Query 020733
Match_columns 322
No_of_seqs 297 out of 1450
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:42:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020733.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020733hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00018 AP2 DNA-binding domain 99.8 1.1E-18 2.3E-23 129.0 7.1 59 43-101 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.7 3.8E-18 8.2E-23 127.4 8.0 61 44-104 1-63 (64)
3 PF02362 B3: B3 DNA binding do 99.7 2.6E-17 5.6E-22 131.5 10.2 87 134-232 1-87 (100)
4 PHA00280 putative NHN endonucl 99.5 6.6E-15 1.4E-19 123.0 6.3 71 24-95 48-119 (121)
5 PF00847 AP2: AP2 domain; Int 99.0 1.1E-09 2.3E-14 79.1 5.8 50 43-92 1-56 (56)
6 PF03754 DUF313: Domain of unk 98.9 5.1E-09 1.1E-13 86.9 8.2 99 117-216 5-114 (114)
7 PF09217 EcoRII-N: Restriction 97.5 0.00025 5.5E-09 61.4 5.8 92 130-228 6-110 (156)
8 PF14657 Integrase_AP2: AP2-li 61.2 27 0.00058 23.8 5.1 36 55-90 1-42 (46)
9 PF10844 DUF2577: Protein of u 57.8 13 0.00028 29.9 3.5 28 213-246 71-98 (100)
10 smart00536 AXH domain in Ataxi 49.7 35 0.00076 28.6 4.8 28 200-227 75-112 (116)
11 PHA02601 int integrase; Provis 45.1 29 0.00064 32.8 4.2 42 47-89 2-46 (333)
12 PF10729 CedA: Cell division a 42.8 39 0.00084 25.8 3.6 39 42-81 30-68 (80)
13 PF04014 Antitoxin-MazE: Antid 38.8 44 0.00095 22.8 3.2 23 212-234 14-36 (47)
14 PF13356 DUF4102: Domain of un 38.8 1.6E+02 0.0035 22.6 6.9 40 50-89 29-74 (89)
15 PRK03760 hypothetical protein; 36.7 1E+02 0.0023 25.5 5.7 26 201-229 89-116 (117)
16 PF08517 AXH: Ataxin-1 and HBP 34.9 29 0.00064 29.0 2.1 29 199-227 73-111 (115)
17 cd06555 ASCH_PF0470_like ASC-1 33.5 71 0.0015 26.4 4.2 31 217-251 30-60 (109)
18 PF12195 End_beta_barrel: Beta 31.4 26 0.00057 27.2 1.2 18 214-231 23-40 (83)
19 PF08846 DUF1816: Domain of un 31.2 1E+02 0.0022 23.4 4.3 35 55-89 9-45 (68)
20 PF05036 SPOR: Sporulation rel 30.9 40 0.00088 24.2 2.2 22 65-86 44-65 (76)
21 PF03120 DNA_ligase_OB: NAD-de 30.3 42 0.00091 26.3 2.2 20 211-230 42-61 (82)
22 PRK10113 cell division modulat 28.3 45 0.00097 25.4 1.9 38 43-81 31-68 (80)
23 PF08471 Ribonuc_red_2_N: Clas 27.5 62 0.0013 26.1 2.7 21 69-89 70-90 (93)
24 cd04516 TBP_eukaryotes eukaryo 25.3 3E+02 0.0064 24.4 7.0 48 42-90 33-81 (174)
25 TIGR02609 doc_partner putative 25.2 1.6E+02 0.0035 22.2 4.6 33 195-230 3-35 (74)
26 cd04459 Rho_CSD Rho_CSD: Rho p 24.6 53 0.0011 24.8 1.8 21 212-232 34-54 (68)
27 PRK11347 antitoxin ChpS; Provi 22.6 2.6E+02 0.0056 21.8 5.4 36 193-231 3-38 (83)
28 PF02643 DUF192: Uncharacteriz 22.0 2.1E+02 0.0046 23.1 5.1 50 177-227 48-106 (108)
29 PF01878 EVE: EVE domain; Int 21.6 90 0.0019 26.1 2.9 16 217-232 38-53 (143)
30 cd00801 INT_P4 Bacteriophage P 20.7 1.9E+02 0.0042 26.9 5.2 37 54-90 10-50 (357)
31 COG4043 Preprotein translocase 20.6 69 0.0015 26.3 1.8 18 212-229 27-44 (111)
No 1
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=99.76 E-value=1.1e-18 Score=128.97 Aligned_cols=59 Identities=47% Similarity=0.821 Sum_probs=56.6
Q ss_pred CceEEEEECCCCeEEEEEeeC--CeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCcc
Q 020733 43 SKFKGVVPQQNGHWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT 101 (322)
