Query 018549
Match_columns 354
No_of_seqs 324 out of 1541
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 09:56:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018549hhsearch_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 7.7E-19 1.7E-23 132.0 7.4 59 43-101 1-61 (61)
2 smart00380 AP2 DNA-binding dom 99.8 1.7E-18 3.6E-23 131.6 8.5 61 44-104 1-63 (64)
3 PF02362 B3: B3 DNA binding do 99.7 4.4E-16 9.6E-21 126.2 10.8 87 166-264 1-87 (100)
4 PHA00280 putative NHN endonucl 99.6 6.2E-15 1.3E-19 125.5 6.8 70 26-96 50-120 (121)
5 PF03754 DUF313: Domain of unk 99.3 1.8E-12 3.9E-17 109.4 7.0 104 144-248 2-114 (114)
6 PF00847 AP2: AP2 domain; Int 99.0 1.4E-09 3.1E-14 79.8 6.2 50 43-92 1-56 (56)
7 PF09217 EcoRII-N: Restriction 98.2 3.8E-06 8.2E-11 74.0 6.6 93 163-262 7-112 (156)
8 PF14657 Integrase_AP2: AP2-li 58.5 34 0.00074 23.9 5.3 36 55-90 1-42 (46)
9 PF10844 DUF2577: Protein of u 58.4 13 0.00028 30.5 3.6 28 245-278 71-98 (100)
10 PHA02601 int integrase; Provis 43.5 31 0.00068 33.1 4.2 40 47-87 2-44 (333)
11 PF10729 CedA: Cell division a 39.0 47 0.001 26.0 3.6 39 42-81 30-68 (80)
12 PF04014 Antitoxin-MazE: Antid 33.5 58 0.0013 22.7 3.2 34 230-266 3-36 (47)
13 PF03120 DNA_ligase_OB: NAD-de 29.7 42 0.00091 26.9 2.1 19 243-261 42-60 (82)
14 TIGR02609 doc_partner putative 29.5 1.2E+02 0.0026 23.4 4.6 33 227-262 3-35 (74)
15 PRK03760 hypothetical protein; 29.2 1.6E+02 0.0035 24.9 5.8 26 233-261 89-116 (117)
16 smart00536 AXH domain in Ataxi 27.8 1.3E+02 0.0027 25.9 4.8 27 233-259 76-112 (116)
17 PF05036 SPOR: Sporulation rel 27.3 45 0.00098 24.5 1.9 22 65-86 44-65 (76)
18 PRK11347 antitoxin ChpS; Provi 27.1 1.8E+02 0.004 23.1 5.4 35 225-262 3-37 (83)
19 cd06555 ASCH_PF0470_like ASC-1 27.0 1.1E+02 0.0023 25.9 4.2 31 249-283 30-60 (109)
20 PRK10113 cell division modulat 26.1 53 0.0011 25.6 2.0 37 43-80 31-67 (80)
21 PF13356 DUF4102: Domain of un 25.1 3.3E+02 0.0073 21.2 6.8 39 51-89 30-74 (89)
22 PF00352 TBP: Transcription fa 24.6 1.6E+02 0.0034 23.2 4.7 46 43-89 36-82 (86)
23 PF08846 DUF1816: Domain of un 22.7 1.6E+02 0.0035 22.9 4.2 37 55-91 9-47 (68)
24 cd00801 INT_P4 Bacteriophage P 22.3 1.5E+02 0.0033 28.0 5.0 38 53-90 9-50 (357)
25 PLN00062 TATA-box-binding prot 22.2 3.5E+02 0.0076 24.6 7.0 48 42-90 33-81 (179)
26 PF08471 Ribonuc_red_2_N: Clas 21.6 97 0.0021 25.6 2.9 21 69-89 70-90 (93)
27 PRK05449 aspartate alpha-decar 21.5 5.5E+02 0.012 22.4 8.6 76 165-262 10-90 (126)
28 cd04516 TBP_eukaryotes eukaryo 21.4 3.8E+02 0.0083 24.2 7.1 47 43-90 34-81 (174)
29 cd06919 Asp_decarbox Aspartate 20.9 5.3E+02 0.011 22.0 8.6 79 165-263 9-90 (111)
30 PF12195 End_beta_barrel: Beta 20.8 60 0.0013 25.9 1.4 16 246-261 23-38 (83)
31 cd04459 Rho_CSD Rho_CSD: Rho p 20.8 77 0.0017 24.5 2.1 23 244-266 34-56 (68)
32 TIGR00223 panD L-aspartate-alp 20.5 5.7E+02 0.012 22.2 8.6 77 165-263 10-91 (126)
33 TIGR01164 rplP_bact ribosomal 20.3 1.7E+02 0.0038 25.1 4.4 34 55-89 91-124 (126)
34 PRK09203 rplP 50S ribosomal pr 20.3 1.6E+02 0.0034 25.8 4.1 36 55-91 92-127 (138)
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=99.77 E-value=7.7e-19 Score=132.02 Aligned_cols=59 Identities=47% Similarity=0.821 Sum_probs=56.6
Q ss_pred CceEEeEECCCCeEEEEEEeC--CeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCC
Q 018549 43 SKFKGVVPQQNGHWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWT 101 (354)
Q Consensus 43 SgyrGV~~~~~gkw~A~I~~~--~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~ 101 (354)
|+|+||+++++|+|+|+|++. ++++|||+|+|+||||.|||.|+++++|..+.+|||.+
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 789999988889999999998 99999999999999999999999999999999999964
No 2
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.76 E-value=1.7e-18 Score=131.62 Aligned_cols=61 Identities=41% Similarity=0.768 Sum_probs=58.7
