Query 027641
Match_columns 220
No_of_seqs 25 out of 27
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 12:59:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027641.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027641hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF15384 DUF4610: Domain of un 97.1 0.0067 1.5E-07 53.4 10.8 113 26-149 13-130 (197)
2 PF06632 XRCC4: DNA double-str 95.6 0.43 9.3E-06 44.8 13.8 141 25-172 15-168 (342)
3 cd07694 Ig2_CD4 Second immunog 71.3 2.8 6.1E-05 32.8 1.8 44 13-61 31-75 (88)
4 PF05013 FGase: N-formylglutam 65.0 8.9 0.00019 32.7 3.8 84 39-126 130-218 (222)
5 KOG4552 Vitamin-D-receptor int 60.3 9 0.00019 35.2 3.1 55 145-200 58-126 (272)
6 cd07766 DHQ_Fe-ADH Dehydroquin 53.7 11 0.00025 33.3 2.6 28 104-131 92-120 (332)
7 KOG2430 Glycosyl hydrolase, fa 51.3 11 0.00023 37.2 2.2 77 35-128 222-300 (587)
8 PF14147 Spore_YhaL: Sporulati 46.0 88 0.0019 22.8 5.7 41 134-174 8-52 (52)
9 PF02362 B3: B3 DNA binding do 45.9 8.8 0.00019 27.8 0.6 47 39-90 33-79 (100)
10 PF14088 DUF4268: Domain of un 44.4 1.4E+02 0.003 23.7 7.2 72 74-155 7-82 (140)
11 PF07889 DUF1664: Protein of u 43.1 50 0.0011 27.3 4.6 52 126-180 36-90 (126)
12 PF11740 KfrA_N: Plasmid repli 39.0 1.7E+02 0.0037 22.2 8.7 27 61-88 22-48 (120)
13 KOG3919 Kinesin-associated fas 37.6 22 0.00048 34.4 2.0 35 57-91 40-78 (374)
14 PF02318 FYVE_2: FYVE-type zin 37.5 98 0.0021 24.3 5.3 36 145-180 14-49 (118)
15 cd06843 PLPDE_III_PvsE_like Ty 36.8 62 0.0013 29.4 4.7 59 59-117 192-276 (377)
16 smart00327 VWA von Willebrand 36.4 46 0.001 25.1 3.3 45 37-83 105-156 (177)
17 cd00198 vWFA Von Willebrand fa 35.0 58 0.0013 23.5 3.5 49 34-83 98-153 (161)
18 PF02731 SKIP_SNW: SKIP/SNW do 33.6 1.2E+02 0.0026 26.2 5.6 37 111-150 77-122 (158)
19 PF09314 DUF1972: Domain of un 27.0 2.6E+02 0.0056 24.2 6.6 67 72-147 17-84 (185)
20 PF13580 SIS_2: SIS domain; PD 24.9 40 0.00087 26.6 1.2 47 74-122 88-137 (138)
21 KOG1369 Hexokinase [Carbohydra 23.7 42 0.00092 33.3 1.4 50 65-114 413-471 (474)
22 PLN03086 PRLI-interacting fact 23.6 87 0.0019 31.8 3.5 28 146-173 5-33 (567)
23 smart00243 GAS2 Growth-Arrest- 23.2 49 0.0011 25.5 1.3 16 67-82 49-64 (73)
24 PRK02220 4-oxalocrotonate taut 23.1 1.6E+02 0.0034 19.7 3.8 29 116-147 1-29 (61)
25 PF12209 SAC3: Leucine permeas 22.9 83 0.0018 23.9 2.5 18 133-150 37-54 (79)
26 cd08180 PDD 1,3-propanediol de 22.5 80 0.0017 28.4 2.8 18 114-131 108-125 (332)
27 COG0219 CspR Predicted rRNA me 22.4 3E+02 0.0065 23.8 6.1 73 70-149 60-149 (155)
28 PF02187 GAS2: Growth-Arrest-S 22.4 25 0.00055 26.9 -0.3 18 66-83 48-65 (73)
29 PRK02289 4-oxalocrotonate taut 22.3 1.6E+02 0.0036 20.2 3.8 30 116-148 1-30 (60)
30 PF07946 DUF1682: Protein of u 22.0 2.7E+02 0.0058 25.6 6.1 33 115-147 213-248 (321)
31 PF09260 DUF1966: Domain of un 21.9 63 0.0014 24.9 1.8 26 104-129 63-88 (91)
32 PRK00745 4-oxalocrotonate taut 21.8 1.7E+02 0.0038 19.6 3.8 29 116-147 1-29 (62)
33 KOG0945 Alpha-aminoadipic semi 21.8 88 0.0019 29.6 3.0 76 9-97 89-164 (289)
34 KOG1789 Endocytosis protein RM 21.7 1.6E+02 0.0035 33.5 5.2 72 105-177 1878-1958(2235)
35 cd08169 DHQ-like Dehydroquinat 21.5 1.2E+02 0.0026 27.9 3.7 22 104-125 97-119 (344)
36 cd08549 G1PDH_related Glycerol 21.5 1.7E+02 0.0037 26.5 4.7 23 104-127 94-116 (332)
37 PRK00002 aroB 3-dehydroquinate 21.5 1.5E+02 0.0032 27.2 4.3 34 89-125 94-128 (358)
38 PRK09423 gldA glycerol dehydro 21.0 54 0.0012 30.0 1.4 27 104-131 98-124 (366)
39 PF06670 Etmic-2: Microneme pr 20.6 1.1E+02 0.0023 29.2 3.3 110 22-132 201-326 (379)
No 1
>PF15384 DUF4610: Domain of unknown function (DUF4610)
Probab=97.10 E-value=0.0067 Score=53.44 Aligned_cols=113 Identities=18% Similarity=0.282 Sum_probs=96.3
Q ss_pred cceEEEEeCC-----CCCCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccceEeecCCCCC
Q 027641 26 GRFLFHVSAP-----DSSHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDVKLILEGHSNA 100 (220)
Q Consensus 26 ~pfLFh~~a~-----ds~hL~v~vTDfHSntW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~aslsS~~VkL~l~~~s~s 100 (220)
-+|+++-+-. +.+...|+|||--. -|.+.++-++|+.+|+-.|.- +..||..-|.+.+..+.|.|-|-.+
T Consensus 13 ~ryvCyce~~~~~~~~~g~~~i~vTDg~d-vW~t~~t~dsL~~~k~~~~L~-~~Edy~~rfR~Ac~~~~vtvtlqed--- 87 (197)
T PF15384_consen 13 PRYVCYCEGEGSGDGDAGVWNIYVTDGAD-VWSTCFTPDSLAALKARFGLS-SAEDYFSRFRAACEQQAVTVTLQED--- 87 (197)
T ss_pred CcEEEEEeCCCCCCCCCCeeEEEecccHH-hhhhccCHHHHHHHHhhcccc-hHHHHHHHHHHHhhcCeeEEEEecC---
Confidence 3588888877 78889999999874 499999999999999999984 6889999999999999999999863
Q ss_pred CCcchheeeeeccCCCCeeEEecccccchhHHHHHHHhhHHHHHHHHHh
Q 027641 101 DGAAYAKIVAQKSKGMPRISISLTRLTGSAATEAMAKLSLELFTAFRSM 149 (220)
Q Consensus 101 ~G~~~akLVA~KaKGmPrItI~L~kl~~saa~D~ma~lsl~lf~a~rs~ 149 (220)
+++-+-+.|-.-|++.|.|+.+..+...+..+-+.|.+.....
