Query psy13626
Match_columns 127
No_of_seqs 38 out of 40
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 16:05:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13626hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12205 GIT1_C: G protein-cou 100.0 2.3E-49 5E-54 295.0 9.7 110 17-127 5-123 (123)
2 KOG0818|consensus 100.0 7.8E-33 1.7E-37 244.9 10.7 120 7-127 539-669 (669)
3 smart00307 ILWEQ I/LWEQ domain 95.4 0.24 5.2E-06 40.0 10.1 106 19-124 3-138 (200)
4 PF03623 Focal_AT: Focal adhes 94.8 0.7 1.5E-05 35.6 10.7 102 22-125 7-124 (139)
5 PF12026 DUF3513: Domain of un 92.3 1.7 3.8E-05 35.4 9.5 102 23-124 93-207 (210)
6 PF08913 VBS: Vinculin Binding 83.0 18 0.00038 27.2 10.3 102 23-126 6-120 (125)
7 PF02845 CUE: CUE domain; Int 77.8 4 8.6E-05 24.4 3.3 28 62-90 3-30 (42)
8 PF13324 GCIP: Grap2 and cycli 69.3 41 0.0009 27.3 8.3 69 57-125 8-83 (275)
9 PF01608 I_LWEQ: I/LWEQ domain 64.6 44 0.00096 26.0 7.2 79 23-124 9-91 (152)
10 PRK12793 flaF flagellar biosyn 63.2 47 0.001 24.6 6.9 56 29-88 21-82 (115)
11 smart00546 CUE Domain that may 60.9 16 0.00035 21.7 3.4 26 62-88 4-29 (43)
12 smart00283 MA Methyl-accepting 55.4 82 0.0018 23.6 7.2 20 27-46 139-158 (262)
13 cd07909 YciF YciF bacterial st 54.3 30 0.00064 26.4 4.7 69 31-99 16-86 (147)
14 smart00307 ILWEQ I/LWEQ domain 53.8 89 0.0019 25.3 7.5 49 77-125 56-107 (200)
15 KOG0980|consensus 47.6 1.6E+02 0.0034 29.4 9.3 43 82-124 798-854 (980)
16 PF00015 MCPsignal: Methyl-acc 46.6 88 0.0019 23.1 6.1 19 28-46 89-107 (213)
17 PF07499 RuvA_C: RuvA, C-termi 43.5 15 0.00033 22.5 1.3 30 58-88 18-47 (47)
18 PF04458 DUF505: Protein of un 40.5 70 0.0015 30.1 5.6 57 51-122 514-574 (591)
19 PF02269 TFIID-18kDa: Transcri 40.5 63 0.0014 22.7 4.2 58 12-75 11-68 (93)
20 PF00015 MCPsignal: Methyl-acc 40.1 1.5E+02 0.0032 21.8 10.0 38 78-115 145-182 (213)
21 PRK04330 hypothetical protein; 35.7 1.6E+02 0.0034 21.3 5.7 30 52-83 25-54 (88)
22 PF12205 GIT1_C: G protein-cou 35.5 1E+02 0.0022 23.2 4.9 20 52-71 103-122 (123)
23 PRK15041 methyl-accepting chem 32.5 2.2E+02 0.0047 25.3 7.2 19 28-46 408-426 (554)
24 PF13324 GCIP: Grap2 and cycli 31.8 1.6E+02 0.0035 23.9 5.9 50 18-68 25-74 (275)
25 PF08701 GN3L_Grn1: GNL3L/Grn1 31.5 86 0.0019 21.9 3.7 22 20-41 41-62 (79)
26 PRK11166 chemotaxis regulator 28.4 3.3E+02 0.0072 22.3 9.5 101 14-120 42-160 (214)
27 cd01075 NAD_bind_Leu_Phe_Val_D 28.0 2.1E+02 0.0045 22.2 5.8 41 23-67 158-198 (200)
28 COG1698 Uncharacterized protei 27.7 2.3E+02 0.0049 20.8 5.4 43 34-83 16-58 (93)
29 PF06103 DUF948: Bacterial pro 25.8 88 0.0019 21.1 2.9 23 24-46 43-65 (90)
30 PF15015 NYD-SP12_N: Spermatog 25.7 1.2E+02 0.0026 28.2 4.6 39 22-60 419-457 (569)
31 PF10157 DUF2365: Uncharacteri 25.2 3.2E+02 0.007 21.1 9.4 89 24-126 55-145 (149)
32 PF06248 Zw10: Centromere/kine 24.9 2.9E+02 0.0063 24.9 6.8 22 22-43 8-29 (593)
33 PF01044 Vinculin: Vinculin fa 24.7 4.2E+02 0.0092 25.9 8.2 21 104-124 921-941 (968)
34 smart00283 MA Methyl-accepting 24.3 3E+02 0.0066 20.5 8.5 20 105-124 237-256 (262)
35 cd05094 PTKc_TrkC Catalytic do 24.3 2.1E+02 0.0046 21.8 5.1 46 44-89 238-284 (291)
36 PF12725 DUF3810: Protein of u 23.8 3.3E+02 0.0071 23.0 6.6 67 19-85 93-165 (318)
37 PRK12794 flaF flagellar biosyn 23.8 3.1E+02 0.0067 20.3 6.4 63 24-89 17-85 (122)
38 PF01322 Cytochrom_C_2: Cytoch 23.7 2.7E+02 0.0057 19.6 5.5 28 51-78 34-61 (122)
39 COG2036 HHT1 Histones H3 and H 23.6 2.8E+02 0.0061 19.8 5.4 56 59-120 8-68 (91)
40 PF14916 CCDC92: Coiled-coil d 23.4 74 0.0016 21.4 2.1 26 78-103 17-42 (60)
41 PRK14562 haloacid dehalogenase 23.4 3E+02 0.0066 21.8 6.0 67 23-90 20-89 (204)
42 cd05072 PTKc_Lyn Catalytic dom 23.0 2E+02 0.0042 21.4 4.6 35 51-85 224-259 (261)
43 TIGR00153 conserved hypothetic 22.6 2.6E+02 0.0056 21.7 5.4 9 53-61 45-53 (216)
44 PF02910 Succ_DH_flav_C: Fumar 22.3 2.7E+02 0.0058 20.0 5.1 16 105-120 57-72 (129)
45 COG4225 Predicted unsaturated 22.3 2.8E+02 0.0061 24.7 6.0 106 15-120 139-281 (357)
46 cd05064 PTKc_EphR_A10 Catalyti 22.0 2.9E+02 0.0063 20.8 5.4 32 54-85 231-263 (266)
47 TIGR03751 conj_TIGR03751 conju 21.9 65 0.0014 24.4 1.8 20 60-79 59-78 (116)
48 PF13581 HATPase_c_2: Histidin 21.7 1.4E+02 0.003 20.3 3.3 44 71-114 1-45 (125)
49 COG2219 PRI2 Eukaryotic-type D 21.7 69 0.0015 27.9 2.1 14 62-75 275-288 (363)
50 PRK15048 methyl-accepting chem 21.7 5.5E+02 0.012 22.4 9.6 18 29-46 407-424 (553)
51 PF09304 Cortex-I_coil: Cortex 20.8 3.7E+02 0.0079 20.1 6.2 44 76-120 38-81 (107)
52 PF10018 Med4: Vitamin-D-recep 20.3 4.1E+02 0.0089 20.5 9.8 82 24-121 5-99 (188)
53 PF12792 CSS-motif: CSS motif 20.3 2.9E+02 0.0062 20.0 4.9 45 23-71 11-55 (208)
54 KOG4514|consensus 20.1 5.1E+02 0.011 21.5 8.7 86 27-126 131-218 (222)
No 1
>PF12205 GIT1_C: G protein-coupled receptor kinase-interacting protein 1 C term; InterPro: IPR022018 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF01412 from PFAM, PF00023 from PFAM, PF08518 from PFAM. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodeling and membrane trafficking. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C-terminal and the LD motifs of paxillin. The C-terminal folds into a four helix bundle. ; PDB: 2JX0_A.
