Query 001821
Match_columns 1009
No_of_seqs 318 out of 571
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 10:07:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001821.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001821hhsearch_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 5.9E-36 1.3E-40 270.0 7.7 83 241-323 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 2.1E-18 4.6E-23 155.0 11.1 98 115-217 1-100 (100)
3 KOG0644 Uncharacterized conser 99.6 2.9E-15 6.3E-20 175.3 6.1 149 193-349 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.3 2.5E-06 5.5E-11 85.8 10.2 90 111-202 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.8 5.2E-05 1.1E-09 73.5 6.5 80 110-190 19-114 (114)
6 KOG3598 Thyroid hormone recept 89.4 0.052 1.1E-06 69.4 -2.6 68 129-201 1663-1741(2220)
7 KOG3598 Thyroid hormone recept 83.8 0.23 4.9E-06 64.1 -1.4 16 696-711 2176-2191(2220)
8 KOG0644 Uncharacterized conser 67.6 3.4 7.4E-05 51.9 2.4 66 23-89 872-939 (1113)
9 PRK10737 FKBP-type peptidyl-pr 66.0 13 0.00028 39.8 6.0 65 237-308 44-114 (196)
10 PF10844 DUF2577: Protein of u 64.6 33 0.00072 32.8 7.9 28 187-214 71-98 (100)
11 PF13163 DUF3999: Protein of u 55.3 1.1E+02 0.0024 36.2 11.6 165 118-329 9-197 (429)
12 PF04014 Antitoxin-MazE: Antid 52.5 15 0.00033 30.3 3.0 28 186-213 14-41 (47)
13 KOG3207 Beta-tubulin folding c 49.0 19 0.00041 43.1 4.1 43 279-335 3-45 (505)
14 PF05641 Agenet: Agenet domain 43.7 42 0.0009 29.8 4.6 42 279-330 1-42 (68)
15 smart00743 Agenet Tudor-like d 40.8 36 0.00078 29.0 3.6 38 278-328 2-39 (61)
16 cd04451 S1_IF1 S1_IF1: Transla 39.2 1.1E+02 0.0025 26.6 6.5 38 154-204 15-52 (64)
17 PF13388 DUF4106: Protein of u 38.1 37 0.00081 38.8 4.1 11 359-369 72-82 (422)
18 TIGR01439 lp_hng_hel_AbrB loop 37.0 43 0.00093 26.3 3.3 27 186-212 14-40 (43)
19 PRK03760 hypothetical protein; 37.0 59 0.0013 32.1 4.9 48 154-204 62-117 (117)
20 PF11515 Cul7: Mouse developme 34.5 55 0.0012 30.9 4.0 57 267-330 6-62 (78)
21 cd06919 Asp_decarbox Aspartate 33.8 1.9E+02 0.0041 29.1 7.7 74 117-203 12-88 (111)
22 smart00333 TUDOR Tudor domain. 33.6 57 0.0012 27.0 3.6 52 278-346 2-53 (57)
23 COG1047 SlpA FKBP-type peptidy 32.4 1.9E+02 0.0041 31.0 7.9 66 236-308 44-115 (174)
24 PF01878 EVE: EVE domain; Int 30.9 49 0.0011 32.7 3.3 26 191-216 38-64 (143)
25 PRK14699 replication factor A; 30.7 1.5E+02 0.0033 35.9 7.8 65 110-201 68-132 (484)
26 CHL00010 infA translation init 30.4 2.4E+02 0.0053 26.0 7.4 51 154-218 21-74 (78)
27 TIGR00223 panD L-aspartate-alp 30.4 2.5E+02 0.0053 28.9 8.0 72 117-203 13-89 (126)
28 PRK05449 aspartate alpha-decar 28.5 2.7E+02 0.0059 28.5 7.9 72 117-203 13-89 (126)
29 PF02261 Asp_decarbox: Asparta 28.4 2.4E+02 0.0053 28.5 7.5 71 117-202 13-88 (116)
30 cd04491 SoSSB_OBF SoSSB_OBF: A 27.7 2.8E+02 0.0061 24.8 7.3 49 151-215 23-75 (82)
31 PF15057 DUF4537: Domain of un 25.2 2.3E+02 0.0049 28.3 6.7 79 196-307 1-82 (124)
32 PF02513 Spin-Ssty: Spin/Ssty 24.5 1E+02 0.0022 27.0 3.6 31 281-311 1-31 (50)
33 cd00367 PTS-HPr_like Histidine 23.4 2.6E+02 0.0057 25.0 6.3 58 232-295 9-67 (77)
34 PF12690 BsuPI: Intracellular 23.4 56 0.0012 30.3 2.1 41 152-203 25-66 (82)
35 PF02643 DUF192: Uncharacteriz 22.4 1.4E+02 0.003 28.9 4.5 46 153-201 50-106 (108)
36 PF06003 SMN: Survival motor n 22.4 70 0.0015 35.6 2.9 56 276-346 66-121 (264)
37 PF13275 S4_2: S4 domain; PDB: 21.9 58 0.0013 29.6 1.8 27 182-211 38-64 (65)
38 PF00381 PTS-HPr: PTS HPr comp 21.2 1.9E+02 0.0042 26.3 5.0 60 230-295 11-71 (84)
39 TIGR01439 lp_hng_hel_AbrB loop 21.1 1.4E+02 0.0031 23.4 3.6 33 125-164 4-37 (43)
40 PF03120 DNA_ligase_OB: NAD-de 20.3 66 0.0014 30.4 1.9 34 185-218 42-76 (82)
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=5.9e-36 Score=270.02 Aligned_cols=83 Identities=64% Similarity=1.097 Sum_probs=81.7
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcc
Q 001821 241 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWR 320 (1009)
Q Consensus 241 Aa~aaa~~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR 320 (1009)
