Query 025423
Match_columns 253
No_of_seqs 28 out of 30
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 05:39:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025423.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025423hhsearch_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 97.2 0.011 2.4E-07 53.1 13.1 112 26-148 13-129 (197)
2 PF06632 XRCC4: DNA double-str 95.4 0.2 4.3E-06 47.9 11.2 141 26-173 16-169 (342)
3 PF05013 FGase: N-formylglutam 59.5 13 0.00028 32.5 3.9 84 39-126 130-218 (222)
4 cd07694 Ig2_CD4 Second immunog 58.4 8.1 0.00018 30.9 2.2 44 13-61 31-75 (88)
5 KOG4552 Vitamin-D-receptor int 56.3 11 0.00024 35.2 3.1 55 144-199 57-125 (272)
6 cd07766 DHQ_Fe-ADH Dehydroquin 55.1 10 0.00023 34.4 2.7 28 104-131 92-120 (332)
7 KOG2430 Glycosyl hydrolase, fa 54.8 8.7 0.00019 38.5 2.2 76 35-127 222-299 (587)
8 PF11740 KfrA_N: Plasmid repli 49.1 1.2E+02 0.0027 23.5 8.5 28 61-89 22-49 (120)
9 PF14088 DUF4268: Domain of un 48.6 1.3E+02 0.0027 24.5 7.7 70 74-153 7-80 (140)
10 PF14147 Spore_YhaL: Sporulati 47.1 84 0.0018 23.3 5.8 41 134-174 8-52 (52)
11 PF02362 B3: B3 DNA binding do 45.8 8.9 0.00019 28.4 0.6 47 39-90 33-79 (100)
12 KOG2441 mRNA splicing factor/p 41.8 53 0.0012 33.4 5.4 39 109-150 248-295 (506)
13 PF02731 SKIP_SNW: SKIP/SNW do 38.9 82 0.0018 27.8 5.5 37 111-150 77-122 (158)
14 smart00327 VWA von Willebrand 37.9 42 0.00091 26.0 3.3 44 38-83 106-156 (177)
15 KOG3919 Kinesin-associated fas 36.9 23 0.0005 34.9 2.0 35 57-91 40-78 (374)
16 cd00198 vWFA Von Willebrand fa 35.9 54 0.0012 24.3 3.5 49 34-83 98-153 (161)
17 cd06843 PLPDE_III_PvsE_like Ty 35.5 72 0.0016 29.7 5.0 58 59-116 192-275 (377)
18 PF02318 FYVE_2: FYVE-type zin 33.4 1.2E+02 0.0027 24.3 5.4 36 145-180 14-49 (118)
19 PF11995 DUF3490: Domain of un 30.1 51 0.0011 29.3 2.9 47 148-194 71-119 (161)
20 PF07889 DUF1664: Protein of u 28.6 1.2E+02 0.0025 25.7 4.7 53 125-180 35-90 (126)
21 PF09314 DUF1972: Domain of un 26.8 2.4E+02 0.0053 24.9 6.6 67 72-147 17-84 (185)
22 PF06670 Etmic-2: Microneme pr 25.3 76 0.0016 30.7 3.3 110 22-132 201-326 (379)
23 PF12209 SAC3: Leucine permeas 25.2 69 0.0015 24.8 2.6 18 133-150 37-54 (79)
24 smart00243 GAS2 Growth-Arrest- 24.5 44 0.00095 26.3 1.3 16 67-82 49-64 (73)
25 COG0219 CspR Predicted rRNA me 24.1 2.7E+02 0.0058 24.6 6.2 73 70-149 60-149 (155)
26 PF02187 GAS2: Growth-Arrest-S 23.9 23 0.00049 27.6 -0.3 18 66-83 48-65 (73)
27 cd08180 PDD 1,3-propanediol de 22.6 77 0.0017 29.2 2.8 18 114-131 108-125 (332)
28 cd00953 KDG_aldolase KDG (2-ke 21.7 2.8E+02 0.006 25.2 6.1 93 54-167 135-234 (279)
29 KOG0894 Ubiquitin-protein liga 21.3 48 0.001 31.1 1.2 24 38-61 84-107 (244)
30 PLN02537 diaminopimelate decar 20.8 2.5E+02 0.0054 26.6 5.8 48 67-114 224-288 (410)
31 cd01464 vWA_subfamily VWA subf 20.3 97 0.0021 25.3 2.7 42 38-81 108-157 (176)
32 cd08169 DHQ-like Dehydroquinat 20.2 1.2E+02 0.0026 28.6 3.5 22 104-125 97-119 (344)
No 1
>PF15384 DUF4610: Domain of unknown function (DUF4610)
Probab=97.18 E-value=0.011 Score=53.05 Aligned_cols=112 Identities=18% Similarity=0.276 Sum_probs=95.3
Q ss_pred cceEEEEeCC-----CCCCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccceEeecCCCCC
Q 025423 26 GRFLFHVSAP-----DSSHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDVKLILEGHSNA 100 (253)
Q Consensus 26 ~pfLFh~~a~-----d~~hL~v~vTDfHS~tW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~~slsS~~VkL~l~~~s~s 100 (253)
-+|+++-+-. +.+...|+|||--. -|...|+-++|+.+|+-.|.- +..||.--|.+.+..|.|.|-|-.+
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 67889999999874 499999999999999999984 6889999999999999999999863
Q ss_pred CCcccceeeeeccCCCCeeEEeeccccchhHHHHHHHhhHHHHHHHHH
Q 025423 101 DGAAYAKIVAQKSKGMPRISISLTRLTGSAATEAMAKLSLELFTAFRS 148 (253)
Q Consensus 101 ~G~~~akLVa~KaKGmP~ItI~L~~l~~saa~D~ma~~sl~Lf~afrs 148 (253)
+++-+-+.|-.-|++.|.++.++-+...+-.|-|.|.+....
