Query 002396
Match_columns 928
No_of_seqs 273 out of 546
Neff 3.5
Searched_HMMs 46136
Date Thu Mar 28 23:05:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002396.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002396hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 1.2E-35 2.5E-40 265.7 8.6 83 197-280 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 2.1E-18 4.5E-23 153.2 10.7 98 71-173 1-100 (100)
3 KOG0644 Uncharacterized conser 99.5 2.7E-14 5.9E-19 166.1 5.0 149 149-306 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.3 4.2E-06 9.2E-11 83.6 10.0 90 67-158 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.8 4.3E-05 9.3E-10 73.3 6.3 80 66-146 19-114 (114)
6 KOG3598 Thyroid hormone recept 93.4 0.06 1.3E-06 68.4 3.7 44 113-157 1693-1741(2220)
7 KOG3598 Thyroid hormone recept 91.3 0.25 5.3E-06 63.3 5.2 7 92-98 1670-1676(2220)
8 PRK10737 FKBP-type peptidyl-pr 79.5 5 0.00011 42.4 6.7 104 148-265 2-114 (196)
9 smart00743 Agenet Tudor-like d 58.2 14 0.00031 31.0 3.8 28 235-265 2-29 (61)
10 PF11498 Activator_LAG-3: Tran 55.0 4 8.7E-05 46.7 0.0 6 376-381 272-277 (468)
11 PF04014 Antitoxin-MazE: Antid 49.1 17 0.00037 29.6 2.8 28 142-169 14-41 (47)
12 PF10844 DUF2577: Protein of u 46.0 26 0.00056 33.1 3.8 29 143-171 71-99 (100)
13 KOG3207 Beta-tubulin folding c 45.8 24 0.00051 42.0 4.2 43 236-292 3-45 (505)
14 PF13163 DUF3999: Protein of u 45.2 1.4E+02 0.003 35.0 10.2 164 74-285 9-196 (429)
15 COG1047 SlpA FKBP-type peptidy 44.7 87 0.0019 33.1 7.7 105 148-265 2-115 (174)
16 smart00333 TUDOR Tudor domain. 36.8 51 0.0011 27.0 3.8 53 235-304 2-54 (57)
17 PRK03760 hypothetical protein; 35.5 72 0.0016 31.2 5.2 48 110-160 62-117 (117)
18 PF11515 Cul7: Mouse developme 34.3 39 0.00084 31.6 2.9 71 224-305 7-77 (78)
19 TIGR01439 lp_hng_hel_AbrB loop 30.4 62 0.0014 25.1 3.2 27 142-168 14-40 (43)
20 PF05641 Agenet: Agenet domain 30.3 82 0.0018 27.6 4.2 42 236-287 1-42 (68)
21 cd04451 S1_IF1 S1_IF1: Transla 29.2 2.1E+02 0.0047 24.6 6.5 38 110-160 15-52 (64)
22 PF06003 SMN: Survival motor n 28.6 54 0.0012 36.1 3.4 57 234-305 67-123 (264)
23 PF01878 EVE: EVE domain; Int 27.6 64 0.0014 31.5 3.4 27 147-173 38-65 (143)
24 KOG4369 RTK signaling protein 25.3 24 0.00052 45.9 0.1 25 134-159 1353-1377(2131)
25 cd04491 SoSSB_OBF SoSSB_OBF: A 25.2 3.5E+02 0.0075 24.0 7.3 50 106-171 22-75 (82)
26 KOG4369 RTK signaling protein 24.2 30 0.00065 45.2 0.6 9 253-261 1620-1628(2131)
27 PF02513 Spin-Ssty: Spin/Ssty 24.2 1.1E+02 0.0024 26.5 3.8 31 238-268 1-31 (50)
28 smart00536 AXH domain in Ataxi 23.6 1.7E+02 0.0037 29.2 5.5 28 130-158 76-113 (116)
29 PF06752 E_Pc_C: Enhancer of P 23.0 68 0.0015 35.2 2.8 14 529-542 6-19 (230)
30 PRK15095 FKBP-type peptidyl-pr 22.5 2.3E+02 0.0051 28.8 6.4 105 148-265 4-118 (156)
31 PF15057 DUF4537: Domain of un 22.4 3.8E+02 0.0082 26.5 7.6 79 152-264 1-82 (124)
32 cd06919 Asp_decarbox Aspartate 20.3 4.2E+02 0.0092 26.4 7.3 73 72-159 11-88 (111)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=1.2e-35 Score=265.67 Aligned_cols=83 Identities=67% Similarity=1.128 Sum_probs=81.6
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCcceeehHHHHHHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCc
Q 002396 197 AAHAAANNSPFTVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQW 276 (928)
Q Consensus 197 Aa~aaat~spFtV~YyPRas~sEFVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~W 276 (928)
|+|||+++++|+|+||||++++|||||++||++|++ ++|++||||||.||+||+++++|+|||+||+++||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999998 9999999999999999999999999999999999999999999
Q ss_pred ccee
Q 002396 277 RNLQ 280 (928)
