Query 017738
Match_columns 366
No_of_seqs 319 out of 812
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 02:59:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017738.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017738hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06203 CCT: CCT motif; Inte 99.8 2.4E-20 5.1E-25 135.1 3.4 45 300-344 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00021 4.5E-09 48.7 2.4 38 20-63 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.2 0.00019 4.2E-09 48.9 2.2 39 62-107 1-39 (39)
4 smart00336 BBOX B-Box-type zin 96.9 0.00091 2E-08 46.2 2.7 41 60-107 2-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.8 0.00062 1.4E-08 47.6 1.3 40 61-107 3-42 (42)
6 KOG1601 GATA-4/5/6 transcripti 96.5 0.00075 1.6E-08 61.4 0.6 94 18-113 5-104 (340)
7 smart00336 BBOX B-Box-type zin 96.2 0.0038 8.2E-08 43.0 2.6 40 18-63 3-42 (42)
8 PF09425 CCT_2: Divergent CCT 96.1 0.0033 7.2E-08 41.4 1.6 26 297-323 1-26 (27)
9 PF00643 zf-B_box: B-box zinc 95.9 0.0054 1.2E-07 42.8 2.1 40 18-63 3-42 (42)
10 KOG4367 Predicted Zn-finger pr 95.3 0.0058 1.3E-07 63.3 0.7 78 18-95 162-257 (699)
11 KOG1601 GATA-4/5/6 transcripti 78.2 3.7 8.1E-05 37.2 4.8 42 296-337 289-330 (340)
12 KOG4367 Predicted Zn-finger pr 63.2 2.7 5.9E-05 44.3 0.4 45 63-108 164-210 (699)
13 PF04438 zf-HIT: HIT zinc fing 51.6 8 0.00017 25.9 1.0 23 62-85 3-25 (30)
14 PRK14873 primosome assembly pr 49.3 9.5 0.00021 42.0 1.8 37 38-79 392-428 (665)
15 PF08149 BING4CT: BING4CT (NUC 44.2 35 0.00075 28.1 3.8 45 250-310 25-70 (80)
16 PF02045 CBFB_NFYA: CCAAT-bind 44.2 24 0.00053 27.4 2.8 38 302-339 12-58 (58)
17 PF14776 UNC-79: Cation-channe 43.4 12 0.00026 40.2 1.3 63 38-101 227-309 (525)
18 PF07649 C1_3: C1-like domain; 41.7 9.3 0.0002 25.0 0.2 26 20-50 2-27 (30)
19 TIGR00622 ssl1 transcription f 40.5 26 0.00057 30.4 2.8 21 73-93 81-101 (112)
20 PF13248 zf-ribbon_3: zinc-rib 38.6 23 0.00049 22.6 1.6 25 17-47 1-25 (26)
21 KOG1705 Uncharacterized conser 37.4 26 0.00056 29.8 2.2 48 26-73 4-55 (110)
22 smart00521 CBF CCAAT-Binding t 37.1 56 0.0012 25.7 3.8 25 317-341 36-61 (62)
23 PF12773 DZR: Double zinc ribb 36.9 35 0.00077 24.3 2.6 28 36-69 10-37 (50)
24 PRK14559 putative protein seri 36.2 28 0.00062 38.3 2.9 50 19-85 2-53 (645)
25 PF07975 C1_4: TFIIH C1-like d 35.9 13 0.00027 28.1 0.1 22 72-93 20-41 (51)
26 cd02335 ZZ_ADA2 Zinc finger, Z 32.8 44 0.00096 24.3 2.6 39 63-101 2-44 (49)
27 COG1198 PriA Primosomal protei 32.2 29 0.00064 38.8 2.2 49 18-82 435-484 (730)
28 PF09776 Mitoc_L55: Mitochondr 30.0 26 0.00056 30.7 1.1 41 260-311 50-93 (116)
29 TIGR00595 priA primosomal prot 29.4 32 0.00069 36.5 1.8 36 38-78 222-258 (505)
30 PF09416 UPF1_Zn_bind: RNA hel 27.1 83 0.0018 28.8 3.8 69 20-88 2-94 (152)
31 PF03660 PHF5: PHF5-like prote 26.7 14 0.00031 31.8 -1.1 22 41-69 30-51 (106)
32 KOG0954 PHD finger protein [Ge 25.7 36 0.00079 38.2 1.5 58 17-77 270-330 (893)
33 KOG0129 Predicted RNA-binding 24.7 25 0.00054 37.7 0.1 32 63-94 457-495 (520)
34 cd02341 ZZ_ZZZ3 Zinc finger, Z 24.6 63 0.0014 23.8 2.1 28 64-91 3-36 (48)
35 PRK14890 putative Zn-ribbon RN 23.7 53 0.0012 25.6 1.7 49 18-80 7-55 (59)
36 PRK14714 DNA polymerase II lar 22.6 60 0.0013 38.6 2.5 29 315-343 1150-1178(1337)
37 PRK04023 DNA polymerase II lar 22.3 67 0.0015 37.4 2.8 30 316-345 935-964 (1121)
38 PRK04023 DNA polymerase II lar 22.1 69 0.0015 37.4 2.8 10 18-27 626-635 (1121)
39 KOG2177 Predicted E3 ubiquitin 22.0 76 0.0017 28.5 2.6 17 72-88 96-112 (386)
40 KOG1561 CCAAT-binding factor, 20.8 86 0.0019 31.7 2.9 49 299-347 191-247 (307)
41 smart00249 PHD PHD zinc finger 20.3 94 0.002 20.6 2.3 26 21-51 2-27 (47)
42 PF14239 RRXRR: RRXRR protein 20.2 85 0.0018 29.3 2.6 37 305-343 92-128 (176)
No 1
