Query 001931
Match_columns 995
No_of_seqs 286 out of 550
Neff 3.4
Searched_HMMs 46136
Date Thu Mar 28 12:39:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001931hhsearch_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 8.4E-36 1.8E-40 268.1 7.7 83 227-309 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 2E-18 4.4E-23 154.0 11.1 98 101-203 1-100 (100)
3 KOG0644 Uncharacterized conser 99.5 3.6E-15 7.9E-20 174.0 5.3 150 179-335 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.2 8.3E-06 1.8E-10 82.0 10.2 90 97-188 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.8 4.9E-05 1.1E-09 73.4 6.5 81 95-176 18-114 (114)
6 KOG3598 Thyroid hormone recept 89.6 0.066 1.4E-06 68.4 -1.6 68 115-187 1663-1741(2220)
7 KOG3598 Thyroid hormone recept 84.3 2 4.4E-05 56.0 6.8 17 682-698 2176-2192(2220)
8 PRK10737 FKBP-type peptidyl-pr 66.4 12 0.00026 39.9 5.8 104 178-294 2-114 (196)
9 PF04014 Antitoxin-MazE: Antid 54.0 14 0.00029 30.4 2.9 29 172-200 14-42 (47)
10 KOG3207 Beta-tubulin folding c 53.0 14 0.0003 44.0 3.8 44 265-322 3-46 (505)
11 COG1047 SlpA FKBP-type peptidy 43.2 94 0.002 33.1 7.7 105 178-294 2-115 (174)
12 PF10844 DUF2577: Protein of u 42.9 84 0.0018 30.0 6.7 28 173-200 71-98 (100)
13 PF13163 DUF3999: Protein of u 41.1 2.4E+02 0.0052 33.3 11.4 165 104-315 9-197 (429)
14 cd04451 S1_IF1 S1_IF1: Transla 40.7 1E+02 0.0022 26.7 6.4 38 140-190 15-52 (64)
15 smart00743 Agenet Tudor-like d 40.0 37 0.00079 28.8 3.5 28 264-294 2-29 (61)
16 PF05641 Agenet: Agenet domain 39.0 44 0.00095 29.5 3.9 42 265-316 1-42 (68)
17 TIGR01439 lp_hng_hel_AbrB loop 37.0 42 0.0009 26.3 3.2 28 171-198 13-40 (43)
18 PRK03760 hypothetical protein; 34.0 68 0.0015 31.6 4.8 48 140-190 62-117 (117)
19 PF01878 EVE: EVE domain; Int 33.6 42 0.00091 32.9 3.3 27 177-203 38-65 (143)
20 smart00333 TUDOR Tudor domain. 31.7 61 0.0013 26.7 3.5 52 264-332 2-53 (57)
21 PF11515 Cul7: Mouse developme 31.2 43 0.00094 31.5 2.7 71 253-333 6-76 (78)
22 CHL00010 infA translation init 30.6 2.9E+02 0.0062 25.5 7.9 28 177-204 45-74 (78)
23 PF02513 Spin-Ssty: Spin/Ssty 24.8 97 0.0021 27.1 3.5 31 267-297 1-31 (50)
24 PRK14129 heat shock protein Hs 24.4 83 0.0018 31.2 3.5 52 262-331 3-55 (105)
25 KOG4369 RTK signaling protein 23.5 52 0.0011 43.4 2.4 9 20-28 1068-1076(2131)
26 PF15057 DUF4537: Domain of un 23.3 2.7E+02 0.0058 27.7 6.8 79 182-293 1-82 (124)
27 PF13275 S4_2: S4 domain; PDB: 21.5 57 0.0012 29.5 1.7 27 168-197 38-64 (65)
28 PF06003 SMN: Survival motor n 20.2 80 0.0017 35.0 2.8 57 262-333 66-122 (264)
29 cd00367 PTS-HPr_like Histidine 20.2 3.4E+02 0.0074 24.2 6.3 57 218-280 9-66 (77)
30 PRK14699 replication factor A; 20.1 3.5E+02 0.0077 32.8 8.2 66 96-188 68-133 (484)
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=8.4e-36 Score=268.08 Aligned_cols=83 Identities=64% Similarity=1.097 Sum_probs=81.7
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCccccchHhHHHHHhcccccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCcc
Q 001931 227 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWR 306 (995)
Q Consensus 227 Aahaaat~~~FtV~Y~PRas~sEFVVp~~kY~eAm~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR 306 (995)