Q Consensus 277 R~Lq 280 (928)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9996
No 2
>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=99.77 E-value=2.1e-18 Score=153.22 Aligned_cols=98 Identities=29% Similarity=0.414 Sum_probs=74.9
Q ss_pred EEEEcccccCCCCCceeeecchhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 002396 71 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFSMQPPAQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLF 150 (928)
Q Consensus 71 F~KtLTaSDVs~~GrfsVPkr~AE~~FPpLD~s~~~psq~LvakDl~Gk~W~FRhiyRg~prRhlLTTGWS~FVreKkLv 150 (928)
|.|+|+++|+.+.++|.||++++++|.. + ...+.++.++|..|++|.+++.|++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~--~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGG--N---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC--C---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 8999999999999999999999999721 1 1235689999999999999999998888899999999999999999
Q ss_pred CCCEEEEEEcc--CccEEEEEEecc
Q 002396 151 AGDSVLFIRDE--KQQLLLGIRRAN 173 (928)
Q Consensus 151 aGDsVVF~R~e--~GeL~VGIRRA~ 173 (928)
+||.|+|+..+ ..++.|+|+|+.
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE---
T ss_pred CCCEEEEEEecCCCceEEEEEEECc
Confidence 99999999875 455699999873
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.47 E-value=2.7e-14 Score=166.14 Aligned_cols=149 Identities=22% Similarity=0.390 Sum_probs=122.1
Q ss_pred CCCCCEEEEEEccCccEEEEEEeccCCCCC---------------------CCCCccCCCccccchHHHHHHHHhcCCcE
Q 002396 149 LFAGDSVLFIRDEKQQLLLGIRRANRQPAN---------------------LSSSVLSSDSMHIGILAAAAHAAANNSPF 207 (928)
Q Consensus 149 LvaGDsVVF~R~e~GeL~VGIRRA~r~~~~---------------------~~ssv~ssdsm~~gvLaaAa~aaat~spF 207 (928)
...||.|+++|.+..+|.-.+|+.+..-++ .|.+.-+.=.|.+.||.-|.|+ -+..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 457999999998877777777766654322 1122223335889999888864 45789
Q ss_pred EEEEcCCCCCCcceeehHHHHHHHhcCCCccCCeeeEee--eccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccc
Q 002396 208 TVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMF--ETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDE 285 (928)
Q Consensus 208 tV~YyPRas~sEFVVp~~kY~kAm~~~~ws~GMRFRM~F--EtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE 285 (928)
.+.|......+||+|.+..|+.|+. ++|..|+|||..+ ++||. .+||.|+|.++.+..| .+|+|+|+|+.|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999998 9999999999998 33342 3899999999999888 8999999999999999
Q ss_pred cCCCCCCCccccceeeecCCC
Q 002396 286 STAGEKRNRVSIWEIEPVTAP 306 (928)
Q Consensus 286 ~~~~~r~~RVSPWEIEpv~~~ 306 (928)
.+. +.-||||.|++...
T Consensus 1029 ~e~----~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1029 TET----ELHSPWEMEPIPDE 1045 (1113)
T ss_pred Ccc----cccCccccCCCccc
Confidence 974 77899999999863
No 4
>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=98.28 E-value=4.2e-06 Score=83.58 Aligned_cols=90 Identities=26% Similarity=0.351 Sum_probs=60.2
Q ss_pred cceEEEEEcccccCCCCC----ceeeecchhhhcCCCCCC-CCCCCceEEEEEecCC--CeEEEEEEEeCC------CCc
Q 002396 67 QTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDF-SMQPPAQELMARDLHD--NIWTFRHIYRGQ------PKR 133 (928)
Q Consensus 67 ~~~~F~KtLTaSDVs~~G----rfsVPkr~AE~~FPpLD~-s~~~psq~LvakDl~G--k~W~FRhiyRg~------prR 133 (928)
....|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||++|.|+ ++.
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 456899999999999875 799999999999998655 5567889999999887 679999999975 677
Q ss_pred eeec--ccchhhhccCCCCCCCEEEEE
Q 002396 134 HLLT--TGWSLFVSGKRLFAGDSVLFI 158 (928)
Q Consensus 134 hlLT--TGWS~FVreKkLvaGDsVVF~ 158 (928)
+.|| +|-..|.+. =..||-+||.
