Query 019028
Match_columns 347
No_of_seqs 264 out of 835
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 06:05:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019028.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019028hhsearch_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 8.1E-21 1.8E-25 135.6 3.3 45 282-326 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.3 0.00016 3.5E-09 48.8 2.2 39 4-48 1-39 (39)
3 cd00021 BBOX B-Box-type zinc f 97.1 0.0003 6.4E-09 47.5 1.7 38 48-91 2-39 (39)
4 smart00336 BBOX B-Box-type zin 96.7 0.0012 2.5E-08 45.2 2.2 41 45-91 2-42 (42)
5 KOG1601 GATA-4/5/6 transcripti 96.6 0.00061 1.3E-08 62.0 0.8 95 3-98 5-105 (340)
6 PF00643 zf-B_box: B-box zinc 96.6 0.00095 2.1E-08 46.2 1.1 40 46-91 3-42 (42)
7 smart00336 BBOX B-Box-type zin 96.3 0.003 6.4E-08 43.2 2.4 40 3-48 3-42 (42)
8 PF09425 CCT_2: Divergent CCT 96.2 0.0028 6.2E-08 40.9 1.6 25 280-305 2-26 (27)
9 PF00643 zf-B_box: B-box zinc 96.0 0.0043 9.3E-08 42.9 1.9 40 3-48 3-42 (42)
10 KOG4367 Predicted Zn-finger pr 94.9 0.008 1.7E-07 61.6 0.2 76 3-78 162-256 (699)
11 KOG1601 GATA-4/5/6 transcripti 71.6 5.2 0.00011 36.2 4.0 42 278-319 289-330 (340)
12 KOG4367 Predicted Zn-finger pr 68.5 1.9 4.2E-05 44.8 0.5 47 47-93 163-211 (699)
13 PF13248 zf-ribbon_3: zinc-rib 48.1 14 0.00029 23.3 1.6 25 2-32 1-25 (26)
14 PF04438 zf-HIT: HIT zinc fing 47.2 9 0.00019 25.2 0.7 24 46-70 2-25 (30)
15 smart00521 CBF CCAAT-Binding t 45.4 32 0.0007 26.5 3.6 25 299-323 36-61 (62)
16 PF12773 DZR: Double zinc ribb 39.5 28 0.0006 24.6 2.4 29 20-54 9-37 (50)
17 PF07649 C1_3: C1-like domain; 39.5 11 0.00024 24.2 0.3 27 4-35 1-27 (30)
18 PRK14873 primosome assembly pr 39.2 18 0.00039 39.6 1.9 45 14-63 382-427 (665)
19 PF02045 CBFB_NFYA: CCAAT-bind 36.4 32 0.00069 26.3 2.3 22 300-321 36-58 (58)
20 PF07975 C1_4: TFIIH C1-like d 35.3 17 0.00038 26.9 0.8 22 14-35 20-41 (51)
21 KOG0129 Predicted RNA-binding 35.1 13 0.00028 39.4 0.0 36 2-37 454-496 (520)
22 PF03660 PHF5: PHF5-like prote 33.5 16 0.00034 31.0 0.3 50 23-72 20-76 (106)
23 cd02335 ZZ_ADA2 Zinc finger, Z 30.3 51 0.0011 23.6 2.5 29 48-76 2-34 (49)
24 PRK14559 putative protein seri 29.7 38 0.00083 37.0 2.5 47 4-67 2-50 (645)
25 TIGR02563 cas_Csy4 CRISPR-asso 27.4 38 0.00082 31.3 1.7 12 336-347 169-185 (185)
26 PF14776 UNC-79: Cation-channe 27.3 25 0.00054 37.4 0.6 57 23-79 227-303 (525)
27 cd02342 ZZ_UBA_plant Zinc fing 26.7 43 0.00092 24.1 1.5 30 5-34 2-35 (43)
28 TIGR00595 priA primosomal prot 24.9 46 0.00099 35.1 2.1 45 14-63 212-258 (505)
29 PRK14714 DNA polymerase II lar 24.8 45 0.00098 39.2 2.1 24 68-96 711-734 (1337)
30 KOG1705 Uncharacterized conser 23.8 56 0.0012 27.3 1.9 39 11-53 4-50 (110)
31 COG1198 PriA Primosomal protei 23.6 55 0.0012 36.4 2.4 46 14-64 434-481 (730)
32 PF10587 EF-1_beta_acid: Eukar 22.2 62 0.0013 21.3 1.5 14 280-293 15-28 (28)