|+|||+++++|+|+||||++++|||||++||++||+++|++||||||.||+||+++++|+|||+||+++||+|||+|+||
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 cee
Q 001931 307 NLQ 309 (995)
Q Consensus 307 ~Lq 309 (995)
|||
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=2e-18 Score=153.96 Aligned_cols=98 Identities=29% Similarity=0.430 Sum_probs=74.9
Q ss_pred EEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001931 101 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLF 180 (995)
Q Consensus 101 F~KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsQeLvakDlhGkeW~FRhiyRgqprRhlLTtGWS~FVreKkLv 180 (995)
|.|+|+++|+.+.++|.||+++++++.. + ...+.++.++|..|++|.+++.+++.+++++|++||..||++++|+
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 1135689999999999999999998888899999999999999999
Q ss_pred CCCeEEEEecC--CCcEEEEEEecc
Q 001931 181 AGDSVLFIRDE--KSQLLLGIRRAN 203 (995)
Q Consensus 181 aGDsVVF~R~e--~GeL~VGIRRA~ 203 (995)
+||+|+|+..+ ..++.|+|+|+.
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 455699999973
No 3
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.54 E-value=3.6e-15 Score=173.98 Aligned_cols=150 Identities=20% Similarity=0.356 Sum_probs=123.5
Q ss_pred CCCCCeEEEEecCCCcEEEEEEeccCCCCCC---------------------CCcccCCCccccchHHHHHHHHhcCCcE
Q 001931 179 LFAGDSVLFIRDEKSQLLLGIRRANRQQPAL---------------------SSSVISSDSMHIGILAAAAHAAANNSPF 237 (995)
Q Consensus 179 LvaGDsVVF~R~e~GeL~VGIRRA~r~~~~~---------------------~ssvissdsm~~gvLAaAahaaat~~~F 237 (995)
...||.|+++|.+..+|.-.+|+.+....+. +.+.-+-=.|.+.|+..|.|+. +..|
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 4589999999998888888888776643321 1122122248888888887554 5789
Q ss_pred EEEEcCCCCCCccccchHhHHHHHhcccccCceeeeeeeec-cCcccceeeEEEEeccCCCCCCCCCCccceeeccccCC
Q 001931 238 TIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETE-ESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 316 (995)
Q Consensus 238 tV~Y~PRas~sEFVVp~~kY~eAm~~~Ws~GMRFRM~FEtE-dss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~ 316 (995)
.+.|....+.+||+|.+..|++|+.++|.+|+|||..+..+ |...+||.|+|.++.+..| .+|+|+|+|+.|+||..+
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp-~fpdSpwery~v~~~~~e 1030 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSP-DFPDSPWERYIVRYDNTE 1030 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHhhccccccceeEEEccCCCcCCceeeeeeeeccCCCC-CCCCCcceeEEEEecCCc
Confidence 99999999999999999999999999999999999999543 2335899999999999888 999999999999999997
Q ss_pred CCCCCCCcccCcccccCCC
Q 001931 317 AGERPSRVSLWETEPVVTP 335 (995)
Q Consensus 317 ~~~r~~RVSPWEIEPv~~p 335 (995)
.+.-||||.|++..-
T Consensus 1031 ----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1031 ----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred ----ccccCccccCCCccc
Confidence 478899999999753
No 4
>PF09217 EcoRII-N: Restriction endonuclease EcoRII, N-terminal; InterPro: IPR023372 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the N-terminal effector-binding domain of the type II restriction endonuclease EcoRII, which has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not []. The domain represented by this entry is only found in bacterial proteins.; PDB: 3HQF_A 1NA6_A.