|+|||+++++|+|+||||++++||||+++||++||+++|++||||||+||+||+++++|+|||+||++.||+|||+|+||
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 001821 321 NLQ 323 (1009)
Q Consensus 321 ~Lq 323 (1009)
|||
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=2.1e-18 Score=155.05 Aligned_cols=98 Identities=29% Similarity=0.420 Sum_probs=74.7
Q ss_pred EEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001821 115 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLF 194 (1009)
Q Consensus 115 F~KtLT~SDVs~~GrfsVPkr~AE~~FPpLD~s~~~psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr~KkLv 194 (1009)
|.|+|+++|+.+.++|.||+++++++. ++ ...+.++.++|..|++|++++.|++.+++++|++||..||++++|+
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 CCCeEEEEEcc--CCcEEEEEEecc
Q 001821 195 AGDSVLFIRDE--KSQLLLGIRRAN 217 (1009)
Q Consensus 195 aGDsVVF~R~e--~GeL~VGIRRA~ 217 (1009)
+||.|+|+..+ ..++.|.|+|+.
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 445699999973
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.55 E-value=2.9e-15 Score=175.34 Aligned_cols=149 Identities=21% Similarity=0.364 Sum_probs=122.2
Q ss_pred CCCCCeEEEEEccCCcEEEEEEeccCCCCCC---------------------CCcccCCCccccchHHHHHHHHhcCCcE
Q 001821 193 LFAGDSVLFIRDEKSQLLLGIRRANRQQPAL---------------------SSSVISSDSMHIGILAAAAHAAANNSPF 251 (1009)
Q Consensus 193 LvaGDsVVF~R~e~GeL~VGIRRA~r~~~~~---------------------~ssv~ssdsm~~gvLaaAa~aaa~~~~F 251 (1009)
...||.|+++|.+..+|.-.+|+.+....+. +.+.-+.=.|.+.||..|.++. +..|
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 4589999999998888777777766532221 1222222248888998888654 5689
Q ss_pred EEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeee--eccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccC
Q 001821 252 TIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFE--TEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDES 329 (1009)
Q Consensus 252 ~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~FE--tEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~ 329 (1009)
.+.|....+.+||+|.+..|++|+.++|.+|+|||..+. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||..
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 3443 4899999999999888 99999999999999999
Q ss_pred CCCCCCCCcccCccccccCC
Q 001821 330 TAGERPSRVSLWETEPVVTP 349 (1009)
Q Consensus 330 ~~~~~~~RVSPWEIEpv~~~ 349 (1009)
+ .+.-||||.|++..-
T Consensus 1030 e----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred c----ccccCccccCCCccc
Confidence 7 468899999999753
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=98.34 E-value=2.5e-06 Score=85.84 Aligned_cols=90 Identities=26% Similarity=0.368 Sum_probs=60.4
Q ss_pred CceeEEEeccccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 001821 111 PTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDY-SMQPPAQEIVARDLHD--TTWTFRHIYRGQ------PKR 177 (1009)
Q Consensus 111 ~~~~F~KtLT~SDVs~~G----rfsVPkr~AE~~FPpLD~-s~~~psq~LvakDlhG--k~W~FRhiyRg~------prR 177 (1009)
....|+|.|++.|++..| |+.|||..++..||.+.. +...|..+|.+++..| .+|+||+||.++ ++.
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 346799999999999875 799999999999988655 5567899999999888 679999999965 677
Q ss_pred eeec--ccchhhhccCCCCCCCeEEEE
Q 001821 178 HLLT--TGWSVFVSTKRLFAGDSVLFI 202 (1009)
Q Consensus 178 hlLT--TGWS~FVr~KkLvaGDsVVF~ 202 (1009)
+.|| +|-..|.+. =..||.+||-
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 7886 333333332 2478888886
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=97.76 E-value=5.2e-05 Score=73.46 Aligned_cols=80 Identities=23% Similarity=0.305 Sum_probs=62.1
Q ss_pred CCceeEEEeccccCCCCC-CceeechhhhhhcCCCCC------------CCCCCCceEEEEEeCCCCeEEEEEEEeCC--
Q 001821 110 QPTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLD------------YSMQPPAQEIVARDLHDTTWTFRHIYRGQ-- 174 (1009)
Q Consensus 110 ~~~~~F~KtLT~SDVs~~-GrfsVPkr~AE~~FPpLD------------~s~~~psq~LvakDlhGk~W~FRhiyRg~-- 174 (1009)
.....|+|+|+.||+..+ .||+||-..... ...|. .....-++++.+.|..++.|..++..|..
