Query 016775
Match_columns 383
No_of_seqs 253 out of 715
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:41:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016775.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016775hhsearch_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 1.1E-19 2.4E-24 132.5 3.1 45 333-377 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00028 6.1E-09 48.4 2.8 38 59-102 2-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.0 0.00043 9.4E-09 47.4 2.1 38 16-59 2-39 (39)
4 smart00336 BBOX B-Box-type zin 96.7 0.0017 3.8E-08 45.0 3.2 41 56-102 2-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.7 0.001 2.2E-08 46.8 1.9 40 57-102 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.2 0.0034 7.4E-08 43.5 2.3 39 14-58 3-41 (42)
7 PF00643 zf-B_box: B-box zinc 95.8 0.0059 1.3E-07 42.9 2.1 41 13-59 2-42 (42)
8 PF09425 CCT_2: Divergent CCT 95.7 0.0058 1.2E-07 40.6 1.6 26 330-356 1-26 (27)
9 KOG1601 GATA-4/5/6 transcripti 95.3 0.0068 1.5E-07 55.4 1.0 42 329-370 289-330 (340)
10 KOG4367 Predicted Zn-finger pr 93.9 0.013 2.9E-07 61.1 -0.7 76 12-87 160-253 (699)
11 PF12773 DZR: Double zinc ribb 60.7 11 0.00024 27.2 3.1 30 31-66 9-38 (50)
12 smart00521 CBF CCAAT-Binding t 49.2 22 0.00048 28.1 3.3 25 350-374 36-61 (62)
13 cd02335 ZZ_ADA2 Zinc finger, Z 48.1 22 0.00047 26.2 3.0 30 59-88 2-35 (49)
14 PF04438 zf-HIT: HIT zinc fing 41.0 17 0.00037 24.5 1.4 24 57-81 2-25 (30)
15 KOG4367 Predicted Zn-finger pr 39.3 9.6 0.00021 40.6 -0.1 44 58-101 163-208 (699)
16 PRK14559 putative protein seri 38.8 23 0.00051 39.3 2.7 34 16-66 3-36 (645)
17 PRK14873 primosome assembly pr 35.3 21 0.00045 39.7 1.7 38 25-67 382-420 (665)
18 cd02341 ZZ_ZZZ3 Zinc finger, Z 33.8 42 0.00091 25.0 2.6 40 59-101 2-47 (48)
19 PF07975 C1_4: TFIIH C1-like d 32.8 22 0.00047 27.0 0.9 23 25-47 20-42 (51)
20 PF14239 RRXRR: RRXRR protein 32.7 38 0.00082 31.8 2.7 38 335-374 88-126 (176)
21 PF02045 CBFB_NFYA: CCAAT-bind 32.7 31 0.00068 27.0 1.8 23 350-372 35-58 (58)
22 KOG4301 Beta-dystrobrevin [Cyt 32.6 13 0.00028 38.5 -0.4 40 59-98 242-285 (434)
23 PF13248 zf-ribbon_3: zinc-rib 32.3 35 0.00076 21.9 1.7 24 14-43 2-25 (26)
24 PF07649 C1_3: C1-like domain; 26.8 22 0.00049 23.3 0.1 26 16-46 2-27 (30)
25 KOG3576 Ovo and related transc 24.9 13 0.00029 36.0 -1.7 49 8-57 111-167 (267)
26 PRK14714 DNA polymerase II lar 23.9 50 0.0011 39.5 2.2 18 15-32 668-685 (1337)
27 KOG1601 GATA-4/5/6 transcripti 22.4 1.1E+02 0.0024 27.8 3.8 48 16-64 7-54 (340)
28 PF04216 FdhE: Protein involve 21.1 60 0.0013 31.9 1.9 63 13-84 171-245 (290)
29 TIGR00595 priA primosomal prot 20.6 57 0.0012 34.9 1.7 37 25-66 212-249 (505)
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=99.77 E-value=1.1e-19 Score=132.48 Aligned_cols=45 Identities=64% Similarity=0.976 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHhhccCCCCcccchhhhhhhhcCCCCCcccccCCC
Q 016775 333 RGNAMLRYKEKKKNRSYGKQIRYESRKARADTRKRVKGRFVKASE 377 (383)
Q Consensus 333 R~~~~~ry~eKr~~R~~~k~irY~~Rk~~A~~R~RvkGrFvk~~~ 377 (383)
|+++|+||++||++|+|+|+|+|++||++||.|||||||||+.+|
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 688999999999999999999999999999999999999999875
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=97.21 E-value=0.00028 Score=48.35 Aligned_cols=38 Identities=39% Similarity=0.823 Sum_probs=33.1
Q ss_pred ccCCCCCCCeeEEecCCCccccCccCCCCCCCCCCCCCCceeee
