Query 017035
Match_columns 378
No_of_seqs 414 out of 1583
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 05:02:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017035.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017035hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.8 2.4E-18 5.2E-23 140.8 12.2 98 207-308 1-98 (100)
2 cd00018 AP2 DNA-binding domain 99.8 4.9E-19 1.1E-23 134.7 7.1 59 69-127 1-61 (61)
3 smart00380 AP2 DNA-binding dom 99.7 4E-18 8.6E-23 131.2 8.1 60 70-129 1-62 (64)
4 PHA00280 putative NHN endonucl 99.5 1.6E-14 3.5E-19 124.7 6.6 71 50-121 48-119 (121)
5 PF00847 AP2: AP2 domain; Int 98.9 1.6E-09 3.5E-14 80.5 5.2 50 69-118 1-56 (56)
6 PF03754 DUF313: Domain of unk 98.8 8.8E-09 1.9E-13 88.4 6.7 80 201-281 18-114 (114)
7 PF09217 EcoRII-N: Restriction 98.0 1.5E-05 3.3E-10 71.3 7.8 90 203-293 6-110 (156)
8 PF10844 DUF2577: Protein of u 64.0 31 0.00068 28.7 6.9 77 205-305 19-97 (100)
9 PF14657 Integrase_AP2: AP2-li 53.7 36 0.00079 24.1 4.8 35 81-115 1-41 (46)
10 PF02261 Asp_decarbox: Asparta 49.8 1.3E+02 0.0029 26.2 8.4 74 206-293 10-88 (116)
11 TIGR00223 panD L-aspartate-alp 48.8 1.1E+02 0.0024 27.1 7.9 74 206-293 10-88 (126)
12 cd06919 Asp_decarbox Aspartate 42.8 1.7E+02 0.0036 25.4 7.9 74 206-293 9-87 (111)
13 smart00536 AXH domain in Ataxi 41.3 14 0.00029 32.2 1.1 27 266-292 76-112 (116)
14 PRK05449 aspartate alpha-decar 41.1 1.7E+02 0.0038 25.8 7.9 74 206-293 10-88 (126)
15 PF04014 Antitoxin-MazE: Antid 39.2 62 0.0014 22.9 4.2 37 264-305 4-40 (47)
16 PF03120 DNA_ligase_OB: NAD-de 37.8 28 0.0006 28.4 2.4 21 276-296 42-62 (82)
17 PRK03760 hypothetical protein; 37.3 82 0.0018 27.1 5.4 26 266-294 89-116 (117)
18 PHA02601 int integrase; Provis 36.3 46 0.001 32.3 4.2 42 73-115 2-46 (333)
19 PF02643 DUF192: Uncharacteriz 32.4 1.1E+02 0.0023 25.8 5.2 48 244-292 50-106 (108)
20 PRK09570 rpoH DNA-directed RNA 32.4 66 0.0014 26.2 3.7 30 277-307 45-74 (79)
21 PRK06461 single-stranded DNA-b 29.4 1.5E+02 0.0032 25.7 5.8 33 244-293 42-74 (129)
22 cd04491 SoSSB_OBF SoSSB_OBF: A 28.1 2.4E+02 0.0053 21.8 6.3 34 244-293 25-58 (82)
23 PF01191 RNA_pol_Rpb5_C: RNA p 27.9 1.3E+02 0.0027 24.2 4.6 31 276-307 41-71 (74)
24 PF08846 DUF1816: Domain of un 27.9 1.1E+02 0.0023 24.3 4.1 29 81-109 9-39 (68)
25 TIGR01643 YD_repeat_2x YD repe 27.1 93 0.002 20.9 3.3 20 242-261 4-23 (42)
26 PF12195 End_beta_barrel: Beta 25.3 44 0.00095 27.2 1.5 17 279-295 23-39 (83)
27 PF09853 DUF2080: Putative tra 25.2 77 0.0017 24.0 2.7 29 201-231 12-42 (53)
28 TIGR02609 doc_partner putative 24.9 1.2E+02 0.0027 23.8 4.0 33 261-296 4-36 (74)
29 PF08517 AXH: Ataxin-1 and HBP 24.8 14 0.0003 32.1 -1.5 27 266-292 75-111 (115)
30 PF05036 SPOR: Sporulation rel 24.3 51 0.0011 24.5 1.7 22 91-112 44-65 (76)
31 PRK11347 antitoxin ChpS; Provi 23.7 2E+02 0.0043 23.3 5.1 36 258-296 3-38 (83)
32 PF01878 EVE: EVE domain; Int 22.9 90 0.002 27.0 3.2 15 282-296 38-52 (143)
33 cd01753 PLAT_LOX PLAT domain o 22.8 1E+02 0.0022 26.1 3.4 55 213-273 57-112 (113)
34 PF13356 DUF4102: Domain of un 22.3 3.8E+02 0.0083 21.2 6.6 37 75-111 28-70 (89)
35 PF05593 RHS_repeat: RHS Repea 22.2 1.4E+02 0.003 20.2 3.4 20 242-261 4-23 (38)
36 TIGR01439 lp_hng_hel_AbrB loop 21.6 1.5E+02 0.0034 19.8 3.6 21 276-296 13-33 (43)
No 1