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 899999876532 12221 11234578999999999999999999964
Q ss_pred -CCceeecccchhhhcc
Q 001821 175 -PKRHLLTTGWSVFVST 190 (1009)
Q Consensus 175 -prRhlLTTGWS~FVr~ 190 (1009)
...|+|++||..+|.+
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=89.43 E-value=0.052 Score=69.45 Aligned_cols=68 Identities=24% Similarity=0.297 Sum_probs=39.0
Q ss_pred ceeechhhhhhcCCCCCCCCCCCceEEE------EEeCCC-CeEEEEEEEeCCCCceeec----ccchhhhccCCCCCCC
Q 001821 129 GFSVPRRAAEKIFPPLDYSMQPPAQEIV------ARDLHD-TTWTFRHIYRGQPKRHLLT----TGWSVFVSTKRLFAGD 197 (1009)
Q Consensus 129 rfsVPkr~AE~~FPpLD~s~~~psq~Lv------akDlhG-k~W~FRhiyRg~prRhlLT----TGWS~FVr~KkLvaGD 197 (1009)
||+=-.+....+||......+ .|. ..|..| +.=.|.-|+.+. ..++.| .-|--|--.|.++.|-
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 455445556666775444321 121 346666 455677776433 235554 4588888888887776
Q ss_pred eEEE
Q 001821 198 SVLF 201 (1009)
Q Consensus 198 sVVF 201 (1009)
.-.|
T Consensus 1738 W~wF 1741 (2220)
T KOG3598|consen 1738 WKWF 1741 (2220)
T ss_pred ceee
Confidence 5444
No 7
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=83.84 E-value=0.23 Score=64.06 Aligned_cols=16 Identities=44% Similarity=0.310 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHh
Q 001821 696 QLQSQLQQKLQQQQQQ 711 (1009)
Q Consensus 696 q~Q~QlLQklQQQQq~ 711 (1009)
..+-|=||+.|||||.
T Consensus 2176 lf~RQglqqtqqQqqt 2191 (2220)
T KOG3598|consen 2176 LFRRQGLQQTQQQQQT 2191 (2220)
T ss_pred hhHHHHHHHHHHHHHH
Confidence 4455667777777775
No 8
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=67.62 E-value=3.4 Score=51.86 Aligned_cols=66 Identities=27% Similarity=0.468 Sum_probs=45.8
Q ss_pred CCCCCCCEEEEecCcchhhhhcccccCCccCCCC-C-CCCCceeEEEeeeeeecCCCchhhhhhhceec
Q 001821 23 SLPPVGSLVVYFPQGHSEQVAASMQKENDFIPNY-P-NLPSKLICMLHSVTLHADPETDEVYAQMTLQP 89 (1009)
Q Consensus 23 ~lP~vGs~VyYFPQGH~Eq~~as~~~~~~~~p~~-~-~lP~~ilCrV~~V~L~AD~eTDEVYAqitL~P 89 (1009)
-||..|+.|.||-|||-|-+.+....+++ .-++ | ++=..=+|.|..+..--=+....-..+|+|.=
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 33345588888887766666666666666653
No 9
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.96 E-value=13 Score=39.80 Aligned_cols=65 Identities=20% Similarity=0.263 Sum_probs=43.8
Q ss_pred hHHHHHHHHhcCCcEEEEEcCCCC------CCccccchHhHhHHHhcCccccceeeeeeeeccCccceeeeEEEEecc
Q 001821 237 ILAAAAHAAANNSPFTIFYNPRAS------PSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 308 (1009)
Q Consensus 237 vLaaAa~aaa~~~~F~V~Y~PRas------~sEFVVp~~ky~~Am~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d 308 (1009)
-|.+|..-.+.|..|+|..-|-.. -.-+.||++.|... ....+||||.+ ++++. .+.++|+.|.+
T Consensus 44 glE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV~~vpr~~F~~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 44 GLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred HHHHHHcCCCCCCEEEEEEChHHhcCCCChHHEEEecHHHCCCc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 456677777778889998665322 22357788877532 24789999886 44443 36889999975
No 10
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=64.60 E-value=33 Score=32.77 Aligned_cols=28 Identities=29% Similarity=0.358 Sum_probs=22.8
Q ss_pred hhccCCCCCCCeEEEEEccCCcEEEEEE
Q 001821 187 FVSTKRLFAGDSVLFIRDEKSQLLLGIR 214 (1009)
Q Consensus 187 FVr~KkLvaGDsVVF~R~e~GeL~VGIR 214 (1009)
|.-...|++||.|+.+|.++|..++=+-
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVlD 98 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVLD 98 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEEE
Confidence 6677889999999999988887665443
No 11
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=55.34 E-value=1.1e+02 Score=36.18 Aligned_cols=165 Identities=18% Similarity=0.270 Sum_probs=98.5
Q ss_pred eccccCCCCCCceeechhh-hhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCC-----CCceeecccchh-hhcc
Q 001821 118 TLTASDTSTHGGFSVPRRA-AEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQ-----PKRHLLTTGWSV-FVST 190 (1009)
Q Consensus 118 tLT~SDVs~~GrfsVPkr~-AE~~FPpLD~s~~~psq~LvakDlhGk~W~FRhiyRg~-----prRhlLTTGWS~-FVr~ 190 (1009)
.|+.+.-+--.++.+|..- +...-|-| .+|.|.|-.|+.-.|..+.... +.++-| -|.. .+..