>PF06203 CCT: CCT motif; InterPro: IPR010402 The CCT (CONSTANS, CO-like, and TOC1) domain is a highly conserved basic module of ~43 amino acids, which is found near the C terminus of plant proteins often involved in light signal transduction. The CCT domain is found in association with other domains, such as the B-box zinc finger, the GATA-type zinc finger, the ZIM motif or the response regulatory domain. The CCT domain contains a putative nuclear localisation signal within the second half of the CCT motif and has been shown to be involved in nuclear localization and probably also has a role in protein-protein interaction [].; GO: 0005515 protein binding
Probab=99.80 E-value=2.4e-20 Score=135.11 Aligned_cols=45 Identities=71% Similarity=1.074 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhhhhcccccccchhhhhhhhhCCCCCcccccCCc
Q 017738 300 RVAKVLRYREKRKARRFEKKIRYASRKAYAEARPRVKGRFARKTE 344 (366)
Q Consensus 300 R~~~~~ryreKrk~R~f~k~irY~~Rk~~A~~RpRvkGrF~k~~~ 344 (366)
|+++|+||+|||++|+|+|+|+|++||++|+.|||||||||+.++
T Consensus 1 R~~~l~Ry~~Kr~~R~f~kkirY~~Rk~~A~~R~RvkGRFvk~~e 45 (45)
T PF06203_consen 1 REEKLQRYREKRKRRNFEKKIRYESRKAVADKRPRVKGRFVKKSE 45 (45)
T ss_pred CHHHHHHHHHHHHhhcccccCCcchHHHHHhhCCccCCcccCCCC
Confidence 689999999999999999999999999999999999999999864
No 2
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=97.24 E-value=0.00021 Score=48.73 Aligned_cols=38 Identities=32% Similarity=0.652 Sum_probs=33.7
Q ss_pred cCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccc
Q 017738 20 TCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWV 63 (366)
Q Consensus 20 ~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~L 63 (366)
.|+.++.+++.+||..|.+.+|..|+...|. .|.+++|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 6999998899999999999999999988774 5888765
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=97.24 E-value=0.00019 Score=48.87 Aligned_cols=39 Identities=31% Similarity=0.487 Sum_probs=33.6
Q ss_pred cccccCCCCcceeEecccccccccccccCCCCCCcccCCCCCcccc
Q 017738 62 WVSAACENGQATFSCNTDAASLRLSCDADKHLANFLAHHHHARVPA 107 (366)
Q Consensus 62 ~LCe~C~~~PA~v~C~aD~a~LC~sCD~~iHsaN~la~rH~~RvPv 107 (366)
++|+.|+..++.+||..|...+|..|+...|. .| .++||
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H-~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GH-RRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CC-CEeeC
Confidence 36888888899999999999999999998863 68 88775
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.85 E-value=0.00091 Score=46.15 Aligned_cols=41 Identities=27% Similarity=0.326 Sum_probs=34.6
Q ss_pred cccccccCCCCcceeEecccccccccccccCCCCCCcccCCCCCcccc
Q 017738 60 RMWVSAACENGQATFSCNTDAASLRLSCDADKHLANFLAHHHHARVPA 107 (366)
Q Consensus 60 Rv~LCe~C~~~PA~v~C~aD~a~LC~sCD~~iHsaN~la~rH~~RvPv 107 (366)
|.++|+.|+..++.+||..|...||..|....| +.| .++||
T Consensus 2 ~~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H-~~~~l 42 (42)
T smart00336 2 RPPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGH-TVVLL 42 (42)
T ss_pred cCCcCCCCCCCceEEECCCCCcccccccChhhc------CCC-ceecC
Confidence 577899999889999999999999999998755 457 66654
No 5
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.75 E-value=0.00062 Score=47.59 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=33.9
Q ss_pred ccccccCCCCcceeEecccccccccccccCCCCCCcccCCCCCcccc
Q 017738 61 MWVSAACENGQATFSCNTDAASLRLSCDADKHLANFLAHHHHARVPA 107 (366)
Q Consensus 61 v~LCe~C~~~PA~v~C~aD~a~LC~sCD~~iHsaN~la~rH~~RvPv 107 (366)
.++|..|+..++.+||..|..+||..|....|.. | ..+||
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H-~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------H-KIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------S-EEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC------C-EEeEC
Confidence 4689999998899999999999999999999753 7 77765
No 6
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=96.54 E-value=0.00075 Score=61.36 Aligned_cols=94 Identities=26% Similarity=0.219 Sum_probs=68.4
Q ss_pred cccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccccccCCCCcce--eEeccccccc----ccccccCC
Q 017738 18 MRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWVSAACENGQAT--FSCNTDAASL----RLSCDADK 91 (366)
Q Consensus 18 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~PA~--v~C~aD~a~L----C~sCD~~i 91 (366)
...|+.|....... |..|...+|..|+.+++..+.+...|.++.++..|...++. +.+..+...+ +..++...
