Query 026095
Match_columns 243
No_of_seqs 153 out of 473
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:43:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026095.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026095hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.2 0.00028 6.1E-09 45.3 2.2 37 4-46 2-39 (39)
2 smart00336 BBOX B-Box-type zin 96.4 0.0025 5.5E-08 41.3 2.4 38 3-46 4-42 (42)
3 PF00643 zf-B_box: B-box zinc 95.7 0.0049 1.1E-07 40.6 1.3 39 2-46 3-42 (42)
4 KOG4367 Predicted Zn-finger pr 89.5 0.059 1.3E-06 53.8 -1.7 80 3-83 163-258 (699)
5 smart00336 BBOX B-Box-type zin 78.1 1.7 3.6E-05 27.9 1.8 31 43-77 2-32 (42)
6 cd00021 BBOX B-Box-type zinc f 76.1 1.6 3.6E-05 27.5 1.4 29 46-78 2-30 (39)
7 PF13248 zf-ribbon_3: zinc-rib 51.9 11 0.00023 23.0 1.5 25 1-30 1-25 (26)
8 PF13406 SLT_2: Transglycosyla 46.9 26 0.00056 32.4 3.9 46 169-224 58-106 (262)
9 PRK10760 murein hydrolase B; P 45.8 28 0.00061 33.9 4.1 46 169-224 120-168 (359)
10 cd00043 CYCLIN Cyclin box fold 42.0 1.1E+02 0.0024 20.8 7.6 77 130-219 8-87 (88)
11 smart00385 CYCLIN domain prese 39.0 1.2E+02 0.0026 20.4 7.5 74 133-219 5-81 (83)
12 KOG2682 NAD-dependent histone 36.6 15 0.00032 34.8 0.7 25 196-220 127-151 (314)
13 TIGR02282 MltB lytic murein tr 33.6 59 0.0013 30.7 4.1 45 169-223 53-100 (290)
14 PF12773 DZR: Double zinc ribb 31.0 59 0.0013 21.8 2.8 30 18-53 9-38 (50)
15 TIGR02283 MltB_2 lytic murein 30.1 74 0.0016 30.2 4.2 46 169-224 59-107 (300)
16 PRK00415 rps27e 30S ribosomal 28.5 28 0.00062 25.8 0.9 31 1-31 10-40 (59)
17 PF08224 DUF1719: Domain of un 28.0 94 0.002 28.8 4.4 50 168-217 3-52 (234)
18 PF07649 C1_3: C1-like domain; 27.7 19 0.00041 22.3 -0.1 26 4-33 2-27 (30)
19 PF00382 TFIIB: Transcription 27.6 2.3E+02 0.005 20.2 6.5 64 132-210 2-69 (71)
20 COG2951 MltB Membrane-bound ly 22.5 55 0.0012 31.7 1.9 33 193-225 111-146 (343)
21 PF13625 Helicase_C_3: Helicas 20.2 1.9E+02 0.0041 23.1 4.3 45 177-225 44-90 (129)
No 1
>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=97.16 E-value=0.00028 Score=45.27 Aligned_cols=37 Identities=41% Similarity=0.801 Sum_probs=32.4
Q ss_pred cccccCC-CceEEecCCccccCcccccccccCccccCCcccccc
Q 026095 4 ACELCSQ-EAALHCASDEAFLCFDCDDRVHKANFLVARHVRQTL 46 (243)
Q Consensus 4 ~Cd~C~~-pA~vyC~aD~A~LC~~CDa~vH~AN~La~rH~RvpL 46 (243)
.|+.++. +..+||..|...+|..|+...|. .|.++|+
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 5888987 99999999999999999988875 5888764
No 2
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.43 E-value=0.0025 Score=41.30 Aligned_cols=38 Identities=29% Similarity=0.578 Sum_probs=31.8
Q ss_pred ccccccC-CCceEEecCCccccCcccccccccCccccCCcccccc
Q 026095 3 RACELCS-QEAALHCASDEAFLCFDCDDRVHKANFLVARHVRQTL 46 (243)
Q Consensus 3 ~~Cd~C~-~pA~vyC~aD~A~LC~~CDa~vH~AN~La~rH~RvpL 46 (243)
..|+.++ .+..+||..|...+|..|....| ..|..++|
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 5789998 59999999999999999998866 35777654
No 3
>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=95.74 E-value=0.0049 Score=40.60 Aligned_cols=39 Identities=23% Similarity=0.442 Sum_probs=32.4