T Consensus 88 ------~a~Ltls~g~s~L~~dL~k~p~~Ea~~~Lq~L~f~lAe~v~~ 129 (197)
T PF15384_consen 88 ------RASLTLSGGPSALTFDLSKVPAPEAAPRLQALTFRLAERVCS 129 (197)
T ss_pred ------eEEEEecCCCccceEEhhhCCCchhhHHHHHHHHHHHHHHHH
Confidence 444455888999999999999999998888888887765533
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=95.39 E-value=0.2 Score=47.93 Aligned_cols=141 Identities=14% Similarity=0.213 Sum_probs=85.5
Q ss_pred cceEEEEeCCCC--CCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccc-----cceEeecCCC
Q 025423 26 GRFLFHVSAPDS--SHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSE-----DVKLILEGHS 98 (253)
Q Consensus 26 ~pfLFh~~a~d~--~hL~v~vTDfHS~tW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~~slsS~-----~VkL~l~~~s 98 (253)
..++.++.-... +|+.|.+||-|+ +|.+..|-.++....++. ++++.+|++-+.-.|-.+ .-.+.+-.
T Consensus 16 ~~yfL~~~W~~~~~~~F~i~lTDG~s-aW~g~vs~~ei~~~A~~~--~~~~~eYv~~l~kaL~~~~~~~~~y~f~~~~-- 90 (342)
T PF06632_consen 16 SIYFLQVSWEKDLGSGFDITLTDGQS-AWSGTVSEEEIRQRAKDW--DMEVEEYVQELKKALTGQQQPSSEYSFDLTE-- 90 (342)
T ss_dssp SEEEEEEEESSSGGGEEEEEEESSSS-EEEEEEEHHHHHHHHHHT--TS-HHHHHHHHHHHHTSSSSSSSEEEEEE----
T ss_pred ceEEEEEEeccCCCCceEEEEecCCC-ceeeecCHHHHHHHHHHh--cCCHHHHHHHHHHHHhcCCCCCCcceEEEee--
Confidence 345666655432 589999999995 899999999999988875 688999999999999654 23444421
Q ss_pred CCCCcccceeeeeccCCCCeeEEee-----ccccchhH-HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025423 99 NADGAAYAKIVAQKSKGMPRISISL-----TRLTGSAA-TEAMAKLSLELFTAFRSMQTLIVQEQERCLQLEKEAAAEKE 172 (253)
Q Consensus 99 ~s~G~~~akLVa~KaKGmP~ItI~L-----~~l~~saa-~D~ma~~sl~Lf~afrs~q~~~~~eqe~~s~L~~~LsaEKe 172 (253)
...|....++ +..|-+.-|++-| .....-+. -.-|-++++.....+...-.++.+|-++..+-.+.+-++-|
T Consensus 91 ~~~~~~~l~~--t~~K~~~~it~rLGsv~L~~~~~p~e~i~el~d~~l~~~~~l~~~~~~L~~enerL~~e~~~~~~qlE 168 (342)
T PF06632_consen 91 DRESNKSLSF--TIEKRLKDITFRLGSVKLKQVDNPAEVIRELFDWCLDANSRLQAENEHLQKENERLESEANKLLKQLE 168 (342)
T ss_dssp ---ETTTTEE--EEEEEESSEEEEEEEEE-EE-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCCceEEE--EEEEecCCceEEEeeEECCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1223333333 3333345566655 33333221 11245667777777776666776666665544444444433
Q ss_pred h
Q 025423 173 R 173 (253)
Q Consensus 173 k 173 (253)
+
T Consensus 169 ~ 169 (342)
T PF06632_consen 169 K 169 (342)
T ss_dssp H
T ss_pred H
Confidence 3
No 3
>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=59.48 E-value=13 Score=32.55 Aligned_cols=84 Identities=14% Similarity=0.143 Sum_probs=50.5
Q ss_pred CeEEEEecccccchhhccccchhhhhHh-hhcCCCC---hHHHHHHHHHhcc-cccceEeecCCCCCCCcccceeeeecc
Q 025423 39 HLLIQVTDFRSNTWEAKRSVLQLDDMRD-EIGIGGS---WSEFIDYVVASIK-SEDVKLILEGHSNADGAAYAKIVAQKS 113 (253)
Q Consensus 39 hL~v~vTDfHS~tW~~slSv~~LeDlRD-~VGIGGS---wsdF~dYl~~sls-S~~VkL~l~~~s~s~G~~~akLVa~Ka 113 (253)
|-.+++-|+||-++...-.-.. ..+| +||+..+ +.++++.+.++|. +.-.++....+=. |....+=..+.+
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 5678889999998875433222 3333 4676554 8899999999999 5555666655422 222222255567
Q ss_pred CCCCeeEEeeccc
Q 025423 114 KGMPRISISLTRL 126 (253)
Q Consensus 114 KGmP~ItI~L~~l 126 (253)
+|.+-|.|.+.+-
T Consensus 206 ~~v~~iqiEi~~~ 218 (222)
T PF05013_consen 206 RGVHAIQIEINRD 218 (222)
T ss_dssp CTEEEEEEEEEGG