T Consensus 88 ------~a~Ltls~g~s~L~~dL~k~p~~Ea~~~Lq~L~f~lAe~v~~L 130 (197)
T PF15384_consen 88 ------RASLTLSGGPSALTFDLSKVPAPEAAPRLQALTFRLAERVCSL 130 (197)
T ss_pred ------eEEEEecCCCccceEEhhhCCCchhhHHHHHHHHHHHHHHHHH
Confidence 4445568889999999999999999998888888877655333
No 2
>PF06632 XRCC4: DNA double-strand break repair and V(D)J recombination protein XRCC4; InterPro: IPR010585 This entry represents the DNA double-strand break repair and V(D)J recombination protein XRCC4, which is found in certain Metazoans, fungi and plants. XRCC4 binds to DNA, and to DNA ligase IV (LIG4) to form the LIG4-XRCC4 complex []. The LIG4-XRCC4 complex is responsible for the ligation step in the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair. XRCC4 enhances the joining activity of LIG4. It is thought that XRCC4 and LIG4 are essential for alignment-based gap filling, as well as for final ligation of the breaks []. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. ; GO: 0003677 DNA binding, 0006302 double-strand break repair, 0006310 DNA recombination, 0005634 nucleus; PDB: 3RWR_R 1IK9_B 3SR2_E 3Q4F_H 3II6_B 1FU1_A 3MUD_B.
Probab=95.58 E-value=0.43 Score=44.78 Aligned_cols=141 Identities=14% Similarity=0.199 Sum_probs=83.0
Q ss_pred ccceEEEEeCCCC--CCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhccccc-----ceEeecCC
Q 027641 25 LGRFLFHVSAPDS--SHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSED-----VKLILEGH 97 (220)
Q Consensus 25 ~~pfLFh~~a~ds--~hL~v~vTDfHSntW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~aslsS~~-----VkL~l~~~ 97 (220)
-..++.++.-... +|+.|.+||-|+ +|.+..|-.++....++. ++++.+|++-+.-.|-.++ -.+.+-.
T Consensus 15 ~~~yfL~~~W~~~~~~~F~i~lTDG~s-aW~g~vs~~ei~~~A~~~--~~~~~eYv~~l~kaL~~~~~~~~~y~f~~~~- 90 (342)
T PF06632_consen 15 DSIYFLQVSWEKDLGSGFDITLTDGQS-AWSGTVSEEEIRQRAKDW--DMEVEEYVQELKKALTGQQQPSSEYSFDLTE- 90 (342)
T ss_dssp SSEEEEEEEESSSGGGEEEEEEESSSS-EEEEEEEHHHHHHHHHHT--TS-HHHHHHHHHHHHTSSSSSSSEEEEEE---
T ss_pred CceEEEEEEeccCCCCceEEEEecCCC-ceeeecCHHHHHHHHHHh--cCCHHHHHHHHHHHHhcCCCCCCcceEEEee-
Confidence 3446666655432 589999999995 899999999999988875 6889999999999996542 3444421
Q ss_pred CCCCCcchheeeeeccCCCCeeEEec-----ccccchhH-HHHHHHhhHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHH
Q 027641 98 SNADGAAYAKIVAQKSKGMPRISISL-----TRLTGSAA-TEAMAKLSLELFTAFRSMQTLIVQEQERCLQLEKEAAAEK 171 (220)
Q Consensus 98 s~s~G~~~akLVA~KaKGmPrItI~L-----~kl~~saa-~D~ma~lsl~lf~a~rs~~~~~~~eqe~~s~L~~~L~sEk 171 (220)
...|.....+-=. |-..-|++-| ..+..-+. -.-|-++++.....+...-.++.+|-++..+-.+.+.++-
T Consensus 91 -~~~~~~~l~~t~~--K~~~~it~rLGsv~L~~~~~p~e~i~el~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~ql 167 (342)
T PF06632_consen 91 -DRESNKSLSFTIE--KRLKDITFRLGSVKLKQVDNPAEVIRELFDWCLDANSRLQAENEHLQKENERLESEANKLLKQL 167 (342)
T ss_dssp ----ETTTTEEEEE--EEESSEEEEEEEEE-EE-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred -ccCCCceEEEEEE--EecCCceEEEeeEECCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2223344444333 3344566554 33333321 1123455677777776666666666655444333333333
Q ss_pred h
Q 027641 172 E 172 (220)
Q Consensus 172 e 172 (220)
|
T Consensus 168 E 168 (342)
T PF06632_consen 168 E 168 (342)
T ss_dssp H
T ss_pred H
Confidence 3
No 3
>cd07694 Ig2_CD4 Second immunoglobulin (Ig) domain of CD4. Ig2_CD4; second immunoglobulin (Ig) domain of CD4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.
Probab=71.29 E-value=2.8 Score=32.82 Aligned_cols=44 Identities=27% Similarity=0.351 Sum_probs=33.0
Q ss_pred CcccccCCCCCCccceEEEEeCCCCCCeEE-EEecccccchhhccccchh
Q 027641 13 PKAEWADSRSDSLGRFLFHVSAPDSSHLLI-QVTDFRSNTWEAKRSVLQL 61 (220)
Q Consensus 13 ak~e~~~~~s~~~~pfLFh~~a~ds~hL~v-~vTDfHSntW~~slSv~~L 61 (220)
++.+|-+|.+-.- +...++...|.+ .|+..||++|.+..++++-
T Consensus 31 ~~i~w~~P~n~~~-----~~~~~~~ktL~~~qv~~qdSG~WtC~V~~~~k 75 (88)
T cd07694 31 FKVEWRGPGNKSK-----QILNQDKKTLNLVQLGPNDSGTWDCIVSVNSS 75 (88)
T ss_pred ccEEEeCCCCccc-----eeccCCccEEEeceeCcccCCEEEEEEEECce
Confidence 3678888775532 556677777655 6999999999999998753
No 4
>PF05013 FGase: N-formylglutamate amidohydrolase; InterPro: IPR007709 Formylglutamate amidohydrolase (FGase) catalyzes the terminal reaction in the five-step pathway for histidine utilization in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolyzed to produce L-glutamate plus formate [].; PDB: 2ODF_G 2Q7S_A.
