Query 001787
Match_columns 1013
No_of_seqs 322 out of 573
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 09:18:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001787.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001787hhsearch_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 4.2E-36 9.1E-41 271.1 7.7 83 245-327 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 1.6E-18 3.5E-23 155.8 11.1 98 119-221 1-100 (100)
3 KOG0644 Uncharacterized conser 99.6 1.7E-15 3.8E-20 177.2 6.0 149 197-353 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.4 1.7E-06 3.7E-11 87.1 10.0 90 115-206 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.7 7.1E-05 1.5E-09 72.6 6.5 80 114-194 19-114 (114)
6 KOG3598 Thyroid hormone recept 93.1 0.043 9.3E-07 70.2 1.8 68 133-205 1663-1741(2220)
7 KOG3598 Thyroid hormone recept 84.5 0.13 2.7E-06 66.3 -3.2 7 232-238 1852-1858(2220)
8 KOG0644 Uncharacterized conser 65.8 4.2 9.1E-05 51.1 2.6 66 27-93 872-939 (1113)
9 PRK10737 FKBP-type peptidyl-pr 65.3 14 0.0003 39.6 6.0 66 240-312 43-114 (196)
10 PF10844 DUF2577: Protein of u 64.7 34 0.00073 32.7 7.9 29 191-219 71-99 (100)
11 KOG3207 Beta-tubulin folding c 52.8 15 0.00033 43.9 4.1 43 283-339 3-45 (505)
12 PF13163 DUF3999: Protein of u 52.1 1.3E+02 0.0028 35.7 11.5 165 122-333 9-197 (429)
13 PF04014 Antitoxin-MazE: Antid 51.5 16 0.00034 30.2 2.9 28 190-217 14-41 (47)
14 PF09606 Med15: ARC105 or Med1 46.1 6.7 0.00015 49.5 0.0 16 916-931 624-639 (799)
15 PF05641 Agenet: Agenet domain 44.3 41 0.00088 29.8 4.6 42 283-334 1-42 (68)
16 smart00743 Agenet Tudor-like d 41.3 35 0.00076 29.0 3.6 38 282-332 2-39 (61)
17 PRK03760 hypothetical protein; 40.8 46 0.001 32.9 4.8 48 158-208 62-117 (117)
18 cd06919 Asp_decarbox Aspartate 39.2 1.4E+02 0.003 30.0 7.7 75 120-207 11-88 (111)
19 cd04451 S1_IF1 S1_IF1: Transla 38.4 1.2E+02 0.0026 26.4 6.5 38 158-208 15-52 (64)
20 PF13388 DUF4106: Protein of u 38.2 37 0.00081 38.8 4.1 9 364-372 73-81 (422)
21 PF11515 Cul7: Mouse developme 37.6 49 0.0011 31.3 4.1 57 271-334 6-62 (78)
22 TIGR01439 lp_hng_hel_AbrB loop 36.3 44 0.00096 26.2 3.2 27 190-216 14-40 (43)
23 COG1047 SlpA FKBP-type peptidy 33.7 1.7E+02 0.0038 31.2 7.9 67 239-312 43-115 (174)
24 TIGR00223 panD L-aspartate-alp 32.7 2E+02 0.0043 29.5 7.7 73 120-207 12-89 (126)
25 smart00333 TUDOR Tudor domain. 32.5 62 0.0013 26.8 3.7 52 282-350 2-53 (57)
26 PF02261 Asp_decarbox: Asparta 32.1 2.2E+02 0.0047 28.9 7.8 72 120-206 12-88 (116)
27 PF01878 EVE: EVE domain; Int 31.5 48 0.001 32.7 3.4 26 195-220 38-64 (143)
28 PRK05449 aspartate alpha-decar 30.1 2.3E+02 0.005 29.1 7.7 73 120-207 12-89 (126)
29 CHL00010 infA translation init 28.2 2.9E+02 0.0062 25.6 7.5 28 194-221 44-73 (78)
30 PF02513 Spin-Ssty: Spin/Ssty 26.8 94 0.002 27.2 3.8 31 285-315 1-31 (50)
31 PRK14699 replication factor A; 26.6 1.6E+02 0.0035 35.7 7.1 66 114-206 68-133 (484)
32 cd04491 SoSSB_OBF SoSSB_OBF: A 26.4 2.9E+02 0.0063 24.8 7.1 49 155-219 23-75 (82)
33 PF02643 DUF192: Uncharacteriz 25.5 1E+02 0.0022 29.7 4.3 46 157-205 50-106 (108)
34 PF15057 DUF4537: Domain of un 25.4 2.2E+02 0.0047 28.5 6.6 79 200-311 1-82 (124)
35 PF06003 SMN: Survival motor n 22.8 71 0.0015 35.6 3.1 57 280-351 66-122 (264)
36 PF12690 BsuPI: Intracellular 22.8 59 0.0013 30.2 2.1 41 156-207 25-66 (82)
37 PF00381 PTS-HPr: PTS HPr comp 22.4 1.8E+02 0.0038 26.6 5.0 60 234-299 11-71 (84)
38 cd00367 PTS-HPr_like Histidine 21.9 3E+02 0.0065 24.7 6.3 58 236-299 9-67 (77)
39 PF13275 S4_2: S4 domain; PDB: 20.5 65 0.0014 29.3 1.8 27 186-215 38-64 (65)
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=4.2e-36 Score=271.06 Aligned_cols=83 Identities=64% Similarity=1.097 Sum_probs=81.7
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcc
Q 001787 245 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWR 324 (1013)
Q Consensus 245 Aahaaat~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR 324 (1013)
|+|||+++++|+|+||||++++||||+++||++||+++|++||||||+||+||+++++|+|||+||+++||+|||+|+||
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~WR 80 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALNHPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKWR 80 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhcCCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCcc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eee
Q 001787 325 NLQ 327 (1013)
Q Consensus 325 ~Lq 327 (1013)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 996
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=1.6e-18 Score=155.81 Aligned_cols=98 Identities=29% Similarity=0.420 Sum_probs=74.7
Q ss_pred EEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCccEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001787 119 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLF 198 (1013)
Q Consensus 119 F~KtLT~SDVst~GrfsVPKr~AE~~FPpLD~s~~~Psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWs~FVr~KkLv 198 (1013)
|.|+|+++|+.+.++|.||+++++++. ++ ...+.++.++|..|++|.+++.|++.+++++|++||..||++++|+
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 FFKVLKPSDVSSSCRLIIPKEFAKKHG--GN---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhC--CC---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 899999999999999999999999972 11 1135689999999999999999998888899999999999999999
Q ss_pred CCCeEEEEEcCC--CcEEEEEEecc
Q 001787 199 AGDSVLFIRDEK--SQLLLGIRRAN 221 (1013)
Q Consensus 199 aGDsVVF~R~e~--GeL~VGIRRa~ 221 (1013)
+||.|+|++.++ .++.|+|+|+.