Probab=100.00 E-value=2.3e-49 Score=294.96 Aligned_cols=110 Identities=47% Similarity=0.774 Sum_probs=99.0
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHH
Q psy13626 17 TTRMPQSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQA 96 (127)
Q Consensus 17 ~~~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~ 96 (127)
++++||+|||+||||+|||+|||||++||+++ +++|+||||+|++||+||++|||++|.+++||++|++|++++.+||+
T Consensus 5 ~~~~p~~e~Vi~~TE~vTk~IqeLl~aAQ~~~-~~s~~pcae~I~~aV~~m~~LfP~~~~~e~vr~~L~~L~~~~~~Lq~ 83 (123)
T PF12205_consen 5 DPNLPSTEDVIRRTEQVTKRIQELLRAAQEGR-HDSFAPCAERIRSAVTEMAALFPKDPRSETVRSSLRQLTSSAYRLQA 83 (123)
T ss_dssp BSS-S-HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHTS-SSB--HHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhcc-cccchhHHHHHHHHHHHHHHhCCCccCChHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999999999975 68999999999999999999999999999999999999999999999
Q ss_pred hhhh---------hHhhHHHHHHHHHHHHHhHhhhhhhcC
Q psy13626 97 ECAQ---------LEGSAERVRSCAYNMAKANKQLLTQFQ 127 (127)
Q Consensus 97 eC~~---------lq~~t~qv~~cAYdIAKAaK~LvT~f~ 127 (127)
||.. ++..++|||+||||||||||+|||+|+
T Consensus 84 eC~~~~~~~~~~~~~~~t~qvi~~AYdIAKAaKqLvT~~~ 123 (123)
T PF12205_consen 84 ECQKAQPEDDAVDIQLVTQQVIQCAYDIAKAAKQLVTIFT 123 (123)
T ss_dssp HHHS---S--SS-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhcccCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 9965 456699999999999999999999984
No 2
>KOG0818|consensus
Probab=99.98 E-value=7.8e-33 Score=244.90 Aligned_cols=120 Identities=39% Similarity=0.545 Sum_probs=115.4
Q ss_pred CchhHhhhccCCCCCChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHH
Q psy13626 7 NNYMECFQSTTTRMPQSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRS 86 (127)
Q Consensus 7 ~~~~~~~~~~~~~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~ 86 (127)
.|+.|+|.|.++++|+.|||+.+||+||++||||+++||+. ++++|+||+|+|+.||++|++|||+.|.++.+|++|++
T Consensus 539 ~~tssl~~~~~~~~p~~eev~i~te~vt~~~~el~ra~qe~-~~~s~~p~~eli~~avt~~~al~ak~pa~d~~r~sl~L 617 (669)
T KOG0818|consen 539 PSTSSLSRSSQPGLPSTEEVIIKTEQVTKNIQELLRAAQEQ-KHDSTRPCSELIHHAVTEMAALFAKGPASDPVRASLRL 617 (669)
T ss_pred cCccccccCCCCCCCccchheecHHHHhHHHHHHHHHHHhh-hccccccHHHHHHHHhhhHHHhccCCCccchHHHHHHH
Confidence 48899999999999999999999999999999999999987 56999999999999999999999999999999999999
Q ss_pred hhhhhHHHHHhh-----------hhhHhhHHHHHHHHHHHHHhHhhhhhhcC
Q psy13626 87 LNTSTVRLQAEC-----------AQLEGSAERVRSCAYNMAKANKQLLTQFQ 127 (127)
Q Consensus 87 L~~~a~~Lq~eC-----------~~lq~~t~qv~~cAYdIAKAaK~LvT~f~ 127 (127)
|+.++.+||+|| +++|+.++|||+||||||||+|+|||+|+
T Consensus 618 lt~~~~~lqhEc~kav~~d~~~~~~~ql~t~~VidcA~~IA~a~k~lV~~f~ 669 (669)
T KOG0818|consen 618 LTISAYRLQHECIKAVPLDPGKPNDPQLMTQQVIDCAYDIAKAAKQLVTIFT 669 (669)
T ss_pred HHHHhHHHHHHHHhhcCCCCCCCCchhhhhHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999 46788899999999999999999999995
No 3
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=95.40 E-value=0.24 Score=40.02 Aligned_cols=106 Identities=15% Similarity=0.212 Sum_probs=79.5
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHhhc--------C--------------CCCCCccchHHHHHHHHHHHHhhcCC---
Q psy13626 19 RMPQSEEVVRRTDQVTKRIQELAAHMRS--------S--------------DKCHSFVPHAERIRIAVSELSAIFPQ--- 73 (127)
Q Consensus 19 ~~P~~e~Vir~TE~vTr~IqeLl~aaq~--------~--------------~~~~~fvpcae~I~~AV~el~aLFP~--- 73 (127)
.+..-|.+......||+.|..|+.++-. | +-.+..+.+|..|..|+..|..-...
T Consensus 3 ~l~v~e~IL~aa~~i~~a~~~Lv~aA~~~Q~Eiv~~gr~~~~~~~fY~kn~~w~EgLisAAkaV~~a~~~Lv~aA~~~~~ 82 (200)
T smart00307 3 ELEVDESILEAAKAITKAIAALVKAATNAQREIVAQGRGGASPGEFYKKNSRWTEGLISAAKAVAAATNVLVEAADGVVT 82 (200)
T ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcccccccCCcccHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566778888899999999999976543 1 11233457888888888777544332
Q ss_pred -CCCcHHHHHHHHHhhhhhHHHHHhhhh----hHhhHHHHHHHHHHHHHhHhhhhh
Q psy13626 74 -NTNNDLIRHALRSLNTSTVRLQAECAQ----LEGSAERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 74 -~~~~e~vr~~L~~L~~~a~~Lq~eC~~----lq~~t~qv~~cAYdIAKAaK~LvT 124 (127)
...+|.+-.+-+....+|.+|-.-|.- .-...+++..++=.|+.|++.||-
T Consensus 83 g~~~~E~LI~aAk~VAasTaQLVaAsrvka~~~S~~~~~L~~Ask~V~~At~~LVa 138 (200)
T smart00307 83 GKGSEEELIVAAKEVAASTAQLVAASRVKADKDSQAQDRLQAASKAVTNATANLVA 138 (200)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCChhHHHHHHHHHHHHHHHHHHHH
Confidence 347899999999999999999988831 123478899999999999999985
No 4
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=94.81 E-value=0.7 Score=35.65 Aligned_cols=102 Identities=19% Similarity=0.260 Sum_probs=73.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHH-------HHHhhcCCCCCcHHHHHHHHHhhhhhHHH
Q psy13626 22 QSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVS-------ELSAIFPQNTNNDLIRHALRSLNTSTVRL 94 (127)
Q Consensus 22 ~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~-------el~aLFP~~~~~e~vr~~L~~L~~~a~~L 94 (127)
..|.|.+.|-.|-|.+-+|=...+.. ..+.|+.|-..|..+.. ++...||... -.+|.-+=+.|+..-..|
T Consensus 7 ~~D~Vy~at~~VVkaV~~Ls~~v~~~-~~~~y~~~VK~VG~~Lr~Ll~sVd~~~~~l~~s~-~~EVema~klL~~DM~eL 84 (139)
T PF03623_consen 7 TNDKVYDATTGVVKAVMQLSNSVQTA-KPEEYVDLVKNVGLALRDLLTSVDQILPSLPSSV-RREVEMAHKLLSKDMAEL 84 (139)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHTTTS-SHHHHHHHHHHHHHHHHHHHHHHHHHGGGSHTTS-HHHHHHHHHHHHHHHHHH
T ss_pred ccChHHHHHHHHHHHHHHHHhhhccC-ChHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHH-HHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999997 47999999999887654 4556777665 555665555555443333
Q ss_pred HH------hhhh---hHhhHHHHHHHHHHHHHhHhhhhhh
Q psy13626 95 QA------ECAQ---LEGSAERVRSCAYNMAKANKQLLTQ 125 (127)
Q Consensus 95 q~------eC~~---lq~~t~qv~~cAYdIAKAaK~LvT~ 125 (127)
.. ++.. ..-.-.++..+||-+|.-+|.|+.-
T Consensus 85 i~~mklaq~~~~ttl~~eyrr~ml~aah~LA~daKnLlD~ 124 (139)
T PF03623_consen 85 ISAMKLAQQNSNTTLDEEYRRQMLSAAHVLAMDAKNLLDV 124 (139)
T ss_dssp HHHHHHHHHTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 22 2211 0111457889999999999999863
No 5
>PF12026 DUF3513: Domain of unknown function (DUF3513); InterPro: IPR021901 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 192 to 218 amino acids in length. This domain is found associated with PF00018 from PFAM, PF08824 from PFAM. This domain has a conserved QPP sequence motif. ; PDB: 3T6G_D 1X27_N.
Probab=92.33 E-value=1.7 Score=35.39 Aligned_cols=102 Identities=13% Similarity=0.181 Sum_probs=73.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH---hhcCCCCCcHHHHHHHHHhhhhhHHHHHhhh
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELS---AIFPQNTNNDLIRHALRSLNTSTVRLQAECA 99 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~---aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~ 99 (127)
++........++++|..++.....+.-+..|+++|-.|..+-.+|+ .-.=+.-...+||.-+-.-++.=.-+...|.
T Consensus 93 ~~q~~~~~~~L~~AId~F~~sv~~nQPP~iFv~~sK~VIl~ahkLVfiGDTl~r~~~~~dvr~~v~~~s~~Lc~~LK~~v 172 (210)
T PF12026_consen 93 SEQCRLHFGALQKAIDAFFSSVSNNQPPKIFVAHSKFVILSAHKLVFIGDTLCREAQSADVRNEVLCSSNQLCDLLKTLV 172 (210)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHHC--SHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccCCCcchhhhcCcEEEEEeeeeeeeccHHHHHhcchHHHHHHHHHHHHHHHHHHHHH
Confidence 3455567788899999999999998878899999999999999999 5554555677777766544444334444442
Q ss_pred h------hH----hhHHHHHHHHHHHHHhHhhhhh
Q psy13626 100 Q------LE----GSAERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 100 ~------lq----~~t~qv~~cAYdIAKAaK~LvT 124 (127)
. ++ ..+++..+++-++++.|.++=+
T Consensus 173 ~aTK~AAl~yPs~~AlqeMvd~v~eLs~~A~qfr~ 207 (210)
T PF12026_consen 173 LATKKAALQYPSPSALQEMVDRVKELSQHAQQFRT 207 (210)
T ss_dssp HHHHHHHHT-S-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHH
Confidence 2 11 2389999999999999998744
No 6
>PF08913 VBS: Vinculin Binding Site; InterPro: IPR015009 Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod []. ; PDB: 2L10_A 2KVP_A 2B0H_A 1RKC_B 1XWJ_B.
