Query 026427
Match_columns 238
No_of_seqs 45 out of 47
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 07:52:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026427.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026427hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12674 Zn_ribbon_2: Putative 71.1 6.3 0.00014 30.4 3.7 45 135-186 34-79 (81)
2 PF13618 Gluconate_2-dh3: Gluc 53.0 22 0.00048 27.9 3.9 70 144-218 46-118 (131)
3 PF13565 HTH_32: Homeodomain-l 41.2 55 0.0012 23.1 4.1 30 150-182 34-63 (77)
4 cd00090 HTH_ARSR Arsenical Res 37.9 72 0.0016 20.9 4.1 53 155-212 12-71 (78)
5 PF09813 Coiled-coil_56: Coile 37.8 21 0.00045 29.2 1.6 34 150-186 9-42 (100)
6 TIGR03299 LGT_TIGR03299 phage/ 35.7 37 0.0008 32.1 3.2 52 161-215 207-269 (309)
7 cd07485 Peptidases_S8_Fervidol 33.9 43 0.00094 29.2 3.1 43 136-180 230-273 (273)
8 PF10026 DUF2268: Predicted Zn 31.4 82 0.0018 27.0 4.3 38 147-184 96-137 (195)
9 cd07498 Peptidases_S8_15 Pepti 31.4 52 0.0011 27.8 3.1 43 136-180 200-242 (242)
10 TIGR01610 phage_O_Nterm phage 31.2 46 0.001 25.5 2.5 57 135-192 3-79 (95)
11 cd00610 OAT_like Acetyl ornith 30.8 32 0.00068 31.1 1.8 43 190-233 27-71 (413)
12 PF12668 DUF3791: Protein of u 28.3 51 0.0011 23.6 2.2 26 153-178 2-27 (62)
13 PF14495 Cytochrom_C550: Cytoc 28.2 62 0.0013 27.8 3.0 35 163-201 101-135 (135)
14 PF07725 LRR_3: Leucine Rich R 27.6 26 0.00056 21.0 0.4 12 187-198 9-20 (20)
15 PF02212 GED: Dynamin GTPase e 27.5 94 0.002 23.5 3.7 27 23-49 65-91 (92)
16 cd07477 Peptidases_S8_Subtilis 26.8 68 0.0015 26.6 3.0 41 137-180 188-229 (229)
17 PF08586 Rsc14: RSC complex, R 26.6 73 0.0016 26.2 3.0 49 146-200 5-56 (101)
18 PF14246 TetR_C_7: AefR-like t 25.9 45 0.00098 22.3 1.5 15 144-158 41-55 (55)
19 cd07981 TAF12 TATA Binding Pro 24.1 1.3E+02 0.0027 22.3 3.7 36 145-181 33-68 (72)
20 cd07481 Peptidases_S8_Bacillop 24.0 99 0.0021 26.9 3.6 44 137-180 219-262 (264)
21 cd07490 Peptidases_S8_6 Peptid 23.9 97 0.0021 26.3 3.5 23 155-180 230-252 (254)
22 PHA02941 hypothetical protein; 23.8 63 0.0014 30.9 2.5 30 77-106 240-269 (356)
23 PF09312 SurA_N: SurA N-termin 23.7 56 0.0012 25.8 1.9 32 140-179 65-96 (118)
24 PF06067 DUF932: Domain of unk 23.6 71 0.0015 28.0 2.7 50 163-215 140-200 (239)
25 PF05402 PqqD: Coenzyme PQQ sy 23.6 1.6E+02 0.0034 20.4 3.9 41 138-183 2-45 (68)
26 PF02344 Myc-LZ: Myc leucine z 23.4 91 0.002 20.9 2.5 21 22-42 9-29 (32)
27 cd07487 Peptidases_S8_1 Peptid 23.2 1E+02 0.0023 26.1 3.5 24 154-180 239-262 (264)
28 PF02734 Dak2: DAK2 domain; I 23.1 1.3E+02 0.0029 25.4 4.1 44 151-195 54-97 (175)
29 cd05833 Ribosomal_P2 Ribosomal 22.5 86 0.0019 25.5 2.7 27 153-179 2-29 (109)
30 PF07030 DUF1320: Protein of u 22.3 1.7E+02 0.0036 23.7 4.4 52 138-190 51-106 (130)
31 KOG3167 Box H/ACA snoRNP compo 21.4 1.4E+02 0.0031 26.1 3.9 64 142-205 12-83 (153)
32 PF09371 Tex_N: Tex-like prote 21.2 1.2E+02 0.0026 26.7 3.6 41 153-195 26-69 (193)
33 PF09045 L27_2: L27_2; InterP 20.6 81 0.0018 23.6 2.0 30 80-110 23-52 (58)
34 PF02426 MIase: Muconolactone 20.3 73 0.0016 25.2 1.9 30 166-195 13-45 (91)
35 cd07474 Peptidases_S8_subtilis 20.0 2.3E+02 0.0049 24.7 5.0 44 137-182 227-270 (295)
No 1
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=71.08 E-value=6.3 Score=30.35 Aligned_cols=45 Identities=16% Similarity=0.384 Sum_probs=36.8
Q ss_pred CCCCeEE-eccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhh
Q 026427 135 DREDYVL-VSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKR 186 (238)
Q Consensus 135 d~e~YVl-V~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~kr 186 (238)
.++.|+- ++-|+.++..+-||+..-- ++|+++.+.+.+.|..+||
T Consensus 34 ~~G~Ft~~~t~eemie~~~~~~~~~~~-------~~~~~a~~~~~~~lp~LkR 79 (81)
T PF12674_consen 34 QNGEFTQDITMEEMIEFCVPFMDEFNG-------MTPEEARKMMPRYLPTLKR 79 (81)
T ss_pred cCCceeecCCHHHHHHHHHHHHHHhCC-------CCHHHHHHHHHHHccCCcc
Confidence 4566777 7888889988888886543 9999999999999987776
No 2
>PF13618 Gluconate_2-dh3: Gluconate 2-dehydrogenase subunit 3
Probab=53.00 E-value=22 Score=27.87 Aligned_cols=70 Identities=20% Similarity=0.285 Sum_probs=32.6
Q ss_pred cchhHHHHHHHHHHHHhccccc-cCCChHHHHHHHHHHHhhhhhhhhhhhhhcc--cceEeeehhhhhhHHHhhcCHH
Q 026427 144 EEDIVDGIACFMAAYLLSLKQA-KNLTPNQLQEALSKTFSVKKRKGKLRKAWDG--SKVIYNVASWGATAVGIYQNPV 218 (238)
Q Consensus 144 eEDIVDGIA~FmA~yIlSlpkA-K~ltP~qLQkALskafs~~krkgKlrk~Wd~--gKviY~~aSWg~ta~GlYqNp~ 218 (238)
++.+.+|++.|-+.+...+.+. ..|+++|-.+.|...-.... .-..|+. ++.+| -.-...|+.|.|.+|.