T Consensus 86 ~RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 86 YRITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEEE---TTSGGG-G--GGTT-EEEEE
T ss_pred eEEeeecCCCccCCc--cccccEEEEE
Confidence 8885 332233332 3478988887
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=97.78 E-value=4.3e-05 Score=73.31 Aligned_cols=80 Identities=21% Similarity=0.243 Sum_probs=62.7
Q ss_pred CcceEEEEEcccccCCCC-CceeeecchhhhcCCCCC------------CCCCCCceEEEEEecCCCeEEEEEEEeCC--
Q 002396 66 PQTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLD------------FSMQPPAQELMARDLHDNIWTFRHIYRGQ-- 130 (928)
Q Consensus 66 ~~~~~F~KtLTaSDVs~~-GrfsVPkr~AE~~FPpLD------------~s~~~psq~LvakDl~Gk~W~FRhiyRg~-- 130 (928)
.+..+|+|+|+.||+..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
T Consensus 19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 456899999999999987 899999876533 12221 11235678899999999999999999964
Q ss_pred -CCceeecccchhhhcc
Q 002396 131 -PKRHLLTTGWSLFVSG 146 (928)
Q Consensus 131 -prRhlLTTGWS~FVre 146 (928)
...|+|++||..+|.+
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 4579999999999864
No 6
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=93.45 E-value=0.06 Score=68.37 Aligned_cols=44 Identities=25% Similarity=0.282 Sum_probs=26.2
Q ss_pred EEecCC-CeEEEEEEEeCCCCceeec----ccchhhhccCCCCCCCEEEE
Q 002396 113 ARDLHD-NIWTFRHIYRGQPKRHLLT----TGWSLFVSGKRLFAGDSVLF 157 (928)
Q Consensus 113 akDl~G-k~W~FRhiyRg~prRhlLT----TGWS~FVreKkLvaGDsVVF 157 (928)
..|..| +.=.|.-|+... ..++.| .-|-.|--.|.+..|-.--|
T Consensus 1693 lidtkgnkiagFdsi~kK~-Glqvstkqk~spwdlFEg~k~~aplsW~wF 1741 (2220)
T KOG3598|consen 1693 LIDTKGNKIAGFDSIEKKN-GLQVSTKQKKSPWDLFEGTKHLAPLSWKWF 1741 (2220)
T ss_pred ccccccceeccchhhhhhc-CceeccccccCcchhhccCCCCCCccceee
Confidence 346666 444566666432 235554 45888888888877665544
No 7
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=91.31 E-value=0.25 Score=63.31 Aligned_cols=7 Identities=14% Similarity=0.667 Sum_probs=2.8
Q ss_pred hhhhcCC
Q 002396 92 AAEKIFP 98 (928)
Q Consensus 92 ~AE~~FP 98 (928)
....+||
T Consensus 1670 kvrqlLP 1676 (2220)
T KOG3598|consen 1670 KVRQLLP 1676 (2220)
T ss_pred HHHHhcC
Confidence 3333444
No 8
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=79.53 E-value=5 Score=42.42 Aligned_cols=104 Identities=20% Similarity=0.191 Sum_probs=63.8
Q ss_pred CCCCCCEEEEE---EccCccEEEEEEeccCCCCCCCCCccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCC------
Q 002396 148 RLFAGDSVLFI---RDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPS------ 218 (928)
Q Consensus 148 kLvaGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaat~spFtV~YyPRas~s------ 218 (928)
++..|++|.|. |.++|+++-.-+ . ..|..++-....-+--|.+|+.-.+.|..|+|..-|-....
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 34567777763 345676533321 1 12333332233334457778888888999999976654332
Q ss_pred cceeehHHHHHHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEeec
Q 002396 219 EFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 265 (928)
Q Consensus 219 EFVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd 265 (928)
-+.||++.|.... ...+||||.+ ++++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~~~~---~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGVD---ELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCcc---CCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 3567888764332 3789999886 45552 36889999975
No 9
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=58.18 E-value=14 Score=30.99 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=23.8
Q ss_pred CCccCCeeeEeeeccCCCcceeeEEEEEeec
Q 002396 235 QISLGMRFRMMFETEESGTRRYMGTITGISD 265 (928)
Q Consensus 235 ~ws~GMRFRM~FEtEDss~rry~GTI~gVsd 265 (928)
.|++|+++...++.++ .||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~---~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEED---SWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCC---EEEEEEEEEECC
Confidence 5899999999996543 899999999964
No 10
>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12 []. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1 []. ; PDB: 2FO1_D.
