Query 015643
Match_columns 403
No_of_seqs 257 out of 670
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:13:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015643.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015643hhsearch_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 3.4E-19 7.4E-24 131.7 2.8 45 347-391 1-45 (45)
2 cd00021 BBOX B-Box-type zinc f 97.5 7.7E-05 1.7E-09 51.4 3.0 38 19-62 2-39 (39)
3 smart00336 BBOX B-Box-type zin 96.8 0.0013 2.8E-08 45.9 3.2 40 17-62 3-42 (42)
4 PF00643 zf-B_box: B-box zinc 96.7 0.0012 2.7E-08 46.6 2.7 40 17-62 3-42 (42)
5 KOG1601 GATA-4/5/6 transcripti 96.4 0.0012 2.7E-08 59.4 1.1 41 344-384 290-330 (340)
6 PF09425 CCT_2: Divergent CCT 95.0 0.015 3.2E-07 39.5 1.6 25 345-370 2-26 (27)
7 KOG4367 Predicted Zn-finger pr 51.5 4.5 9.8E-05 43.5 -0.3 50 17-66 162-213 (699)
8 KOG4582 Uncharacterized conser 35.7 82 0.0018 31.5 5.8 38 18-55 153-196 (278)
9 smart00521 CBF CCAAT-Binding t 34.3 48 0.001 26.8 3.1 25 364-388 36-61 (62)
10 PRK14714 DNA polymerase II lar 32.1 36 0.00078 40.9 2.9 50 18-73 668-722 (1337)
11 PF02045 CBFB_NFYA: CCAAT-bind 31.0 32 0.0007 27.4 1.6 22 365-386 36-58 (58)
12 PF14951 DUF4503: Domain of un 29.7 36 0.00078 35.9 2.2 46 18-65 275-320 (389)
13 PF07649 C1_3: C1-like domain; 28.8 17 0.00037 24.3 -0.2 26 19-49 2-27 (30)
14 cd02335 ZZ_ADA2 Zinc finger, Z 26.7 71 0.0015 23.7 2.8 40 19-58 2-45 (49)
15 cd02342 ZZ_UBA_plant Zinc fing 23.7 48 0.001 25.0 1.3 31 19-49 2-36 (43)
16 PF09702 Cas_Csa5: CRISPR-asso 23.3 59 0.0013 28.7 2.0 24 174-197 67-90 (105)
17 PF13240 zinc_ribbon_2: zinc-r 22.0 55 0.0012 21.2 1.2 22 20-47 2-23 (23)
18 KOG0129 Predicted RNA-binding 21.2 28 0.00061 37.9 -0.4 45 17-64 455-506 (520)
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=99.75 E-value=3.4e-19 Score=131.68 Aligned_cols=45 Identities=64% Similarity=1.054 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHhhccCCCCcccchhhhhhcccCCCCCccccccCC
Q 015643 347 REARVSRYREKRRTRLFSKKIRYEVRKLNAEKRPRMKGRFVKRTS 391 (403)
Q Consensus 347 R~~~v~RYreKr~~R~f~KkirY~~RK~~A~~RpRvKGRFvk~~~ 391 (403)
|+++|+||++||++|+|+|+|+|++||.+|+.|||||||||+..+
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 689999999999999999999999999999999999999999863
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=97.53 E-value=7.7e-05 Score=51.42 Aligned_cols=38 Identities=45% Similarity=0.795 Sum_probs=34.6
Q ss_pred CccccCCCceEEEecccccccccccccCCcCCCCCCCCCceeee
Q 015643 19 ACDGCLRKRARWYCVADDAFLCQGCDASVHSANQLASRHERVRL 62 (403)
Q Consensus 19 lCD~C~~apA~vyC~aD~A~LC~~CDa~vHsAN~La~rH~RvpL 62 (403)
.|+.+..+++.+||..|.+.+|..|+...|. .|.++||
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 6999998899999999999999999998885 5999886
No 3
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.80 E-value=0.0013 Score=45.86 Aligned_cols=40 Identities=33% Similarity=0.646 Sum_probs=35.2
Q ss_pred CCCccccCCCceEEEecccccccccccccCCcCCCCCCCCCceeee
Q 015643 17 ARACDGCLRKRARWYCVADDAFLCQGCDASVHSANQLASRHERVRL 62 (403)