Q ss_pred ceEEeEECCCCeEEEEEEe--CCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Q 018549 44 KFKGVVPQQNGHWGAQIYA--NHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHRNFPWTKIT 104 (354)
Q Consensus 44 gyrGV~~~~~gkw~A~I~~--~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~NFp~~~y~ 104 (354)
+|+||+++++|+|+|+|++ +++++|||+|+|+||||.|||.|+++++|..+.+|||.++|+
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 4899988889999999999 999999999999999999999999999999999999999986
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=99.67 E-value=4.4e-16 Score=126.24 Aligned_cols=87 Identities=36% Similarity=0.583 Sum_probs=68.9
Q ss_pred eeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCCceEEEEEEEeCCCCeeeEccChHHH
Q 018549 166 FQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSMKLWKFRYCYWKSSQSFVFTRGWNRF 245 (354)
Q Consensus 166 F~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g~~W~fr~~~~~~sr~yvLt~GW~~F 245 (354)
|.|+|+++|+...++|.||++.+.+|... ...++.+.+.|..|+.|.+++++++.+.+|+|++||..|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~------------~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~F 68 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN------------KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKF 68 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS--------------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHH
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC------------cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHH
Confidence 78999999999889999999999988211 135678999999999999999999998889999999999
Q ss_pred HhhcCCCCCCEEEEEEeec
Q 018549 246 VKENQLKANDTICFYLCEL 264 (354)
Q Consensus 246 Vr~k~Lk~GD~I~F~r~~~ 264 (354)
|++++|++||.|+|+...+
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=6.2e-15 Score=125.52 Aligned_cols=70 Identities=16% Similarity=0.115 Sum_probs=62.2
Q ss_pred CCCCCCCCcccCCCCCCCceEEeEE-CCCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHhcCCCCCC
Q 018549 26 STPLIPATKRLRHASAVSKFKGVVP-QQNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRGVDSHR 96 (354)
Q Consensus 26 ~~~~~~~~~r~~~~~~~SgyrGV~~-~~~gkw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~~a~~ 96 (354)
.|..++..+++.+++|+|||+||++ +..|||+|+|.++||+++||.|+++|+|+.||+ ++.++||.+|+.
T Consensus 50 ~T~~eN~~N~~~~~~N~SG~kGV~~~k~~~kw~A~I~~~gK~~~lG~f~~~e~A~~a~~-~~~~lhGeFa~~ 120 (121)
T PHA00280 50 ALPKENSWNMKTPKSNTSGLKGLSWSKEREMWRGTVTAEGKQHNFRSRDLLEVVAWIYR-TRRELHGQFARF 120 (121)
T ss_pred cCHHHHhcccCCCCCCCCCCCeeEEecCCCeEEEEEEECCEEEEcCCCCCHHHHHHHHH-HHHHHhhccccC
Confidence 4566778888889999999999965 568999999999999999999999999999997 778999999853
No 5
>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=99.35 E-value=1.8e-12 Score=109.43 Aligned_cols=104 Identities=25% Similarity=0.473 Sum_probs=83.1
Q ss_pred cccccccccccCCCCcccccceeeeeccccccCC-CCceeechhhhhhcCCCCchhh-----hhhccccCCCCeEEEEEe
Q 018549 144 EEDVIFTQMRAGTDGWMMCRQLFQKELTPSDVGK-LNRLVIPKKYAVKYFPQISERV-----EEHAENDKADDVQLVFHD 217 (354)
Q Consensus 144 et~~~~~~~~~~~~~~~~~~~lF~K~LT~SDv~~-~~rL~IPk~~a~~~fP~l~~~~-----~~~~~~~~~~gv~v~v~D 217 (354)
+.|+|+..++..+.+..+..++++|+|++|||.+ ++||+||...+.. ..+|..+. +++.......|+.|.++|
T Consensus 2 e~P~~l~~~m~~~~g~~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvd 80 (114)
T PF03754_consen 2 ELPEWLKNVMREMNGAEDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVD 80 (114)
T ss_pred CchHHHHHHHHHhcCCCCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEEC
Confidence 5678888888877666677999999999999987 9999999888755 24444211 112234567899999999
Q ss_pred CCCceEEEEEEEeCC---CCeeeEccChHHHHhh
Q 018549 218 KSMKLWKFRYCYWKS---SQSFVFTRGWNRFVKE 248 (354)
Q Consensus 218 ~~g~~W~fr~~~~~~---sr~yvLt~GW~~FVr~ 248 (354)
..++.|.++++.|.. +..|+|+.||+++|+.