Probab=65.04 E-value=8.9 Score=32.74 Aligned_cols=84 Identities=14% Similarity=0.143 Sum_probs=50.4
Q ss_pred CeEEEEecccccchhhccccchhhhhHh-hhcCCCC---hHHHHHHHHHhcc-cccceEeecCCCCCCCcchheeeeecc
Q 027641 39 HLLIQVTDFRSNTWEAKRSVLQLDDMRD-EIGIGGS---WSEFIDYVVASIK-SEDVKLILEGHSNADGAAYAKIVAQKS 113 (220)
Q Consensus 39 hL~v~vTDfHSntW~~slSv~~LeDlRD-~VGIGGS---wsdF~dYl~asls-S~~VkL~l~~~s~s~G~~~akLVA~Ka 113 (220)
|-.+++-|+||-++...-.-.. ..+| +||+... +.++++.+.+.|. +.-.++....+=. |....+=..+.+
T Consensus 130 ~g~~illd~HS~~~~~~~~~~~--~~~~~~lG~~~~~s~~~~l~~~~~~~l~~~~g~~v~~N~Py~--Gg~~~~~~~~~~ 205 (222)
T PF05013_consen 130 FGKVILLDCHSMPPVPPGREDD--PRPDIVLGTLHGPSCDPELVDALAEALEASDGYSVRVNEPYS--GGYITRYYGRPA 205 (222)
T ss_dssp CS-EEEEEEEEE-TCCCCCCT------SECEECCTTTSS-HHHHHHHHHHCC-CTTS-EEETSS----GGHCCCHHHCCC
T ss_pred cCceEEEEeccCCCcccccccC--CCCCeEEEcCCCCCCCHHHHHHHHHHhhcccCcEEeeCCCCC--CcchhcEEecCC
Confidence 5678889999998875433322 3333 4676544 8899999999999 5555666655422 222222255567
Q ss_pred CCCCeeEEecccc
Q 027641 114 KGMPRISISLTRL 126 (220)
Q Consensus 114 KGmPrItI~L~kl 126 (220)
+|.|-|.|.+.+-
T Consensus 206 ~~v~~iqiEi~~~ 218 (222)
T PF05013_consen 206 RGVHAIQIEINRD 218 (222)
T ss_dssp CTEEEEEEEEEGG
T ss_pred CCceEEEEEEEHh
Confidence 8999999988763
No 5
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=60.32 E-value=9 Score=35.22 Aligned_cols=55 Identities=27% Similarity=0.330 Sum_probs=39.7
Q ss_pred HHHHhhHhHHHHHHHHHHHHHHHHHHHhhh-hccc-CC--cch----------HHHHHhhhhCCCCCccc
Q 027641 145 AFRSMQTLIVQEQERCLQLEKEAAAEKERN-ENIQ-NQ--PLY----------SKRQKLQKMNFSDKTDI 200 (220)
Q Consensus 145 a~rs~~~~~~~eqe~~s~L~~~L~sEkekn-e~iq-~q--~~~----------s~~qKlqk~n~s~k~~~ 200 (220)
.||+.. .++-||+...|+|+.|.++-||+ +.|| .| +-+ .-+|||..|+.-+|--|
T Consensus 58 ef~~ll-kla~eq~k~e~~m~~Lea~VEkrD~~IQqLqk~LK~aE~iLtta~fqA~qKLksi~~A~krpv 126 (272)
T KOG4552|consen 58 EFKTLL-KLAPEQQKREQLMRTLEAHVEKRDEVIQQLQKNLKSAEVILTTACFQANQKLKSIKEAEKRPV 126 (272)
T ss_pred HHHHHH-HHhHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 466655 46779999999999999988876 3443 33 111 45799999999888643
No 6
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=53.73 E-value=11 Score=33.31 Aligned_cols=28 Identities=39% Similarity=0.451 Sum_probs=20.0
Q ss_pred chheeeeecc-CCCCeeEEecccccchhH
Q 027641 104 AYAKIVAQKS-KGMPRISISLTRLTGSAA 131 (220)
Q Consensus 104 ~~akLVA~Ka-KGmPrItI~L~kl~~saa 131 (220)
|.||.+|-.. +|+|.|.||-|-.+|++.
T Consensus 92 D~aK~ia~~~~~~~p~i~iPTt~~tgse~ 120 (332)
T cd07766 92 DTAKAVAALLNRGLPIIIVPTTAATGSEV 120 (332)
T ss_pred HHHHHHHHHhcCCCCEEEEeCCCchhhcc
Confidence 6777776655 488888888877777544
No 7
>KOG2430 consensus Glycosyl hydrolase, family 47 [Carbohydrate transport and metabolism]
Probab=51.29 E-value=11 Score=37.24 Aligned_cols=77 Identities=22% Similarity=0.390 Sum_probs=52.2
Q ss_pred CCCCCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccceEeecCCCCCC--Ccchheeeeec
Q 027641 35 PDSSHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDVKLILEGHSNAD--GAAYAKIVAQK 112 (220)
Q Consensus 35 ~ds~hL~v~vTDfHSntW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~aslsS~~VkL~l~~~s~s~--G~~~akLVA~K 112 (220)
+.++.|.=++-+.||+.|. |.+-|||.+...|.+|+.... ++|+.+|--+ ..-+--+.--+
T Consensus 222 ~rss~l~g~~inihsgdw~-----------rkdsgigagidsyyey~lkay------illgddsfldrfn~hydai~ryi 284 (587)
T KOG2430|consen 222 HRSSDLMGTTINIHSGDWT-----------RKDSGIGAGIDSYYEYLLKAY------ILLGDDSFLDRFNKHYDAIKRYI 284 (587)
T ss_pred cccccccceeEEeccCcce-----------ecccCcCcchHHHHHHHHHHh------heeccHHHHHHHHHHHHHHHHHh
Confidence 4567799999999999997 678899999999999987553 3444332100 01122345556
Q ss_pred cCCCCeeEEecccccc
Q 027641 113 SKGMPRISISLTRLTG 128 (220)
Q Consensus 113 aKGmPrItI~L~kl~~ 128 (220)
+||--.+.+-.+|-+-
T Consensus 285 ~k~pi~ldvhihkp~l 300 (587)
T KOG2430|consen 285 NKGPIFLDVHIHKPML 300 (587)
T ss_pred cCCCeEEEEecccchh
Confidence 7887677777776554
No 8
>PF14147 Spore_YhaL: Sporulation protein YhaL
Probab=45.96 E-value=88 Score=22.79 Aligned_cols=41 Identities=17% Similarity=0.187 Sum_probs=30.6
Q ss_pred HHHHhhHHHHHHHHHhhHhHHHHHHHHHH----HHHHHHHHHhhh
Q 027641 134 AMAKLSLELFTAFRSMQTLIVQEQERCLQ----LEKEAAAEKERN 174 (220)
Q Consensus 134 ~ma~lsl~lf~a~rs~~~~~~~eqe~~s~----L~~~L~sEkekn 174 (220)
+++-+-++-|-+.+++++--..||+.+.+ -|+.+..||||+
T Consensus 8 vi~gI~~S~ym~v~t~~eE~~~dq~~IEkEGevymeR~e~ererR 52 (52)
T PF14147_consen 8 VIAGIIFSGYMAVKTAKEEREIDQEFIEKEGEVYMERMEEERERR 52 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHhHHHHHHHHHHHhccC
Confidence 45666778888889998888888888765 466777777763
No 9
>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=45.90 E-value=8.8 Score=27.80 Aligned_cols=47 Identities=19% Similarity=0.389 Sum_probs=33.2
Q ss_pred CeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccc
Q 027641 39 HLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDV 90 (220)
Q Consensus 39 hL~v~vTDfHSntW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~aslsS~~V 90 (220)
...|.+.|-....|...+++ ..=.....|+++|.+|+. ...|+-||+
T Consensus 33 ~~~v~l~~~~g~~W~v~~~~---~~~~~~~~l~~GW~~Fv~--~n~L~~GD~ 79 (100)
T PF02362_consen 33 SREVTLKDPDGRSWPVKLKY---RKNSGRYYLTGGWKKFVR--DNGLKEGDV 79 (100)
T ss_dssp -CEEEEEETTTEEEEEEEEE---ECCTTEEEEETTHHHHHH--HCT--TT-E
T ss_pred CeEEEEEeCCCCEEEEEEEE---EccCCeEEECCCHHHHHH--HcCCCCCCE
Confidence 45788899889999999866 222344889999999986 467777775
No 10
>PF14088 DUF4268: Domain of unknown function (DUF4268)
Probab=44.36 E-value=1.4e+02 Score=23.69 Aligned_cols=72 Identities=17% Similarity=0.221 Sum_probs=42.4
Q ss_pred hHHHHHHHHHhcccccceEeecCCCC----CCCcchheeeeeccCCCCeeEEecccccchhHHHHHHHhhHHHHHHHHHh
Q 027641 74 WSEFIDYVVASIKSEDVKLILEGHSN----ADGAAYAKIVAQKSKGMPRISISLTRLTGSAATEAMAKLSLELFTAFRSM 149 (220)
Q Consensus 74 wsdF~dYl~aslsS~~VkL~l~~~s~----s~G~~~akLVA~KaKGmPrItI~L~kl~~saa~D~ma~lsl~lf~a~rs~ 149 (220)
|+.|++|+...- ..++-.=+.+.+ +.|.+...|...-.+. .+.|.|.--.+. ....-++|+.+...