Q Consensus 17 ~~lCD~C~~apA~vyC~aD~A~LC~~CDa~vHsAN~La~rH~RvpL 62 (403)
.+.|..|...++.+||..|.+.+|..|....| +.|.++||
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 56799999899999999999999999998877 45888775
No 4
>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=96.73 E-value=0.0012 Score=46.65 Aligned_cols=40 Identities=23% Similarity=0.463 Sum_probs=35.5
Q ss_pred CCCccccCCCceEEEecccccccccccccCCcCCCCCCCCCceeee
Q 015643 17 ARACDGCLRKRARWYCVADDAFLCQGCDASVHSANQLASRHERVRL 62 (403)
Q Consensus 17 ~~lCD~C~~apA~vyC~aD~A~LC~~CDa~vHsAN~La~rH~RvpL 62 (403)
.+.|..|...++.+||..+...+|..|....|.. |..+||
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 4679999998899999999999999999999965 988886
No 5
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=96.39 E-value=0.0012 Score=59.44 Aligned_cols=41 Identities=59% Similarity=0.862 Sum_probs=39.8
Q ss_pred hhhHHHHHHHHHHHhhccCCCCcccchhhhhhcccCCCCCc
Q 015643 344 GGGREARVSRYREKRRTRLFSKKIRYEVRKLNAEKRPRMKG 384 (403)
Q Consensus 344 ~~~R~~~v~RYreKr~~R~f~KkirY~~RK~~A~~RpRvKG 384 (403)
...|...+.||+++++.|.|.++|+|..|+.+|+.|||+||
T Consensus 290 ~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (340)
T KOG1601|consen 290 SHQRVAEVRRYRESRDGRYFDKGIRYASRKSNAESRPRLKG 330 (340)
T ss_pred cchHHHHHhhccCccCCcccccccccccccccchhcccccc
Confidence 57999999999999999999999999999999999999999
No 6
>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=94.95 E-value=0.015 Score=39.49 Aligned_cols=25 Identities=40% Similarity=0.606 Sum_probs=9.9
Q ss_pred hhHHHHHHHHHHHhhccCCCCcccch
Q 015643 345 GGREARVSRYREKRRTRLFSKKIRYE 370 (403)
Q Consensus 345 ~~R~~~v~RYreKr~~R~f~KkirY~ 370 (403)
..|.++|+||.||||.|+.. +.-|.
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 46899999999999999987 66664
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=51.51 E-value=4.5 Score=43.48 Aligned_cols=50 Identities=24% Similarity=0.447 Sum_probs=41.5
Q ss_pred CCCccccCCCc--eEEEecccccccccccccCCcCCCCCCCCCceeeecCCC
Q 015643 17 ARACDGCLRKR--ARWYCVADDAFLCQGCDASVHSANQLASRHERVRLETAS 66 (403)
Q Consensus 17 ~~lCD~C~~ap--A~vyC~aD~A~LC~~CDa~vHsAN~La~rH~RvpL~~~~ 66 (403)
+..|..|.++| |+|+|..++.|.|..|-...|-+-..+.+|.-+|-....
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~gr 213 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGR 213 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCc
Confidence 34688888875 899999999999999999999887777888777665543
No 8
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=35.66 E-value=82 Score=31.52 Aligned_cols=38 Identities=32% Similarity=0.684 Sum_probs=27.6
Q ss_pred CCccccCCC---ceEEEeccccc-ccccccccCC--cCCCCCCC
Q 015643 18 RACDGCLRK---RARWYCVADDA-FLCQGCDASV--HSANQLAS 55 (403)
Q Consensus 18 ~lCD~C~~a---pA~vyC~aD~A-~LC~~CDa~v--HsAN~La~ 55 (403)
..||.|+.. -..+-|.-+.. -||..|.+.. |.+-.+++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceee
Confidence 479999983 57888977754 4999999995 44444444
No 9
>smart00521 CBF CCAAT-Binding transcription Factor.