Q Consensus 43 S~yrGV~~~~~gkw~A~I~~~--~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~ 101 (322)
|+|+||+++++|+|+|+|+.+ ++++|||+|+|+||||.|||.|+++++|.++.+|||.+
T Consensus 1 s~~~GV~~~~~gkw~A~I~~~~~gk~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~ 61 (61)
T cd00018 1 SKYRGVRQRPWGKWVAEIRDPSGGRRIWLGTFDTAEEAARAYDRAALKLRGSSAVLNFPDS 61 (61)
T ss_pred CCccCEEECCCCcEEEEEEeCCCCceEccCCCCCHHHHHHHHHHHHHHhcCCccccCCCCC
Confidence 799999998889999999998 99999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.75 E-value=3.8e-18 Score=127.38 Aligned_cols=61 Identities=41% Similarity=0.768 Sum_probs=58.5
Q ss_pred ceEEEEECCCCeEEEEEee--CCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCccccc
Q 020733 44 KFKGVVPQQNGHWGAQIYA--NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKIT 104 (322)
Q Consensus 44 ~yrGV~~~~~gkw~A~I~~--~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~~NFp~~~y~ 104 (322)
+|+||+++++|+|+|+|+. +++.+|||+|+|+||||.|||.|+++++|..+.+|||.++|+
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y~ 63 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLYD 63 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccCC
Confidence 4899998888999999999 999999999999999999999999999999999999999884
No 3
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.72 E-value=2.6e-17 Score=131.48 Aligned_cols=87 Identities=34% Similarity=0.563 Sum_probs=68.3
Q ss_pred cccccCccccccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCCceEEEEEEEeCCCCceEEccChHHH
Q 020733 134 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRF 213 (322)
Q Consensus 134 F~K~LT~SDV~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~gk~W~fr~~~~~~~~~yvLt~GW~~F 213 (322)
|.|+|++||+...++|.||+++++.|.... ..+..+.+.|..|+.|.+++++++.+.+++|++||..|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~------------~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~F 68 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNK------------RKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKF 68 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS--S------------S--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHH
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCCc------------CCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHH
Confidence 789999999988889999999999973111 24668888999999999999999988889999999999
Q ss_pred HhhcCCCCCCEEEEEEeec
Q 020733 214 VKENQLKANDTICFYLCEL 232 (322)
Q Consensus 214 V~~k~L~~GD~i~F~~~~~ 232 (322)
|++|+|++||+|+|+...+
T Consensus 69 v~~n~L~~GD~~~F~~~~~ 87 (100)
T PF02362_consen 69 VRDNGLKEGDVCVFELIGN 87 (100)
T ss_dssp HHHCT--TT-EEEEEE-SS
T ss_pred HHHcCCCCCCEEEEEEecC
Confidence 9999999999999999865
No 4
>PHA00280 putative NHN endonuclease
Probab=99.55 E-value=6.6e-15 Score=123.01 Aligned_cols=71 Identities=15% Similarity=0.107 Sum_probs=63.9
Q ss_pred CCCCCCCCcCcccCCCCCCCceEEEEE-CCCCeEEEEEeeCCeeEEecCCCCHHHHHHHHHHHHHHhcCCCCC
Q 020733 24 ISSTPLIPATKRLRHASAVSKFKGVVP-QQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSH 95 (322)
Q Consensus 24 ~~~~~~~~~~~r~~~~~~~S~yrGV~~-~~~gkw~A~I~~~~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~~a~ 95 (322)
+..+...+..+++.+++|+|||+||++ ++.|||+|+|.++||+++||.|+++|+|+.||+ ++.+|||.+|.