>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=99.78 E-value=2.4e-18 Score=140.80 Aligned_cols=98 Identities=34% Similarity=0.577 Sum_probs=73.6
Q ss_pred eeeccccCCCCCCCceeechhhHhhcCCCCCCCCCCceEEEEEeCCCCeEEEEEEEecCCCceEEecCHHHHHhhcCCCC
Q 017035 207 FEKAVTPSDVGKLNRLVIPKQHAEKHFPLQSGSTSKGLLLNFEDVTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKA 286 (378)
Q Consensus 207 F~K~LT~SDV~~~~rLvIPk~~ae~~lP~~~~~~~~gv~l~v~D~~Gk~W~Fr~s~~~~s~~yvLt~GW~~FVk~k~Lk~ 286 (378)
|.|+|+++|+...++|.||++++++|... ...++.+.++|..|++|.+++++++.+..|+|++||.+||++|+|++
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~----~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~ 76 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGN----KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKE 76 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--T
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCC----cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCC
Confidence 88999999999889999999999988211 12347899999999999999999988888999999999999999999
Q ss_pred CCEEEEEEecCCCceEEEEEee
Q 017035 287 GDIVSFHRSTGGDRQLYIDWKA 308 (378)
Q Consensus 287 GD~I~F~r~~~~~~~l~i~~r~ 308 (378)
||+|+|+...+....+.+.+-+
T Consensus 77 GD~~~F~~~~~~~~~~~v~i~~ 98 (100)
T PF02362_consen 77 GDVCVFELIGNSNFTLKVHIFR 98 (100)
T ss_dssp T-EEEEEE-SSSCE-EEEEEE-
T ss_pred CCEEEEEEecCCCceEEEEEEE
Confidence 9999999986555545555543
No 2
>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=4.9e-19 Score=134.69 Aligned_cols=59 Identities=54% Similarity=0.929 Sum_probs=56.6
Q ss_pred CceEEeEECCCCeEEEEEEeC--CeEEEecCCCCHHHHHHHHHHHHHhhcCCCCCCCCCcc
Q 017035 69 SKYKGVVPQPNGRWGAQIYEK--HQRVWLGTFNEEEEAARAYDIAAQRFRGRDAVTNFKQI 127 (378)
Q Consensus 69 S~yrGV~~~~~grW~A~I~~~--gkr~~LGtf~t~EeAArAYD~Aa~~~~G~~a~~NFp~~ 127 (378)
|+|+||+++++|+|+|+|+.+ ++++|||+|+|+||||+|||.|+++++|..+.+|||++
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 689999999899999999998 99999999999999999999999999999999999973
No 3
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=99.75 E-value=4e-18 Score=131.16 Aligned_cols=60 Identities=57% Similarity=0.928 Sum_probs=57.1
Q ss_pred ceEEeEECCCCeEEEEEEe--CCeEEEecCCCCHHHHHHHHHHHHHhhcCCCCCCCCCcccc
Q 017035 70 KYKGVVPQPNGRWGAQIYE--KHQRVWLGTFNEEEEAARAYDIAAQRFRGRDAVTNFKQISC 129 (378)
Q Consensus 70 ~yrGV~~~~~grW~A~I~~--~gkr~~LGtf~t~EeAArAYD~Aa~~~~G~~a~~NFp~~~~ 129 (378)
+|+||+++++|+|+|+|+. .++++|||+|+|+||||+|||.|+++++|..+.+|||...|
T Consensus 1 ~~kGV~~~~~gkw~A~I~~~~~~k~~~lG~f~t~eeAa~Ayd~a~~~~~g~~a~~Nf~~~~y 62 (64)
T smart00380 1 KYRGVRQRPWGKWVAEIRDPSKGKRVWLGTFDTAEEAARAYDRAAFKFRGRSARLNFPNSLY 62 (64)
T ss_pred CEeeEEeCCCCeEEEEEEecCCCcEEecCCCCCHHHHHHHHHHHHHHhcCCccccCCCCccC
Confidence 5899998889999999999 99999999999999999999999999999999999999664
No 4
>PHA00280 putative NHN endonuclease
Probab=99.52 E-value=1.6e-14 Score=124.68 Aligned_cols=71 Identities=17% Similarity=0.185 Sum_probs=65.2
Q ss_pred ceecccccccccccCCCCCCceEEeEEC-CCCeEEEEEEeCCeEEEecCCCCHHHHHHHHHHHHHhhcCCCCC
Q 017035 50 SVILDSEAGVEAESRKLPSSKYKGVVPQ-PNGRWGAQIYEKHQRVWLGTFNEEEEAARAYDIAAQRFRGRDAV 121 (378)
Q Consensus 50 s~v~~~en~~n~~~~~~~~S~yrGV~~~-~~grW~A~I~~~gkr~~LGtf~t~EeAArAYD~Aa~~~~G~~a~ 121 (378)
..++.++|..|++.++.++|+|+||+++ ..|||.|+|+.+||+++||.|+++|+|+.||+ ++.+++|.+|.