Probab=34.34 E-value=48 Score=26.78 Aligned_cols=25 Identities=44% Similarity=0.652 Sum_probs=21.7
Q ss_pred CCcccchhhhhhcccCCC-CCccccc
Q 015643 364 SKKIRYEVRKLNAEKRPR-MKGRFVK 388 (403)
Q Consensus 364 ~KkirY~~RK~~A~~RpR-vKGRFvk 388 (403)
.|+.-|++|-+-|-+||| --|||.+
T Consensus 36 rkpYlhESRH~HAm~R~Rg~gGRFl~ 61 (62)
T smart00521 36 RKPYLHESRHLHAMRRPRGSGGRFLN 61 (62)
T ss_pred cCCcccchhHHHHHccCcCCCCCCCC
Confidence 567889999999999999 5589975
No 10
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.05 E-value=36 Score=40.91 Aligned_cols=50 Identities=16% Similarity=0.236 Sum_probs=37.0
Q ss_pred CCccccCCCceEEEeccccccc-----ccccccCCcCCCCCCCCCceeeecCCCCCCCCcc
Q 015643 18 RACDGCLRKRARWYCVADDAFL-----CQGCDASVHSANQLASRHERVRLETASSCNNNNK 73 (403)
Q Consensus 18 ~lCD~C~~apA~vyC~aD~A~L-----C~~CDa~vHsAN~La~rH~RvpL~~~~~~p~~~~ 73 (403)
+.|..|+..--..+|..|.+.+ |+.|.+.+.... +. ..-|.+|+.|..+.
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~de-----s~-a~~CP~CGtplv~~ 722 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPDE-----SG-RVECPRCDVELTPY 722 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCCceeCccCCCccCCCc-----cc-cccCCCCCCccccc
Confidence 6899999876667999988776 999999987542 22 22478888776554
No 11
>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=31.03 E-value=32 Score=27.43 Aligned_cols=22 Identities=45% Similarity=0.581 Sum_probs=18.2
Q ss_pred CcccchhhhhhcccCCCC-Cccc
Q 015643 365 KKIRYEVRKLNAEKRPRM-KGRF 386 (403)
Q Consensus 365 KkirY~~RK~~A~~RpRv-KGRF 386 (403)
|+.-|++|-+-|-+|||- -|||
T Consensus 36 k~YlheSRH~HA~~R~Rg~gGRF 58 (58)
T PF02045_consen 36 KPYLHESRHKHAMRRPRGPGGRF 58 (58)
T ss_pred HHHHHHHHHHHHHcCccCCCCCC
Confidence 456799999999999994 5677
No 12
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=29.66 E-value=36 Score=35.87 Aligned_cols=46 Identities=26% Similarity=0.411 Sum_probs=36.5
Q ss_pred CCccccCCCceEEEecccccccccccccCCcCCCCCCCCCceeeecCC
Q 015643 18 RACDGCLRKRARWYCVADDAFLCQGCDASVHSANQLASRHERVRLETA 65 (403)
Q Consensus 18 ~lCD~C~~apA~vyC~aD~A~LC~~CDa~vHsAN~La~rH~RvpL~~~ 65 (403)
|.||.|++..=-..=..-.++.|..|..-| .+++.++|.-|-|...
T Consensus 275 PvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V--~sP~~r~~LeVfl~Cp 320 (389)
T PF14951_consen 275 PVCDRCGNGRLEQSPEDRGAFSCGDCSRVV--TSPVLRMHLEVFLDCP 320 (389)
T ss_pred ccccccCCccceeCccCCCceeccchhhhc--cCcceeeeEEEEEeCC
Confidence 699999987655555556779999999998 6788999988877643
No 13
>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=28.83 E-value=17 Score=24.28 Aligned_cols=26 Identities=27% Similarity=0.646 Sum_probs=8.9
Q ss_pred CccccCCCceEEEecccccccccccccCCcC
Q 015643 19 ACDGCLRKRARWYCVADDAFLCQGCDASVHS 49 (403)
Q Consensus 19 lCD~C~~apA~vyC~aD~A~LC~~CDa~vHs 49 (403)
.|+.|+...-. +..+-|..||..+|.