Probab=82.96 E-value=18 Score=27.20 Aligned_cols=102 Identities=17% Similarity=0.267 Sum_probs=77.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH-------HhhcCCCCCcHHHHHHHHHhhhhhHHHH
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSEL-------SAIFPQNTNNDLIRHALRSLNTSTVRLQ 95 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el-------~aLFP~~~~~e~vr~~L~~L~~~a~~Lq 95 (127)
.+.+++.++.|.+-++|+......+ ++...+.|.++-.-..+| ++.-|+......||.+++.|..+...|-
T Consensus 6 Qt~mv~~ak~ia~~a~emv~ks~~~--p~eL~~la~~lt~~y~~La~~~~~aaat~~~~ev~~~i~~~vq~LG~sc~~Lv 83 (125)
T PF08913_consen 6 QTRMVEAAKEIARTAQEMVTKSRTN--PEELGTLANDLTHDYSQLAQDAKGAAATTPSAEVQNRIKSAVQDLGMSCIELV 83 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHCCSSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCC--hHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999887764 578888888776655554 3456665567788999999999888886
Q ss_pred HhhhhhH------hhHHHHHHHHHHHHHhHhhhhhhc
Q psy13626 96 AECAQLE------GSAERVRSCAYNMAKANKQLLTQF 126 (127)
Q Consensus 96 ~eC~~lq------~~t~qv~~cAYdIAKAaK~LvT~f 126 (127)
..+..++ ..-+++..+|-++....-++|.-.
T Consensus 84 ~aag~~~~~P~d~~~k~~L~~~AR~v~EkVs~VlaaL 120 (125)
T PF08913_consen 84 QAAGAVQSNPSDPYAKRELADAARAVSEKVSQVLAAL 120 (125)
T ss_dssp HHHHHHHH-TT-HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHhCcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6665543 347889999999988877777543
No 7
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=77.82 E-value=4 Score=24.40 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=22.1
Q ss_pred HHHHHHHhhcCCCCCcHHHHHHHHHhhhh
Q psy13626 62 IAVSELSAIFPQNTNNDLIRHALRSLNTS 90 (127)
Q Consensus 62 ~AV~el~aLFP~~~~~e~vr~~L~~L~~~ 90 (127)
..|..|.++||..+ .+.|+.+|+.-+.+
T Consensus 3 ~~v~~L~~mFP~~~-~~~I~~~L~~~~~~ 30 (42)
T PF02845_consen 3 EMVQQLQEMFPDLD-REVIEAVLQANNGD 30 (42)
T ss_dssp HHHHHHHHHSSSS--HHHHHHHHHHTTTT
T ss_pred HHHHHHHHHCCCCC-HHHHHHHHHHcCCC
Confidence 46889999999998 88899988766544
No 8
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=69.31 E-value=41 Score=27.33 Aligned_cols=69 Identities=19% Similarity=0.249 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHhhc--CCCCCcHHHHHHHHHhhhhhHHHHHhhhhhH-----hhHHHHHHHHHHHHHhHhhhhhh
Q psy13626 57 AERIRIAVSELSAIF--PQNTNNDLIRHALRSLNTSTVRLQAECAQLE-----GSAERVRSCAYNMAKANKQLLTQ 125 (127)
Q Consensus 57 ae~I~~AV~el~aLF--P~~~~~e~vr~~L~~L~~~a~~Lq~eC~~lq-----~~t~qv~~cAYdIAKAaK~LvT~ 125 (127)
+..|..-+|.+.=+| |+.|..+++...+..+..+...|-.-|..+. ..-..|++.+.+|-++..+|+..
T Consensus 8 ~~~~s~~aTkl~l~~~~~~~P~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~G~tL~~~i~~~v~~lv~~~~~L~~~ 83 (275)
T PF13324_consen 8 AKALSHEATKLSLVFSKPPLPSPEEAQELCESLFNALLGLLSLYHGLPKGQGPTLRKEIRSAVKSLVDSSIQLVEE 83 (275)
T ss_dssp HHHHHHHHHHHHHHTTSSS---HHHHHHHHHHHHHHHHHHHHHHTTS-GGG-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHhhCcHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566778889999999 6677888898888888888777777775432 12678888888888888888754
No 9
>PF01608 I_LWEQ: I/LWEQ domain; InterPro: IPR002558 I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin P26039 from SWISSPROT and yeast Sla2p P33338 from SWISSPROT interact with F-actin []. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks []. I/LWEQ domains can be placed into four major groups based on sequence similarity: Metazoan talin. Dictyostelium discoideum (Slime mould) TalA/TalB P54633 from SWISSPROT and SLA110. Metazoan Hip1p O00291 from SWISSPROT. Saccharomyces cerevisiae Sla2p P33338 from SWISSPROT. ; GO: 0003779 actin binding; PDB: 2QDQ_A 2JSW_A 1R0D_B.
Probab=64.59 E-value=44 Score=26.02 Aligned_cols=79 Identities=15% Similarity=0.204 Sum_probs=53.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHHhhh---
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECA--- 99 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~--- 99 (127)
+|-+|--...|......|+.+|.+--. .....|.+-.+-+...++|.+|.+-|.
T Consensus 9 teGLISAAKaVa~at~~LveaA~~vv~-----------------------g~~~~E~LIvaa~eVAasTAQLv~AsrVKa 65 (152)
T PF01608_consen 9 TEGLISAAKAVAAATNMLVEAADGVVQ-----------------------GTGSEEELIVAAKEVAASTAQLVAASRVKA 65 (152)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------------TS--HHHHHHHHHHHHHHHHHHHHHHCTTS
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHh-----------------------CCCcHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 566777778888888888888775211 222566777788888888888888882
Q ss_pred -hhHhhHHHHHHHHHHHHHhHhhhhh
Q psy13626 100 -QLEGSAERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 100 -~lq~~t~qv~~cAYdIAKAaK~LvT 124 (127)
..-....++.+++=.|.+|++.||.
T Consensus 66 ~~~S~~~~~L~~As~~V~~At~~LV~ 91 (152)
T PF01608_consen 66 DPNSKTQDRLEQASKAVKKATENLVA 91 (152)
T ss_dssp -TTSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 1123467777777777777777764
No 10
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=63.23 E-value=47 Score=24.61 Aligned_cols=56 Identities=18% Similarity=0.207 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhc------CCCCCcHHHHHHHHHhh
Q psy13626 29 RTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIF------PQNTNNDLIRHALRSLN 88 (127)
Q Consensus 29 ~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLF------P~~~~~e~vr~~L~~L~ 88 (127)
.-+.++|.+..|-.+...+ .+|....+.++. -.+||++| |.++-|+++|.-|-.|.
T Consensus 21 E~~~l~r~~~~L~~a~~~~---~~~~~~~eAL~~-NrrLWt~~~~Dl~~p~N~LP~eLRa~lisL~ 82 (115)
T PRK12793 21 ERQAFDRSIDLLEAARAKG---AYSREAIEALYF-TRRLWTVLIEDLGSPENALPEELRADLISIG 82 (115)
T ss_pred HHHHHHHHHHHHHHHHhcC---CChHHHHHHHHH-HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHH
Confidence 3467888888888777764 266666666654 36788888 78889999999887776
No 11
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=60.86 E-value=16 Score=21.67 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=21.0
Q ss_pred HHHHHHHhhcCCCCCcHHHHHHHHHhh
Q psy13626 62 IAVSELSAIFPQNTNNDLIRHALRSLN 88 (127)
Q Consensus 62 ~AV~el~aLFP~~~~~e~vr~~L~~L~ 88 (127)
.+|..|..+||.-+ .+.|+.+|+.-+
T Consensus 4 ~~v~~L~~mFP~l~-~~~I~~~L~~~~ 29 (43)
T smart00546 4 EALHDLKDMFPNLD-EEVIKAVLEANN 29 (43)
T ss_pred HHHHHHHHHCCCCC-HHHHHHHHHHcC
Confidence 47888999999988 888888887543
No 12
>smart00283 MA Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.
Probab=55.39 E-value=82 Score=23.58 Aligned_cols=20 Identities=20% Similarity=0.411 Sum_probs=11.1
Q ss_pred HHHHHHHHHHHHHHHHHhhc
Q psy13626 27 VRRTDQVTKRIQELAAHMRS 46 (127)
Q Consensus 27 ir~TE~vTr~IqeLl~aaq~ 46 (127)
...|..++..|+.|+...+.