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 999999998754 45699999973
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.57 E-value=1.7e-15 Score=177.22 Aligned_cols=149 Identities=21% Similarity=0.369 Sum_probs=122.7
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeccCCCCC---------------------CCCcccCCCccccchHHHHHHHHhcCCcE
Q 001787 197 LFAGDSVLFIRDEKSQLLLGIRRANRQQPA---------------------LSSSVISSDSMHIGILAAAAHAAANNSPF 255 (1013)
Q Consensus 197 LvaGDsVVF~R~e~GeL~VGIRRa~r~~~~---------------------~~ssv~ss~sm~~gvLaaAahaaat~~~F 255 (1013)
...||.|+++|.+..+|.-.+|+.+..-.+ .+.+.-+.=+|.+.||..|.++. +..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~~--~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKLM--DKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhhh--hccc
Confidence 458999999998887777777776553222 12222223358999998888554 5699
Q ss_pred EEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeee--cccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccC
Q 001787 256 TIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFE--TEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDES 333 (1013)
Q Consensus 256 ~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~fE--tEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~ 333 (1013)
.+.|......+||+|.+..|++|+.++|..|+|||..+. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||..
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~~ 1029 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDNT 1029 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecCC
Confidence 999999999999999999999999999999999999994 4444 4899999999999888 99999999999999999
Q ss_pred CCCCCCCCccccccccccCC
Q 001787 334 TAGERPSRVSLWETEPVVTP 353 (1013)
Q Consensus 334 ~~~~~~~RVSPWEIEpv~~~ 353 (1013)
+ .+..||||.|++..-
T Consensus 1030 e----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred c----ccccCccccCCCccc
Confidence 7 478899999999753
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=98.38 E-value=1.7e-06 Score=87.09 Aligned_cols=90 Identities=26% Similarity=0.368 Sum_probs=60.8
Q ss_pred CceEEEEeccccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCccEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 001787 115 PTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDY-SMQPPAQEIVARDLHD--TTWTFRHIYRGQ------PKR 181 (1013)
Q Consensus 115 ~~~sF~KtLT~SDVst~G----rfsVPKr~AE~~FPpLD~-s~~~Psq~LvakDlhG--k~W~FRhiyRg~------prR 181 (1013)
....|+|.|++.|++..| |+.|||..++..||.+.. +..+|..+|.+++..| ..|+||+||.|+ ++.
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 356799999999999875 799999999999998655 5677899999999988 679999999975 677
Q ss_pred eeec--ccchhhhccCCCCCCCeEEEE
Q 001787 182 HLLT--TGWSVFVSTKRLFAGDSVLFI 206 (1013)
Q Consensus 182 hlLT--TGWs~FVr~KkLvaGDsVVF~ 206 (1013)
+.|| +|-..|.+. =..||.+||-
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 8886 333333332 2478988886
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=97.70 E-value=7.1e-05 Score=72.58 Aligned_cols=80 Identities=23% Similarity=0.305 Sum_probs=62.1
Q ss_pred CCceEEEEeccccCCCCC-CceeechhhhhhcCCCCC------------CCCCCCccEEEEEeCCCCeEEEEEEEeCC--
Q 001787 114 QPTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLD------------YSMQPPAQEIVARDLHDTTWTFRHIYRGQ-- 178 (1013)
Q Consensus 114 ~~~~sF~KtLT~SDVst~-GrfsVPKr~AE~~FPpLD------------~s~~~Psq~LvakDlhGk~W~FRhiyRg~-- 178 (1013)
+..-.|+|+|+.||+..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
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 345789999999999986 899999876533 12221 11234578999999999999999999964
Q ss_pred -CCceeecccchhhhcc
Q 001787 179 -PKRHLLTTGWSVFVST 194 (1013)
Q Consensus 179 -prRhlLTTGWs~FVr~ 194 (1013)
...|+|++||..+|++
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 5679999999999864
No 6
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=93.11 E-value=0.043 Score=70.17 Aligned_cols=68 Identities=24% Similarity=0.297 Sum_probs=37.7
Q ss_pred ceeechhhhhhcCCCCCCCCCCCccEEE------EEeCCC-CeEEEEEEEeCCCCceeec----ccchhhhccCCCCCCC
Q 001787 133 GFSVPRRAAEKIFPPLDYSMQPPAQEIV------ARDLHD-TTWTFRHIYRGQPKRHLLT----TGWSVFVSTKRLFAGD 201 (1013)
Q Consensus 133 rfsVPKr~AE~~FPpLD~s~~~Psq~Lv------akDlhG-k~W~FRhiyRg~prRhlLT----TGWs~FVr~KkLvaGD 201 (1013)
||+=-.+....+||......+ .|. +.|..| +.=.|.-|+.+. ..++.| .-|-.|--.|.++.|-
T Consensus 1663 r~sds~~kvrqlLPlpKqt~d----vItcep~gslidtkgnkiagFdsi~kK~-Glqvstkqk~spwdlFEg~k~~apls 1737 (2220)