T Consensus 81 p~~~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 81 PSLRKWTMRLKKWNMGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CcCcEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence 999999999999987 6689999999999863
No 6
>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=98.96 E-value=1.4e-09 Score=79.80 Aligned_cols=50 Identities=36% Similarity=0.468 Sum_probs=44.4
Q ss_pred CceEEeEEC-CCCeEEEEEEeC-----CeEEEecCCCCHHHHHHHHHHHHHHhcCC
Q 018549 43 SKFKGVVPQ-QNGHWGAQIYAN-----HQRIWLGTFKSEKDAAMAYDSAAIRLRGV 92 (354)
Q Consensus 43 SgyrGV~~~-~~gkw~A~I~~~-----~k~~~LG~f~t~EeAa~Ayd~aa~~~~g~ 92 (354)
|+|+||++. ..++|+|+|++. ++.++||.|++++||++||+.++..++|+
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 789999765 589999999982 49999999999999999999999999874
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=98.18 E-value=3.8e-06 Score=74.04 Aligned_cols=93 Identities=19% Similarity=0.305 Sum_probs=58.9
Q ss_pred cceeeeeccccccCC----CCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEeCCC--ceEEEEEEEeCC----
Q 018549 163 RQLFQKELTPSDVGK----LNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHDKSM--KLWKFRYCYWKS---- 232 (354)
Q Consensus 163 ~~lF~K~LT~SDv~~----~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D~~g--~~W~fr~~~~~~---- 232 (354)
-.+|+|.|++.|++. +.++.|||..+..+||.+.. ..+.++.+.|.+.+..+ ..|+||++|.++
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~------~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~ 80 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINH------TKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFG 80 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-S------SSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTT
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCc------ccccCCceeEEEEECCCCccceeEEEEEEcccccC
Confidence 358999999999975 78899999999999999874 23346889999988766 568899999987
Q ss_pred --CCeeeEccChHHHHhhcC-CCCCCEEEEEEe
Q 018549 233 --SQSFVFTRGWNRFVKENQ-LKANDTICFYLC 262 (354)
Q Consensus 233 --sr~yvLt~GW~~FVr~k~-Lk~GD~I~F~r~ 262 (354)
...|.|| +|.....--+ =.+||.++|-=.
T Consensus 81 gTRNE~RIT-~~G~~~~~~~~~~tGaL~vlaf~ 112 (156)
T PF09217_consen 81 GTRNEYRIT-RFGRGFPLQNPENTGALLVLAFD 112 (156)
T ss_dssp SS--EEEEE----TTSGGG-GGGTT-EEEEEEE
T ss_pred CCcCceEEe-eecCCCccCCccccccEEEEEEc
Confidence 4559997 7877433222 468998888744
No 8
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=58.50 E-value=34 Score=23.85 Aligned_cols=36 Identities=22% Similarity=0.329 Sum_probs=28.0
Q ss_pred eEEEEEE-e---CC--eEEEecCCCCHHHHHHHHHHHHHHhc
Q 018549 55 HWGAQIY-A---NH--QRIWLGTFKSEKDAAMAYDSAAIRLR 90 (354)
Q Consensus 55 kw~A~I~-~---~~--k~~~LG~f~t~EeAa~Ayd~aa~~~~ 90 (354)
+|...|. . .| ++++-+.|.|..||..+...+...+.
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~~ 42 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAELE 42 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHHH
Confidence 5788883 3 33 67888999999999999888766654
No 9
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=58.40 E-value=13 Score=30.54 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=20.9
Q ss_pred HHhhcCCCCCCEEEEEEeecCCccccceeEEEEE
Q 018549 245 FVKENQLKANDTICFYLCELRDIAKGTKTFGMID 278 (354)
Q Consensus 245 FVr~k~Lk~GD~I~F~r~~~g~~~~~~~~~~~i~ 278 (354)
|.-..+|++||.|.+.+...| +.|+++|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~g------Q~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGG------QKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCC------CEEEEEE
Confidence 445678999999999994444 5567766
No 10
>PHA02601 int integrase; Provisional
Probab=43.50 E-value=31 Score=33.12 Aligned_cols=40 Identities=25% Similarity=0.420 Sum_probs=28.2
Q ss_pred EeEECCCCeEEEEEEeC---CeEEEecCCCCHHHHHHHHHHHHH
Q 018549 47 GVVPQQNGHWGAQIYAN---HQRIWLGTFKSEKDAAMAYDSAAI 87 (354)
Q Consensus 47 GV~~~~~gkw~A~I~~~---~k~~~LG~f~t~EeAa~Ayd~aa~ 87 (354)
+|++.++|+|+++++.. |+++. .+|.|..||.........