33 PF02318 FYVE_2: FYVE-type zin 21.9 46 0.001 28.1 1.1 44 3-54 54-102 (118)
34 PRK14890 putative Zn-ribbon RN 21.5 68 0.0015 24.6 1.8 17 48-64 38-54 (59)
35 KOG4571 Activating transcripti 21.2 65 0.0014 32.0 2.1 17 280-296 233-249 (294)
36 PRK04023 DNA polymerase II lar 20.8 78 0.0017 36.5 2.9 29 297-325 934-962 (1121)
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=99.81 E-value=8.1e-21 Score=135.63 Aligned_cols=45 Identities=64% Similarity=1.082 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHhhhccccccccchhhhhhhhhCCCCCceeecCCC
Q 019028 282 REARVLRYREKRKNRKFEKTIRYASRKAYAEMRPRIKGRFAKRTD 326 (347)
Q Consensus 282 R~~~~~ry~eKr~~r~f~k~irY~~Rk~~A~~r~R~kGrf~k~~~ 326 (347)
|+++|+||+|||++|+|+|+|+|++||++|+.|||||||||+.++
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 789999999999999999999999999999999999999999864
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=97.29 E-value=0.00016 Score=48.83 Aligned_cols=39 Identities=41% Similarity=0.915 Sum_probs=34.0
Q ss_pred ccccccCCCCceEEeeCCCcccccccccccccccccccccccccc
Q 019028 4 KLCDSCKSATATVFCRADSAFLCVNCDTKIHAANKLASRHARVWV 48 (347)
Q Consensus 4 ~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~L 48 (347)
..|+.++.+++.+||..|.+.+|..|+...|. .|.+++|
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 36999998899999999999999999988775 4888764
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=97.07 E-value=0.0003 Score=47.50 Aligned_cols=38 Identities=42% Similarity=0.927 Sum_probs=32.5
Q ss_pred ccccccCCCceeeccCccccccccccCCCCCCCCcCCCcccccc
Q 019028 48 VCEVCEQAPAHVTCKADAAALCVTCDRDIHSANPLARRHERVPV 91 (347)
Q Consensus 48 LCe~C~~~PA~v~C~~d~a~LC~~CD~~~Hsan~la~rH~Rvpv 91 (347)
+|+.++..|+.+||..|...||..|+...|. .|.++||
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 5778887799999999999999999976664 7888876
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.69 E-value=0.0012 Score=45.21 Aligned_cols=41 Identities=37% Similarity=0.601 Sum_probs=34.6
Q ss_pred cccccccccCCCceeeccCccccccccccCCCCCCCCcCCCcccccc
Q 019028 45 RVWVCEVCEQAPAHVTCKADAAALCVTCDRDIHSANPLARRHERVPV 91 (347)
Q Consensus 45 Rv~LCe~C~~~PA~v~C~~d~a~LC~~CD~~~Hsan~la~rH~Rvpv 91 (347)
|.++|+.++..++.+||..|...||..|....| +.|.++||
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 577899998889999999999999999986555 56777765
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=96.64 E-value=0.00061 Score=61.98 Aligned_cols=95 Identities=24% Similarity=0.273 Sum_probs=68.7
Q ss_pred CccccccCCCCceEEeeCCCcccccccccccccccccccccccccccccccCCCce--eeccCccccc----cccccCCC
Q 019028 3 SKLCDSCKSATATVFCRADSAFLCVNCDTKIHAANKLASRHARVWVCEVCEQAPAH--VTCKADAAAL----CVTCDRDI 76 (347)
Q Consensus 3 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~PA~--v~C~~d~a~L----C~~CD~~~ 76 (347)
...|+.|....... |..|.+.+|..|+.+++..+.+...|.++.++..+...++. +.+..+...+ +..+....