T Consensus 48 r~~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~ 119 (121)
T PHA00280 48 RLALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFAR 119 (121)
T ss_pred hhcCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhcccc
Confidence 456667788888889999999999987 678999999999999999999999999999997 77899999875
No 5
>PF00847 AP2: AP2 domain; InterPro: IPR001471 Pathogenesis-related genes transcriptional activator binds to the GCC-box pathogenesis-related promoter element and activates the plant's defence genes. Ethylene, chemically the simplest plant hormone, participates in a number of stress responses and developmental processes: e.g., fruit ripening, inhibition of stem and root elongation, promotion of seed germination and flowering, senescence of leaves and flowers, and sex determination []. DNA sequence elements that confer ethylene responsiveness have been shown to contain two 11bp GCC boxes, which are necessary and sufficient for transcriptional control by ethylene. Ethylene responsive element binding proteins (EREBPs) have now been identified in a variety of plants. The proteins share a similar domain of around 59 amino acids, which interacts directly with the GCC box in the ERE.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3IGM_A 3GCC_A 1GCC_A 2GCC_A.
Probab=98.98 E-value=1.1e-09 Score=79.07 Aligned_cols=50 Identities=36% Similarity=0.472 Sum_probs=44.5
Q ss_pred CceEEEEE-CCCCeEEEEEeeC-----CeeEEecCCCCHHHHHHHHHHHHHHhcCC
Q 020733 43 SKFKGVVP-QQNGHWGAQIYAN-----HQRIWLGTFKSEKDAAMAYDSAAIRLRGV 92 (322)
Q Consensus 43 S~yrGV~~-~~~gkw~A~I~~~-----~k~~~LG~f~t~eeAa~Ayd~aa~~~~g~ 92 (322)
|+|+||++ +..++|+|+|++. ++.++||.|+++++|+.|++.++..++|.
T Consensus 1 s~~~GV~~~~~~~~W~a~i~~~~~~g~~k~f~~g~fg~~~eA~~~a~~~r~~~~~e 56 (56)
T PF00847_consen 1 SGYKGVSWDKRRGRWRAQIRVWSENGKRKRFSVGKFGFEEEAKRAAIEARKELEGE 56 (56)
T ss_dssp SSSTTEEEETTTTEEEEEEEECCCTTEEEEEEECCCCCHHHHHHHHHHHHHHCTS-
T ss_pred CCcEEEEEcCCCCEEEEEEEEcccCcccEEEeCccCCCHHHHHHHHHHHHHHhcCC
Confidence 78999987 5689999999982 49999999999999999999999999873
No 6
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=98.91 E-value=5.1e-09 Score=86.89 Aligned_cols=99 Identities=28% Similarity=0.601 Sum_probs=75.6
Q ss_pred hhHhhhhhc--CCCccccccccccCcccc-ccccccccchhhHhhcCCCCchh---h--hhhcccCCCCCeEEEEEeCCC
Q 020733 117 EAVINMIRD--GSYSSRQLFQKELTPSDV-GKLNRLVIPKKYAVKYFPQISER---V--EEHAENDKADDVQLVFHDKSM 188 (322)
Q Consensus 117 Eevi~aLR~--gs~s~~~~F~K~LT~SDV-~~~~rL~IPk~~a~~~lP~l~~~---~--~~~~~~~~~~~~~l~~~D~~g 188 (322)
+.+.+.++. +.+....++.|.|+.||| .+++||.||...+.. ..+|... . +++.......|+.+.+.|..+
T Consensus 5 ~~l~~~m~~~~g~~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~ 83 (114)
T PF03754_consen 5 EWLKNVMREMNGAEDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSL 83 (114)
T ss_pred HHHHHHHHHhcCCCCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcC
Confidence 344455553 335568899999999999 568999999998866 4555521 1 112233556899999999999
Q ss_pred ceEEEEEEEeCC---CCceEEccChHHHHhh
Q 020733 189 KLWKFRYCYWKS---SQSFVFTRGWNRFVKE 216 (322)
Q Consensus 189 k~W~fr~~~~~~---~~~yvLt~GW~~FV~~ 216 (322)
+.|.++++.|.. +..|+|..||+.+|.+
T Consensus 84 ~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 84 RKWTMRLKKWNMGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred cEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence 999999999987 5789999999999864
No 7
