Query 001728
Match_columns 1020
No_of_seqs 325 out of 573
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 07:54:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001728.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001728hhsearch_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 5.5E-36 1.2E-40 270.2 7.6 83 252-334 1-83 (83)
2 PF02362 B3: B3 DNA binding do 99.8 2.1E-18 4.6E-23 154.7 11.1 98 126-228 1-100 (100)
3 KOG0644 Uncharacterized conser 99.6 2.7E-15 5.8E-20 175.6 5.9 149 204-360 874-1045(1113)
4 PF09217 EcoRII-N: Restriction 98.3 2.9E-06 6.2E-11 85.5 10.2 90 122-213 6-110 (156)
5 PF03754 DUF313: Domain of unk 97.8 4.6E-05 1E-09 73.8 6.5 80 121-201 19-114 (114)
6 KOG3598 Thyroid hormone recept 88.9 0.064 1.4E-06 68.7 -2.4 68 140-212 1663-1741(2220)
7 KOG3598 Thyroid hormone recept 87.3 0.16 3.5E-06 65.3 -0.3 10 237-246 1850-1859(2220)
8 PF11498 Activator_LAG-3: Tran 80.3 0.54 1.2E-05 53.7 0.0 6 435-440 270-275 (468)
9 KOG0644 Uncharacterized conser 68.0 3.5 7.7E-05 51.7 2.6 66 33-99 871-938 (1113)
10 PRK10737 FKBP-type peptidyl-pr 64.8 14 0.00031 39.5 6.0 66 247-319 43-114 (196)
11 PF10844 DUF2577: Protein of u 63.6 37 0.0008 32.5 8.0 28 198-225 71-98 (100)
12 KOG3207 Beta-tubulin folding c 54.9 13 0.00028 44.4 4.1 44 290-347 3-46 (505)
13 PF04014 Antitoxin-MazE: Antid 53.0 15 0.00032 30.3 3.0 29 197-225 14-42 (47)
14 PF13163 DUF3999: Protein of u 52.5 1.2E+02 0.0027 35.7 11.4 165 129-340 9-197 (429)
15 PF05641 Agenet: Agenet domain 41.4 44 0.00096 29.6 4.4 42 290-341 1-42 (68)
16 smart00743 Agenet Tudor-like d 39.0 38 0.00082 28.8 3.5 38 289-339 2-39 (61)
17 cd04451 S1_IF1 S1_IF1: Transla 38.8 1.2E+02 0.0025 26.5 6.5 38 165-215 15-52 (64)
18 TIGR01439 lp_hng_hel_AbrB loop 36.4 44 0.00096 26.2 3.3 27 197-223 14-40 (43)
19 PRK03760 hypothetical protein; 36.2 63 0.0014 32.0 4.9 48 165-215 62-117 (117)
20 cd06919 Asp_decarbox Aspartate 36.0 1.7E+02 0.0036 29.5 7.7 74 128-214 12-88 (111)
21 COG1047 SlpA FKBP-type peptidy 34.5 1.6E+02 0.0035 31.5 7.8 67 246-319 43-115 (174)
22 KOG4274 Positive cofactor 2 (P 32.8 33 0.00071 42.2 2.8 16 921-936 571-586 (742)
23 PF11515 Cul7: Mouse developme 32.5 63 0.0014 30.6 4.0 57 278-341 6-62 (78)
24 PF13388 DUF4106: Protein of u 31.8 55 0.0012 37.5 4.2 9 371-379 73-81 (422)
25 PF01878 EVE: EVE domain; Int 31.2 49 0.0011 32.6 3.4 26 202-227 38-64 (143)
26 smart00333 TUDOR Tudor domain. 31.1 62 0.0014 26.8 3.5 52 289-357 2-53 (57)
27 TIGR00223 panD L-aspartate-alp 29.8 2.4E+02 0.0051 29.0 7.7 72 128-214 13-89 (126)
28 CHL00010 infA translation init 29.5 2.6E+02 0.0056 25.9 7.4 50 165-228 21-73 (78)
29 PRK05449 aspartate alpha-decar 28.9 2.7E+02 0.0058 28.6 8.0 74 128-214 13-89 (126)
30 cd04491 SoSSB_OBF SoSSB_OBF: A 26.8 3E+02 0.0066 24.6 7.3 49 162-226 23-75 (82)
31 PF15057 DUF4537: Domain of un 24.4 2.5E+02 0.0053 28.1 6.8 79 207-318 1-82 (124)
32 PF02513 Spin-Ssty: Spin/Ssty 23.2 1.1E+02 0.0024 26.9 3.6 31 292-322 1-31 (50)
33 PF00381 PTS-HPr: PTS HPr comp 23.0 1.8E+02 0.0038 26.6 5.1 60 241-306 11-71 (84)
34 cd00367 PTS-HPr_like Histidine 23.0 2.8E+02 0.006 24.9 6.3 59 242-306 8-67 (77)
35 PF02643 DUF192: Uncharacteriz 22.3 1.4E+02 0.0029 28.9 4.5 46 164-212 50-106 (108)
36 PRK14699 replication factor A; 21.8 3.1E+02 0.0066 33.4 8.1 66 121-213 68-133 (484)
37 PF06003 SMN: Survival motor n 21.7 74 0.0016 35.4 2.9 57 287-358 66-122 (264)
38 TIGR01439 lp_hng_hel_AbrB loop 21.6 1.4E+02 0.003 23.5 3.7 33 136-175 4-37 (43)
39 PF03120 DNA_ligase_OB: NAD-de 21.1 62 0.0013 30.6 1.9 34 196-229 42-76 (82)
40 PF12690 BsuPI: Intracellular 21.0 67 0.0015 29.9 2.1 41 163-214 25-66 (82)
41 PF13275 S4_2: S4 domain; PDB: 20.3 65 0.0014 29.3 1.8 27 193-222 38-64 (65)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=5.5e-36 Score=270.19 Aligned_cols=83 Identities=64% Similarity=1.097 Sum_probs=81.7
Q ss_pred HHHHHhcCCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcc
Q 001728 252 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWR 331 (1020)
Q Consensus 252 Aahaaat~~~F~V~Y~PRas~sEFVVp~~kY~kAm~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR 331 (1020)
|+|||+++++|+|+||||++++||||+++||++||+++|++||||||+||+||+++++|+|||+||++.||+|||+|+||
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 001728 332 NLQ 334 (1020)
Q Consensus 332 ~Lq 334 (1020)
|||
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=154.70 Aligned_cols=98 Identities=29% Similarity=0.420 Sum_probs=74.7
Q ss_pred EEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCC
Q 001728 126 FCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLF 205 (1020)
Q Consensus 126 F~KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsqeLvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVreKkLv 205 (1020)
|.|+|+++|+.+.++|.||++++++|. ++ ...+.++.++|..|++|.+++.|++.+++++|++||..||++++|+
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 001728 206 AGDSVLFIRDE--KSQLLLGIRRAN 228 (1020)
Q Consensus 206 aGDsVVF~R~e--~GeL~VGIRRA~ 228 (1020)
+||.|+|+..+ ..++.|.|+|+.