T ss_pred CCceEEEEEEEHh
Confidence 8999999998763
No 4
>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=58.41 E-value=8.1 Score=30.88 Aligned_cols=44 Identities=27% Similarity=0.354 Sum_probs=31.3
Q ss_pred CcccccCCCCCCccceEEEEeCCCCCCeE-EEEecccccchhhccccchh
Q 025423 13 PKAEWADSRSDSLGRFLFHVSAPDSSHLL-IQVTDFRSNTWEAKRSVLQL 61 (253)
Q Consensus 13 ak~e~~~~~s~~~~pfLFh~~a~d~~hL~-v~vTDfHS~tW~~slSv~~L 61 (253)
++.+|-+|..-.- +...++...|. ..++..||++|.+..++++-
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 3668877654321 55566666665 46999999999999998754
No 5
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=56.29 E-value=11 Score=35.25 Aligned_cols=55 Identities=24% Similarity=0.308 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh--hcccCCc------------chhHHHhhhhcCCCCCCc
Q 025423 144 TAFRSMQTLIVQEQERCLQLEKEAAAEKERN--ENIQNQP------------LYSKRQKLQKMNFSDKTD 199 (253)
Q Consensus 144 ~afrs~q~~~~~eqe~~s~L~~~LsaEKekn--E~mq~q~------------~~~~~~Kl~~~s~~dk~~ 199 (253)
+.|+++.+ ++.||+...|+|..|.++-||. +|-|.|- .+--+|||.-|+--+|+-
T Consensus 57 ~ef~~llk-la~eq~k~e~~m~~Lea~VEkrD~~IQqLqk~LK~aE~iLtta~fqA~qKLksi~~A~krp 125 (272)
T KOG4552|consen 57 DEFKTLLK-LAPEQQKREQLMRTLEAHVEKRDEVIQQLQKNLKSAEVILTTACFQANQKLKSIKEAEKRP 125 (272)
T ss_pred HHHHHHHH-HhHhHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 45777764 5678999999999999987765 4444441 114569999999988875
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=55.07 E-value=10 Score=34.37 Aligned_cols=28 Identities=39% Similarity=0.451 Sum_probs=20.3
Q ss_pred ccceeeeecc-CCCCeeEEeeccccchhH
Q 025423 104 AYAKIVAQKS-KGMPRISISLTRLTGSAA 131 (253)
Q Consensus 104 ~~akLVa~Ka-KGmP~ItI~L~~l~~saa 131 (253)
|.||.+|-.. +|+|.|.||-|-.+|++.
T Consensus 92 D~aK~ia~~~~~~~p~i~iPTt~~tgse~ 120 (332)
T cd07766 92 DTAKAVAALLNRGLPIIIVPTTAATGSEV 120 (332)
T ss_pred HHHHHHHHHhcCCCCEEEEeCCCchhhcc
Confidence 6777776655 488888888887777654
No 7
>KOG2430 consensus Glycosyl hydrolase, family 47 [Carbohydrate transport and metabolism]
Probab=54.76 E-value=8.7 Score=38.50 Aligned_cols=76 Identities=22% Similarity=0.415 Sum_probs=50.7
Q ss_pred CCCCCeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccceEeecCCCCCC--Ccccceeeeec
Q 025423 35 PDSSHLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDVKLILEGHSNAD--GAAYAKIVAQK 112 (253)
Q Consensus 35 ~d~~hL~v~vTDfHS~tW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~~slsS~~VkL~l~~~s~s~--G~~~akLVa~K 112 (253)
+.++.|.=++-+.||+.|. |.+-|||.+...|.+|+.... ++|+.+|--+ ..-+--+.--+
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 4567899999999999997 678899999999999986543 3444332100 01122344556
Q ss_pred cCCCCeeEEeecccc
Q 025423 113 SKGMPRISISLTRLT 127 (253)
Q Consensus 113 aKGmP~ItI~L~~l~ 127 (253)
+||--.+.+-+++-+
T Consensus 285 ~k~pi~ldvhihkp~ 299 (587)
T KOG2430|consen 285 NKGPIFLDVHIHKPM 299 (587)
T ss_pred cCCCeEEEEecccch
Confidence 777666666666644
No 8
>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=49.06 E-value=1.2e+02 Score=23.46 Aligned_cols=28 Identities=21% Similarity=0.393 Sum_probs=22.4
Q ss_pred hhhhHhhhcCCCChHHHHHHHHHhccccc
Q 025423 61 LDDMRDEIGIGGSWSEFIDYVVASIKSED 89 (253)
Q Consensus 61 LeDlRD~VGIGGSwsdF~dYl~~slsS~~ 89 (253)
...+|..+| |||.++-..||..-.....