T Consensus 139 a~~t~~~~~ev~~~~~~~~~ 158 (262)
T smart00283 139 AERSAESAKEIESLIKEIQE 158 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44555556666666665443
No 13
>cd07909 YciF YciF bacterial stress response protein, ferritin-like iron-binding domain. YciF is a bacterial protein of unknown function that is up-regulated when bacteria experience stress conditions, and is highly conserved in a broad range of bacterial species. YciF has a ferritin-like domain. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterio
Probab=54.35 E-value=30 Score=26.44 Aligned_cols=69 Identities=22% Similarity=0.252 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCC-CcHHHH-HHHHHhhhhhHHHHHhhh
Q psy13626 31 DQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNT-NNDLIR-HALRSLNTSTVRLQAECA 99 (127)
Q Consensus 31 E~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~-~~e~vr-~~L~~L~~~a~~Lq~eC~ 99 (127)
.|+.+....+.+++.++..++.|..|.+-++.=|.+|-.+|=... .++.++ .+...|...+..+-.++.
T Consensus 16 ~Q~~~al~~m~~~a~~peLk~~l~~H~~eT~~qi~rLe~if~~lg~~~~~~~c~~m~gli~e~~~~~~~~~ 86 (147)
T cd07909 16 KQLVKALPKMAKAATSEELKEAFESHLEETEGQVERLEQIFESLGEKPEGKKCKAMEGLIKEAEELIEETG 86 (147)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCccCcchHHHHHHHHHHHHHhccC
Confidence 577888888888888888888999999999999999888886433 445555 666667666666766663
No 14
>smart00307 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function.
Probab=53.75 E-value=89 Score=25.33 Aligned_cols=49 Identities=20% Similarity=0.252 Sum_probs=33.2
Q ss_pred cHHHHHHHHHhhhhhHHHHHhhhhh---HhhHHHHHHHHHHHHHhHhhhhhh
Q psy13626 77 NDLIRHALRSLNTSTVRLQAECAQL---EGSAERVRSCAYNMAKANKQLLTQ 125 (127)
Q Consensus 77 ~e~vr~~L~~L~~~a~~Lq~eC~~l---q~~t~qv~~cAYdIAKAaK~LvT~ 125 (127)
+|-+=++-+....++..|--..+.. ....+++|.+|-.||.+|-|||+-
T Consensus 56 ~EgLisAAkaV~~a~~~Lv~aA~~~~~g~~~~E~LI~aAk~VAasTaQLVaA 107 (200)
T smart00307 56 TEGLISAAKAVAAATNVLVEAADGVVTGKGSEEELIVAAKEVAASTAQLVAA 107 (200)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555555555553333332 345899999999999999999974
No 15
>KOG0980|consensus
Probab=47.64 E-value=1.6e+02 Score=29.39 Aligned_cols=43 Identities=26% Similarity=0.177 Sum_probs=33.3
Q ss_pred HHHHHhhhhhHHHHHhhhhhH--------------hhHHHHHHHHHHHHHhHhhhhh
Q psy13626 82 HALRSLNTSTVRLQAECAQLE--------------GSAERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 82 ~~L~~L~~~a~~Lq~eC~~lq--------------~~t~qv~~cAYdIAKAaK~LvT 124 (127)
.++..|--++..||+|=..-. .-|+=+|.+|-.||+||-.||+
T Consensus 798 ~aI~~Lv~as~~lQ~EIVasgrgsas~~eFY~kNsrWTEGLISAaKAVa~aatvLVe 854 (980)
T KOG0980|consen 798 EAIMALVKASRELQTEIVASGRGSASPNEFYKKNSRWTEGLISAAKAVAWAATVLVE 854 (980)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHhcCchhHHHHHHHHHHHHHHHHHHH
Confidence 567778888888998874321 1288899999999999988885
No 16
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=46.60 E-value=88 Score=23.06 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q psy13626 28 RRTDQVTKRIQELAAHMRS 46 (127)
Q Consensus 28 r~TE~vTr~IqeLl~aaq~ 46 (127)
..|...|+.|..++..++.
T Consensus 89 ~~t~~~~~~I~~~i~~i~~ 107 (213)
T PF00015_consen 89 EQTSESAKEISEIIEEIQE 107 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhHHHHHHHHHhhhhh
Confidence 3455666666666666665
No 17
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=43.51 E-value=15 Score=22.55 Aligned_cols=30 Identities=33% Similarity=0.406 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhhcCCCCCcHHHHHHHHHhh
Q psy13626 58 ERIRIAVSELSAIFPQNTNNDLIRHALRSLN 88 (127)
Q Consensus 58 e~I~~AV~el~aLFP~~~~~e~vr~~L~~L~ 88 (127)
..|..||.++.. .|..+-++-||.+|+.|+
T Consensus 18 ~e~~~av~~~~~-~~~~~~e~~ik~aLk~Ls 47 (47)
T PF07499_consen 18 AEAQKAVSKLLE-KPGMDVEELIKQALKLLS 47 (47)
T ss_dssp HHHHHHHHHHHH-STTS-HHHHHHHHHCCCT
T ss_pred HHHHHHHHHhhc-CCCCCHHHHHHHHHhhcC
Confidence 346777777777 777777888888887763
No 18
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=40.54 E-value=70 Score=30.08 Aligned_cols=57 Identities=14% Similarity=0.190 Sum_probs=46.2
Q ss_pred CCccchHHHHHHHHHHHHhhcCCCC----CcHHHHHHHHHhhhhhHHHHHhhhhhHhhHHHHHHHHHHHHHhHhhh
Q psy13626 51 HSFVPHAERIRIAVSELSAIFPQNT----NNDLIRHALRSLNTSTVRLQAECAQLEGSAERVRSCAYNMAKANKQL 122 (127)
Q Consensus 51 ~~fvpcae~I~~AV~el~aLFP~~~----~~e~vr~~L~~L~~~a~~Lq~eC~~lq~~t~qv~~cAYdIAKAaK~L 122 (127)
...-|...|+-.|+.+.-++|++.. .++..+.+++.++ .+.+.++-|+.+|+++|.+
T Consensus 514 ~PVtP~~~rVL~Ai~~~g~lyvKe~KvRi~pk~~ke~~K~sg---------------L~~e~f~kaL~~aR~~~~i 574 (591)
T PF04458_consen 514 FPVTPTIYRVLKAIREVGTLYVKEKKVRILPKNIKEAIKLSG---------------LTPEEFKKALEVAREAGFI 574 (591)
T ss_pred CCCCHHHHHHHHHHHHhhhhhhhhhhhhcCccchHHHHHhcC---------------CCHHHHHHHHHHHHHhccc
Confidence 5677999999999999999998876 6677777665554 5778899999999999865
No 19
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=40.45 E-value=63 Score=22.69 Aligned_cols=58 Identities=19% Similarity=0.187 Sum_probs=29.3
Q ss_pred hhhccCCCCCChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCC
Q psy13626 12 CFQSTTTRMPQSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNT 75 (127)
Q Consensus 12 ~~~~~~~~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~ 75 (127)
||-.++..-|..|.|..--|.|+.-|.+|+..|..-.... - +-+.-+.|+.=++=++|
T Consensus 11 My~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~r----g--~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 11 MYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRR----G--SKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp HHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------------
T ss_pred HHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcc----c--cCcCcHHHHHHHHhcCH
Confidence 6777788899999999999999999999999998732111 1 11335566665554444
No 20
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=40.06 E-value=1.5e+02 Score=21.80 Aligned_cols=38 Identities=13% Similarity=0.228 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhhhHHHHHhhhhhHhhHHHHHHHHHHH
Q psy13626 78 DLIRHALRSLNTSTVRLQAECAQLEGSAERVRSCAYNM 115 (127)
Q Consensus 78 e~vr~~L~~L~~~a~~Lq~eC~~lq~~t~qv~~cAYdI 115 (127)
+.+...+..+..++..+......+...++++-+.+-++
T Consensus 145 ~~i~~~i~~i~~~~~~~~~~~~~i~~~i~~i~~~~~~~ 182 (213)
T PF00015_consen 145 EEISDSIEEISESAEEQSESIEQINESIEEISEISEQI 182 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHhhhhHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666666655555555444433333333333
No 21
>PRK04330 hypothetical protein; Provisional
Probab=35.66 E-value=1.6e+02 Score=21.29 Aligned_cols=30 Identities=30% Similarity=0.385 Sum_probs=22.5
Q ss_pred CccchHHHHHHHHHHHHhhcCCCCCcHHHHHH
Q psy13626 52 SFVPHAERIRIAVSELSAIFPQNTNNDLIRHA 83 (127)
Q Consensus 52 ~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~ 83 (127)
.-|| ++||.|.++..+..=++..+..||.+
T Consensus 25 ~sVP--RNIRraa~ea~~~L~~e~~~~~vRaA 54 (88)
T PRK04330 25 TSVP--RNIRRAATEAKEILLNEEESPGVRAA 54 (88)
T ss_pred CCCC--hHHHHHHHHHHHHHhCcCcchhHHHH
Confidence 4455 68899998888888777777777753
No 22
>PF12205 GIT1_C: G protein-coupled receptor kinase-interacting protein 1 C term; InterPro: IPR022018 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF01412 from PFAM, PF00023 from PFAM, PF08518 from PFAM. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodeling and membrane trafficking. To perform this function, it localises p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C-terminal and the LD motifs of paxillin. The C-terminal folds into a four helix bundle. ; PDB: 2JX0_A.