Q ss_pred CccccccCC-CceEEecCCccccCcccccccccCccccCCcccccc
Q 026095 2 KRACELCSQ-EAALHCASDEAFLCFDCDDRVHKANFLVARHVRQTL 46 (243)
Q Consensus 2 ~~~Cd~C~~-pA~vyC~aD~A~LC~~CDa~vH~AN~La~rH~RvpL 46 (243)
...|+.|.. ++.+||..+...+|..|....|.. |..++|
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 367999997 599999999999999999999864 776654
No 4
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=89.53 E-value=0.059 Score=53.83 Aligned_cols=80 Identities=25% Similarity=0.433 Sum_probs=62.2
Q ss_pred ccccccCC---CceEEecCCccccCcccccccccCccccCCccccccc-------------cccccCCcceeeccCCCCC
Q 026095 3 RACELCSQ---EAALHCASDEAFLCFDCDDRVHKANFLVARHVRQTLC-------------SQCKSLTGKFISGERSSSS 66 (243)
Q Consensus 3 ~~Cd~C~~---pA~vyC~aD~A~LC~~CDa~vH~AN~La~rH~RvpLC-------------~~C~~~pa~~~c~~~~~~d 66 (243)
..|.+|++ .|.|+|.....+.|..|..+.|-+--.+.+|.=+|-- ..|-.|+.....-||.. +
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~-c 241 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQ-C 241 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEe-c
Confidence 46999994 6999999999999999999999988888899876543 45667776655555554 7
Q ss_pred CcccCCCCCCCCCCCCC
Q 026095 67 LVPICPSCCSSTTSTSS 83 (243)
Q Consensus 67 ~~~LC~~Cd~~~~~~~s 83 (243)
.+++|-.|-.++-++.+
T Consensus 242 k~pvc~~clee~khs~h 258 (699)
T KOG4367|consen 242 KMPVCYQCLEEGKHSSH 258 (699)
T ss_pred CChHHHHHHHhhcccch
Confidence 88888888777666543
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=78.14 E-value=1.7 Score=27.87 Aligned_cols=31 Identities=19% Similarity=0.439 Sum_probs=25.2
Q ss_pred ccccccccccCCcceeeccCCCCCCcccCCCCCCC
Q 026095 43 RQTLCSQCKSLTGKFISGERSSSSLVPICPSCCSS 77 (243)
Q Consensus 43 RvpLC~~C~~~pa~~~c~~~~~~d~~~LC~~Cd~~ 77 (243)
|.++|+.++..+..+||.. +...+|..|...
T Consensus 2 ~~~~C~~h~~~~~~~~C~~----c~~~iC~~C~~~ 32 (42)
T smart00336 2 RPPKCDSHGDEPAEFFCEE----CGALLCRTCDEA 32 (42)
T ss_pred cCCcCCCCCCCceEEECCC----CCcccccccChh
Confidence 4677888887777888875 889999999865
No 6
>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=76.10 E-value=1.6 Score=27.51 Aligned_cols=29 Identities=17% Similarity=0.326 Sum_probs=23.0
Q ss_pred cccccccCCcceeeccCCCCCCcccCCCCCCCC
Q 026095 46 LCSQCKSLTGKFISGERSSSSLVPICPSCCSST 78 (243)
Q Consensus 46 LC~~C~~~pa~~~c~~~~~~d~~~LC~~Cd~~~ 78 (243)
+|+.++..|..++|.. |...+|..|+..+
T Consensus 2 ~C~~H~~~~~~~fC~~----~~~~iC~~C~~~~ 30 (39)
T cd00021 2 LCDEHGEEPLSLFCET----DRALLCVDCDLSV 30 (39)
T ss_pred CCCccCCcceEEEeCc----cChhhhhhcChhh
Confidence 4666666677888876 9999999999765
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=51.92 E-value=11 Score=23.01 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=17.3
Q ss_pred CCccccccCCCceEEecCCccccCcccccc
Q 026095 1 MKRACELCSQEAALHCASDEAFLCFDCDDR 30 (243)
Q Consensus 1 M~~~Cd~C~~pA~vyC~aD~A~LC~~CDa~ 30 (243)
|...|..|+.+ ..+.+..|..|..+
T Consensus 1 m~~~Cp~Cg~~-----~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAE-----IDPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCc-----CCcccccChhhCCC
Confidence 78889999962 14557777777654
No 8
>PF13406 SLT_2: Transglycosylase SLT domain; PDB: 1LTM_A 1D0L_A 1QDT_A 1D0K_A 1D0M_A 1QDR_A 1QUT_A 1QUS_A 4ANR_A.