T Consensus 22 ~~~Vr~~lG-~GS~~ti~~~l~~w~~~~~ 49 (120)
T PF11740_consen 22 VRAVRERLG-GGSMSTISKHLKEWREERE 49 (120)
T ss_pred HHHHHHHHC-CCCHHHHHHHHHHHHHhhh
Confidence 467899999 9999999888887655433
No 9
>PF14088 DUF4268: Domain of unknown function (DUF4268)
Probab=48.56 E-value=1.3e+02 Score=24.49 Aligned_cols=70 Identities=17% Similarity=0.228 Sum_probs=42.4
Q ss_pred hHHHHHHHHHhcccccceEeecCCCC----CCCcccceeeeeccCCCCeeEEeeccccchhHHHHHHHhhHHHHHHHHHH
Q 025423 74 WSEFIDYVVASIKSEDVKLILEGHSN----ADGAAYAKIVAQKSKGMPRISISLTRLTGSAATEAMAKLSLELFTAFRSM 149 (253)
Q Consensus 74 wsdF~dYl~~slsS~~VkL~l~~~s~----s~G~~~akLVa~KaKGmP~ItI~L~~l~~saa~D~ma~~sl~Lf~afrs~ 149 (253)
|+.|++|+...- ..++-.=+.+.+ +.|.+...|...-.+. .+.|.|.--.+. ....-.+|+.|...
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 889999987654 222222222222 6688888887777755 666666655443 34456678888666
Q ss_pred HHHH
Q 025423 150 QTLI 153 (253)
Q Consensus 150 q~~~ 153 (253)
++.+
T Consensus 77 k~~I 80 (140)
T PF14088_consen 77 KEEI 80 (140)
T ss_pred HHHH
Confidence 6333
No 10
>PF14147 Spore_YhaL: Sporulation protein YhaL
Probab=47.08 E-value=84 Score=23.32 Aligned_cols=41 Identities=17% Similarity=0.187 Sum_probs=31.9
Q ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHhhh
Q 025423 134 AMAKLSLELFTAFRSMQTLIVQEQERCLQ----LEKEAAAEKERN 174 (253)
Q Consensus 134 ~ma~~sl~Lf~afrs~q~~~~~eqe~~s~----L~~~LsaEKekn 174 (253)
+++-+-++-|-+.+++++--.-||+.+.+ -|+.+..||+|.
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 46677788899999999888888888765 567777777763
No 11
>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=45.79 E-value=8.9 Score=28.44 Aligned_cols=47 Identities=19% Similarity=0.389 Sum_probs=33.2
Q ss_pred CeEEEEecccccchhhccccchhhhhHhhhcCCCChHHHHHHHHHhcccccc
Q 025423 39 HLLIQVTDFRSNTWEAKRSVLQLDDMRDEIGIGGSWSEFIDYVVASIKSEDV 90 (253)
Q Consensus 39 hL~v~vTDfHS~tW~~slSv~~LeDlRD~VGIGGSwsdF~dYl~~slsS~~V 90 (253)
...|.+.|-....|...+++ ..=.....|+++|.+|+. ...|+-||+
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 35788899989999999866 222334889999999986 467777775
No 12
>KOG2441 consensus mRNA splicing factor/probable chromatin binding snw family nuclear protein [RNA processing and modification; Chromatin structure and dynamics]
Probab=41.80 E-value=53 Score=33.36 Aligned_cols=39 Identities=31% Similarity=0.376 Sum_probs=28.9
Q ss_pred eeecc-CCCCeeEEeeccccch--------hHHHHHHHhhHHHHHHHHHHH
Q 025423 109 VAQKS-KGMPRISISLTRLTGS--------AATEAMAKLSLELFTAFRSMQ 150 (253)
Q Consensus 109 Va~Ka-KGmP~ItI~L~~l~~s--------aa~D~ma~~sl~Lf~afrs~q 150 (253)
--||+ || .||+|++=.+. -.||..|.||-.||-|=|.+-
T Consensus 248 SNWKNpkG---YTipLdkRlaadgrglq~v~INdnFaKlseALy~adrKAR 295 (506)
T KOG2441|consen 248 SNWKNPKG---YTIPLDKRLAADGRGLQDVHINDNFAKLSEALYIADRKAR 295 (506)
T ss_pred hcCcCCCC---ceecchhhhhhccCCcccceecccHHHHHHHHHHHHHHHH
Confidence 34666 66 59999985443 367889999999999876553
No 13
>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=38.89 E-value=82 Score=27.80 Aligned_cols=37 Identities=35% Similarity=0.459 Sum_probs=28.4
Q ss_pred ecc-CCCCeeEEeecc--------ccchhHHHHHHHhhHHHHHHHHHHH
Q 025423 111 QKS-KGMPRISISLTR--------LTGSAATEAMAKLSLELFTAFRSMQ 150 (253)
Q Consensus 111 ~Ka-KGmP~ItI~L~~--------l~~saa~D~ma~~sl~Lf~afrs~q 150 (253)
||+ || .||+|++ +.+.-.||..+.||-+||.|=+..-
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 4445689999999999999987665
No 14
>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=37.85 E-value=42 Score=25.95 Aligned_cols=44 Identities=20% Similarity=0.299 Sum_probs=29.0
Q ss_pred CCeEEEEecccccchhhccccchhhhhHhh------hcCCCC-hHHHHHHHHH
Q 025423 38 SHLLIQVTDFRSNTWEAKRSVLQLDDMRDE------IGIGGS-WSEFIDYVVA 83 (253)
Q Consensus 38 ~hL~v~vTDfHS~tW~~slSv~~LeDlRD~------VGIGGS-wsdF~dYl~~ 83 (253)
.++.|++||...+.+ ....+-++.++.. ||+|.. +.+++..+-.