T Consensus 46 ~~~~~~gl~~ld~~a~~~~g~~F~~l~~~~~~~lL~~~~~~~~----~~~~~~~~~~~~ff-~~lr~~~~~gyyt~p~ 118 (131)
T PF13618_consen 46 RRAFRAGLAALDAYAQKRYGKSFAELSPAQREALLDALEKSEA----AGPDWDGIPGARFF-QQLRNLTLQGYYTSPE 118 (131)
T ss_pred HHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHhccc----cccccccCcHHHHH-HHHHHHHHHHHhcCCc
Confidence 4455555555555554443332 45555555444443332111 0011211 12233 3445677788888876
No 3
>PF13565 HTH_32: Homeodomain-like domain
Probab=41.21 E-value=55 Score=23.12 Aligned_cols=30 Identities=20% Similarity=0.232 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhccccccCCChHHHHHHHHHHHh
Q 026427 150 GIACFMAAYLLSLKQAKNLTPNQLQEALSKTFS 182 (238)
Q Consensus 150 GIA~FmA~yIlSlpkAK~ltP~qLQkALskafs 182 (238)
-+..+|-+.+.++| .+||.+|+..|..-|.
T Consensus 34 e~~~~i~~~~~~~p---~wt~~~i~~~L~~~~g 63 (77)
T PF13565_consen 34 EQRERIIALIEEHP---RWTPREIAEYLEEEFG 63 (77)
T ss_pred HHHHHHHHHHHhCC---CCCHHHHHHHHHHHhC
Confidence 34478888888999 9999999999999886
No 4
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=37.89 E-value=72 Score=20.87 Aligned_cols=53 Identities=21% Similarity=0.354 Sum_probs=33.3
Q ss_pred HHHHHhccccccCCChHHHHHH-------HHHHHhhhhhhhhhhhhhcccceEeeehhhhhhHHH
Q 026427 155 MAAYLLSLKQAKNLTPNQLQEA-------LSKTFSVKKRKGKLRKAWDGSKVIYNVASWGATAVG 212 (238)
Q Consensus 155 mA~yIlSlpkAK~ltP~qLQkA-------Lskafs~~krkgKlrk~Wd~gKviY~~aSWg~ta~G 212 (238)
|..||...| ++..++.+. +.+.+..+.++|-+..........|.+.. |-.++-
T Consensus 12 il~~l~~~~----~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~ 71 (78)
T cd00090 12 ILRLLLEGP----LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLA 71 (78)
T ss_pred HHHHHHHCC----cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHH
Confidence 344555544 777777765 45555556667777776666678888876 544443
No 5
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=37.76 E-value=21 Score=29.22 Aligned_cols=34 Identities=29% Similarity=0.252 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhh
Q 026427 150 GIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKR 186 (238)
Q Consensus 150 GIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~kr 186 (238)
|-|-|.=++ .|..-.|+|+|||=.=.--+...+|
T Consensus 9 ~~a~~a~ri---dp~~e~L~~~q~~fmr~vE~~~~kr 42 (100)
T PF09813_consen 9 GEAPFAQRI---DPSKEKLSPAQLQFMRQVELQQLKR 42 (100)
T ss_pred cccchhhhC---CcccccCCHHHHHHHHHHHHHHHHH
Confidence 445554444 8888899999998544333444444
No 6
>TIGR03299 LGT_TIGR03299 phage/plasmid-related protein TIGR03299. Members of this uncharacterized protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. The function is unknown.