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=99.55 E-value=2.7e-15 Score=175.60 Aligned_cols=149 Identities=21% Similarity=0.364 Sum_probs=122.7
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeccCCCCCC---------------------CCcccCCCccccchHHHHHHHHhcCCcE
Q 001728 204 LFAGDSVLFIRDEKSQLLLGIRRANRQQPAL---------------------SSSVISSDSMHIGILAAAAHAAANNSPF 262 (1020)
Q Consensus 204 LvaGDsVVF~R~e~GeL~VGIRRA~r~~~~~---------------------~ssv~ssdsm~~gvLAaAahaaat~~~F 262 (1020)
...||.|+++|.+..+|.-.+|+.++...+. +.+.-+.=+|.+.||..|.++. +..|
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 4579999999998888777777766533221 2222223358999998888554 5689
Q ss_pred EEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeee--cccccccceeeEEEEeccCCCCCCCCCCcceeeeecccC
Q 001728 263 TIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFE--TEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDES 340 (1020)
Q Consensus 263 ~V~Y~PRas~sEFVVp~~kY~kAm~~~Ws~GMRFKM~FE--tEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~ 340 (1020)
.+.|......+||+|.+..|++|+.++|.+|+|||..+. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||..
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 4443 4899999999999988 99999999999999999
Q ss_pred CCCCCCCCccccccccccCC
Q 001728 341 TAGERPSRVSLWETEPVVTP 360 (1020)
Q Consensus 341 ~~~~r~~RVSPWEIEpv~~~ 360 (1020)
+ .+.-||||.|++..-
T Consensus 1030 e----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1030 E----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred c----ccccCccccCCCccc
Confidence 7 468899999999763
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=98.33 E-value=2.9e-06 Score=85.51 Aligned_cols=90 Identities=26% Similarity=0.368 Sum_probs=60.4
Q ss_pred CceeEEEeccccCCCCCC----ceeechhhhhhcCCCCCC-CCCCCceEEEEEeCCC--CeEEEEEEEeCC------CCc
Q 001728 122 PTEFFCKTLTASDTSTHG----GFSVPRRAAEKIFPPLDY-SMQPPAQEIVARDLHD--TTWTFRHIYRGQ------PKR 188 (1020)
Q Consensus 122 ~~~~F~KtLTaSDVs~~G----rfsVPKr~AE~~FPpLD~-s~~~PsqeLvakDlhG--k~W~FRhiyRg~------prR 188 (1020)
....|+|.|++.|++..| |+.|||..++..||.+.. +...|..+|.+++..| ..|+||+||.|+ ++.
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 799999999999987655 5667899999999888 679999999975 677
Q ss_pred eeec--ccchhhhccCCCCCCCeEEEE
Q 001728 189 HLLT--TGWSVFVSTKRLFAGDSVLFI 213 (1020)
Q Consensus 189 hlLT--TGWS~FVreKkLvaGDsVVF~ 213 (1020)
+.|| +|-..|.+. =..||.+||-
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=97.78 E-value=4.6e-05 Score=73.82 Aligned_cols=80 Identities=23% Similarity=0.305 Sum_probs=62.4
Q ss_pred CCceeEEEeccccCCCCC-CceeechhhhhhcCCCCC------------CCCCCCceEEEEEeCCCCeEEEEEEEeCC--
Q 001728 121 QPTEFFCKTLTASDTSTH-GGFSVPRRAAEKIFPPLD------------YSMQPPAQEIVARDLHDTTWTFRHIYRGQ-- 185 (1020)
Q Consensus 121 ~~~~~F~KtLTaSDVs~~-GrfsVPKr~AE~~FPpLD------------~s~~~PsqeLvakDlhGk~W~FRhiyRg~-- 185 (1020)
.....|+|+|+.||+..+ .||+||-..... ...|. .....-++.+.+.|..++.|..++..|..
