Query psy4310
Match_columns 203
No_of_seqs 125 out of 1024
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 22:18:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4310.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4310hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0541 Ffh Signal recognition 100.0 3.2E-57 7E-62 418.0 16.4 159 3-167 275-434 (451)
2 KOG0780|consensus 100.0 8.2E-57 1.8E-61 411.0 18.8 195 3-202 276-471 (483)
3 PRK00771 signal recognition pa 100.0 1.8E-52 3.8E-57 389.3 16.2 155 4-164 269-424 (437)
4 PRK10867 signal recognition pa 100.0 2.8E-52 6.1E-57 387.5 16.5 151 4-164 277-428 (433)
5 TIGR00959 ffh signal recogniti 100.0 3.3E-51 7.1E-56 379.9 14.9 152 4-160 276-428 (428)
6 TIGR01425 SRP54_euk signal rec 100.0 6E-50 1.3E-54 371.5 13.9 151 4-157 276-429 (429)
7 PF02978 SRP_SPB: Signal pepti 100.0 7.2E-40 1.6E-44 252.4 10.3 101 53-158 1-104 (104)
8 PF08671 SinI: Anti-repressor 79.4 1.7 3.7E-05 26.6 2.0 21 131-151 9-29 (30)
9 PF10392 COG5: Golgi transport 65.1 15 0.00032 29.0 4.9 63 10-79 6-77 (132)
10 PF08700 Vps51: Vps51/Vps67; 57.4 26 0.00057 24.9 4.7 60 9-69 3-63 (87)
11 PRK14001 potassium-transportin 54.4 10 0.00022 32.5 2.3 25 129-153 141-165 (189)
12 PRK14723 flhF flagellar biosyn 52.5 6.3 0.00014 40.3 0.9 27 4-30 360-387 (767)
13 PRK00315 potassium-transportin 52.2 11 0.00024 32.4 2.2 25 129-153 141-165 (193)
14 PF10376 Mei5: Double-strand r 51.5 24 0.00053 30.7 4.3 39 26-64 171-212 (221)
15 PRK13997 potassium-transportin 51.4 11 0.00024 32.4 2.2 25 129-153 143-167 (193)
16 PRK14003 potassium-transportin 51.3 13 0.00028 32.1 2.5 25 129-153 144-168 (194)
17 PF02669 KdpC: K+-transporting 50.9 13 0.00028 31.8 2.5 25 129-153 140-164 (188)
18 TIGR00681 kdpC K+-transporting 50.5 13 0.00028 31.9 2.3 25 129-153 139-163 (187)
19 PRK14002 potassium-transportin 49.3 14 0.00029 31.7 2.3 25 129-153 137-161 (186)
20 PRK13999 potassium-transportin 48.8 14 0.00031 32.0 2.4 25 129-153 150-174 (201)
21 PRK13995 potassium-transportin 48.7 14 0.00031 32.0 2.4 25 129-153 151-175 (203)
22 PF02206 WSN: Domain of unknow 48.1 19 0.00042 25.2 2.6 45 3-50 23-67 (69)
23 PRK13996 potassium-transportin 47.4 15 0.00033 31.7 2.4 25 129-153 147-171 (197)
24 PRK14000 potassium-transportin 47.3 13 0.00029 31.8 2.0 25 129-153 140-164 (185)
25 PF07200 Mod_r: Modifier of ru 46.1 15 0.00033 29.1 2.1 30 40-69 110-139 (150)
26 PF01418 HTH_6: Helix-turn-hel 45.7 27 0.00059 24.8 3.1 47 99-150 4-57 (77)
27 PRK13998 potassium-transportin 45.2 16 0.00034 31.3 2.1 25 129-153 139-163 (186)
28 PRK13994 potassium-transportin 45.1 16 0.00034 32.2 2.1 25 129-153 171-195 (222)
29 COG1737 RpiR Transcriptional r 41.9 31 0.00067 30.4 3.5 58 98-160 5-74 (281)
30 PF04675 DNA_ligase_A_N: DNA l 32.0 1.9E+02 0.0042 23.1 6.5 45 51-115 108-152 (177)
31 PF09015 NgoMIV_restric: NgoMI 30.1 75 0.0016 28.8 4.0 41 13-53 216-264 (278)
32 cd00591 HU_IHF Integration hos 29.4 52 0.0011 23.3 2.5 24 130-153 6-29 (87)
33 PRK14101 bifunctional glucokin 29.3 1.2E+02 0.0026 29.9 5.7 92 64-160 294-412 (638)
34 smart00027 EH Eps15 homology d 29.3 1.3E+02 0.0029 21.7 4.7 46 24-70 29-77 (96)
35 PF12108 SF3a60_bindingd: Spli 28.8 55 0.0012 19.7 2.1 14 55-68 8-21 (28)
36 PRK12751 cpxP periplasmic stre 28.2 2.7E+02 0.0059 23.1 6.8 53 43-116 85-137 (162)