Q 016775 59 ICDNCRAEPVSVRCCTENLMLCQDCDWDSHYNSSVSSVHERSSV 102 (383)
Q Consensus 59 LCd~C~~~pAsv~C~~d~a~LC~~CD~~~H~anslas~H~R~pv 102 (383)
+|+.|..+++.+||..|...+|..|++..|. .|.+.||
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 6999999899999999999999999987663 5888775
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=97.01 E-value=0.00043 Score=47.42 Aligned_cols=38 Identities=39% Similarity=0.756 Sum_probs=33.0
Q ss_pred cCcccCCCCcEEEeeCCCcccchhhhccccccchhhhhcccccc
Q 016775 16 LCDFCNSKLAVLYCTADSAKLCLFCDQQIHSANALSLRHLRSQI 59 (383)
Q Consensus 16 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv~L 59 (383)
.|+.++.+++.+||..|.+.+|..|+...|. .|.++++
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 6899998899999999999999999988775 5777653
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.69 E-value=0.0017 Score=45.00 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=33.9
Q ss_pred cccccCCCCCCCeeEEecCCCccccCccCCCCCCCCCCCCCCceeee
Q 016775 56 RSQICDNCRAEPVSVRCCTENLMLCQDCDWDSHYNSSVSSVHERSSV 102 (383)
Q Consensus 56 Rv~LCd~C~~~pAsv~C~~d~a~LC~~CD~~~H~anslas~H~R~pv 102 (383)
|...|+.|...++.+||..|...+|..|....| ..|.+.||
T Consensus 2 ~~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 2 RPPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred cCCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 567899999999999999999999999986544 35766654
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=96.67 E-value=0.001 Score=46.80 Aligned_cols=40 Identities=28% Similarity=0.543 Sum_probs=33.8
Q ss_pred ccccCCCCCCCeeEEecCCCccccCccCCCCCCCCCCCCCCceeee
Q 016775 57 SQICDNCRAEPVSVRCCTENLMLCQDCDWDSHYNSSVSSVHERSSV 102 (383)
Q Consensus 57 v~LCd~C~~~pAsv~C~~d~a~LC~~CD~~~H~anslas~H~R~pv 102 (383)
.+.|+.|...++.+||..|..++|..|....|.. |..+||
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 4689999999999999999999999999877753 877765
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.22 E-value=0.0034 Score=43.52 Aligned_cols=39 Identities=28% Similarity=0.457 Sum_probs=33.0
Q ss_pred CccCcccCCCCcEEEeeCCCcccchhhhccccccchhhhhccccc
Q 016775 14 LALCDFCNSKLAVLYCTADSAKLCLFCDQQIHSANALSLRHLRSQ 58 (383)
Q Consensus 14 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv~ 58 (383)
...|..+...++.+||..|.+.+|..|....| +.|.+.+
T Consensus 3 ~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~ 41 (42)
T smart00336 3 PPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVL 41 (42)
T ss_pred CCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceec
Confidence 56899999889999999999999999998766 3466554
No 7
>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=95.82 E-value=0.0059 Score=42.89 Aligned_cols=41 Identities=22% Similarity=0.322 Sum_probs=34.1
Q ss_pred CCccCcccCCCCcEEEeeCCCcccchhhhccccccchhhhhcccccc
Q 016775 13 MLALCDFCNSKLAVLYCTADSAKLCLFCDQQIHSANALSLRHLRSQI 59 (383)
Q Consensus 13 ~~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv~L 59 (383)
....|..|...++.+||..+...+|..|....|.. |..++|
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 35689999998899999999999999999998864 766543
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=95.74 E-value=0.0058 Score=40.57 Aligned_cols=26 Identities=27% Similarity=0.454 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHhhccCCCCcccch
Q 016775 330 AKNRGNAMLRYKEKKKNRSYGKQIRYE 356 (383)
Q Consensus 330 ~~~R~~~~~ry~eKr~~R~~~k~irY~ 356 (383)
|..|...|+||.||||.|... +..|.