T Consensus 7 Wt~f~~~~~~~~--~~~~~~~p~~~~W~~~~~G~sg~~~~~~~~~~--~~~V~l~I~~~d------~~~n~~~fe~L~~~ 76 (140)
T PF14088_consen 7 WTEFLEYLKEKP--PLFSNRKPSPDHWINYSTGISGVSLSFVFNKK--RARVELYIDRPD------KEENKEIFEQLKSQ 76 (140)
T ss_pred HHHHHHHHHhcc--cccccCCCCCCcceEecCCCCCEEEEEEEeCC--EEEEEEEEcCCC------HHHHHHHHHHHHHH
Confidence 888999987654 222222222222 6678888887776655 666666554443 23345678888776
Q ss_pred hHhHHH
Q 027641 150 QTLIVQ 155 (220)
Q Consensus 150 ~~~~~~ 155 (220)
++.+.+
T Consensus 77 k~~IE~ 82 (140)
T PF14088_consen 77 KEEIEE 82 (140)
T ss_pred HHHHHH
Confidence 644443
No 11
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=43.07 E-value=50 Score=27.30 Aligned_cols=52 Identities=17% Similarity=0.312 Sum_probs=39.1
Q ss_pred ccchhHHHHHHHhhHH---HHHHHHHhhHhHHHHHHHHHHHHHHHHHHHhhhhcccCC
Q 027641 126 LTGSAATEAMAKLSLE---LFTAFRSMQTLIVQEQERCLQLEKEAAAEKERNENIQNQ 180 (220)
Q Consensus 126 l~~saa~D~ma~lsl~---lf~a~rs~~~~~~~eqe~~s~L~~~L~sEkekne~iq~q 180 (220)
+|-+..+|+.+.++=. +++++..++.|+. +|+..|-..|..=+|-.+.|+.+
T Consensus 36 vTrr~m~~A~~~v~kql~~vs~~l~~tKkhLs---qRId~vd~klDe~~ei~~~i~~e 90 (126)
T PF07889_consen 36 VTRRSMSDAVASVSKQLEQVSESLSSTKKHLS---QRIDRVDDKLDEQKEISKQIKDE 90 (126)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhHHHHHHHHHHHHHH
Confidence 4666777888877654 7999999999998 67777777777777766666655
No 12
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=39.04 E-value=1.7e+02 Score=22.15 Aligned_cols=27 Identities=22% Similarity=0.374 Sum_probs=21.7
Q ss_pred hhhhHhhhcCCCChHHHHHHHHHhcccc
Q 027641 61 LDDMRDEIGIGGSWSEFIDYVVASIKSE 88 (220)
Q Consensus 61 LeDlRD~VGIGGSwsdF~dYl~aslsS~ 88 (220)
.+.+|..+| |||.++-..||..--...
T Consensus 22 ~~~Vr~~lG-~GS~~ti~~~l~~w~~~~ 48 (120)
T PF11740_consen 22 VRAVRERLG-GGSMSTISKHLKEWREER 48 (120)
T ss_pred HHHHHHHHC-CCCHHHHHHHHHHHHHhh
Confidence 467899999 999999888888765443
No 13
>KOG3919 consensus Kinesin-associated fasciculation and elongation protein involved in axonal transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.56 E-value=22 Score=34.40 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=28.8
Q ss_pred ccchhhhhHhhhcCCCChHHHHHHH----HHhcccccce
Q 027641 57 SVLQLDDMRDEIGIGGSWSEFIDYV----VASIKSEDVK 91 (220)
Q Consensus 57 Sv~~LeDlRD~VGIGGSwsdF~dYl----~aslsS~~Vk 91 (220)
|++.||..+|+||-+||..|.|+-| ..||.-.++|
T Consensus 40 sls~lE~~s~ei~~~~SmEDLVn~FDEKi~vCf~ny~~~ 78 (374)
T KOG3919|consen 40 SLSGEERGSDELGAPGSLEDLVNLFDEKIPVCFPNYEGR 78 (374)
T ss_pred ccchhhhccchhcCCccHHHHHHhhhhhhhhcccccccc
Confidence 9999999999999999999998875 4556555544
No 14
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=37.49 E-value=98 Score=24.33 Aligned_cols=36 Identities=31% Similarity=0.396 Sum_probs=29.2
Q ss_pred HHHHhhHhHHHHHHHHHHHHHHHHHHHhhhhcccCC
Q 027641 145 AFRSMQTLIVQEQERCLQLEKEAAAEKERNENIQNQ 180 (220)
Q Consensus 145 a~rs~~~~~~~eqe~~s~L~~~L~sEkekne~iq~q 180 (220)
.++.....-.+|++|+.+|...|..|..|..++..+
T Consensus 14 Vl~R~~~l~~~E~~Ri~kLk~~L~~e~~r~~~~~~~ 49 (118)
T PF02318_consen 14 VLQRDEELRKKEEERIRKLKQELQKEKMRREALGNS 49 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCS
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 444566666899999999999998888888888764
No 15
>cd06843 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity.
Probab=36.80 E-value=62 Score=29.39 Aligned_cols=59 Identities=17% Similarity=0.164 Sum_probs=39.6
Q ss_pred chhhhhHhhhc-------CCCCh-------------HHHHHHHHHhccc--ccceEeecCCCC---CCCcchheeeeecc
Q 027641 59 LQLDDMRDEIG-------IGGSW-------------SEFIDYVVASIKS--EDVKLILEGHSN---ADGAAYAKIVAQKS 113 (220)
Q Consensus 59 ~~LeDlRD~VG-------IGGSw-------------sdF~dYl~aslsS--~~VkL~l~~~s~---s~G~~~akLVA~Ka 113 (220)
..++++.+..| |||+| .+|.+.+...+.. .+++|.+|+-.. ..|.--+|.+..|.
T Consensus 192 ~~~~~l~~~~g~~~~~idiGGGf~~~y~~~~~~~~~~~~~~~i~~~~~~~~~~~~l~~EpGR~lva~ag~lv~~V~~~k~ 271 (377)
T cd06843 192 ETARQWAAEHGLDLDVVNVGGGIGVNYADPEEQFDWAGFCEGLDQLLAEYEPGLTLRFECGRYISAYCGYYVTEVLDLKR 271 (377)
T ss_pred HHHHHHHHHhCCCCcEEEecCccccccCCCCCCCCHHHHHHHHHHHHHhcCCCCEEEEccChhhhcCceEEEEEEEEEee
Confidence 34556665544 78887 4777878887765 479999996533 55666777777776
Q ss_pred C-CCC
Q 027641 114 K-GMP 117 (220)
Q Consensus 114 K-GmP 117 (220)
. |..
T Consensus 272 ~~~~~ 276 (377)
T cd06843 272 SHGEW 276 (377)
T ss_pred cCCcE
Confidence 3 543
No 16
>smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Probab=36.35 E-value=46 Score=25.05 Aligned_cols=45 Identities=20% Similarity=0.301 Sum_probs=28.0
Q ss_pred CCCeEEEEecccccchhhccccchhhhhHhh------hcCCCC-hHHHHHHHHH
Q 027641 37 SSHLLIQVTDFRSNTWEAKRSVLQLDDMRDE------IGIGGS-WSEFIDYVVA 83 (220)
Q Consensus 37 s~hL~v~vTDfHSntW~~slSv~~LeDlRD~------VGIGGS-wsdF~dYl~a 83 (220)
..++.|++||...+.+ ....+-++.++.. ||+|.. ..+++..+-.