37 cd05027 S-100B S-100B: S-100B 27.6 1.5E+02 0.0034 21.6 4.8 46 22-67 27-81 (88)
38 smart00549 TAFH TAF homology. 27.5 2.3E+02 0.0049 21.8 5.7 48 28-75 10-61 (92)
39 TIGR01597 PYST-B Plasmodium yo 27.4 68 0.0015 28.7 3.2 48 51-117 52-99 (255)
40 PF00216 Bac_DNA_binding: Bact 27.3 64 0.0014 22.9 2.6 24 130-153 7-30 (90)
41 PF02375 JmjN: jmjN domain; I 27.1 27 0.00059 21.8 0.5 25 56-80 10-34 (34)
42 PRK11302 DNA-binding transcrip 26.8 84 0.0018 27.0 3.7 57 99-160 4-72 (284)
43 PF12167 DUF3596: Domain of un 26.5 1.4E+02 0.003 20.8 4.2 34 22-59 26-59 (64)
44 PRK00153 hypothetical protein; 25.6 74 0.0016 24.1 2.8 32 23-55 1-32 (104)
45 PF11304 DUF3106: Protein of u 25.2 1.1E+02 0.0025 23.4 3.8 49 96-156 28-76 (107)
46 cd00052 EH Eps15 homology doma 25.0 1E+02 0.0022 19.9 3.1 29 38-66 31-62 (67)
47 PRK00464 nrdR transcriptional 24.0 1.9E+02 0.0041 23.8 5.1 13 9-21 58-70 (154)
48 smart00417 H4 Histone H4. 23.2 82 0.0018 23.0 2.5 25 128-152 17-47 (74)
49 PRK14621 hypothetical protein; 23.1 82 0.0018 24.6 2.6 29 22-51 1-29 (111)
50 TIGR00103 DNA_YbaB_EbfC DNA-bi 22.8 80 0.0017 24.0 2.5 33 22-55 2-34 (102)
51 KOG0512|consensus 22.1 2.7E+02 0.0058 24.3 5.8 71 51-150 15-85 (228)
52 PF14098 SSPI: Small, acid-sol 21.9 58 0.0013 23.4 1.5 23 77-115 33-55 (65)
53 PF00390 malic: Malic enzyme, 21.8 27 0.00059 29.7 -0.3 10 19-28 76-85 (182)
54 PRK14721 flhF flagellar biosyn 21.8 36 0.00079 32.3 0.5 20 7-26 367-386 (420)
55 cd05022 S-100A13 S-100A13: S-1 21.7 1.7E+02 0.0037 21.6 4.0 47 22-68 26-78 (89)
56 PF09592 DUF2031: Protein of u 21.1 1E+02 0.0022 27.3 3.1 48 51-117 51-98 (228)
No 1
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=100.00 E-value=3.2e-57 Score=418.03 Aligned_cols=159 Identities=34% Similarity=0.511 Sum_probs=146.0
Q ss_pred ccccccccccCCchhHHhhcCCCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCC
Q psy4310 3 QIGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPG 81 (203)
Q Consensus 3 ~~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG 81 (203)
.+.++|||+|||+||||||||||||.||+||+++ +++++++++.+|+.+|+|||+|||+|+++++||||+++|++||||
T Consensus 275 GEki~dLE~F~P~R~asRILGMGDv~sLvEk~~~~~d~e~a~~~~~kl~~g~FtL~Df~~Ql~~m~kmGpl~~ll~miPG 354 (451)
T COG0541 275 GEKIDDLEPFHPDRFASRILGMGDVLSLIEKAEEVVDEEEAEKLAEKLKKGKFTLEDFLEQLEQMKKMGPLSKLLSMIPG 354 (451)
T ss_pred CCCcccCCCcChHHHHHHhcCcccHHHHHHHHHHhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHccCCHHHHHHhCCC
Confidence 3678999999999999999999999999999999 588999999999999999999999999999999999999999999
Q ss_pred CCcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHh
Q psy4310 82 FSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKM 161 (203)
Q Consensus 82 ~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km~kkm 161 (203)
++ ...+....+.++++++||++||+|||++||+||+++ ++||++|||+||||+++|||+||+||++|++|||+|
T Consensus 355 ~~-~~~~~~~~~~~e~~~kr~~aIi~SMT~~Er~nP~ii-----~~SR~rRIA~GSG~sv~dVn~Llkq~~~m~~mmk~m 428 (451)
T COG0541 355 MG-MKDSDKDIELDEKKLKRIEAIIDSMTPEERENPDII-----NASRKRRIARGSGTSVQDVNKLLKQFKQMKKMMKKM 428 (451)
T ss_pred CC-CCCchhhhhccHHHHHHHHHHHHcCCHHHhhCcccc-----ChHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 98 223334456789999999999999999999999854 799999999999999999999999999999999999
Q ss_pred cCCCCC
Q psy4310 162 GGIKGL 167 (203)
Q Consensus 162 ~~~~g~ 167 (203)
++..|.