T KOG3598|consen 1663 RFSDSTRKVRQLLPLPKQTMD----VITCEPYGSLIDTKGNKIAGFDSIEKKN-GLQVSTKQKKSPWDLFEGTKHLAPLS 1737 (2220)
T ss_pred hhhHHHHHHHHhcCCCccccc----eeeecccccccccccceeccchhhhhhc-CceeccccccCcchhhccCCCCCCcc
Confidence 444444555556665443321 222 346666 456677776432 335554 4588888888887665
Q ss_pred eEEE
Q 001787 202 SVLF 205 (1013)
Q Consensus 202 sVVF 205 (1013)
.--|
T Consensus 1738 W~wF 1741 (2220)
T KOG3598|consen 1738 WKWF 1741 (2220)
T ss_pred ceee
Confidence 5443
No 7
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=84.47 E-value=0.13 Score=66.27 Aligned_cols=7 Identities=29% Similarity=0.344 Sum_probs=2.7
Q ss_pred cCCCccc
Q 001787 232 ISSDSMH 238 (1013)
Q Consensus 232 ~ss~sm~ 238 (1013)
+|++.||
T Consensus 1852 ~s~~~~h 1858 (2220)
T KOG3598|consen 1852 TSEKNEH 1858 (2220)
T ss_pred CChHhhc
Confidence 3333333
No 8
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=65.76 E-value=4.2 Score=51.14 Aligned_cols=66 Identities=27% Similarity=0.468 Sum_probs=44.8
Q ss_pred CCCCCCCEEEEecCcchhhhccccccCCccCCCC-C-CCCCccEEEEeeEeeecCCCchhhheeeceec
Q 001787 27 SLPPVGSLVVYFPQGHSEQVAASMQKENDFIPNY-P-NLPSKLICMLHSVTLHADPETDEVYAQMTLQP 93 (1013)
Q Consensus 27 ~lP~vGs~VyYFPQGH~Eq~~as~~~~~~~~p~~-p-~lP~~ilCrV~~V~L~AD~eTDEVYAqitL~P 93 (1013)
-||..|+.|.||-|||-|-+.+....+++ .-++ | ++=..=+|.|..+..--=+-...--.+|+|.=
T Consensus 872 yipQmgDEViyfrQghqeyl~~~~~n~~~-~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~ 939 (1113)
T KOG0644|consen 872 YIPQMGDEVIYFRQGHQEYLEAVRLNNIE-LNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAV 939 (1113)
T ss_pred ccccccceeehhhhhhHHHHhhhhhcccc-ccccCcccccchhhheeeeeeeeeccCCCcchheeeeee
Confidence 58999999999999999999986544433 1111 0 33335588888877666555555566666643
No 9
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.33 E-value=14 Score=39.64 Aligned_cols=66 Identities=20% Similarity=0.261 Sum_probs=44.6
Q ss_pred chHHHHHHHHhcCCcEEEEEcCCCC------CCccccchHhHhHHHhcCccccceeeeeeecccCccceeeeEEEEecc
Q 001787 240 GILAAAAHAAANNSPFTIFYNPRAS------PSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 312 (1013)
Q Consensus 240 gvLaaAahaaat~~~F~V~Y~PRas------~sEFVVp~~ky~~Am~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~d 312 (1013)
-.|.+|..-.+.|..|+|..-|-.. -.-+.||++.|... ....+||||.+ ++++. .+.++|+.|.+
T Consensus 43 pglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV~~vpr~~F~~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 43 SGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred HHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHEEEecHHHCCCc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 3456677777788889998665422 23457788877532 24789999886 44443 36889999975
No 10
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=64.74 E-value=34 Score=32.74 Aligned_cols=29 Identities=28% Similarity=0.377 Sum_probs=23.3
Q ss_pred hhccCCCCCCCeEEEEEcCCCcEEEEEEe
Q 001787 191 FVSTKRLFAGDSVLFIRDEKSQLLLGIRR 219 (1013)
Q Consensus 191 FVr~KkLvaGDsVVF~R~e~GeL~VGIRR 219 (1013)
|.-..+|++||.|..+|.++|..++-+-|
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlDk 99 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLDK 99 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEEe
Confidence 66778899999999999888876655433
No 11
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=52.85 E-value=15 Score=43.91 Aligned_cols=43 Identities=26% Similarity=0.642 Sum_probs=30.5
Q ss_pred ccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCC
Q 001787 283 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERP 339 (1013)
Q Consensus 283 ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~ 339 (1013)
..+|.|+|..+|- +..||.|+|.| |++ +| +-|.||++.-+.+.
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 4689999988762 35666776655 444 45 78999999876543
No 12
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=52.12 E-value=1.3e+02 Score=35.70 Aligned_cols=165 Identities=18% Similarity=0.262 Sum_probs=98.3
Q ss_pred eccccCCCCCCceeechhh-hhhcCCCCCCCCCCCccEEEEEeCCCCeEEEEEEEeCC-----CCceeecccchh-hhcc
Q 001787 122 TLTASDTSTHGGFSVPRRA-AEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQ-----PKRHLLTTGWSV-FVST 194 (1013)
Q Consensus 122 tLT~SDVst~GrfsVPKr~-AE~~FPpLD~s~~~Psq~LvakDlhGk~W~FRhiyRg~-----prRhlLTTGWs~-FVr~ 194 (1013)
.|+.+.-+--.++.+|..- ....-|-| .+|.|.|-.|+.-.|..+.... +.++-| -|.. .+..
