Query 012439
Match_columns 463
No_of_seqs 294 out of 516
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:39:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012439.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012439hhsearch_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 8.5E-37 1.8E-41 254.3 8.4 83 263-345 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 2.7E-18 5.9E-23 143.4 11.5 97 137-238 1-99 (100)
3 KOG0644 Uncharacterized conser 99.5 1.1E-14 2.3E-19 159.6 5.8 148 215-369 874-1044(1113)
4 PF09217 EcoRII-N: Restriction 98.2 1E-05 2.2E-10 75.0 9.2 89 134-224 7-110 (156)
5 PF03754 DUF313: Domain of unk 97.9 2E-05 4.4E-10 70.0 5.9 77 135-212 22-114 (114)
6 PRK10737 FKBP-type peptidyl-pr 69.9 16 0.00036 35.5 7.2 104 214-330 2-114 (196)
7 KOG0644 Uncharacterized conser 63.8 4 8.8E-05 47.4 1.9 65 40-104 871-940 (1113)
8 PF04014 Antitoxin-MazE: Antid 62.2 13 0.00028 27.6 3.8 27 208-234 14-40 (47)
9 smart00743 Agenet Tudor-like d 60.7 15 0.00031 28.3 4.0 28 300-330 2-29 (61)
10 TIGR01439 lp_hng_hel_AbrB loop 49.9 28 0.00061 24.5 3.8 26 208-233 14-39 (43)
11 KOG3207 Beta-tubulin folding c 48.1 26 0.00056 38.5 4.7 42 301-356 3-44 (505)
12 PF10844 DUF2577: Protein of u 45.9 30 0.00065 29.9 4.0 27 209-235 71-97 (100)
13 PF02513 Spin-Ssty: Spin/Ssty 44.8 36 0.00078 26.6 3.8 31 303-333 1-31 (50)
14 PF05641 Agenet: Agenet domain 44.0 48 0.001 26.5 4.6 40 301-350 1-40 (68)
15 PRK03760 hypothetical protein; 34.1 94 0.002 27.8 5.4 48 176-226 62-117 (117)
16 PF11302 DUF3104: Protein of u 32.3 1E+02 0.0022 26.0 4.9 41 301-346 6-51 (75)
17 PF01878 EVE: EVE domain; Int 31.6 50 0.0011 29.6 3.2 26 213-238 38-64 (143)
18 smart00333 TUDOR Tudor domain. 31.2 85 0.0018 23.3 4.0 52 300-368 2-54 (57)
19 COG1430 Uncharacterized conser 28.4 1.1E+02 0.0025 27.9 5.0 50 175-227 64-123 (126)
20 COG1047 SlpA FKBP-type peptidy 28.0 3.5E+02 0.0076 26.2 8.4 106 213-330 1-115 (174)
21 PF03120 DNA_ligase_OB: NAD-de 26.1 57 0.0012 27.7 2.4 31 207-237 42-73 (82)
22 PF04225 OapA: Opacity-associa 23.7 64 0.0014 27.2 2.3 18 214-231 42-59 (85)
23 PF11604 CusF_Ec: Copper bindi 21.8 1.4E+02 0.0031 24.1 3.9 27 212-238 40-69 (70)
24 cd04451 S1_IF1 S1_IF1: Transla 21.8 3.6E+02 0.0079 20.9 6.2 38 176-226 15-52 (64)
25 PF02643 DUF192: Uncharacteriz 21.6 2E+02 0.0043 25.0 5.1 46 175-223 50-106 (108)
26 PF13275 S4_2: S4 domain; PDB: 21.5 59 0.0013 26.5 1.6 18 206-223 40-57 (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=8.5e-37 Score=254.33 Aligned_cols=83 Identities=59% Similarity=1.035 Sum_probs=81.8
Q ss_pred HHHHHHcCCceEEEEeCCCCCCceeEehhhHhhhcCCCcccCCeEEEEeeccccccceeeeEEEEeecCCCCCCCCCCce
Q 012439 263 VVDAIARKRAFSISYNPRASASEFVIPVNKFLKSLDHPFAEGMRFKMRSETEDAAEQRCSGLIVGVSDMDPVRWPGSKWR 342 (463)