T Consensus 429 ~~~~~~ 434 (451)
T COG0541 429 SGGGGK 434 (451)
T ss_pred hCCCCc
Confidence 875433
No 2
>KOG0780|consensus
Probab=100.00 E-value=8.2e-57 Score=411.03 Aligned_cols=195 Identities=55% Similarity=0.875 Sum_probs=182.0
Q ss_pred ccccccccccCCchhHHhhcCCCCHHHHHHHHHhccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCC
Q psy4310 3 QIGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82 (203)
Q Consensus 3 ~~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~ 82 (203)
.+.+||||+|+|++|||||||||||.||+||++++..++++++.++|.+|+|||+|||+|+++|.||||++++++|||||
T Consensus 276 GEhmdDlE~F~pk~FvsrlLGmGDi~glvek~~ev~~~d~~el~~kl~~gkFtlrd~y~Qfq~imkmGp~s~v~~MiPG~ 355 (483)
T KOG0780|consen 276 GEHMDDLEPFDPKPFVSRLLGMGDIEGLVEKVQEVGKDDAKELVEKLKQGKFTLRDFYDQFQNIMKMGPLSQVLGMIPGM 355 (483)
T ss_pred CccccccCCCChHHHHHHHhccccHHHHHHHHHHHhhhhHHHHHHHHHhCCccHHHHHHHHHHHHhhCCHHHHHhhCCCc
Confidence 36799999999999999999999999999999998788999999999999999999999999999999999999999999
Q ss_pred CcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHhc
Q psy4310 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMG 162 (203)
Q Consensus 83 ~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km~kkm~ 162 (203)
+ .+++.++++++.++|||+++|||||++|||+|+ +|..++||+.||||||||+++||.+||.||++++.++++++
T Consensus 356 s--~m~~~~e~Es~~~~krm~~mmDsMt~~Elds~~---~f~~~p~R~~RvArgSG~~v~eV~ell~q~~~~~~~~kk~~ 430 (483)
T KOG0780|consen 356 S--MMSKGNEEESSAKLKRMMTMMDSMTDEELDSPE---LFVEEPSRIMRVARGSGTSVQEVMELLAQYKKFAAMMKKIG 430 (483)
T ss_pred c--cCCCcchhHHHHHHHHHHHHHHhcChhhccCcc---ccccCchHhhhhhccCCccHHHHHHHHHHHHHHHHHHHHhc
Confidence 9 478889999999999999999999999999995 56678999999999999999999999999999999999999
Q ss_pred CCCCCCCC-CCcccCccHHHHHHHHHHHHhcCCHHHHhhcC
Q psy4310 163 GIKGLFKG-GDITKNVNQTQMMKLNQQMAKMMDPRVLHQMG 202 (203)
Q Consensus 163 ~~~g~~~~-~~~~~~~~~~~~~~~~~qm~~~~~p~~~~~mg 202 (203)
+.+|.... |..+.++++.+++.+.+|+.++.+|.++++||
T Consensus 431 ~~~G~~~~lg~~~~~~~~~~~~~l~q~~~~~~~~~~~~~mg 471 (483)
T KOG0780|consen 431 GIKGIFGALGNPNKNMNPAPMAKLKQQMAKMGPQRLLQQMG 471 (483)
T ss_pred CCCCcccccCCcccccCcCChHHHHHHHHhcccHHHHHHhc
Confidence 88887754 55456778878888899999999999999998
No 3
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=100.00 E-value=1.8e-52 Score=389.26 Aligned_cols=155 Identities=34% Similarity=0.569 Sum_probs=142.2
Q ss_pred cccccccccCCchhHHhhcCCCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCC
Q psy4310 4 IGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82 (203)
Q Consensus 4 ~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~ 82 (203)
+.|||||+|||+|||+||||||||.+|+|++++ +++++++++.+|+.+|+|||+|||+|+++|+||||+++|++||||+
T Consensus 269 e~v~Dle~f~~~~~~~~ilgmgd~~~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~~~~~kmG~~~~~~~m~pg~ 348 (437)
T PRK00771 269 EKIDDLERFDPDRFISRLLGMGDLESLLEKVEEALDEEEEEKDVEKMMKGKFTLKDMYKQLEAMNKMGPLKQILQMLPGL 348 (437)
T ss_pred CCcccCCcCCHHHHHHHHhCCCChHHHHHHHHHhhhHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhcCCHHHHHHhCcCc
Confidence 457999999999999999999999999999999 5878899999999999999999999999999999999999999999
Q ss_pred CcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHhc
Q psy4310 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMG 162 (203)
Q Consensus 83 ~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km~kkm~ 162 (203)
++. ++....+.+++++++|++||+|||++||+||++ | ++||++|||+||||+++|||+||++|++|++||++|+
T Consensus 349 ~~~-~~~~~~~~~~~~~~~~~~ii~SMt~~Er~~p~~---~--~~sR~~Ria~GsG~~~~~v~~ll~~~~~~~~~~~~~~ 422 (437)
T PRK00771 349 GGK-LPDEALEVTEEKLKKYKAIMDSMTEEELENPEI---I--NASRIRRIARGSGTTVEDVRELLKYYKMMKKAMKQLK 422 (437)
T ss_pred ccc-chhhhhcccHHHHHHHHHHHHcCCHHHHhCccc---c--cHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 852 222233567899999999999999999999974 3 7999999999999999999999999999999999998
Q ss_pred CC
Q psy4310 163 GI 164 (203)
Q Consensus 163 ~~ 164 (203)
+.
