssp ---------------------------------------
T ss_pred cccccccccccccccc---------cccccccccccccc
Confidence 3568999999999974 37899986656775
No 62
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.05 E-value=39 Score=18.33 Aligned_cols=20 Identities=25% Similarity=0.743 Sum_probs=12.7
Q ss_pred cccccCcccccCCCCCCChhHHHHhhcc
Q 029499 61 VCEVCSVSIETTGEFGEGEKTMLEKHKK 88 (192)
Q Consensus 61 ~CPlC~~~v~~~~~~g~~~n~~v~~Hi~ 88 (192)
.|.+|++.+.. ...+..|+.
T Consensus 2 ~C~~C~~~f~s--------~~~~~~H~~ 21 (25)
T PF12874_consen 2 YCDICNKSFSS--------ENSLRQHLR 21 (25)
T ss_dssp EETTTTEEESS--------HHHHHHHHT
T ss_pred CCCCCCCCcCC--------HHHHHHHHC
Confidence 47788776653 245677775
Done!