Probab=35.46 E-value=1e+02 Score=23.15 Aligned_cols=20 Identities=30% Similarity=0.360 Sum_probs=13.4
Q ss_pred CccchHHHHHHHHHHHHhhc
Q psy13626 52 SFVPHAERIRIAVSELSAIF 71 (127)
Q Consensus 52 ~fvpcae~I~~AV~el~aLF 71 (127)
....||+.|-.|-..|+.+|
T Consensus 103 qvi~~AYdIAKAaKqLvT~~ 122 (123)
T PF12205_consen 103 QVIQCAYDIAKAAKQLVTIF 122 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhc
Confidence 45567777777777776665
No 23
>PRK15041 methyl-accepting chemotaxis protein I; Provisional
Probab=32.48 E-value=2.2e+02 Score=25.30 Aligned_cols=19 Identities=21% Similarity=0.356 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHhhc
Q psy13626 28 RRTDQVTKRIQELAAHMRS 46 (127)
Q Consensus 28 r~TE~vTr~IqeLl~aaq~ 46 (127)
.+|..-|+.|+.++..+++
T Consensus 408 ~~s~~at~~I~~~i~~~~~ 426 (554)
T PRK15041 408 QRSAQAAREIKSLIEDSVG 426 (554)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3455567777777766554
No 24
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=31.79 E-value=1.6e+02 Score=23.88 Aligned_cols=50 Identities=18% Similarity=0.143 Sum_probs=33.1
Q ss_pred CCCCChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHH
Q psy13626 18 TRMPQSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELS 68 (127)
Q Consensus 18 ~~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~ 68 (127)
+..|+.+++....+.+-..++.|+...+.. ..+.-..-...|+.+|..++
T Consensus 25 ~~~P~~~~~~~~~~~~~~~l~~l~~~~~~~-~~~~G~tL~~~i~~~v~~lv 74 (275)
T PF13324_consen 25 PPLPSPEEAQELCESLFNALLGLLSLYHGL-PKGQGPTLRKEIRSAVKSLV 74 (275)
T ss_dssp SS---HHHHHHHHHHHHHHHHHHHHHHTTS--GGG-HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHhhC-cHhhHHHHHHHHHHHHHHHH
Confidence 347999999999999999999999988864 23344444566666665543
No 25
>PF08701 GN3L_Grn1: GNL3L/Grn1 putative GTPase; InterPro: IPR014813 Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA []. This family contains a potential nuclear localisation signal.
Probab=31.48 E-value=86 Score=21.87 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=17.1
Q ss_pred CCChhHHHHHHHHHHHHHHHHH
Q psy13626 20 MPQSEEVVRRTDQVTKRIQELA 41 (127)
Q Consensus 20 ~P~~e~Vir~TE~vTr~IqeLl 41 (127)
.||-|++....|+--+.+.+.-
T Consensus 41 ~PfKe~iL~eie~~k~~~ee~k 62 (79)
T PF08701_consen 41 FPFKEEILKEIEEKKERAEEEK 62 (79)
T ss_pred CcCHHHHHHHHHHHHHHHHHHH
Confidence 5999999999988766665543
No 26
>PRK11166 chemotaxis regulator CheZ; Provisional
Probab=28.43 E-value=3.3e+02 Score=22.29 Aligned_cols=101 Identities=14% Similarity=0.144 Sum_probs=69.9
Q ss_pred hccCCCCCChh----HHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCC-Cc-------HHHH
Q psy13626 14 QSTTTRMPQSE----EVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNT-NN-------DLIR 81 (127)
Q Consensus 14 ~~~~~~~P~~e----~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~-~~-------e~vr 81 (127)
+.+...+|... .|+..||+-+.+|=..+..++. ..+.....+..+...+.++.+ ++ .. ..++
T Consensus 42 ~~a~~~iPDArdRL~YVi~~TEqAA~rtLnaVE~a~p--~~d~l~~~a~~L~~~w~~l~~----~~~~~~e~~~L~~~~~ 115 (214)
T PRK11166 42 EEAAEAIPDARDRLDYVAQMTEQAAERVLNAVEAAQP--HQDQLEKEAKALDARWDEWFA----NPIELADARELVTDTR 115 (214)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh--HHHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHHHHHHH
Confidence 45566778764 5999999999999999999886 346666777777776666655 33 22 3455
Q ss_pred HHHHHhhhhhHHHHHhhhh------hHhhHHHHHHHHHHHHHhHh
Q psy13626 82 HALRSLNTSTVRLQAECAQ------LEGSAERVRSCAYNMAKANK 120 (127)
Q Consensus 82 ~~L~~L~~~a~~Lq~eC~~------lq~~t~qv~~cAYdIAKAaK 120 (127)
.-|..+...+..+.+...+ +|-.|-|||+---++.+-.+
T Consensus 116 ~fL~~v~~~t~~~~~~L~eI~mAqdFQDLTGQvI~kVi~~v~~vE 160 (214)
T PRK11166 116 AFLADVPEHTSFTNAQLLEIMMAQDFQDLTGQVIKRMMDVIQEIE 160 (214)
T ss_pred HHHHHhHhhHHHHHHHHHHHHHHccchHhHhHHHHHHHHHHHHHH
Confidence 6667777777777777743 46557777766666655443
No 27
>cd01075 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily inc
Probab=28.01 E-value=2.1e+02 Score=22.15 Aligned_cols=41 Identities=12% Similarity=0.244 Sum_probs=30.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHH
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSEL 67 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el 67 (127)
.|+|.++.+.+.+.+.+.|..+++. ...|..-.-..|+.+|
T Consensus 158 ~~~~~~~~~~~~~~~~~v~~~a~~~----~~~~~~aA~~~a~~r~ 198 (200)
T cd01075 158 EARVLAKVEAIYDTLLEIFAQAKQD----GITTLEAADRMAEERI 198 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh----CcCHHHHHHHHHHHHh
Confidence 6789999999999999999999873 3345444445555544
No 28
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.73 E-value=2.3e+02 Score=20.77 Aligned_cols=43 Identities=23% Similarity=0.319 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHH
Q psy13626 34 TKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHA 83 (127)
Q Consensus 34 Tr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~ 83 (127)
-++++-|-..+|+ .-|| ++||.|..+.....-+...++.||.+
T Consensus 16 ~q~~~lL~~Ii~D-----ttVP--RNIRraA~~a~e~L~~e~e~p~vRaA 58 (93)
T COG1698 16 NQVMQLLDEIIQD-----TTVP--RNIRRAAEEAKEALNNEGESPAVRAA 58 (93)
T ss_pred HHHHHHHHHHHcc-----cccc--HHHHHHHHHHHHHHhCCCCCchhHHH
Confidence 3444455555554 3345 68888888888888777777777754
No 29
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=25.78 E-value=88 Score=21.07 Aligned_cols=23 Identities=9% Similarity=0.310 Sum_probs=11.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhc
Q psy13626 24 EEVVRRTDQVTKRIQELAAHMRS 46 (127)
Q Consensus 24 e~Vir~TE~vTr~IqeLl~aaq~ 46 (127)
|.+...++.+.+...+++.+.++
T Consensus 43 ~~i~~e~~~ll~~~n~l~~dv~~ 65 (90)
T PF06103_consen 43 DPITKEINDLLHNTNELLEDVNE 65 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555555554
No 30
>PF15015 NYD-SP12_N: Spermatogenesis-associated, N-terminal
Probab=25.75 E-value=1.2e+02 Score=28.21 Aligned_cols=39 Identities=28% Similarity=0.394 Sum_probs=35.2
Q ss_pred ChhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHH
Q psy13626 22 QSEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERI 60 (127)
Q Consensus 22 ~~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I 60 (127)
+.||-.|.-|.+.++|=-.+.-+++.+..++|-||++-|
T Consensus 419 t~~~~~~~~et~gkrIlpildfirST~l~~~~~~cs~vi 457 (569)
T PF15015_consen 419 TREDAVRQMETMGKRILPILDFIRSTKLNGSFCACSGVI 457 (569)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHhhcccccCCcCCcHHHH
Confidence 458889999999999999999999999999999999754
No 31
>PF10157 DUF2365: Uncharacterized conserved protein (DUF2365); InterPro: IPR019314 This entry is found in a highly conserved family of proteins which have no known function.