Q Consensus 263 a~~a~~tg~~F~V~Y~Pr~~~~EFvVp~~ky~~a~~~~w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~~dp~~Wp~S~WR 342 (463)
|+||+++|++|+|+||||++++|||||++||++||+++|++||||||+||+||+++++|+|||+||++.||++||+|+||
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 012439 343 CLL 345 (463)
Q Consensus 343 ~L~ 345 (463)
|||
T Consensus 81 ~Lq 83 (83)
T PF06507_consen 81 MLQ 83 (83)
T ss_pred cCc
Confidence 997
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=2.7e-18 Score=143.44 Aligned_cols=97 Identities=32% Similarity=0.483 Sum_probs=74.8
Q ss_pred EEEeccccCCCCCCceeeeccchhhcCCCCCcCCCCCceEEEEEeCCCCEEEEEEEEeCCCCceeeccchhHHHhhcCCC
Q 012439 137 FCKTLTASDTSTCGGFSVPRRAAEDCFPPLDYMQQRPSQQLVAKDLHGVEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLV 216 (463)
Q Consensus 137 F~K~LT~SDv~~~grfsVPk~~Ae~~FP~Ld~~~~~p~q~L~~~D~~G~~W~Fr~~yrg~prr~lLTtGWs~FV~~K~L~ 216 (463)
|.|+|++||+.+.++|.||+++++.+.. + ...++++.++|..|++|.+++.+++.+++++|++||..||++++|+
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~--~---~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~ 75 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGG--N---KRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLK 75 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS-------SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCC--C---cCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCC
Confidence 8999999999999999999999999721 1 1235789999999999999999998888899999999999999999
Q ss_pred CCCEEEEEecCC--CcEEEEEEEc
Q 012439 217 SGDAVLFLRGED--GELKIGIRRA 238 (463)
Q Consensus 217 aGD~VvF~R~~~--G~l~VgIRRa 238 (463)
+||.|+|+...+ .++.|.|+|+
T Consensus 76 ~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 76 EGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CCCEEEEEEecCCCceEEEEEEEC
Confidence 999999998754 5569999986
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.51 E-value=1.1e-14 Score=159.62 Aligned_cols=148 Identities=18% Similarity=0.339 Sum_probs=117.5
Q ss_pred CCCCCEEEEEecCCCcEEEEEEEcccccCC-------------------C--CCCcccCCCCCCccHHHHHHHHHcCCce
Q 012439 215 LVSGDAVLFLRGEDGELKIGIRRAAQVKNG-------------------A--TFPSFCNQHSSTSSVTEVVDAIARKRAF 273 (463)
Q Consensus 215 L~aGD~VvF~R~~~G~l~VgIRRa~~~~~~-------------------~--~~~~~~~~~~~~~~l~~a~~a~~tg~~F 273 (463)
.+.||.|+.+|....++.-.+|+.+.-.++ . |-+..+.-.|.+.++.-|.++. ...|
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 458999999998776665555554332111 0 1122222346777888888554 5679
Q ss_pred EEEEeCCCCCCceeEehhhHhhhcCCCcccCCeEEEEeecc--ccccceeeeEEEEeecCCCCCCCCCCceeeEEeecCC
Q 012439 274 SISYNPRASASEFVIPVNKFLKSLDHPFAEGMRFKMRSETE--DAAEQRCSGLIVGVSDMDPVRWPGSKWRCLLVRWDDV 351 (463)
Q Consensus 274 ~V~Y~Pr~~~~EFvVp~~ky~~a~~~~w~~GmRFkM~fE~E--Ds~e~r~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~ 351 (463)
.+.|+.....+||+|.++.|++|++++|..+++||.-+..+ +. -.||.|+|.++.+.+| .+|+|+|+|+.|+||..