T Consensus 105 ~~~~iviitDg~~~~~--~~~~~~~~~~~~~~i~i~~i~~~~~~~~~~l~~~~~ 156 (177)
T smart00327 105 APKVLILITDGESNDG--GDLLKAAKELKRSGVKVFVVGVGNDVDEEELKKLAS 156 (177)
T ss_pred CCeEEEEEcCCCCCCC--ccHHHHHHHHHHCCCEEEEEEccCccCHHHHHHHhC
Confidence 3679999999988755 2223344444443 677766 6666666543
No 17
>cd00198 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Probab=34.98 E-value=58 Score=23.45 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=30.9
Q ss_pred CCCCCCeEEEEecccccchhhccccchhhhhHh------hhcCCC-ChHHHHHHHHH
Q 027641 34 APDSSHLLIQVTDFRSNTWEAKRSVLQLDDMRD------EIGIGG-SWSEFIDYVVA 83 (220)
Q Consensus 34 a~ds~hL~v~vTDfHSntW~~slSv~~LeDlRD------~VGIGG-SwsdF~dYl~a 83 (220)
.++...+.|++||.+.+.+. .-....++.++. .||+|+ .=..+++.|..
T Consensus 98 ~~~~~~~lvvitDg~~~~~~-~~~~~~~~~~~~~~v~v~~v~~g~~~~~~~l~~l~~ 153 (161)
T cd00198 98 RPNARRVIILLTDGEPNDGP-ELLAEAARELRKLGITVYTIGIGDDANEDELKEIAD 153 (161)
T ss_pred CCCCceEEEEEeCCCCCCCc-chhHHHHHHHHHcCCEEEEEEcCCCCCHHHHHHHhc
Confidence 45678899999999976554 222334555554 677777 55555555543
No 18
>PF02731 SKIP_SNW: SKIP/SNW domain; InterPro: IPR004015 SKIP (SKI-interacting protein) is an essential spliceosomal component and transcriptional coregulator, which may provide regulatory coupling of transcription initiation and splicing []. SKIP was identified in a yeast 2-hybrid screen, where it was shown to interact with both the cellular and viral forms of SKI through the highly conserved region on SKIP known as the SNW domain []. SKIP is now known to interact with a number of other proteins as well. SKIP potentiates the activity of important transcription factors, such as vitamin D receptor, CBF1 (RBP-Jkappa), Smad2/3, and MyoD. It works with Ski in overcoming pRb-mediated cell cycle arrest, and it is targeted by the viral transactivators EBNA2 and E7 []. This entry represents the SNW domain.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=33.55 E-value=1.2e+02 Score=26.24 Aligned_cols=37 Identities=35% Similarity=0.459 Sum_probs=27.9
Q ss_pred ecc-CCCCeeEEeccc--------ccchhHHHHHHHhhHHHHHHHHHhh
Q 027641 111 QKS-KGMPRISISLTR--------LTGSAATEAMAKLSLELFTAFRSMQ 150 (220)
Q Consensus 111 ~Ka-KGmPrItI~L~k--------l~~saa~D~ma~lsl~lf~a~rs~~ 150 (220)
||+ || .||+|++ +.+.-.||..+.||-+||.|=+.+.
T Consensus 77 WKN~kG---ytIpLDKRlaadgr~l~~~~INd~Fa~LseAL~~Ad~~aR 122 (158)
T PF02731_consen 77 WKNPKG---YTIPLDKRLAADGRGLQDVEINDKFAKLSEALYIADRKAR 122 (158)
T ss_pred ccCCCC---CccCHHHHHhhcccccCCccccHHHHHHHHHHHHHHHHHH
Confidence 666 56 4888875 3344578999999999999887665
No 19
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=27.01 E-value=2.6e+02 Score=24.20 Aligned_cols=67 Identities=21% Similarity=0.316 Sum_probs=41.7
Q ss_pred CChHHHHHHHHHhcccccceEeecCCCCCCCcchheeeeecc-CCCCeeEEecccccchhHHHHHHHhhHHHHHHHH
Q 027641 72 GSWSEFIDYVVASIKSEDVKLILEGHSNADGAAYAKIVAQKS-KGMPRISISLTRLTGSAATEAMAKLSLELFTAFR 147 (220)
Q Consensus 72 GSwsdF~dYl~aslsS~~VkL~l~~~s~s~G~~~akLVA~Ka-KGmPrItI~L~kl~~saa~D~ma~lsl~lf~a~r 147 (220)
|+|..|+++|..-+.+..+++..--.+...+. + ... +|+.++.|+..+. ++ .+++.--.+++..+.+
T Consensus 17 GGfET~ve~L~~~l~~~g~~v~Vyc~~~~~~~---~---~~~y~gv~l~~i~~~~~-g~--~~si~yd~~sl~~al~ 84 (185)
T PF09314_consen 17 GGFETFVEELAPRLVSKGIDVTVYCRSDYYPY---K---EFEYNGVRLVYIPAPKN-GS--AESIIYDFLSLLHALR 84 (185)
T ss_pred CcHHHHHHHHHHHHhcCCceEEEEEccCCCCC---C---CcccCCeEEEEeCCCCC-Cc--hHHHHHHHHHHHHHHH
Confidence 89999999999999988776655432221111 1 444 7999999987753 31 2344443444555553
No 20
>PF13580 SIS_2: SIS domain; PDB: 1TK9_C 2I22_B 2I2W_A 1X92_A 3BJZ_D 2XBL_B 2X3Y_F 2YVA_B 3CVJ_D 3TRJ_D ....
Probab=24.88 E-value=40 Score=26.61 Aligned_cols=47 Identities=21% Similarity=0.343 Sum_probs=26.6
Q ss_pred hHHHHHHHHHh--cccccceEeecCCCCCCCcchhee-eeeccCCCCeeEEe
Q 027641 74 WSEFIDYVVAS--IKSEDVKLILEGHSNADGAAYAKI-VAQKSKGMPRISIS 122 (220)
Q Consensus 74 wsdF~dYl~as--lsS~~VkL~l~~~s~s~G~~~akL-VA~KaKGmPrItI~ 122 (220)
...|.+.+..- +..|||=+++...-++. .-.+. -.-|.+||+.|.|.