Probab=46.92 E-value=26 Score=32.45 Aligned_cols=46 Identities=35% Similarity=0.419 Sum_probs=34.0
Q ss_pred CCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCCchhHHHH---HHHHHHHHhh
Q 026095 169 ALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGVPAKLIVA---VEGKIARVMA 224 (243)
Q Consensus 169 ~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgvpa~lila---ve~~~~r~~~ 224 (243)
.-|.||..+..||-+-+ ..|.++|+-.|||..+|+| ||+..++.+.
T Consensus 58 v~~~ri~~G~~~~~~~~----------~~l~~~e~~yGVp~~iivAi~GvET~yG~~~G 106 (262)
T PF13406_consen 58 VSPARIARGRAFLKEHR----------ALLDRAEKRYGVPPEIIVAIWGVETNYGRYTG 106 (262)
T ss_dssp SSHHHHHHHHHHHHHTH----------HHHHHHHHHH---HHHHHHHHHHHHTTTTS--
T ss_pred cCHHHHHHHHHHHHHHH----------HHHHHHHHHHCcCHHHHHHHHHHHhccccccC
Confidence 35789999999998665 8999999999999999876 6887765543
No 9
>PRK10760 murein hydrolase B; Provisional
Probab=45.80 E-value=28 Score=33.86 Aligned_cols=46 Identities=33% Similarity=0.487 Sum_probs=38.0
Q ss_pred CCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCCchhHHHH---HHHHHHHHhh
Q 026095 169 ALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGVPAKLIVA---VEGKIARVMA 224 (243)
Q Consensus 169 ~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgvpa~lila---ve~~~~r~~~ 224 (243)
.-|.||.-...||-+-+ ..|.|+|+-.|||..+|+| +|+..++.+.
T Consensus 120 v~~~ri~~G~~~~~~~~----------~~l~~~e~~yGVp~~iivAi~GvET~yG~~~G 168 (359)
T PRK10760 120 ITPDNVQNGVVFWNQYE----------DALNRAWQVYGVPPEIIVGIIGVETRWGRVMG 168 (359)
T ss_pred CCHHHHHHHHHHHHHhH----------HHHHHHHHHHCcCHHHHHHHHHhhcccccccC
Confidence 35788999999998766 8999999999999999876 6877776554
No 10
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=41.97 E-value=1.1e+02 Score=20.82 Aligned_cols=77 Identities=21% Similarity=0.263 Sum_probs=52.0
Q ss_pred HHHHHHHHhCCCCCCCCCchhhHHHHHHHHHhhhh--hhccCCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCC
Q 026095 130 IFAIWCRRLGLNGNNSNCNSVVVVSLASRALGLFL--ERTTALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGV 207 (243)
Q Consensus 130 vl~~w~rrlgl~~~~~~~~~~~~~~~A~~a~~~~~--~~~~~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgv 207 (243)
-+..-++.++++.. +...|..-+-+.+ .....-++....+++++.+.++.+. ...++.+...+|.