Probab=35.73 E-value=37 Score=32.14 Aligned_cols=52 Identities=17% Similarity=0.283 Sum_probs=39.5
Q ss_pred ccccccCCChHHHHHHHHHHHhhh-----------hhhhhhhhhhcccceEeeehhhhhhHHHhhc
Q 026427 161 SLKQAKNLTPNQLQEALSKTFSVK-----------KRKGKLRKAWDGSKVIYNVASWGATAVGIYQ 215 (238)
Q Consensus 161 SlpkAK~ltP~qLQkALskafs~~-----------krkgKlrk~Wd~gKviY~~aSWg~ta~GlYq 215 (238)
.-=++..|||.|.++-+..+|-.- ++..++..+|++. =++++|+=|+.|+|+
T Consensus 207 ~~m~~~~ls~~e~~~f~~~~lp~~~~~~~~~~~~~~~~~~v~~l~~~~---~~l~~~~gTawg~~n 269 (309)
T TIGR03299 207 KRLAERPVSDRQFAAFLDDVLPVPDASDRDRTNNEKARDTVTRLFAGA---ARLEPVRGTAWGLLQ 269 (309)
T ss_pred HHHhcCCCCHHHHHHHHHHhcCCCCccccchhhHHHHHHHHHHHHhcc---hhcccccccHHHHHH
Confidence 334567899999999888888322 3345577888876 578899999999997
No 7
>cd07485 Peptidases_S8_Fervidolysin_like Peptidase S8 family domain in Fervidolysin. Fervidolysin found in Fervidobacterium pennivorans is an extracellular subtilisin-like keratinase. It is contains a signal peptide, a propeptide, and a catalytic region. The tertiary structure of fervidolysin is similar to that of subtilisin. It contains a Asp/His/Ser catalytic triad and is a member of the peptidase S8 (subtilisin and kexin) family. The catalytic triad is similar to that found in trypsin-like proteases, but it does not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. Howev
Probab=33.94 E-value=43 Score=29.24 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=26.7
Q ss_pred CCCeEEeccchhHHH-HHHHHHHHHhccccccCCChHHHHHHHHHH
Q 026427 136 REDYVLVSEEDIVDG-IACFMAAYLLSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 136 ~e~YVlV~eEDIVDG-IA~FmA~yIlSlpkAK~ltP~qLQkALska 180 (238)
++.|..++==-..-. ||--+|-.+.-+|+ .|+|+|+++.|..|
T Consensus 230 ~~~~~~~sGTS~AaP~VaG~aAll~~~~~~--~~~~~~i~~~L~~T 273 (273)
T cd07485 230 GGNYEYLSGTSMAAPHVSGVAALVLSKFPD--VFTPEQIRKLLEES 273 (273)
T ss_pred CCCeEeeccHHHHHHHHHHHHHHHHHhCCC--CCCHHHHHHHHHhC
Confidence 556766553332222 23344445555777 89999999999764
No 8
>PF10026 DUF2268: Predicted Zn-dependent protease (DUF2268); InterPro: IPR018728 This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=31.39 E-value=82 Score=27.03 Aligned_cols=38 Identities=18% Similarity=0.281 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHhcccc----ccCCChHHHHHHHHHHHhhh
Q 026427 147 IVDGIACFMAAYLLSLKQ----AKNLTPNQLQEALSKTFSVK 184 (238)
Q Consensus 147 IVDGIA~FmA~yIlSlpk----AK~ltP~qLQkALskafs~~ 184 (238)
|.||+|+|.|+-+.-... .+.++.+++++...+.+...
T Consensus 96 I~EGlAe~f~~~~~g~~~~~~w~~~~~~~~~~~~~~~~~~~~ 137 (195)
T PF10026_consen 96 IMEGLAEYFAEELYGEEYLGPWVTYYDEEELKELWKEFIKEN 137 (195)
T ss_pred HHhhHHHHHHHHHcCCCCCchhhhcCCHHHHHHHHHHHHHHh
Confidence 779999999999987766 88999999998877776544
No 9
>cd07498 Peptidases_S8_15 Peptidase S8 family domain, uncharacterized subfamily 15. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=31.36 E-value=52 Score=27.84 Aligned_cols=43 Identities=30% Similarity=0.393 Sum_probs=26.2
Q ss_pred CCCeEEeccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHH
Q 026427 136 REDYVLVSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 136 ~e~YVlV~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALska 180 (238)
+..|...+---..=.+++=+|+.|++ +-.+|||+||++.|..+
T Consensus 200 ~~~~~~~~GTS~Aap~vaG~~All~~--~~p~l~~~~i~~~L~~t 242 (242)
T cd07498 200 GGGYGSFSGTSFASPVAAGVAALILS--ANPNLTPAEVEDILTST 242 (242)
T ss_pred CCceEeeCcHHHHHHHHHHHHHHHHH--hCCCCCHHHHHHHHHhC
Confidence 45566555444444444445555554 23479999999998753
No 10
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=31.16 E-value=46 Score=25.51 Aligned_cols=57 Identities=12% Similarity=0.214 Sum_probs=39.2
Q ss_pred CCCCeEEeccchhHHHHHHH-----HHHHHhccc--------cccCCChHHHHH-------HHHHHHhhhhhhhhhhh
Q 026427 135 DREDYVLVSEEDIVDGIACF-----MAAYLLSLK--------QAKNLTPNQLQE-------ALSKTFSVKKRKGKLRK 192 (238)
Q Consensus 135 d~e~YVlV~eEDIVDGIA~F-----mA~yIlSlp--------kAK~ltP~qLQk-------ALskafs~~krkgKlrk 192 (238)
-++||+-... ..++.++.+ .|+||+-+- ....+|+.||-+ .++++++.+.++|-+.+
T Consensus 3 ~~~g~t~~~~-~~~e~l~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 3 LSNGYTRMAN-ELQEALPGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred cccchhhhhH-HHHHHHHhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 3678888776 455656544 667776554 578899999975 45677777777776654
No 11
>cd00610 OAT_like Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation.