T Consensus 423 ~~ 424 (437)
T PRK00771 423 KG 424 (437)
T ss_pred CC
Confidence 63
No 4
>PRK10867 signal recognition particle protein; Provisional
Probab=100.00 E-value=2.8e-52 Score=387.51 Aligned_cols=151 Identities=34% Similarity=0.518 Sum_probs=140.8
Q ss_pred cccccccccCCchhHHhhcCCCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCC
Q psy4310 4 IGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82 (203)
Q Consensus 4 ~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~ 82 (203)
+.++|||+|||+|||+||||||||.+|+|++++ +++++++++.+|+.+|+|||+|||+|+++|+||||+++|++||||+
T Consensus 277 e~v~DLe~f~p~~~~~~ilgmgD~~~l~e~~~~~~~~~~~~~~~~~~~~g~f~l~d~~~q~~~~~kmG~~~~~~~m~Pg~ 356 (433)
T PRK10867 277 EKLDDLEPFHPDRMASRILGMGDVLSLIEKAQEVVDEEKAEKLAKKLKKGKFDLEDFLEQLQQMKKMGGLGSLLGMLPGM 356 (433)
T ss_pred CccccCccCCHHHHHHHHhCCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHhCCCc
Confidence 568999999999999999999999999999999 6888899999999999999999999999999999999999999999
Q ss_pred CcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHhc
Q psy4310 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKKMG 162 (203)
Q Consensus 83 ~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km~kkm~ 162 (203)
++ +. . +.+++++++|++||+|||++||+||++ | ++||++|||+||||+++|||+||++|++|++||++|+
T Consensus 357 ~~-~~-~---~~~~~~~~~~~~ii~SMt~~Er~~p~~---~--~~sR~~RIa~GsG~~~~~v~~ll~~~~~~~~~~~~~~ 426 (433)
T PRK10867 357 GN-MK-A---QLDDKELKRIEAIINSMTPKERANPDI---L--NGSRKRRIAKGSGTTVQEVNRLLKQFEQMKKMMKKMK 426 (433)
T ss_pred cc-cc-c---cccHHHHHHHHHHHHcCCHHHHhCccc---c--chHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 85 22 1 356799999999999999999999974 3 7899999999999999999999999999999999998
Q ss_pred CC
Q psy4310 163 GI 164 (203)
Q Consensus 163 ~~ 164 (203)
+.
T Consensus 427 ~~ 428 (433)
T PRK10867 427 GK 428 (433)
T ss_pred CC
Confidence 73
No 5
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=100.00 E-value=3.3e-51 Score=379.93 Aligned_cols=152 Identities=32% Similarity=0.475 Sum_probs=137.6
Q ss_pred cccccccccCCchhHHhhcCCCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCC
Q psy4310 4 IGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82 (203)
Q Consensus 4 ~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~ 82 (203)
+.++|||+|+|+|||+||||||||.+|+|++++ +++++++++.+++.+|+|||+|||+|+++|+||||+++|++||||+
T Consensus 276 e~i~dl~~f~p~~~~~~iLg~gD~~~l~e~~~~~~~~~~~~~~~~~~~~~~f~l~d~~~q~~~~~kmG~~~~~~~~~Pg~ 355 (428)
T TIGR00959 276 EKIDDLEPFHPERMASRILGMGDILSLVEKAQEVVDEEEAKKLAEKMKKGQFDLEDFLEQLRQIKKMGPLSSLLKMIPGM 355 (428)
T ss_pred CChhhCccCCHHHHHHHHhCCCChHHHHHHHHHhhCHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhcCCHHHHHHhCcCc
Confidence 457999999999999999999999999999999 5888899999999999999999999999999999999999999999
Q ss_pred CcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHHHHH
Q psy4310 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAVVKK 160 (203)
Q Consensus 83 ~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km~kk 160 (203)
++...+....+.+++++++|++||+|||++||+||++ | ++||++|||+||||+++|||+||++|++|++||++
T Consensus 356 ~~~~~~~~~~~~~~~~~~~~~~ii~SMt~~Er~~p~~---~--~~sR~~RIa~GsG~~~~~v~~ll~~~~~~~~~~~~ 428 (428)
T TIGR00959 356 GGVKPSLSDLELDEKQFKRIEAIISSMTPEERRNPKI---L--NPSRRKRIAAGSGTTVQDVNKLIKRFEQMKKMMKK 428 (428)
T ss_pred cccccccccccccHHHHHHHHHHHHcCCHHHHhCccc---c--cHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcc
Confidence 8521111122457899999999999999999999974 3 79999999999999999999999999999999864
No 6
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=100.00 E-value=6e-50 Score=371.51 Aligned_cols=151 Identities=56% Similarity=0.878 Sum_probs=135.4
Q ss_pred cccccccccCCchhHHhhcCCCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCC