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 58888876432 345679999998883
No 14
>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=26.68 E-value=71 Score=23.72 Aligned_cols=40 Identities=23% Similarity=0.402 Sum_probs=28.8
Q ss_pred CccccCCCceE---EEeccc-ccccccccccCCcCCCCCCCCCc
Q 015643 19 ACDGCLRKRAR---WYCVAD-DAFLCQGCDASVHSANQLASRHE 58 (403)
Q Consensus 19 lCD~C~~apA~---vyC~aD-~A~LC~~CDa~vHsAN~La~rH~ 58 (403)
.|+.|.+.+-. +.|... +--||..|=......+.....|.
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~~~~H~~~H~ 45 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAEIGKHRNDHN 45 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCCCCCCCCCCC
Confidence 59999987655 889887 78899999876654444444454
No 15
>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=23.70 E-value=48 Score=25.01 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=23.2
Q ss_pred CccccCCCc---eEEEecccccc-cccccccCCcC
Q 015643 19 ACDGCLRKR---ARWYCVADDAF-LCQGCDASVHS 49 (403)
Q Consensus 19 lCD~C~~ap---A~vyC~aD~A~-LC~~CDa~vHs 49 (403)
.||.|+..| .++.|....-+ ||..|-...-+
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~~n 36 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSRMGN 36 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhhhcC
Confidence 599999866 56788766555 99999776643
No 16
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=23.32 E-value=59 Score=28.74 Aligned_cols=24 Identities=33% Similarity=0.594 Sum_probs=20.4
Q ss_pred CCCCCCCCcccHHHHHHHHHHhhc
Q 015643 174 DLHGFLPSDLDLAEFAADVESLLG 197 (403)
Q Consensus 174 ~~~gf~ptD~eLaeFaADvEsLLg 197 (403)
-+.|-+|||.|...|..|||.=.+
T Consensus 67 i~~g~lPt~~eVe~Fl~~v~~di~ 90 (105)
T PF09702_consen 67 IIVGYLPTDEEVEDFLDDVERDIY 90 (105)
T ss_pred EecCCCCChHHHHHHHHHHHHHHH
Confidence 367899999999999999997543
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=21.96 E-value=55 Score=21.17 Aligned_cols=22 Identities=32% Similarity=0.887 Sum_probs=14.3
Q ss_pred ccccCCCceEEEecccccccccccccCC
Q 015643 20 CDGCLRKRARWYCVADDAFLCQGCDASV 47 (403)
Q Consensus 20 CD~C~~apA~vyC~aD~A~LC~~CDa~v 47 (403)
|-.|++. -.+.+.+|..|...+
T Consensus 2 Cp~CG~~------~~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 2 CPNCGAE------IEDDAKFCPNCGTPL 23 (23)
T ss_pred CcccCCC------CCCcCcchhhhCCcC
Confidence 5566654 246778888887653
No 18
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=21.21 E-value=28 Score=37.94 Aligned_cols=45 Identities=27% Similarity=0.569 Sum_probs=35.0
Q ss_pred CCCccccCC-----CceEEEecc--cccccccccccCCcCCCCCCCCCceeeecC
Q 015643 17 ARACDGCLR-----KRARWYCVA--DDAFLCQGCDASVHSANQLASRHERVRLET 64 (403)
Q Consensus 17 ~~lCD~C~~-----apA~vyC~a--D~A~LC~~CDa~vHsAN~La~rH~RvpL~~ 64 (403)
...||.|+. +.|-+||++ +--+.|..|=+.+|+- ..+|.-.||..
T Consensus 455 Dq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPlvr 506 (520)
T KOG0129|consen 455 DQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPLVR 506 (520)
T ss_pred ccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCceec
Confidence 358999998 899999965 5678999999999986 35555555543
Done!