T Consensus 5 ~~~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (340)
T KOG1601|consen 5 AEDLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFV 83 (340)
T ss_pred cccccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccc
Confidence 34566666655555 99999999999999999998777789999999988733322 4555555555 56688888
Q ss_pred CCCCcccCCCCCccccCCCCCC
Q 017738 92 HLANFLAHHHHARVPAPPFSDL 113 (366)
Q Consensus 92 HsaN~la~rH~~RvPv~~~~~~ 113 (366)
+..++...+| ..+++.+....
T Consensus 84 ~~~~~~~~~~-~~~~~~~~~~~ 104 (340)
T KOG1601|consen 84 SENNPNSLRH-PPVPSMPSSNS 104 (340)
T ss_pred ccccCCCCCC-CCccccccccc
Confidence 8777777788 66766666543
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.22 E-value=0.0038 Score=43.01 Aligned_cols=40 Identities=23% Similarity=0.541 Sum_probs=33.6
Q ss_pred cccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccc
Q 017738 18 MRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWV 63 (366)
Q Consensus 18 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~L 63 (366)
.+.|..|...++.+||..|.+.+|..|....| +.|.+++|
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 46799999889999999999999999998766 45776654
No 8
>PF09425 CCT_2: Divergent CCT motif; InterPro: IPR018467 The short CCT (CO, COL, TOC1) motif is found in a number of plant proteins, including Constans (CO), Constans-like (COL) and TOC1. The CCT motif is about 45 amino acids long and contains a putative nuclear localisation signal within the second half of the CCT motif []. The CCT motif is found in the Arabidopsis circadian rhythm protein TOC1, an autoregulatory response regulator homologue the controls the photoperiodic flowering through its clock function []. ; GO: 0005515 protein binding; PDB: 3OGK_V 3OGL_S 3OGM_W.
Probab=96.10 E-value=0.0033 Score=41.37 Aligned_cols=26 Identities=42% Similarity=0.588 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHhhhhcccccccch
Q 017738 297 PMNRVAKVLRYREKRKARRFEKKIRYA 323 (366)
Q Consensus 297 ~~~R~~~~~ryreKrk~R~f~k~irY~ 323 (366)
|..|.+.|+||.||||.|... +..|.
T Consensus 1 P~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 1 PIARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp -----HHHHHHHHHH------------
T ss_pred CchHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 357999999999999999987 66664
No 9
>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=95.90 E-value=0.0054 Score=42.80 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=34.2
Q ss_pred cccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccc
Q 017738 18 MRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWV 63 (366)
Q Consensus 18 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~L 63 (366)
...|..|...++.+||..+...||..|....|.. |..++|
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 5689999998899999999999999999988864 777654
No 10
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=95.30 E-value=0.0058 Score=63.33 Aligned_cols=78 Identities=18% Similarity=0.365 Sum_probs=61.8
Q ss_pred cccCcccCCC--CeeEEeeCCCccccccccccccccccCcCCcccccc----------------cccCCCCcceeEeccc
Q 017738 18 MRTCNTCKAA--VSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWV----------------SAACENGQATFSCNTD 79 (366)
Q Consensus 18 ~~~Cd~C~~~--~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~L----------------Ce~C~~~PA~v~C~aD 79 (366)
.-.|.+|+++ .|+|+|..+..|.|.-|..+.|-+-.-.++|.-++- |.-.+-..-..||..|
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~c 241 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQC 241 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEec
Confidence 4579999885 499999999999999999999987777777765442 4343444457999999
Q ss_pred ccccccccccCCCCCC
Q 017738 80 AASLRLSCDADKHLAN 95 (366)
Q Consensus 80 ~a~LC~sCD~~iHsaN 95 (366)
.+++|-.|-.++-++|
T Consensus 242 k~pvc~~clee~khs~ 257 (699)
T KOG4367|consen 242 KMPVCYQCLEEGKHSS 257 (699)
T ss_pred CChHHHHHHHhhcccc
Confidence 9999999988874443
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=78.18 E-value=3.7 Score=37.19 Aligned_cols=42 Identities=64% Similarity=0.956 Sum_probs=40.6
Q ss_pred CHHHHHHHHHHHHHHhhhhcccccccchhhhhhhhhCCCCCc
Q 017738 296 SPMNRVAKVLRYREKRKARRFEKKIRYASRKAYAEARPRVKG 337 (366)
Q Consensus 296 ~~~~R~~~~~ryreKrk~R~f~k~irY~~Rk~~A~~RpRvkG 337 (366)
....|++.+.||++|++.|.|.|+|+|..||..|+.|||+||
T Consensus 289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 577999999999999999999999999999999999999999
No 12
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=63.22 E-value=2.7 Score=44.25 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=37.8
Q ss_pred ccccCCCCc--ceeEecccccccccccccCCCCCCcccCCCCCccccC
Q 017738 63 VSAACENGQ--ATFSCNTDAASLRLSCDADKHLANFLAHHHHARVPAP 108 (366)
Q Consensus 63 LCe~C~~~P--A~v~C~aD~a~LC~sCD~~iHsaN~la~rH~~RvPv~ 108 (366)
.|..|+.+| |.++|..|....|.-|....|-+-+..++| ..+|-.