T Consensus 106 ~~~iviitDg~~~~~--~~~~~~~~~~~~~~i~i~~i~~~~~~~~~~l~~~~~ 156 (177)
T smart00327 106 PKVLILITDGESNDG--GDLLKAAKELKRSGVKVFVVGVGNDVDEEELKKLAS 156 (177)
T ss_pred CeEEEEEcCCCCCCC--ccHHHHHHHHHHCCCEEEEEEccCccCHHHHHHHhC
Confidence 679999999988755 2223444445443 677777 7777776643
No 15
>KOG3919 consensus Kinesin-associated fasciculation and elongation protein involved in axonal transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=36.89 E-value=23 Score=34.95 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=29.0
Q ss_pred ccchhhhhHhhhcCCCChHHHHHHH----HHhcccccce
Q 025423 57 SVLQLDDMRDEIGIGGSWSEFIDYV----VASIKSEDVK 91 (253)
Q Consensus 57 Sv~~LeDlRD~VGIGGSwsdF~dYl----~~slsS~~Vk 91 (253)
|++.||..+|+||-+||..|.|+-| -.||.-.++|
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 4566655544
No 16
>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=35.89 E-value=54 Score=24.26 Aligned_cols=49 Identities=20% Similarity=0.314 Sum_probs=32.0
Q ss_pred CCCCCCeEEEEecccccchhhccccchhhhhHh------hhcCCC-ChHHHHHHHHH
Q 025423 34 APDSSHLLIQVTDFRSNTWEAKRSVLQLDDMRD------EIGIGG-SWSEFIDYVVA 83 (253)
Q Consensus 34 a~d~~hL~v~vTDfHS~tW~~slSv~~LeDlRD------~VGIGG-SwsdF~dYl~~ 83 (253)
.++...+.|++||.+.+.+. .-....++.++. .||||+ .-..+++.|..
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 35678899999999976554 222344555555 678887 55666665544
No 17
>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=35.52 E-value=72 Score=29.67 Aligned_cols=58 Identities=17% Similarity=0.195 Sum_probs=38.8
Q ss_pred chhhhhHhhhc-------CCCCh-------------HHHHHHHHHhccc--ccceEeecCCCC---CCCcccceeeeecc
Q 025423 59 LQLDDMRDEIG-------IGGSW-------------SEFIDYVVASIKS--EDVKLILEGHSN---ADGAAYAKIVAQKS 113 (253)
Q Consensus 59 ~~LeDlRD~VG-------IGGSw-------------sdF~dYl~~slsS--~~VkL~l~~~s~---s~G~~~akLVa~Ka 113 (253)
..++++.+..| |||+| .+|.+.+...+.. .+++|.+|+-.. ..|.--++.+..|.
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 34556655444 78888 4777778887765 479999996532 55666677777776
Q ss_pred C-CC
Q 025423 114 K-GM 116 (253)
Q Consensus 114 K-Gm 116 (253)
. |.
T Consensus 272 ~~~~ 275 (377)
T cd06843 272 SHGE 275 (377)
T ss_pred cCCc
Confidence 3 54
No 18
>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=33.41 E-value=1.2e+02 Score=24.30 Aligned_cols=36 Identities=31% Similarity=0.396 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccCC
Q 025423 145 AFRSMQTLIVQEQERCLQLEKEAAAEKERNENIQNQ 180 (253)
Q Consensus 145 afrs~q~~~~~eqe~~s~L~~~LsaEKeknE~mq~q 180 (253)
.++.....-.+|++|+.+|...|..|..|..++..+
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 344666677899999999999998888888888764
No 19
>PF11995 DUF3490: Domain of unknown function (DUF3490); InterPro: IPR021881 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with PF00225 from PFAM. This domain is found associated with PF00225 from PFAM. This domain has two conserved sequence motifs: EVE and ESA.