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 3444444545688888753 22323332 2599999999998888766421 222222 1222 3455
Q ss_pred CCCCCCCe-EEEEEccCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCccccchH
Q 001821 191 KRLFAGDS-VLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASPSEFVIPLA 269 (1009)
Q Consensus 191 KkLvaGDs-VVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaa~~~~F~V~Y~PRas~sEFVVp~~ 269 (1009)
.. ..||. +.+.|+.+|.+ |.|+++......... ...|++.++
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 55 67774 88899999999 999998764321110 012344433
Q ss_pred hHh---HHHhcCc-ccccee--eeeeeeccCcccee----eeEEEEeccC------CCCCCCCCCcceeeeecccC
Q 001821 270 KYN---KAMYTQV-SLGMRF--RMMFETEESGVRRY----MGTITSISDL------DPLRWKNSQWRNLQVGWDES 329 (1009)
Q Consensus 270 ky~---~Am~~~w-s~GMRF--KM~FEtEdss~r~y----~GTI~gv~d~------DP~rWp~S~WR~LqV~WDE~ 329 (1009)
..+ .++.-.| .....+ |..+|+-|.-..|+ .|+|..+..- +-+.-|++..|.|+|.|++.
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 333 3455677 344444 66666655445564 4777777532 23667899999999999653
No 12
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=52.48 E-value=15 Score=30.25 Aligned_cols=28 Identities=14% Similarity=0.143 Sum_probs=23.1
Q ss_pred hhhccCCCCCCCeEEEEEccCCcEEEEE
Q 001821 186 VFVSTKRLFAGDSVLFIRDEKSQLLLGI 213 (1009)
Q Consensus 186 ~FVr~KkLvaGDsVVF~R~e~GeL~VGI 213 (1009)
.|....+|.+||.|.|.-+++|++.|--
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 5667889999999999999998666543
No 13
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=49.02 E-value=19 Score=43.13 Aligned_cols=43 Identities=26% Similarity=0.642 Sum_probs=30.6
Q ss_pred ccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCC
Q 001821 279 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERP 335 (1009)
Q Consensus 279 ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~ 335 (1009)
..+|.|+|..+|- +..||.|+|.| |++ +| +-|.||++.-+.+.
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 4689999988773 35667777665 444 45 78999999876543
No 14
>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=43.71 E-value=42 Score=29.76 Aligned_cols=42 Identities=12% Similarity=0.106 Sum_probs=27.4
Q ss_pred ccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001821 279 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 330 (1009)
Q Consensus 279 ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~~ 330 (1009)
|..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 46899999887766666899999999987521 6789987554
No 15
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=40.79 E-value=36 Score=28.95 Aligned_cols=38 Identities=11% Similarity=0.078 Sum_probs=29.0
Q ss_pred CccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeeccc
Q 001821 278 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDE 328 (1009)
Q Consensus 278 ~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE 328 (1009)
.|++|+++-..|+. ...||.|+|+.+.. -..+.|.-+.
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 16
>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=39.25 E-value=1.1e+02 Score=26.57 Aligned_cols=38 Identities=13% Similarity=0.065 Sum_probs=22.8
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEEc
Q 001821 154 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIRD 204 (1009)
Q Consensus 154 ~LvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr~KkLvaGDsVVF~R~ 204 (1009)
.+.+++..|. .++|..||.-|+ +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~--~~~c~~rGklr~-----------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGH--EVLAHISGKMRM-----------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCC--EEEEEECceeec-----------CCcccCCCCEEEEEEe
Confidence 4556677776 444445542110 2334899999999864
No 17
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=38.09 E-value=37 Score=38.80 Aligned_cols=11 Identities=27% Similarity=0.190 Sum_probs=5.0
Q ss_pred CCCCCCCCCCC
Q 001821 359 RPKFPKQPGMP 369 (1009)
Q Consensus 359 ~~Kr~r~~~~~ 369 (1009)
.-|+.+..|+.
T Consensus 72 sgkklksegfd 82 (422)
T PF13388_consen 72 SGKKLKSEGFD 82 (422)
T ss_pred cccccccchhh
Confidence 34445444443
No 18
>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=37.03 E-value=43 Score=26.31 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=22.8
Q ss_pred hhhccCCCCCCCeEEEEEccCCcEEEE
Q 001821 186 VFVSTKRLFAGDSVLFIRDEKSQLLLG 212 (1009)
Q Consensus 186 ~FVr~KkLvaGDsVVF~R~e~GeL~VG 212 (1009)
.|.+.-++..||.|.+...++|.+.+.