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~-~~f~tk~eA~~~~~~~~~ 44 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIR-KRFATKGEALAFENYTMA 44 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhh-hhhcCHHHHHHHHHHHHH
Confidence 46666788999999863 66665 369999888765554433
No 11
>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=38.98 E-value=47 Score=25.99 Aligned_cols=39 Identities=15% Similarity=0.151 Sum_probs=27.5
Q ss_pred CCceEEeEECCCCeEEEEEEeCCeEEEecCCCCHHHHHHH
Q 018549 42 VSKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAMA 81 (354)
Q Consensus 42 ~SgyrGV~~~~~gkw~A~I~~~~k~~~LG~f~t~EeAa~A 81 (354)
--||+-||.-+ |||.|.+..+..-..--.|..+|.|-+=
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 37899997544 9999999887766667788888887653
No 12
>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=33.49 E-value=58 Score=22.69 Aligned_cols=34 Identities=12% Similarity=0.030 Sum_probs=24.7
Q ss_pred eCCCCeeeEccChHHHHhhcCCCCCCEEEEEEeecCC
Q 018549 230 WKSSQSFVFTRGWNRFVKENQLKANDTICFYLCELRD 266 (354)
Q Consensus 230 ~~~sr~yvLt~GW~~FVr~k~Lk~GD~I~F~r~~~g~ 266 (354)
|+++..-.|= ..|.+..+|++||.|.|.-..+|.
T Consensus 3 vg~s~~v~iP---k~~~~~l~l~~Gd~v~i~~~~~g~ 36 (47)
T PF04014_consen 3 VGNSGQVTIP---KEIREKLGLKPGDEVEIEVEGDGK 36 (47)
T ss_dssp ETTCSEEEE----HHHHHHTTSSTTTEEEEEEETTSE
T ss_pred ECCCceEECC---HHHHHHcCCCCCCEEEEEEeCCCE
Confidence 3444444554 358888999999999999987764
No 13
>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=29.72 E-value=42 Score=26.93 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=15.9
Q ss_pred HHHHhhcCCCCCCEEEEEE
Q 018549 243 NRFVKENQLKANDTICFYL 261 (354)
Q Consensus 243 ~~FVr~k~Lk~GD~I~F~r 261 (354)
.+|+++++|..||.|.++|
T Consensus 42 ~~~i~~~~i~~Gd~V~V~r 60 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTR 60 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEE
Confidence 4799999999999999999
No 14
>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=29.48 E-value=1.2e+02 Score=23.44 Aligned_cols=33 Identities=15% Similarity=0.034 Sum_probs=24.7
Q ss_pred EEEeCCCCeeeEccChHHHHhhcCCCCCCEEEEEEe
Q 018549 227 YCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLC 262 (354)
Q Consensus 227 ~~~~~~sr~yvLt~GW~~FVr~k~Lk~GD~I~F~r~ 262 (354)
...|++|..-.|- ..++..-+|..||.|.|...
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 4567777555665 36899999999999977553
No 15
>PRK03760 hypothetical protein; Provisional
Probab=29.18 E-value=1.6e+02 Score=24.89 Aligned_cols=26 Identities=12% Similarity=0.268 Sum_probs=20.0
Q ss_pred CCeeeE--ccChHHHHhhcCCCCCCEEEEEE
Q 018549 233 SQSFVF--TRGWNRFVKENQLKANDTICFYL 261 (354)
Q Consensus 233 sr~yvL--t~GW~~FVr~k~Lk~GD~I~F~r 261 (354)
+-.||| ..|| +.+.++++||.|.|-+
T Consensus 89 ~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 89 PARYIIEGPVGK---IRVLKVEVGDEIEWID 116 (117)
T ss_pred cceEEEEeCCCh---HHHcCCCCCCEEEEee
Confidence 455888 4454 6789999999998764
No 16
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=27.80 E-value=1.3e+02 Score=25.85 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=21.4
Q ss_pred CCeeeEccChHHHH----------hhcCCCCCCEEEE
Q 018549 233 SQSFVFTRGWNRFV----------KENQLKANDTICF 259 (354)
Q Consensus 233 sr~yvLt~GW~~FV----------r~k~Lk~GD~I~F 259 (354)
-..||...||+.|- ....|++||+++-
T Consensus 76 HPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 76 HPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred CCeEEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 46689999999873 4567899999874
No 17
>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=27.30 E-value=45 Score=24.46 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=17.9
Q ss_pred eEEEecCCCCHHHHHHHHHHHH
Q 018549 65 QRIWLGTFKSEKDAAMAYDSAA 86 (354)
Q Consensus 65 k~~~LG~f~t~EeAa~Ayd~aa 86 (354)
-++.+|.|++.++|..+.....