T Consensus 5 ~~~~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (340)
T KOG1601|consen 5 AEDLDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFV 83 (340)
T ss_pred cccccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhcccccccccccccccccccccccccc
Confidence 34577777766666 99999999999999999998777788999999887633322 4444444445 55577667
Q ss_pred CCCCCcCCCcccccccCCCCCC
Q 019028 77 HSANPLARRHERVPVTPFYDSV 98 (347)
Q Consensus 77 Hsan~la~rH~Rvpv~~~~~~~ 98 (347)
|..++...+|..+++.+.....
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~ 105 (340)
T KOG1601|consen 84 SENNPNSLRHPPVPSMPSSNSS 105 (340)
T ss_pred ccccCCCCCCCCcccccccccc
Confidence 7777777788877766665443
No 6
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.56 E-value=0.00095 Score=46.19 Aligned_cols=40 Identities=25% Similarity=0.507 Sum_probs=33.4
Q ss_pred ccccccccCCCceeeccCccccccccccCCCCCCCCcCCCcccccc
Q 019028 46 VWVCEVCEQAPAHVTCKADAAALCVTCDRDIHSANPLARRHERVPV 91 (347)
Q Consensus 46 v~LCe~C~~~PA~v~C~~d~a~LC~~CD~~~Hsan~la~rH~Rvpv 91 (347)
.++|..++..++.+||..|...||..|....|.. |..+||
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 4678889988899999999999999999766754 888876
No 7
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.32 E-value=0.003 Score=43.15 Aligned_cols=40 Identities=35% Similarity=0.651 Sum_probs=33.5
Q ss_pred CccccccCCCCceEEeeCCCcccccccccccccccccccccccccc
Q 019028 3 SKLCDSCKSATATVFCRADSAFLCVNCDTKIHAANKLASRHARVWV 48 (347)
Q Consensus 3 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~L 48 (347)
.+.|..|...++.+||..|.+.+|..|....| +.|.+++|
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 46799999889999999999999999998767 34776653
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=96.19 E-value=0.0028 Score=40.95 Aligned_cols=25 Identities=36% Similarity=0.494 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHhhhccccccccch
Q 019028 280 ADREARVLRYREKRKNRKFEKTIRYA 305 (347)
Q Consensus 280 ~~R~~~~~ry~eKr~~r~f~k~irY~ 305 (347)
..|.+.|+||.||||.|... +..|.