T Consensus 19 d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~-~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 19 DPKLIIEKTLFKTDVDPHQSRLSMPFNQIID-NDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCeEEEeeeecccCCCCCCceeeccHHHhcc-cccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 345789999999999986 899999876533 12221 11234588999999999999999999965
Q ss_pred -CCceeecccchhhhcc
Q 001728 186 -PKRHLLTTGWSVFVST 201 (1020)
Q Consensus 186 -prRhlLTTGWS~FVre 201 (1020)
...|+|++||..+|.+
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=88.90 E-value=0.064 Score=68.70 Aligned_cols=68 Identities=24% Similarity=0.292 Sum_probs=39.0
Q ss_pred ceeechhhhhhcCCCCCCCCCCCceEE------EEEeCCC-CeEEEEEEEeCCCCceeec----ccchhhhccCCCCCCC
Q 001728 140 GFSVPRRAAEKIFPPLDYSMQPPAQEI------VARDLHD-TTWTFRHIYRGQPKRHLLT----TGWSVFVSTKRLFAGD 208 (1020)
Q Consensus 140 rfsVPKr~AE~~FPpLD~s~~~PsqeL------vakDlhG-k~W~FRhiyRg~prRhlLT----TGWS~FVreKkLvaGD 208 (1020)
||+=-.+.+...||......+ .| ...|..| +.=.|.-|+.+. ..++.| .-|-.|--.|.++.|-
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 444444555666775444321 12 2446776 556677777532 335554 4588888888887766
Q ss_pred eEEE
Q 001728 209 SVLF 212 (1020)
Q Consensus 209 sVVF 212 (1020)
.--|
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=87.31 E-value=0.16 Score=65.29 Aligned_cols=10 Identities=30% Similarity=0.298 Sum_probs=6.0
Q ss_pred cccCCCcccc
Q 001728 237 SVISSDSMHI 246 (1020)
Q Consensus 237 sv~ssdsm~~ 246 (1020)
.|+|++.||+
T Consensus 1850 ~~~s~~~~hh 1859 (2220)
T KOG3598|consen 1850 DVTSEKNEHH 1859 (2220)
T ss_pred CCCChHhhcC
Confidence 4566666665
No 8
>PF11498 Activator_LAG-3: Transcriptional activator LAG-3; InterPro: IPR021587 The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12 []. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1 []. ; PDB: 2FO1_D.
Probab=80.30 E-value=0.54 Score=53.75 Aligned_cols=6 Identities=17% Similarity=0.179 Sum_probs=0.0
Q ss_pred CCcccc
Q 001728 435 FFPSMV 440 (1020)
Q Consensus 435 ~~~~~~ 440 (1020)
+-|+.|
T Consensus 270 LgpDtY 275 (468)
T PF11498_consen 270 LGPDTY 275 (468)
T ss_dssp ------
T ss_pred cCccch
Confidence 334444
No 9
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=67.96 E-value=3.5 Score=51.74 Aligned_cols=66 Identities=27% Similarity=0.467 Sum_probs=45.2
Q ss_pred CCCCCCCCEEEEecCcchhhhhccccccCccCCCC-C-CCCCceEEEEeeEeeecCCCchhhheeeccc
Q 001728 33 VSLPPVGSLVVYFPQGHSEQVAASMQKENDFIPNY-P-NLPSKLICMLHSVTLHADPETDEVYAQMTLQ 99 (1020)
Q Consensus 33 V~lP~vGs~VyYFPQGH~EQ~~as~~~~~~~~p~~-p-~lP~~ilCrV~~V~L~AD~eTDEVYAqitL~ 99 (1020)
--||..|+.|.||-|||-|-+.+....+++ .-++ | ++=..=+|.|..+...-=+-...-..+|+|.
T Consensus 871 ryipQmgDEViyfrQghqeyl~~~~~n~~~-~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~ 938 (1113)
T KOG0644|consen 871 RYIPQMGDEVIYFRQGHQEYLEAVRLNNIE-LNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLA 938 (1113)
T ss_pred cccccccceeehhhhhhHHHHhhhhhcccc-ccccCcccccchhhheeeeeeeeeccCCCcchheeeee
Confidence 368999999999999999999987544433 1111 1 3444567888887666655555556666654
No 10
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=64.83 E-value=14 Score=39.50 Aligned_cols=66 Identities=18% Similarity=0.222 Sum_probs=44.2
Q ss_pred chHHHHHHHHhcCCcEEEEEcCCCCC------CccccchHhHhHHHhcCccccceeeeeeecccccccceeeEEEEecc
Q 001728 247 GILAAAAHAAANNSPFTIFYNPRASP------SEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 319 (1020)
Q Consensus 247 gvLAaAahaaat~~~F~V~Y~PRas~------sEFVVp~~kY~kAm~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd 319 (1020)
-.|.+|..-.+.|..|+|..-|-..- .-+.||++.|... ....+||||.+. +++. .+.++|+.|.+
T Consensus 43 pglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV~~vpr~~F~~~--~~l~~G~~~~~~--~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 43 SGLETALEGHEVGDKFDVAVGANDAYGQYDENLVQRVPKDVFMGV--DELQVGMRFLAE--TDQG---PVPVEITAVED 114 (196)
T ss_pred HHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHEEEecHHHCCCc--cCCCCCCEEEEe--CCCC---cEEEEEEEEcC
Confidence 34566777777888899986554322 2356788877532 247899998864 4433 36889999975
No 11
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=63.59 E-value=37 Score=32.48 Aligned_cols=28 Identities=29% Similarity=0.358 Sum_probs=22.8
Q ss_pred hhccCCCCCCCeEEEEEcCCCcEEEEEE
Q 001728 198 FVSTKRLFAGDSVLFIRDEKSQLLLGIR 225 (1020)
Q Consensus 198 FVreKkLvaGDsVVF~R~e~GeL~VGIR 225 (1020)
|.-...|++||.|+.+|.++|..++=+-
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 12
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=54.92 E-value=13 Score=44.38 Aligned_cols=44 Identities=25% Similarity=0.631 Sum_probs=30.9
Q ss_pred ccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCC
Q 001728 290 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPS 347 (1020)
Q Consensus 290 Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~ 347 (1020)
..+|.|+|..+|- +..||.|+|.| |++ +| +-|.||++.-+.+.-
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 4689999988762 35566666655 445 55 789999998775543
No 13
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=53.00 E-value=15 Score=30.34 Aligned_cols=29 Identities=14% Similarity=0.115 Sum_probs=23.6
Q ss_pred hhhccCCCCCCCeEEEEEcCCCcEEEEEE
Q 001728 197 VFVSTKRLFAGDSVLFIRDEKSQLLLGIR 225 (1020)
Q Consensus 197 ~FVreKkLvaGDsVVF~R~e~GeL~VGIR 225 (1020)
.|....+|.+||.|.|.-+++|++.|--.