Probab=55.03 E-value=4 Score=46.65 Aligned_cols=6 Identities=0% Similarity=0.041 Sum_probs=0.0
Q ss_pred cccccC
Q 002396 376 SSYMHS 381 (928)
Q Consensus 376 ~~~~~~ 381 (928)
|+.|..
T Consensus 272 pDtYD~ 277 (468)
T PF11498_consen 272 PDTYDT 277 (468)
T ss_dssp ------
T ss_pred ccchHH
Confidence 444433
No 11
>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=49.08 E-value=17 Score=29.59 Aligned_cols=28 Identities=14% Similarity=0.101 Sum_probs=22.8
Q ss_pred hhhccCCCCCCCEEEEEEccCccEEEEE
Q 002396 142 LFVSGKRLFAGDSVLFIRDEKQQLLLGI 169 (928)
Q Consensus 142 ~FVreKkLvaGDsVVF~R~e~GeL~VGI 169 (928)
+|....+|.+||.|.|.-+++|++.+.-
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 5666889999999999998888666543
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=45.96 E-value=26 Score=33.12 Aligned_cols=29 Identities=24% Similarity=0.320 Sum_probs=24.1
Q ss_pred hhccCCCCCCCEEEEEEccCccEEEEEEe
Q 002396 143 FVSGKRLFAGDSVLFIRDEKQQLLLGIRR 171 (928)
Q Consensus 143 FVreKkLvaGDsVVF~R~e~GeL~VGIRR 171 (928)
|.-...|++||.|..+|.++|..++=+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 66788999999999999988887765544
No 13
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=45.83 E-value=24 Score=41.98 Aligned_cols=43 Identities=30% Similarity=0.720 Sum_probs=30.1
Q ss_pred CccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccccCCCCCC
Q 002396 236 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKR 292 (928)
Q Consensus 236 ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~ 292 (928)
..+|.|+|.-+|- +..||.|+|.| |++ +| +.|.||++.-+.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccC
Confidence 5689999987652 33566676655 444 45 78999999977553
No 14
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=45.25 E-value=1.4e+02 Score=35.02 Aligned_cols=164 Identities=16% Similarity=0.240 Sum_probs=98.0
Q ss_pred EcccccCCCCCceeeecc-hhhhcCCCCCCCCCCCceEEEEEecCCCeEEEEEEEeCC-----CCceeecccchhh-hcc
Q 002396 74 TLTASDTSTHGGFSVPRR-AAEKIFPPLDFSMQPPAQELMARDLHDNIWTFRHIYRGQ-----PKRHLLTTGWSLF-VSG 146 (928)
Q Consensus 74 tLTaSDVs~~GrfsVPkr-~AE~~FPpLD~s~~~psq~LvakDl~Gk~W~FRhiyRg~-----prRhlLTTGWS~F-Vre 146 (928)
.|+.+.-+--.++.+|.. .....-|-| .+|.|.|-.|+.-.|....... +.++-| -|... +..
T Consensus 9 ~L~~~~~~~~y~l~Lp~~vy~~~~~~dL--------~DvrVfn~~G~~vP~al~~~~~~~~~~~~~~~~--~~fpl~~~~ 78 (429)
T PF13163_consen 9 PLQLSGSAPWYRLTLPLAVYAASRRPDL--------GDVRVFNAAGEPVPYALLPPRAPAAQAPTRQPV--PWFPLPASA 78 (429)
T ss_pred eeecCCCCceEEEECCHHHHHhhccccc--------cceEEECCCCCCCceeecccccccCCCCceeee--eeeecCCcc
Confidence 344444444467888876 333334444 3699999999998887775521 222222 23333 445
Q ss_pred CCCCCCCE-EEEEEccCccEEEEEEeccCCCCCCCCCccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCcceeehH
Q 002396 147 KRLFAGDS-VLFIRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEFVVPLA 225 (928)
Q Consensus 147 KkLvaGDs-VVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaat~spFtV~YyPRas~sEFVVp~~ 225 (928)
.. ..||. +.+.|+.+|.+ |.|+++......... ...|+|.+.