Probab=98.20 E-value=8.3e-06 Score=82.03 Aligned_cols=90 Identities=26% Similarity=0.368 Sum_probs=59.9
Q ss_pred CceeEEEeccccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 001931 97 PTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDY-SMQPPAQEIVARDLHD--TTWTFRHIYRGQ------PKR 163 (995)
Q Consensus 97 ~~~sF~KtLTaSDVs~~G----rfsVPKr~AE~~FPpLD~-s~~~PsQeLvakDlhG--keW~FRhiyRgq------prR 163 (995)
....|+|.|++.|++..| |+.|||..++..||.+.. ....|...|.+++..| ..|+||+||.|+ ++.
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 346799999999999864 799999999999987654 5567889999999888 679999999975 666
Q ss_pred eeec--ccchhhhccCCCCCCCeEEEE
Q 001931 164 HLLT--TGWSVFVSTKRLFAGDSVLFI 188 (995)
Q Consensus 164 hlLT--tGWS~FVreKkLvaGDsVVF~ 188 (995)
+.|| +|-..|.+. =..||.+||.
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 7776 333334332 2478988886
No 5
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=97.77 E-value=4.9e-05 Score=73.36 Aligned_cols=81 Identities=22% Similarity=0.303 Sum_probs=63.2
Q ss_pred CCCceeEEEeccccCCCCC-CceeechhhhhhcCCCCC------------CCCCCCceEEEEEeCCCCeEEEEEEEeCC-
Q 001931 95 RQPTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLD------------YSMQPPAQEIVARDLHDTTWTFRHIYRGQ- 160 (995)
Q Consensus 95 ~~~~~sF~KtLTaSDVs~~-GrfsVPKr~AE~~FPpLD------------~s~~~PsQeLvakDlhGkeW~FRhiyRgq- 160 (995)
..+...|+|+|+.||+..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg 96 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMG 96 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEeccc
Confidence 3456789999999999986 899999876633 12221 11234578999999999999999999965
Q ss_pred --CCceeecccchhhhcc
Q 001931 161 --PKRHLLTTGWSVFVST 176 (995)
Q Consensus 161 --prRhlLTtGWS~FVre 176 (995)
...|+|++||..+|++
T Consensus 97 ~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 97 NGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEEEcChHhhccC
Confidence 5679999999999864
No 6
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=89.61 E-value=0.066 Score=68.37 Aligned_cols=68 Identities=24% Similarity=0.297 Sum_probs=39.5
Q ss_pred ceeechhhhhhcCCCCCCCCCCCceEEE------EEeCCC-CeEEEEEEEeCCCCceeec----ccchhhhccCCCCCCC
Q 001931 115 GFSVPRRAAEKIFPPLDYSMQPPAQEIV------ARDLHD-TTWTFRHIYRGQPKRHLLT----TGWSVFVSTKRLFAGD 183 (995)
Q Consensus 115 rfsVPKr~AE~~FPpLD~s~~~PsQeLv------akDlhG-keW~FRhiyRgqprRhlLT----tGWS~FVreKkLvaGD 183 (995)
||+=-.+.....||......+ .|. ..|..| +.=.|.-|+.+. ..++.| .-|..|--.|.+..|-
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 455445556666775544321 222 446776 456677777533 234554 5688888888887765
Q ss_pred eEEE
Q 001931 184 SVLF 187 (995)
Q Consensus 184 sVVF 187 (995)
.--|
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=84.27 E-value=2 Score=55.97 Aligned_cols=17 Identities=41% Similarity=0.288 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHh
Q 001931 682 QLQSQLQQKLQQQQQQQ 698 (995)
Q Consensus 682 qlQlQLLQkLQQQQq~~ 698 (995)
..+-|=||..|||||.-
T Consensus 2176 lf~RQglqqtqqQqqta 2192 (2220)
T KOG3598|consen 2176 LFRRQGLQQTQQQQQTA 2192 (2220)
T ss_pred hhHHHHHHHHHHHHHHH
Confidence 44556778888888863
No 8
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=66.44 E-value=12 Score=39.89 Aligned_cols=104 Identities=17% Similarity=0.184 Sum_probs=59.7
Q ss_pred CCCCCCeEEEE---ecCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCC------C
Q 001931 178 RLFAGDSVLFI---RDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASP------S 248 (995)
Q Consensus 178 kLvaGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssvissdsm~~gvLAaAahaaat~~~FtV~Y~PRas~------s 248 (995)
++..|++|.|. |.++|+++-.-+ . ..|-.++--...-+-.|.+|..-...|..|+|..-|-..- .