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 677899999999999998878876654
No 19
>PRK03760 hypothetical protein; Provisional
Probab=36.99 E-value=59 Score=32.15 Aligned_cols=48 Identities=21% Similarity=0.429 Sum_probs=29.8
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCeEEEEEc
Q 001821 154 EIVARDLHDTTWTFRH-----IYR-GQPKRHLL--TTGWSVFVSTKRLFAGDSVLFIRD 204 (1009)
Q Consensus 154 ~LvakDlhGk~W~FRh-----iyR-g~prRhlL--TTGWS~FVr~KkLvaGDsVVF~R~ 204 (1009)
++++.|.+|++-.... +|. ..+-+|+| ..||. ...++++||.|.|.|+
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 3555565555433211 122 23456777 57765 7889999999998774
No 20
>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=34.54 E-value=55 Score=30.92 Aligned_cols=57 Identities=23% Similarity=0.330 Sum_probs=31.2
Q ss_pred chHhHhHHHhcCccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001821 267 PLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 330 (1009)
Q Consensus 267 p~~ky~~Am~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~~ 330 (1009)
..+.|-.=+.-++.+||++||.=.-||-. .-=.|+|..++. | .-|+ -.++|.|...+
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 1121 24788887765
No 21
>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=33.79 E-value=1.9e+02 Score=29.07 Aligned_cols=74 Identities=15% Similarity=0.258 Sum_probs=51.5
Q ss_pred EeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccCCC
Q 001821 117 KTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTKRL 193 (1009)
Q Consensus 117 KtLT~SDVs~~GrfsVPkr~AE~~FPpLD~s~~~psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVr~KkL 193 (1009)
-+.|..|..-.|.+.|..+.++. -+.- |...+.+.|. +|..|+- |.+.|.+ +.-.|.+. -.+..
T Consensus 12 atVT~a~L~YeGSitID~~Ll~a----agi~---~~E~V~I~Nv~NG~Rf~T-YvI~g~~gSg~I~lNGA-----AAr~~ 78 (111)
T cd06919 12 ATVTEADLNYEGSITIDEDLLEA----AGIL---PYEKVLVVNVNNGARFET-YVIPGERGSGVICLNGA-----AARLG 78 (111)
T ss_pred eEEeccccccceeEEECHHHHHh----cCCC---CCCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HHhcC
Confidence 46788999889999999987765 2221 3345778886 5888875 6667754 33344333 56778
Q ss_pred CCCCeEEEEE
Q 001821 194 FAGDSVLFIR 203 (1009)
Q Consensus 194 vaGDsVVF~R 203 (1009)
..||.|+++-
T Consensus 79 ~~GD~vII~s 88 (111)
T cd06919 79 QPGDRVIIMA 88 (111)
T ss_pred CCCCEEEEEE
Confidence 8999999863
No 22
>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=33.62 E-value=57 Score=27.04 Aligned_cols=52 Identities=12% Similarity=0.169 Sum_probs=37.1
Q ss_pred CccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCcccCccccc
Q 001821 278 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 346 (1009)
Q Consensus 278 ~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~~RVSPWEIEpv 346 (1009)
.|.+|..+...| .+ ..||.|+|+++.. + ....|.-++-+.. +-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~-------~---~~~~V~f~D~G~~---~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDG-------E---QLYEVFFIDYGNE---EVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECC-------C---CEEEEEEECCCcc---EEEeHHHeecC
Confidence 588999999998 32 6899999999963 2 4567888775533 45555555554
No 23
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=32.41 E-value=1.9e+02 Score=30.99 Aligned_cols=66 Identities=20% Similarity=0.306 Sum_probs=46.2
Q ss_pred chHHHHHHHHhcCCcEEEEEcCCCCCCcc------ccchHhHhHHHhcCccccceeeeeeeeccCccceeeeEEEEecc
Q 001821 236 GILAAAAHAAANNSPFTIFYNPRASPSEF------VIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 308 (1009)
Q Consensus 236 gvLaaAa~aaa~~~~F~V~Y~PRas~sEF------VVp~~ky~~Am~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d 308 (1009)
.-|.+|..-..-|..|+|.--|-..-.|+ .||+++|...= ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 44 ~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 44 PGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDLVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred hhHHHHHhCCCCCceeEEEeCchHhcCCCChHHeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 34677888888899999998886544443 46666665432 6889999875 4444 446799999974
No 24
>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=30.87 E-value=49 Score=32.70 Aligned_cols=26 Identities=31% Similarity=0.526 Sum_probs=17.5
Q ss_pred CCCCCCCeEEEEEcc-CCcEEEEEEec
Q 001821 191 KRLFAGDSVLFIRDE-KSQLLLGIRRA 216 (1009)
Q Consensus 191 KkLvaGDsVVF~R~e-~GeL~VGIRRA 216 (1009)
++++.||.|+||... .+.-+|||=|-
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 25
>PRK14699 replication factor A; Provisional
Probab=30.71 E-value=1.5e+02 Score=35.92 Aligned_cols=65 Identities=14% Similarity=0.258 Sum_probs=44.0
Q ss_pred CCceeEEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc
Q 001821 110 QPTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS 189 (1009)
Q Consensus 110 ~~~~~F~KtLT~SDVs~~GrfsVPkr~AE~~FPpLD~s~~~psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr 189 (1009)
..+.++.|+|+.+++.+ |-..|++ ..-...+.+.|..| +.|++.|... -..+.