Probab=30.06 E-value=51 Score=29.28 Aligned_cols=47 Identities=28% Similarity=0.278 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcccCC--cchhHHHhhhhcCC
Q 025423 148 SMQTLIVQEQERCLQLEKEAAAEKERNENIQNQ--PLYSKRQKLQKMNF 194 (253)
Q Consensus 148 s~q~~~~~eqe~~s~L~~~LsaEKeknE~mq~q--~~~~~~~Kl~~~s~ 194 (253)
+....+.+|++-.++.|..=-++.||.++.++= ++.+|+.|||..+-
T Consensus 71 sS~kaL~rER~~L~k~m~~rls~eere~ly~kWgI~l~sK~RrlQL~~~ 119 (161)
T PF11995_consen 71 SSIKALRREREMLAKQMQKRLSREEREELYKKWGIPLDSKQRRLQLANR 119 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhcCCCCcchHHHHHHHHH
Confidence 455677899999999997777777999988876 78899999987754
No 20
>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=28.59 E-value=1.2e+02 Score=25.70 Aligned_cols=53 Identities=17% Similarity=0.287 Sum_probs=40.5
Q ss_pred cccchhHHHHHHHhhHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccCC
Q 025423 125 RLTGSAATEAMAKLSLE---LFTAFRSMQTLIVQEQERCLQLEKEAAAEKERNENIQNQ 180 (253)
Q Consensus 125 ~l~~saa~D~ma~~sl~---Lf~afrs~q~~~~~eqe~~s~L~~~LsaEKeknE~mq~q 180 (253)
=+|-+..+|+.++++=. +++++..++.|+. +|+..|-..|..=+|-++.|+.+
T Consensus 35 ~vTrr~m~~A~~~v~kql~~vs~~l~~tKkhLs---qRId~vd~klDe~~ei~~~i~~e 90 (126)
T PF07889_consen 35 FVTRRSMSDAVASVSKQLEQVSESLSSTKKHLS---QRIDRVDDKLDEQKEISKQIKDE 90 (126)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhHHHHHHHHHHHHHH
Confidence 35667788888888864 5889999999998 67777777777777766666665
No 21
>PF09314 DUF1972: Domain of unknown function (DUF1972); InterPro: IPR015393 This domain is functionally uncharacterised and found in bacterial glycosyltransferases and rhamnosyltransferases.
Probab=26.77 E-value=2.4e+02 Score=24.90 Aligned_cols=67 Identities=19% Similarity=0.311 Sum_probs=42.4
Q ss_pred CChHHHHHHHHHhcccccceEeecCCCCCCCcccceeeeecc-CCCCeeEEeeccccchhHHHHHHHhhHHHHHHHH
Q 025423 72 GSWSEFIDYVVASIKSEDVKLILEGHSNADGAAYAKIVAQKS-KGMPRISISLTRLTGSAATEAMAKLSLELFTAFR 147 (253)
Q Consensus 72 GSwsdF~dYl~~slsS~~VkL~l~~~s~s~G~~~akLVa~Ka-KGmP~ItI~L~~l~~saa~D~ma~~sl~Lf~afr 147 (253)
|+|..|+++|..-+.+..+++..--.+...+. + ... +|+.++.|+..+. + ..+++.--.++|..+++
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-G--SAESIIYDFLSLLHALR 84 (185)
T ss_pred CcHHHHHHHHHHHHhcCCceEEEEEccCCCCC---C---CcccCCeEEEEeCCCCC-C--chHHHHHHHHHHHHHHH
Confidence 89999999999999988666655432221111 1 344 7999999987752 2 22455544555555553
No 22
>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=25.33 E-value=76 Score=30.71 Aligned_cols=110 Identities=19% Similarity=0.234 Sum_probs=76.1
Q ss_pred CCCccceEEEEeCCCCCCeEEEEecccccchhh-------ccccchhhh-hHhhhcCCCChHHHHHHHHHhcccccceEe
Q 025423 22 SDSLGRFLFHVSAPDSSHLLIQVTDFRSNTWEA-------KRSVLQLDD-MRDEIGIGGSWSEFIDYVVASIKSEDVKLI 93 (253)
Q Consensus 22 s~~~~pfLFh~~a~d~~hL~v~vTDfHS~tW~~-------slSv~~LeD-lRD~VGIGGSwsdF~dYl~~slsS~~VkL~ 93 (253)
.++..||..-+.-.+.....|.+--..+-.+-+ .+-+++.=. -||.-|=.|||-|-.--+..+|+--||.++
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 356689999998888888777774444433322 233444333 378889999998866667899999999999
Q ss_pred ecC--CCC--CCCcccceeeeeccC----CCCeeEEeeccccchhHH
Q 025423 94 LEG--HSN--ADGAAYAKIVAQKSK----GMPRISISLTRLTGSAAT 132 (253)
Q Consensus 94 l~~--~s~--s~G~~~akLVa~KaK----GmP~ItI~L~~l~~saa~ 132 (253)
+.. +++ ..|.++|-||+-|.| -=|. -|.||+--.++++
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 973 333 789999999998875 1232 2566766665554
No 23
>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=25.17 E-value=69 Score=24.84 Aligned_cols=18 Identities=39% Similarity=0.497 Sum_probs=15.0
Q ss_pred HHHHHhhHHHHHHHHHHH
Q 025423 133 EAMAKLSLELFTAFRSMQ 150 (253)
Q Consensus 133 D~ma~~sl~Lf~afrs~q 150 (253)
..|.+||=+||.||-+-+
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 469999999999996643
No 24
>smart00243 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain
Probab=24.52 E-value=44 Score=26.27 Aligned_cols=16 Identities=25% Similarity=0.904 Sum_probs=14.1
Q ss_pred hhcCCCChHHHHHHHH
Q 025423 67 EIGIGGSWSEFIDYVV 82 (253)
Q Consensus 67 ~VGIGGSwsdF~dYl~ 82 (253)
.|-+||+|.++=+||.