Probab=30.76 E-value=32 Score=31.07 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=33.9
Q ss_pred hhhhhc-ccceEeeehh-hhhhHHHhhcCHHHHHHHHHHHHHHhHH
Q 026427 190 LRKAWD-GSKVIYNVAS-WGATAVGIYQNPVILRAASKAFWTSCHV 233 (238)
Q Consensus 190 lrk~Wd-~gKviY~~aS-Wg~ta~GlYqNp~ilk~A~ka~~ts~rv 233 (238)
=..+|| .|+.+....+ |++..+| |.+|.|++++.+++.+..++
T Consensus 27 g~~~~d~dG~~~id~~~~~~~~~lG-~~~p~v~~a~~~~~~~~~~~ 71 (413)
T cd00610 27 GAYLYDVDGNRYLDFLSGIGVLNLG-HNHPEVVEALKEQLAKLTHF 71 (413)
T ss_pred cCEEEeCCCCEEEEcCccHHhhccC-CCCHHHHHHHHHHHHhCcCc
Confidence 345785 6788888887 8988888 69999999999998654443
No 12
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=28.31 E-value=51 Score=23.56 Aligned_cols=26 Identities=8% Similarity=0.139 Sum_probs=22.3
Q ss_pred HHHHHHHhccccccCCChHHHHHHHH
Q 026427 153 CFMAAYLLSLKQAKNLTPNQLQEALS 178 (238)
Q Consensus 153 ~FmA~yIlSlpkAK~ltP~qLQkALs 178 (238)
.|+..||-..-+.+++||.|.=+.+.
T Consensus 2 ~F~v~~Ie~~A~~~~~s~~ea~~~~~ 27 (62)
T PF12668_consen 2 EFVVFCIEEFAKKLNISGEEAYNYFK 27 (62)
T ss_pred hHHHHHHHHHHHHHCcCHHHHHHHHH
Confidence 48899999999999999998766554
No 13
>PF14495 Cytochrom_C550: Cytochrome c-550 domain; PDB: 3ARC_V 1IZL 3A0H_V 3A0B_v 1E29_A 1F1C_B 1S5L_V 4FBY_i 3PRR_V 3PRQ_V ....
Probab=28.22 E-value=62 Score=27.78 Aligned_cols=35 Identities=29% Similarity=0.518 Sum_probs=17.9
Q ss_pred ccccCCChHHHHHHHHHHHhhhhhhhhhhhhhcccceEe
Q 026427 163 KQAKNLTPNQLQEALSKTFSVKKRKGKLRKAWDGSKVIY 201 (238)
Q Consensus 163 pkAK~ltP~qLQkALskafs~~krkgKlrk~Wd~gKviY 201 (238)
|+-.+||-++|+..-+--+..-|..| . |-+||+-|
T Consensus 101 p~mr~ltdddL~~iAg~IL~~pk~~~---~-WGggk~yy 135 (135)
T PF14495_consen 101 PKMRNLTDDDLYAIAGYILRQPKVAG---G-WGGGKIYY 135 (135)
T ss_dssp GGGTS--HHHHHHHHHHHHHHHHHHC---G-CCTCTTC-
T ss_pred HhhcCCCHHHHHHHHHHHHhcccccC---C-cCCCcccC
Confidence 55555666666555444444333332 2 99998766
No 14
>PF07725 LRR_3: Leucine Rich Repeat; InterPro: IPR011713 Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [, ].Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response []. Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterised by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the beta-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions []. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats []. This entry includes some LRRs that fail to be detected by the IPR001611 from INTERPRO model.
Probab=27.57 E-value=26 Score=21.04 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=9.7
Q ss_pred hhhhhhhhcccc
Q 026427 187 KGKLRKAWDGSK 198 (238)
Q Consensus 187 kgKlrk~Wd~gK 198 (238)
-.|+.++|+|.|
T Consensus 9 ~S~lekLW~G~k 20 (20)
T PF07725_consen 9 YSKLEKLWEGVK 20 (20)
T ss_pred CCChHHhcCccC
Confidence 468999999865
No 15
>PF02212 GED: Dynamin GTPase effector domain; InterPro: IPR003130 Dynamin GTPase effector domain found in proteins related to dynamin. Dynamin is a GTP-hydrolysing protein that is an essential participant in clathrin-mediated endocytosis by cells. It self-assembles into 'collars' in vivo at the necks of invaginated coated pits; the self-assembly of dynamin being coordinated by the GTPase domain. Mutation studies indicate that dynamin functions as a molecular regulator of receptor-mediated endocytosis [].; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 3ZYS_B 3SZR_A 3LJB_B 3T35_C 3T34_A 2X2F_D 2X2E_D 3SNH_A 3ZYC_D 3ZVR_A.