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh-~l~~~~ 210 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKH-RLVPPA 210 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhc-ccCCcc
Confidence 488888887 889999999999999999999777767788 666643
No 13
>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=51.60 E-value=8 Score=25.89 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=17.6
Q ss_pred cccccCCCCcceeEeccccccccc
Q 017738 62 WVSAACENGQATFSCNTDAASLRL 85 (366)
Q Consensus 62 ~LCe~C~~~PA~v~C~aD~a~LC~ 85 (366)
.+|.+|+. ++.+.|+.|.+..|.
T Consensus 3 ~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-EESEE-TTT--EESS
T ss_pred CCCccCcC-CCEEECCCcCCceeC
Confidence 58999998 999999999999884
No 14
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.33 E-value=9.5 Score=42.00 Aligned_cols=37 Identities=11% Similarity=0.183 Sum_probs=23.0
Q ss_pred ccccccccccccccccCcCCcccccccccCCCCcceeEeccc
Q 017738 38 AYFCDSCDERVHAYNSMALPHERMWVSAACENGQATFSCNTD 79 (366)
Q Consensus 38 A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~PA~v~C~aD 79 (366)
..-|..||..+-.. +..+...|..|+.......|+.|
T Consensus 392 ~~~C~~C~~~L~~h-----~~~~~l~Ch~CG~~~~p~~Cp~C 428 (665)
T PRK14873 392 PARCRHCTGPLGLP-----SAGGTPRCRWCGRAAPDWRCPRC 428 (665)
T ss_pred eeECCCCCCceeEe-----cCCCeeECCCCcCCCcCccCCCC
Confidence 67788888754321 23456789999875444445444
No 15
>PF08149 BING4CT: BING4CT (NUC141) domain; InterPro: IPR012952 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This C-terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins [].
Probab=44.25 E-value=35 Score=28.13 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=29.0
Q ss_pred CCcccccccc-ccCCCCCccccccccCCCCCCCCCCCCCCccccCCCCHHHHHHHHHHHHHH
Q 017738 250 SMSQTVPVSG-ILPKATRADISSSYTKYSQGTNDLFPNFSFFVPLQFSPMNRVAKVLRYREK 310 (366)
Q Consensus 250 s~s~svs~ss-vvp~~~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~R~~~~~ryreK 310 (366)
.++|+-.+|| |||.+..+.+.. +-.+|.+ -..+.||.-|.+-.||
T Consensus 25 gvGh~~G~sSiiVPGsGe~NfDs------------~e~NP~e----t~kqRrE~EV~~LLeK 70 (80)
T PF08149_consen 25 GVGHSKGFSSIIVPGSGEPNFDS------------LEANPFE----TKKQRREREVRSLLEK 70 (80)
T ss_pred EeeccCceeEEeccCCCCCCCCc------------ccCCccc----chhHHhHHHHHHHHHh
Confidence 5688888889 999987654422 1122332 2456777778888877
No 16
>PF02045 CBFB_NFYA: CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B; InterPro: IPR001289 The CCAAT-binding factor (CBFB/NF-YA) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin []. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding []. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The B subunit contains a region of similarity with the yeast protein HAP2 []. For the B subunit it has been suggested that the N-terminal portion of the conserved region is involved in subunit interaction and the C-terminal region involved in DNA-binding [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=44.15 E-value=24 Score=27.36 Aligned_cols=38 Identities=37% Similarity=0.463 Sum_probs=26.1
Q ss_pred HHHHHHHHHhhhhcc--------cccccchhhhhhhhhCCC-CCccc
Q 017738 302 AKVLRYREKRKARRF--------EKKIRYASRKAYAEARPR-VKGRF 339 (366)
Q Consensus 302 ~~~~ryreKrk~R~f--------~k~irY~~Rk~~A~~RpR-vkGrF 339 (366)
.+|+|-|+.|.+--- .|+.-++||-..|-.||| --|||
T Consensus 12 ~rIlrRR~~Rakle~~~k~~~~~rk~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 12 HRILRRRQARAKLEAEGKLSPKKRKPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred HHHHHHHHHHHHHHHhCCcchhhhHHHHHHHHHHHHHcCccCCCCCC
Confidence 455555555544333 344578899999999999 67787
No 17
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=43.44 E-value=12 Score=40.18 Aligned_cols=63 Identities=21% Similarity=0.425 Sum_probs=40.5
Q ss_pred ccccccccccccccccCcCC-ccccc------ccc--cCCCC--cceeEec---------ccccccccccccCCCCCCcc
Q 017738 38 AYFCDSCDERVHAYNSMALP-HERMW------VSA--ACENG--QATFSCN---------TDAASLRLSCDADKHLANFL 97 (366)
Q Consensus 38 A~LC~~CDa~vH~aN~La~r-H~Rv~------LCe--~C~~~--PA~v~C~---------aD~a~LC~sCD~~iHsaN~l 97 (366)