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 357899999999999999987 66664
No 9
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=95.28 E-value=0.0068 Score=55.42 Aligned_cols=42 Identities=40% Similarity=0.703 Sum_probs=40.2
Q ss_pred cHHHHHHHHHHHHHHhhccCCCCcccchhhhhhhhcCCCCCc
Q 016775 329 LAKNRGNAMLRYKEKKKNRSYGKQIRYESRKARADTRKRVKG 370 (383)
Q Consensus 329 ~~~~R~~~~~ry~eKr~~R~~~k~irY~~Rk~~A~~R~RvkG 370 (383)
....|...+.||+++++.|.|.++|+|..||..|+.|+|+||
T Consensus 289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 577889999999999999999999999999999999999999
No 10
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=93.87 E-value=0.013 Score=61.11 Aligned_cols=76 Identities=18% Similarity=0.399 Sum_probs=64.1
Q ss_pred CCCccCcccCCCC--cEEEeeCCCcccchhhhccccccchhhhhcccc----------------cccCCCCCCCeeEEec
Q 016775 12 SMLALCDFCNSKL--AVLYCTADSAKLCLFCDQQIHSANALSLRHLRS----------------QICDNCRAEPVSVRCC 73 (383)
Q Consensus 12 ~~~~~Cd~C~~~~--A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv----------------~LCd~C~~~pAsv~C~ 73 (383)
...-.|.+|++++ |.|+|..+..+.|..|..+.|-+-.-..+|--+ ..|..+..+.-+.||.
T Consensus 160 ~aa~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~ 239 (699)
T KOG4367|consen 160 AAALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCV 239 (699)
T ss_pred HHhhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEE
Confidence 3456799999866 999999999999999999999876656677433 3599999999999999
Q ss_pred CCCccccCccCCCC
Q 016775 74 TENLMLCQDCDWDS 87 (383)
Q Consensus 74 ~d~a~LC~~CD~~~ 87 (383)
.|.+++|-.|-.+.
T Consensus 240 ~ck~pvc~~clee~ 253 (699)
T KOG4367|consen 240 QCKMPVCYQCLEEG 253 (699)
T ss_pred ecCChHHHHHHHhh
Confidence 99999999997653
No 11
>PF12773 DZR: Double zinc ribbon
Probab=60.67 E-value=11 Score=27.22 Aligned_cols=30 Identities=37% Similarity=0.749 Sum_probs=19.3
Q ss_pred CCCcccchhhhccccccchhhhhcccccccCCCCCC
Q 016775 31 ADSAKLCLFCDQQIHSANALSLRHLRSQICDNCRAE 66 (383)
Q Consensus 31 aD~A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~~~ 66 (383)
.+.+.+|..|...+- .......+|..|+..
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 456788888887665 223344577777764
No 12
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=49.17 E-value=22 Score=28.12 Aligned_cols=25 Identities=40% Similarity=0.457 Sum_probs=21.9
Q ss_pred CCcccchhhhhhhhcCCC-CCccccc
Q 016775 350 GKQIRYESRKARADTRKR-VKGRFVK 374 (383)
Q Consensus 350 ~k~irY~~Rk~~A~~R~R-vkGrFvk 374 (383)
.|..-+++|-..|-.|+| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567889999999999999 5689976
No 13
>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=48.09 E-value=22 Score=26.16 Aligned_cols=30 Identities=23% Similarity=0.661 Sum_probs=23.3
Q ss_pred ccCCCCCCCee---EEecCC-CccccCccCCCCC
Q 016775 59 ICDNCRAEPVS---VRCCTE-NLMLCQDCDWDSH 88 (383)
Q Consensus 59 LCd~C~~~pAs---v~C~~d-~a~LC~~CD~~~H 88 (383)
.|+.|...+.. +.|..| ..-||..|-....