Probab=27.52 E-value=94 Score=23.53 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=23.6
Q ss_pred hhhhhHhHHHHHHHHHHHHHHHHhhhc
Q 026427 23 KEKVRVKRKTLEAVLQQCQRALELLSN 49 (238)
Q Consensus 23 ~~~~r~~r~tl~~vl~~~qrale~l~~ 49 (238)
.+.+.-||+.|+.-++.+++|++.|++
T Consensus 65 d~~i~~kR~~l~~~~~~L~~A~~~L~~ 91 (92)
T PF02212_consen 65 DPEIAEKREELKKKLERLKKAQQILSE 91 (92)
T ss_dssp GHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 357888999999999999999998863
No 16
>cd07477 Peptidases_S8_Subtilisin_subset Peptidase S8 family domain in Subtilisin proteins. This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain. TK-subtilisin is matured from pro-TK-subtilisin upon autoprocessing and degradation of the propeptide. Unlike other subtilisins though, the folding of the unprocessed form of pro-TK-subtilisin is induced by Ca2+ binding which is almost completed prior to autoprocessing. Ca2+ is required for activity unlike the bacterial subtilisins. The propeptide is not required for folding of the mature domain unlike the bacterial subtilases because of the stability produced from Ca2+ binding. Subtilisin Carlsberg is extremely similar in structure to subtilisin BPN'/Novo thoug
Probab=26.75 E-value=68 Score=26.64 Aligned_cols=41 Identities=29% Similarity=0.346 Sum_probs=23.6
Q ss_pred CCeEEeccchhHHHHHHHHHHHH-hccccccCCChHHHHHHHHHH
Q 026427 137 EDYVLVSEEDIVDGIACFMAAYL-LSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 137 e~YVlV~eEDIVDGIA~FmA~yI-lSlpkAK~ltP~qLQkALska 180 (238)
.+|..+.=--..=.+.+=+|+.| .-+|+ |+|+|++..|.++
T Consensus 188 ~~~~~~~GTS~Aap~vag~~All~~~~~~---~~~~~i~~~l~~t 229 (229)
T cd07477 188 NDYAYLSGTSMATPHVAGVAALVWSKRPE---LTNAQVRQALNKT 229 (229)
T ss_pred CCEEEEccHHHHHHHHHHHHHHHHHhCCC---CCHHHHHHHHHhC
Confidence 44555443333333334444444 44555 9999999998764
No 17
>PF08586 Rsc14: RSC complex, Rsc14/Ldb7 subunit; InterPro: IPR013895 RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions [].
Probab=26.58 E-value=73 Score=26.21 Aligned_cols=49 Identities=20% Similarity=0.304 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhhhh---hhhhhhcccceE
Q 026427 146 DIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKRKG---KLRKAWDGSKVI 200 (238)
Q Consensus 146 DIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~krkg---Klrk~Wd~gKvi 200 (238)
||+-|++||=. .+-=.+|++|||.-......+.+.+. .-++-|+-+|.+
T Consensus 5 dvIagLsalE~------S~~Vtfs~~eL~eLt~~~~~~r~~~~~~~~~~~~~~~~kRv 56 (101)
T PF08586_consen 5 DVIAGLSALER------SHQVTFSQEELQELTKQEKDNRKDRDDPELKRKDEKKSKRV 56 (101)
T ss_pred HHhhchHhhhc------ccccccCHHHHHHHHhchhhhhhhccchhhhhcccccccee
Confidence 56777777743 23346899999999988886665433 345567666665
No 18
>PF14246 TetR_C_7: AefR-like transcriptional repressor, C-terminal region; PDB: 3BHQ_B 3CDL_A.
Probab=25.87 E-value=45 Score=22.30 Aligned_cols=15 Identities=27% Similarity=0.527 Sum_probs=11.1
Q ss_pred cchhHHHHHHHHHHH
Q 026427 144 EEDIVDGIACFMAAY 158 (238)
Q Consensus 144 eEDIVDGIA~FmA~y 158 (238)
+..|-.+|..|+++|
T Consensus 41 ~~~v~~aV~~FL~aY 55 (55)
T PF14246_consen 41 ERIVESAVDMFLRAY 55 (55)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhC
Confidence 345667888888887
No 19
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=24.11 E-value=1.3e+02 Score=22.28 Aligned_cols=36 Identities=17% Similarity=0.284 Sum_probs=28.9
Q ss_pred chhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHH
Q 026427 145 EDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTF 181 (238)
Q Consensus 145 EDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskaf 181 (238)
|+.|+-|+.+..+| .-|.+.+.+.++.+|-+|.+.+
T Consensus 33 e~fv~~v~~~a~~l-AkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 33 DDFVDDVVEDACRL-AKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred HHHHHHHHHHHHHH-HHHcCCCCCCHHHHHHHHHHhc
Confidence 56677777776654 5789999999999999998876
No 20
>cd07481 Peptidases_S8_BacillopeptidaseF-like Peptidase S8 family domain in BacillopeptidaseF-like proteins. Bacillus subtilis produces and secretes proteases and other types of exoenzymes at the end of the exponential phase of growth. The ones that make up this group is known as bacillopeptidase F, encoded by bpr, a serine protease with high esterolytic activity which is inhibited by PMSF. Like other members of the peptidases S8 family these have a Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity.