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 3444444445688888753 22333332 2599999999998887665421 222222 1333 3444
Q ss_pred CCCCCCCe-EEEEEcCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCccccchH
Q 001787 195 KRLFAGDS-VLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASPSEFVIPLA 273 (1013)
Q Consensus 195 KkLvaGDs-VVF~R~e~GeL~VGIRRa~r~~~~~~ssv~ss~sm~~gvLaaAahaaat~~~F~V~Y~PRas~sEFVVp~~ 273 (1013)
.. ..||. +.+.|+.+|.+ |.|+++......... ...|+|.+.
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 44 67774 88889999999 999987764321100 012344433
Q ss_pred hH---hHHHhcCc-ccccee--eeeeecccCcccee----eeEEEEeccC------CCCCCCCCCcceeeeecccC
Q 001787 274 KY---NKAMYTQV-SLGMRF--RMMFETEESGVRRY----MGTITSISDL------DPLRWKNSQWRNLQVGWDES 333 (1013)
Q Consensus 274 ky---~~Am~~~w-s~GMRF--KM~fEtEdss~r~~----~GTItgv~d~------DP~rWp~S~WR~LqV~WDE~ 333 (1013)
.. ..++.-.| .....+ |..+|+-|.-..|+ .|+|..+..- +-+.-|++..|-|+|.|++.
T Consensus 122 ~~~~~l~~L~L~w~~~~~~~~~~v~VeaSdDl~~W~~l~~~~~l~~L~~~~~~l~~~~I~L~~~~~rYLRl~~~~~ 197 (429)
T PF13163_consen 122 ALKEPLDALRLDWPQSNFNWQARVSVEASDDLQHWRPLAGDAQLMDLSNGGQRLVQDRIELPGSNARYLRLTWNDP 197 (429)
T ss_pred ccccchhheEEEeecCCCCceEEEEEEEecCcccceEccCCceEEEeccCCcceeeeeEccCCCCCceEEEEeCCC
Confidence 33 33455677 344454 66666655445564 4777777532 23667899999999999653
No 13
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=51.55 E-value=16 Score=30.19 Aligned_cols=28 Identities=14% Similarity=0.143 Sum_probs=23.0
Q ss_pred hhhccCCCCCCCeEEEEEcCCCcEEEEE
Q 001787 190 VFVSTKRLFAGDSVLFIRDEKSQLLLGI 217 (1013)
Q Consensus 190 ~FVr~KkLvaGDsVVF~R~e~GeL~VGI 217 (1013)
+|....+|.+||.|.|.-+++|++.|--
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 5668889999999999999998665543
No 14
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=46.06 E-value=6.7 Score=49.48 Aligned_cols=16 Identities=19% Similarity=0.343 Sum_probs=0.0
Q ss_pred cccCCCCccccccccC
Q 001787 916 ANIDGMAPDTLLSRGY 931 (1013)
Q Consensus 916 ~n~d~~~~d~ll~~~~ 931 (1013)
+|+|+-.-+..|.|.|
T Consensus 624 ~~l~sp~~nhtL~rtf 639 (799)
T PF09606_consen 624 SNLQSPVFNHTLQRTF 639 (799)
T ss_dssp ----------------
T ss_pred hhcCCcccchhHHHHH
Confidence 3555544444555544
No 15
>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=44.35 E-value=41 Score=29.84 Aligned_cols=42 Identities=12% Similarity=0.106 Sum_probs=27.6
Q ss_pred ccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001787 283 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 334 (1013)
Q Consensus 283 ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~~ 334 (1013)
|..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 56899999987766666899999999987522 6789987654
No 16
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=41.31 E-value=35 Score=29.04 Aligned_cols=38 Identities=11% Similarity=0.078 Sum_probs=29.0
Q ss_pred CccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeeccc
Q 001787 282 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDE 332 (1013)
Q Consensus 282 ~ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE 332 (1013)
.|++|+++-..++. ...||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~---~~~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKE---EDSWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECC---CCEEEEEEEEEECC----------CCEEEEEECC
Confidence 58899999999953 36899999999964 1235677665
No 17
>PRK03760 hypothetical protein; Provisional
Probab=40.83 E-value=46 Score=32.92 Aligned_cols=48 Identities=21% Similarity=0.429 Sum_probs=30.3
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCeEEEEEc
Q 001787 158 EIVARDLHDTTWTFRH-----IYR-GQPKRHLL--TTGWSVFVSTKRLFAGDSVLFIRD 208 (1013)
Q Consensus 158 ~LvakDlhGk~W~FRh-----iyR-g~prRhlL--TTGWs~FVr~KkLvaGDsVVF~R~ 208 (1013)
++++.|.+|++-.... +|. ..+-+|+| ..||. ...++++||.|.|.|+
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~~---~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGKI---RVLKVEVGDEIEWIDE 117 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCChH---HHcCCCCCCEEEEeeC
Confidence 3566666665433211 122 23456777 57765 8899999999998763
No 18
>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=39.20 E-value=1.4e+02 Score=29.98 Aligned_cols=75 Identities=15% Similarity=0.245 Sum_probs=52.6
Q ss_pred EEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCccEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccCC
Q 001787 120 CKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTKR 196 (1013)
Q Consensus 120 ~KtLT~SDVst~GrfsVPKr~AE~~FPpLD~s~~~Psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWs~FVr~Kk 196 (1013)
.-+.|..|..-.|.+.|..+.++. -+.. |...+.+.|. +|..|.- |...|.+ +.-.|.+. -.+.