T Consensus 88 ~~~~~~~~~~~~~~~~gDvli~iS~SG~s~--~vi~a~~~Ak~~G~~vIalT 137 (138)
T PF13580_consen 88 DEGFARQLLALYDIRPGDVLIVISNSGNSP--NVIEAAEEAKERGMKVIALT 137 (138)
T ss_dssp GGTHHHHHHHHTT--TT-EEEEEESSS-SH--HHHHHHHHHHHTT-EEEEEE
T ss_pred hhHHHHHHHHHcCCCCCCEEEEECCCCCCH--HHHHHHHHHHHCCCEEEEEe
Confidence 35688888877 99999999998752322 11111 11245799998873
No 21
>KOG1369 consensus Hexokinase [Carbohydrate transport and metabolism]
Probab=23.67 E-value=42 Score=33.30 Aligned_cols=50 Identities=34% Similarity=0.528 Sum_probs=40.1
Q ss_pred HhhhcCCCCh----HHHHHHHHHhcc-----cccceEeecCCCCCCCcchheeeeeccC
Q 027641 65 RDEIGIGGSW----SEFIDYVVASIK-----SEDVKLILEGHSNADGAAYAKIVAQKSK 114 (220)
Q Consensus 65 RD~VGIGGSw----sdF~dYl~asls-----S~~VkL~l~~~s~s~G~~~akLVA~KaK 114 (220)
|=.||.+||. +.|-+|++..++ +-.|++.+..+.++.||+-+-.|+.+.|
T Consensus 413 ~~~VgvdGsly~~yP~f~~~m~~~l~eLlg~~~~v~i~~s~dgSg~GAAL~Aav~~~~~ 471 (474)
T KOG1369|consen 413 RVTVGVDGSLYKNHPFFREYLKEALRELLGPSIHVKLVLSEDGSGRGAALIAAVASRLK 471 (474)
T ss_pred ceEEEeccchhHcCchHHHHHHHHHHHHhCCCceEEEEECCCCccccHHHHHHHHhhhh
Confidence 4458999996 568888888887 4689999999999999988777777665
No 22
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.60 E-value=87 Score=31.84 Aligned_cols=28 Identities=21% Similarity=0.280 Sum_probs=14.8
Q ss_pred HHHhhHhHHHHH-HHHHHHHHHHHHHHhh
Q 027641 146 FRSMQTLIVQEQ-ERCLQLEKEAAAEKER 173 (220)
Q Consensus 146 ~rs~~~~~~~eq-e~~s~L~~~L~sEkek 173 (220)
||.+.+.+.+|| +|..|+..-+..|+..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (567)
T PLN03086 5 LRRAREKLEREQRERKQRAKLKLERERKA 33 (567)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555566665 4555555555555443
No 23
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=23.19 E-value=49 Score=25.53 Aligned_cols=16 Identities=25% Similarity=0.904 Sum_probs=14.0
Q ss_pred hhcCCCChHHHHHHHH
Q 027641 67 EIGIGGSWSEFIDYVV 82 (220)
Q Consensus 67 ~VGIGGSwsdF~dYl~ 82 (220)
.|-+||+|.++=+||.
T Consensus 49 MVRVGGGW~tL~~fL~ 64 (73)
T smart00243 49 MVRVGGGWETLDEYLL 64 (73)
T ss_pred EEEECCcHHHHHHHHH
Confidence 5788999999999985
No 24
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=23.06 E-value=1.6e+02 Score=19.73 Aligned_cols=29 Identities=28% Similarity=0.453 Sum_probs=18.7
Q ss_pred CCeeEEecccccchhHHHHHHHhhHHHHHHHH
Q 027641 116 MPRISISLTRLTGSAATEAMAKLSLELFTAFR 147 (220)
Q Consensus 116 mPrItI~L~kl~~saa~D~ma~lsl~lf~a~r 147 (220)
||.|+|.+-+ |+ --+....|+-++.+++.
T Consensus 1 MP~i~i~~~~--Gr-s~eqk~~l~~~it~~l~ 29 (61)
T PRK02220 1 MPYVHIKLIE--GR-TEEQLKALVKDVTAAVS 29 (61)
T ss_pred CCEEEEEEcC--CC-CHHHHHHHHHHHHHHHH
Confidence 8999997665 43 33555666666666553
No 25
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=22.87 E-value=83 Score=23.92 Aligned_cols=18 Identities=39% Similarity=0.497 Sum_probs=15.1
Q ss_pred HHHHHhhHHHHHHHHHhh
Q 027641 133 EAMAKLSLELFTAFRSMQ 150 (220)
Q Consensus 133 D~ma~lsl~lf~a~rs~~ 150 (220)
.+|.+||=|||+||-+-+
T Consensus 37 ~iI~sLs~ELy~AFi~E~ 54 (79)
T PF12209_consen 37 QIIDSLSEELYDAFIHEQ 54 (79)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 569999999999996644
No 26
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=22.51 E-value=80 Score=28.41 Aligned_cols=18 Identities=39% Similarity=0.218 Sum_probs=11.3
Q ss_pred CCCCeeEEecccccchhH
Q 027641 114 KGMPRISISLTRLTGSAA 131 (220)
Q Consensus 114 KGmPrItI~L~kl~~saa 131 (220)
+|+|.|.||=|--+|+.+
T Consensus 108 ~~~p~i~VPTtagtgse~ 125 (332)
T cd08180 108 KKPLFIAIPTTSGTGSEV 125 (332)
T ss_pred CCCCEEEeCCCCcchHhh
Confidence 456777777666666544
No 27
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=22.43 E-value=3e+02 Score=23.82 Aligned_cols=73 Identities=18% Similarity=0.276 Sum_probs=40.2
Q ss_pred CCCChHHHHHHHHHhcccccceEeec---CCCC-CC---CcchheeeeeccCCCC----------eeEEecccccchhHH
Q 027641 70 IGGSWSEFIDYVVASIKSEDVKLILE---GHSN-AD---GAAYAKIVAQKSKGMP----------RISISLTRLTGSAAT 132 (220)
Q Consensus 70 IGGSwsdF~dYl~aslsS~~VkL~l~---~~s~-s~---G~~~akLVA~KaKGmP----------rItI~L~kl~~saa~ 132 (220)
.=.||.+|++.... ..+|++- +... ++ -..-.-|-..-++|+| .|.||.. -..++.|
T Consensus 60 ~h~s~e~fl~~~~~-----~~rl~~~tt~~~~~~~~~~f~~~d~llFG~Es~GLP~~i~~~~~~~~irIPm~-~~~RSLN 133 (155)
T COG0219 60 EHDSLEAFLEAEPI-----GGRLFALTTKGTTTYTDVSFQKGDYLLFGPESRGLPEEILDAAPDRCIRIPMR-PGVRSLN 133 (155)
T ss_pred EeCCHHHHHhhccC-----CceEEEEEeccccccccccCCCCCEEEECCCCCCCCHHHHHhCccceEEeccC-CCCccch
Confidence 34688899876653 2333322 1111 11 1122456667778888 5999998 2224443
Q ss_pred HHHHHhhHHHHHHHHHh
Q 027641 133 EAMAKLSLELFTAFRSM 149 (220)
Q Consensus 133 D~ma~lsl~lf~a~rs~ 149 (220)
=+ .+.+.-+|+++|..
T Consensus 134 Ls-nsvavv~yEa~RQ~ 149 (155)
T COG0219 134 LS-NTVAVVLYEALRQL 149 (155)
T ss_pred HH-HHHHHHHHHHHHHh
Confidence 22 23456699999754
No 28
>PF02187 GAS2: Growth-Arrest-Specific Protein 2 Domain; InterPro: IPR003108 The growth-arrest-specific protein 2 domain is found associated with the spectrin repeat, calponin homology domain and EF hand in many proteins. It is found among others in the growth arrest-specific protein 2 [].; GO: 0007050 cell cycle arrest; PDB: 1V5R_A.
Probab=22.39 E-value=25 Score=26.86 Aligned_cols=18 Identities=22% Similarity=0.682 Sum_probs=15.3
Q ss_pred hhhcCCCChHHHHHHHHH
Q 027641 66 DEIGIGGSWSEFIDYVVA 83 (220)
Q Consensus 66 D~VGIGGSwsdF~dYl~a 83 (220)
-.|-+||+|.++-.||..