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 99999999999999999999999999999999999999522 21 2399999999999999 99999999999999998
Q ss_pred CCCCCCCccccceeecCC
Q 012439 352 ESNRHNRVSPWEIEPSGS 369 (463)
Q Consensus 352 ~~~~~~RVSPWeIEpv~~ 369 (463)
|+ +.-||||.|++..
T Consensus 1030 e~---~~~spwe~~~i~d 1044 (1113)
T KOG0644|consen 1030 ET---ELHSPWEMEPIPD 1044 (1113)
T ss_pred cc---cccCccccCCCcc
Confidence 87 6789999999987
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=98.16 E-value=1e-05 Score=74.98 Aligned_cols=89 Identities=26% Similarity=0.384 Sum_probs=59.3
Q ss_pred cceEEEeccccCCCCCC----ceeeeccchhhcCCCCCc-CCCCCceEEEEEeCCC--CEEEEEEEEeCC------CCce
Q 012439 134 PHMFCKTLTASDTSTCG----GFSVPRRAAEDCFPPLDY-MQQRPSQQLVAKDLHG--VEWKFRHIYRGQ------PRRH 200 (463)
Q Consensus 134 ~~~F~K~LT~SDv~~~g----rfsVPk~~Ae~~FP~Ld~-~~~~p~q~L~~~D~~G--~~W~Fr~~yrg~------prr~ 200 (463)
-..|+|.|++.|++..| |+.|||..++..||.+.. +...|...|.+++..| ..|+||++|.++ .+.+
T Consensus 7 ~~~~~K~LSaNDtGaTGgHQaGiyIpk~~~~~lFp~~~~~~~~Np~~~~~~~~~s~~~~~~~~r~iYYnn~~~~gTRNE~ 86 (156)
T PF09217_consen 7 WAIYCKRLSANDTGATGGHQAGIYIPKSAAELLFPSINHTKEENPDIWLKARWQSHFVTDSQVRFIYYNNRLFGGTRNEY 86 (156)
T ss_dssp EEEEEEE--CCCCTTTSSS--EEEE-HHHHHHH-GGG-SSSSSS-EEEEEEEETTTT---EEEEEEEE-CCCTTSS--EE
T ss_pred eEEEEEEccCCCCCCcCcccceeEecccHHHHhCCCCCcccccCCceeEEEEECCCCccceeEEEEEEcccccCCCcCce
Confidence 45899999999999765 799999999999998765 5566899999999888 569999999976 5567
Q ss_pred eec--cchhHHHhhcCCCCCCEEEEE
Q 012439 201 LLT--TGWSAFVNKKKLVSGDAVLFL 224 (463)
Q Consensus 201 lLT--tGWs~FV~~K~L~aGD~VvF~ 224 (463)
-|| ++=..|.+. =..||-+||.
T Consensus 87 RIT~~G~~~~~~~~--~~tGaL~vla 110 (156)
T PF09217_consen 87 RITRFGRGFPLQNP--ENTGALLVLA 110 (156)
T ss_dssp EEE---TTSGGG-G--GGTT-EEEEE
T ss_pred EEeeecCCCccCCc--cccccEEEEE
Confidence 776 332333332 2478888887
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=97.90 E-value=2e-05 Score=69.95 Aligned_cols=77 Identities=19% Similarity=0.270 Sum_probs=61.0
Q ss_pred ceEEEeccccCCCCC-CceeeeccchhhcCCCCCc------------CCCCCceEEEEEeCCCCEEEEEEEEeCC---CC
Q 012439 135 HMFCKTLTASDTSTC-GGFSVPRRAAEDCFPPLDY------------MQQRPSQQLVAKDLHGVEWKFRHIYRGQ---PR 198 (463)
Q Consensus 135 ~~F~K~LT~SDv~~~-grfsVPk~~Ae~~FP~Ld~------------~~~~p~q~L~~~D~~G~~W~Fr~~yrg~---pr 198 (463)
..|+|+|++||+..+ .||+||-..... ...|.. .....++.+.+.|..++.|..++..|.. ..