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=97.45 E-value=0.00025 Score=61.42 Aligned_cols=92 Identities=23% Similarity=0.380 Sum_probs=57.0
Q ss_pred cccccccccCcccc----ccccccccchhhHhhcCCCCchhhhhhcccCCCCCeEEEEEeCCC--ceEEEEEEEeCC---
Q 020733 130 SRQLFQKELTPSDV----GKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM--KLWKFRYCYWKS--- 200 (322)
Q Consensus 130 ~~~~F~K~LT~SDV----~~~~rL~IPk~~a~~~lP~l~~~~~~~~~~~~~~~~~l~~~D~~g--k~W~fr~~~~~~--- 200 (322)
...+|.|.|++.|+ +++.++.||+..+..+||.+... ....+.+.|.+.+..+ ..|.||++|.++
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~------~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~ 79 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHT------KEENPDIWLKARWQSHFVTDSQVRFIYYNNRLF 79 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SS------SSSS-EEEEEEEETTTT---EEEEEEEE-CCCT
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcc------cccCCceeEEEEECCCCccceeEEEEEEccccc
Confidence 45679999999999 56789999999999999887632 2335788888888766 568899999987
Q ss_pred ---CCceEEccChHH-HHhhcCCCCCCEEEEE
Q 020733 201 ---SQSFVFTRGWNR-FVKENQLKANDTICFY 228 (322)
Q Consensus 201 ---~~~yvLt~GW~~-FV~~k~L~~GD~i~F~ 228 (322)
+.-|-|| .|.. |--.+-=.+||.++|-
T Consensus 80 ~gTRNE~RIT-~~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 80 GGTRNEYRIT-RFGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp TSS--EEEEE----TTSGGG-GGGTT-EEEEE
T ss_pred CCCcCceEEe-eecCCCccCCccccccEEEEE
Confidence 4557785 7776 4333334689988886
No 8
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=61.20 E-value=27 Score=23.83 Aligned_cols=36 Identities=22% Similarity=0.329 Sum_probs=27.4
Q ss_pred eEEEEEe-e---CC--eeEEecCCCCHHHHHHHHHHHHHHhc
Q 020733 55 HWGAQIY-A---NH--QRIWLGTFKSEKDAAMAYDSAAIRLR 90 (322)
Q Consensus 55 kw~A~I~-~---~~--k~~~LG~f~t~eeAa~Ayd~aa~~~~ 90 (322)
+|...|. . .| ++++-+.|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5878883 3 34 57788999999999999887766553
No 9
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=57.79 E-value=13 Score=29.90 Aligned_cols=28 Identities=14% Similarity=0.236 Sum_probs=21.7
Q ss_pred HHhhcCCCCCCEEEEEEeeccCceecceeEEEEe
Q 020733 213 FVKENQLKANDTICFYLCELRDIAKGTKTFGMID 246 (322)
Q Consensus 213 FV~~k~L~~GD~i~F~~~~~~~~~~~~~~~~~i~ 246 (322)
|.-...|++||.|.+.+...|. .|++++
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ------~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQ------KYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCC------EEEEEE
Confidence 5667899999999999965554 466665
No 10
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=49.70 E-value=35 Score=28.55 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=22.4
Q ss_pred CCCceEEccChHHHH----------hhcCCCCCCEEEE
Q 020733 200 SSQSFVFTRGWNRFV----------KENQLKANDTICF 227 (322)
Q Consensus 200 ~~~~yvLt~GW~~FV----------~~k~L~~GD~i~F 227 (322)
..+-||...||+-|- .-..|++||+|+-
T Consensus 75 eHPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 75 EHPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred CCCeEEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 457789999999763 4568999999975
No 11
>PHA02601 int integrase; Provisional
Probab=45.12 E-value=29 Score=32.76 Aligned_cols=42 Identities=24% Similarity=0.417 Sum_probs=28.9
Q ss_pred EEEECCCCeEEEEEeeC---CeeEEecCCCCHHHHHHHHHHHHHHh
Q 020733 47 GVVPQQNGHWGAQIYAN---HQRIWLGTFKSEKDAAMAYDSAAIRL 89 (322)
Q Consensus 47 GV~~~~~gkw~A~I~~~---~k~~~LG~f~t~eeAa~Ayd~aa~~~ 89 (322)
+|+..++|+|+++++.. |+++. .+|.|..||....+......