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~ 35 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGA 35 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcC
Confidence 48888887654 889888 6789999976543
No 14
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=40.96 E-value=17 Score=24.49 Aligned_cols=24 Identities=25% Similarity=0.693 Sum_probs=17.8
Q ss_pred ccccCCCCCCCeeEEecCCCccccC
Q 016775 57 SQICDNCRAEPVSVRCCTENLMLCQ 81 (383)
Q Consensus 57 v~LCd~C~~~pAsv~C~~d~a~LC~ 81 (383)
..+|..|+. ++.+.|..+.+..|.
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESS
T ss_pred cCCCccCcC-CCEEECCCcCCceeC
Confidence 358999999 899999999998885
No 15
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=39.32 E-value=9.6 Score=40.59 Aligned_cols=44 Identities=20% Similarity=0.474 Sum_probs=36.7
Q ss_pred cccCCCCCCC--eeEEecCCCccccCccCCCCCCCCCCCCCCceee
Q 016775 58 QICDNCRAEP--VSVRCCTENLMLCQDCDWDSHYNSSVSSVHERSS 101 (383)
Q Consensus 58 ~LCd~C~~~p--Asv~C~~d~a~LC~~CD~~~H~anslas~H~R~p 101 (383)
.-|..|..+| |.|+|..|..+.|.-|....|-.-...+.|..+|
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~ 208 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVP 208 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCC
Confidence 4688888775 8999999999999999998888766667787665
No 16
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=38.75 E-value=23 Score=39.25 Aligned_cols=34 Identities=24% Similarity=0.803 Sum_probs=23.1
Q ss_pred cCcccCCCCcEEEeeCCCcccchhhhccccccchhhhhcccccccCCCCCC
Q 016775 16 LCDFCNSKLAVLYCTADSAKLCLFCDQQIHSANALSLRHLRSQICDNCRAE 66 (383)
Q Consensus 16 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~~~ 66 (383)
.|-.|+.. -.+.|++|..|...+- | ..|..|+..
T Consensus 3 ~Cp~Cg~~------n~~~akFC~~CG~~l~--------~---~~Cp~CG~~ 36 (645)
T PRK14559 3 ICPQCQFE------NPNNNRFCQKCGTSLT--------H---KPCPQCGTE 36 (645)
T ss_pred cCCCCCCc------CCCCCccccccCCCCC--------C---CcCCCCCCC
Confidence 68888865 2467888888876552 1 258888875
No 17
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.34 E-value=21 Score=39.71 Aligned_cols=38 Identities=16% Similarity=0.320 Sum_probs=24.8
Q ss_pred cEEEeeCCC-cccchhhhccccccchhhhhcccccccCCCCCCC
Q 016775 25 AVLYCTADS-AKLCLFCDQQIHSANALSLRHLRSQICDNCRAEP 67 (383)
Q Consensus 25 A~vyC~aD~-A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~~~p 67 (383)
..|+|+.+. ..-|..||..+-.. +..+.+.|..|+...
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~h-----~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGLP-----SAGGTPRCRWCGRAA 420 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeEe-----cCCCeeECCCCcCCC
Confidence 456677653 67899999654321 234567899999753
No 18
>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=33.84 E-value=42 Score=24.96 Aligned_cols=40 Identities=33% Similarity=0.621 Sum_probs=26.1
Q ss_pred ccCCCCCCCe---eEEecCCC---ccccCccCCCCCCCCCCCCCCceee
Q 016775 59 ICDNCRAEPV---SVRCCTEN---LMLCQDCDWDSHYNSSVSSVHERSS 101 (383)
Q Consensus 59 LCd~C~~~pA---sv~C~~d~---a~LC~~CD~~~H~anslas~H~R~p 101 (383)
-|+.|...|. -+.|..|. --||+.|-+... .....|.-++
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~ 47 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVK 47 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCcC---CCCCCCceee
Confidence 3888888664 46777776 789999976542 1224465544
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=32.82 E-value=22 Score=27.03 Aligned_cols=23 Identities=26% Similarity=0.586 Sum_probs=15.0
Q ss_pred cEEEeeCCCcccchhhhcccccc
Q 016775 25 AVLYCTADSAKLCLFCDQQIHSA 47 (383)
Q Consensus 25 A~vyC~aD~A~LC~~CD~~VHsa 47 (383)
...-|......+|.+||.-||..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 45678888889999999999874
No 20
>PF14239 RRXRR: RRXRR protein
Probab=32.72 E-value=38 Score=31.84 Aligned_cols=38 Identities=37% Similarity=0.654 Sum_probs=30.0
Q ss_pred HHH-HHHHHHhhccCCCCcccchhhhhhhhcCCCCCccccc
Q 016775 335 NAM-LRYKEKKKNRSYGKQIRYESRKARADTRKRVKGRFVK 374 (383)
Q Consensus 335 ~~~-~ry~eKr~~R~~~k~irY~~Rk~~A~~R~RvkGrFvk 374 (383)
++| ...+.-|..|+|+++.|| ||.+=+.|.|-+|.+..