T Consensus 22 li~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~ 100 (114)
T PF03754_consen 22 LIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTS 100 (114)
T ss_pred EEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCce
Confidence 589999999999965 799999876633 233321 1244678899999999999999999965 56
Q ss_pred ceeeccchhHHHhh
Q 012439 199 RHLLTTGWSAFVNK 212 (463)
Q Consensus 199 r~lLTtGWs~FV~~ 212 (463)
.|+|++||..+|.+
T Consensus 101 ~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 101 NYVLNSGWNKVVED 114 (114)
T ss_pred EEEEEcChHhhccC
Confidence 79999999999864
No 6
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=69.89 E-value=16 Score=35.53 Aligned_cols=104 Identities=20% Similarity=0.217 Sum_probs=62.8
Q ss_pred CCCCCCEEEEE---ecCCCcEEEEEEEcccccCCCCCCcccCCCCCCccHHHHHHHHHcCCceEEEEeCCC------CCC
Q 012439 214 KLVSGDAVLFL---RGEDGELKIGIRRAAQVKNGATFPSFCNQHSSTSSVTEVVDAIARKRAFSISYNPRA------SAS 284 (463)
Q Consensus 214 ~L~aGD~VvF~---R~~~G~l~VgIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~tg~~F~V~Y~Pr~------~~~ 284 (463)
++..|+.|.+. |.++|+++-.-+ ...|...+-....-...|.+|..-...|..|+|..-|-. ...
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~------~~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP------VSAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC------CCCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 35567777762 345677533211 012222222223334567777777888999999865543 223
Q ss_pred ceeEehhhHhhhcCCCcccCCeEEEEeeccccccceeeeEEEEeec
Q 012439 285 EFVIPVNKFLKSLDHPFAEGMRFKMRSETEDAAEQRCSGLIVGVSD 330 (463)
Q Consensus 285 EFvVp~~ky~~a~~~~w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~ 330 (463)
-..||++.|.... ...+||||.+. +++. ...++|+.|.+
T Consensus 76 V~~vpr~~F~~~~--~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGVD--ELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCcc--CCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 4678888885322 36899998874 4554 35788888865
No 7
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=63.82 E-value=4 Score=47.36 Aligned_cols=65 Identities=22% Similarity=0.319 Sum_probs=45.3
Q ss_pred cCCCCCCCeEEEecCcccccccccccccccC-CCCCCc----eeEEEEeeeecccCCCcceeeeeeeecc
Q 012439 40 ISLPKRGSVVVYFPQGHLEHVSDFSAAASAA-YDIPPH----LFCRVADVKLHADAASDEVYAQVSLVHD 104 (463)
Q Consensus 40 v~lP~~gs~V~YFPqGH~Eq~~~~~~~~~~~-~~lP~~----i~CrV~~V~l~Ad~~TDEVyA~i~L~P~ 104 (463)
--||.+|+.|.||-|||-|-+.+..-..... -..|.. =.|.|..+..--=+..+.--.+|.|.=.