Probab=25.18 E-value=3.2e+02 Score=21.07 Aligned_cols=89 Identities=25% Similarity=0.346 Sum_probs=55.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCC--CCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHHhhhhh
Q psy13626 24 EEVVRRTDQVTKRIQELAAHMRSSDK--CHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECAQL 101 (127)
Q Consensus 24 e~Vir~TE~vTr~IqeLl~aaq~~~~--~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~~l 101 (127)
.++-+.+..|..+.-.|+...+..-+ .+--+.|-+--+-+|..+-. +|..+++ +++.|-+.|+.+
T Consensus 55 ~~LE~~a~~ia~svd~ll~~L~~~L~~mS~~Tv~~~~~y~~sv~~~cd---------svD~sik----~~y~liakceEL 121 (149)
T PF10157_consen 55 HDLERDAQAIAESVDSLLRSLRSSLHSMSAITVEHMETYKDSVDKLCD---------SVDASIK----SMYTLIAKCEEL 121 (149)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHH----HHHHHHHHHHHH
Confidence 34556666666666777777665321 12345555555666655532 2333333 255788999999
Q ss_pred HhhHHHHHHHHHHHHHhHhhhhhhc
Q psy13626 102 EGSAERVRSCAYNMAKANKQLLTQF 126 (127)
Q Consensus 102 q~~t~qv~~cAYdIAKAaK~LvT~f 126 (127)
..++..|...|-+| |-.|.+|-.|
T Consensus 122 n~~M~~v~~La~qI-K~Ik~~lD~l 145 (149)
T PF10157_consen 122 NESMKPVYKLAQQI-KDIKKLLDLL 145 (149)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 99888888877777 5566666655
No 32
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus
Probab=24.87 E-value=2.9e+02 Score=24.89 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=9.6
Q ss_pred ChhHHHHHHHHHHHHHHHHHHH
Q psy13626 22 QSEEVVRRTDQVTKRIQELAAH 43 (127)
Q Consensus 22 ~~e~Vir~TE~vTr~IqeLl~a 43 (127)
+.|++-.+...+.++|.++-..
T Consensus 8 ~~edl~~~I~~L~~~i~~~k~e 29 (593)
T PF06248_consen 8 SKEDLRKSISRLSRRIEELKEE 29 (593)
T ss_pred CHhHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444333
No 33
>PF01044 Vinculin: Vinculin family; InterPro: IPR006077 Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques []. In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins. Vinculin is a large protein of 116 kDa (about a 1000 residues). Structurally the protein consists of an acidic N-terminal domain of about 90 kDa separated from a basic C-terminal domain of about 25 kDa by a proline-rich region of about 50 residues. The central part of the N-terminal domain consists of a variable number (3 in vertebrates, 2 in Caenorhabditis elegans) of repeats of a 110 amino acids domain. Alpha-catenins are evolutionary related to vinculin IPR001033 from INTERPRO []. Catenins are proteins that associate with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Three different types of catenins seem to exist: alpha, beta, and gamma. Alpha-catenins are proteins of about 100 kDa which are evolutionary related to vinculin. In terms of their structure the most significant differences are the absence, in alpha-catenin, of the repeated domain and of the proline-rich segment.; GO: 0005198 structural molecule activity, 0007155 cell adhesion, 0015629 actin cytoskeleton; PDB: 3S90_B 1TR2_B 2IBF_A 1RKC_A 3TJ5_A 3RF3_B 4DJ9_A 2GWW_A 2HSQ_A 3TJ6_A ....
Probab=24.67 E-value=4.2e+02 Score=25.92 Aligned_cols=21 Identities=29% Similarity=0.218 Sum_probs=18.0
Q ss_pred hHHHHHHHHHHHHHhHhhhhh
Q psy13626 104 SAERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 104 ~t~qv~~cAYdIAKAaK~LvT 124 (127)
+++.+++||=++-+|-++.|.
T Consensus 921 ~~~~li~~aknLm~~V~~~v~ 941 (968)
T PF01044_consen 921 SAESLIQNAKNLMNAVVETVK 941 (968)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999888775
No 34
>smart00283 MA Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.
Probab=24.33 E-value=3e+02 Score=20.47 Aligned_cols=20 Identities=15% Similarity=0.272 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHhHhhhhh
Q psy13626 105 AERVRSCAYNMAKANKQLLT 124 (127)
Q Consensus 105 t~qv~~cAYdIAKAaK~LvT 124 (127)
++++-..+.++.+.+..|..
T Consensus 237 ~~~~~~~~~~l~~~~~~l~~ 256 (262)
T smart00283 237 SEEISAAAEELSGLAEELKE 256 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45555555555555555543
No 35
>cd05094 PTKc_TrkC Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some n
Probab=24.30 E-value=2.1e+02 Score=21.84 Aligned_cols=46 Identities=13% Similarity=-0.009 Sum_probs=28.8
Q ss_pred hhcCCCCCCccchHHHHHHHHHHHHhhcCCCC-CcHHHHHHHHHhhh
Q psy13626 44 MRSSDKCHSFVPHAERIRIAVSELSAIFPQNT-NNDLIRHALRSLNT 89 (127)
Q Consensus 44 aq~~~~~~~fvpcae~I~~AV~el~aLFP~~~-~~e~vr~~L~~L~~ 89 (127)
+..+........+...++..+..++..=|++. .-++|...|+.+..
T Consensus 238 ~~~~~~~~~~~~~~~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~~~ 284 (291)
T cd05094 238 ITQGRVLERPRVCPKEVYDIMLGCWQREPQQRLNIKEIYKILHALGK 284 (291)
T ss_pred HhCCCCCCCCccCCHHHHHHHHHHcccChhhCcCHHHHHHHHHHHHh
Confidence 34433323334466778888888888888766 44666666666643
No 36
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=23.82 E-value=3.3e+02 Score=23.05 Aligned_cols=67 Identities=16% Similarity=0.132 Sum_probs=52.1
Q ss_pred CCCChhHHHHHHHHHHHHHHHHHHHhhcCCCC-----CCccchHHHHHHHHHHHHhhcCCCC-CcHHHHHHHH
Q psy13626 19 RMPQSEEVVRRTDQVTKRIQELAAHMRSSDKC-----HSFVPHAERIRIAVSELSAIFPQNT-NNDLIRHALR 85 (127)
Q Consensus 19 ~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~-----~~fvpcae~I~~AV~el~aLFP~~~-~~e~vr~~L~ 85 (127)
.-.+.||+..-++.++.++-+|-..+...... .+...=.+.++.+...|...||... ....+|.+|-
T Consensus 93 ~~~~~~eL~~l~~~li~~~N~l~~~i~~~~~~~~~~~~~~~~i~~~~~~~y~~l~~~~p~l~~~~~~~K~~l~ 165 (318)
T PF12725_consen 93 EEYSTEELKELTEYLIEKANELREQITEDDNGVVDIPYDKEEIFEEAREGYENLAERYPFLSGYYPSPKPSLF 165 (318)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhcCCCccccccCCCCHHHHHHHHHHHHHHHHHhCCccCCCCCCCcHhhc
Confidence 35899999999999999999999988875321 1233447788899999999999877 6667777664
No 37
>PRK12794 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=23.77 E-value=3.1e+02 Score=20.34 Aligned_cols=63 Identities=19% Similarity=0.210 Sum_probs=46.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhc------CCCCCcHHHHHHHHHhhh
Q psy13626 24 EEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIF------PQNTNNDLIRHALRSLNT 89 (127)
Q Consensus 24 e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLF------P~~~~~e~vr~~L~~L~~ 89 (127)
+-=-+.-+.++|.+..|-.+...+ .++|....+.++. -.+||++| |.++.++++|.-|-.|.-
T Consensus 17 ~~Re~E~~~l~~~~~~L~~a~~~~--~~~~~~~~~AL~~-NrrLWt~~~~dl~~~~N~LP~eLRa~lisL~~ 85 (122)
T PRK12794 17 TPRETEYQLLAKATRQLKDAQTNG--PDRFAALAEALHF-NRKLWSIFASDVADPDNPLPIELRARIFNLSL 85 (122)
T ss_pred ChHHHHHHHHHHHHHHHHHHHhcC--CccHHHHHHHHHH-HHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Confidence 333455678899999888887764 3566666666654 35777777 788899999998888763
No 38
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=23.72 E-value=2.7e+02 Score=19.56 Aligned_cols=28 Identities=14% Similarity=0.334 Sum_probs=22.1
Q ss_pred CCccchHHHHHHHHHHHHhhcCCCCCcH
Q psy13626 51 HSFVPHAERIRIAVSELSAIFPQNTNND 78 (127)
Q Consensus 51 ~~fvpcae~I~~AV~el~aLFP~~~~~e 78 (127)
..|...+..|......+...||++....