T Consensus 2 kI~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~l 75 (196)
T PRK10737 2 KVAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENL 75 (196)
T ss_pred ccCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHH
Confidence 34567777662 345676533221 1 1122222222222334566777777788899987664322 2
Q ss_pred ccccchHhHHHHHhcccccCceeeeeeeeccCcccceeeEEEEecc
Q 001931 249 EFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 294 (995)
Q Consensus 249 EFVVp~~kY~eAm~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd 294 (995)
-+.||++.|... ....+||||.+ ++++. .+.++|+.|.+
T Consensus 76 V~~vpr~~F~~~--~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 76 VQRVPKDVFMGV--DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEEecHHHCCCc--cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 356788777432 24789999886 44433 36889999975
No 9
>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=53.98 E-value=14 Score=30.44 Aligned_cols=29 Identities=14% Similarity=0.115 Sum_probs=23.7
Q ss_pred hhhccCCCCCCCeEEEEecCCCcEEEEEE
Q 001931 172 VFVSTKRLFAGDSVLFIRDEKSQLLLGIR 200 (995)
Q Consensus 172 ~FVreKkLvaGDsVVF~R~e~GeL~VGIR 200 (995)
.|....+|.+||.|.|.-+++|++.|--.
T Consensus 14 ~~~~~l~l~~Gd~v~i~~~~~g~i~i~p~ 42 (47)
T PF04014_consen 14 EIREKLGLKPGDEVEIEVEGDGKIVIRPV 42 (47)
T ss_dssp HHHHHTTSSTTTEEEEEEETTSEEEEEES
T ss_pred HHHHHcCCCCCCEEEEEEeCCCEEEEEEC
Confidence 56688899999999999999987666443
No 10
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=52.97 E-value=14 Score=44.04 Aligned_cols=44 Identities=25% Similarity=0.631 Sum_probs=30.3
Q ss_pred cccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCccceeeccccCCCCCCCC
Q 001931 265 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPS 322 (995)
Q Consensus 265 Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~ 322 (995)
..+|.|+|.-+|- +..||.|+|.| |++ +| +-|.||++.-+.+.-
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g--------~~~-~w--~GvEWDd~~RGKH~G 46 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEG--------NNS-KW--YGVEWDDPVRGKHDG 46 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcC--------CCC-cc--eeeEecCCCccccCc
Confidence 4689999987662 34566666654 444 44 789999998775543
No 11
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=43.21 E-value=94 Score=33.06 Aligned_cols=105 Identities=18% Similarity=0.236 Sum_probs=62.5
Q ss_pred CCCCCCeEEEE---ecCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCcc----
Q 001931 178 RLFAGDSVLFI---RDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASPSEF---- 250 (995)
Q Consensus 178 kLvaGDsVVF~---R~e~GeL~VGIRRA~r~~~~~~ssvissdsm~~gvLAaAahaaat~~~FtV~Y~PRas~sEF---- 250 (995)
++..||.|.+. |.++|+++=--+- ..-|-.++--+..-+.-|.+|..-..-|..|+|.--|-..-.||
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 45677777763 3444544322111 01122222222233334677888888899999998886544443
Q ss_pred --ccchHhHHHHHhcccccCceeeeeeeeccCcccceeeEEEEecc
Q 001931 251 --VIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 294 (995)
Q Consensus 251 --VVp~~kY~eAm~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd 294 (995)
.||+++|...- ...+||+|.. ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 46666665432 6889999875 5544 456799999974
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=42.87 E-value=84 Score=29.99 Aligned_cols=28 Identities=29% Similarity=0.358 Sum_probs=22.8
Q ss_pred hhccCCCCCCCeEEEEecCCCcEEEEEE
Q 001931 173 FVSTKRLFAGDSVLFIRDEKSQLLLGIR 200 (995)
Q Consensus 173 FVreKkLvaGDsVVF~R~e~GeL~VGIR 200 (995)
|.-...|++||.|+.+|.++|..++-+=