T Consensus 79 ~~-~~~~~~~~v~~~~~G~~-ve~~~~~~~~~~~~~-----------------------------------~~~~Lld~s 121 (429)
T PF13163_consen 79 DA-ARGDPQLRVERDADGAL-VEVRPASGAAPADGQ-----------------------------------ARGWLLDLS 121 (429)
T ss_pred cc-ccCCccEEEEECCCCcE-EEecccCCCCccccc-----------------------------------ccEEEEECc
Confidence 45 67774 78889999999 999987764322110 013444443
Q ss_pred HH---HHHHhcCCC-ccCCee--eEeeeccCCCccee----eEEEEEeecCC------CCCCCCCCccceeccccc
Q 002396 226 KY---YKAVHSNQI-SLGMRF--RMMFETEESGTRRY----MGTITGISDLD------PVRWKNSQWRNLQVGWDE 285 (928)
Q Consensus 226 kY---~kAm~~~~w-s~GMRF--RM~FEtEDss~rry----~GTI~gVsd~D------P~rWp~S~WR~LqV~WDE 285 (928)
.. ..++. -.| .....+ |..+|+-|.-..|+ .|+|..+..-+ -+.-|++..|-|+|.|++
T Consensus 122 ~~~~~l~~L~-L~w~~~~~~~~~~v~VeaSdDl~~W~~l~~~~~l~~L~~~~~~l~~~~I~L~~~~~rYLRl~~~~ 196 (429)
T PF13163_consen 122 ALKEPLDALR-LDWPQSNFNWQARVSVEASDDLQHWRPLAGDAQLMDLSNGGQRLVQDRIELPGSNARYLRLTWND 196 (429)
T ss_pred ccccchhheE-EEeecCCCCceEEEEEEEecCcccceEccCCceEEEeccCCcceeeeeEccCCCCCceEEEEeCC
Confidence 33 23343 456 334444 66666655555664 47777776322 356789999999999965
No 15
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=44.72 E-value=87 Score=33.07 Aligned_cols=105 Identities=19% Similarity=0.226 Sum_probs=65.8
Q ss_pred CCCCCCEEEEE---EccCccEEEEEEeccCCCCCCCCCccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCcc----
Q 002396 148 RLFAGDSVLFI---RDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEF---- 220 (928)
Q Consensus 148 kLvaGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaat~spFtV~YyPRas~sEF---- 220 (928)
++..||.|.+. |.++|+++=.-. . ...|..++-.+..-+.-|.+|..-..-|..|+|.--|-....||
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~-e----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTD-E----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEccc-c----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 45678888773 445555432211 1 01233333333333445778888889999999999887665554
Q ss_pred --eeehHHHHHHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEeec
Q 002396 221 --VVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 265 (928)
Q Consensus 221 --VVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd 265 (928)
.||+++|...- ...+||+|.. ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~---~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG---ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC---CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 46666655431 5789999874 4554 556799999974
No 16
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=36.82 E-value=51 Score=26.96 Aligned_cols=53 Identities=11% Similarity=0.216 Sum_probs=37.8
Q ss_pred CCccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccccCCCCCCCccccceeeecC
Q 002396 235 QISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVT 304 (928)
Q Consensus 235 ~ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEpv~ 304 (928)
.|.+|..+...+ .+. .||.|+|+++.. + ..+.|.-++-+. .+-|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecCC
Confidence 588999999999 433 899999999964 1 446788776442 3566666665554
No 17
>PRK03760 hypothetical protein; Provisional
Probab=35.46 E-value=72 Score=31.24 Aligned_cols=48 Identities=21% Similarity=0.404 Sum_probs=30.2
Q ss_pred EEEEEecCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCEEEEEEc
Q 002396 110 ELMARDLHDNIWTFRH-----IYR-GQPKRHLL--TTGWSLFVSGKRLFAGDSVLFIRD 160 (928)
Q Consensus 110 ~LvakDl~Gk~W~FRh-----iyR-g~prRhlL--TTGWS~FVreKkLvaGDsVVF~R~ 160 (928)
++++.|.+|++-.... +|. ..+-+|+| ..||.+ +.++++||.|.|.|+
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~~---~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKIR---VLKVEVGDEIEWIDE 117 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChHH---HcCCCCCCEEEEeeC
Confidence 4566666665443211 122 23456787 677754 889999999998863
No 18
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=34.34 E-value=39 Score=31.59 Aligned_cols=71 Identities=23% Similarity=0.247 Sum_probs=35.1
Q ss_pred hHHHHHHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccccCCCCCCCccccceeeec
Q 002396 224 LAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPV 303 (928)
Q Consensus 224 ~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEpv 303 (928)
.+.|..-+. -++.+||++||.=.-||-. ..=.|+|..++.- .-|+ -.++|.|...+. .-.|--=.||.+
T Consensus 7 ~d~Ya~YVr-~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~d---g~~~---lnvqv~W~~~G~---tyWV~~~~vEii 75 (78)
T PF11515_consen 7 NDDYAEYVR-DNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDRD---GLHD---LNVQVDWQSKGR---TYWVHWHHVEII 75 (78)
T ss_dssp SHHHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE-T---TSSE-----EEEEETTTTE---EEEEEGGGEEE-
T ss_pred hhHHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeeccC---CCCC---cceEEEeeecCc---eEEEEEEEEEEe
Confidence 456777776 7799999999974333321 2236777666631 1122 357899987652 234444466666
Q ss_pred CC
Q 002396 304 TA 305 (928)
Q Consensus 304 ~~ 305 (928)
+.