Q psy4310 4 IGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGF 82 (203)
Q Consensus 4 ~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~ 82 (203)
+.++|||+|||++||+||||||||.+|+||+++ +++++++++.+|+.+|+|||+|||+|+++|+||||+++|++||||+
T Consensus 276 e~v~Dle~f~p~~~~~rilgmgDi~~L~ek~~~~~~~~~~~~~~~k~~~~~f~l~D~~~q~~~i~kmG~~~~i~~m~Pg~ 355 (429)
T TIGR01425 276 EHIDDFEIFKTQPFISKLLGMGDIEGLIDKVQDLKLDDNEKALIEKLKEGTFTLRDMYEQFQNLLKMGPLGQILSMIPGF 355 (429)
T ss_pred CChhhcCcCChHHHHHHHhcCCCcHHHHHHHHHhhhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHhccCHHHHHHhCcCc
Confidence 568999999999999999999999999999999 5777899999999999999999999999999999999999999999
Q ss_pred CcccccccchhhHHHHHHHHHHHHhCCChHhhcC--CccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHHH
Q psy4310 83 SQDFLSKGSEQESMARLKRLMTIMDSMNDGELDN--RDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAAV 157 (203)
Q Consensus 83 ~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~--p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~km 157 (203)
++.+.+....+.++++++||++||+|||++||+| |+ +|..++||++|||+||||+++|||+||++|++|++|
T Consensus 356 ~~~~~~~~~~~~~~~~~~~~~aii~SMT~~Er~~~~p~---i~~~~~sR~~RIa~GSG~~~~~V~~ll~~~~~~~~~ 429 (429)
T TIGR01425 356 STDFMSKGNEEESMAKIKKLMTIMDSMTDQELDSTDGK---VFSKQPSRIQRVARGSGRSIRDVQELLEQYKKFAQM 429 (429)
T ss_pred chhhhhhhcccccHHHHHhHHHHHhcCCHHHHccCCCc---cccCCccHHHHHHccCCCCHHHHHHHHHHHHHHhcC
Confidence 8422122223567899999999999999999999 75 443368999999999999999999999999999874
No 7
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=100.00 E-value=7.2e-40 Score=252.44 Aligned_cols=101 Identities=43% Similarity=0.691 Sum_probs=90.3
Q ss_pred CCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcc--ccc-ccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchh
Q psy4310 53 QFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQD--FLS-KGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGR 129 (203)
Q Consensus 53 ~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~--~~~-~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR 129 (203)
+|||+|||+|+++|.||||+++|++||||+++. .++ ....+.+++++++|++||+|||++||+||++ | +.||
T Consensus 1 ~F~l~Df~~Q~~~i~kmG~l~~i~~miPG~~~~~~~~~~~~~~~~~~~~lk~~~~Ii~SMT~~Er~~p~l---l--~~sR 75 (104)
T PF02978_consen 1 KFTLRDFLEQLQQIKKMGPLSKIMSMIPGMGNMMESLPSEQEEEEDEKKLKRMEAIIDSMTPEERDNPKL---L--NESR 75 (104)
T ss_dssp SSCHHHHHHHHHHHHHTSTTHHHHTTSSSSSSS-SSTTCSSSSHHHHHHHHHHHHHHTTSBHHHHHCGGG---H--HHHH
T ss_pred CCCHHHHHHHHHHHHhcCCHHHHHHHCcCccccccccchhcchhhhHHHHHHHHHHHHCcCHHHHhCccc---c--chHH
Confidence 699999999999999999999999999999863 123 3445678999999999999999999999974 4 6799
Q ss_pred HHHhhccCCCCHHHHHHHHHHHHHHHHHH
Q psy4310 130 ITRVAQGAGVTEKEVKDLISQYTKFAAVV 158 (203)
Q Consensus 130 ~~RIA~GSG~~~~eVn~Llkq~~~m~km~ 158 (203)
++|||+||||+++|||+||++|+++++||
T Consensus 76 ~~RIA~GSG~~~~eV~~ll~~f~~~~~mm 104 (104)
T PF02978_consen 76 RRRIARGSGTTVQEVNELLKQFKQMKKMM 104 (104)
T ss_dssp HHHHHHHTTS-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHhhC
Confidence 99999999999999999999999999986
No 8
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=79.36 E-value=1.7 Score=26.62 Aligned_cols=21 Identities=14% Similarity=0.474 Sum_probs=15.5
Q ss_pred HHhhccCCCCHHHHHHHHHHH
Q psy4310 131 TRVAQGAGVTEKEVKDLISQY 151 (203)
Q Consensus 131 ~RIA~GSG~~~~eVn~Llkq~ 151 (203)
..=|+.+|.|++||.++|+.-
T Consensus 9 i~eA~~~Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHhC
Confidence 345889999999999999754
No 9
>PF10392 COG5: Golgi transport complex subunit 5; InterPro: IPR019465 The conserved oligomeric Golgi (COG) complex is a peripheral membrane complex involved in intra-Golgi protein trafficking. Subunit 5 is located in the smaller, B lobe, together with subunits 6-8, and has been shown to bind subunits 1 and 7 [].