T Consensus 871 ryipQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~i 940 (1113)
T KOG0644|consen 871 RYIPQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVI 940 (1113)
T ss_pred cccccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeee
Confidence 3689999999999999999988764311111 123332 3588888877766777777777777644
No 8
>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=62.19 E-value=13 Score=27.55 Aligned_cols=27 Identities=30% Similarity=0.319 Sum_probs=22.9
Q ss_pred HHHhhcCCCCCCEEEEEecCCCcEEEE
Q 012439 208 AFVNKKKLVSGDAVLFLRGEDGELKIG 234 (463)
Q Consensus 208 ~FV~~K~L~aGD~VvF~R~~~G~l~Vg 234 (463)
.|....+|.+||.|.|.-.++|++.+-
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 678888999999999999998865543
No 9
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=60.70 E-value=15 Score=28.29 Aligned_cols=28 Identities=25% Similarity=0.372 Sum_probs=23.7
Q ss_pred CcccCCeEEEEeeccccccceeeeEEEEeec
Q 012439 300 PFAEGMRFKMRSETEDAAEQRCSGLIVGVSD 330 (463)
Q Consensus 300 ~w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~ 330 (463)
.|++|+++-..++.+++ ||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~~~~---W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDS---WWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCE---EEEEEEEEECC
Confidence 58899999999975454 99999999875
No 10
>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=49.86 E-value=28 Score=24.54 Aligned_cols=26 Identities=35% Similarity=0.493 Sum_probs=22.4
Q ss_pred HHHhhcCCCCCCEEEEEecCCCcEEE
Q 012439 208 AFVNKKKLVSGDAVLFLRGEDGELKI 233 (463)
Q Consensus 208 ~FV~~K~L~aGD~VvF~R~~~G~l~V 233 (463)
.|.++-++..||.|.+....+|.+.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 78999999999999999877776654
No 11
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=48.06 E-value=26 Score=38.51 Aligned_cols=42 Identities=36% Similarity=0.587 Sum_probs=27.7
Q ss_pred cccCCeEEEEeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeecCCCCCCC
Q 012439 301 FAEGMRFKMRSETEDAAEQRCSGLIVGVSDMDPVRWPGSKWRCLLVRWDDVESNRH 356 (463)
Q Consensus 301 w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe~~~~~~ 356 (463)
..+|+|+|..++ -+..||.|+|.| |++ +| +.|.||++.-..+
T Consensus 3 ~~IG~RvkI~~~---~~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH 44 (505)
T KOG3207|consen 3 MEIGTRVKIGGE---IATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKH 44 (505)
T ss_pred eeccceEEEcCE---EEEEEEEEEEcC--------CCC-cc--eeeEecCCCcccc
Confidence 468999998765 123356665543 555 55 8899999665443
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=45.85 E-value=30 Score=29.89 Aligned_cols=27 Identities=33% Similarity=0.419 Sum_probs=21.9
Q ss_pred HHhhcCCCCCCEEEEEecCCCcEEEEE
Q 012439 209 FVNKKKLVSGDAVLFLRGEDGELKIGI 235 (463)
Q Consensus 209 FV~~K~L~aGD~VvF~R~~~G~l~VgI 235 (463)
|.-...|++||.|..+|.++|..++=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 556678999999999998888766544
No 13
>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=44.84 E-value=36 Score=26.58 Aligned_cols=31 Identities=19% Similarity=0.357 Sum_probs=24.6
Q ss_pred cCCeEEEEeeccccccceeeeEEEEeecCCC
Q 012439 303 EGMRFKMRSETEDAAEQRCSGLIVGVSDMDP 333 (463)
Q Consensus 303 ~GmRFkM~fE~EDs~e~r~~GtI~gv~~~dp 333 (463)
+|-|+.-.||.++.+...|.|+|...-+..|
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 5889999999888887788999999988877
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=43.98 E-value=48 Score=26.46 Aligned_cols=40 Identities=20% Similarity=0.322 Sum_probs=26.1
Q ss_pred cccCCeEEEEeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeecC
Q 012439 301 FAEGMRFKMRSETEDAAEQRCSGLIVGVSDMDPVRWPGSKWRCLLVRWDD 350 (463)