T Consensus 34 ~~~~~~a~~l~~~a~~~~~~F~~gs~~~ 61 (122)
T PF01322_consen 34 AAVAAAADALAALAKSLPDHFPEGSDGG 61 (122)
T ss_dssp HHHHHHHHHHHHHHTSGGGGGSTTCSST
T ss_pred HHHHHHHHHHHHHHhhhhhhCCCCCCCC
Confidence 5567788888888888999999887433
No 39
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=23.57 E-value=2.8e+02 Score=19.81 Aligned_cols=56 Identities=21% Similarity=0.289 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHHhhh-hh----HhhHHHHHHHHHHHHHhHh
Q psy13626 59 RIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECA-QL----EGSAERVRSCAYNMAKANK 120 (127)
Q Consensus 59 ~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~-~l----q~~t~qv~~cAYdIAKAaK 120 (127)
.|+.--..+..++|..|-.--+|.+... +.+..+. .+ ..-..+|-.-|..+|+++|
T Consensus 8 ~~r~~~~~~~~~Lp~apv~Ri~r~~~~~------Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~ 68 (91)
T COG2036 8 EIRRYQRSTDLLLPKAPVRRILRKAGAE------RVSSSAIEELQEALEEYLEEIAEDAVELAEHAK 68 (91)
T ss_pred HHHhhhhhhhhhcCchHHHHHHHHHhHH------HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 4455556677788888855555555544 6776662 23 3337788888999999887
No 40
>PF14916 CCDC92: Coiled-coil domain of unknown function
Probab=23.44 E-value=74 Score=21.37 Aligned_cols=26 Identities=23% Similarity=0.213 Sum_probs=21.3
Q ss_pred HHHHHHHHHhhhhhHHHHHhhhhhHh
Q psy13626 78 DLIRHALRSLNTSTVRLQAECAQLEG 103 (127)
Q Consensus 78 e~vr~~L~~L~~~a~~Lq~eC~~lq~ 103 (127)
++=...|+.|-..-.+|+.+|.++++
T Consensus 17 ~eH~~tL~~LH~EIe~Lq~~~~dL~~ 42 (60)
T PF14916_consen 17 QEHAQTLKGLHAEIERLQKRNKDLTF 42 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHhccccce
Confidence 34457789999999999999988764
No 41
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=23.44 E-value=3e+02 Score=21.78 Aligned_cols=67 Identities=12% Similarity=0.184 Sum_probs=42.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCC---cHHHHHHHHHhhhh
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTN---NDLIRHALRSLNTS 90 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~---~e~vr~~L~~L~~~ 90 (127)
-|++++.+-.||+.=+..+.+++.+. .+....--..++.-+.+|..++|+.|. ...+..+++.+..+
T Consensus 20 RE~iik~sRdI~~~Sk~~I~~lHr~~-~~~a~~~l~~a~~~~~~l~~~~~~~~~~~y~~~~~~~lQEyvEA 89 (204)
T PRK14562 20 REEALKLSREIVRLSGDAIRAIHRGD-FEEAEKLLKEAEELVKELKELLKDHPELYYAGYVGTALQEYVEA 89 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc-HHHHHHHHHHHHHHHHHHHHHhccCchhhhhhhcchHHHHHHHH
Confidence 36778888888888777787777652 233333334445556777888877662 35556666666533
No 42
>cd05072 PTKc_Lyn Catalytic domain of the Protein Tyrosine Kinase, Lyn. Protein Tyrosine Kinase (PTK) family; Lyn kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lyn is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) tyr kinases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that regulate cytokine and growth fa
Probab=23.00 E-value=2e+02 Score=21.37 Aligned_cols=35 Identities=6% Similarity=-0.006 Sum_probs=24.3
Q ss_pred CCccchHHHHHHHHHHHHhhcCCCC-CcHHHHHHHH
Q psy13626 51 HSFVPHAERIRIAVSELSAIFPQNT-NNDLIRHALR 85 (127)
Q Consensus 51 ~~fvpcae~I~~AV~el~aLFP~~~-~~e~vr~~L~ 85 (127)
.....+.+.+...+..++..-|++. .-+++...|+
T Consensus 224 ~~~~~~~~~~~~li~~~l~~~p~~Rp~~~~i~~~l~ 259 (261)
T cd05072 224 PRMENCPDELYDIMKTCWKEKAEERPTFDYLQSVLD 259 (261)
T ss_pred CCCCCCCHHHHHHHHHHccCCcccCcCHHHHHHHHh
Confidence 4455677888888888888877776 5555555554
No 43
>TIGR00153 conserved hypothetical protein TIGR00153. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport.
Probab=22.58 E-value=2.6e+02 Score=21.70 Aligned_cols=9 Identities=11% Similarity=-0.226 Sum_probs=3.7
Q ss_pred ccchHHHHH
Q psy13626 53 FVPHAERIR 61 (127)
Q Consensus 53 fvpcae~I~ 61 (127)
+......|.
T Consensus 45 ~~~~~~~I~ 53 (216)
T TIGR00153 45 DEELRKEII 53 (216)
T ss_pred HHHHHHHHH
Confidence 334444443
No 44
>PF02910 Succ_DH_flav_C: Fumarate reductase flavoprotein C-term; InterPro: IPR004112 In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate (1.3.99.1 from EC): fumarate reductase (Frd) is used in anaerobic growth, and succinate dehydrogenase (Sdh) is used in aerobic growth. Both complexes consist of two main components: a membrane-extrinsic component composed of a FAD-binding flavoprotein and an iron-sulphur protein; and an hydrophobic component composed of a membrane anchor protein and/or a cytochrome B. In eukaryotes mitochondrial succinate dehydrogenase (ubiquinone) (1.3.5.1 from EC) is an enzyme composed of two subunits: a FAD flavoprotein and and iron-sulphur protein. The flavoprotein subunit is a protein of about 60 to 70 Kd to which FAD is covalently bound to a histidine residue which is located in the N-terminal section of the protein []. The sequence around that histidine is well conserved in Frd and Sdh from various bacterial and eukaryotic species []. This family includes members that bind FAD such as the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. ; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3AEF_A 3AE9_A 3AE5_A 3AEA_A 3SFD_A 3AE7_A 3AEB_A 3AE8_A 1ZP0_A 3AE6_A ....
Probab=22.33 E-value=2.7e+02 Score=20.05 Aligned_cols=16 Identities=25% Similarity=0.036 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHhHh
Q psy13626 105 AERVRSCAYNMAKANK 120 (127)
Q Consensus 105 t~qv~~cAYdIAKAaK 120 (127)
+...+.+|.-|++||-
T Consensus 57 l~n~l~~a~~i~~aAl 72 (129)
T PF02910_consen 57 LRNMLLVAELIAKAAL 72 (129)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHHHH
Confidence 6777888888888874
No 45
>COG4225 Predicted unsaturated glucuronyl hydrolase involved in regulation of bacterial surface properties, and related proteins [General function prediction only]
Probab=22.28 E-value=2.8e+02 Score=24.68 Aligned_cols=106 Identities=15% Similarity=0.205 Sum_probs=68.0
Q ss_pred ccCCCCCChhHHHHHHHHHHHHHHHHHHHhhcCCCC------------------CCccch----HHH---HHHHHHHHHh
Q psy13626 15 STTTRMPQSEEVVRRTDQVTKRIQELAAHMRSSDKC------------------HSFVPH----AER---IRIAVSELSA 69 (127)
Q Consensus 15 ~~~~~~P~~e~Vir~TE~vTr~IqeLl~aaq~~~~~------------------~~fvpc----ae~---I~~AV~el~a 69 (127)
|+++.+-..-.+..+.|.+-..+.+-+-+.+..+++ ..+..| |+. +-.|+.+++.
T Consensus 139 Ma~~F~ak~g~~~~~~e~~d~~~~QF~~~~~~l~Dp~TGL~YH~wd~~~~~~w~~~~sG~~~fWaRg~gW~~mal~d~le 218 (357)
T COG4225 139 MAGLFLAKYGQVTGRPEYFDEALYQFSLHEKYLRDPETGLYYHGWDEDGTMPWANNESGEPAFWARGNGWYAMALADLLE 218 (357)
T ss_pred hhhHHHHHHHHHhCCHHHHHHHHHHHHHHHHHccCCCcCceEEeeccCCCCccccccCCCceeeecccchHHHHHHHHHH
Confidence 444444555666677777777777776666553222 222222 222 4567889999
Q ss_pred hcCCCC-CcHHHHHHHHHhhhhhHHHHHhhhhh-----------HhhHHHHHHHHHHHHHhHh
Q psy13626 70 IFPQNT-NNDLIRHALRSLNTSTVRLQAECAQL-----------EGSAERVRSCAYNMAKANK 120 (127)
Q Consensus 70 LFP~~~-~~e~vr~~L~~L~~~a~~Lq~eC~~l-----------q~~t~qv~~cAYdIAKAaK 120 (127)
+.|++. .--.+...|+.+-++-.+.|.|=.-- -+.+--..--||.|+|+..
T Consensus 219 ~lp~~~~~r~~l~~~l~d~v~al~r~Qde~GlW~tiLDd~~~~sy~EsSaSa~faYallkgi~ 281 (357)
T COG4225 219 LLPEDHPDRRELLNVLRDLVDALIRYQDESGLWHTILDDGRPGSYLESSASAGFAYALLKGIN 281 (357)
T ss_pred hCCCCCchHHHHHHHHHHHHHHHHHhhccccchhhhhccCCCCCchhhhHHHHHHHHHHHHHh
Confidence 999887 77788899999999988988865110 1113445667888888654
No 46
>cd05064 PTKc_EphR_A10 Catalytic domain of the Protein Tyrosine Kinase, Ephrin Receptor A10. Protein Tyrosine Kinase (PTK) family; Ephrin Receptor (EphR) subfamily; EphA10 receptor; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchor
Probab=21.97 E-value=2.9e+02 Score=20.77 Aligned_cols=32 Identities=6% Similarity=-0.116 Sum_probs=20.9
Q ss_pred cchHHHHHHHHHHHHhhcCCCC-CcHHHHHHHH
Q psy13626 54 VPHAERIRIAVSELSAIFPQNT-NNDLIRHALR 85 (127)
Q Consensus 54 vpcae~I~~AV~el~aLFP~~~-~~e~vr~~L~ 85 (127)
..|...++..+..++..-|+.. .-+++...|.