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 4577899999999999999999999987 57999999999999999999999999999997 77899998874
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=98.92 E-value=1.6e-09 Score=80.53 Aligned_cols=50 Identities=44% Similarity=0.554 Sum_probs=45.0
Q ss_pred CceEEeEECC-CCeEEEEEEeC-----CeEEEecCCCCHHHHHHHHHHHHHhhcCC
Q 017035 69 SKYKGVVPQP-NGRWGAQIYEK-----HQRVWLGTFNEEEEAARAYDIAAQRFRGR 118 (378)
Q Consensus 69 S~yrGV~~~~-~grW~A~I~~~-----gkr~~LGtf~t~EeAArAYD~Aa~~~~G~ 118 (378)
|+|+||++++ .++|.|+|++. +++++||.|++++||++||+.+++.++|+
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 6899999885 79999999982 49999999999999999999999999874
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=98.81 E-value=8.8e-09 Score=88.36 Aligned_cols=80 Identities=25% Similarity=0.517 Sum_probs=67.1
Q ss_pred ccccceeeeccccCCCC-CCCceeechhhHhhcCCCCCCC-------------CCCceEEEEEeCCCCeEEEEEEEecC-
Q 017035 201 KARDQLFEKAVTPSDVG-KLNRLVIPKQHAEKHFPLQSGS-------------TSKGLLLNFEDVTGKVWRFRYSYWNS- 265 (378)
Q Consensus 201 ~~~~~lF~K~LT~SDV~-~~~rLvIPk~~ae~~lP~~~~~-------------~~~gv~l~v~D~~Gk~W~Fr~s~~~~- 265 (378)
.+...+|.|+|+.|||. +++||.||...+.. ..+|... ...|+.+.++|..++.|..+++.|.-
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 35689999999999998 88999999888744 2444421 45689999999999999999999965
Q ss_pred --CCceEEecCHHHHHhh
Q 017035 266 --SQSYVLTKGWSRFVKE 281 (378)
Q Consensus 266 --s~~yvLt~GW~~FVk~ 281 (378)
...|+|..||.++|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 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=98.05 E-value=1.5e-05 Score=71.35 Aligned_cols=90 Identities=20% Similarity=0.344 Sum_probs=58.5
Q ss_pred ccceeeeccccCCCC----CCCceeechhhHhhcCCCCCCC--CCCceEEEEEeCCC--CeEEEEEEEecC------CCc
Q 017035 203 RDQLFEKAVTPSDVG----KLNRLVIPKQHAEKHFPLQSGS--TSKGLLLNFEDVTG--KVWRFRYSYWNS------SQS 268 (378)
Q Consensus 203 ~~~lF~K~LT~SDV~----~~~rLvIPk~~ae~~lP~~~~~--~~~gv~l~v~D~~G--k~W~Fr~s~~~~------s~~ 268 (378)
-..+|.|.|++.|++ |+..++|||..++.+||.+... ..+.++|.+.+..+ ..|+||++|.|+ ...
T Consensus 6 ~~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE 85 (156)
T PF09217_consen 6 SWAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNE 85 (156)
T ss_dssp SEEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--E
T ss_pred ceEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCc
Confidence 356899999999998 8889999999999999886643 45678999998877 568899999987 477
Q ss_pred eEEecCHHHHHh-hcCCCCCCEEEEE
Q 017035 269 YVLTKGWSRFVK-EKNLKAGDIVSFH 293 (378)
Q Consensus 269 yvLt~GW~~FVk-~k~Lk~GD~I~F~ 293 (378)
|.||. |..... .+-=.+||.++|-
T Consensus 86 ~RIT~-~G~~~~~~~~~~tGaL~vla 110 (156)
T PF09217_consen 86 YRITR-FGRGFPLQNPENTGALLVLA 110 (156)
T ss_dssp EEEE----TTSGGG-GGGTT-EEEEE
T ss_pred eEEee-ecCCCccCCccccccEEEEE
Confidence 99986 777333 2334689998886
No 8
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=64.03 E-value=31 Score=28.73 Aligned_cols=77 Identities=18% Similarity=0.213 Sum_probs=43.5
Q ss_pred ceeeeccccCCCC--CCCceeechhhHhhcCCCCCCCCCCceEEEEEeCCCCeEEEEEEEecCCCceEEecCHHHHHhhc
Q 017035 205 QLFEKAVTPSDVG--KLNRLVIPKQHAEKHFPLQSGSTSKGLLLNFEDVTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEK 282 (378)
Q Consensus 205 ~lF~K~LT~SDV~--~~~rLvIPk~~ae~~lP~~~~~~~~gv~l~v~D~~Gk~W~Fr~s~~~~s~~yvLt~GW~~FVk~k 282 (378)
..|.++++.+-+. -.++|.||++++ ++|.... .....+.+.... .....+ |.-..
T Consensus 19 i~~G~V~s~~PL~I~i~~~liL~~~~L--~i~~~l~--~~~~~~~~~~~~--------------~~~~~~-----i~~~~ 75 (100)
T PF10844_consen 19 IVIGTVVSVPPLKIKIDQKLILDKDFL--IIPELLK--DYTRDITIEHNS--------------ETDNIT-----ITFTD 75 (100)
T ss_pred eEEEEEEecccEEEEECCeEEEchHHE--Eeehhcc--ceEEEEEEeccc--------------ccccee-----EEEec
Confidence 3789999999854 333599998876 2333221 122223322211 111000 55567
Q ss_pred CCCCCCEEEEEEecCCCceEEEE
Q 017035 283 NLKAGDIVSFHRSTGGDRQLYID 305 (378)
Q Consensus 283 ~Lk~GD~I~F~r~~~~~~~l~i~ 305 (378)
+|++||.|.+.+..++ ..|+|-
T Consensus 76 ~Lk~GD~V~ll~~~~g-Q~yiVl 97 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGG-QKYIVL 97 (100)
T ss_pred CCcCCCEEEEEEecCC-CEEEEE
Confidence 8999999999997543 444443
No 9
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=53.75 E-value=36 Score=24.13 Aligned_cols=35 Identities=17% Similarity=0.287 Sum_probs=27.3
Q ss_pred eEEEEEE-e---CC--eEEEecCCCCHHHHHHHHHHHHHhh
Q 017035 81 RWGAQIY-E---KH--QRVWLGTFNEEEEAARAYDIAAQRF 115 (378)
Q Consensus 81 rW~A~I~-~---~g--kr~~LGtf~t~EeAArAYD~Aa~~~ 115 (378)
+|...|. . .| ++++-+.|.|..||-.+...+...+
T Consensus 1 ~w~~~v~g~~~~~Gkrk~~~k~GF~TkkeA~~~~~~~~~~~ 41 (46)
T PF14657_consen 1 TWYYRVYGYDDETGKRKQKTKRGFKTKKEAEKALAKIEAEL 41 (46)
T ss_pred CEEEEEEEEECCCCCEEEEEcCCCCcHHHHHHHHHHHHHHH
Confidence 5788884 3 23 6789999999999999988776654
No 10
>PF02261 Asp_decarbox: Aspartate decarboxylase; InterPro: IPR003190 Decarboxylation of aspartate is the major route of alanine production in bacteria, and is catalysed by the enzyme aspartate decarboxylase. The enzyme is translated as an inactive proenzyme of two chains, A and B. This family contains both chains of aspartate decarboxylase.; GO: 0004068 aspartate 1-decarboxylase activity, 0006523 alanine biosynthetic process; PDB: 1PYU_C 1AW8_A 1PYQ_B 3TM7_C 1PT1_A 1PQH_A 1PPY_B 1PT0_B 1PQF_A 1PQE_A ....