T Consensus 11 ratVT~a~L~YeGSitID~~Ll~a----agi~---~~E~V~I~Nv~NG~Rf~T-YvI~g~~gSg~I~lNGA-----AAr~ 77 (111)
T cd06919 11 RATVTEADLNYEGSITIDEDLLEA----AGIL---PYEKVLVVNVNNGARFET-YVIPGERGSGVICLNGA-----AARL 77 (111)
T ss_pred ceEEeccccccceeEEECHHHHHh----cCCC---CCCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HHhc
Confidence 347889999999999999987776 2221 3345778886 5888886 6667753 43444443 5677
Q ss_pred CCCCCeEEEEE
Q 001787 197 LFAGDSVLFIR 207 (1013)
Q Consensus 197 LvaGDsVVF~R 207 (1013)
...||.|+++=
T Consensus 78 ~~~GD~vII~s 88 (111)
T cd06919 78 GQPGDRVIIMA 88 (111)
T ss_pred CCCCCEEEEEE
Confidence 78999999863
No 19
>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=38.43 E-value=1.2e+02 Score=26.43 Aligned_cols=38 Identities=13% Similarity=0.065 Sum_probs=22.8
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEEc
Q 001787 158 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIRD 208 (1013)
Q Consensus 158 ~LvakDlhGk~W~FRhiyRg~prRhlLTTGWs~FVr~KkLvaGDsVVF~R~ 208 (1013)
...+++..|+. ++|..||+-|+ +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~~--~~c~~rGklr~-----------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGHE--VLAHISGKMRM-----------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCCE--EEEEECceeec-----------CCcccCCCCEEEEEEe
Confidence 45566777764 44445542110 2334899999999864
No 20
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=38.25 E-value=37 Score=38.83 Aligned_cols=9 Identities=33% Similarity=0.265 Sum_probs=3.9
Q ss_pred CCCCCCCCC
Q 001787 364 PKFPKQPGM 372 (1013)
Q Consensus 364 ~Krpr~~~~ 372 (1013)
-|+.+..|+
T Consensus 73 gkklksegf 81 (422)
T PF13388_consen 73 GKKLKSEGF 81 (422)
T ss_pred ccccccchh
Confidence 344444443
No 21
>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=37.62 E-value=49 Score=31.27 Aligned_cols=57 Identities=23% Similarity=0.330 Sum_probs=31.0
Q ss_pred chHhHhHHHhcCccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001787 271 PLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 334 (1013)
Q Consensus 271 p~~ky~~Am~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~~ 334 (1013)
..+.|-.=+.-+..+||++||.=.-||-. .-=.|+|..++. | .-|+ -.++|.|....
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~-d--g~~~---lnvqv~W~~~G 62 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-D--GLHD---LNVQVDWQSKG 62 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB--TT-EEE-EEEE--T--TSSE-----EEEEETTTT
T ss_pred chhHHHHHHHHhCCCCcEEEEeccccccc-ccccceeEeecc-C--CCCC---cceEEEeeecC
Confidence 45778888889999999999985444433 223677666653 1 1122 24788887765
No 22
>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=36.26 E-value=44 Score=26.25 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=22.7
Q ss_pred hhhccCCCCCCCeEEEEEcCCCcEEEE
Q 001787 190 VFVSTKRLFAGDSVLFIRDEKSQLLLG 216 (1013)
Q Consensus 190 ~FVr~KkLvaGDsVVF~R~e~GeL~VG 216 (1013)
.|.+.-++..||.|.+...++|.+.+.
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 677999999999999998877776653
No 23
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=33.69 E-value=1.7e+02 Score=31.25 Aligned_cols=67 Identities=21% Similarity=0.321 Sum_probs=46.9
Q ss_pred cchHHHHHHHHhcCCcEEEEEcCCCCCCcc------ccchHhHhHHHhcCccccceeeeeeecccCccceeeeEEEEecc
Q 001787 239 IGILAAAAHAAANNSPFTIFYNPRASPSEF------VIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 312 (1013)
Q Consensus 239 ~gvLaaAahaaat~~~F~V~Y~PRas~sEF------VVp~~ky~~Am~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~d 312 (1013)
+.-|.+|.....-|..|+|.--|-..-.|+ .||+++|...= ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 43 i~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 43 IPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDLVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred chhHHHHHhCCCCCceeEEEeCchHhcCCCChHHeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 344677888888899999998886544443 45666665432 6889999874 4544 446799999974
No 24
>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=32.69 E-value=2e+02 Score=29.53 Aligned_cols=73 Identities=11% Similarity=0.223 Sum_probs=52.1
Q ss_pred EEeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCccEEEEEeC-CCCeEEEEEEEeCCC--Cceeecccchhhhcc
Q 001787 120 CKTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVST 194 (1013)
Q Consensus 120 ~KtLT~SDVst~GrfsVPKr~AE~--~FPpLD~s~~~Psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWs~FVr~ 194 (1013)
.-+.|..|..-.|.+.|-.+.++. ++| ...+.+.|. +|.+|+. |...|.+ +.-.|.+. -.