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 4788999999999988876654
No 18
>PRK11347 antitoxin ChpS; Provisional
Probab=27.07 E-value=1.8e+02 Score=23.14 Aligned_cols=35 Identities=20% Similarity=0.308 Sum_probs=29.4
Q ss_pred EEEEEeCCCCeeeEccChHHHHhhcCCCCCCEEEEEEe
Q 018549 225 FRYCYWKSSQSFVFTRGWNRFVKENQLKANDTICFYLC 262 (354)
Q Consensus 225 fr~~~~~~sr~yvLt~GW~~FVr~k~Lk~GD~I~F~r~ 262 (354)
...+.|++|..-.|- ..|++.-+|..||.|.+.-.
T Consensus 3 ~~v~kwGNS~~vriP---k~il~~l~l~~G~~v~i~v~ 37 (83)
T PRK11347 3 ITIKRWGNSAGMVIP---NIVMKELNLQPGQSVEAQVS 37 (83)
T ss_pred EEEEEEcCceeEEeC---HHHHHHcCCCCCCEEEEEEE
Confidence 356789999888887 47999999999999988763
No 19
>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=26.95 E-value=1.1e+02 Score=25.86 Aligned_cols=31 Identities=23% Similarity=0.276 Sum_probs=21.5
Q ss_pred cCCCCCCEEEEEEeecCCccccceeEEEEEeeecC
Q 018549 249 NQLKANDTICFYLCELRDIAKGTKTFGMIDAKKGE 283 (354)
Q Consensus 249 k~Lk~GD~I~F~r~~~g~~~~~~~~~~~i~~~~~~ 283 (354)
+++++||.|+|.--.++.. ...-++++++=+
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 6799999999988666554 333456666554
No 20
>PRK10113 cell division modulator; Provisional
Probab=26.06 E-value=53 Score=25.62 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=28.4
Q ss_pred CceEEeEECCCCeEEEEEEeCCeEEEecCCCCHHHHHH
Q 018549 43 SKFKGVVPQQNGHWGAQIYANHQRIWLGTFKSEKDAAM 80 (354)
Q Consensus 43 SgyrGV~~~~~gkw~A~I~~~~k~~~LG~f~t~EeAa~ 80 (354)
-+|+-||.-+ |||.|.+..+..-..--.|..+|.|-+
T Consensus 31 d~frDVW~Lr-GKYVAFvl~ge~FrRSPaFs~PEsAQR 67 (80)
T PRK10113 31 DSFRDVWMLR-GKYVAFVLMGESFLRSPAFSVPESAQR 67 (80)
T ss_pred cchhhhheec-cceEEEEEechhhccCCccCCcHHHHH
Confidence 6889997654 999999987655555667888887765
No 21
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=25.07 E-value=3.3e+02 Score=21.20 Aligned_cols=39 Identities=18% Similarity=0.175 Sum_probs=25.2
Q ss_pred CCCC--eEEEEEEeCCe--EEEecCCCC--HHHHHHHHHHHHHHh
Q 018549 51 QQNG--HWGAQIYANHQ--RIWLGTFKS--EKDAAMAYDSAAIRL 89 (354)
Q Consensus 51 ~~~g--kw~A~I~~~~k--~~~LG~f~t--~EeAa~Ayd~aa~~~ 89 (354)
.++| .|..+.+.+|+ ++.||.|.. ..+|..........+
T Consensus 30 ~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~~~~~ 74 (89)
T PF13356_consen 30 TPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKARELRALV 74 (89)
T ss_dssp -TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHHHHHH
T ss_pred EeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHHHHHH
Confidence 4443 59988888776 688999975 555555544444433
No 22
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=24.59 E-value=1.6e+02 Score=23.16 Aligned_cols=46 Identities=24% Similarity=0.351 Sum_probs=35.1
Q ss_pred CceEEeEEC-CCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHh
Q 018549 43 SKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRL 89 (354)
Q Consensus 43 SgyrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~ 89 (354)
..|.||..+ ..-+-.+.|+..||-+..|. .++++|..|.+.....+
T Consensus 36 e~fpgl~~r~~~p~~t~~IF~sGki~itGa-ks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 36 ERFPGLIYRLRNPKATVLIFSSGKIVITGA-KSEEEAKKAIEKILPIL 82 (86)
T ss_dssp TTESSEEEEETTTTEEEEEETTSEEEEEEE-SSHHHHHHHHHHHHHHH
T ss_pred ccCCeEEEeecCCcEEEEEEcCCEEEEEec-CCHHHHHHHHHHHHHHH
Confidence 568888554 34567888888999998886 67888888888776554
No 23
>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=22.67 E-value=1.6e+02 Score=22.85 Aligned_cols=37 Identities=22% Similarity=0.372 Sum_probs=26.6
Q ss_pred eEEEEEEeC--CeEEEecCCCCHHHHHHHHHHHHHHhcC
Q 018549 55 HWGAQIYAN--HQRIWLGTFKSEKDAAMAYDSAAIRLRG 91 (354)
Q Consensus 55 kw~A~I~~~--~k~~~LG~f~t~EeAa~Ayd~aa~~~~g 91 (354)
.|=++|.-. .-.+|.|-|+|.+||..+...-...+..