Probab=65.07 E-value=15 Score=29.02 Aligned_cols=63 Identities=11% Similarity=0.174 Sum_probs=42.8
Q ss_pred cccCCchhHHhhcC--------CCCHHHHHHHHHh-ccHhhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcC
Q psy4310 10 CHYLNFPLYCGICC--------MGDIEGLIDKVNE-LKLDDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMI 79 (203)
Q Consensus 10 E~F~P~rf~sRiLG--------mGDi~~Liek~~~-v~~~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~mi 79 (203)
+-|+|.+||+.+|. -.|+..-++|+.. +. +-.+++-+.+. =...|++.|...+... ..++..+
T Consensus 6 ~dFd~~~fan~ll~~~~~~~~~~ld~~~~l~kL~~~i~-eld~~i~~~v~---~~~~~LL~q~~~~~~~---~~~l~~v 77 (132)
T PF10392_consen 6 PDFDPVQFANDLLKSTNNNSDSELDISTPLKKLNFDIQ-ELDKRIRSQVT---SNHEDLLSQASSIEEL---ESVLQAV 77 (132)
T ss_pred CCCCHHHHHHHHHHhhcCCCCCcccHHHHHHHHHHHHH-HHHHHHHHHHH---hCHHHHHHHHHhHHHH---HHHHHHH
Confidence 46999999999999 9999999999975 32 21122222222 2567888887777664 4455555
No 10
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=57.40 E-value=26 Score=24.93 Aligned_cols=60 Identities=18% Similarity=0.148 Sum_probs=38.0
Q ss_pred ccccCCchhHHhhcCCCCHHHHHHHHHhccHhhHHHHHHHHHcC-CCCHHHHHHHHHHHHhc
Q psy4310 9 LCHYLNFPLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIKHG-QFTLRDMYEQFQNIMKM 69 (203)
Q Consensus 9 lE~F~P~rf~sRiLGmGDi~~Liek~~~v~~~~~~~l~~ki~~G-~Ftl~Df~~Ql~~i~kM 69 (203)
-+-|+|+.++..+|.=-.+..+....+.+. .+.......+.+- --+++||..--+.|.+|
T Consensus 3 ~~~fd~~~~~~~~l~~~s~~~i~~~~~~L~-~~i~~~~~eLr~~V~~nY~~fI~as~~I~~m 63 (87)
T PF08700_consen 3 SENFDVDEYFKDLLKNSSIKEIRQLENKLR-QEIEEKDEELRKLVYENYRDFIEASDEISSM 63 (87)
T ss_pred CCcCCHHHHHHHHHhhCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 468999999998888666666555544432 1112222233333 24788999888888875
No 11
>PRK14001 potassium-transporting ATPase subunit C; Provisional
Probab=54.38 E-value=10 Score=32.53 Aligned_cols=25 Identities=32% Similarity=0.465 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 141 Qv~RVA~argl~~~~v~~LV~~~t~ 165 (189)
T PRK14001 141 QAPRVAQARNISIRQVERLIEDHTD 165 (189)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 12
>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=52.51 E-value=6.3 Score=40.28 Aligned_cols=27 Identities=11% Similarity=-0.266 Sum_probs=21.9
Q ss_pred ccc-ccccccCCchhHHhhcCCCCHHHH
Q psy4310 4 IGY-LMLCHYLNFPLYCGICCMGDIEGL 30 (203)
Q Consensus 4 ~~~-~~lE~F~P~rf~sRiLGmGDi~~L 30 (203)
..| ||||+|+|+.||.+|||.+.-.++
T Consensus 360 Q~VPdDL~~a~~~~lv~~ll~~~~~~~~ 387 (767)
T PRK14723 360 QKVPEHLELAQADELVDRAFATPRRGAL 387 (767)
T ss_pred CCChhhcccCCHHHHHHHHhcccccCCC
Confidence 356 999999999999999997554443
No 13
>PRK00315 potassium-transporting ATPase subunit C; Reviewed
Probab=52.17 E-value=11 Score=32.41 Aligned_cols=25 Identities=32% Similarity=0.553 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 141 Qv~RVA~argl~~~~v~~LI~~~t~ 165 (193)
T PRK00315 141 QIPRVAAARQLPVEQVAQLVAAYTQ 165 (193)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 14
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=51.53 E-value=24 Score=30.73 Aligned_cols=39 Identities=21% Similarity=0.406 Sum_probs=31.9
Q ss_pred CHHHHHHHHHhccHhhHHHHHHHHHc--C-CCCHHHHHHHHH
Q psy4310 26 DIEGLIDKVNELKLDDNEELIEKIKH--G-QFTLRDMYEQFQ 64 (203)
Q Consensus 26 Di~~Liek~~~v~~~~~~~l~~ki~~--G-~Ftl~Df~~Ql~ 64 (203)
++.+||++.+.+..+.+.++...+.. | +||+.+|+++|.