T Consensus 49 MVRVGGGW~tL~~fL~ 64 (73)
T smart00243 49 MVRVGGGWETLDEYLL 64 (73)
T ss_pred EEEECCcHHHHHHHHH
Confidence 6789999999999985
No 25
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=24.09 E-value=2.7e+02 Score=24.62 Aligned_cols=73 Identities=18% Similarity=0.276 Sum_probs=41.1
Q ss_pred CCCChHHHHHHHHHhcccccceEeec---CCCC-CC---CcccceeeeeccCCCC----------eeEEeeccccchhHH
Q 025423 70 IGGSWSEFIDYVVASIKSEDVKLILE---GHSN-AD---GAAYAKIVAQKSKGMP----------RISISLTRLTGSAAT 132 (253)
Q Consensus 70 IGGSwsdF~dYl~~slsS~~VkL~l~---~~s~-s~---G~~~akLVa~KaKGmP----------~ItI~L~~l~~saa~ 132 (253)
.=.||.+|++.... ..+|++- +... ++ -..-.-|-..-++|+| .|.||.. -..+++|
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 34688999876653 2333321 1111 11 1122456677778888 4999998 2224444
Q ss_pred HHHHHhhHHHHHHHHHH
Q 025423 133 EAMAKLSLELFTAFRSM 149 (253)
Q Consensus 133 D~ma~~sl~Lf~afrs~ 149 (253)
=+ .+.+.-+|+++|..
T Consensus 134 Ls-nsvavv~yEa~RQ~ 149 (155)
T COG0219 134 LS-NTVAVVLYEALRQL 149 (155)
T ss_pred HH-HHHHHHHHHHHHHh
Confidence 22 23567799999754
No 26
>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=23.92 E-value=23 Score=27.65 Aligned_cols=18 Identities=22% Similarity=0.682 Sum_probs=15.4
Q ss_pred hhhcCCCChHHHHHHHHH
Q 025423 66 DEIGIGGSWSEFIDYVVA 83 (253)
Q Consensus 66 D~VGIGGSwsdF~dYl~~ 83 (253)
-.|-+||+|.++-.||..
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 27
>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=22.57 E-value=77 Score=29.21 Aligned_cols=18 Identities=39% Similarity=0.218 Sum_probs=11.7
Q ss_pred CCCCeeEEeeccccchhH
Q 025423 114 KGMPRISISLTRLTGSAA 131 (253)
Q Consensus 114 KGmP~ItI~L~~l~~saa 131 (253)
+|+|.|.||=|-.+||.+
T Consensus 108 ~~~p~i~VPTtagtgse~ 125 (332)
T cd08180 108 KKPLFIAIPTTSGTGSEV 125 (332)
T ss_pred CCCCEEEeCCCCcchHhh
Confidence 467777777666666554
No 28
>cd00953 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases.
Probab=21.68 E-value=2.8e+02 Score=25.18 Aligned_cols=93 Identities=11% Similarity=0.079 Sum_probs=52.7
Q ss_pred hccccchhhhhHh----hhcCCCChHH---HHHHHHHhcccccceEeecCCCCCCCcccceeeeeccCCCCeeEEeeccc
Q 025423 54 AKRSVLQLDDMRD----EIGIGGSWSE---FIDYVVASIKSEDVKLILEGHSNADGAAYAKIVAQKSKGMPRISISLTRL 126 (253)
Q Consensus 54 ~slSv~~LeDlRD----~VGIGGSwsd---F~dYl~~slsS~~VkL~l~~~s~s~G~~~akLVa~KaKGmP~ItI~L~~l 126 (253)
..++++.++.|-+ .|||..|-.+ |.+|... .+++.+..+.+.- ..-....=++|. .