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 13
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=41.11 E-value=2.4e+02 Score=33.28 Aligned_cols=165 Identities=16% Similarity=0.250 Sum_probs=98.8
Q ss_pred eccccCCCCCCceeechhhhhh-cCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCC-----CCceeecccchh-hhcc
Q 001931 104 TLTASDTSTHGGFSVPRRAAEK-IFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQ-----PKRHLLTTGWSV-FVST 176 (995)
Q Consensus 104 tLTaSDVs~~GrfsVPKr~AE~-~FPpLD~s~~~PsQeLvakDlhGkeW~FRhiyRgq-----prRhlLTtGWS~-FVre 176 (995)
.|+.+.-+--.++.+|..--.. .-|-| .+|.|.|-.|+.-.|..+.... +.++-| -|.. .+.+
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 3444544555688888754222 22322 2699999999998888776531 222222 1222 3455
Q ss_pred CCCCCCCe-EEEEecCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCccccchH
Q 001931 177 KRLFAGDS-VLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASPSEFVIPLA 255 (995)
Q Consensus 177 KkLvaGDs-VVF~R~e~GeL~VGIRRA~r~~~~~~ssvissdsm~~gvLAaAahaaat~~~FtV~Y~PRas~sEFVVp~~ 255 (995)
.. ..||. +.+.|+.+|.+ |.|+++......... ...|+|.+.
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 012344444
Q ss_pred hHH---HHHhccc-ccCcee--eeeeeeccCcccce----eeEEEEeccCC------CCCCCCCCccceeeccccC
Q 001931 256 KYN---KAMYTQV-SLGMRF--RMMFETEESGVRRY----MGTITSISDLD------PLRWKNSQWRNLQVGWDES 315 (995)
Q Consensus 256 kY~---eAm~~~W-s~GMRF--RM~FEtEdss~rwy----~GTItgIsd~D------P~rWp~S~WR~LqV~WDE~ 315 (995)
..+ .++.-.| .....+ |..+|+-|.-..|+ .|+|..+..-+ -+..|+...|.|+|.|++.
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 3445677 344444 55566544444564 47777776422 3567899999999999653
No 14
>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=40.73 E-value=1e+02 Score=26.72 Aligned_cols=38 Identities=13% Similarity=0.065 Sum_probs=22.8
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEec
Q 001931 140 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIRD 190 (995)
Q Consensus 140 eLvakDlhGkeW~FRhiyRgqprRhlLTtGWS~FVreKkLvaGDsVVF~R~ 190 (995)
...+++..|. .++|..||+-|+ +...+.+||.|.|...
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 4556676776 344445543211 2334899999999864
No 15
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=39.95 E-value=37 Score=28.79 Aligned_cols=28 Identities=11% Similarity=0.159 Sum_probs=23.6
Q ss_pred ccccCceeeeeeeeccCcccceeeEEEEecc
Q 001931 264 QVSLGMRFRMMFETEESGVRRYMGTITSISD 294 (995)
Q Consensus 264 ~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd 294 (995)
.|.+|+++-..++. ...||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~---~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE---EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC---CCEEEEEEEEEECC
Confidence 58899999999953 36899999999964
No 16
>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=39.00 E-value=44 Score=29.51 Aligned_cols=42 Identities=12% Similarity=0.106 Sum_probs=27.3
Q ss_pred cccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCccceeeccccCC
Q 001931 265 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 316 (995)
Q Consensus 265 Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~ 316 (995)
|..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 46799999887766666899999999997521 6788886554
No 17
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=36.99 E-value=42 Score=26.27 Aligned_cols=28 Identities=25% Similarity=0.310 Sum_probs=23.2
Q ss_pred hhhhccCCCCCCCeEEEEecCCCcEEEE
Q 001931 171 SVFVSTKRLFAGDSVLFIRDEKSQLLLG 198 (995)
Q Consensus 171 S~FVreKkLvaGDsVVF~R~e~GeL~VG 198 (995)
..|.+.-++..||.|.+...++|.+.|.