Probab=49.77 E-value=1.3e+02 Score=26.19 Aligned_cols=74 Identities=18% Similarity=0.276 Sum_probs=47.8
Q ss_pred eeeeccccCCCCCCCceeechhhHhhc--CCCCCCCCCCceEEEEEeC-CCCeEEEEEEEec--CCCceEEecCHHHHHh
Q 017035 206 LFEKAVTPSDVGKLNRLVIPKQHAEKH--FPLQSGSTSKGLLLNFEDV-TGKVWRFRYSYWN--SSQSYVLTKGWSRFVK 280 (378)
Q Consensus 206 lF~K~LT~SDV~~~~rLvIPk~~ae~~--lP~~~~~~~~gv~l~v~D~-~Gk~W~Fr~s~~~--~s~~yvLt~GW~~FVk 280 (378)
|-.-++|..|+...|-+.|..+.++.. +|.- .+.+++. +|..|.- |.+.. .+..-.|.+. -
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~E--------~V~V~Nv~nG~Rf~T-YvI~g~~GSg~I~lNGa-----A 75 (116)
T PF02261_consen 10 IHRATVTEADLNYEGSITIDEDLLDAAGILPYE--------QVQVVNVNNGERFET-YVIPGERGSGVICLNGA-----A 75 (116)
T ss_dssp EEEEE--EEETTSTSCEEEEHHHHHHCT--TTB--------EEEEEETTT--EEEE-EEEEESTTTT-EEEEGG-----G
T ss_pred hcceEEeccccccceeeEECHHHHHHcCCCcCC--------EEEEEECCCCcEEEE-EEEEccCCCcEEEECCH-----H
Confidence 445678999999999999999998774 4433 3678887 6887763 44443 3456777664 7
Q ss_pred hcCCCCCCEEEEE
Q 017035 281 EKNLKAGDIVSFH 293 (378)
Q Consensus 281 ~k~Lk~GD~I~F~ 293 (378)
++..++||.|++.
T Consensus 76 Arl~~~GD~vII~ 88 (116)
T PF02261_consen 76 ARLVQVGDRVIIM 88 (116)
T ss_dssp GGCS-TT-EEEEE
T ss_pred HhccCCCCEEEEE
Confidence 7888999999984
No 11
>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=48.80 E-value=1.1e+02 Score=27.08 Aligned_cols=74 Identities=18% Similarity=0.282 Sum_probs=54.3
Q ss_pred eeeeccccCCCCCCCceeechhhHhhc--CCCCCCCCCCceEEEEEeC-CCCeEEEEEEEecC--CCceEEecCHHHHHh
Q 017035 206 LFEKAVTPSDVGKLNRLVIPKQHAEKH--FPLQSGSTSKGLLLNFEDV-TGKVWRFRYSYWNS--SQSYVLTKGWSRFVK 280 (378)
Q Consensus 206 lF~K~LT~SDV~~~~rLvIPk~~ae~~--lP~~~~~~~~gv~l~v~D~-~Gk~W~Fr~s~~~~--s~~yvLt~GW~~FVk 280 (378)
|-.-++|..|+..-+-+.|..+.++.. +|.- .+.++|. +|..|. .|.+... |..-.|.+ .-
T Consensus 10 IHratVT~a~L~Y~GSItID~~Lm~aagi~p~E--------~V~V~Nv~NG~Rf~-TYvI~G~~GSg~I~lNG-----AA 75 (126)
T TIGR00223 10 LHRATVTHANLNYEGSITIDEDLLDAAGILENE--------KVDIVNVNNGKRFS-TYAIAGKRGSRIICVNG-----AA 75 (126)
T ss_pred hcceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC-----HH
Confidence 345578999999889999999998774 4433 3678887 688776 3555533 45577766 36
Q ss_pred hcCCCCCCEEEEE
Q 017035 281 EKNLKAGDIVSFH 293 (378)
Q Consensus 281 ~k~Lk~GD~I~F~ 293 (378)
++..++||.|++.