T Consensus 171 ~Lq~lI~Kwr~~~q~~l~eL~~~~~~~e~~~~TM~eL~~~l~ 212 (221)
T PF10376_consen 171 QLQSLIKKWRSASQEALYELQSEMSEEEGEKFTMGELIKRLG 212 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhccccCccHHHHHHHhC
Confidence 57788888888777777888888877 3 999999999873
No 15
>PRK13997 potassium-transporting ATPase subunit C; Provisional
Probab=51.40 E-value=11 Score=32.37 Aligned_cols=25 Identities=16% Similarity=0.417 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 143 Qv~RVA~argls~~~v~~LV~~~t~ 167 (193)
T PRK13997 143 QVERISKLTNIPKETLDQLIKDQTE 167 (193)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHcc
Confidence 4899999999999999999999984
No 16
>PRK14003 potassium-transporting ATPase subunit C; Provisional
Probab=51.29 E-value=13 Score=32.07 Aligned_cols=25 Identities=32% Similarity=0.525 Sum_probs=23.4
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 144 Qv~RVA~argl~~~~v~~LI~~~t~ 168 (194)
T PRK14003 144 QIERVAKARGLPPDQLEILITKNTD 168 (194)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 4899999999999999999999984
No 17
>PF02669 KdpC: K+-transporting ATPase, c chain; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex []. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA []. The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane
Probab=50.94 E-value=13 Score=31.81 Aligned_cols=25 Identities=40% Similarity=0.676 Sum_probs=23.0
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 140 Qv~RVA~argl~~~~v~~li~~~t~ 164 (188)
T PF02669_consen 140 QVPRVAKARGLSEEEVEALIDKHTE 164 (188)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4889999999999999999999884
No 18
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=50.48 E-value=13 Score=31.88 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=23.4
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 139 Qv~RVA~argl~~~~v~~LI~~~t~ 163 (187)
T TIGR00681 139 QFPRVAKARNISPQQLQSLITKHTE 163 (187)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 5899999999999999999999984
No 19
>PRK14002 potassium-transporting ATPase subunit C; Provisional
Probab=49.32 E-value=14 Score=31.71 Aligned_cols=25 Identities=36% Similarity=0.655 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 137 Qv~RVA~argl~~~~v~~LV~~~t~ 161 (186)
T PRK14002 137 QVKRVAKARGMSEEKVKQLVDQHVE 161 (186)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 20
>PRK13999 potassium-transporting ATPase subunit C; Provisional
Probab=48.79 E-value=14 Score=31.98 Aligned_cols=25 Identities=28% Similarity=0.618 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 150 Qv~RVA~argls~~~v~~LV~~~t~ 174 (201)
T PRK13999 150 QVPRVAKARGLPEDRLRDLVAAQVE 174 (201)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 21
>PRK13995 potassium-transporting ATPase subunit C; Provisional
Probab=48.70 E-value=14 Score=31.99 Aligned_cols=25 Identities=24% Similarity=0.573 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|..
T Consensus 151 Qv~RVA~argl~~~~v~~LV~~~t~ 175 (203)
T PRK13995 151 QIPAVSKATGISESKLKKIVKDNTE 175 (203)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 22
>PF02206 WSN: Domain of unknown function; InterPro: IPR003125 This domain has no known function and is found in Caenorhabditis elegans proteins normally at the N-terminal.
Probab=48.09 E-value=19 Score=25.18 Aligned_cols=45 Identities=13% Similarity=0.238 Sum_probs=31.3
Q ss_pred ccccccccccCCchhHHhhcCCCCHHHHHHHHHhccHhhHHHHHHHHH
Q psy4310 3 QIGYLMLCHYLNFPLYCGICCMGDIEGLIDKVNELKLDDNEELIEKIK 50 (203)
Q Consensus 3 ~~~~~~lE~F~P~rf~sRiLGmGDi~~Liek~~~v~~~~~~~l~~ki~ 50 (203)
|.|.-+ ..+.|+-+++-+|.+|+. -++++..++.....+..+++.
T Consensus 23 q~~l~~-gsi~~~~vIsElL~~~~~--~~~~i~~~d~~~~~~~l~~l~ 67 (69)
T PF02206_consen 23 QNGLMN-GSIDIDDVISELLNIGSV--SLSDIINLDVSKVKKFLDKLK 67 (69)
T ss_pred HHHHHc-CCCCHHHHHHHHHcCCCC--CHHHHHhcCHHHHHHHHHHHh
Confidence 344443 567899999999999998 556666666555555555554
No 23
>PRK13996 potassium-transporting ATPase subunit C; Provisional
Probab=47.44 E-value=15 Score=31.67 Aligned_cols=25 Identities=32% Similarity=0.699 Sum_probs=23.3
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 147 Qv~RVA~argls~~~v~~LV~~~t~ 171 (197)
T PRK13996 147 QVDRIAKNNNMSVKDVEDIIDKYTS 171 (197)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHhc
Confidence 4899999999999999999999984
No 24
>PRK14000 potassium-transporting ATPase subunit C; Provisional
Probab=47.32 E-value=13 Score=31.75 Aligned_cols=25 Identities=16% Similarity=0.461 Sum_probs=23.5
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 140 Qv~RVA~argls~~~v~~LV~~~t~ 164 (185)
T PRK14000 140 QVKRIAKERNIDASKINHLIDENKQ 164 (185)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHhcc
Confidence 4899999999999999999999986
No 25
>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.
Probab=46.07 E-value=15 Score=29.11 Aligned_cols=30 Identities=30% Similarity=0.594 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHcCCCCHHHHHHHHHHHHhc
Q psy4310 40 DDNEELIEKIKHGQFTLRDMYEQFQNIMKM 69 (203)
Q Consensus 40 ~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kM 69 (203)
++.+++++.+..|.-+++||++++....+.
T Consensus 110 eeSe~lae~fl~g~~d~~~Fl~~f~~~R~~ 139 (150)
T PF07200_consen 110 EESEELAEEFLDGEIDVDDFLKQFKEKRKL 139 (150)
T ss_dssp HHHHHHC-S-SSSHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 566788899999999999999999988764
No 26
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=45.66 E-value=27 Score=24.80 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=29.3
Q ss_pred HHHHHHHHhCCChHhhc-------CCccccccccCchhHHHhhccCCCCHHHHHHHHHH
Q psy4310 99 LKRLMTIMDSMNDGELD-------NRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQ 150 (203)
Q Consensus 99 lk~~~~IIdSMT~~Er~-------~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq 150 (203)
+.++....+++|+.|+. ||+- + ...-+.-||+-+||++.-|.++.+.