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 5677777521 13344
Q ss_pred cCCCCCCCeEEE
Q 001821 190 TKRLFAGDSVLF 201 (1009)
Q Consensus 190 ~KkLvaGDsVVF 201 (1009)
+-+|++||+|.+
T Consensus 121 ~g~l~~GDvv~I 132 (484)
T PRK14699 121 AGKIKAGQTLQI 132 (484)
T ss_pred hcCCCCCCEEEE
Confidence 557999999987
No 26
>CHL00010 infA translation initiation factor 1
Probab=30.44 E-value=2.4e+02 Score=26.03 Aligned_cols=51 Identities=16% Similarity=0.090 Sum_probs=28.2
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc-cCCCCCCCeEEEEE--ccCCcEEEEEEeccC
Q 001821 154 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS-TKRLFAGDSVLFIR--DEKSQLLLGIRRANR 218 (1009)
Q Consensus 154 ~LvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr-~KkLvaGDsVVF~R--~e~GeL~VGIRRA~r 218 (1009)
.+.+++..|+ .+.|..||. |.+ ..++.+||.|.|.- .++++-+|-.|-.++
T Consensus 21 ~y~V~~~~g~--~~~c~~rGk------------lr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 21 MFRVRLDNGC--QVLGYISGK------------IRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEeCCCC--EEEEEeccc------------eecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 3555666665 344445542 222 34578999999984 344444554444443
No 27
>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=30.37 E-value=2.5e+02 Score=28.86 Aligned_cols=72 Identities=13% Similarity=0.270 Sum_probs=50.8
Q ss_pred EeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccC
Q 001821 117 KTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTK 191 (1009)
Q Consensus 117 KtLT~SDVs~~GrfsVPkr~AE~--~FPpLD~s~~~psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVr~K 191 (1009)
-+.|..|..-.|.+.|-.+.++. ++| ...+.+.|. +|..|+- |.+.|.+ +.-.|. | .-.+
T Consensus 13 atVT~a~L~Y~GSItID~~Lm~aagi~p---------~E~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~lN-G----AAAr 77 (126)
T TIGR00223 13 ATVTHANLNYEGSITIDEDLLDAAGILE---------NEKVDIVNVNNGKRFST-YAIAGKRGSRIICVN-G----AAAR 77 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeC-C----HHHh
Confidence 46788899888999999987665 333 335777786 5888886 6667754 333343 3 2566
Q ss_pred CCCCCCeEEEEE
Q 001821 192 RLFAGDSVLFIR 203 (1009)
Q Consensus 192 kLvaGDsVVF~R 203 (1009)
....||.|+++=
T Consensus 78 l~~~GD~VII~s 89 (126)
T TIGR00223 78 CVSVGDIVIIAS 89 (126)
T ss_pred cCCCCCEEEEEE
Confidence 778999999863
No 28
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=28.52 E-value=2.7e+02 Score=28.54 Aligned_cols=72 Identities=14% Similarity=0.272 Sum_probs=51.1
Q ss_pred EeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCCCc--eeecccchhhhccC
Q 001821 117 KTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQPKR--HLLTTGWSVFVSTK 191 (1009)
Q Consensus 117 KtLT~SDVs~~GrfsVPkr~AE~--~FPpLD~s~~~psq~LvakDl-hGk~W~FRhiyRg~prR--hlLTTGWS~FVr~K 191 (1009)
-+.|..|..-.|.+.|-.+.++. ++| ...+.+.|. +|..|+- |.+.|.+.. -.|.+. -.+
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~NG~Rf~T-YvI~g~~GSg~I~lNGA-----AAr 77 (126)
T PRK05449 13 ATVTEADLNYEGSITIDEDLLDAAGILE---------NEKVQIVNVNNGARFET-YVIAGERGSGVICLNGA-----AAR 77 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HHh
Confidence 46788999888999999987776 333 335777786 5888876 666775433 334333 567
Q ss_pred CCCCCCeEEEEE
Q 001821 192 RLFAGDSVLFIR 203 (1009)
Q Consensus 192 kLvaGDsVVF~R 203 (1009)
....||.|+++=
T Consensus 78 ~~~~GD~vII~a 89 (126)
T PRK05449 78 LVQVGDLVIIAA 89 (126)
T ss_pred cCCCCCEEEEEE
Confidence 788999999763
No 29
>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=28.42 E-value=2.4e+02 Score=28.52 Aligned_cols=71 Identities=15% Similarity=0.326 Sum_probs=44.2
Q ss_pred EeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccC