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHHhc
Confidence 45666788999999864 66654 36899888876655543333
No 12
>PF10729 CedA: Cell division activator CedA; InterPro: IPR019666 CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet [, ]. ; GO: 0003677 DNA binding, 0051301 cell division; PDB: 2BN8_A 2D35_A.
Probab=42.83 E-value=39 Score=25.80 Aligned_cols=39 Identities=15% Similarity=0.151 Sum_probs=27.8
Q ss_pred CCceEEEEECCCCeEEEEEeeCCeeEEecCCCCHHHHHHH
Q 020733 42 VSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMA 81 (322)
Q Consensus 42 ~S~yrGV~~~~~gkw~A~I~~~~k~~~LG~f~t~eeAa~A 81 (322)
--||+-||..+ |||.|.+..+..-..--.|..+|.|.+-
T Consensus 30 ~dgfrdvw~lr-gkyvafvl~ge~f~rsp~fs~pesaqrw 68 (80)
T PF10729_consen 30 MDGFRDVWQLR-GKYVAFVLMGEHFRRSPAFSVPESAQRW 68 (80)
T ss_dssp TTTECCECCCC-CEEEEEEESSS-EEE---BSSHHHHHHH
T ss_pred cccccceeeec-cceEEEEEecchhccCCCcCCcHHHHHH
Confidence 37899996654 9999999877655556788889888775
No 13
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=38.84 E-value=44 Score=22.80 Aligned_cols=23 Identities=13% Similarity=0.034 Sum_probs=20.0
Q ss_pred HHHhhcCCCCCCEEEEEEeeccC
Q 020733 212 RFVKENQLKANDTICFYLCELRD 234 (322)
Q Consensus 212 ~FV~~k~L~~GD~i~F~~~~~~~ 234 (322)
.|.+..+|++||.|.|.-..+|.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~ 36 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGK 36 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCE
Confidence 68888999999999999887764
No 14
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=38.77 E-value=1.6e+02 Score=22.57 Aligned_cols=40 Identities=20% Similarity=0.173 Sum_probs=25.1
Q ss_pred ECCCC--eEEEEEeeCCe--eEEecCCC--CHHHHHHHHHHHHHHh
Q 020733 50 PQQNG--HWGAQIYANHQ--RIWLGTFK--SEKDAAMAYDSAAIRL 89 (322)
Q Consensus 50 ~~~~g--kw~A~I~~~~k--~~~LG~f~--t~eeAa~Ayd~aa~~~ 89 (322)
..++| .|..+.+.+|+ ++-||.|. |..+|..........+
T Consensus 29 v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 29 VTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp E-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 34554 59888888876 56799997 5666665544443333
No 15
>PRK03760 hypothetical protein; Provisional
Probab=36.66 E-value=1e+02 Score=25.53 Aligned_cols=26 Identities=12% Similarity=0.271 Sum_probs=20.0
Q ss_pred CCceEE--ccChHHHHhhcCCCCCCEEEEEE
Q 020733 201 SQSFVF--TRGWNRFVKENQLKANDTICFYL 229 (322)
Q Consensus 201 ~~~yvL--t~GW~~FV~~k~L~~GD~i~F~~ 229 (322)
+-.|+| ..| ++.+.++++||.|.|-+
T Consensus 89 ~a~~VLEl~aG---~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 89 PARYIIEGPVG---KIRVLKVEVGDEIEWID 116 (117)
T ss_pred cceEEEEeCCC---hHHHcCCCCCCEEEEee
Confidence 356887 444 56789999999998865
No 16