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 3677899999999999998878876654
No 18
>PRK03760 hypothetical protein; Provisional
Probab=34.04 E-value=68 Score=31.63 Aligned_cols=48 Identities=21% Similarity=0.429 Sum_probs=29.7
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCeEEEEec
Q 001931 140 EIVARDLHDTTWTFRH-----IYR-GQPKRHLL--TTGWSVFVSTKRLFAGDSVLFIRD 190 (995)
Q Consensus 140 eLvakDlhGkeW~FRh-----iyR-gqprRhlL--TtGWS~FVreKkLvaGDsVVF~R~ 190 (995)
++++.|.+|++-.... +|. ..+-+|+| ..||. .+.++++||.|.|.|+
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 4555555555433211 122 23455777 57765 7889999999998764
No 19
>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=33.63 E-value=42 Score=32.94 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=18.5
Q ss_pred CCCCCCCeEEEEecC-CCcEEEEEEecc
Q 001931 177 KRLFAGDSVLFIRDE-KSQLLLGIRRAN 203 (995)
Q Consensus 177 KkLvaGDsVVF~R~e-~GeL~VGIRRA~ 203 (995)
++++.||.|+||... .+.-+|||=|-.
T Consensus 38 ~~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 38 KRMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp HC--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred hcCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 489999999999987 677778777654
No 20
>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=31.75 E-value=61 Score=26.71 Aligned_cols=52 Identities=12% Similarity=0.171 Sum_probs=36.7
Q ss_pred ccccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCccceeeccccCCCCCCCCCcccCccccc
Q 001931 264 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 332 (995)
Q Consensus 264 ~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEPv 332 (995)
.|.+|..+...+ .+ ..||.|+|+++.. + ....|.-++-+. .+-|...+|-++
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecC
Confidence 578999999988 32 5899999999964 2 456777777542 245666665554
No 21
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=31.18 E-value=43 Score=31.55 Aligned_cols=71 Identities=21% Similarity=0.260 Sum_probs=36.4
Q ss_pred chHhHHHHHhcccccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCccceeeccccCCCCCCCCCcccCccccc
Q 001931 253 PLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 332 (995)
Q Consensus 253 p~~kY~eAm~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEPv 332 (995)
..+.|..=+.-++.+||++||.=.-||-. .-=.|+|.-++. | .-|+ -+++|.|-.... .-.|--=.||.+
T Consensus 6 s~d~Ya~YVr~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~-d--g~~~---lnvqv~W~~~G~---tyWV~~~~vEii 75 (78)
T PF11515_consen 6 SNDDYAEYVRDNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-D--GLHD---LNVQVDWQSKGR---TYWVHWHHVEII 75 (78)
T ss_dssp SSHHHHHHHHHH--TT-EEEESS-BTTB--TT-EEE-EEEE--T--TSSE-----EEEEETTTTE---EEEEEGGGEEE-
T ss_pred chhHHHHHHHHhCCCCcEEEEeccccccc-ccccceeEeecc-C--CCCC---cceEEEeeecCc---eEEEEEEEEEEe
Confidence 45778888889999999999975444433 223677766664 1 1122 247888877652 223444455555
Q ss_pred C
Q 001931 333 V 333 (995)
Q Consensus 333 ~ 333 (995)
.