T Consensus 135 ~~l~~~~l~~L~~~~p~vvgiK~s~~d~~~~~~~~~~---~~~~~v~~G~d~~-----~~~~l~~Ga~G~---i------ 197 (279)
T cd00953 135 YDINARMAKEIKKAGGDIIGVKDTNEDISHMLEYKRL---VPDFKVYSGPDSL-----IFSALRSGLDGS---V------ 197 (279)
T ss_pred CCCCHHHHHHHHhcCCCEEEEEeCccCHHHHHHHHHh---CCCeEEEEccHHH-----HHHHHHcCCCeE---E------
Confidence 3567777777753 4788766544 5554321 2367655443210 000001112221 1
Q ss_pred cchhHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025423 127 TGSAATEAMAKLSLELFTAFRSMQTLIVQEQERCLQLEKEA 167 (253)
Q Consensus 127 ~~saa~D~ma~~sl~Lf~afrs~q~~~~~eqe~~s~L~~~L 167 (253)
++.+.++-.+..++|++|. .+.+.+.|.++..|+..+
T Consensus 198 --~~~~n~~P~~~~~l~~a~~--~~~a~~~q~~~~~l~~~~ 234 (279)
T cd00953 198 --AAASNYLPEVFVKIKDHVA--IEDAFKLQFLINEVLDAS 234 (279)
T ss_pred --echhhccHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 3466778888999999996 445556677777777755
No 29
>KOG0894 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.29 E-value=48 Score=31.06 Aligned_cols=24 Identities=25% Similarity=0.661 Sum_probs=20.4
Q ss_pred CCeEEEEecccccchhhccccchh
Q 025423 38 SHLLIQVTDFRSNTWEAKRSVLQL 61 (253)
Q Consensus 38 ~hL~v~vTDfHS~tW~~slSv~~L 61 (253)
..|++-.||||-.+|.-.-||+-+
T Consensus 84 tRLCLSiSDfHPdsWNP~WsVStI 107 (244)
T KOG0894|consen 84 TRLCLSISDFHPDSWNPGWSVSTI 107 (244)
T ss_pred ceEEEeccccCcCcCCCcccHHHH
Confidence 459999999999999988887653
No 30
>PLN02537 diaminopimelate decarboxylase
Probab=20.80 E-value=2.5e+02 Score=26.62 Aligned_cols=48 Identities=25% Similarity=0.384 Sum_probs=32.8
Q ss_pred hhcCCCCh--------------HHHHHHHHHhcccccceEeecCCCC---CCCcccceeeeeccC
Q 025423 67 EIGIGGSW--------------SEFIDYVVASIKSEDVKLILEGHSN---ADGAAYAKIVAQKSK 114 (253)
Q Consensus 67 ~VGIGGSw--------------sdF~dYl~~slsS~~VkL~l~~~s~---s~G~~~akLVa~KaK 114 (253)
.|-|||+| .+|.+-+...+...+++|.+|+-.. ..|.--++.+..|-.
T Consensus 224 ~idiGGGf~v~y~~~~~~~~~~~~~~~~i~~~~~~~~~~li~EPGR~lva~ag~lv~~V~~~k~~ 288 (410)
T PLN02537 224 YLNIGGGLGIDYYHAGAVLPTPRDLIDTVRELVLSRDLTLIIEPGRSLIANTCCFVNRVTGVKTN 288 (410)
T ss_pred EEEcCCCccccCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEccChhhhccceEEEEEEEEEeec
Confidence 47799998 2466777778887789999997533 444455555666654
No 31
>cd01464 vWA_subfamily VWA subfamily: 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
Probab=20.29 E-value=97 Score=25.35 Aligned_cols=42 Identities=14% Similarity=0.228 Sum_probs=26.2
Q ss_pred CCeEEEEecccccc-hhhccccchhhhhHh------hhcCCC-ChHHHHHHH
Q 025423 38 SHLLIQVTDFRSNT-WEAKRSVLQLDDMRD------EIGIGG-SWSEFIDYV 81 (253)
Q Consensus 38 ~hL~v~vTDfHS~t-W~~slSv~~LeDlRD------~VGIGG-SwsdF~dYl 81 (253)
....|+.||=+.+. |... .+.+.++++ .||||- ...++|..|
T Consensus 108 ~~~iillTDG~~~~~~~~~--~~~~~~~~~~~~~i~~igiG~~~~~~~L~~i 157 (176)
T cd01464 108 RPWVFLLTDGEPTDDLTAA--IERIKEARDSKGRIVACAVGPKADLDTLKQI 157 (176)
T ss_pred CcEEEEEcCCCCCchHHHH--HHHHHhhcccCCcEEEEEeccccCHHHHHHH
Confidence 45789999998753 4433 255666665 589995 444444443
No 32
>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=20.25 E-value=1.2e+02 Score=28.59 Aligned_cols=22 Identities=27% Similarity=0.306 Sum_probs=12.3
Q ss_pred ccceeeeecc-CCCCeeEEeecc
Q 025423 104 AYAKIVAQKS-KGMPRISISLTR 125 (253)
Q Consensus 104 ~~akLVa~Ka-KGmP~ItI~L~~ 125 (253)
|.||.+|-.. .|+|.|.||-|.
T Consensus 97 D~ak~vA~~~~rgip~i~VPTTl 119 (344)
T cd08169 97 DVAGFVASTLFRGIAFIRVPTTL 119 (344)
T ss_pred HHHHHHHHHhccCCcEEEecCCc
Confidence 5555555432 466666666653
Done!