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 56678899999999999999987666443
No 14
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=52.52 E-value=1.2e+02 Score=35.74 Aligned_cols=165 Identities=18% Similarity=0.270 Sum_probs=98.6
Q ss_pred eccccCCCCCCceeechhh-hhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCC-----CCceeecccchh-hhcc
Q 001728 129 TLTASDTSTHGGFSVPRRA-AEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQ-----PKRHLLTTGWSV-FVST 201 (1020)
Q Consensus 129 tLTaSDVs~~GrfsVPKr~-AE~~FPpLD~s~~~PsqeLvakDlhGk~W~FRhiyRg~-----prRhlLTTGWS~-FVre 201 (1020)
.|+.+.-+--.++.+|..- ....-|-| .+|.|.|-.|+.-.|..+.... +.++-| -|.. .+..
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 3444444555688888753 22333333 2599999999998888765421 222222 1222 3445
Q ss_pred CCCCCCCe-EEEEEcCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEcCCCCCCccccchH
Q 001728 202 KRLFAGDS-VLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYNPRASPSEFVIPLA 280 (1020)
Q Consensus 202 KkLvaGDs-VVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLAaAahaaat~~~F~V~Y~PRas~sEFVVp~~ 280 (1020)
.. ..||. +.+.|+.+|.+ |.|+++......... ...|+|.++
T Consensus 79 ~~-~~~~~~~~v~~~~~G~~-ve~~~~~~~~~~~~~-----------------------------------~~~~Lld~s 121 (429)
T PF13163_consen 79 DA-ARGDPQLRVERDADGAL-VEVRPASGAAPADGQ-----------------------------------ARGWLLDLS 121 (429)
T ss_pred cc-ccCCccEEEEECCCCcE-EEecccCCCCccccc-----------------------------------ccEEEEECc
Confidence 45 67774 88899999999 999998764321110 012344443
Q ss_pred hHh---HHHhcCc-ccccee--eeeeecccccccce----eeEEEEeccC------CCCCCCCCCcceeeeecccC
Q 001728 281 KYN---KAMYTQV-SLGMRF--RMMFETEESGVRRY----MGTITSISDL------DPLRWKNSQWRNLQVGWDES 340 (1020)
Q Consensus 281 kY~---kAm~~~W-s~GMRF--KM~FEtEdss~rwy----~GTI~gVsd~------DP~rWp~S~WR~LqV~WDE~ 340 (1020)
..+ .++.-.| .....+ |..+|+-|.-..|+ .|+|..+..- +-+.-|++..|.|+|.|++.
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 334444 66666655445564 4777777532 23667899999999999653
No 15
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=41.44 E-value=44 Score=29.61 Aligned_cols=42 Identities=12% Similarity=0.106 Sum_probs=27.5
Q ss_pred ccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001728 290 VSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 341 (1020)
Q Consensus 290 Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~ 341 (1020)
|..|+++-..-+.+.....||.|||+.....+ .+.|+.++-.
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 46899999887766666899999999987421 6789987554
No 16
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=39.05 E-value=38 Score=28.82 Aligned_cols=38 Identities=11% Similarity=0.078 Sum_probs=28.9
Q ss_pred CccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeeccc
Q 001728 289 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDE 339 (1020)
Q Consensus 289 ~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE 339 (1020)
.|++|+++-..|+. ...||.|+|+.+.. -..+.|.-+.
T Consensus 2 ~~~~G~~Ve~~~~~---~~~W~~a~V~~~~~----------~~~~~V~~~~ 39 (61)
T smart00743 2 DFKKGDRVEVFSKE---EDSWWEAVVTKVLG----------DGKYLVRYLT 39 (61)
T ss_pred CcCCCCEEEEEECC---CCEEEEEEEEEECC----------CCEEEEEECC
Confidence 58899999999953 36899999999964 1235677665
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=38.84 E-value=1.2e+02 Score=26.52 Aligned_cols=38 Identities=13% Similarity=0.065 Sum_probs=22.8
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEEc
Q 001728 165 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIRD 215 (1020)
Q Consensus 165 eLvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVreKkLvaGDsVVF~R~ 215 (1020)
.+.+++..|.. ++|..||+-|+ +...+.+||.|.|...
T Consensus 15 ~~~V~~~~g~~--~~c~~rGklr~-----------~~~~~~vGD~V~~~~~ 52 (64)
T cd04451 15 MFRVELENGHE--VLAHISGKMRM-----------NYIRILPGDRVKVELS 52 (64)
T ss_pred EEEEEeCCCCE--EEEEECceeec-----------CCcccCCCCEEEEEEe
Confidence 45566777764 44445542110 2334899999999864
No 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=36.40 E-value=44 Score=26.24 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=22.8
Q ss_pred hhhccCCCCCCCeEEEEEcCCCcEEEE
Q 001728 197 VFVSTKRLFAGDSVLFIRDEKSQLLLG 223 (1020)
Q Consensus 197 ~FVreKkLvaGDsVVF~R~e~GeL~VG 223 (1020)
.|.+.-++..||.|.+...++|.+.+.