T Consensus 76 g~ 77 (78)
T PF11515_consen 76 GF 77 (78)
T ss_dssp --
T ss_pred cC
Confidence 53
No 19
>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=30.36 E-value=62 Score=25.09 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=22.3
Q ss_pred hhhccCCCCCCCEEEEEEccCccEEEE
Q 002396 142 LFVSGKRLFAGDSVLFIRDEKQQLLLG 168 (928)
Q Consensus 142 ~FVreKkLvaGDsVVF~R~e~GeL~VG 168 (928)
.|.+.-++..||.|.+...++|.+.+.
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 677899999999999998777776553
No 20
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=30.27 E-value=82 Score=27.62 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=26.5
Q ss_pred CccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccccC
Q 002396 236 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDEST 287 (928)
Q Consensus 236 ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~ 287 (928)
|..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 46899999887655544579999999997522 6678886544
No 21
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=29.18 E-value=2.1e+02 Score=24.57 Aligned_cols=38 Identities=13% Similarity=0.080 Sum_probs=22.6
Q ss_pred EEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCEEEEEEc
Q 002396 110 ELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRD 160 (928)
Q Consensus 110 ~LvakDl~Gk~W~FRhiyRg~prRhlLTTGWS~FVreKkLvaGDsVVF~R~ 160 (928)
...+++..|+ .++|..||+-| . +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~--~~~c~~rGklr-----~------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGH--EVLAHISGKMR-----M------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCC--EEEEEECceee-----c------CCcccCCCCEEEEEEe
Confidence 3445666676 44455555311 0 2334899999999864
No 22
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=28.61 E-value=54 Score=36.07 Aligned_cols=57 Identities=16% Similarity=0.297 Sum_probs=34.0
Q ss_pred CCCccCCeeeEeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeccccccCCCCCCCccccceeeecCC
Q 002396 234 NQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVTA 305 (928)
Q Consensus 234 ~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEpv~~ 305 (928)
..|.+|++.+..|..|. .+|.+||++|..-+- .| .|..++=+ +.+.|..=+|.+...
T Consensus 67 ~~WkvGd~C~A~~s~Dg---~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSEDG---QYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPSEG 123 (264)
T ss_dssp T---TT-EEEEE-TTTS---SEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEETT-
T ss_pred cCCCCCCEEEEEECCCC---CEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhccccc
Confidence 68999999999995433 799999999974221 23 37776543 335566666666554
No 23
>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=27.61 E-value=64 Score=31.47 Aligned_cols=27 Identities=30% Similarity=0.498 Sum_probs=18.0
Q ss_pred CCCCCCCEEEEEEcc-CccEEEEEEecc
Q 002396 147 KRLFAGDSVLFIRDE-KQQLLLGIRRAN 173 (928)
Q Consensus 147 KkLvaGDsVVF~R~e-~GeL~VGIRRA~ 173 (928)
++++.||.|+||... ++.-+|||=|-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 489999999999987 667777776553
No 24
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=25.34 E-value=24 Score=45.93 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=13.8
Q ss_pred eeecccchhhhccCCCCCCCEEEEEE
Q 002396 134 HLLTTGWSLFVSGKRLFAGDSVLFIR 159 (928)
Q Consensus 134 hlLTTGWS~FVreKkLvaGDsVVF~R 159 (928)
.|++.|= .=|+.-+|..|-.+-+.+
T Consensus 1353 RVig~gg-snVna~r~~tga~ielek 1377 (2131)
T KOG4369|consen 1353 RVIGDGG-SNVNAARLGTGALIELEK 1377 (2131)
T ss_pred hhhccCc-chhhhHhhccceEEehhh
Confidence 3555552 236666666666665555
No 25
>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=25.21 E-value=3.5e+02 Score=23.95 Aligned_cols=50 Identities=20% Similarity=0.186 Sum_probs=34.5
Q ss_pred CCceEEEEEecCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCEEEEEE----ccCccEEEEEEe
Q 002396 106 PPAQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIR----DEKQQLLLGIRR 171 (928)
Q Consensus 106 ~psq~LvakDl~Gk~W~FRhiyRg~prRhlLTTGWS~FVreKkLvaGDsVVF~R----~e~GeL~VGIRR 171 (928)
.....+.+.|..| ..++.+|+.. . ...|..||.|.+.. .-+|.+.+.+.+
T Consensus 22 ~~~~~~~l~D~TG---~i~~~~W~~~----------~---~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 22 GKVQSGLVGDETG---TIRFTLWDEK----------A---ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred eEEEEEEEECCCC---EEEEEEECch----------h---cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 3456788999988 5778888642 1 45588999988872 236677776664
No 26
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=24.18 E-value=30 Score=45.17 Aligned_cols=9 Identities=44% Similarity=0.645 Sum_probs=5.1
Q ss_pred cceeeEEEE
Q 002396 253 TRRYMGTIT 261 (928)
Q Consensus 253 ~rry~GTI~ 261 (928)
+.+|.|||.