T Consensus 12 ratVT~a~L~Y~GSItID~~Lm~aagi~p---------~E~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~lNGA-----AA 76 (126)
T TIGR00223 12 RATVTHANLNYEGSITIDEDLLDAAGILE---------NEKVDIVNVNNGKRFST-YAIAGKRGSRIICVNGA-----AA 76 (126)
T ss_pred ceEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HH
Confidence 357788899888999999987765 333 335778886 5898886 6667754 33444433 56
Q ss_pred CCCCCCCeEEEEE
Q 001787 195 KRLFAGDSVLFIR 207 (1013)
Q Consensus 195 KkLvaGDsVVF~R 207 (1013)
+....||.|+++=
T Consensus 77 rl~~~GD~VII~s 89 (126)
T TIGR00223 77 RCVSVGDIVIIAS 89 (126)
T ss_pred hcCCCCCEEEEEE
Confidence 6778999999863
No 25
>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=32.51 E-value=62 Score=26.84 Aligned_cols=52 Identities=12% Similarity=0.171 Sum_probs=37.3
Q ss_pred CccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCccccccccc
Q 001787 282 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 350 (1013)
Q Consensus 282 ~ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~~RVSPWEIEpv 350 (1013)
.|.+|..+...| .+ ..||.|+|+++.. + ....|.-++-.. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 588999999999 32 5899999999974 2 456788877543 245666665554
No 26
>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=32.14 E-value=2.2e+02 Score=28.87 Aligned_cols=72 Identities=15% Similarity=0.311 Sum_probs=45.4
Q ss_pred EEeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCccEEEEEeC-CCCeEEEEEEEeCCC--Cceeecccchhhhcc
Q 001787 120 CKTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVST 194 (1013)
Q Consensus 120 ~KtLT~SDVst~GrfsVPKr~AE~--~FPpLD~s~~~Psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWs~FVr~ 194 (1013)
.-+.|..|..-.|.+.|..+.++. ++| ...+.+.+. +|..|.- |...|.+ +.-.|.+. -+
T Consensus 12 ratVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~nG~Rf~T-YvI~g~~GSg~I~lNGa-----AA 76 (116)
T PF02261_consen 12 RATVTEADLNYEGSITIDEDLLDAAGILP---------YEQVQVVNVNNGERFET-YVIPGERGSGVICLNGA-----AA 76 (116)
T ss_dssp EEE--EEETTSTSCEEEEHHHHHHCT--T---------TBEEEEEETTT--EEEE-EEEEESTTTT-EEEEGG-----GG
T ss_pred ceEEeccccccceeeEECHHHHHHcCCCc---------CCEEEEEECCCCcEEEE-EEEEccCCCcEEEECCH-----HH
Confidence 347889999999999999987665 344 335777786 6999886 5666654 33444443 56
Q ss_pred CCCCCCCeEEEE
Q 001787 195 KRLFAGDSVLFI 206 (1013)
Q Consensus 195 KkLvaGDsVVF~ 206 (1013)
+...+||.|+++
T Consensus 77 rl~~~GD~vII~ 88 (116)
T PF02261_consen 77 RLVQVGDRVIIM 88 (116)
T ss_dssp GCS-TT-EEEEE
T ss_pred hccCCCCEEEEE
Confidence 778899999986
No 27
>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=31.55 E-value=48 Score=32.74 Aligned_cols=26 Identities=31% Similarity=0.526 Sum_probs=17.4
Q ss_pred CCCCCCCeEEEEEcC-CCcEEEEEEec
Q 001787 195 KRLFAGDSVLFIRDE-KSQLLLGIRRA 220 (1013)
Q Consensus 195 KkLvaGDsVVF~R~e-~GeL~VGIRRa 220 (1013)
++++.||.|+||... .+.-+|||=|-
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V 64 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEV 64 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEE
Confidence 489999999999987 66777777664
No 28
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=30.06 E-value=2.3e+02 Score=29.08 Aligned_cols=73 Identities=14% Similarity=0.251 Sum_probs=52.3
Q ss_pred EEeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCccEEEEEeC-CCCeEEEEEEEeCCC--Cceeecccchhhhcc
Q 001787 120 CKTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVST 194 (1013)
Q Consensus 120 ~KtLT~SDVst~GrfsVPKr~AE~--~FPpLD~s~~~Psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWs~FVr~ 194 (1013)
.-+.|..|..-.|.+.|-.+.++. ++| ...+.+.|. +|..|.. |...|.+ +.-.|.+. -+
T Consensus 12 ratVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~NG~Rf~T-YvI~g~~GSg~I~lNGA-----AA 76 (126)
T PRK05449 12 RATVTEADLNYEGSITIDEDLLDAAGILE---------NEKVQIVNVNNGARFET-YVIAGERGSGVICLNGA-----AA 76 (126)
T ss_pred ceEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HH
Confidence 357889999989999999988776 333 335777886 5898886 6667754 33444443 56
Q ss_pred CCCCCCCeEEEEE
Q 001787 195 KRLFAGDSVLFIR 207 (1013)
Q Consensus 195 KkLvaGDsVVF~R 207 (1013)
+....||.|+++=
T Consensus 77 r~~~~GD~vII~a 89 (126)
T PRK05449 77 RLVQVGDLVIIAA 89 (126)
T ss_pred hcCCCCCEEEEEE
Confidence 7788999999863
No 29
>CHL00010 infA translation initiation factor 1
Probab=28.17 E-value=2.9e+02 Score=25.61 Aligned_cols=28 Identities=21% Similarity=0.172 Sum_probs=17.0
Q ss_pred cCCCCCCCeEEEEE--cCCCcEEEEEEecc
Q 001787 194 TKRLFAGDSVLFIR--DEKSQLLLGIRRAN 221 (1013)
Q Consensus 194 ~KkLvaGDsVVF~R--~e~GeL~VGIRRa~ 221 (1013)
..++.+||.|.|.- .++++-+|-.|-.+
T Consensus 44 ~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 44 SIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred CcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 34478999999984 33434444444443
No 30
>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=26.84 E-value=94 Score=27.25 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=23.9
Q ss_pred ccceeeeeeecccCccceeeeEEEEeccCCC
Q 001787 285 LGMRFRMMFETEESGVRRYMGTITSISDLDP 315 (1013)
Q Consensus 285 ~GMRFKM~fEtEdss~r~~~GTItgv~d~DP 315 (1013)
+|-|+.-.||.++.+...|.|+|..--+..|
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 5889999999998888888999999877654
No 31
>PRK14699 replication factor A; Provisional
Probab=26.57 E-value=1.6e+02 Score=35.65 Aligned_cols=66 Identities=14% Similarity=0.245 Sum_probs=44.0
Q ss_pred CCceEEEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCccEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc
Q 001787 114 QPTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS 193 (1013)
Q Consensus 114 ~~~~sF~KtLT~SDVst~GrfsVPKr~AE~~FPpLD~s~~~Psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWs~FVr 193 (1013)
..+.++.|+|+.+++.+ |-..|++ ..-...|.+.|..| +.||+.|... ...+.