.|||..|...||+.-+.... +.=-| .|+ .|.++ .|++.|. .-...+|..|....|+ |.-
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 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHN-NRR 305 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhcc-ccc
Confidence 57999999999975433222 11111 366 57544 4888884 3456899999998885 444
Q ss_pred cCCC
Q 017738 98 AHHH 101 (366)
Q Consensus 98 a~rH 101 (366)
...|
T Consensus 306 ~~dH 309 (525)
T PF14776_consen 306 GSDH 309 (525)
T ss_pred ccce
Confidence 4456
No 18
>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=41.67 E-value=9.3 Score=24.98 Aligned_cols=26 Identities=27% Similarity=0.758 Sum_probs=9.3
Q ss_pred cCcccCCCCeeEEeeCCCccccccccccccc
Q 017738 20 TCNTCKAAVSTLYCHTHLAYFCDSCDERVHA 50 (366)
Q Consensus 20 ~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~ 50 (366)
.|+.|+...-. +..|-|..||..+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 58888874332 356789999998884
No 19
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.47 E-value=26 Score=30.44 Aligned_cols=21 Identities=19% Similarity=0.407 Sum_probs=19.1
Q ss_pred eeEecccccccccccccCCCC
Q 017738 73 TFSCNTDAASLRLSCDADKHL 93 (366)
Q Consensus 73 ~v~C~aD~a~LC~sCD~~iHs 93 (366)
.+.|..|.-.+|.+||+-||.
T Consensus 81 ~y~C~~C~~~FC~dCD~fiHe 101 (112)
T TIGR00622 81 RYVCAVCKNVFCVDCDVFVHE 101 (112)
T ss_pred ceeCCCCCCccccccchhhhh
Confidence 467999999999999999995
No 20
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=38.64 E-value=23 Score=22.63 Aligned_cols=25 Identities=28% Similarity=0.644 Sum_probs=16.5
Q ss_pred CcccCcccCCCCeeEEeeCCCcccccccccc
Q 017738 17 WMRTCNTCKAAVSTLYCHTHLAYFCDSCDER 47 (366)
Q Consensus 17 ~~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~ 47 (366)
|...|-.|+... .+.+..|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 456777787732 4567778777664
No 21
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=37.36 E-value=26 Score=29.77 Aligned_cols=48 Identities=17% Similarity=0.480 Sum_probs=27.0
Q ss_pred CCCeeEEeeCC----CccccccccccccccccCcCCcccccccccCCCCcce
Q 017738 26 AAVSTLYCHTH----LAYFCDSCDERVHAYNSMALPHERMWVSAACENGQAT 73 (366)
Q Consensus 26 ~~~A~vyC~aD----~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~PA~ 73 (366)
+.+-.|.|+-- -..||..||.+----..-++--.-|.+|+.|.-..-.
T Consensus 4 HhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q 55 (110)
T KOG1705|consen 4 HHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQ 55 (110)
T ss_pred cCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCcccc
Confidence 34667777753 3578888887643222212222336678888654433
No 22
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=37.12 E-value=56 Score=25.70 Aligned_cols=25 Identities=40% Similarity=0.456 Sum_probs=21.9
Q ss_pred cccccchhhhhhhhhCCC-CCccccc
Q 017738 317 EKKIRYASRKAYAEARPR-VKGRFAR 341 (366)
Q Consensus 317 ~k~irY~~Rk~~A~~RpR-vkGrF~k 341 (366)
.|..-++||-..|-.||| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567889999999999999 6789975
No 23
>PF12773 DZR: Double zinc ribbon
Probab=36.91 E-value=35 Score=24.32 Aligned_cols=28 Identities=21% Similarity=0.495 Sum_probs=14.8
Q ss_pred CCccccccccccccccccCcCCcccccccccCCC
Q 017738 36 HLAYFCDSCDERVHAYNSMALPHERMWVSAACEN 69 (366)
Q Consensus 36 D~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~ 69 (366)
+.+..|..|...+- .......+|..|..
T Consensus 10 ~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP------PPDQSKKICPNCGA 37 (50)
T ss_pred ccccCChhhcCChh------hccCCCCCCcCCcC
Confidence 45666666665544 12333445666654
No 24
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.19 E-value=28 Score=38.34 Aligned_cols=50 Identities=18% Similarity=0.418 Sum_probs=31.6
Q ss_pred ccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccccccCCCC--cceeEeccccccccc
Q 017738 19 RTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWVSAACENG--QATFSCNTDAASLRL 85 (366)
Q Consensus 19 ~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~--PA~v~C~aD~a~LC~ 85 (366)
..|-.|+.. -.+.+++|..|.+.+- + ..|..|+.. +..-||..|...+=.