T Consensus 2 ~aRK~SLqRFLeKRK~R~~~-~~PY~ 26 (27)
T PF09425_consen 2 IARKASLQRFLEKRKDRLAA-KSPYQ 26 (27)
T ss_dssp ----HHHHHHHHHH------------
T ss_pred chHHHHHHHHHHHHHHhhcc-CCCCC
Confidence 57999999999999999987 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=95.99 E-value=0.0043 Score=42.88 Aligned_cols=40 Identities=23% Similarity=0.458 Sum_probs=34.0
Q ss_pred CccccccCCCCceEEeeCCCcccccccccccccccccccccccccc
Q 019028 3 SKLCDSCKSATATVFCRADSAFLCVNCDTKIHAANKLASRHARVWV 48 (347)
Q Consensus 3 ~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~L 48 (347)
...|+.|...++.+||..+...||..|....|.. |..++|
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 4689999998899999999999999999998864 776654
No 10
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.86 E-value=0.008 Score=61.63 Aligned_cols=76 Identities=25% Similarity=0.516 Sum_probs=58.6
Q ss_pred CccccccCCCC--ceEEeeCCCcccccccccccccccccccccccccccc-------------cccCCC---ceeeccCc
Q 019028 3 SKLCDSCKSAT--ATVFCRADSAFLCVNCDTKIHAANKLASRHARVWVCE-------------VCEQAP---AHVTCKAD 64 (347)
Q Consensus 3 ~~~Cd~C~~~~--A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~LCe-------------~C~~~P---A~v~C~~d 64 (347)
+-.|..|++++ |+|+|..+..+.|.-|..+.|-+-.-..+|.-++--+ .|..+| -.+||.+|
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 34699999887 9999999999999999999997666566665443321 265554 57899999
Q ss_pred ccccccccc-CCCCC
Q 019028 65 AAALCVTCD-RDIHS 78 (347)
Q Consensus 65 ~a~LC~~CD-~~~Hs 78 (347)
.+++|-.|- .+-|+
T Consensus 242 k~pvc~~clee~khs 256 (699)
T KOG4367|consen 242 KMPVCYQCLEEGKHS 256 (699)
T ss_pred CChHHHHHHHhhccc
Confidence 999999996 34443
No 11
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=71.56 E-value=5.2 Score=36.19 Aligned_cols=42 Identities=62% Similarity=0.904 Sum_probs=40.6
Q ss_pred CHHHHHHHHHHHHHHhhhccccccccchhhhhhhhhCCCCCc
Q 019028 278 SAADREARVLRYREKRKNRKFEKTIRYASRKAYAEMRPRIKG 319 (347)
Q Consensus 278 ~~~~R~~~~~ry~eKr~~r~f~k~irY~~Rk~~A~~r~R~kG 319 (347)
....|++.+.||++|++.|.|.|+|+|..||..|+.|||+||
T Consensus 289 ~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 289 SSHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred ccchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 477999999999999999999999999999999999999999
No 12
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=68.54 E-value=1.9 Score=44.77 Aligned_cols=47 Identities=30% Similarity=0.603 Sum_probs=39.0
Q ss_pred cccccccCCC--ceeeccCccccccccccCCCCCCCCcCCCcccccccC
Q 019028 47 WVCEVCEQAP--AHVTCKADAAALCVTCDRDIHSANPLARRHERVPVTP 93 (347)
Q Consensus 47 ~LCe~C~~~P--A~v~C~~d~a~LC~~CD~~~Hsan~la~rH~Rvpv~~ 93 (347)
.-|..|+.+| |.|+|..|....|.-|.-..|-+-...++|..+|-+.
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~ 211 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQ 211 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCccc
Confidence 4588899876 7999999999999999988887666678898887544
No 13
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=48.12 E-value=14 Score=23.28 Aligned_cols=25 Identities=28% Similarity=0.696 Sum_probs=17.8
Q ss_pred CCccccccCCCCceEEeeCCCcccccccccc
Q 019028 2 ASKLCDSCKSATATVFCRADSAFLCVNCDTK 32 (347)
Q Consensus 2 ~~~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~ 32 (347)
|...|-.|+... .+.+.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 567788888632 5668888888765
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=47.25 E-value=9 Score=25.21 Aligned_cols=24 Identities=33% Similarity=0.722 Sum_probs=17.3
Q ss_pred ccccccccCCCceeeccCccccccc
Q 019028 46 VWVCEVCEQAPAHVTCKADAAALCV 70 (347)
Q Consensus 46 v~LCe~C~~~PA~v~C~~d~a~LC~ 70 (347)
..+|.+|+. ++...|..|.+.+|.