T Consensus 1620 is~~q~tiq 1628 (2131)
T KOG4369|consen 1620 ISMYQGTIQ 1628 (2131)
T ss_pred ccccCCccc
Confidence 345666664
No 27
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=24.17 E-value=1.1e+02 Score=26.50 Aligned_cols=31 Identities=16% Similarity=0.358 Sum_probs=24.0
Q ss_pred cCCeeeEeeeccCCCcceeeEEEEEeecCCC
Q 002396 238 LGMRFRMMFETEESGTRRYMGTITGISDLDP 268 (928)
Q Consensus 238 ~GMRFRM~FEtEDss~rry~GTI~gVsd~DP 268 (928)
+|-|+.-.||.++.++..|.|+|..--+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCC
Confidence 5889999999888888888999999877655
No 28
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=23.61 E-value=1.7e+02 Score=29.23 Aligned_cols=28 Identities=29% Similarity=0.445 Sum_probs=21.3
Q ss_pred CCCceeecccchhhhcc----------CCCCCCCEEEEE
Q 002396 130 QPKRHLLTTGWSLFVSG----------KRLFAGDSVLFI 158 (928)
Q Consensus 130 ~prRhlLTTGWS~FVre----------KkLvaGDsVVF~ 158 (928)
+|- ++..+||+.|--+ +.|.+||+|+..
T Consensus 76 HPf-FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~l 113 (116)
T smart00536 76 HPF-FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLSL 113 (116)
T ss_pred CCe-EEcCccccccChhhhhhhcCCcceecccCCEEecc
Confidence 454 7778999998654 478999999853
No 29
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=23.00 E-value=68 Score=35.17 Aligned_cols=14 Identities=50% Similarity=0.534 Sum_probs=11.2
Q ss_pred cccHHHHHHHHhHH
Q 002396 529 QMSDKQIQLHLLQK 542 (928)
Q Consensus 529 ~~~~~q~~~qlLQk 542 (928)
|+.++|+||.+|||
T Consensus 6 QyQqHQqQL~~MQk 19 (230)
T PF06752_consen 6 QYQQHQQQLVLMQK 19 (230)
T ss_pred HHHHHHHHHHHHHH
Confidence 56678888888888
No 30
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=22.48 E-value=2.3e+02 Score=28.79 Aligned_cols=105 Identities=14% Similarity=0.102 Sum_probs=60.2
Q ss_pred CCCCCCEEEEE---EccCccEEEEEEeccCCCCCCCCCc-cCCCccccchHHHHHHHHhcCCcEEEEEcCCCCC------
Q 002396 148 RLFAGDSVLFI---RDEKQQLLLGIRRANRQPANLSSSV-LSSDSMHIGILAAAAHAAANNSPFTVFYNPRASP------ 217 (928)
Q Consensus 148 kLvaGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssv-~ssdsm~~gvLaaAa~aaat~spFtV~YyPRas~------ 217 (928)
....||+|.+. +.++|+.+=.-+ .. ..|..+ +....+ +--+.+|..-...|..++|..-|-...