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l~ 40 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIILR 40 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEEE
Confidence 677899999999999998877876654
No 19
>PRK03760 hypothetical protein; Provisional
Probab=36.20 E-value=63 Score=32.01 Aligned_cols=48 Identities=21% Similarity=0.429 Sum_probs=29.9
Q ss_pred EEEEEeCCCCeEEEEE-----EEe-CCCCceee--cccchhhhccCCCCCCCeEEEEEc
Q 001728 165 EIVARDLHDTTWTFRH-----IYR-GQPKRHLL--TTGWSVFVSTKRLFAGDSVLFIRD 215 (1020)
Q Consensus 165 eLvakDlhGk~W~FRh-----iyR-g~prRhlL--TTGWS~FVreKkLvaGDsVVF~R~ 215 (1020)
++++.|.+|++-.... +|. ..+-+|+| ..||. ...++++||.|.|.|+
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 4555665555433211 122 23456777 57765 7889999999998763
No 20
>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=36.05 E-value=1.7e+02 Score=29.46 Aligned_cols=74 Identities=15% Similarity=0.258 Sum_probs=51.9
Q ss_pred EeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccCCC
Q 001728 128 KTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTKRL 204 (1020)
Q Consensus 128 KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsqeLvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVreKkL 204 (1020)
-+.|..|..-.|.+.|..+.++. -+.- |...+.+.|. +|..|.- |.+.|.+ +.-.|.+. -.+..
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 46788999999999999987776 2221 3445778886 5888875 6667753 43344433 56778
Q ss_pred CCCCeEEEEE
Q 001728 205 FAGDSVLFIR 214 (1020)
Q Consensus 205 vaGDsVVF~R 214 (1020)
..||.|+++-
T Consensus 79 ~~GD~vII~s 88 (111)
T cd06919 79 QPGDRVIIMA 88 (111)
T ss_pred CCCCEEEEEE
Confidence 8999999864
No 21
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=34.51 E-value=1.6e+02 Score=31.49 Aligned_cols=67 Identities=21% Similarity=0.321 Sum_probs=47.2
Q ss_pred cchHHHHHHHHhcCCcEEEEEcCCCCCCcc------ccchHhHhHHHhcCccccceeeeeeecccccccceeeEEEEecc
Q 001728 246 IGILAAAAHAAANNSPFTIFYNPRASPSEF------VIPLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISD 319 (1020)
Q Consensus 246 ~gvLAaAahaaat~~~F~V~Y~PRas~sEF------VVp~~kY~kAm~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd 319 (1020)
+.-|.+|..-..-|..|+|.--|-..-.|+ .||+++|...= ...+||+|.+ ++++ .-.-|+|+.|..
T Consensus 43 i~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~lvq~vp~~~F~~~~--~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 43 IPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDLVQRVPRDEFQGVG--ELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred chhHHHHHhCCCCCceeEEEeCchHhcCCCChHHeEEecHHHhCcCC--CCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 344677888888899999998876544444 46666665532 6889999875 4444 456799999974
No 22
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=32.80 E-value=33 Score=42.16 Aligned_cols=16 Identities=19% Similarity=0.017 Sum_probs=6.7
Q ss_pred cccccCCCCccccccc
Q 001728 921 FVANIDGMAPDTLLSR 936 (1020)
Q Consensus 921 ~~~n~d~~~~d~ll~~ 936 (1020)
++.++-.-..|.+|-|
T Consensus 571 i~s~~~spv~nh~lYr 586 (742)
T KOG4274|consen 571 IGSMGGSPVLNHLLYR 586 (742)
T ss_pred cccccCCCcccchhhh
Confidence 4444433333444444
No 23
>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=32.50 E-value=63 Score=30.61 Aligned_cols=57 Identities=23% Similarity=0.330 Sum_probs=31.0
Q ss_pred chHhHhHHHhcCccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeecccCC
Q 001728 278 PLAKYNKAMYTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDEST 341 (1020)
Q Consensus 278 p~~kY~kAm~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~ 341 (1020)
..+.|..=+.-+..+||++||.=.-||-. .-=.|+|..++. | .-|+ -.++|.|....