T Consensus 76 g 76 (78)
T PF11515_consen 76 G 76 (78)
T ss_dssp -
T ss_pred c
Confidence 3
No 22
>CHL00010 infA translation initiation factor 1
Probab=30.63 E-value=2.9e+02 Score=25.51 Aligned_cols=28 Identities=21% Similarity=0.186 Sum_probs=17.4
Q ss_pred CCCCCCCeEEEEe--cCCCcEEEEEEeccC
Q 001931 177 KRLFAGDSVLFIR--DEKSQLLLGIRRANR 204 (995)
Q Consensus 177 KkLvaGDsVVF~R--~e~GeL~VGIRRA~r 204 (995)
.++.+||.|.|.- .++++-+|-.|-.++
T Consensus 45 i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 45 IRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred cccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 4478999999984 334444554454443
No 23
>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=24.76 E-value=97 Score=27.12 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=24.0
Q ss_pred cCceeeeeeeeccCcccceeeEEEEeccCCC
Q 001931 267 LGMRFRMMFETEESGVRRYMGTITSISDLDP 297 (995)
Q Consensus 267 ~GMRFRM~FEtEdss~rwy~GTItgIsd~DP 297 (995)
+|-|+.-.||+++.+...|.|+|..--+..|
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 5889999999998888888999999876544
No 24
>PRK14129 heat shock protein HspQ; Provisional
Probab=24.44 E-value=83 Score=31.16 Aligned_cols=52 Identities=21% Similarity=0.369 Sum_probs=35.0
Q ss_pred hcccccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCC-CCccceeeccccCCCCCCCCCcccCcccc
Q 001931 262 YTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKN-SQWRNLQVGWDESTAGERPSRVSLWETEP 331 (995)
Q Consensus 262 ~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~-S~WR~LqV~WDE~~~~~r~~RVSPWEIEP 331 (995)
..++.+|.-+|-+.- .|.|.|++| || .+.+ .+| |++-... ++.|=.||===.
T Consensus 3 ~akF~IGQ~VrHrl~-------~yrGVV~DV---DP-~fs~~e~w------~~~ia~~-~p~kdqPwYHvl 55 (105)
T PRK14129 3 ASKFGIGQQVRHSLL-------GYLGVVVDI---DP-EYSLEEPS------PDELAVN-DELRAAPWYHVV 55 (105)
T ss_pred cccccCCcEEEEeec-------CCCeEEEee---CC-CcCCCchh------HHhhccC-CCccCCCceEEE
Confidence 357889999998643 489999999 44 3433 345 5655543 777888885333
No 25
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=23.47 E-value=52 Score=43.42 Aligned_cols=9 Identities=11% Similarity=-0.101 Sum_probs=4.7
Q ss_pred cCCCchhhh
Q 001931 20 LLPSRPQRV 28 (995)
Q Consensus 20 f~qGH~EQv 28 (995)
|--||.|-|
T Consensus 1068 fRKgh~~iV 1076 (2131)
T KOG4369|consen 1068 FRKGHFAIV 1076 (2131)
T ss_pred HHhchhhee
Confidence 445555544
No 26
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=23.26 E-value=2.7e+02 Score=27.71 Aligned_cols=79 Identities=22% Similarity=0.305 Sum_probs=52.9
Q ss_pred CCeEEEEecCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcC-CC--CCCccccchHhHH
Q 001931 182 GDSVLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNP-RA--SPSEFVIPLAKYN 258 (995)
Q Consensus 182 GDsVVF~R~e~GeL~VGIRRA~r~~~~~~ssvissdsm~~gvLAaAahaaat~~~FtV~Y~P-Ra--s~sEFVVp~~kY~ 258 (995)
|..|+=-++++|.|+.|.-++.- +...|.|.|+- +. -..+|||...