T Consensus 48 vMVRVGGGW~tL~~~L~k 65 (73)
T PF02187_consen 48 VMVRVGGGWDTLEEYLDK 65 (73)
T ss_dssp EEEEETTEEEEHHHHHHH
T ss_pred EEEEeCCcHHHHHHHhhc
Confidence 468899999999999863
No 29
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=22.28 E-value=1.6e+02 Score=20.17 Aligned_cols=30 Identities=27% Similarity=0.367 Sum_probs=20.3
Q ss_pred CCeeEEecccccchhHHHHHHHhhHHHHHHHHH
Q 027641 116 MPRISISLTRLTGSAATEAMAKLSLELFTAFRS 148 (220)
Q Consensus 116 mPrItI~L~kl~~saa~D~ma~lsl~lf~a~rs 148 (220)
||.|+|.+-. |+ -.|-...|+-++.++...
T Consensus 1 MP~i~i~~~~--Gr-s~EqK~~L~~~it~a~~~ 30 (60)
T PRK02289 1 MPFVRIDLFE--GR-SQEQKNALAREVTEVVSR 30 (60)
T ss_pred CCEEEEEECC--CC-CHHHHHHHHHHHHHHHHH
Confidence 8999999977 43 345666666666666643
No 30
>PF07946 DUF1682: Protein of unknown function (DUF1682); InterPro: IPR012879 The members of this family are all hypothetical eukaryotic proteins of unknown function. One member (Q920S6 from SWISSPROT) is described as being an adipocyte-specific protein, but no evidence of this was found.
Probab=22.03 E-value=2.7e+02 Score=25.55 Aligned_cols=33 Identities=24% Similarity=0.249 Sum_probs=21.8
Q ss_pred CCCeeEEecccccchh---HHHHHHHhhHHHHHHHH
Q 027641 115 GMPRISISLTRLTGSA---ATEAMAKLSLELFTAFR 147 (220)
Q Consensus 115 GmPrItI~L~kl~~sa---a~D~ma~lsl~lf~a~r 147 (220)
.-|+|.|++..-.... .-..+-++.+.|.+.+.
T Consensus 213 ~~~~l~~~~~lp~~~~~~~~~~~l~~~v~~l~D~~~ 248 (321)
T PF07946_consen 213 PKKRLIFSFRLPSSSDDMEALEPLLKLVFYLIDKLA 248 (321)
T ss_pred cCcEEEEEEEeCCCcccHHHHHHHHHHHHHHHHHhh
Confidence 5677777766655555 44555667888887774
No 31
>PF09260 DUF1966: Domain of unknown function (DUF1966); InterPro: IPR015340 Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This domain is found in various fungal alpha-amylase proteins. Its exact function has not, as yet, been defined []. ; GO: 0004556 alpha-amylase activity, 0005509 calcium ion binding, 0016052 carbohydrate catabolic process; PDB: 2AAA_A 2GUY_A 2TAA_B 6TAA_A 2GVY_B 7TAA_A 3KWX_A.
Probab=21.89 E-value=63 Score=24.93 Aligned_cols=26 Identities=27% Similarity=0.445 Sum_probs=18.9
Q ss_pred chheeeeeccCCCCeeEEecccccch
Q 027641 104 AYAKIVAQKSKGMPRISISLTRLTGS 129 (220)
Q Consensus 104 ~~akLVA~KaKGmPrItI~L~kl~~s 129 (220)
+.+.|.....+|+|+|=+|-.++.++
T Consensus 63 ~~G~l~v~m~~G~P~Vl~P~~~l~gs 88 (91)
T PF09260_consen 63 SNGTLTVPMSNGEPRVLYPASLLSGS 88 (91)
T ss_dssp TTS-EEEEESTT--EEEEECHHHTTS
T ss_pred CCCEEEEEEcCCceEEEEEHHHccCC
Confidence 45567778888999999999888775
No 32
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=21.76 E-value=1.7e+02 Score=19.60 Aligned_cols=29 Identities=31% Similarity=0.353 Sum_probs=18.9
Q ss_pred CCeeEEecccccchhHHHHHHHhhHHHHHHHH
Q 027641 116 MPRISISLTRLTGSAATEAMAKLSLELFTAFR 147 (220)
Q Consensus 116 mPrItI~L~kl~~saa~D~ma~lsl~lf~a~r 147 (220)
||.|+|.+.. |+ -.+....|+-.+.+++.
T Consensus 1 MP~i~I~~~~--gr-s~eqk~~l~~~it~~l~ 29 (62)
T PRK00745 1 MPTFHIELFE--GR-TVEQKRKLVEEITRVTV 29 (62)
T ss_pred CCEEEEEEcC--CC-CHHHHHHHHHHHHHHHH
Confidence 8999999876 33 33556666656666553
No 33
>KOG0945 consensus Alpha-aminoadipic semialdehyde dehydrogenase-phosphopantetheinyl transferase [Amino acid transport and metabolism; Coenzyme transport and metabolism]
Probab=21.76 E-value=88 Score=29.56 Aligned_cols=76 Identities=14% Similarity=0.173 Sum_probs=54.0
Q ss_pred ccCCCcccccCCCCCCccceEEEEeCCCCCCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccc
Q 027641 9 IFGEPKAEWADSRSDSLGRFLFHVSAPDSSHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSE 88 (220)
Q Consensus 9 IFgeak~e~~~~~s~~~~pfLFh~~a~ds~hL~v~vTDfHSntW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~aslsS~ 88 (220)
-+|+| .-|-+...+...+|=|.+... +.|.+++|+.|.+.==..+.+. -.++=.||+.-+...|+-.
T Consensus 89 ~~GKP-~l~qn~~~p~~~~f~fNvSH~--gd~iv~at~~~~~VGIDIm~~~----------~r~~~~e~l~~~kr~fS~~ 155 (289)
T KOG0945|consen 89 EYGKP-VLWQNYSNPFSPTFGFNVSHQ--GDLIVVATTVHVPVGIDIMRPK----------ERKTAHEELELFKRVFSED 155 (289)
T ss_pred cCCCc-chhhcccCCCCCCccceeeee--ceEEEEeccCCcccceeeeecc----------cccchHHHHHHHHHhcCHH
Confidence 46777 667775555677777777766 5899999999876321111111 2355678999999999999
Q ss_pred cceEeecCC
Q 027641 89 DVKLILEGH 97 (220)
Q Consensus 89 ~VkL~l~~~ 97 (220)
++|.+...+
T Consensus 156 E~k~l~s~~ 164 (289)
T KOG0945|consen 156 EWKMLKSAP 164 (289)
T ss_pred HHHHHHcCC
Confidence 999998863
No 34
>KOG1789 consensus Endocytosis protein RME-8, contains DnaJ domain [Intracellular trafficking, secretion, and vesicular transport; Posttranslational modification, protein turnover, chaperones]
Probab=21.73 E-value=1.6e+02 Score=33.53 Aligned_cols=72 Identities=17% Similarity=0.274 Sum_probs=46.1
Q ss_pred hheeeeeccCCCCeeEEecccccchhHHHHHHHhhHH---HHHHHHHhhHhHH------HHHHHHHHHHHHHHHHHhhhh
Q 027641 105 YAKIVAQKSKGMPRISISLTRLTGSAATEAMAKLSLE---LFTAFRSMQTLIV------QEQERCLQLEKEAAAEKERNE 175 (220)
Q Consensus 105 ~akLVA~KaKGmPrItI~L~kl~~saa~D~ma~lsl~---lf~a~rs~~~~~~------~eqe~~s~L~~~L~sEkekne 175 (220)
-|||+|+|=.| ||++|.|-|..-+...|+|-+=.=. +|+.-..+-+++= +--.++...+..+=.|++|+-
T Consensus 1878 laKl~Adkl~G-PrV~ITL~kFLP~~f~d~~RD~PEAaVH~fE~T~EnPELiWn~~~r~kvS~~i~tM~~~~y~~QQk~p 1956 (2235)
T KOG1789|consen 1878 LAKLQADKLTG-PRVTITLIKFLPEIFADSLRDSPEAAVHMFESTSENPELIWNEVTRQKVSGIIDTMVGKLYEQQQKDP 1956 (2235)
T ss_pred HHHhhhccccC-CceeeehHHhchHHHHHHHhcCHHHHHHHHhccCCCcccccCHhHHHHHHHHHHHHHHHHHHHhccCC
Confidence 47999999988 9999999999999999999875533 4443322222222 222344444555556666664
Q ss_pred cc
Q 027641 176 NI 177 (220)
Q Consensus 176 ~i 177 (220)
.+
T Consensus 1957 ~~ 1958 (2235)
T KOG1789|consen 1957 TV 1958 (2235)
T ss_pred cc
Confidence 43
No 35
>cd08169 DHQ-like Dehydroquinate synthase-like which includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. Dehydroquinate synthase-like. This group contains dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. They exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-Deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes ne
Probab=21.54 E-value=1.2e+02 Score=27.93 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=13.1
Q ss_pred chheeeeecc-CCCCeeEEeccc
Q 027641 104 AYAKIVAQKS-KGMPRISISLTR 125 (220)
Q Consensus 104 ~~akLVA~Ka-KGmPrItI~L~k 125 (220)
|.||.+|-.. +|+|.|.||-|.