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~gyieDL~~ 47 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALPGYIEDLES 47 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhccHHHHHHh
Confidence 466888653 4678999999999999886554444443
No 24
>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=22.35 E-value=1.5e+02 Score=28.04 Aligned_cols=38 Identities=24% Similarity=0.306 Sum_probs=26.7
Q ss_pred CCeEEEEEEeCCeE--EEecCCC--CHHHHHHHHHHHHHHhc
Q 018549 53 NGHWGAQIYANHQR--IWLGTFK--SEKDAAMAYDSAAIRLR 90 (354)
Q Consensus 53 ~gkw~A~I~~~~k~--~~LG~f~--t~EeAa~Ayd~aa~~~~ 90 (354)
.+.|..+++.+|++ +.||+|+ +.++|..+.......+.
T Consensus 9 ~~~~~~~~~~~g~~~~~~~g~~~~~~~~~A~~~~~~~~~~~~ 50 (357)
T cd00801 9 SKSWRFRYRLAGKRKRLTLGSYPAVSLAEAREKADEARALLA 50 (357)
T ss_pred CEEEEEEeccCCceeEEeCcCCCCCCHHHHHHHHHHHHHHHH
Confidence 35699998887765 6689995 67777766665555443
No 25
>PLN00062 TATA-box-binding protein; Provisional
Probab=22.17 E-value=3.5e+02 Score=24.65 Aligned_cols=48 Identities=25% Similarity=0.332 Sum_probs=37.0
Q ss_pred CCceEEeEEC-CCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 018549 42 VSKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLR 90 (354)
Q Consensus 42 ~SgyrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~~ 90 (354)
...|-|+..| ..-+=.+-|+..||-+-.|. .++|+|..|.+..+..+.
T Consensus 33 Pe~fpgli~Rl~~Pk~t~lIF~SGKiviTGa-ks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 33 PKRFAAVIMRIREPKTTALIFASGKMVCTGA-KSEHDSKLAARKYARIIQ 81 (179)
T ss_pred CccCcEEEEEeCCCcEEEEEECCCeEEEEec-CCHHHHHHHHHHHHHHHH
Confidence 3678999655 45566888999999988775 678888888888777774
No 26
>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=21.64 E-value=97 Score=25.56 Aligned_cols=21 Identities=38% Similarity=0.493 Sum_probs=17.6
Q ss_pred ecCCCCHHHHHHHHHHHHHHh
Q 018549 69 LGTFKSEKDAAMAYDSAAIRL 89 (354)
Q Consensus 69 LG~f~t~EeAa~Ayd~aa~~~ 89 (354)
-|+|+|+|+|..=||..+-.|
T Consensus 70 ~GYF~t~eDA~~FydEl~~mL 90 (93)
T PF08471_consen 70 GGYFATEEDAEAFYDELTYML 90 (93)
T ss_pred CCCcCCHHHHHHHHHHHHHHH
Confidence 589999999999999876544
No 27
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=21.50 E-value=5.5e+02 Score=22.36 Aligned_cols=76 Identities=8% Similarity=0.114 Sum_probs=53.3
Q ss_pred eeeeeccccccCCCCceeechhhhhhc--CCCCchhhhhhccccCCCCeEEEEEe-CCCceEEEEEEEeCC--CCeeeEc
Q 018549 165 LFQKELTPSDVGKLNRLVIPKKYAVKY--FPQISERVEEHAENDKADDVQLVFHD-KSMKLWKFRYCYWKS--SQSFVFT 239 (354)
Q Consensus 165 lF~K~LT~SDv~~~~rL~IPk~~a~~~--fP~l~~~~~~~~~~~~~~gv~v~v~D-~~g~~W~fr~~~~~~--sr~yvLt 239 (354)
|=.-+.|..|+.-.|.+.|..+..++. +|. -.|.++| ..|..|. .|.+.+. |..-.|+