T Consensus 76 Arl~~~GD~VII~ 88 (126)
T TIGR00223 76 ARCVSVGDIVIIA 88 (126)
T ss_pred HhcCCCCCEEEEE
Confidence 7888999999985
No 12
>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=42.83 E-value=1.7e+02 Score=25.39 Aligned_cols=74 Identities=19% Similarity=0.234 Sum_probs=54.3
Q ss_pred eeeeccccCCCCCCCceeechhhHhhc--CCCCCCCCCCceEEEEEeC-CCCeEEEEEEEec--CCCceEEecCHHHHHh
Q 017035 206 LFEKAVTPSDVGKLNRLVIPKQHAEKH--FPLQSGSTSKGLLLNFEDV-TGKVWRFRYSYWN--SSQSYVLTKGWSRFVK 280 (378)
Q Consensus 206 lF~K~LT~SDV~~~~rLvIPk~~ae~~--lP~~~~~~~~gv~l~v~D~-~Gk~W~Fr~s~~~--~s~~yvLt~GW~~FVk 280 (378)
|-.-++|..|+...+-+.|..+.++.. +|.- .+.++|. +|..|. .|.+.. .|..-.|.+ .-
T Consensus 9 iHratVT~a~L~YeGSitID~~Ll~aagi~~~E--------~V~I~Nv~NG~Rf~-TYvI~g~~gSg~I~lNG-----AA 74 (111)
T cd06919 9 IHRATVTEADLNYEGSITIDEDLLEAAGILPYE--------KVLVVNVNNGARFE-TYVIPGERGSGVICLNG-----AA 74 (111)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC-----HH
Confidence 345578999999889999999998774 4432 3778887 688665 355553 356677766 36
Q ss_pred hcCCCCCCEEEEE
Q 017035 281 EKNLKAGDIVSFH 293 (378)
Q Consensus 281 ~k~Lk~GD~I~F~ 293 (378)
++..++||.|+++
T Consensus 75 Ar~~~~GD~vII~ 87 (111)
T cd06919 75 ARLGQPGDRVIIM 87 (111)
T ss_pred HhcCCCCCEEEEE
Confidence 7888999999985
No 13
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=41.33 E-value=14 Score=32.23 Aligned_cols=27 Identities=30% Similarity=0.443 Sum_probs=22.1
Q ss_pred CCceEEecCHHHHH----------hhcCCCCCCEEEE
Q 017035 266 SQSYVLTKGWSRFV----------KEKNLKAGDIVSF 292 (378)
Q Consensus 266 s~~yvLt~GW~~FV----------k~k~Lk~GD~I~F 292 (378)
-+-||..+||+-|- .-..|++||+|+.
T Consensus 76 HPfFV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 76 HPFFVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred CCeEEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 57899999999874 4567899999975
No 14
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=41.12 E-value=1.7e+02 Score=25.85 Aligned_cols=74 Identities=16% Similarity=0.259 Sum_probs=54.2
Q ss_pred eeeeccccCCCCCCCceeechhhHhhc--CCCCCCCCCCceEEEEEeC-CCCeEEEEEEEecC--CCceEEecCHHHHHh
Q 017035 206 LFEKAVTPSDVGKLNRLVIPKQHAEKH--FPLQSGSTSKGLLLNFEDV-TGKVWRFRYSYWNS--SQSYVLTKGWSRFVK 280 (378)
Q Consensus 206 lF~K~LT~SDV~~~~rLvIPk~~ae~~--lP~~~~~~~~gv~l~v~D~-~Gk~W~Fr~s~~~~--s~~yvLt~GW~~FVk 280 (378)
|=.-++|..|+...|-+.|..+.+++. +|.- .+.++|. +|..|. .|.+... |..-.|.+ .-
T Consensus 10 iHratVT~a~L~Y~GSitID~~Ll~aagi~p~E--------~V~V~Nv~NG~Rf~-TYvI~g~~GSg~I~lNG-----AA 75 (126)
T PRK05449 10 IHRATVTEADLNYEGSITIDEDLLDAAGILENE--------KVQIVNVNNGARFE-TYVIAGERGSGVICLNG-----AA 75 (126)
T ss_pred ccceEEeccccccceeEEECHHHHHhcCCCCCC--------EEEEEECCCCcEEE-EEEEEcCCCCCEEEeCC-----HH
Confidence 345578999999889999999998774 4433 3678887 688665 3555533 45577766 36
Q ss_pred hcCCCCCCEEEEE
Q 017035 281 EKNLKAGDIVSFH 293 (378)
Q Consensus 281 ~k~Lk~GD~I~F~ 293 (378)
++..++||.|++.
T Consensus 76 Ar~~~~GD~vII~ 88 (126)
T PRK05449 76 ARLVQVGDLVIIA 88 (126)
T ss_pred HhcCCCCCEEEEE
Confidence 7888999999985
No 15
>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=39.16 E-value=62 Score=22.92 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=24.6
Q ss_pred cCCCceEEecCHHHHHhhcCCCCCCEEEEEEecCCCceEEEE
Q 017035 264 NSSQSYVLTKGWSRFVKEKNLKAGDIVSFHRSTGGDRQLYID 305 (378)
Q Consensus 264 ~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F~r~~~~~~~l~i~ 305 (378)
.++..-.|- .+|.+..+|++||.|.|.-+.++ .+.|.
T Consensus 4 g~s~~v~iP---k~~~~~l~l~~Gd~v~i~~~~~g--~i~i~ 40 (47)
T PF04014_consen 4 GNSGQVTIP---KEIREKLGLKPGDEVEIEVEGDG--KIVIR 40 (47)
T ss_dssp TTCSEEEE----HHHHHHTTSSTTTEEEEEEETTS--EEEEE
T ss_pred CCCceEECC---HHHHHHcCCCCCCEEEEEEeCCC--EEEEE
Confidence 344444454 36788899999999999987433 45443
No 16
>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=37.75 E-value=28 Score=28.44 Aligned_cols=21 Identities=29% Similarity=0.542 Sum_probs=17.4
Q ss_pred HHHHhhcCCCCCCEEEEEEec
Q 017035 276 SRFVKEKNLKAGDIVSFHRST 296 (378)
Q Consensus 276 ~~FVk~k~Lk~GD~I~F~r~~ 296 (378)
.+|+++++|..||.|.++|..