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~--------~---~~Cp~CG~~~~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLT--------H---KPCPQCGTEVPVDEAHCPNCGAETGT 53 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCC--------C---CcCCCCCCCCCcccccccccCCcccc
Confidence 468888875 2467888999977652 1 258888764 234456655555433
No 25
>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=35.88 E-value=13 Score=28.07 Aligned_cols=22 Identities=18% Similarity=0.431 Sum_probs=15.3
Q ss_pred ceeEecccccccccccccCCCC
Q 017738 72 ATFSCNTDAASLRLSCDADKHL 93 (366)
Q Consensus 72 A~v~C~aD~a~LC~sCD~~iHs 93 (366)
..+.|+.|...+|..||+-||.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTT
T ss_pred CeEECCCCCCccccCcChhhhc
Confidence 5688999999999999999995
No 26
>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=32.76 E-value=44 Score=24.30 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=26.6
Q ss_pred ccccCCCCcc---eeEeccc-ccccccccccCCCCCCcccCCC
Q 017738 63 VSAACENGQA---TFSCNTD-AASLRLSCDADKHLANFLAHHH 101 (366)
Q Consensus 63 LCe~C~~~PA---~v~C~aD-~a~LC~sCD~~iHsaN~la~rH 101 (366)
.|+.|...+. .+.|..| ..-||..|-......+..-..|
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H 44 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDH 44 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCC
Confidence 4788876664 3778888 7789999988775443333334
No 27
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.20 E-value=29 Score=38.81 Aligned_cols=49 Identities=16% Similarity=0.308 Sum_probs=32.3
Q ss_pred cccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccccccCCCC-cceeEecccccc
Q 017738 18 MRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWVSAACENG-QATFSCNTDAAS 82 (366)
Q Consensus 18 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~-PA~v~C~aD~a~ 82 (366)
...|..|+. ..=|..||..+-. .++.+...|..|+.+ +-...|+.|...
T Consensus 435 ~l~C~~Cg~-----------v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGY-----------IAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCC-----------cccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 446777776 5668889876432 245688889999877 555555555443
No 28
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=30.03 E-value=26 Score=30.69 Aligned_cols=41 Identities=17% Similarity=0.283 Sum_probs=24.7
Q ss_pred ccCCCCCccccccccCCCCCCCCCCCCCCcccc---CCCCHHHHHHHHHHHHHHh
Q 017738 260 ILPKATRADISSSYTKYSQGTNDLFPNFSFFVP---LQFSPMNRVAKVLRYREKR 311 (366)
Q Consensus 260 vvp~~~~~d~~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~~R~~~~~ryreKr 311 (366)
|-||++...|....++ -. ++|| ..||+++|.+++.+-+-|+
T Consensus 50 V~pDGSTI~Iry~EPR---~i--------i~mPlDl~~LSeeERk~rl~kR~pk~ 93 (116)
T PF09776_consen 50 VRPDGSTINIRYHEPR---RI--------IKMPLDLDTLSEEERKARLRKRKPKK 93 (116)
T ss_pred EecCCCEEEEeccChH---HH--------hccccCcccCCHHHHHHHHHHhCCcc
Confidence 7789876666443221 11 2233 3579999999987654443
No 29
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.38 E-value=32 Score=36.54 Aligned_cols=36 Identities=17% Similarity=0.336 Sum_probs=21.7
Q ss_pred ccccccccccccccccCcCCcccccccccCCCCcc-eeEecc
Q 017738 38 AYFCDSCDERVHAYNSMALPHERMWVSAACENGQA-TFSCNT 78 (366)
Q Consensus 38 A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~PA-~v~C~a 78 (366)
..-|..||..+-.. ++.+...|..|+.... ...|+.