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~----------------E~V~V~Nv~NG~Rf~-TYvI~g~~GSg~I~lN 72 (126)
T PRK05449 10 IHRATVTEADLNYEGSITIDEDLLDAAGILEN----------------EKVQIVNVNNGARFE-TYVIAGERGSGVICLN 72 (126)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCCC----------------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeC
Confidence 445678999998888999998887763 443 3567777 4666665 3444443 5557776
Q ss_pred cChHHHHhhcCCCCCCEEEEEEe
Q 018549 240 RGWNRFVKENQLKANDTICFYLC 262 (354)
Q Consensus 240 ~GW~~FVr~k~Lk~GD~I~F~r~ 262 (354)
| .-++..+.||.|++.--
T Consensus 73 G-----AAAr~~~~GD~vII~ay 90 (126)
T PRK05449 73 G-----AAARLVQVGDLVIIAAY 90 (126)
T ss_pred C-----HHHhcCCCCCEEEEEEC
Confidence 5 46778899999998863
No 28
>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=21.35 E-value=3.8e+02 Score=24.24 Aligned_cols=47 Identities=21% Similarity=0.296 Sum_probs=36.5
Q ss_pred CceEEeEEC-CCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHhc
Q 018549 43 SKFKGVVPQ-QNGHWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLR 90 (354)
Q Consensus 43 SgyrGV~~~-~~gkw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~~ 90 (354)
..|-|+..| ..-+=.+-|+..||-+-.|.. |+|+|..|.++.+..+.
T Consensus 34 e~fpgli~Rl~~Pk~t~lIF~SGKiviTGak-s~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 34 KRFAAVIMRIREPKTTALIFSSGKMVCTGAK-SEDDSKLAARKYARIIQ 81 (174)
T ss_pred ccCcEEEEEeCCCcEEEEEECCCeEEEEecC-CHHHHHHHHHHHHHHHH
Confidence 678899655 445667899999999988874 67888888888777664
No 29
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=20.87 E-value=5.3e+02 Score=21.97 Aligned_cols=79 Identities=8% Similarity=0.068 Sum_probs=53.7
Q ss_pred eeeeeccccccCCCCceeechhhhhhcCCCCchhhhhhccccCCCCeEEEEEe-CCCceEEEEEEEeCC--CCeeeEccC
Q 018549 165 LFQKELTPSDVGKLNRLVIPKKYAVKYFPQISERVEEHAENDKADDVQLVFHD-KSMKLWKFRYCYWKS--SQSFVFTRG 241 (354)
Q Consensus 165 lF~K~LT~SDv~~~~rL~IPk~~a~~~fP~l~~~~~~~~~~~~~~gv~v~v~D-~~g~~W~fr~~~~~~--sr~yvLt~G 241 (354)
|=.-+.|..|+.-.|.+.|..+..++. +-.+.-.|.++| ..|..|. .|.+.+. |+.-.|+|
T Consensus 9 iHratVT~a~L~YeGSitID~~Ll~aa--------------gi~~~E~V~I~Nv~NG~Rf~-TYvI~g~~gSg~I~lNG- 72 (111)
T cd06919 9 IHRATVTEADLNYEGSITIDEDLLEAA--------------GILPYEKVLVVNVNNGARFE-TYVIPGERGSGVICLNG- 72 (111)
T ss_pred ccceEEeccccccceeEEECHHHHHhc--------------CCCCCCEEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC-
Confidence 445678999998888999998887752 012333577778 4666665 3444443 56677765
Q ss_pred hHHHHhhcCCCCCCEEEEEEee
Q 018549 242 WNRFVKENQLKANDTICFYLCE 263 (354)
Q Consensus 242 W~~FVr~k~Lk~GD~I~F~r~~ 263 (354)
.-++..+.||.|++.--.