Probab=24.01 E-value=99 Score=26.87 Aligned_cols=44 Identities=18% Similarity=0.067 Sum_probs=28.9
Q ss_pred CCeEEeccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHH
Q 026427 137 EDYVLVSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 137 e~YVlV~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALska 180 (238)
.+|..++==-..=-+.+=+|+.|++.-..+.|+|.|++..|..+
T Consensus 219 ~~~~~~~GTS~AaP~vaG~aAll~~~~p~~~l~~~~v~~~L~~t 262 (264)
T cd07481 219 GGYGSSSGTSMAAPHVAGVAALLWSANPSLIGDVDATEAILTET 262 (264)
T ss_pred CceEeeCcHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHh
Confidence 44555443333334555566677766555789999999999875
No 21
>cd07490 Peptidases_S8_6 Peptidase S8 family domain, uncharacterized subfamily 6. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=23.91 E-value=97 Score=26.32 Aligned_cols=23 Identities=30% Similarity=0.478 Sum_probs=16.6
Q ss_pred HHHHHhccccccCCChHHHHHHHHHH
Q 026427 155 MAAYLLSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 155 mA~yIlSlpkAK~ltP~qLQkALska 180 (238)
+|-.+.-+|. |+|.||+..|.++
T Consensus 230 aAl~~~~~p~---~~~~~i~~~L~~t 252 (254)
T cd07490 230 AALLAAAHPD---LSPEQIKDALTET 252 (254)
T ss_pred HHHHHHHCCC---CCHHHHHHHHHHh
Confidence 3344445564 9999999999865
No 22
>PHA02941 hypothetical protein; Provisional
Probab=23.78 E-value=63 Score=30.87 Aligned_cols=30 Identities=23% Similarity=0.391 Sum_probs=25.4
Q ss_pred CccchHHHHHHHHhhcCChHHHHHHHHhhh
Q 026427 77 IDREADELCDLLRSRVECPDFLDKLEYAQL 106 (238)
Q Consensus 77 ~d~~td~Lyd~Lks~Vesp~FL~kLe~~q~ 106 (238)
..+-.-+||+.+||++.|.+||.+....|-
T Consensus 240 asefilqlyemikskitsedflk~~m~~~l 269 (356)
T PHA02941 240 ASEFILQLYEMIKSKITSEDFLKHVMVYQL 269 (356)
T ss_pred HHHHHHHHHHHHHhhcchHHHHHHHHHhhc
Confidence 334567899999999999999999998774
No 23
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=23.73 E-value=56 Score=25.77 Aligned_cols=32 Identities=31% Similarity=0.520 Sum_probs=20.4
Q ss_pred EEeccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHH
Q 026427 140 VLVSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSK 179 (238)
Q Consensus 140 VlV~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALsk 179 (238)
+-|++++|=..|+.+. +..+||++||.++|.+
T Consensus 65 I~vsd~evd~~i~~ia--------~~n~ls~~ql~~~L~~ 96 (118)
T PF09312_consen 65 IKVSDEEVDEAIANIA--------KQNNLSVEQLRQQLEQ 96 (118)
T ss_dssp ----HHHHHHHHHHHH--------HHTT--HHHHHHHCHH
T ss_pred CCCCHHHHHHHHHHHH--------HHcCCCHHHHHHHHHH
Confidence 3567777777777754 5678999999999875
No 24
>PF06067 DUF932: Domain of unknown function (DUF932); InterPro: IPR017686 Members of this uncharacterised protein are found in various Mycobacterium phage genomes, in Streptomyces coelicolor Plasmid SCP1 and in bacterial genomes near various markers that suggest lateral gene transfer. The function of this protein is unknown.
Probab=23.60 E-value=71 Score=28.02 Aligned_cols=50 Identities=22% Similarity=0.437 Sum_probs=40.0
Q ss_pred ccccCCChHHHHHHHHHHHhhh-----------hhhhhhhhhhcccceEeeehhhhhhHHHhhc
Q 026427 163 KQAKNLTPNQLQEALSKTFSVK-----------KRKGKLRKAWDGSKVIYNVASWGATAVGIYQ 215 (238)
Q Consensus 163 pkAK~ltP~qLQkALskafs~~-----------krkgKlrk~Wd~gKviY~~aSWg~ta~GlYq 215 (238)
=+...|++.|.++-+..+|... ++..++..+|..... +..|+-|+.|+|+
T Consensus 140 l~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~t~w~~~N 200 (239)
T PF06067_consen 140 LAQIELTDDEFEAFADAALPLRYDSERKQRNNPKRRDQLLRLRRSEDR---LAGWGGTLWGAYN 200 (239)
T ss_pred HHhcCCCHHHHHHHHHHHhccCcccccccccccccHHHHHHHHhcCcc---cccCCCCHHHHHH
Confidence 3467899999999888888644 225678888887776 8999999999997
No 25
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.57 E-value=1.6e+02 Score=20.45 Aligned_cols=41 Identities=27% Similarity=0.451 Sum_probs=21.8
Q ss_pred CeEEeccch---hHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHhh
Q 026427 138 DYVLVSEED---IVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSV 183 (238)
Q Consensus 138 ~YVlV~eED---IVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~ 183 (238)
+|||+..+. .++++|.||-..+- ...|.+++-++|...|..
T Consensus 2 e~vll~~~~~~~~Ln~~a~~Iw~~~~-----g~~t~~ei~~~l~~~y~~ 45 (68)
T PF05402_consen 2 EYVLLDPESGEFTLNETAAFIWELLD-----GPRTVEEIVDALAEEYDV 45 (68)
T ss_dssp EEEEE----------THHHHHHHH-------SSS-HHHHHHHHHHHTT-
T ss_pred CEEEEeCCCCCccccHHHHHHHHHcc-----CCCCHHHHHHHHHHHcCC
Confidence 455555444 56888999888883 346777777777777743
No 26
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=23.38 E-value=91 Score=20.93 Aligned_cols=21 Identities=38% Similarity=0.578 Sum_probs=16.4
Q ss_pred chhhhhHhHHHHHHHHHHHHH
Q 026427 22 EKEKVRVKRKTLEAVLQQCQR 42 (238)
Q Consensus 22 ~~~~~r~~r~tl~~vl~~~qr 42 (238)
.++.+|=||.-|+.-|||+|.