T Consensus 8 ~l~~~~~~~~~~~~--------~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~-----~~~~~~~~~~~~~ 74 (88)
T cd00043 8 FLRRVAKALGLSPE--------TLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI-----PPWLKDLVHVTGY 74 (88)
T ss_pred HHHHHHHHcCCCHH--------HHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCC-----CCCHHHHhHHhCC
Confidence 34455666777655 4555555444443 2234677888889999999998775 4667788899998
Q ss_pred -chhHHHHHHHHH
Q 026095 208 -PAKLIVAVEGKI 219 (243)
Q Consensus 208 -pa~lilave~~~ 219 (243)
..+-|...|..|
T Consensus 75 ~~~~~i~~~e~~i 87 (88)
T cd00043 75 ATEEEILRMEKLL 87 (88)
T ss_pred CCHHHHHHHHHHh
Confidence 777777666543
No 11
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=38.98 E-value=1.2e+02 Score=20.43 Aligned_cols=74 Identities=20% Similarity=0.277 Sum_probs=48.4
Q ss_pred HHHHHhCCCCCCCCCchhhHHHHHHHHHhhhhh--hccCCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCC-ch
Q 026095 133 IWCRRLGLNGNNSNCNSVVVVSLASRALGLFLE--RTTALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGV-PA 209 (243)
Q Consensus 133 ~w~rrlgl~~~~~~~~~~~~~~~A~~a~~~~~~--~~~~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgv-pa 209 (243)
.-+++++++.. +...|..-+-+.+. ...+-++-...+|+++.+-+..+.. +..+.+...+|+ ..
T Consensus 5 ~~~~~~~~~~~--------~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~-----~~~~~~~~~~~~~~~ 71 (83)
T smart00385 5 RVCKALNLDPE--------TLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIP-----PWTKELVHYTGYFTE 71 (83)
T ss_pred HHHHHcCCCHH--------HHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCC-----CCchhHhHhhCCCCH
Confidence 34566777543 34555543333321 2335778888899999999988743 345677888999 87
Q ss_pred hHHHHHHHHH
Q 026095 210 KLIVAVEGKI 219 (243)
Q Consensus 210 ~lilave~~~ 219 (243)
+-|...|..|
T Consensus 72 ~~i~~~~~~i 81 (83)
T smart00385 72 EEILRMEKLL 81 (83)
T ss_pred HHHHHHHHHH
Confidence 7777776654
No 12
>KOG2682 consensus NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=36.59 E-value=15 Score=34.76 Aligned_cols=25 Identities=40% Similarity=0.658 Sum_probs=21.9
Q ss_pred hhhhhhHHhhCCchhHHHHHHHHHH
Q 026095 196 PNLRRLEAISGVPAKLIVAVEGKIA 220 (243)
Q Consensus 196 ~~l~rle~~sgvpa~lilave~~~~ 220 (243)
||++-||.++|||.+.|+-+....+
T Consensus 127 QNIDtLER~aGv~d~~lvEAHGtFa 151 (314)
T KOG2682|consen 127 QNIDTLERIAGVPDEDLVEAHGTFA 151 (314)
T ss_pred ccchHHHHhcCCCHHHHHHhcccee
Confidence 9999999999999999998776543
No 13
>TIGR02282 MltB lytic murein transglycosylase B. This family consists of lytic murein transglycosylases (murein hydrolases) in the family of MltB, which is a membrane-bound lipoprotein in Escherichia coli. The N-terminal lipoprotein modification motif is conserved in about half the members of this family. The term Slt35 describes a naturally occurring soluble fragment of MltB. Members of this family never contain the putative peptidoglycan binding domain described by Pfam model pfam01471, which is associated with several classes of bacterial cell wall lytic enzymes.
Probab=33.63 E-value=59 Score=30.74 Aligned_cols=45 Identities=38% Similarity=0.505 Sum_probs=36.7
Q ss_pred CCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCCchhHHHH---HHHHHHHHh
Q 026095 169 ALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGVPAKLIVA---VEGKIARVM 223 (243)
Q Consensus 169 ~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgvpa~lila---ve~~~~r~~ 223 (243)
.-|.||.-.-.||-.-+ +.|.++|+-.|||..+|+| +|+..++.+
T Consensus 53 v~~~ri~~G~~~~~~~~----------~~l~~~e~~yGVp~~ii~AiwGvET~yG~~~ 100 (290)
T TIGR02282 53 ITPKRIQDGVEFWKQHE----------DALNRAEQRYGVPPEIIVAIIGVETNYGRNM 100 (290)
T ss_pred cCHHHHHHHHHHHHHhH----------HHHHHHHHHHCcCHHHHHHHHHHHhcccccc
Confidence 45778888888887544 8999999999999999886 688877655
No 14
>PF12773 DZR: Double zinc ribbon
Probab=30.96 E-value=59 Score=21.80 Aligned_cols=30 Identities=20% Similarity=0.581 Sum_probs=17.3
Q ss_pred CCccccCcccccccccCccccCCccccccccccccC
Q 026095 18 SDEAFLCFDCDDRVHKANFLVARHVRQTLCSQCKSL 53 (243)
Q Consensus 18 aD~A~LC~~CDa~vH~AN~La~rH~RvpLC~~C~~~ 53 (243)
.+.+..|..|...+- ........|..|...