T Consensus 73 ----AAAr~~~~GD~vII~sy~ 90 (111)
T cd06919 73 ----AAARLGQPGDRVIIMAYA 90 (111)
T ss_pred ----HHHhcCCCCCEEEEEECc
Confidence 467788999999998643
No 30
>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=20.79 E-value=60 Score=25.87 Aligned_cols=16 Identities=19% Similarity=0.250 Sum_probs=8.7
Q ss_pred HhhcCCCCCCEEEEEE
Q 018549 246 VKENQLKANDTICFYL 261 (354)
Q Consensus 246 Vr~k~Lk~GD~I~F~r 261 (354)
+.+++|.+||.|.|.-
T Consensus 23 l~~HGl~vGD~VnFsn 38 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSN 38 (83)
T ss_dssp -TT----TT-EEEEES
T ss_pred EccCceeecceEEEec
Confidence 5689999999999975
No 31
>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=20.78 E-value=77 Score=24.46 Aligned_cols=23 Identities=13% Similarity=0.224 Sum_probs=17.9
Q ss_pred HHHhhcCCCCCCEEEEEEeecCC
Q 018549 244 RFVKENQLKANDTICFYLCELRD 266 (354)
Q Consensus 244 ~FVr~k~Lk~GD~I~F~r~~~g~ 266 (354)
..+|..+|+.||.|.=.-.+..+
T Consensus 34 ~~Irr~~LR~GD~V~G~vr~p~~ 56 (68)
T cd04459 34 SQIRRFNLRTGDTVVGQIRPPKE 56 (68)
T ss_pred HHHHHhCCCCCCEEEEEEeCCCC
Confidence 58999999999999865544333
No 32
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=20.50 E-value=5.7e+02 Score=22.23 Aligned_cols=77 Identities=9% Similarity=0.091 Sum_probs=53.9
Q ss_pred eeeeeccccccCCCCceeechhhhhhc--CCCCchhhhhhccccCCCCeEEEEEe-CCCceEEEEEEEeCC--CCeeeEc
Q 018549 165 LFQKELTPSDVGKLNRLVIPKKYAVKY--FPQISERVEEHAENDKADDVQLVFHD-KSMKLWKFRYCYWKS--SQSFVFT 239 (354)
Q Consensus 165 lF~K~LT~SDv~~~~rL~IPk~~a~~~--fP~l~~~~~~~~~~~~~~gv~v~v~D-~~g~~W~fr~~~~~~--sr~yvLt 239 (354)
|=.-+.|..|+.-.|.+.|..+..++. +|. -.|.++| ..|..|. .|.+.+. |+.-.|+
T Consensus 10 IHratVT~a~L~Y~GSItID~~Lm~aagi~p~----------------E~V~V~Nv~NG~Rf~-TYvI~G~~GSg~I~lN 72 (126)
T TIGR00223 10 LHRATVTHANLNYEGSITIDEDLLDAAGILEN----------------EKVDIVNVNNGKRFS-TYAIAGKRGSRIICVN 72 (126)
T ss_pred hcceEEeccccccceeEEECHHHHHhcCCCCC----------------CEEEEEECCCCcEEE-EEEEEcCCCCCEEEeC
Confidence 445678999998888999998887762 443 3567777 5677666 3444443 5567776
Q ss_pred cChHHHHhhcCCCCCCEEEEEEee
Q 018549 240 RGWNRFVKENQLKANDTICFYLCE 263 (354)
Q Consensus 240 ~GW~~FVr~k~Lk~GD~I~F~r~~ 263 (354)
| .-++..++||.|++.--.
T Consensus 73 G-----AAArl~~~GD~VII~sy~ 91 (126)
T TIGR00223 73 G-----AAARCVSVGDIVIIASYV 91 (126)
T ss_pred C-----HHHhcCCCCCEEEEEECC
Confidence 5 467788999999988643
No 33
>TIGR01164 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10
Probab=20.33 E-value=1.7e+02 Score=25.10 Aligned_cols=34 Identities=24% Similarity=0.217 Sum_probs=29.5
Q ss_pred eEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHh
Q 018549 55 HWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRL 89 (354)
Q Consensus 55 kw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~ 89 (354)
.|.|.|..+..-+-++. .+++.|..|...|+.+|
T Consensus 91 ~~varV~~G~ilfEi~~-~~~~~a~~al~~a~~KL 124 (126)
T TIGR01164 91 YWVAVVKPGKILFEIAG-VPEEVAREAFRLAASKL 124 (126)
T ss_pred EEEEEECCCCEEEEEeC-CCHHHHHHHHHHHHhcC
Confidence 59999998888888877 89999999999988765
No 34
>PRK09203 rplP 50S ribosomal protein L16; Reviewed
Probab=20.28 E-value=1.6e+02 Score=25.81 Aligned_cols=36 Identities=25% Similarity=0.124 Sum_probs=30.6
Q ss_pred eEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHHhcC
Q 018549 55 HWGAQIYANHQRIWLGTFKSEKDAAMAYDSAAIRLRG 91 (354)
Q Consensus 55 kw~A~I~~~~k~~~LG~f~t~EeAa~Ayd~aa~~~~g 91 (354)
.|.|+|..+..-+-++. .+++.|..|...|+.+|-+
T Consensus 92 ~~varVk~G~iifEi~~-~~~~~a~~al~~a~~KLP~ 127 (138)
T PRK09203 92 YWVAVVKPGRILFEIAG-VSEELAREALRLAAAKLPI 127 (138)
T ss_pred EEEEEECCCCEEEEEeC-CCHHHHHHHHHHHhccCCC
Confidence 59999998888888877 8999999999999877644
Done!