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raG 62 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAG 62 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEET
T ss_pred HHHHHHcCCCCCCEEEEEECC
Confidence 679999999999999999973
No 17
>PRK03760 hypothetical protein; Provisional
Probab=37.26 E-value=82 Score=27.12 Aligned_cols=26 Identities=15% Similarity=0.438 Sum_probs=20.1
Q ss_pred CCceEE--ecCHHHHHhhcCCCCCCEEEEEE
Q 017035 266 SQSYVL--TKGWSRFVKEKNLKAGDIVSFHR 294 (378)
Q Consensus 266 s~~yvL--t~GW~~FVk~k~Lk~GD~I~F~r 294 (378)
.-.||| ..| ++.+.++++||.|.|-+
T Consensus 89 ~a~~VLEl~aG---~~~~~gi~~Gd~v~~~~ 116 (117)
T PRK03760 89 PARYIIEGPVG---KIRVLKVEVGDEIEWID 116 (117)
T ss_pred cceEEEEeCCC---hHHHcCCCCCCEEEEee
Confidence 355887 445 56899999999998865
No 18
>PHA02601 int integrase; Provisional
Probab=36.30 E-value=46 Score=32.27 Aligned_cols=42 Identities=21% Similarity=0.371 Sum_probs=28.9
Q ss_pred EeEECCCCeEEEEEEeC---CeEEEecCCCCHHHHHHHHHHHHHhh
Q 017035 73 GVVPQPNGRWGAQIYEK---HQRVWLGTFNEEEEAARAYDIAAQRF 115 (378)
Q Consensus 73 GV~~~~~grW~A~I~~~---gkr~~LGtf~t~EeAArAYD~Aa~~~ 115 (378)
+|++.++|+|.++++.. |+++.. +|.|..||-...+.....+
T Consensus 2 ~~~~~~~g~w~~~~~~~~~~g~r~~~-~f~tk~eA~~~~~~~~~~~ 46 (333)
T PHA02601 2 AVRKLKDGKWLCEIYPNGRDGKRIRK-RFATKGEALAFENYTMAEV 46 (333)
T ss_pred ceEEcCCCCEEEEEEECCCCCchhhh-hhcCHHHHHHHHHHHHHhc
Confidence 45556788999999863 666653 6999888866555544333
No 19
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=32.42 E-value=1.1e+02 Score=25.77 Aligned_cols=48 Identities=25% Similarity=0.342 Sum_probs=27.6
Q ss_pred eEEEEEeCCCCeEEEEEEEe---------cCCCceEEecCHHHHHhhcCCCCCCEEEE
Q 017035 244 LLLNFEDVTGKVWRFRYSYW---------NSSQSYVLTKGWSRFVKEKNLKAGDIVSF 292 (378)
Q Consensus 244 v~l~v~D~~Gk~W~Fr~s~~---------~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F 292 (378)
+.+.+.|.+|++-....-.. ..+-+|||.-. ..++...+|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~-aG~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELP-AGWFEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEE-TTHHHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcC-CCchhhcCCCCCCEEEe
Confidence 66777787776655543331 12246888542 34779999999999987
No 20
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=32.41 E-value=66 Score=26.18 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=21.6
Q ss_pred HHHhhcCCCCCCEEEEEEecCCCceEEEEEe
Q 017035 277 RFVKEKNLKAGDIVSFHRSTGGDRQLYIDWK 307 (378)
Q Consensus 277 ~FVk~k~Lk~GD~I~F~r~~~~~~~l~i~~r 307 (378)
..++..+|+.||+|.+.|.....+. ++.+|
T Consensus 45 Pv~r~~g~k~GdVvkI~R~S~taG~-~v~YR 74 (79)
T PRK09570 45 PVVKAIGAKPGDVIKIVRKSPTAGE-AVYYR 74 (79)
T ss_pred hhhhhcCCCCCCEEEEEECCCCCCc-cEEEE
Confidence 4778889999999999998533332 34444
No 21
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=29.44 E-value=1.5e+02 Score=25.71 Aligned_cols=33 Identities=24% Similarity=0.512 Sum_probs=25.2
Q ss_pred eEEEEEeCCCCeEEEEEEEecCCCceEEecCHHHHHhhcCCCCCCEEEEE
Q 017035 244 LLLNFEDVTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFH 293 (378)
Q Consensus 244 v~l~v~D~~Gk~W~Fr~s~~~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F~ 293 (378)
..+.+.|..|. .+++.|.. ....|++||+|.+.
T Consensus 42 ~~~~l~D~TG~---I~~tlW~~--------------~a~~l~~GdvV~I~ 74 (129)
T PRK06461 42 SEAVVGDETGR---VKLTLWGE--------------QAGSLKEGEVVEIE 74 (129)
T ss_pred EEEEEECCCCE---EEEEEeCC--------------ccccCCCCCEEEEE
Confidence 45788999995 67888854 13468999999996
No 22
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=28.08 E-value=2.4e+02 Score=21.80 Aligned_cols=34 Identities=26% Similarity=0.549 Sum_probs=25.8
Q ss_pred eEEEEEeCCCCeEEEEEEEecCCCceEEecCHHHHHhhcCCCCCCEEEEE
Q 017035 244 LLLNFEDVTGKVWRFRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFH 293 (378)
Q Consensus 244 v~l~v~D~~Gk~W~Fr~s~~~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F~ 293 (378)
..+.+.|..| ..++++|.... ...|++||+|.+.
T Consensus 25 ~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~ 58 (82)
T cd04491 25 QSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIE 58 (82)
T ss_pred EEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEE
Confidence 6678899888 57888885431 4568999999886
No 23
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=27.90 E-value=1.3e+02 Score=24.19 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=20.7
Q ss_pred HHHHhhcCCCCCCEEEEEEecCCCceEEEEEe
Q 017035 276 SRFVKEKNLKAGDIVSFHRSTGGDRQLYIDWK 307 (378)
Q Consensus 276 ~~FVk~k~Lk~GD~I~F~r~~~~~~~l~i~~r 307 (378)
-..++..+++.||+|-+.|.....+ -++-+|
T Consensus 41 DPv~r~~g~k~GdVvkI~R~S~taG-~~v~YR 71 (74)
T PF01191_consen 41 DPVARYLGAKPGDVVKIIRKSETAG-EYVTYR 71 (74)
T ss_dssp SHHHHHTT--TTSEEEEEEEETTTS-EEEEEE
T ss_pred ChhhhhcCCCCCCEEEEEecCCCCC-CcEEEE
Confidence 3588889999999999999864333 334444
No 24
>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=27.90 E-value=1.1e+02 Score=24.33 Aligned_cols=29 Identities=28% Similarity=0.493 Sum_probs=23.6
Q ss_pred eEEEEEEe--CCeEEEecCCCCHHHHHHHHH
Q 017035 81 RWGAQIYE--KHQRVWLGTFNEEEEAARAYD 109 (378)
Q Consensus 81 rW~A~I~~--~gkr~~LGtf~t~EeAArAYD 109 (378)
-|-++|.- ..-..|.|-|.+.+||..+.-
T Consensus 9 aWWveI~T~~P~ctYyFGPF~s~~eA~~~~~ 39 (68)
T PF08846_consen 9 AWWVEIETQNPNCTYYFGPFDSREEAEAALP 39 (68)
T ss_pred cEEEEEEcCCCCEEEEeCCcCCHHHHHHHhc
Confidence 47788875 457899999999999998753
No 25
>TIGR01643 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.