T Consensus 222 ~~~C~~C~~~l~~h-----~~~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 222 ILCCPNCDVSLTYH-----KKEGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred ccCCCCCCCceEEe-----cCCCeEEcCCCcCcCCCCCCCCC
Confidence 67788998754221 3455677888876543 334443
No 30
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=27.10 E-value=83 Score=28.79 Aligned_cols=69 Identities=19% Similarity=0.431 Sum_probs=35.1
Q ss_pred cCcccC--CCCeeEEeeCCCcccccccccc--ccccccC-cCCccccc------------ccccCCCCcc----eeEecc
Q 017738 20 TCNTCK--AAVSTLYCHTHLAYFCDSCDER--VHAYNSM-ALPHERMW------------VSAACENGQA----TFSCNT 78 (366)
Q Consensus 20 ~Cd~C~--~~~A~vyC~aD~A~LC~~CDa~--vH~aN~L-a~rH~Rv~------------LCe~C~~~PA----~v~C~a 78 (366)
.|.+|+ ...++|.|....-.+|-+=+.. -|--|-| .+||.-|. -|-.|+.... .+-.++
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~NvF~LGFipak~ 81 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKS 81 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT----TTTEEEEEETT
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCCceeeEEEEEecc
Confidence 599999 7889999999999999865531 2222222 34555433 2777876653 344555
Q ss_pred cc--cccccc-cc
Q 017738 79 DA--ASLRLS-CD 88 (366)
Q Consensus 79 D~--a~LC~s-CD 88 (366)
+. ..||+. |-
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 55 578876 63
No 31
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=26.70 E-value=14 Score=31.78 Aligned_cols=22 Identities=23% Similarity=0.617 Sum_probs=7.5
Q ss_pred cccccccccccccCcCCcccccccccCCC
Q 017738 41 CDSCDERVHAYNSMALPHERMWVSAACEN 69 (366)
Q Consensus 41 C~~CDa~vH~aN~La~rH~Rv~LCe~C~~ 69 (366)
|.-||.-|.- ...|.+|+.|..
T Consensus 30 CpiCDS~Vrp-------~~~VrICdeCs~ 51 (106)
T PF03660_consen 30 CPICDSYVRP-------CTKVRICDECSF 51 (106)
T ss_dssp -TTT--------------EE-EEEHHHHT
T ss_pred ccccCCccCC-------cceEEECCcCCC
Confidence 5555554443 355667665543
No 32
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=25.71 E-value=36 Score=38.25 Aligned_cols=58 Identities=22% Similarity=0.457 Sum_probs=36.1
Q ss_pred CcccCcccCCCCeeEEeeCCCcccccccccccccccc-CcCCcccccccccCCC--CcceeEec
Q 017738 17 WMRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNS-MALPHERMWVSAACEN--GQATFSCN 77 (366)
Q Consensus 17 ~~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~-La~rH~Rv~LCe~C~~--~PA~v~C~ 77 (366)
-..+||+|+..-.- .++...+|..|..-||.+=. |..--.--|||..|.. .|.-|.|+
T Consensus 270 edviCDvCrspD~e---~~neMVfCd~Cn~cVHqaCyGIle~p~gpWlCr~Calg~~ppCvLCP 330 (893)
T KOG0954|consen 270 EDVICDVCRSPDSE---EANEMVFCDKCNICVHQACYGILEVPEGPWLCRTCALGIEPPCVLCP 330 (893)
T ss_pred ccceeceecCCCcc---ccceeEEeccchhHHHHhhhceeecCCCCeeehhccccCCCCeeecc
Confidence 46799999985332 14566778888888887532 3334446678777743 23344453
No 33
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=24.74 E-value=25 Score=37.71 Aligned_cols=32 Identities=28% Similarity=0.326 Sum_probs=28.2
Q ss_pred ccccCCC-----CcceeEec--ccccccccccccCCCCC
Q 017738 63 VSAACEN-----GQATFSCN--TDAASLRLSCDADKHLA 94 (366)
Q Consensus 63 LCe~C~~-----~PA~v~C~--aD~a~LC~sCD~~iHsa 94 (366)
+|+.|+. ..|.+||. .|--..|..|-..+|+-
T Consensus 457 ~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 457 LCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG 495 (520)
T ss_pred chhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC
Confidence 5998887 78999995 69999999999999975
No 34
>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=24.60 E-value=63 Score=23.84 Aligned_cols=28 Identities=14% Similarity=0.345 Sum_probs=21.1
Q ss_pred cccCCCCc---ceeEecccc---cccccccccCC
Q 017738 64 SAACENGQ---ATFSCNTDA---ASLRLSCDADK 91 (366)
Q Consensus 64 Ce~C~~~P---A~v~C~aD~---a~LC~sCD~~i 91 (366)
|+.|...| ..+.|..|. --||..|-...
T Consensus 3 Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 3 CDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 77777755 346777776 78999997765
No 35
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.74 E-value=53 Score=25.60 Aligned_cols=49 Identities=14% Similarity=0.567 Sum_probs=26.7
Q ss_pred cccCcccCCCCeeEEeeCCCccccccccccccccccCcCCcccccccccCCCCcceeEecccc
Q 017738 18 MRTCNTCKAAVSTLYCHTHLAYFCDSCDERVHAYNSMALPHERMWVSAACENGQATFSCNTDA 80 (366)
Q Consensus 18 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~aN~La~rH~Rv~LCe~C~~~PA~v~C~aD~ 80 (366)
.+.|..|+..-+-. ..-..+.|..|.+. -++.|..|..+...+.|+.|.
T Consensus 7 ~~~CtSCg~~i~~~--~~~~~F~CPnCG~~------------~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 7 PPKCTSCGIEIAPR--EKAVKFLCPNCGEV------------IIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred CccccCCCCcccCC--CccCEeeCCCCCCe------------eEeechhHHhcCCceECCCCC
Confidence 45677776533211 01245677777553 123477776666666666654
No 36
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.56 E-value=60 Score=38.64 Aligned_cols=29 Identities=21% Similarity=0.304 Sum_probs=22.6
Q ss_pred cccccccchhhhhhhhhCCCCCcccccCC
Q 017738 315 RFEKKIRYASRKAYAEARPRVKGRFARKT 343 (366)
Q Consensus 315 ~f~k~irY~~Rk~~A~~RpRvkGrF~k~~ 343 (366)
-|+++.+|+.=|.+.+..-||+-|.-+..