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 357999998 999999999988874
No 15
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=45.37 E-value=32 Score=26.54 Aligned_cols=25 Identities=40% Similarity=0.446 Sum_probs=22.0
Q ss_pred cccccchhhhhhhhhCCC-CCceeec
Q 019028 299 EKTIRYASRKAYAEMRPR-IKGRFAK 323 (347)
Q Consensus 299 ~k~irY~~Rk~~A~~r~R-~kGrf~k 323 (347)
.|..-++||-..|-.||| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567889999999999999 6789975
No 16
>PF12773 DZR: Double zinc ribbon
Probab=39.49 E-value=28 Score=24.57 Aligned_cols=29 Identities=24% Similarity=0.568 Sum_probs=18.4
Q ss_pred CCCcccccccccccccccccccccccccccccccC
Q 019028 20 ADSAFLCVNCDTKIHAANKLASRHARVWVCEVCEQ 54 (347)
Q Consensus 20 aD~A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~ 54 (347)
.+.+.+|..|...+- .......+|..|+.
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGA 37 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcC
Confidence 456788888877666 22344566777764
No 17
>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=39.45 E-value=11 Score=24.22 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=9.1
Q ss_pred ccccccCCCCceEEeeCCCccccccccccccc
Q 019028 4 KLCDSCKSATATVFCRADSAFLCVNCDTKIHA 35 (347)
Q Consensus 4 ~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~ 35 (347)
+.|+.|+..... +..|-|..||-.+|.
T Consensus 1 ~~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 1 FRCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp ---TTTS----S-------EEE-TTT-----H
T ss_pred CcCCcCCCcCCC-----CceEECccCCCccCh
Confidence 368888865532 346779999988884
No 18
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.24 E-value=18 Score=39.58 Aligned_cols=45 Identities=16% Similarity=0.364 Sum_probs=29.4
Q ss_pred ceEEeeCCC-cccccccccccccccccccccccccccccccCCCceeeccC
Q 019028 14 ATVFCRADS-AFLCVNCDTKIHAANKLASRHARVWVCEVCEQAPAHVTCKA 63 (347)
Q Consensus 14 A~vyC~aD~-A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~PA~v~C~~ 63 (347)
..++|+.+. ..-|..||..... ++..+.+.|..|+.......|..
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~-----h~~~~~l~Ch~CG~~~~p~~Cp~ 427 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGL-----PSAGGTPRCRWCGRAAPDWRCPR 427 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeE-----ecCCCeeECCCCcCCCcCccCCC
Confidence 467788774 7889999975542 12355788999997533333443
No 19
>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=36.37 E-value=32 Score=26.29 Aligned_cols=22 Identities=45% Similarity=0.507 Sum_probs=18.4
Q ss_pred ccccchhhhhhhhhCCC-CCcee
Q 019028 300 KTIRYASRKAYAEMRPR-IKGRF 321 (347)
Q Consensus 300 k~irY~~Rk~~A~~r~R-~kGrf 321 (347)
|+.-++||-..|-.|+| -.|||
T Consensus 36 k~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 36 KPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred HHHHHHHHHHHHHcCccCCCCCC
Confidence 45568999999999999 67787
No 20
>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=35.33 E-value=17 Score=26.90 Aligned_cols=22 Identities=27% Similarity=0.682 Sum_probs=14.6
Q ss_pred ceEEeeCCCccccccccccccc
Q 019028 14 ATVFCRADSAFLCVNCDTKIHA 35 (347)
Q Consensus 14 A~vyC~aD~A~LC~~CDa~vH~ 35 (347)
..+-|......+|..||.-||.