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 55666666789999988766442 34556677722 21 1456777655
Q ss_pred HHHhcccccCceeeeeeeeccCcccceeeEEEEec
Q 001931 259 KAMYTQVSLGMRFRMMFETEESGVRRYMGTITSIS 293 (995)
Q Consensus 259 eAm~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIs 293 (995)
.|+.+...+|+.+-+..|.. ..++.=|||++.-
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 56689999999999985533 2345569999864
No 27
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=21.51 E-value=57 Score=29.52 Aligned_cols=27 Identities=22% Similarity=0.204 Sum_probs=12.9
Q ss_pred ccchhhhccCCCCCCCeEEEEecCCCcEEE
Q 001931 168 TGWSVFVSTKRLFAGDSVLFIRDEKSQLLL 197 (995)
Q Consensus 168 tGWS~FVreKkLvaGDsVVF~R~e~GeL~V 197 (995)
.|=...-|.++|++||.|.| ++..+.|
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 4444443
No 28
>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=20.22 E-value=80 Score=35.02 Aligned_cols=57 Identities=19% Similarity=0.233 Sum_probs=32.7
Q ss_pred hcccccCceeeeeeeeccCcccceeeEEEEeccCCCCCCCCCCccceeeccccCCCCCCCCCcccCcccccC
Q 001931 262 YTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPVV 333 (995)
Q Consensus 262 ~~~Ws~GMRFRM~FEtEdss~rwy~GTItgIsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEPv~ 333 (995)
...|.+|++.+-.|..+ ..+|-+||++|..-+- .| .|+.++-+ +.+.|+.=+|.+..
T Consensus 66 ~~~WkvGd~C~A~~s~D---g~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSED---GQYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPSE 122 (264)
T ss_dssp TT---TT-EEEEE-TTT---SSEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEETT
T ss_pred ccCCCCCCEEEEEECCC---CCEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhcccc
Confidence 36899999999998543 4689999999974221 23 36666543 23455555555543
No 29
>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=20.22 E-value=3.4e+02 Score=24.20 Aligned_cols=57 Identities=16% Similarity=0.057 Sum_probs=40.9
Q ss_pred ccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHHHHHhcccccCceeeeeeeeccC
Q 001931 218 SMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEES 280 (995)
Q Consensus 218 sm~~gvLAaAahaaat-~~~FtV~Y~PRas~sEFVVp~~kY~eAm~~~Ws~GMRFRM~FEtEds 280 (995)
.+|....+.-++.|.+ .+.++|.|. ...|++..+..-|.-.+..|+++...++++|.
T Consensus 9 GlHaRpa~~~v~~a~~~~~~v~i~~~------~~~vdakSil~i~~L~~~~G~~i~i~~~G~de 66 (77)
T cd00367 9 GLHARPAALLVQLASKFKSDITLRKG------GRKANAKSILGLMSLGAKQGDEITLSAEGEDA 66 (77)
T ss_pred CCcHHHHHHHHHHHHhCCCEEEEEEC------CEEEcHHhHHHHHHcCCCCCCEEEEEEECcCH
Confidence 4554443333344433 455666664 45899999999999999999999999998775
No 30
>PRK14699 replication factor A; Provisional
Probab=20.14 E-value=3.5e+02 Score=32.75 Aligned_cols=66 Identities=14% Similarity=0.245 Sum_probs=44.9
Q ss_pred CCceeEEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc
Q 001931 96 QPTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS 175 (995)
Q Consensus 96 ~~~~sF~KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsQeLvakDlhGkeW~FRhiyRgqprRhlLTtGWS~FVr 175 (995)
..+.++.|+|+.+++.+ |-..|++ ..-...+.+.|..| +.||+.|... -..+.
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 45778999999999865 4334443 12234678999999 5777877421 13344
Q ss_pred cCCCCCCCeEEEE
Q 001931 176 TKRLFAGDSVLFI 188 (995)
Q Consensus 176 eKkLvaGDsVVF~ 188 (995)
+-+|++||+|.+-
T Consensus 121 ~g~l~~GDvv~I~ 133 (484)
T PRK14699 121 AGKIKAGQTLQIS 133 (484)
T ss_pred hcCCCCCCEEEEc
Confidence 5579999999983
Done!