T Consensus 88 ~~lr~~RR~~RR~RR~~rk~Ry--R~~RF~NR~r~~gwL~P 126 (176)
T PF14239_consen 88 DRLRTQRRAYRRGRRYNRKTRY--RKARFDNRKRPKGWLPP 126 (176)
T ss_pred HHHHHHHHHHhhhccccccccc--ccccccccCCCCCCcCc
Confidence 344 566777888888888888 88888899998898764
No 21
>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=32.70 E-value=31 Score=26.99 Aligned_cols=23 Identities=43% Similarity=0.459 Sum_probs=19.0
Q ss_pred CCcccchhhhhhhhcCCC-CCccc
Q 016775 350 GKQIRYESRKARADTRKR-VKGRF 372 (383)
Q Consensus 350 ~k~irY~~Rk~~A~~R~R-vkGrF 372 (383)
.|+.-++||-..|-.|+| --|||
T Consensus 35 rk~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 35 RKPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred hHHHHHHHHHHHHHcCccCCCCCC
Confidence 355679999999999999 56777
No 22
>KOG4301 consensus Beta-dystrobrevin [Cytoskeleton]
Probab=32.65 E-value=13 Score=38.52 Aligned_cols=40 Identities=35% Similarity=0.740 Sum_probs=31.3
Q ss_pred ccCCCCCCCe---eEEecCCCc-cccCccCCCCCCCCCCCCCCc
Q 016775 59 ICDNCRAEPV---SVRCCTENL-MLCQDCDWDSHYNSSVSSVHE 98 (383)
Q Consensus 59 LCd~C~~~pA---sv~C~~d~a-~LC~~CD~~~H~anslas~H~ 98 (383)
.|+.|...+. .+.|..|+- -||++|-|.+|...+.+-+|+
T Consensus 242 ~cs~c~srs~~gfry~cq~C~nyqlcq~cfwrG~~g~~hsnqh~ 285 (434)
T KOG4301|consen 242 ECSYCRSRSMMGFRYRCQQCHNYQLCQQCFWRGHAGGSHSNQHQ 285 (434)
T ss_pred cCcceecccccchhhhHhhcCCccccchhhccccCCCCcchHHH
Confidence 6999998874 557887765 799999999998766555554
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.26 E-value=35 Score=21.93 Aligned_cols=24 Identities=25% Similarity=0.685 Sum_probs=15.8
Q ss_pred CccCcccCCCCcEEEeeCCCcccchhhhcc
Q 016775 14 LALCDFCNSKLAVLYCTADSAKLCLFCDQQ 43 (383)
Q Consensus 14 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CD~~ 43 (383)
...|-.|+... .+.+.+|..|.+.
T Consensus 2 ~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcC------CcccccChhhCCC
Confidence 45677787632 4567788877664
No 24
>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=26.84 E-value=22 Score=23.34 Aligned_cols=26 Identities=27% Similarity=0.533 Sum_probs=8.9
Q ss_pred cCcccCCCCcEEEeeCCCcccchhhhccccc
Q 016775 16 LCDFCNSKLAVLYCTADSAKLCLFCDQQIHS 46 (383)
Q Consensus 16 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHs 46 (383)
.|+.|+..... +..+-|..||-.+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 58888875432 245678999998885
No 25
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=24.90 E-value=13 Score=36.04 Aligned_cols=49 Identities=29% Similarity=0.556 Sum_probs=38.7
Q ss_pred CCCCCCCccCcccCCCC-------cEEEeeCC-Ccccchhhhccccccchhhhhcccc
Q 016775 8 SPGSSMLALCDFCNSKL-------AVLYCTAD-SAKLCLFCDQQIHSANALSLRHLRS 57 (383)
Q Consensus 8 ~~~~~~~~~Cd~C~~~~-------A~vyC~aD-~A~LC~~CD~~VHsaN~L~~RH~Rv 57 (383)
++.+.....|++|++.- --+-|++| .-+||..|..-.|-+ +=..||.|.