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 4678889999999999999984
No 21
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=35.10 E-value=13 Score=39.37 Aligned_cols=36 Identities=36% Similarity=0.801 Sum_probs=31.1
Q ss_pred CCccccccCC-----CCceEEeeC--CCccccccccccccccc
Q 019028 2 ASKLCDSCKS-----ATATVFCRA--DSAFLCVNCDTKIHAAN 37 (347)
Q Consensus 2 ~~~~Cd~C~~-----~~A~vyC~a--D~A~LC~~CDa~vH~AN 37 (347)
-..+||.|+. ..|-.||++ +--|.|..|=+.+|+.-
T Consensus 454 eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~ 496 (520)
T KOG0129|consen 454 EDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP 496 (520)
T ss_pred cccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC
Confidence 3568999988 889999998 56999999999999853
No 22
>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=33.52 E-value=16 Score=31.04 Aligned_cols=50 Identities=24% Similarity=0.540 Sum_probs=18.4
Q ss_pred cccccccccccccccccccccccccccccccCCCceeeccCcc-------ccccccc
Q 019028 23 AFLCVNCDTKIHAANKLASRHARVWVCEVCEQAPAHVTCKADA-------AALCVTC 72 (347)
Q Consensus 23 A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~PA~v~C~~d~-------a~LC~~C 72 (347)
..||..||.+----+...+-...|.+|+-|....-.-.|.-|. |..|..|
T Consensus 20 G~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 20 GRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp -EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred hhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhh
Confidence 3444444443332222333356788888776443333333333 4557777
No 23
>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=30.31 E-value=51 Score=23.62 Aligned_cols=29 Identities=21% Similarity=0.552 Sum_probs=20.1
Q ss_pred ccccccCCCce---eeccCc-cccccccccCCC
Q 019028 48 VCEVCEQAPAH---VTCKAD-AAALCVTCDRDI 76 (347)
Q Consensus 48 LCe~C~~~PA~---v~C~~d-~a~LC~~CD~~~ 76 (347)
.|+.|...+.. +.|..| .--||..|-...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 47778766543 668887 557999997543
No 24
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.72 E-value=38 Score=37.02 Aligned_cols=47 Identities=21% Similarity=0.574 Sum_probs=29.2
Q ss_pred ccccccCCCCceEEeeCCCcccccccccccccccccccccccccccccccCC--CceeeccCcccc
Q 019028 4 KLCDSCKSATATVFCRADSAFLCVNCDTKIHAANKLASRHARVWVCEVCEQA--PAHVTCKADAAA 67 (347)
Q Consensus 4 ~~Cd~C~~~~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~--PA~v~C~~d~a~ 67 (347)
..|-.|+.. -.+.|.+|..|.+.+. + ..|..|+.. +..-||..|.+.
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~--------~---~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLT--------H---KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCC--------C---CcCCCCCCCCCcccccccccCCc
Confidence 478889875 3467888888877652 1 247777754 223355555443
No 25
>TIGR02563 cas_Csy4 CRISPR-associated protein, Csy4 family. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4.
Probab=27.41 E-value=38 Score=31.28 Aligned_cols=12 Identities=33% Similarity=0.733 Sum_probs=9.5
Q ss_pred CCCCCcc-----cccCC
Q 019028 336 SSIYGFG-----IVPSF 347 (347)
Q Consensus 336 ~~~~~yg-----vVPsf 347 (347)
...++|| +||||
T Consensus 169 g~F~sYGLS~~aTVPwf 185 (185)
T TIGR02563 169 GKFNAYGLSNTATVPWF 185 (185)
T ss_pred CCCCccccCCCCCCCCC
Confidence 3467888 99999
No 26
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=27.29 E-value=25 Score=37.42 Aligned_cols=57 Identities=28% Similarity=0.574 Sum_probs=35.9
Q ss_pred cccccccccccccccccccc-ccc------cccccc--ccCC--CceeeccC--c-------cccccccccCCCCCC
Q 019028 23 AFLCVNCDTKIHAANKLASR-HAR------VWVCEV--CEQA--PAHVTCKA--D-------AAALCVTCDRDIHSA 79 (347)
Q Consensus 23 A~LC~~CDa~vH~AN~La~R-H~R------v~LCe~--C~~~--PA~v~C~~--d-------~a~LC~~CD~~~Hsa 79 (347)
.|||..|...||+.-+.... +.- ...||. |.+. .|+++|-. | .+.+|..|....|..