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=34.89 E-value=29 Score=28.97 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=17.4
Q ss_pred CCCCceEEccChHHH----------HhhcCCCCCCEEEE
Q 020733 199 KSSQSFVFTRGWNRF----------VKENQLKANDTICF 227 (322)
Q Consensus 199 ~~~~~yvLt~GW~~F----------V~~k~L~~GD~i~F 227 (322)
-..+-||...||+-| ..-+.|++||+|+-
T Consensus 73 ~ehPFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl~ 111 (115)
T PF08517_consen 73 VEHPFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCLS 111 (115)
T ss_dssp TT-EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEEE
T ss_pred CCCceEEeCCcccccCcchhceecCCcccccccCCEEec
Confidence 345678889999754 34568899999974
No 17
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=33.46 E-value=71 Score=26.36 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=21.0
Q ss_pred cCCCCCCEEEEEEeeccCceecceeEEEEeeeeCC
Q 020733 217 NQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE 251 (322)
Q Consensus 217 k~L~~GD~i~F~~~~~~~~~~~~~~~~~i~~~~~~ 251 (322)
.++++||.|+|.--.++.. ...-++++.+=+
T Consensus 30 ~~ikvGD~I~f~~~~~~~~----l~v~V~~i~~Y~ 60 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQ----LLVKVVDIRKYD 60 (109)
T ss_pred hcCCCCCEEEEEEcCCCcE----EEEEEEEEEecC
Confidence 6799999999987766554 333455555443
No 18
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=31.40 E-value=26 Score=27.21 Aligned_cols=18 Identities=17% Similarity=0.224 Sum_probs=9.3
Q ss_pred HhhcCCCCCCEEEEEEee
Q 020733 214 VKENQLKANDTICFYLCE 231 (322)
Q Consensus 214 V~~k~L~~GD~i~F~~~~ 231 (322)
+.+++|.+||.|.|--..
T Consensus 23 l~~HGl~vGD~VnFsnsa 40 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSNSA 40 (83)
T ss_dssp -TT----TT-EEEEES-S
T ss_pred EccCceeecceEEEeccc
Confidence 578999999999997643
No 19
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=31.20 E-value=1e+02 Score=23.44 Aligned_cols=35 Identities=23% Similarity=0.385 Sum_probs=24.8
Q ss_pred eEEEEEeeC--CeeEEecCCCCHHHHHHHHHHHHHHh
Q 020733 55 HWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRL 89 (322)
Q Consensus 55 kw~A~I~~~--~k~~~LG~f~t~eeAa~Ayd~aa~~~ 89 (322)
.|=++|.-. .-..|.|.|.|.+||..+...-...+
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL 45 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDL 45 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHH
Confidence 466788653 35678999999999998854443333
No 20
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=30.93 E-value=40 Score=24.24 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=18.0
Q ss_pred eeEEecCCCCHHHHHHHHHHHH
Q 020733 65 QRIWLGTFKSEKDAAMAYDSAA 86 (322)
Q Consensus 65 k~~~LG~f~t~eeAa~Ayd~aa 86 (322)
-++++|.|+|.++|..+.....