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 355777777776665 223344456666553
No 15
>TIGR02283 MltB_2 lytic murein transglycosylase. Members of this family are closely related to the MltB family lytic murein transglycosylases described by TIGR02282 and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many members of this family (unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (pfam01471), not included in region described by this model. Many sequences appear to contain N-terminal lipoprotein attachment sites, as does E. coli MltB in TIGR02282.
Probab=30.08 E-value=74 Score=30.17 Aligned_cols=46 Identities=24% Similarity=0.377 Sum_probs=37.9
Q ss_pred CCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCCchhHHHH---HHHHHHHHhh
Q 026095 169 ALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGVPAKLIVA---VEGKIARVMA 224 (243)
Q Consensus 169 ~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgvpa~lila---ve~~~~r~~~ 224 (243)
.-|-||.....||-.-+ +.|.|+|+-.|||..+|+| +|+..++.+.
T Consensus 59 v~~~ri~~G~~~~~~~~----------~~L~~~e~~yGVp~~ii~Ai~gvET~yG~~~G 107 (300)
T TIGR02283 59 VSPRRIAIGRAMLQRYA----------ALLARIEKRYGVPAEILLAIWGMESDFGAYQG 107 (300)
T ss_pred cCHHHHHHHHHHHHHHH----------HHHHHHHHHhCcCHHHHHHHHHHHhhcccccC
Confidence 45788899889987665 8899999999999999886 6887776544
No 16
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.52 E-value=28 Score=25.83 Aligned_cols=31 Identities=19% Similarity=0.554 Sum_probs=27.2
Q ss_pred CCccccccCCCceEEecCCccccCccccccc
Q 026095 1 MKRACELCSQEAALHCASDEAFLCFDCDDRV 31 (243)
Q Consensus 1 M~~~Cd~C~~pA~vyC~aD~A~LC~~CDa~v 31 (243)
|+..|.-|+..-.||=++.....|..|...+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 5678999999899999999999999998655
No 17
>PF08224 DUF1719: Domain of unknown function (DUF1719); InterPro: IPR013181 This is a group of rice proteins of unknown function. They may have a role in ATPase activation.
Probab=27.98 E-value=94 Score=28.77 Aligned_cols=50 Identities=18% Similarity=0.254 Sum_probs=40.5
Q ss_pred cCCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCCchhHHHHHHH
Q 026095 168 TALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGVPAKLIVAVEG 217 (243)
Q Consensus 168 ~~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgvpa~lilave~ 217 (243)
..+|-||+-|+--+..-.+.++....+...+||+|..+.-..+.+--||.
T Consensus 3 ssfprRia~a~ksfvss~~~~~~~~~s~s~VrRFEr~AdgA~eFlR~VE~ 52 (234)
T PF08224_consen 3 SSFPRRIAHATKSFVSSIFHGNDDELSRSVVRRFERFADGASEFLRFVEL 52 (234)
T ss_pred ccHHHHHHHHHHHHHHhhcCCCCccccHHHHHHHHHHhhhHHHHHHHHHh
Confidence 46899999998776666666655557779999999999999998888874
No 18
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=27.66 E-value=19 Score=22.32 Aligned_cols=26 Identities=23% Similarity=0.616 Sum_probs=8.3
Q ss_pred cccccCCCceEEecCCccccCccccccccc
Q 026095 4 ACELCSQEAALHCASDEAFLCFDCDDRVHK 33 (243)
Q Consensus 4 ~Cd~C~~pA~vyC~aD~A~LC~~CDa~vH~ 33 (243)
.|+.|+.+-.- +..+-|..||-.+|.