T Consensus 68 ~~v~i~~rVl~i~~~r~--------------f~r~dG~-~g~v~~~~iaDeTG---~ir~tlW~~~---------a~~~~ 120 (484)
T PRK14699 68 GPVNFIARVVSVFDTKE--------------FTRNDGT-IGRVGNLIVGDETG---KIKLTLWDNM---------ADLIK 120 (484)
T ss_pred ceEEEEEEEEEecCceE--------------EecCCCC-ceEEEEEEEecCCC---eEEEEEecCc---------cchhh
Confidence 35678999999998865 4334443 11234678999999 5677777421 13344
Q ss_pred cCCCCCCCeEEEE
Q 001787 194 TKRLFAGDSVLFI 206 (1013)
Q Consensus 194 ~KkLvaGDsVVF~ 206 (1013)
+-+|++||+|.+-
T Consensus 121 ~g~l~~GDvv~I~ 133 (484)
T PRK14699 121 AGKIKAGQTLQIS 133 (484)
T ss_pred hcCCCCCCEEEEc
Confidence 4579999999883
No 32
>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=26.43 E-value=2.9e+02 Score=24.76 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=33.4
Q ss_pred CccEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE----cCCCcEEEEEEe
Q 001787 155 PAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR----DEKSQLLLGIRR 219 (1013)
Q Consensus 155 Psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWs~FVr~KkLvaGDsVVF~R----~e~GeL~VGIRR 219 (1013)
....+.+.|..| ..++.+|+..- ...|..||.|.+.. .-+|.+.+.+.+
T Consensus 23 ~~~~~~l~D~TG---~i~~~~W~~~~-------------~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~ 75 (82)
T cd04491 23 KVQSGLVGDETG---TIRFTLWDEKA-------------ADDLEPGDVVRIENAYVREFNGRLELSVGK 75 (82)
T ss_pred EEEEEEEECCCC---EEEEEEECchh-------------cccCCCCCEEEEEeEEEEecCCcEEEEeCC
Confidence 456789999998 47778886321 34588999888762 235666666554
No 33
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=25.53 E-value=1e+02 Score=29.75 Aligned_cols=46 Identities=22% Similarity=0.351 Sum_probs=27.2
Q ss_pred cEEEEEeCCCCeEEEEEEEe---------CCCCceee--cccchhhhccCCCCCCCeEEE
Q 001787 157 QEIVARDLHDTTWTFRHIYR---------GQPKRHLL--TTGWSVFVSTKRLFAGDSVLF 205 (1013)
Q Consensus 157 q~LvakDlhGk~W~FRhiyR---------g~prRhlL--TTGWs~FVr~KkLvaGDsVVF 205 (1013)
.++++.|..|++-....... ..+-+|+| ..|| +..++|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG~---~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAGW---FEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETTH---HHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCCc---hhhcCCCCCCEEEe
Confidence 45788888887665554441 12346787 4554 48899999999987
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=25.43 E-value=2.2e+02 Score=28.48 Aligned_cols=79 Identities=22% Similarity=0.316 Sum_probs=53.2
Q ss_pred CCeEEEEEcCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcC-CC--CCCccccchHhHh
Q 001787 200 GDSVLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNP-RA--SPSEFVIPLAKYN 276 (1013)
Q Consensus 200 GDsVVF~R~e~GeL~VGIRRa~r~~~~~~ssv~ss~sm~~gvLaaAahaaat~~~F~V~Y~P-Ra--s~sEFVVp~~ky~ 276 (1013)
|..|+=-++++|-|+.|.-++.- ++..|.|.|+- +. -..+|||...
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 55666666789999998766442 34566777722 11 1356677654
Q ss_pred HHHhcCccccceeeeeeecccCccceeeeEEEEec
Q 001787 277 KAMYTQVSLGMRFRMMFETEESGVRRYMGTITSIS 311 (1013)
Q Consensus 277 ~Am~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~ 311 (1013)
.|+.+...+|+.+-+..|..+ .++.=|||++.-
T Consensus 50 ~~~~~~L~~GD~VLA~~~~~~--~~Y~Pg~V~~~~ 82 (124)
T PF15057_consen 50 DAMRHSLQVGDKVLAPWEPDD--CRYGPGTVIAGP 82 (124)
T ss_pred CcccCcCCCCCEEEEecCcCC--CEEeCEEEEECc
Confidence 567899999999999965433 346679999754
No 35
>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=22.82 E-value=71 Score=35.57 Aligned_cols=57 Identities=19% Similarity=0.233 Sum_probs=33.0
Q ss_pred hcCccccceeeeeeecccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCcccccccccc
Q 001787 280 YTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPVV 351 (1013)
Q Consensus 280 ~~~ws~GMRFKM~fEtEdss~r~~~GTItgv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~~RVSPWEIEpv~ 351 (1013)
...|.+|++.+..|..+ ..+|.+||++|..-+- .| .|+.++=+ +.+.|..=+|.+..