T Consensus 9 ekeqLrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 9 EKEQLRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 368899999999999998875
No 27
>cd07487 Peptidases_S8_1 Peptidase S8 family domain, uncharacterized subfamily 1. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=23.22 E-value=1e+02 Score=26.07 Aligned_cols=24 Identities=29% Similarity=0.318 Sum_probs=16.6
Q ss_pred HHHHHHhccccccCCChHHHHHHHHHH
Q 026427 154 FMAAYLLSLKQAKNLTPNQLQEALSKT 180 (238)
Q Consensus 154 FmA~yIlSlpkAK~ltP~qLQkALska 180 (238)
.+|..+..+| +|+|+|++..|.++
T Consensus 239 ~~All~~~~p---~~~~~~ik~~L~~t 262 (264)
T cd07487 239 AIALLLQANP---ILTPDEVKCILRDT 262 (264)
T ss_pred HHHHHHHHCc---CCCHHHHHHHHHhh
Confidence 3333344445 89999999998765
No 28
>PF02734 Dak2: DAK2 domain; InterPro: IPR004007 Dihydroxyacetone kinase (glycerone kinase) 2.7.1.29 from EC catalyses the phosphorylation of glycerone in the presence of ATP to glycerone phosphate in the glycerol utilization pathway. This is the predicted phosphatase domain of the dihydroxyacetone kinase family.; GO: 0004371 glycerone kinase activity, 0006071 glycerol metabolic process; PDB: 3CR3_B 1UN8_A 1UN9_B 3PNL_B 2BTD_A.
Probab=23.11 E-value=1.3e+02 Score=25.44 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=33.9
Q ss_pred HHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhhhhhhhhhhc
Q 026427 151 IACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKRKGKLRKAWD 195 (238)
Q Consensus 151 IA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~krkgKlrk~Wd 195 (238)
++.|.-+.-..++....++++.|-+++..+....++.|+.+ .+|
T Consensus 54 ~~~~f~~~a~~l~~~~~~~~~~~~~a~~~~~~~i~~~g~a~-~Gd 97 (175)
T PF02734_consen 54 YSQFFMGAAKALKGKEELDAEDLAEAFEAALEAIQARGGAK-PGD 97 (175)
T ss_dssp HHHHHHHHHHHCHTTSECCHHHHHHHHHHHHHHHHHHH----TTS
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHHHHHHHHHHHcCCC-CCc
Confidence 35676677777788888999999999999999999887653 455
No 29
>cd05833 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2
Probab=22.49 E-value=86 Score=25.49 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=22.1
Q ss_pred HHHHHHHhcccccc-CCChHHHHHHHHH
Q 026427 153 CFMAAYLLSLKQAK-NLTPNQLQEALSK 179 (238)
Q Consensus 153 ~FmA~yIlSlpkAK-~ltP~qLQkALsk 179 (238)
.|||+|++-.-.-+ +.|.+++++.|+-
T Consensus 2 kyvaAylL~~l~g~~~pTa~dI~~IL~A 29 (109)
T cd05833 2 KYVAAYLLAVLGGNASPSAADVKKILGS 29 (109)
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 37899998887777 8999999888753
No 30
>PF07030 DUF1320: Protein of unknown function (DUF1320); InterPro: IPR009752 This entry is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.34 E-value=1.7e+02 Score=23.68 Aligned_cols=52 Identities=23% Similarity=0.359 Sum_probs=39.0
Q ss_pred CeEE--eccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhh--hhhh
Q 026427 138 DYVL--VSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKR--KGKL 190 (238)
Q Consensus 138 ~YVl--V~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~kr--kgKl 190 (238)
.|++ ...-.++-.++|=||+|-+..-....- |++.++.-..++.-+++ +||+
T Consensus 51 RY~lPl~~~p~~L~~~~~dIA~y~L~~~~~~~~-~e~~~~rY~~A~~~L~~ia~G~~ 106 (130)
T PF07030_consen 51 RYDLPLAPVPALLKRIACDIARYRLYDRRPSQE-TEPVRERYKDAIKWLEDIAKGKI 106 (130)
T ss_pred hcCCCcccccHHHHHHHHHHHHHHHHhcCCccC-cHHHHHHHHHHHHHHHHHHCCCc
Confidence 3544 456678999999999999866555444 99999999998876655 5554
No 31
>KOG3167 consensus Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification]
Probab=21.44 E-value=1.4e+02 Score=26.11 Aligned_cols=64 Identities=19% Similarity=0.213 Sum_probs=46.1
Q ss_pred eccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHhhhhhhhhhhh--------hhcccceEeeehh
Q 026427 142 VSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFSVKKRKGKLRK--------AWDGSKVIYNVAS 205 (238)
Q Consensus 142 V~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs~~krkgKlrk--------~Wd~gKviY~~aS 205 (238)
..++|.--|--.|=+.++.-+|=||-|.+..|+|-+-|....-.+.+.+|+ +=.|.|.|-.+|.