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n 303 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNN 303 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhhhhccc
Confidence 58999999999974333222 111 234664 6543 57887764 2 235899999888754
No 27
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=26.75 E-value=43 Score=24.12 Aligned_cols=30 Identities=20% Similarity=0.583 Sum_probs=21.0
Q ss_pred cccccCCCC---ceEEeeCCCcc-cccccccccc
Q 019028 5 LCDSCKSAT---ATVFCRADSAF-LCVNCDTKIH 34 (347)
Q Consensus 5 ~Cd~C~~~~---A~vyC~aD~A~-LC~~CDa~vH 34 (347)
.||.|+..| ..+.|....-+ ||..|=.+.-
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~ 35 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMG 35 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhhc
Confidence 589999766 66777765544 8888865543
No 28
>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=24.95 E-value=46 Score=35.05 Aligned_cols=45 Identities=22% Similarity=0.561 Sum_probs=28.8
Q ss_pred ceEEeeCCC-cccccccccccccccccccccccccccccccCCCc-eeeccC
Q 019028 14 ATVFCRADS-AFLCVNCDTKIHAANKLASRHARVWVCEVCEQAPA-HVTCKA 63 (347)
Q Consensus 14 A~vyC~aD~-A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~PA-~v~C~~ 63 (347)
..++|+.+. ..-|..||...-. +++.+...|..|+.... .-.|..
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcCCCCCCCCC
Confidence 456777764 7789999975432 23566788999986543 333443
No 29
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.77 E-value=45 Score=39.16 Aligned_cols=24 Identities=21% Similarity=0.483 Sum_probs=12.6
Q ss_pred ccccccCCCCCCCCcCCCcccccccCCCC
Q 019028 68 LCVTCDRDIHSANPLARRHERVPVTPFYD 96 (347)
Q Consensus 68 LC~~CD~~~Hsan~la~rH~Rvpv~~~~~ 96 (347)
.|..|+... .....+.++|..++.
T Consensus 711 ~CP~CGtpl-----v~~~~~~i~~~~~~~ 734 (1337)
T PRK14714 711 ECPRCDVEL-----TPYQRRTINVKEEYR 734 (1337)
T ss_pred cCCCCCCcc-----cccceEEecHHHHHH
Confidence 577776443 133445666665553
No 30
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=23.85 E-value=56 Score=27.34 Aligned_cols=39 Identities=28% Similarity=0.652 Sum_probs=23.4
Q ss_pred CCCceEEeeCC----Cccccccccccccccccccccccc----cccccccc
Q 019028 11 SATATVFCRAD----SAFLCVNCDTKIHAANKLASRHAR----VWVCEVCE 53 (347)
Q Consensus 11 ~~~A~vyC~aD----~A~LC~~CDa~vH~AN~La~RH~R----v~LCe~C~ 53 (347)
+.|-.+.|+-- -..||..||.+--- -..|.| |.+||.|.