Q Consensus 301 w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe 350 (463)
|.+|+++-..-+.+...--||.|+|+.....+ .+.|+.++
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~ 40 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDD 40 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECC
Confidence 46899999876543332239999999987643 78899987
No 15
>PRK03760 hypothetical protein; Provisional
Probab=34.07 E-value=94 Score=27.78 Aligned_cols=48 Identities=21% Similarity=0.381 Sum_probs=30.5
Q ss_pred EEEEEeCCCCEEEEEE-----EEe-CCCCceee--ccchhHHHhhcCCCCCCEEEEEec
Q 012439 176 QLVAKDLHGVEWKFRH-----IYR-GQPRRHLL--TTGWSAFVNKKKLVSGDAVLFLRG 226 (463)
Q Consensus 176 ~L~~~D~~G~~W~Fr~-----~yr-g~prr~lL--TtGWs~FV~~K~L~aGD~VvF~R~ 226 (463)
++++.|.+|++=.... +|. ..+-+|+| ..|| +.+.++++||.|.|.++
T Consensus 62 DiiFld~~g~Vv~i~~~~P~~~~~~~~~a~~VLEl~aG~---~~~~gi~~Gd~v~~~~~ 117 (117)
T PRK03760 62 DVIFLDSNRRVVDFKTLKPWRIYVPKKPARYIIEGPVGK---IRVLKVEVGDEIEWIDE 117 (117)
T ss_pred EEEEECCCCeEEEEEeCCCccccCCCccceEEEEeCCCh---HHHcCCCCCCEEEEeeC
Confidence 4566666555433211 122 23456776 6776 78999999999998763
No 16
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=32.27 E-value=1e+02 Score=25.99 Aligned_cols=41 Identities=17% Similarity=0.189 Sum_probs=29.4
Q ss_pred cccCCeEEEEeecccc---ccceeeeEEEEeec--CCCCCCCCCCceeeEE
Q 012439 301 FAEGMRFKMRSETEDA---AEQRCSGLIVGVSD--MDPVRWPGSKWRCLLV 346 (463)
Q Consensus 301 w~~GmRFkM~fE~EDs---~e~r~~GtI~gv~~--~dp~~Wp~S~WR~L~V 346 (463)
..+||-+-..=+.+.+ ++-||+|.|+.+.. -|| ..|..+||
T Consensus 6 Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P-----~~~tlFQV 51 (75)
T PF11302_consen 6 VKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDP-----KVPTLFQV 51 (75)
T ss_pred cCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCC-----CCCceEEE
Confidence 4678888776665443 33499999998864 466 56888887
No 17
>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=50 Score=29.61 Aligned_cols=26 Identities=23% Similarity=0.417 Sum_probs=17.4
Q ss_pred cCCCCCCEEEEEecC-CCcEEEEEEEc
Q 012439 213 KKLVSGDAVLFLRGE-DGELKIGIRRA 238 (463)
Q Consensus 213 K~L~aGD~VvF~R~~-~G~l~VgIRRa 238 (463)
++++.||.|+||... .+.-++|+=+-
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 499999999999987 56677777554
No 18
>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=31.16 E-value=85 Score=23.33 Aligned_cols=52 Identities=19% Similarity=0.235 Sum_probs=36.8
Q ss_pred CcccCCeEEEEeeccccccceeeeEEEEeecCCCCCCCCCCceeeEEeecC-CCCCCCCCccccceeecC
Q 012439 300 PFAEGMRFKMRSETEDAAEQRCSGLIVGVSDMDPVRWPGSKWRCLLVRWDD-VESNRHNRVSPWEIEPSG 368 (463)
Q Consensus 300 ~w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~~dp~~Wp~S~WR~L~V~WDe-~~~~~~~RVSPWeIEpv~ 368 (463)
+|.+|..+..++ .+. .||.|+|+++... ....|.-++ ... +-|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~d~---~wyra~I~~~~~~----------~~~~V~f~D~G~~---~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-EDG---EWYRARIIKVDGE----------QLYEVFFIDYGNE---EVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-CCC---CEEEEEEEEECCC----------CEEEEEEECCCcc---EEEeHHHeecCC
Confidence 588999999999 332 4999999999752 456788877 433 446666665543
No 19
>COG1430 Uncharacterized conserved protein [Function unknown]
Probab=28.45 E-value=1.1e+02 Score=27.93 Aligned_cols=50 Identities=22% Similarity=0.325 Sum_probs=33.4
Q ss_pred eEEEEEeCCCCEEEEEEE-------Ee-CCCCceee--ccchhHHHhhcCCCCCCEEEEEecC
Q 012439 175 QQLVAKDLHGVEWKFRHI-------YR-GQPRRHLL--TTGWSAFVNKKKLVSGDAVLFLRGE 227 (463)
Q Consensus 175 q~L~~~D~~G~~W~Fr~~-------yr-g~prr~lL--TtGWs~FV~~K~L~aGD~VvF~R~~ 227 (463)
.++.+.|.+|++=.-.+. +. .-+.+|+| ..|| ++.++++.||.|.|....