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 122677666653 1 1121 24788887764
No 24
>PF13388 DUF4106: Protein of unknown function (DUF4106)
Probab=31.75 E-value=55 Score=37.55 Aligned_cols=9 Identities=33% Similarity=0.265 Sum_probs=3.8
Q ss_pred CCCCCCCCC
Q 001728 371 PKFPKQPGM 379 (1020)
Q Consensus 371 ~Kr~r~~~~ 379 (1020)
-|+.+..|+
T Consensus 73 gkklksegf 81 (422)
T PF13388_consen 73 GKKLKSEGF 81 (422)
T ss_pred ccccccchh
Confidence 344444443
No 25
>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=31.19 E-value=49 Score=32.64 Aligned_cols=26 Identities=31% Similarity=0.526 Sum_probs=17.4
Q ss_pred CCCCCCCeEEEEEcC-CCcEEEEEEec
Q 001728 202 KRLFAGDSVLFIRDE-KSQLLLGIRRA 227 (1020)
Q Consensus 202 KkLvaGDsVVF~R~e-~GeL~VGIRRA 227 (1020)
++++.||.|+||... .+.-+|||=|-
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 56777776664
No 26
>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=31.12 E-value=62 Score=26.79 Aligned_cols=52 Identities=12% Similarity=0.169 Sum_probs=37.2
Q ss_pred CccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCccccccccc
Q 001728 289 QVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPV 357 (1020)
Q Consensus 289 ~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEpv 357 (1020)
.|.+|..+...| .+ ..||.|+|+++.. + ....|.-++-... +-|...+|-++
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 4567888775432 45666665554
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=29.82 E-value=2.4e+02 Score=29.02 Aligned_cols=72 Identities=11% Similarity=0.236 Sum_probs=51.3
Q ss_pred EeccccCCCCCCceeechhhhhh--cCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccC
Q 001728 128 KTLTASDTSTHGGFSVPRRAAEK--IFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTK 202 (1020)
Q Consensus 128 KtLTaSDVs~~GrfsVPKr~AE~--~FPpLD~s~~~PsqeLvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVreK 202 (1020)
-+.|..|..-.|.+.|-.+..+. ++| ...+.+.|. +|..|+- |.+.|.+ +.-.|.+. -.+
T Consensus 13 atVT~a~L~Y~GSItID~~Lm~aagi~p---------~E~V~V~Nv~NG~Rf~T-YvI~G~~GSg~I~lNGA-----AAr 77 (126)
T TIGR00223 13 ATVTHANLNYEGSITIDEDLLDAAGILE---------NEKVDIVNVNNGKRFST-YAIAGKRGSRIICVNGA-----AAR 77 (126)
T ss_pred eEEeccccccceeEEECHHHHHhcCCCC---------CCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HHh
Confidence 47788899888999999987765 333 345777886 5888886 6667754 33344333 566
Q ss_pred CCCCCCeEEEEE
Q 001728 203 RLFAGDSVLFIR 214 (1020)
Q Consensus 203 kLvaGDsVVF~R 214 (1020)
....||.|+++=
T Consensus 78 l~~~GD~VII~s 89 (126)
T TIGR00223 78 CVSVGDIVIIAS 89 (126)
T ss_pred cCCCCCEEEEEE
Confidence 778999999863
No 28
>CHL00010 infA translation initiation factor 1
Probab=29.53 E-value=2.6e+02 Score=25.90 Aligned_cols=50 Identities=16% Similarity=0.074 Sum_probs=27.4
Q ss_pred EEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc-cCCCCCCCeEEEEE--cCCCcEEEEEEecc
Q 001728 165 EIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS-TKRLFAGDSVLFIR--DEKSQLLLGIRRAN 228 (1020)
Q Consensus 165 eLvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr-eKkLvaGDsVVF~R--~e~GeL~VGIRRA~ 228 (1020)
.+.+++..|+ .+.|..||+ |.+ ..++.+||.|.|.- .++++-+|-.|-.+
T Consensus 21 ~y~V~~~~g~--~~~c~~rGk------------lr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 21 MFRVRLDNGC--QVLGYISGK------------IRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred EEEEEeCCCC--EEEEEeccc------------eecCCcccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 3455666665 344445442 222 34478999999984 33434444444444
No 29
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=28.92 E-value=2.7e+02 Score=28.62 Aligned_cols=74 Identities=12% Similarity=0.213 Sum_probs=51.5
Q ss_pred EeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeC-CCCeEEEEEEEeCCC--CceeecccchhhhccCCC
Q 001728 128 KTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDL-HDTTWTFRHIYRGQP--KRHLLTTGWSVFVSTKRL 204 (1020)
Q Consensus 128 KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsqeLvakDl-hGk~W~FRhiyRg~p--rRhlLTTGWS~FVreKkL 204 (1020)
-+.|..|..-.|.+.|-.+.++. -+.- |...+.+.|. +|..|.- |.+.|.+ +.-.|.+. -.+..
T Consensus 13 atVT~a~L~Y~GSitID~~Ll~a----agi~---p~E~V~V~Nv~NG~Rf~T-YvI~g~~GSg~I~lNGA-----AAr~~ 79 (126)
T PRK05449 13 ATVTEADLNYEGSITIDEDLLDA----AGIL---ENEKVQIVNVNNGARFET-YVIAGERGSGVICLNGA-----AARLV 79 (126)
T ss_pred eEEeccccccceeEEECHHHHHh----cCCC---CCCEEEEEECCCCcEEEE-EEEEcCCCCCEEEeCCH-----HHhcC
Confidence 47889999989999999987776 2221 2335777786 5888876 6666754 33344433 56778
Q ss_pred CCCCeEEEEE
Q 001728 205 FAGDSVLFIR 214 (1020)
Q Consensus 205 vaGDsVVF~R 214 (1020)
..||.|+++=
T Consensus 80 ~~GD~vII~a 89 (126)
T PRK05449 80 QVGDLVIIAA 89 (126)
T ss_pred CCCCEEEEEE
Confidence 8999999863
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=26.84 E-value=3e+02 Score=24.62 Aligned_cols=49 Identities=20% Similarity=0.209 Sum_probs=33.6
Q ss_pred CceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE----cCCCcEEEEEEe
Q 001728 162 PAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR----DEKSQLLLGIRR 226 (1020)
Q Consensus 162 PsqeLvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVreKkLvaGDsVVF~R----~e~GeL~VGIRR 226 (1020)
....+.+.|..| ..++.+|+..- ...|..||.|.+.. .-+|.+.+.+.+
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=24.43 E-value=2.5e+02 Score=28.08 Aligned_cols=79 Identities=22% Similarity=0.312 Sum_probs=52.7
Q ss_pred CCeEEEEEcCCCcEEEEEEeccCCCCCCCCcccCCCccccchHHHHHHHHhcCCcEEEEEc-CCC--CCCccccchHhHh
Q 001728 207 GDSVLFIRDEKSQLLLGIRRANRQQPALSSSVISSDSMHIGILAAAAHAAANNSPFTIFYN-PRA--SPSEFVIPLAKYN 283 (1020)
Q Consensus 207 GDsVVF~R~e~GeL~VGIRRA~r~~~~~~ssv~ssdsm~~gvLAaAahaaat~~~F~V~Y~-PRa--s~sEFVVp~~kY~ 283 (1020)
|..|+=-+++||.++.|.-++.- +...|.|.|+ .+. -..+|||...