T Consensus 4 HhpDLi~CrkQPGi~~G~LCEkCDgkC~I----CDS~VRP~tlVRiC~eC~ 50 (110)
T KOG1705|consen 4 HHPDLIMCRKQPGIAIGRLCEKCDGKCVI----CDSYVRPCTLVRICDECN 50 (110)
T ss_pred cCCcEEEEecCCCchhhhhHHhcCCcccc----cccccccceeeeeehhcC
Confidence 45677788764 36789999875332 222333 55666664
No 31
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.58 E-value=55 Score=36.40 Aligned_cols=46 Identities=22% Similarity=0.522 Sum_probs=32.3
Q ss_pred ceEEeeCCC-cccccccccccccccccccccccccccccccCC-CceeeccCc
Q 019028 14 ATVFCRADS-AFLCVNCDTKIHAANKLASRHARVWVCEVCEQA-PAHVTCKAD 64 (347)
Q Consensus 14 A~vyC~aD~-A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~~-PA~v~C~~d 64 (347)
..+.|+.+. ..=|..||...- .+++.+...|..|+.. +-...|..|
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt-----~H~~~~~L~CH~Cg~~~~~p~~Cp~C 481 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLT-----LHKATGQLRCHYCGYQEPIPQSCPEC 481 (730)
T ss_pred ceeecccCCCcccCCCCCcceE-----EecCCCeeEeCCCCCCCCCCCCCCCC
Confidence 456777764 677999998644 2356788999999977 445556655
No 32
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=22.19 E-value=62 Score=21.28 Aligned_cols=14 Identities=36% Similarity=0.517 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHh
Q 019028 280 ADREARVLRYREKR 293 (347)
Q Consensus 280 ~~R~~~~~ry~eKr 293 (347)
..|++||.-|.+||
T Consensus 15 r~reeRla~y~aKK 28 (28)
T PF10587_consen 15 RIREERLAAYAAKK 28 (28)
T ss_pred HHHHHHHHHHHccC
Confidence 46888888898886
No 33
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=21.91 E-value=46 Score=28.07 Aligned_cols=44 Identities=23% Similarity=0.744 Sum_probs=30.8
Q ss_pred CccccccCCC-----CceEEeeCCCcccccccccccccccccccccccccccccccC
Q 019028 3 SKLCDSCKSA-----TATVFCRADSAFLCVNCDTKIHAANKLASRHARVWVCEVCEQ 54 (347)
Q Consensus 3 ~~~Cd~C~~~-----~A~vyC~aD~A~LC~~CDa~vH~AN~La~RH~Rv~LCe~C~~ 54 (347)
.+.|-.|+.. .....|....-..|..|... ......|+|.+|..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~--------~~~~~~WlC~vC~k 102 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY--------SKKEPIWLCKVCQK 102 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE--------TSSSCCEEEHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc--------CCCCCCEEChhhHH
Confidence 4578888753 34577888888888888765 34577899988863
No 34
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=21.53 E-value=68 Score=24.59 Aligned_cols=17 Identities=29% Similarity=0.634 Sum_probs=8.8
Q ss_pred ccccccCCCceeeccCc
Q 019028 48 VCEVCEQAPAHVTCKAD 64 (347)
Q Consensus 48 LCe~C~~~PA~v~C~~d 64 (347)
.|..|...-..+.|..|
T Consensus 38 RC~~CRk~~~~Y~CP~C 54 (59)
T PRK14890 38 RCEKCRKQSNPYTCPKC 54 (59)
T ss_pred echhHHhcCCceECCCC
Confidence 35555555555555443
No 35
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=21.20 E-value=65 Score=31.98 Aligned_cols=17 Identities=29% Similarity=0.597 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHhhhc
Q 019028 280 ADREARVLRYREKRKNR 296 (347)
Q Consensus 280 ~~R~~~~~ry~eKr~~r 296 (347)
+.|..+-.|||+|||.-
T Consensus 233 ~qnk~AAtRYRqKkRae 249 (294)
T KOG4571|consen 233 QQNKAAATRYRQKKRAE 249 (294)
T ss_pred HHhHHHHHHHHHHHHHH
Confidence 45555568999998753
No 36
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.76 E-value=78 Score=36.55 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=20.1
Q ss_pred cccccccchhhhhhhhhCCCCCceeecCC
Q 019028 297 KFEKTIRYASRKAYAEMRPRIKGRFAKRT 325 (347)
Q Consensus 297 ~f~k~irY~~Rk~~A~~r~R~kGrf~k~~ 325 (347)
-|+++.+|+.=|.+.+.--+|+.|.-+..
T Consensus 934 FYeat~~~~~P~ev~~~i~~ve~rlgt~~ 962 (1121)
T PRK04023 934 FYEATLEGADPKEVEDIMDTVEDRLGTPE 962 (1121)
T ss_pred HHHHHhccCCHHHHHHHHHHHHHhcCCch
Confidence 35677778877777777777777765544
Done!