T Consensus 66 ~~~WkvGd~C~A~~s~D---g~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSED---GQYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPSE 122 (264)
T ss_dssp TT---TT-EEEEE-TTT---SSEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEETT
T ss_pred ccCCCCCCEEEEEECCC---CCEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhcccc
Confidence 36899999999999533 3689999999975321 23 37776643 23455555555543
No 36
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=22.78 E-value=59 Score=30.23 Aligned_cols=41 Identities=17% Similarity=0.410 Sum_probs=21.7
Q ss_pred ccEEEEEeCCC-CeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE
Q 001787 156 AQEIVARDLHD-TTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR 207 (1013)
Q Consensus 156 sq~LvakDlhG-k~W~FRhiyRg~prRhlLTTGWs~FVr~KkLvaGDsVVF~R 207 (1013)
.-+|.++|..| ++|++ +....|+ .-..+..|.+|++++|--
T Consensus 25 ~~D~~v~d~~g~~vwrw-------S~~~~Ft----Qal~~~~l~pGe~~~~~~ 66 (82)
T PF12690_consen 25 RYDFVVKDKEGKEVWRW-------SDGKMFT----QALQEETLEPGESLTYEE 66 (82)
T ss_dssp -EEEEEE-TT--EEEET-------TTT-----------EEEEE-TT-EEEEEE
T ss_pred EEEEEEECCCCCEEEEe-------cCCchhh----heeeEEEECCCCEEEEEE
Confidence 45789999988 46665 3334444 345678899999999864
No 37
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=22.39 E-value=1.8e+02 Score=26.58 Aligned_cols=60 Identities=17% Similarity=0.105 Sum_probs=44.3
Q ss_pred CCccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeecccCc
Q 001787 234 SDSMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 299 (1013)
Q Consensus 234 s~sm~~gvLaaAahaaat-~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~fEtEdss 299 (1013)
...+|.-..+.-+++|.+ ++.++|.|.- -.|++..+..-|.-....|+.++..+|++|..
T Consensus 11 ~~GlHaRpa~~lv~~a~~~~~~i~i~~~~------~~vdakSil~l~~L~~~~G~~i~i~~~G~de~ 71 (84)
T PF00381_consen 11 PNGLHARPAAELVQIASKFDSDITIRKGG------KTVDAKSILGLMSLGAKKGDEIEIEAEGEDEE 71 (84)
T ss_dssp TTSSSHHHHHHHHHHHHTSSSEEEEEETT------EEEETTSHHHHHHHTBSTTEEEEEEEESTTHH
T ss_pred CCcccHHHHHHHHHHHhhCCCEEEEEeCc------eeEecCCHHHHhhhhcCCCCEEEEEEECcCHH
Confidence 344565443333444433 5678888774 48999999999999999999999999998864
No 38
>cd00367 PTS-HPr_like Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate is transferred to HPr by enzyme I (EI). Phospho-HPr then transfers the phosphoryl group to one of several sugar-specific phosphoprotein intermediates. The conserved histidine in the N-terminus of HPr serves as an acceptor for the phosphoryl group of EI. In addition to the phosphotransferase proteins HPr and E1, this family also includes the closely related Carbon Catabolite Repressor (CCR) proteins which use the same phosphorylation mechanism and interact with transcriptional regulators to control expression of genes coding for utilization of less favored carbon sources.
Probab=21.91 E-value=3e+02 Score=24.66 Aligned_cols=58 Identities=16% Similarity=0.051 Sum_probs=41.1
Q ss_pred ccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeecccCc
Q 001787 236 SMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 299 (1013)
Q Consensus 236 sm~~gvLaaAahaaat-~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~fEtEdss 299 (1013)
.+|.-..+.-++.|.+ .+.++|.|. ...|.+..+..-|.-.+.-|+++...+|++|..
T Consensus 9 GlHaRpa~~~v~~a~~~~~~v~i~~~------~~~vdakSil~i~~L~~~~G~~i~i~~~G~de~ 67 (77)
T cd00367 9 GLHARPAALLVQLASKFKSDITLRKG------GRKANAKSILGLMSLGAKQGDEITLSAEGEDAE 67 (77)
T ss_pred CCcHHHHHHHHHHHHhCCCEEEEEEC------CEEEcHHhHHHHHHcCCCCCCEEEEEEECcCHH
Confidence 4554433333343333 455666664 458999999999999999999999999988753
No 39
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=20.54 E-value=65 Score=29.28 Aligned_cols=27 Identities=22% Similarity=0.204 Sum_probs=13.0
Q ss_pred ccchhhhccCCCCCCCeEEEEEcCCCcEEE
Q 001787 186 TGWSVFVSTKRLFAGDSVLFIRDEKSQLLL 215 (1013)
Q Consensus 186 TGWs~FVr~KkLvaGDsVVF~R~e~GeL~V 215 (1013)
.|=.+.-|.++|++||.|.| ++..+.|
T Consensus 38 NGe~e~rrg~Kl~~GD~V~~---~~~~~~V 64 (65)
T PF13275_consen 38 NGEVETRRGKKLRPGDVVEI---DGEEYRV 64 (65)
T ss_dssp TTB----SS----SSEEEEE---TTEEEEE
T ss_pred CCEEccccCCcCCCCCEEEE---CCEEEEE
Confidence 34445668899999999999 4444543
Done!