T Consensus 97 D~ak~vA~~~~rgip~i~VPTTl 119 (344)
T cd08169 97 DVAGFVASTLFRGIAFIRVPTTL 119 (344)
T ss_pred HHHHHHHHHhccCCcEEEecCCc
Confidence 5666665432 466777776663
No 36
>cd08549 G1PDH_related Glycerol-1-phosphate_dehydrogenase and related proteins. Bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. The proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH). G1PDH plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids.
Probab=21.54 E-value=1.7e+02 Score=26.53 Aligned_cols=23 Identities=26% Similarity=0.281 Sum_probs=15.3
Q ss_pred chheeeeeccCCCCeeEEeccccc
Q 027641 104 AYAKIVAQKSKGMPRISISLTRLT 127 (220)
Q Consensus 104 ~~akLVA~KaKGmPrItI~L~kl~ 127 (220)
|.||.+|. -.|+|.|.||-|..+
T Consensus 94 D~aK~iA~-~~gip~I~VPTT~~~ 116 (332)
T cd08549 94 DLVKFVSF-KVGKPFISVPTAPSM 116 (332)
T ss_pred HHHHHHHH-HcCCCEEEeCCCccc
Confidence 67777772 247777777777644
No 37
>PRK00002 aroB 3-dehydroquinate synthase; Reviewed
Probab=21.51 E-value=1.5e+02 Score=27.20 Aligned_cols=34 Identities=24% Similarity=0.229 Sum_probs=20.8
Q ss_pred cceEeecCCCCCCCcchheeeee-ccCCCCeeEEeccc
Q 027641 89 DVKLILEGHSNADGAAYAKIVAQ-KSKGMPRISISLTR 125 (220)
Q Consensus 89 ~VkL~l~~~s~s~G~~~akLVA~-KaKGmPrItI~L~k 125 (220)
++=+-+++-+ --|.||.+|- -..|+|.|.||-|-
T Consensus 94 d~IIavGGGs---v~D~aK~iA~~~~~gip~i~IPTT~ 128 (358)
T PRK00002 94 DTLIALGGGV---IGDLAGFAAATYMRGIRFIQVPTTL 128 (358)
T ss_pred CEEEEEcCcH---HHHHHHHHHHHhcCCCCEEEcCchh
Confidence 5555555521 1267777773 22488888888874
No 38
>PRK09423 gldA glycerol dehydrogenase; Provisional
Probab=20.95 E-value=54 Score=29.99 Aligned_cols=27 Identities=26% Similarity=0.294 Sum_probs=18.2
Q ss_pred chheeeeeccCCCCeeEEecccccchhH
Q 027641 104 AYAKIVAQKSKGMPRISISLTRLTGSAA 131 (220)
Q Consensus 104 ~~akLVA~KaKGmPrItI~L~kl~~saa 131 (220)
|.||.+|-.. |+|.|.||-|--+||.+
T Consensus 98 D~aK~iA~~~-~~p~i~IPTtagtgSe~ 124 (366)
T PRK09423 98 DTAKAVADYL-GVPVVIVPTIASTDAPT 124 (366)
T ss_pred HHHHHHHHHc-CCCEEEeCCccccCccc
Confidence 6777777443 67888887776666643
No 39
>PF06670 Etmic-2: Microneme protein Etmic-2; InterPro: IPR009556 This family consists of several Microneme protein Etmic-2 sequences from Eimeria tenella. Etmic-2 is a 50 kDa acidic protein, which is found within the microneme organelles of E. tenella sporozoites and merozoites [].
Probab=20.64 E-value=1.1e+02 Score=29.24 Aligned_cols=110 Identities=19% Similarity=0.241 Sum_probs=75.5
Q ss_pred CCCccceEEEEeCCCCCCeEEEEecccccchhhc-------cccchhhh-hHhhhcCCCChHHHHHHHHHhcccccceEe
Q 027641 22 SDSLGRFLFHVSAPDSSHLLIQVTDFRSNTWEAK-------RSVLQLDD-MRDEIGIGGSWSEFIDYVVASIKSEDVKLI 93 (220)
Q Consensus 22 s~~~~pfLFh~~a~ds~hL~v~vTDfHSntW~~s-------lSv~~LeD-lRD~VGIGGSwsdF~dYl~aslsS~~VkL~ 93 (220)
..+-.||..-+.-.+.-...|.+--..+-.+-++ +-+++.=. -||.-|=.|||-|-.--+..+|+--||.++
T Consensus 201 agpttp~mv~i~q~~p~e~~vr~~~wi~teylcsrrgvsrifkysdfcslcrdas~G~GSW~E~~V~VG~~i~~RD~~V~ 280 (379)
T PF06670_consen 201 AGPTTPLMVLITQQNPKEVEVRVLAWISTEYLCSRRGVSRIFKYSDFCSLCRDASTGDGSWHENFVDVGSSINHRDVMVN 280 (379)
T ss_pred CCCCCceEEEEecCCCceEEEEEEEeecchhhhcccccchhhcccchhhhhccccCCCccceeeeEEecccccCceeEEE
Confidence 4566899999988888878777744443333222 33333333 378889999998866667889999999999
Q ss_pred ecC--CCC--CCCcchheeeeeccC----CCCeeEEecccccchhHH
Q 027641 94 LEG--HSN--ADGAAYAKIVAQKSK----GMPRISISLTRLTGSAAT 132 (220)
Q Consensus 94 l~~--~s~--s~G~~~akLVA~KaK----GmPrItI~L~kl~~saa~ 132 (220)
+.. +++ ..|.++|-||+-|.| -=|. -|.||+--.++++
T Consensus 281 ~SDC~P~SLRiYGSsSADLVT~~E~~C~A~~P~-Li~LT~P~~~~~s 326 (379)
T PF06670_consen 281 VSDCVPHSLRIYGSSSADLVTVDEKMCQADDPQ-LINLTSPHENRTS 326 (379)
T ss_pred ecccCccceEEecccccceEeeccccccCCChh-heeccCCCcccCC
Confidence 983 333 789999999998875 1232 2566665555544
Done!