T Consensus 111 sssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndt-fdlkrh~rt 167 (267)
T KOG3576|consen 111 SSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDT-FDLKRHTRT 167 (267)
T ss_pred CCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccch-hhhhhhhcc
Confidence 44556678999999743 34789998 689999999999986 446899996
No 26
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.90 E-value=50 Score=39.50 Aligned_cols=18 Identities=17% Similarity=0.329 Sum_probs=10.2
Q ss_pred ccCcccCCCCcEEEeeCC
Q 016775 15 ALCDFCNSKLAVLYCTAD 32 (383)
Q Consensus 15 ~~Cd~C~~~~A~vyC~aD 32 (383)
..|..|+...-..+|..+
T Consensus 668 rkCPkCG~~t~~~fCP~C 685 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDC 685 (1337)
T ss_pred EECCCCCCccccccCccc
Confidence 678888875433344333
No 27
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=22.42 E-value=1.1e+02 Score=27.80 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=37.6
Q ss_pred cCcccCCCCcEEEeeCCCcccchhhhccccccchhhhhcccccccCCCC
Q 016775 16 LCDFCNSKLAVLYCTADSAKLCLFCDQQIHSANALSLRHLRSQICDNCR 64 (383)
Q Consensus 16 ~Cd~C~~~~A~vyC~aD~A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~ 64 (383)
.|+.|....... |..|.+.+|..|+..+|..+.+...|.++.+|..+.
T Consensus 7 ~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 54 (340)
T KOG1601|consen 7 DLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPE 54 (340)
T ss_pred cccccCcccccc-cccccccCCcccccccccccccccccccccccchhh
Confidence 455555544444 999999999999999999886666788888887776
No 28
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=21.07 E-value=60 Score=31.92 Aligned_cols=63 Identities=16% Similarity=0.364 Sum_probs=29.0
Q ss_pred CCccCcccCCCCcEEEeeCC-----CcccchhhhccccccchhhhhcccccccCCCCCCCeeEEec-------CCCcccc
Q 016775 13 MLALCDFCNSKLAVLYCTAD-----SAKLCLFCDQQIHSANALSLRHLRSQICDNCRAEPVSVRCC-------TENLMLC 80 (383)
Q Consensus 13 ~~~~Cd~C~~~~A~vyC~aD-----~A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~~~pAsv~C~-------~d~a~LC 80 (383)
....|-.||+.|..-+=+.+ .-..|..|...-|. .| .-|..|+.....-+-. .-.+-.|
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~--------~R-~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C 241 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF--------VR-IKCPYCGNTDHEKLEYFTVEGEPAYRVEVC 241 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE----------T-TS-TTT---SS-EEE--------SEEEEEE
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee--------cC-CCCcCCCCCCCcceeeEecCCCCcEEEEEC
Confidence 35799999998865555544 45678889875443 33 3799999764322111 2245688
Q ss_pred CccC
Q 016775 81 QDCD 84 (383)
Q Consensus 81 ~~CD 84 (383)
..|.
T Consensus 242 ~~C~ 245 (290)
T PF04216_consen 242 ESCG 245 (290)
T ss_dssp TTTT
T ss_pred Cccc
Confidence 8884
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=20.64 E-value=57 Score=34.91 Aligned_cols=37 Identities=19% Similarity=0.383 Sum_probs=23.2
Q ss_pred cEEEeeCCC-cccchhhhccccccchhhhhcccccccCCCCCC
Q 016775 25 AVLYCTADS-AKLCLFCDQQIHSANALSLRHLRSQICDNCRAE 66 (383)
Q Consensus 25 A~vyC~aD~-A~LC~~CD~~VHsaN~L~~RH~Rv~LCd~C~~~ 66 (383)
..|+|+.+. ..-|..||...-. .++.....|..|+..
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQ 249 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCc
Confidence 345666653 6778888864322 134456778888865
Done!