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 55666666789999988766432 3445666662 221 1356677655
Q ss_pred HHHhcCccccceeeeeeecccccccceeeEEEEec
Q 001728 284 KAMYTQVSLGMRFRMMFETEESGVRRYMGTITSIS 318 (1020)
Q Consensus 284 kAm~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVs 318 (1020)
.++.+...+|+.+-+..|..+ .++.=|||++.-
T Consensus 50 ~~~~~~L~~GD~VLA~~~~~~--~~Y~Pg~V~~~~ 82 (124)
T PF15057_consen 50 DAMRHSLQVGDKVLAPWEPDD--CRYGPGTVIAGP 82 (124)
T ss_pred CcccCcCCCCCEEEEecCcCC--CEEeCEEEEECc
Confidence 566899999999999965432 346669999864
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=23.23 E-value=1.1e+02 Score=26.89 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=23.8
Q ss_pred ccceeeeeeecccccccceeeEEEEeccCCC
Q 001728 292 LGMRFRMMFETEESGVRRYMGTITSISDLDP 322 (1020)
Q Consensus 292 ~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP 322 (1020)
+|-|+.-.||.++.+...|.|+|..--+..|
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 5889999999998888888999999876554
No 33
>PF00381 PTS-HPr: PTS HPr component phosphorylation site; InterPro: IPR005698 The histidine-containing phosphocarrier protein (HPr) is a central component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which transfers metabolic carbohydrates across the cell membrane in many bacterial species [, ]. PTS catalyses the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is as follows: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to Enzyme I (EI) of the PTS, which in turn transfers it to the phosphoryl carrier protein (HPr) [, ]. Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease complex (enzymes EII/EIII). HPr [, ] is a small cytoplasmic protein of 70 to 90 amino acid residues. In some bacteria, HPr is a domain in a larger protein that includes a EIII(Fru) (IIA) domain and in some cases also the EI domain. A conserved histidine in the N-terminal section of HPr serves as an acceptor for the phosphoryl group of EI. In the central part of HPr, there is a conserved serine which (in Gram-positive bacteria only) is phosphorylated by an ATP-dependent protein kinase; a process which probably play a regulatory role in sugar transport. The overall architecture of the HPr domain has been described as an open faced beta-sandwich in which a beta-sheet is packed against three alpha-helices. Regulatory phosphorylation at the conserved Ser residue does not appear to induce large structural changes to the HPr domain, in particular in the region of the active site [, ].; GO: 0005351 sugar:hydrogen symporter activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system; PDB: 1TXE_A 1QR5_A 1RZR_S 2NZU_L 2OEN_L 2NZV_L 1Y51_B 1Y4Y_A 1Y50_A 2HPR_A ....
Probab=22.96 E-value=1.8e+02 Score=26.56 Aligned_cols=60 Identities=17% Similarity=0.105 Sum_probs=44.9
Q ss_pred CCccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeeccccc
Q 001728 241 SDSMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 306 (1020)
Q Consensus 241 sdsm~~gvLAaAahaaat-~~~F~V~Y~PRas~sEFVVp~~kY~kAm~~~Ws~GMRFKM~FEtEdss 306 (1020)
...+|....+.-+++|.+ ++.++|.|.- -.|++..+..-|.-....|+.++..+|++|..
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 345665444444444433 5778888774 48999999999999999999999999998864
No 34
>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=22.96 E-value=2.8e+02 Score=24.87 Aligned_cols=59 Identities=15% Similarity=0.028 Sum_probs=42.0
Q ss_pred CccccchHHHHHHHHhc-CCcEEEEEcCCCCCCccccchHhHhHHHhcCccccceeeeeeeccccc
Q 001728 242 DSMHIGILAAAAHAAAN-NSPFTIFYNPRASPSEFVIPLAKYNKAMYTQVSLGMRFRMMFETEESG 306 (1020)
Q Consensus 242 dsm~~gvLAaAahaaat-~~~F~V~Y~PRas~sEFVVp~~kY~kAm~~~Ws~GMRFKM~FEtEdss 306 (1020)
..+|....+.-++.|.+ .+.++|.|. ...|++..+..-|.-.+..|+.+...+|++|..
T Consensus 8 ~GlHaRpa~~~v~~a~~~~~~v~i~~~------~~~vdakSil~i~~L~~~~G~~i~i~~~G~de~ 67 (77)
T cd00367 8 LGLHARPAALLVQLASKFKSDITLRKG------GRKANAKSILGLMSLGAKQGDEITLSAEGEDAE 67 (77)
T ss_pred CCCcHHHHHHHHHHHHhCCCEEEEEEC------CEEEcHHhHHHHHHcCCCCCCEEEEEEECcCHH
Confidence 34554443333444433 455666664 458999999999999999999999999988753
No 35
>PF02643 DUF192: Uncharacterized ACR, COG1430; InterPro: IPR003795 This entry describes proteins of unknown function.; PDB: 3M7A_B 3PJY_B.