T Consensus 44 yrV~~G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 44 YRVRVGPFSSREEAEAALRKLK 65 (76)
T ss_dssp EEEEECCECTCCHHHHHHHHHH
T ss_pred EEEEECCCCCHHHHHHHHHHHh
Confidence 4778999999999988876654
No 21
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=30.30 E-value=42 Score=26.32 Aligned_cols=20 Identities=20% Similarity=0.361 Sum_probs=16.3
Q ss_pred HHHHhhcCCCCCCEEEEEEe
Q 020733 211 NRFVKENQLKANDTICFYLC 230 (322)
Q Consensus 211 ~~FV~~k~L~~GD~i~F~~~ 230 (322)
..|+++++|..||.|.++|.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~ra 61 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRA 61 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEC
Confidence 47999999999999999994
No 22
>PRK10113 cell division modulator; Provisional
Probab=28.32 E-value=45 Score=25.39 Aligned_cols=38 Identities=16% Similarity=0.169 Sum_probs=28.8
Q ss_pred CceEEEEECCCCeEEEEEeeCCeeEEecCCCCHHHHHHH
Q 020733 43 SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMA 81 (322)
Q Consensus 43 S~yrGV~~~~~gkw~A~I~~~~k~~~LG~f~t~eeAa~A 81 (322)
-+|+-||..+ |||.|.+.....-..--.|..+|.|.+-
T Consensus 31 d~frDVW~Lr-GKYVAFvl~ge~FrRSPaFs~PEsAQRW 68 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLMGESFLRSPAFSVPESAQRW 68 (80)
T ss_pred cchhhhheec-cceEEEEEechhhccCCccCCcHHHHHH
Confidence 6888887655 9999999775544445678888888775
No 23
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=27.46 E-value=62 Score=26.08 Aligned_cols=21 Identities=38% Similarity=0.493 Sum_probs=17.5
Q ss_pred ecCCCCHHHHHHHHHHHHHHh
Q 020733 69 LGTFKSEKDAAMAYDSAAIRL 89 (322)
Q Consensus 69 LG~f~t~eeAa~Ayd~aa~~~ 89 (322)
-|+|+|+|+|..-||...-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 589999999999999875443
No 24
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=25.34 E-value=3e+02 Score=24.44 Aligned_cols=48 Identities=21% Similarity=0.277 Sum_probs=37.4
Q ss_pred CCceEEEEEC-CCCeEEEEEeeCCeeEEecCCCCHHHHHHHHHHHHHHhc
Q 020733 42 VSKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLR 90 (322)
Q Consensus 42 ~S~yrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~eeAa~Ayd~aa~~~~ 90 (322)
...|-|+..| +.-+-.+.|+..||-+-.|.. |+|+|..|.++.+..+.
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 33 PKRFAAVIMRIREPKTTALIFSSGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred CccCcEEEEEeCCCcEEEEEECCCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 3678899664 345778899999999988875 77888888888777775
No 25
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=25.24 E-value=1.6e+02 Score=22.22 Aligned_cols=33 Identities=15% Similarity=0.034 Sum_probs=23.6
Q ss_pred EEEeCCCCceEEccChHHHHhhcCCCCCCEEEEEEe
Q 020733 195 YCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLC 230 (322)
Q Consensus 195 ~~~~~~~~~yvLt~GW~~FV~~k~L~~GD~i~F~~~ 230 (322)
...|+++.--.|- ..++..-+|..||.|.|...
T Consensus 3 i~k~GNS~~vtIP---k~i~~~lgl~~Gd~v~v~~~ 35 (74)
T TIGR02609 3 IRKVGNSLVVTLP---KEVLESLGLKEGDTLYVDEE 35 (74)
T ss_pred EEEECCeeEEEEC---HHHHHHcCcCCCCEEEEEEE
Confidence 3466766444454 36899999999999977553
No 26
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=24.58 E-value=53 Score=24.80 Aligned_cols=21 Identities=14% Similarity=0.159 Sum_probs=17.0
Q ss_pred HHHhhcCCCCCCEEEEEEeec
Q 020733 212 RFVKENQLKANDTICFYLCEL 232 (322)
Q Consensus 212 ~FV~~k~L~~GD~i~F~~~~~ 232 (322)
..++..+|+.||.|.=.-.+.