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 58888853210 234568888888874
No 19
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=27.63 E-value=2.3e+02 Score=20.17 Aligned_cols=64 Identities=25% Similarity=0.315 Sum_probs=40.9
Q ss_pred HHHHHHhCCCCCCCCCchhhHHHHHHH----HHhhhhhhccCCchHHHHHHHHHhhhhhcCCCCcCCchhhhhhHHhhCC
Q 026095 132 AIWCRRLGLNGNNSNCNSVVVVSLASR----ALGLFLERTTALPLRACLAASFWFGLRMCGDKTVATWPNLRRLEAISGV 207 (243)
Q Consensus 132 ~~w~rrlgl~~~~~~~~~~~~~~~A~~----a~~~~~~~~~~~p~rv~laa~~w~~~~~~~~~~~~~~~~l~rle~~sgv 207 (243)
..-|.+|||..+ +...|.. +...++. ..| -+....||++++.-+..+.. -.++.+-+.+||
T Consensus 2 ~r~~~~L~L~~~--------v~~~A~~i~~~~~~~~~~-~Gr-~~~~iaAA~iY~acr~~~~~-----~t~~eIa~~~~V 66 (71)
T PF00382_consen 2 PRICSKLGLPED--------VRERAKEIYKKAQERGLL-KGR-SPESIAAACIYLACRLNGVP-----RTLKEIAEAAGV 66 (71)
T ss_dssp HHHHHHTT--HH--------HHHHHHHHHHHHHHTTTS-TTS--HHHHHHHHHHHHHHHTTSS-----SSHHHHHHHCTS
T ss_pred hHHHhHcCCCHH--------HHHHHHHHHHHHHHcCCc-ccC-CHHHHHHHHHHHHHHHcCCC-----cCHHHHHHHhCC
Confidence 345788999875 5666665 4444432 112 35777889999999987743 467888888888
Q ss_pred chh
Q 026095 208 PAK 210 (243)
Q Consensus 208 pa~ 210 (243)
.-+
T Consensus 67 s~~ 69 (71)
T PF00382_consen 67 SEK 69 (71)
T ss_dssp SHH
T ss_pred CCC
Confidence 754
No 20
>COG2951 MltB Membrane-bound lytic murein transglycosylase B [Cell envelope biogenesis, outer membrane]
Probab=22.53 E-value=55 Score=31.66 Aligned_cols=33 Identities=39% Similarity=0.470 Sum_probs=27.3
Q ss_pred CCchhhhhhHHhhCCchhHHHH---HHHHHHHHhhh
Q 026095 193 ATWPNLRRLEAISGVPAKLIVA---VEGKIARVMAV 225 (243)
Q Consensus 193 ~~~~~l~rle~~sgvpa~lila---ve~~~~r~~~~ 225 (243)
.+...|+|.|...|||+.+|++ +|+..++++..
T Consensus 111 ~~~~~l~~~e~~yGVp~~ii~aiWg~Et~fG~~~g~ 146 (343)
T COG2951 111 QYAAALARAERRYGVPAPILVAIWGMETGFGRVMGK 146 (343)
T ss_pred HHHHHHHHHHHHhCCCchheeeeehhhcccccccCc
Confidence 4457999999999999999875 68888887763
No 21
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=20.23 E-value=1.9e+02 Score=23.14 Aligned_cols=45 Identities=22% Similarity=0.231 Sum_probs=35.8
Q ss_pred HHHHHhhhhhcCCCCcCCchhhhhhHHhh--CCchhHHHHHHHHHHHHhhh
Q 026095 177 AASFWFGLRMCGDKTVATWPNLRRLEAIS--GVPAKLIVAVEGKIARVMAV 225 (243)
Q Consensus 177 aa~~w~~~~~~~~~~~~~~~~l~rle~~s--gvpa~lilave~~~~r~~~~ 225 (243)
..|||.++.. |...-+-+..||+.| +||..|...++.|+.+.-+.
T Consensus 44 ~~Sl~~A~~~----G~~~e~i~~~L~~~S~~~lP~~v~~~i~~w~~~~g~v 90 (129)
T PF13625_consen 44 PASLWRAASA----GLTAEEIIEFLERYSKNPLPQNVEQSIEDWARRYGRV 90 (129)
T ss_pred HHHHHHHHHc----CCCHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCE
Confidence 4688888874 455568888999987 69999999999999877553
Done!