T Consensus 64 LDiiFid~dg~i~~i~~~~P~~~~~~~~~~~~~yvLEl~~G~---~~~~~i~vGd~v~~~~~~ 123 (126)
T COG1430 64 LDIIFIDSDGRVVDIVELVPWSTYPCKSYGPVRYVLELPAGW---AARLGIKVGDRVEFRPLG 123 (126)
T ss_pred eEEEEEcCCCCEEEEEeccccccCCCCCCCCccEEEEecCCc---hhhcCCccCCEEEecccC
Confidence 457888877765444331 11 12335776 6887 889999999999997543
No 20
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=27.98 E-value=3.5e+02 Score=26.19 Aligned_cols=106 Identities=21% Similarity=0.293 Sum_probs=65.2
Q ss_pred cCCCCCCEEEEE---ecCCCcEEEEEEEcccccCCCCCCcccCCCCCCccHHHHHHHHHcCCceEEEEeCCCCCCce---
Q 012439 213 KKLVSGDAVLFL---RGEDGELKIGIRRAAQVKNGATFPSFCNQHSSTSSVTEVVDAIARKRAFSISYNPRASASEF--- 286 (463)
Q Consensus 213 K~L~aGD~VvF~---R~~~G~l~VgIRRa~~~~~~~~~~~~~~~~~~~~~l~~a~~a~~tg~~F~V~Y~Pr~~~~EF--- 286 (463)
+++..||.|.+. |.++|++.=--.- ...|...+-.+..-..-|.+|..-..-|.-|+|.--|-..-.++
T Consensus 1 m~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~ 75 (174)
T COG1047 1 MKIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPD 75 (174)
T ss_pred CcccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChH
Confidence 356678888773 3455554321111 11223333333333456888888889999999998887544443
Q ss_pred ---eEehhhHhhhcCCCcccCCeEEEEeeccccccceeeeEEEEeec
Q 012439 287 ---VIPVNKFLKSLDHPFAEGMRFKMRSETEDAAEQRCSGLIVGVSD 330 (463)
Q Consensus 287 ---vVp~~ky~~a~~~~w~~GmRFkM~fE~EDs~e~r~~GtI~gv~~ 330 (463)
.||..+|...- ...+||+|.+ +++| .-.-|+|+.|..
T Consensus 76 lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 76 LVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred HeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 56777765543 6889999876 4444 355789988863
No 21
>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=26.14 E-value=57 Score=27.73 Aligned_cols=31 Identities=23% Similarity=0.387 Sum_probs=21.0
Q ss_pred hHHHhhcCCCCCCEEEEEecCCCc-EEEEEEE
Q 012439 207 SAFVNKKKLVSGDAVLFLRGEDGE-LKIGIRR 237 (463)
Q Consensus 207 s~FV~~K~L~aGD~VvF~R~~~G~-l~VgIRR 237 (463)
..|+++++|..||.|.++|..+.= ..+++-.