Probab=22.32 E-value=1.4e+02 Score=28.93 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=27.1
Q ss_pred eEEEEEeCCCCeEEEEEEEe---------CCCCceee--cccchhhhccCCCCCCCeEEE
Q 001728 164 QEIVARDLHDTTWTFRHIYR---------GQPKRHLL--TTGWSVFVSTKRLFAGDSVLF 212 (1020)
Q Consensus 164 qeLvakDlhGk~W~FRhiyR---------g~prRhlL--TTGWS~FVreKkLvaGDsVVF 212 (1020)
.++.+.|..|++=....... ..+-+|+| ..| ++..++|++||.|.|
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 46778888887655554441 12346888 455 458899999999987
No 36
>PRK14699 replication factor A; Provisional
Probab=21.76 E-value=3.1e+02 Score=33.40 Aligned_cols=66 Identities=14% Similarity=0.245 Sum_probs=44.8
Q ss_pred CCceeEEEeccccCCCCCCceeechhhhhhcCCCCCCCCCCCceEEEEEeCCCCeEEEEEEEeCCCCceeecccchhhhc
Q 001728 121 QPTEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVS 200 (1020)
Q Consensus 121 ~~~~~F~KtLTaSDVs~~GrfsVPKr~AE~~FPpLD~s~~~PsqeLvakDlhGk~W~FRhiyRg~prRhlLTTGWS~FVr 200 (1020)
..+.++.|+|+.+++.+ |-..|++ ..-..++.+.|..| +.||+.|... -..+.
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 4434443 11234678999999 5677877521 13344
Q ss_pred cCCCCCCCeEEEE
Q 001728 201 TKRLFAGDSVLFI 213 (1020)
Q Consensus 201 eKkLvaGDsVVF~ 213 (1020)
+-+|++||+|.+-
T Consensus 121 ~g~l~~GDvv~I~ 133 (484)
T PRK14699 121 AGKIKAGQTLQIS 133 (484)
T ss_pred hcCCCCCCEEEEc
Confidence 5579999999883
No 37
>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=21.68 E-value=74 Score=35.44 Aligned_cols=57 Identities=19% Similarity=0.233 Sum_probs=32.5
Q ss_pred hcCccccceeeeeeecccccccceeeEEEEeccCCCCCCCCCCcceeeeecccCCCCCCCCCcccccccccc
Q 001728 287 YTQVSLGMRFRMMFETEESGVRRYMGTITSISDLDPLRWKNSQWRNLQVGWDESTAGERPSRVSLWETEPVV 358 (1020)
Q Consensus 287 ~~~Ws~GMRFKM~FEtEdss~rwy~GTI~gVsd~DP~rWp~S~WR~LqV~WDE~~~~~r~~RVSPWEIEpv~ 358 (1020)
...|.+|++.+..|..+ ..+|.+||++|..-+- .| .|+.++-+ +.+.|+.=+|.+..
T Consensus 66 ~~~WkvGd~C~A~~s~D---g~~Y~A~I~~i~~~~~--------~~-~V~f~gYg---n~e~v~l~dL~~~~ 122 (264)
T PF06003_consen 66 NKKWKVGDKCMAVYSED---GQYYPATIESIDEEDG--------TC-VVVFTGYG---NEEEVNLSDLKPSE 122 (264)
T ss_dssp TT---TT-EEEEE-TTT---SSEEEEEEEEEETTTT--------EE-EEEETTTT---EEEEEEGGGEEETT
T ss_pred ccCCCCCCEEEEEECCC---CCEEEEEEEEEcCCCC--------EE-EEEEcccC---CeEeeehhhhcccc
Confidence 36899999999999533 3689999999975221 23 37766643 23445554554443
No 38
>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=21.61 E-value=1.4e+02 Score=23.47 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=21.6
Q ss_pred CCCCceeechhhhhhcCCCCCCCCCCCceEEEEE-eCCCCe
Q 001728 136 STHGGFSVPRRAAEKIFPPLDYSMQPPAQEIVAR-DLHDTT 175 (1020)
Q Consensus 136 s~~GrfsVPKr~AE~~FPpLD~s~~~PsqeLvak-DlhGk~ 175 (1020)
+..|++.||++..+. ++.. ++..+.+. +.+|..
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 5444 23456666 445543
No 39
>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=21.10 E-value=62 Score=30.62 Aligned_cols=34 Identities=21% Similarity=0.385 Sum_probs=22.4
Q ss_pred hhhhccCCCCCCCeEEEEEcCCCc-EEEEEEeccC
Q 001728 196 SVFVSTKRLFAGDSVLFIRDEKSQ-LLLGIRRANR 229 (1020)
Q Consensus 196 S~FVreKkLvaGDsVVF~R~e~Ge-L~VGIRRA~r 229 (1020)
..|+++++|..||.|.++|.++.= ..+++-...|
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 378999999999999999987653 3345554444
No 40
>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=21.05 E-value=67 Score=29.85 Aligned_cols=41 Identities=17% Similarity=0.410 Sum_probs=21.6
Q ss_pred ceEEEEEeCCC-CeEEEEEEEeCCCCceeecccchhhhccCCCCCCCeEEEEE
Q 001728 163 AQEIVARDLHD-TTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR 214 (1020)
Q Consensus 163 sqeLvakDlhG-k~W~FRhiyRg~prRhlLTTGWS~FVreKkLvaGDsVVF~R 214 (1020)
.-+|.++|..| ++|+| +....|+ .-..+..|.+|++++|--
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 55889999988 46665 2334443 445678899999999864
No 41
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=20.31 E-value=65 Score=29.27 Aligned_cols=27 Identities=22% Similarity=0.204 Sum_probs=12.9
Q ss_pred ccchhhhccCCCCCCCeEEEEEcCCCcEEE
Q 001728 193 TGWSVFVSTKRLFAGDSVLFIRDEKSQLLL 222 (1020)
Q Consensus 193 TGWS~FVreKkLvaGDsVVF~R~e~GeL~V 222 (1020)
.|=...-|.++|++||.|.| ++..+.|
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
Done!