T Consensus 34 ~~Irr~~LR~GD~V~G~vr~p 54 (68)
T cd04459 34 SQIRRFNLRTGDTVVGQIRPP 54 (68)
T ss_pred HHHHHhCCCCCCEEEEEEeCC
Confidence 589999999999998655443
No 27
>PRK11347 antitoxin ChpS; Provisional
Probab=22.58 E-value=2.6e+02 Score=21.77 Aligned_cols=36 Identities=19% Similarity=0.308 Sum_probs=28.4
Q ss_pred EEEEEeCCCCceEEccChHHHHhhcCCCCCCEEEEEEee
Q 020733 193 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLCE 231 (322)
Q Consensus 193 fr~~~~~~~~~yvLt~GW~~FV~~k~L~~GD~i~F~~~~ 231 (322)
.+.+.|++|.--.|- ..|++.-+|.+||.|.+.-..
T Consensus 3 ~~v~kwGNS~~vriP---k~il~~l~l~~G~~v~i~v~~ 38 (83)
T PRK11347 3 ITIKRWGNSAGMVIP---NIVMKELNLQPGQSVEAQVSN 38 (83)
T ss_pred EEEEEEcCceeEEeC---HHHHHHcCCCCCCEEEEEEEC
Confidence 356688888776676 479999999999999877643
No 28
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=21.98 E-value=2.1e+02 Score=23.05 Aligned_cols=50 Identities=12% Similarity=0.135 Sum_probs=27.7
Q ss_pred CCeEEEEEeCCCceEEEEEEEe---------CCCCceEEccChHHHHhhcCCCCCCEEEE
Q 020733 177 DDVQLVFHDKSMKLWKFRYCYW---------KSSQSFVFTRGWNRFVKENQLKANDTICF 227 (322)
Q Consensus 177 ~~~~l~~~D~~gk~W~fr~~~~---------~~~~~yvLt~GW~~FV~~k~L~~GD~i~F 227 (322)
-.+++.+.|..|++-....... ..+-+|+|.- =..++...+|++||.|.|
T Consensus 48 ~pLDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~-~aG~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 48 FPLDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLEL-PAGWFEKLGIKVGDRVRI 106 (108)
T ss_dssp S-EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEE-ETTHHHHHT--TT-EEE-
T ss_pred eeEEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEc-CCCchhhcCCCCCCEEEe
Confidence 4567778887777655554331 1224688831 123688999999999987
No 29
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=21.61 E-value=90 Score=26.15 Aligned_cols=16 Identities=25% Similarity=0.553 Sum_probs=11.3
Q ss_pred cCCCCCCEEEEEEeec
Q 020733 217 NQLKANDTICFYLCEL 232 (322)
Q Consensus 217 k~L~~GD~i~F~~~~~ 232 (322)
+++++||.|+||...+
T Consensus 38 ~~mk~GD~vifY~s~~ 53 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGC 53 (143)
T ss_dssp HC--TT-EEEEEETSS
T ss_pred hcCCCCCEEEEEEcCC
Confidence 3999999999999883
No 30
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=20.68 E-value=1.9e+02 Score=26.89 Aligned_cols=37 Identities=24% Similarity=0.306 Sum_probs=26.0
Q ss_pred CeEEEEEeeCCee--EEecCCC--CHHHHHHHHHHHHHHhc
Q 020733 54 GHWGAQIYANHQR--IWLGTFK--SEKDAAMAYDSAAIRLR 90 (322)
Q Consensus 54 gkw~A~I~~~~k~--~~LG~f~--t~eeAa~Ayd~aa~~~~ 90 (322)
+.|+.+++.+|++ ..||+|+ +.++|..+.......+.
T Consensus 10 ~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 10 KSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred EEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 4699999888865 4589995 66777766655544443
No 31
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.64 E-value=69 Score=26.29 Aligned_cols=18 Identities=33% Similarity=0.285 Sum_probs=14.9
Q ss_pred HHHhhcCCCCCCEEEEEE
Q 020733 212 RFVKENQLKANDTICFYL 229 (322)
Q Consensus 212 ~FV~~k~L~~GD~i~F~~ 229 (322)
..-+.++.+.||+|+|-.
T Consensus 27 ~d~krr~ik~GD~IiF~~ 44 (111)
T COG4043 27 ADPKRRQIKPGDKIIFNG 44 (111)
T ss_pred cCHhhcCCCCCCEEEEcC
Confidence 345778999999999975
Done!