T Consensus 231 ~~~~~~~~~li~~c~~~~p~~RP~~~~i~~~l~ 263 (266)
T cd05064 231 RNCPNLLHQLMLDCWQKERGERPRFSQIHSILS 263 (266)
T ss_pred CCCCHHHHHHHHHHcCCCchhCCCHHHHHHHHH
Confidence 3466777888888888777665 4445555544
No 47
>TIGR03751 conj_TIGR03751 conjugative transfer region lipoprotein, TIGR03751 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=21.94 E-value=65 Score=24.35 Aligned_cols=20 Identities=40% Similarity=0.649 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhcCCCCCcHH
Q psy13626 60 IRIAVSELSAIFPQNTNNDL 79 (127)
Q Consensus 60 I~~AV~el~aLFP~~~~~e~ 79 (127)
-|+|.+||-.+||..|+++-
T Consensus 59 tRta~nei~~~F~RLPNPdl 78 (116)
T TIGR03751 59 TRTAENEIQQLFPRLPNPDL 78 (116)
T ss_pred chHHHhHHHHhccCCCCCCe
Confidence 58999999999999998764
No 48
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=21.74 E-value=1.4e+02 Score=20.33 Aligned_cols=44 Identities=18% Similarity=0.153 Sum_probs=20.1
Q ss_pred cCCCC-CcHHHHHHHHHhhhhhHHHHHhhhhhHhhHHHHHHHHHH
Q psy13626 71 FPQNT-NNDLIRHALRSLNTSTVRLQAECAQLEGSAERVRSCAYN 114 (127)
Q Consensus 71 FP~~~-~~e~vr~~L~~L~~~a~~Lq~eC~~lq~~t~qv~~cAYd 114 (127)
||.++ .-..++..++.+-.....=...+..+..++.+.+..|+.
T Consensus 1 ~pa~~~~i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~ 45 (125)
T PF13581_consen 1 FPADPEDIREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVE 45 (125)
T ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45554 223333333333322222233445566666666666554
No 49
>COG2219 PRI2 Eukaryotic-type DNA primase, large subunit [DNA replication, recombination, and repair]
Probab=21.74 E-value=69 Score=27.93 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=9.1
Q ss_pred HHHHHHHhhcCCCC
Q psy13626 62 IAVSELSAIFPQNT 75 (127)
Q Consensus 62 ~AV~el~aLFP~~~ 75 (127)
.-|.++..+|+..|
T Consensus 275 ~~~deiv~~fr~~p 288 (363)
T COG2219 275 LSVDEIVELFRNSP 288 (363)
T ss_pred CChhHHHHHhccCC
Confidence 33567777777766
No 50
>PRK15048 methyl-accepting chemotaxis protein II; Provisional
Probab=21.66 E-value=5.5e+02 Score=22.43 Aligned_cols=18 Identities=33% Similarity=0.387 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHhhc
Q psy13626 29 RTDQVTKRIQELAAHMRS 46 (127)
Q Consensus 29 ~TE~vTr~IqeLl~aaq~ 46 (127)
+|..-|+.|++++.....
T Consensus 407 ~t~~st~~I~~~i~~~~~ 424 (553)
T PRK15048 407 RSAQAAKEIKALIEDSVS 424 (553)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455667777777765544
No 51
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=20.75 E-value=3.7e+02 Score=20.06 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=34.8
Q ss_pred CcHHHHHHHHHhhhhhHHHHHhhhhhHhhHHHHHHHHHHHHHhHh
Q psy13626 76 NNDLIRHALRSLNTSTVRLQAECAQLEGSAERVRSCAYNMAKANK 120 (127)
Q Consensus 76 ~~e~vr~~L~~L~~~a~~Lq~eC~~lq~~t~qv~~cAYdIAKAaK 120 (127)
..+.++++++.|.....-+...|.+++..+.+++..-=+ =|-+|
T Consensus 38 qkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~-eK~ak 81 (107)
T PF09304_consen 38 QKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLED-EKQAK 81 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Confidence 467799999999999999999999999888877765322 44444
No 52
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=20.30 E-value=4.1e+02 Score=20.49 Aligned_cols=82 Identities=22% Similarity=0.357 Sum_probs=59.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHHhhhh---
Q psy13626 24 EEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECAQ--- 100 (127)
Q Consensus 24 e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~~--- 100 (127)
++++..-+.+.+.|.+|-..-+.. .+|...-.++.++ ++.++..++.|...=.-|..-|..
T Consensus 5 ~~L~~~d~~L~~~L~~l~~hq~~~----------~~I~~L~~e~~~l------d~~i~~~~~~L~~~~~~L~~~~~~~~~ 68 (188)
T PF10018_consen 5 EDLIEADDELSSALEELQEHQENQ----------ARIQQLRAEIEEL------DEQIRDILKQLKEARKELRTLPDQADE 68 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 566667777777777775544432 4566666666554 678999999999988888888821
Q ss_pred ----h------HhhHHHHHHHHHHHHHhHhh
Q psy13626 101 ----L------EGSAERVRSCAYNMAKANKQ 121 (127)
Q Consensus 101 ----l------q~~t~qv~~cAYdIAKAaK~ 121 (127)
. ....++|+.-|+-|+|.++-
T Consensus 69 ~~~~~~~~~~~~v~~~eLL~YA~rISk~t~~ 99 (188)
T PF10018_consen 69 KLKSIPKAEKRPVDYEELLSYAHRISKFTSA 99 (188)
T ss_pred ccccccccccCCCCHHHHHHHHHHHHHhcCC
Confidence 1 12299999999999998874
No 53
>PF12792 CSS-motif: CSS motif domain associated with EAL ; InterPro: IPR024744 This domain, with its characteristic highly conserved CSS sequence motif, is found N-terminal to the EAL domain (PF00563 from PFAM), found in many putative cyclic diguanylate phosphodiesterases.
Probab=20.27 E-value=2.9e+02 Score=20.00 Aligned_cols=45 Identities=11% Similarity=0.108 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhcCCCCCCccchHHHHHHHHHHHHhhc
Q psy13626 23 SEEVVRRTDQVTKRIQELAAHMRSSDKCHSFVPHAERIRIAVSELSAIF 71 (127)
Q Consensus 23 ~e~Vir~TE~vTr~IqeLl~aaq~~~~~~~fvpcae~I~~AV~el~aLF 71 (127)
.+.++.++|.+....++-+..+.. -...||++.=.....+++...
T Consensus 11 a~~~~~~~e~~~~~~~~~~~~~~~----~~~~~Cs~~~~~~Lr~~~~~~ 55 (208)
T PF12792_consen 11 AQRALQRIESVLDQARQALDALLP----LTGQPCSPAHLNALRQIVARS 55 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh----hcCCCCCHHHHHHHHHHHHhc
Confidence 567788888888888777777754 356778887444444444443
No 54
>KOG4514|consensus
Probab=20.06 E-value=5.1e+02 Score=21.49 Aligned_cols=86 Identities=14% Similarity=0.208 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCC--CCCccchHHHHHHHHHHHHhhcCCCCCcHHHHHHHHHhhhhhHHHHHhhhhhHhh
Q psy13626 27 VRRTDQVTKRIQELAAHMRSSDK--CHSFVPHAERIRIAVSELSAIFPQNTNNDLIRHALRSLNTSTVRLQAECAQLEGS 104 (127)
Q Consensus 27 ir~TE~vTr~IqeLl~aaq~~~~--~~~fvpcae~I~~AV~el~aLFP~~~~~e~vr~~L~~L~~~a~~Lq~eC~~lq~~ 104 (127)
-+.+..+.-+.-.|++.+.+..| .+--+.|-+--|.||..+..-. +..|| ..+.|.++|+.+..+
T Consensus 131 E~~~~el~~~vD~llr~lgg~lh~is~lt~~~vq~yr~aV~kl~d~~-----DanIK--------~~Y~lLAk~EEi~ks 197 (222)
T KOG4514|consen 131 ELEAQELASSVDNLLRNLGGLLHSISSLTADNVQVYRNAVNKLTDTL-----DANIK--------CQYQLLAKAEEITKS 197 (222)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHhhhhHHHHHHHHHHHHHHHh-----hhhhH--------HHHHHHHHHHHHHHH
Confidence 34444555566667776665322 1234566666777787775433 33333 346788899999999
Q ss_pred HHHHHHHHHHHHHhHhhhhhhc
Q psy13626 105 AERVRSCAYNMAKANKQLLTQF 126 (127)
Q Consensus 105 t~qv~~cAYdIAKAaK~LvT~f 126 (127)
++-|.+.|-+| |-.|-||..|
T Consensus 198 m~pv~~La~qi-r~irRlve~l 218 (222)
T KOG4514|consen 198 MKPVEQLAQQI-RQIRRLVEML 218 (222)
T ss_pred HhhHHHHHHHH-HHHHHHHHHH
Confidence 88888888776 4455555443
Done!