T Consensus 42 ~~~i~~~~i~~Gd~V~V~raGdVIP~I~~vv~ 73 (82)
T PF03120_consen 42 YDYIKELDIRIGDTVLVTRAGDVIPKIVGVVK 73 (82)
T ss_dssp HHHHHHTT-BBT-EEEEEEETTTEEEEEEE-G
T ss_pred HHHHHHcCCCCCCEEEEEECCCccceEeEeeh
Confidence 378999999999999999976643 3344433
No 22
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=23.72 E-value=64 Score=27.17 Aligned_cols=18 Identities=39% Similarity=0.674 Sum_probs=11.8
Q ss_pred CCCCCCEEEEEecCCCcE
Q 012439 214 KLVSGDAVLFLRGEDGEL 231 (463)
Q Consensus 214 ~L~aGD~VvF~R~~~G~l 231 (463)
+|++||.|.|..+++|+|
T Consensus 42 ~L~pGq~l~f~~d~~g~L 59 (85)
T PF04225_consen 42 RLKPGQTLEFQLDEDGQL 59 (85)
T ss_dssp G--TT-EEEEEE-TTS-E
T ss_pred hCCCCCEEEEEECCCCCE
Confidence 589999999999999985
No 23
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=21.85 E-value=1.4e+02 Score=24.11 Aligned_cols=27 Identities=33% Similarity=0.364 Sum_probs=15.9
Q ss_pred hcCCCCCCEEEEEe--cCCC-cEEEEEEEc
Q 012439 212 KKKLVSGDAVLFLR--GEDG-ELKIGIRRA 238 (463)
Q Consensus 212 ~K~L~aGD~VvF~R--~~~G-~l~VgIRRa 238 (463)
-.+|++||.|-|.- .++| -....|+++
T Consensus 40 l~~l~~Gd~V~F~~~~~~~~~~~I~~i~~~ 69 (70)
T PF11604_consen 40 LAGLKPGDKVRFTFERTDDGSYVITAIEPA 69 (70)
T ss_dssp ESS-STT-EEEEEEEEETTCEEEEEEEEE-
T ss_pred hhcCCCCCEEEEEEEECCCCcEEEEEEEEC
Confidence 36799999999964 4556 344555554
No 24
>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=21.82 E-value=3.6e+02 Score=20.94 Aligned_cols=38 Identities=18% Similarity=0.160 Sum_probs=22.5
Q ss_pred EEEEEeCCCCEEEEEEEEeCCCCceeeccchhHHHhhcCCCCCCEEEEEec
Q 012439 176 QLVAKDLHGVEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFLRG 226 (463)
Q Consensus 176 ~L~~~D~~G~~W~Fr~~yrg~prr~lLTtGWs~FV~~K~L~aGD~VvF~R~ 226 (463)
...+++..|. .++|..||+-++ +...+.+||.|.|...
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 3445666676 445555553220 2334899999999854
No 25
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=21.63 E-value=2e+02 Score=25.03 Aligned_cols=46 Identities=26% Similarity=0.399 Sum_probs=27.9
Q ss_pred eEEEEEeCCCCEEEEEEEEe---------CCCCceee--ccchhHHHhhcCCCCCCEEEE
Q 012439 175 QQLVAKDLHGVEWKFRHIYR---------GQPRRHLL--TTGWSAFVNKKKLVSGDAVLF 223 (463)
Q Consensus 175 q~L~~~D~~G~~W~Fr~~yr---------g~prr~lL--TtGWs~FV~~K~L~aGD~VvF 223 (463)
.++.+.|..|++=....... ..+-+|+| ..|| +..++|++||.|.|
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 56888888887666555441 12346787 4554 88999999999986
No 26
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=21.51 E-value=59 Score=26.48 Aligned_cols=18 Identities=33% Similarity=0.215 Sum_probs=8.8
Q ss_pred hhHHHhhcCCCCCCEEEE
Q 012439 206 WSAFVNKKKLVSGDAVLF 223 (463)
Q Consensus 206 Ws~FV~~K~L~aGD~VvF 223 (463)
=...-|.++|.+||.|.|
T Consensus 40 e~e~rrg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 40 EVETRRGKKLRPGDVVEI 57 (65)
T ss_dssp B----SS----SSEEEEE
T ss_pred EEccccCCcCCCCCEEEE
Confidence 345567899999999999
Done!