Probab=27.11 E-value=93 Score=20.95 Aligned_cols=20 Identities=30% Similarity=0.503 Sum_probs=16.4
Q ss_pred CceEEEEEeCCCCeEEEEEE
Q 017035 242 KGLLLNFEDVTGKVWRFRYS 261 (378)
Q Consensus 242 ~gv~l~v~D~~Gk~W~Fr~s 261 (378)
.+..+.+.|..|..|.|.|-
T Consensus 4 ~g~l~~~~~p~G~~~~~~YD 23 (42)
T TIGR01643 4 AGRLTGSTDADGTTTRYTYD 23 (42)
T ss_pred CCCEEEEECCCCCEEEEEEC
Confidence 35677899999999999874
No 26
>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=25.29 E-value=44 Score=27.17 Aligned_cols=17 Identities=35% Similarity=0.634 Sum_probs=9.0
Q ss_pred HhhcCCCCCCEEEEEEe
Q 017035 279 VKEKNLKAGDIVSFHRS 295 (378)
Q Consensus 279 Vk~k~Lk~GD~I~F~r~ 295 (378)
+-+++|.+||.|.|.-.
T Consensus 23 l~~HGl~vGD~VnFsns 39 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSNS 39 (83)
T ss_dssp -TT----TT-EEEEES-
T ss_pred EccCceeecceEEEecc
Confidence 56899999999999865
No 27
>PF09853 DUF2080: Putative transposon-encoded protein (DUF2080); InterPro: IPR019205 This entry, found in various hypothetical archaeal proteins, has no known function.
Probab=25.22 E-value=77 Score=23.97 Aligned_cols=29 Identities=28% Similarity=0.437 Sum_probs=24.3
Q ss_pred ccccceeeeccccCCCCCCCcee--echhhHhh
Q 017035 201 KARDQLFEKAVTPSDVGKLNRLV--IPKQHAEK 231 (378)
Q Consensus 201 ~~~~~lF~K~LT~SDV~~~~rLv--IPk~~ae~ 231 (378)
+...+.|.+.+++. ++.+++. +|+++..+
T Consensus 12 ~~i~~~~~~~vk~~--Gnsa~v~p~lPkeyiGK 42 (53)
T PF09853_consen 12 RNIEPTFIGVVKPF--GNSARVYPSLPKEYIGK 42 (53)
T ss_pred eeEEEEEEEEEEec--CcceeEcCCCChHHcCc
Confidence 46778999999988 7778999 99999844
No 28
>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=24.92 E-value=1.2e+02 Score=23.76 Aligned_cols=33 Identities=21% Similarity=0.234 Sum_probs=24.3
Q ss_pred EEecCCCceEEecCHHHHHhhcCCCCCCEEEEEEec
Q 017035 261 SYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFHRST 296 (378)
Q Consensus 261 s~~~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F~r~~ 296 (378)
..|++|.--.|-+ .++..-+|.+||.|.|....
T Consensus 4 ~k~GNS~~vtIPk---~i~~~lgl~~Gd~v~v~~~~ 36 (74)
T TIGR02609 4 RKVGNSLVVTLPK---EVLESLGLKEGDTLYVDEEE 36 (74)
T ss_pred EEECCeeEEEECH---HHHHHcCcCCCCEEEEEEEC
Confidence 4566555555554 68899999999999887653
No 29
>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=24.80 E-value=14 Score=32.09 Aligned_cols=27 Identities=30% Similarity=0.544 Sum_probs=16.7
Q ss_pred CCceEEecCHHHH----------HhhcCCCCCCEEEE
Q 017035 266 SQSYVLTKGWSRF----------VKEKNLKAGDIVSF 292 (378)
Q Consensus 266 s~~yvLt~GW~~F----------Vk~k~Lk~GD~I~F 292 (378)
-+-||..+||+-| ..-+.|++||+|+-
T Consensus 75 hPFFV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl~ 111 (115)
T PF08517_consen 75 HPFFVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCLS 111 (115)
T ss_dssp -EEEETTTEEEESSHHHHHHHHTS--EE--TT-EEEE
T ss_pred CceEEeCCcccccCcchhceecCCcccccccCCEEec
Confidence 4678889999876 34567899999974
No 30
>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=24.35 E-value=51 Score=24.48 Aligned_cols=22 Identities=36% Similarity=0.443 Sum_probs=17.6
Q ss_pred eEEEecCCCCHHHHHHHHHHHH
Q 017035 91 QRVWLGTFNEEEEAARAYDIAA 112 (378)
Q Consensus 91 kr~~LGtf~t~EeAArAYD~Aa 112 (378)
-+|.+|.|++.++|..+-....