Q 001821 117 KTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTK 191 (1009)
Q Consensus 117 KtLT~SDVs~~GrfsVPkr~AE~--~FPpLD~s~~~psq~LvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVr~K 191 (1009)
-+.|..|..-.|.+.|..+.++. ++| ...+.+.+. +|..|.- |.+.|.+ +.-.|.+. -.+
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~aagi~p---------~E~V~V~Nv~nG~Rf~T-YvI~g~~GSg~I~lNGa-----AAr 77 (116)
T PF02261_consen 13 ATVTEADLNYEGSITIDEDLLDAAGILP---------YEQVQVVNVNNGERFET-YVIPGERGSGVICLNGA-----AAR 77 (116)
T ss_dssp EE--EEETTSTSCEEEEHHHHHHCT--T---------TBEEEEEETTT--EEEE-EEEEESTTTT-EEEEGG-----GGG
T ss_pred eEEeccccccceeeEECHHHHHHcCCCc---------CCEEEEEECCCCcEEEE-EEEEccCCCcEEEECCH-----HHh
Confidence 46888999999999999987665 344 335777776 5898886 5666654 33344333 567
Q ss_pred CCCCCCeEEEE
Q 001821 192 RLFAGDSVLFI 202 (1009)
Q Consensus 192 kLvaGDsVVF~ 202 (1009)
...+||.|+++
T Consensus 78 l~~~GD~vII~ 88 (116)
T PF02261_consen 78 LVQVGDRVIIM 88 (116)
T ss_dssp CS-TT-EEEEE
T ss_pred ccCCCCEEEEE
Confidence 78899999985
No 30
>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=27.68 E-value=2.8e+02 Score=24.84 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=33.5
Q ss_pred CceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE----ccCCcEEEEEEe
Q 001821 151 PAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR----DEKSQLLLGIRR 215 (1009)
Q Consensus 151 psq~LvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr~KkLvaGDsVVF~R----~e~GeL~VGIRR 215 (1009)
....+.+.|..| ..++.+|+..- ...|..||.|.+.. .-+|.+.+.+.+
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 456788999998 57788886321 34588999888762 235666666554
No 31
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=25.15 E-value=2.3e+02 Score=28.33 Aligned_cols=79 Identities=22% Similarity=0.305 Sum_probs=52.6
Q ss_pred CCeEEEEEccCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcC-CC--CCCccccchHhHh
Q 001821 196 GDSVLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNP-RA--SPSEFVIPLAKYN 272 (1009)
Q Consensus 196 GDsVVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLaaAa~aaa~~~~F~V~Y~P-Ra--s~sEFVVp~~ky~ 272 (1009)
|..|+=-+++||.++.|.-++.- +...|.|.|+- +. -..+|||...
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 55666666789999988765432 34566777722 21 1356677655
Q ss_pred HHHhcCccccceeeeeeeeccCccceeeeEEEEec
Q 001821 273 KAMYTQVSLGMRFRMMFETEESGVRRYMGTITSIS 307 (1009)
Q Consensus 273 ~Am~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~ 307 (1009)
.|+.+...+|+.+-+..|.. ..++.=|||++.-
T Consensus 50 ~~~~~~L~~GD~VLA~~~~~--~~~Y~Pg~V~~~~ 82 (124)
T PF15057_consen 50 DAMRHSLQVGDKVLAPWEPD--DCRYGPGTVIAGP 82 (124)
T ss_pred CcccCcCCCCCEEEEecCcC--CCEEeCEEEEECc
Confidence 56689999999999996543 2346669999753
No 32
>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=24.46 E-value=1e+02 Score=27.00 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=23.9
Q ss_pred ccceeeeeeeeccCccceeeeEEEEeccCCC
Q 001821 281 LGMRFRMMFETEESGVRRYMGTITSISDLDP 311 (1009)
Q Consensus 281 ~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP 311 (1009)
+|-|+.-.||.++.+...|.|+|..--+..|
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 5889999999998888888999999876654
No 33
>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=23.39 E-value=2.6e+02 Score=25.01 Aligned_cols=58 Identities=16% Similarity=0.051 Sum_probs=41.3
Q ss_pred ccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeeeccCc
Q 001821 232 SMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 295 (1009)
Q Consensus 232 sm~~gvLaaAa~aaa~-~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~FEtEdss 295 (1009)
.+|.-..+.-++.|.+ .+.++|.|. ...|.+..+..-|...+..|+++...++++|..