T Consensus 12 ~a~~~~~s~e~~Y~~~l~~~~PIAkPLA~kkl~kk~~KlvkKa~k~k~lrrGvKevqK~vrkGeKGl~VlAg 83 (153)
T KOG3167|consen 12 DAKGEKTSGEDEYQALLIAVNPIAKPLASKKLAKKVYKLVKKAAKQKGLRRGVKEVQKRVRKGEKGLCVLAG 83 (153)
T ss_pred ccccccccchhHHHHHHHhhcccccccccHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCCcceEEEec
Confidence 344555555667888999999999999999999999888865444333554 5567777766553
No 32
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=21.17 E-value=1.2e+02 Score=26.73 Aligned_cols=41 Identities=27% Similarity=0.313 Sum_probs=25.3
Q ss_pred HHHHHHHhccccccCCChHHHHHHHHHHH---hhhhhhhhhhhhhc
Q 026427 153 CFMAAYLLSLKQAKNLTPNQLQEALSKTF---SVKKRKGKLRKAWD 195 (238)
Q Consensus 153 ~FmA~yIlSlpkAK~ltP~qLQkALskaf---s~~krkgKlrk~Wd 195 (238)
-|||||=-. .+-+|+|+||+.....-- .-.+||..+.+.++
T Consensus 26 PFIARYRKe--~TG~Lde~~lR~i~~~~~~~~~L~~Rk~~il~~i~ 69 (193)
T PF09371_consen 26 PFIARYRKE--MTGGLDEVQLREIQDRYEYLRELEKRKESILKSIE 69 (193)
T ss_dssp HHHHHH-HH--HHTS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhhhhhhh--hhCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 499999654 578999999987654322 12266777766555
No 33
>PF09045 L27_2: L27_2; InterPro: IPR015132 The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer []. ; PDB: 3UIT_A 1VF6_B.
Probab=20.59 E-value=81 Score=23.60 Aligned_cols=30 Identities=23% Similarity=0.152 Sum_probs=21.2
Q ss_pred chHHHHHHHHhhcCChHHHHHHHHhhhcCCC
Q 026427 80 EADELCDLLRSRVECPDFLDKLEYAQLSGPP 110 (238)
Q Consensus 80 ~td~Lyd~Lks~Vesp~FL~kLe~~q~sv~q 110 (238)
...+=...|++++.||-|-+= =.+|+|+.|
T Consensus 23 s~~e~L~~l~~~LqSPLF~~i-L~LQqSi~q 52 (58)
T PF09045_consen 23 SHSEKLSLLKDTLQSPLFNQI-LTLQQSIKQ 52 (58)
T ss_dssp TTHHHHHHHHHHHH-HHHHHH-HHHHHHHCC
T ss_pred ccHHHHHHHHHHHhChHHHHH-HHHHHHHHH
Confidence 345556788999999999654 477887765
No 34
>PF02426 MIase: Muconolactone delta-isomerase; InterPro: IPR003464 This small enzyme forms a homodecameric complex, that catalyses the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway (5.3.3.4 from EC). The protein has a ferredoxin-like fold according to SCOP.; GO: 0006725 cellular aromatic compound metabolic process
Probab=20.31 E-value=73 Score=25.24 Aligned_cols=30 Identities=20% Similarity=0.521 Sum_probs=22.3
Q ss_pred cCCChHHHHHHHHH---HHhhhhhhhhhhhhhc
Q 026427 166 KNLTPNQLQEALSK---TFSVKKRKGKLRKAWD 195 (238)
Q Consensus 166 K~ltP~qLQkALsk---afs~~krkgKlrk~Wd 195 (238)
.+|+|++..+.-++ ....+.+.|||+++|-
T Consensus 13 ~~~~~~~~~~~~a~E~~~a~eLq~~G~~~~lWr 45 (91)
T PF02426_consen 13 PDMPPEEVDRLKAREKARAQELQRQGKWRHLWR 45 (91)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCeeeEEEE
Confidence 57888887765543 3345688999999997
No 35
>cd07474 Peptidases_S8_subtilisin_Vpr-like Peptidase S8 family domain in Vpr-like proteins. The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide. Vpr was identified as one of the proteases, along with WprA, that are capable of processing subtilin. Asp, Ser, His triadPeptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=20.00 E-value=2.3e+02 Score=24.66 Aligned_cols=44 Identities=23% Similarity=0.240 Sum_probs=31.8
Q ss_pred CCeEEeccchhHHHHHHHHHHHHhccccccCCChHHHHHHHHHHHh
Q 026427 137 EDYVLVSEEDIVDGIACFMAAYLLSLKQAKNLTPNQLQEALSKTFS 182 (238)
Q Consensus 137 e~YVlV~eEDIVDGIA~FmA~yIlSlpkAK~ltP~qLQkALskafs 182 (238)
..|+..+=--..=.+.+-+|+.|++.- .+|+|+|++..|..+=.
T Consensus 227 ~~~~~~~GTS~AaP~vaG~aAll~~~~--p~l~~~~v~~~L~~tA~ 270 (295)
T cd07474 227 TGYARMSGTSMAAPHVAGAAALLKQAH--PDWSPAQIKAALMNTAK 270 (295)
T ss_pred CceEEeccHHHHHHHHHHHHHHHHhhC--CCCCHHHHHHHHHhhCc
Confidence 566666665566666666777776643 57999999999987754
Done!