T Consensus 1150 fYeat~~~~~p~ev~~~i~~ve~rlg~~~ 1178 (1337)
T PRK14714 1150 FYEATLEMADPKDVEDLIERVEDRLGTPE 1178 (1337)
T ss_pred HHHHHhccCCHHHHHHHHHHHHHhcCCch
Confidence 36778888888888888888888877654
No 37
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.28 E-value=67 Score=37.44 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=21.3
Q ss_pred ccccccchhhhhhhhhCCCCCcccccCCcc
Q 017738 316 FEKKIRYASRKAYAEARPRVKGRFARKTEM 345 (366)
Q Consensus 316 f~k~irY~~Rk~~A~~RpRvkGrF~k~~~~ 345 (366)
|+++.+|+.=|.+.+..-+|+.|.-+....
T Consensus 935 Yeat~~~~~P~ev~~~i~~ve~rlgt~~qy 964 (1121)
T PRK04023 935 YEATLEGADPKEVEDIMDTVEDRLGTPEQY 964 (1121)
T ss_pred HHHHhccCCHHHHHHHHHHHHHhcCCchhc
Confidence 567778888887777777777777665533
No 38
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.06 E-value=69 Score=37.36 Aligned_cols=10 Identities=30% Similarity=0.840 Sum_probs=6.1
Q ss_pred cccCcccCCC
Q 017738 18 MRTCNTCKAA 27 (366)
Q Consensus 18 ~~~Cd~C~~~ 27 (366)
.+.|..|+..
T Consensus 626 ~RfCpsCG~~ 635 (1121)
T PRK04023 626 RRKCPSCGKE 635 (1121)
T ss_pred CccCCCCCCc
Confidence 4566666664
No 39
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.96 E-value=76 Score=28.50 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=15.8
Q ss_pred ceeEecccccccccccc
Q 017738 72 ATFSCNTDAASLRLSCD 88 (366)
Q Consensus 72 A~v~C~aD~a~LC~sCD 88 (366)
..++|..|...+|..|.
T Consensus 96 ~~~~c~~~~~~~c~~c~ 112 (386)
T KOG2177|consen 96 LKLFCEEDEKLLCVLCR 112 (386)
T ss_pred ceEEecccccccCCCCC
Confidence 47999999999999999
No 40
>KOG1561 consensus CCAAT-binding factor, subunit B (HAP2) [Transcription]
Probab=20.76 E-value=86 Score=31.72 Aligned_cols=49 Identities=29% Similarity=0.320 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHhhhh-------cccccccchhhhhhhhhCCC-CCcccccCCcccc
Q 017738 299 NRVAKVLRYREKRKAR-------RFEKKIRYASRKAYAEARPR-VKGRFARKTEMDF 347 (366)
Q Consensus 299 ~R~~~~~ryreKrk~R-------~f~k~irY~~Rk~~A~~RpR-vkGrF~k~~~~~~ 347 (366)
.-..+|+|-|+-|.+- +=.|+---++|-..|-+||| --|||....+.+.
T Consensus 191 KQY~~IlrRRq~RaKlEa~~klik~RkpYLHESRH~HAmkR~RG~GGRFln~k~~~~ 247 (307)
T KOG1561|consen 191 KQYHRILRRRQARAKLEATTKLIKARKPYLHESRHLHAMKRARGEGGRFLNTKEYHD 247 (307)
T ss_pred HHHHHHHHHHHHHhhhhhcccchhhcCccccchhhHHHhhcccCCCCCCCchhhhhh
Confidence 4455666666655332 22344556899999999999 9999999987654
No 41
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF14239 RRXRR: RRXRR protein
Probab=20.25 E-value=85 Score=29.35 Aligned_cols=37 Identities=38% Similarity=0.596 Sum_probs=30.0
Q ss_pred HHHHHHhhhhcccccccchhhhhhhhhCCCCCcccccCC
Q 017738 305 LRYREKRKARRFEKKIRYASRKAYAEARPRVKGRFARKT 343 (366)
Q Consensus 305 ~ryreKrk~R~f~k~irY~~Rk~~A~~RpRvkGrF~k~~ 343 (366)
...|.-|..|.|..++|| ||+.=+.|.|-+|.++..-
T Consensus 92 ~~RR~~RR~RR~~rk~Ry--R~~RF~NR~r~~gwL~PSl 128 (176)
T PF14239_consen 92 TQRRAYRRGRRYNRKTRY--RKARFDNRKRPKGWLPPSL 128 (176)
T ss_pred HHHHHHhhhccccccccc--ccccccccCCCCCCcCcCH
Confidence 666777888888888898 8888888888889887654
Done!