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 3788999999999988776554
No 31
>PRK11347 antitoxin ChpS; Provisional
Probab=23.70 E-value=2e+02 Score=23.33 Aligned_cols=36 Identities=28% Similarity=0.424 Sum_probs=30.0
Q ss_pred EEEEEecCCCceEEecCHHHHHhhcCCCCCCEEEEEEec
Q 017035 258 FRYSYWNSSQSYVLTKGWSRFVKEKNLKAGDIVSFHRST 296 (378)
Q Consensus 258 Fr~s~~~~s~~yvLt~GW~~FVk~k~Lk~GD~I~F~r~~ 296 (378)
...+.|++|.-..|.+ .|+++-+|.+||.|.+....
T Consensus 3 ~~v~kwGNS~~vriPk---~il~~l~l~~G~~v~i~v~~ 38 (83)
T PRK11347 3 ITIKRWGNSAGMVIPN---IVMKELNLQPGQSVEAQVSN 38 (83)
T ss_pred EEEEEEcCceeEEeCH---HHHHHcCCCCCCEEEEEEEC
Confidence 3567888888888875 79999999999999988764
No 32
>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=22.87 E-value=90 Score=27.03 Aligned_cols=15 Identities=47% Similarity=0.603 Sum_probs=10.7
Q ss_pred cCCCCCCEEEEEEec
Q 017035 282 KNLKAGDIVSFHRST 296 (378)
Q Consensus 282 k~Lk~GD~I~F~r~~ 296 (378)
+.+++||.|+||...
T Consensus 38 ~~mk~GD~vifY~s~ 52 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSG 52 (143)
T ss_dssp HC--TT-EEEEEETS
T ss_pred hcCCCCCEEEEEEcC
Confidence 399999999999986
No 33
>cd01753 PLAT_LOX PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates.
Probab=22.78 E-value=1e+02 Score=26.08 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=32.7
Q ss_pred cCCCCCCCceeechhhHhhcCCCCCCCCCCceEEEEEeCCCCeEEEEEEEec-CCCceEEec
Q 017035 213 PSDVGKLNRLVIPKQHAEKHFPLQSGSTSKGLLLNFEDVTGKVWRFRYSYWN-SSQSYVLTK 273 (378)
Q Consensus 213 ~SDV~~~~rLvIPk~~ae~~lP~~~~~~~~gv~l~v~D~~Gk~W~Fr~s~~~-~s~~yvLt~ 273 (378)
+.|++.+.+|.|=.+..-..-+..- -.|.|.|..|++|.|-|.-|= ....++|..
T Consensus 57 ~~~lG~l~~i~i~~d~~g~~~~W~l------~~V~V~~~~~~~~~F~c~rWl~~~~~~~~~~ 112 (113)
T cd01753 57 PEDLGELLLVRLRKRKYLLFDAWFC------NYITVTGPGGDEYHFPCYRWIEGYGTLELRE 112 (113)
T ss_pred ccCCCCcEEEEEEECCCCCCCCeee------cEEEEEcCCCCEEEEEhHHeECCCCEEEecC
Confidence 3578777777775544311111111 135677888999999999883 334555544
No 34
>PF13356 DUF4102: Domain of unknown function (DUF4102); PDB: 3JU0_A 3RMP_A 3JTZ_A 2KJ8_A.
Probab=22.28 E-value=3.8e+02 Score=21.20 Aligned_cols=37 Identities=19% Similarity=0.152 Sum_probs=23.4
Q ss_pred EECCC--CeEEEEEEeCCe--EEEecCCCC--HHHHHHHHHHH
Q 017035 75 VPQPN--GRWGAQIYEKHQ--RVWLGTFNE--EEEAARAYDIA 111 (378)
Q Consensus 75 ~~~~~--grW~A~I~~~gk--r~~LGtf~t--~EeAArAYD~A 111 (378)
+..+. ..|.-+.+.+|+ ++-||.|++ .++|-......
T Consensus 28 ~v~~~G~kt~~~r~~~~gk~~~~~lG~~p~~sl~~AR~~a~~~ 70 (89)
T PF13356_consen 28 RVTPSGSKTFYFRYRINGKRRRITLGRYPELSLAEAREKAREL 70 (89)
T ss_dssp EE-TTS-EEEEEEEEETTEEEEEEEEECTTS-HHHHHHHHHHH
T ss_pred EEEeCCCeEEEEEEEecceEEEeccCCCccCCHHHHHHHHHHH
Confidence 33444 458888877665 689999976 55555444433
No 35
>PF05593 RHS_repeat: RHS Repeat; InterPro: IPR006530 These sequences contain two tandem copies of a 21-residue extracellular repeat that is found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin [, , ].
Probab=22.25 E-value=1.4e+02 Score=20.20 Aligned_cols=20 Identities=30% Similarity=0.591 Sum_probs=15.8
Q ss_pred CceEEEEEeCCCCeEEEEEE
Q 017035 242 KGLLLNFEDVTGKVWRFRYS 261 (378)
Q Consensus 242 ~gv~l~v~D~~Gk~W~Fr~s 261 (378)
.+..+.+.|..|.+|+|.|-
T Consensus 4 ~G~l~~~~d~~G~~~~y~YD 23 (38)
T PF05593_consen 4 NGRLTSVTDPDGRTTRYTYD 23 (38)
T ss_pred CCCEEEEEcCCCCEEEEEEC
Confidence 45678888999999977654
No 36
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=21.58 E-value=1.5e+02 Score=19.83 Aligned_cols=21 Identities=24% Similarity=0.316 Sum_probs=18.2
Q ss_pred HHHHhhcCCCCCCEEEEEEec
Q 017035 276 SRFVKEKNLKAGDIVSFHRST 296 (378)
Q Consensus 276 ~~FVk~k~Lk~GD~I~F~r~~ 296 (378)
..|.+..++..||.|.+....
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~ 33 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVE 33 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeC
Confidence 468999999999999999763
Done!