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 4554433333344333 455666664 458999999999999999999999999988753
No 34
>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=23.38 E-value=56 Score=30.34 Aligned_cols=41 Identities=17% Similarity=0.410 Sum_probs=21.7
Q ss_pred ceEEEEEeCCC-CeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE
Q 001821 152 AQEIVARDLHD-TTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR 203 (1009)
Q Consensus 152 sq~LvakDlhG-k~W~FRhiyRg~prRhlLTTGWS~FVr~KkLvaGDsVVF~R 203 (1009)
.-+|.++|..| ++|+| +....|| .-..+..|.+|++++|--
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 45899999888 46665 3334444 445678899999999864
No 35
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=22.38 E-value=1.4e+02 Score=28.91 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=27.0
Q ss_pred eEEEEEeCCCCeEEEEEEEe---------CCCCceee--cccchhhhccCCCCCCCeEEE
Q 001821 153 QEIVARDLHDTTWTFRHIYR---------GQPKRHLL--TTGWSVFVSTKRLFAGDSVLF 201 (1009)
Q Consensus 153 q~LvakDlhGk~W~FRhiyR---------g~prRhlL--TTGWS~FVr~KkLvaGDsVVF 201 (1009)
.++++.|..|++=....... ..+-+|+| ..| ++...+|++||.|.|
T Consensus 50 LDi~fld~~g~Vv~i~~~~~P~~~~~~~~~~~a~~vLE~~aG---~~~~~~i~~Gd~v~~ 106 (108)
T PF02643_consen 50 LDIAFLDSDGRVVKIERMVPPWRTYPCPSYKPARYVLELPAG---WFEKLGIKVGDRVRI 106 (108)
T ss_dssp EEEEEE-TTSBEEEEEEEE-TT--S-EEECCEECEEEEEETT---HHHHHT--TT-EEE-
T ss_pred EEEEEECCCCeEEEEEccCCCCccCCCCCCCccCEEEEcCCC---chhhcCCCCCCEEEe
Confidence 45788888887655554441 12346787 455 458899999999987
No 36
>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=22.35 E-value=70 Score=35.62 Aligned_cols=56 Identities=20% Similarity=0.249 Sum_probs=32.1
Q ss_pred hcCccccceeeeeeeeccCccceeeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCcccCccccc
Q 001821 276 YTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 346 (1009)
Q Consensus 276 ~~~ws~GMRFKM~FEtEdss~r~y~GTI~gv~d~DP~rWp~S~WR~LqV~WDE~~~~~~~~RVSPWEIEpv 346 (1009)
...|.+|++.+..|..| ..+|.+||++|..-+- .| .|+.++=+ +.+.|..=+|.+.
T Consensus 66 ~~~WkvGd~C~A~~s~D---g~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~ 121 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSED---GQYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPS 121 (264)
T ss_dssp TT---TT-EEEEE-TTT---SSEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEET
T ss_pred ccCCCCCCEEEEEECCC---CCEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhccc
Confidence 46899999999999533 4699999999975221 23 37776643 2244544444444
No 37
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=21.90 E-value=58 Score=29.56 Aligned_cols=27 Identities=22% Similarity=0.204 Sum_probs=13.0
Q ss_pred ccchhhhccCCCCCCCeEEEEEccCCcEEE
Q 001821 182 TGWSVFVSTKRLFAGDSVLFIRDEKSQLLL 211 (1009)
Q Consensus 182 TGWS~FVr~KkLvaGDsVVF~R~e~GeL~V 211 (1009)
.|=...-|.++|++||.|.| ++..+.|
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 4444544
No 38
>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=21.19 E-value=1.9e+02 Score=26.32 Aligned_cols=60 Identities=17% Similarity=0.105 Sum_probs=44.3
Q ss_pred CCccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeeeccCc
Q 001821 230 SDSMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 295 (1009)
Q Consensus 230 sdsm~~gvLaaAa~aaa~-~~~F~V~Y~PRas~sEFVVp~~ky~~Am~~~ws~GMRFKM~FEtEdss 295 (1009)
...+|.-..+.-+++|.+ ++.++|.|.- -.|++..+..-|......|+.++..+|++|..
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 58999999999999999999999999998864
No 39
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=21.10 E-value=1.4e+02 Score=23.40 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=21.6
Q ss_pred CCCCceeechhhhhhcCCCCCCCCCCCceEEEEE-eCCCCe
Q 001821 125 STHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVAR-DLHDTT 164 (1009)
Q Consensus 125 s~~GrfsVPkr~AE~~FPpLD~s~~~psq~Lvak-DlhGk~ 164 (1009)
+..|+++||++..+. ++.. ++..+.+. +.+|..
T Consensus 4 ~~kgri~iP~~~r~~----l~~~---~gd~~~i~~~~~~~l 37 (43)
T TIGR01439 4 DKKGQIVIPKEIREK----LGLK---EGDRLEVIRVEDGEI 37 (43)
T ss_pred CcCCeEEecHHHHHH----cCcC---CCCEEEEEEeCCCEE
Confidence 346899999999988 5544 23456666 445543
No 40
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=20.33 E-value=66 Score=30.41 Aligned_cols=34 Identities=21% Similarity=0.385 Sum_probs=22.2
Q ss_pred hhhhccCCCCCCCeEEEEEccCCc-EEEEEEeccC
Q 001821 185 SVFVSTKRLFAGDSVLFIRDEKSQ-LLLGIRRANR 218 (1009)
Q Consensus 185 S~FVr~KkLvaGDsVVF~R~e~Ge-L~VGIRRA~r 218 (1009)
..|+++++|..||.|.++|.++.= ..+++-...|
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~~~r 76 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVKEKR 76 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-GGG-
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeehhcC
Confidence 378999999999999999986543 3445544443
Done!