T Consensus 4 ~i~~~~~V~v~Y~~~~~dG~v~dst~-~~----~~P~~f~~G~g~v-i~gle~aL~gm~~Ge~~~v~ipp~~ayG~~d~~ 77 (156)
T PRK15095 4 SVQSNSAVLVHFTLKLDDGSTAESTR-NN----GKPALFRLGDGSL-SEGLEQQLLGLKVGDKKTFSLEPEAAFGVPSPD 77 (156)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEECC-CC----CCCEEEEeCCCCc-cHHHHHHHcCCCCCCEEEEEEChHHhcCCCChH
Confidence 56778888873 345677543322 11 112221 222222 233556777777888888886554322
Q ss_pred CcceeehHHHHHHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEeec
Q 002396 218 SEFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 265 (928)
Q Consensus 218 sEFVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVsd 265 (928)
--+.||++.|.+. ....+||.+.+ ++++ ..++.|+|+.|.+
T Consensus 78 ~v~~vp~~~f~~~---~~~~~G~~~~~--~~~~--G~~~~~~V~~i~~ 118 (156)
T PRK15095 78 LIQYFSRRDFMDA---GEPEIGAIMLF--TAMD--GSEMPGVIREING 118 (156)
T ss_pred HEEEecHHHCCcc---cCCCCCCEEEE--ECCC--CCEEEEEEEEEcC
Confidence 2345677776543 24789998654 4444 2467899999875
No 31
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=22.42 E-value=3.8e+02 Score=26.47 Aligned_cols=79 Identities=20% Similarity=0.309 Sum_probs=53.7
Q ss_pred CCEEEEEEccCccEEEEEEeccCCCCCCCCCccCCCccccchHHHHHHHHhcCCcEEEEEc-CCC--CCCcceeehHHHH
Q 002396 152 GDSVLFIRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYN-PRA--SPSEFVVPLAKYY 228 (928)
Q Consensus 152 GDsVVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaat~spFtV~Yy-PRa--s~sEFVVp~~kY~ 228 (928)
|..|+=-+++||-++.|.-++.- ++..|.|.|+ .+. -..+|||...
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~----------------------------~~~~~lV~f~~~~~~~v~~~~iI~~~--- 49 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCV----------------------------SSGQFLVEFDDGDTQEVPISDIIALS--- 49 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEcc----------------------------CCCEEEEEECCCCEEEeChHHeEEcc---
Confidence 45565556678888888653321 4556777772 222 1478888866
Q ss_pred HHHhcCCCccCCeeeEeeeccCCCcceeeEEEEEee
Q 002396 229 KAVHSNQISLGMRFRMMFETEESGTRRYMGTITGIS 264 (928)
Q Consensus 229 kAm~~~~ws~GMRFRM~FEtEDss~rry~GTI~gVs 264 (928)
.++. +.+.+|+.+-+..|..+ .++.=|||.+.-
T Consensus 50 ~~~~-~~L~~GD~VLA~~~~~~--~~Y~Pg~V~~~~ 82 (124)
T PF15057_consen 50 DAMR-HSLQVGDKVLAPWEPDD--CRYGPGTVIAGP 82 (124)
T ss_pred Cccc-CcCCCCCEEEEecCcCC--CEEeCEEEEECc
Confidence 4665 99999999999975544 346669999854
No 32
>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=20.32 E-value=4.2e+02 Score=26.45 Aligned_cols=73 Identities=18% Similarity=0.323 Sum_probs=51.6
Q ss_pred EEEcccccCCCCCceeeecchhhh--cCCCCCCCCCCCceEEEEEec-CCCeEEEEEEEeCCC--Cceeecccchhhhcc
Q 002396 72 CKTLTASDTSTHGGFSVPRRAAEK--IFPPLDFSMQPPAQELMARDL-HDNIWTFRHIYRGQP--KRHLLTTGWSLFVSG 146 (928)
Q Consensus 72 ~KtLTaSDVs~~GrfsVPkr~AE~--~FPpLD~s~~~psq~LvakDl-~Gk~W~FRhiyRg~p--rRhlLTTGWS~FVre 146 (928)
.-+.|..|....|-+.|..+-.+. ++| ...+.+.|. +|..|. .|.+.|.+ +.--|. | ...
T Consensus 11 ratVT~a~L~YeGSitID~~Ll~aagi~~---------~E~V~I~Nv~NG~Rf~-TYvI~g~~gSg~I~lN-G----AAA 75 (111)
T cd06919 11 RATVTEADLNYEGSITIDEDLLEAAGILP---------YEKVLVVNVNNGARFE-TYVIPGERGSGVICLN-G----AAA 75 (111)
T ss_pred ceEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEE-EEEEEcCCCCCEEEeC-C----HHH
Confidence 457899999999999999986665 333 346788886 588888 46777653 333333 3 346
Q ss_pred CCCCCCCEEEEEE
Q 002396 147 KRLFAGDSVLFIR 159 (928)
Q Consensus 147 KkLvaGDsVVF~R 159 (928)
+....||.|+++-
T Consensus 76 r~~~~GD~vII~s 88 (111)
T cd06919 76 RLGQPGDRVIIMA 88 (111)
T ss_pred hcCCCCCEEEEEE
Confidence 6778999999863
Done!