T Consensus 4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~--~---~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 4 LEKIRSQYNSLSPTEKKIADYILENPDE--I---AFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHHGGGS-HHHHHHHHHHHH-HHH--H---CT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHH--H---HHccHHHHHHHcCCCHHHHHHHHHH
Confidence 34455556667777654 4541 1 2355899999999999999988765
No 27
>PRK13998 potassium-transporting ATPase subunit C; Provisional
Probab=45.17 E-value=16 Score=31.33 Aligned_cols=25 Identities=28% Similarity=0.436 Sum_probs=23.5
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 139 Qv~RVA~argl~~~~v~~LV~~~t~ 163 (186)
T PRK13998 139 QAPRIADARHVSTSRVADLIQHRKQ 163 (186)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHhcc
Confidence 5899999999999999999999975
No 28
>PRK13994 potassium-transporting ATPase subunit C; Provisional
Probab=45.08 E-value=16 Score=32.18 Aligned_cols=25 Identities=28% Similarity=0.473 Sum_probs=23.5
Q ss_pred hHHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 129 RITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 129 R~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
-+.|||+=.|.++++|++|+++|.+
T Consensus 171 Qv~RVA~argls~~~V~~LV~~~t~ 195 (222)
T PRK13994 171 QVHRVAARNGLNVARVQKLVDEHTT 195 (222)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHHcc
Confidence 5899999999999999999999985
No 29
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=41.89 E-value=31 Score=30.41 Aligned_cols=58 Identities=24% Similarity=0.372 Sum_probs=44.6
Q ss_pred HHHHHHHHHhCCChHhhc-------CCccccccccCchhHHHhhccCCCCHHHHHHHHHH-----HHHHHHHHHH
Q psy4310 98 RLKRLMTIMDSMNDGELD-------NRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQ-----YTKFAAVVKK 160 (203)
Q Consensus 98 ~lk~~~~IIdSMT~~Er~-------~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq-----~~~m~km~kk 160 (203)
-+.++....+++|+.||. ||+- + ....+.-+|+-+|+++.-|.+|.+. |..++-.+..
T Consensus 5 l~~~I~~~~~~Lt~~er~iA~yil~~~~~--~---~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~ 74 (281)
T COG1737 5 LLERIRERYDSLTKSERKIADYILANPDE--V---ALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQ 74 (281)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhCHHH--H---HHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 456777888999999984 6652 1 2478999999999999999999875 6666665554
No 30
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=31.98 E-value=1.9e+02 Score=23.07 Aligned_cols=45 Identities=9% Similarity=0.175 Sum_probs=32.2
Q ss_pred cCCCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhc
Q psy4310 51 HGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELD 115 (203)
Q Consensus 51 ~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~ 115 (203)
....|+.|.++.|..|....+ -+ -...+...+..++..+||.|..
T Consensus 108 ~~~lTi~~V~~~L~~la~~~g----------~~----------s~~~k~~~l~~ll~~~s~~E~k 152 (177)
T PF04675_consen 108 PSPLTISEVNETLDELAAASG----------KG----------SQDEKIDILKELLRRCSPEEAK 152 (177)
T ss_dssp SS--BHHHHHHHHHHHHH--S----------TT----------HHHHHHHHHHHHHTTS-HHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhhC----------cc----------chHHHHHHHHHHHHhCCHHHHH
Confidence 467899999999999988642 11 1267888999999999999987
No 31
>PF09015 NgoMIV_restric: NgoMIV restriction enzyme; InterPro: IPR015105 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents NgoMIV-type prokaryotic DNA restriction enzymes exhibiting an alpha/beta structure, with a central region comprising a mixed six-stranded beta-sheet with alpha-helices on each side. A long 'arm' protrudes out of the core of the domain between strands beta2 and beta3 and is mainly involved in the tetramerisation interface of the protein. These restriction enzymes recognise the double-stranded sequence GCCGGC and cleave after G-1 []. ; PDB: 1FIU_C 4ABT_B.
Probab=30.07 E-value=75 Score=28.84 Aligned_cols=41 Identities=32% Similarity=0.418 Sum_probs=30.3
Q ss_pred CCchhHHhhcCCCCHH--------HHHHHHHhccHhhHHHHHHHHHcCC
Q psy4310 13 LNFPLYCGICCMGDIE--------GLIDKVNELKLDDNEELIEKIKHGQ 53 (203)
Q Consensus 13 ~P~rf~sRiLGmGDi~--------~Liek~~~v~~~~~~~l~~ki~~G~ 53 (203)
-|.|++|--||-|||. .|.+.+++...+++.++...+-.|+
T Consensus 216 ~psrlas~a~gtgdid~vyh~al~el~~a~~~~~~~~~~~~l~~~~~g~ 264 (278)
T PF09015_consen 216 LPSRLASLALGTGDIDCVYHFALPELIAAVKELGNDDAADMLRTLIDGK 264 (278)
T ss_dssp -HHHHHHHHSSSSS-SEEEETTHHHHHHHHHHHT-HHHHHHHHHHHHTT
T ss_pred ChHHHHHHHcCCCccceeeeecHHHHHHHHHHhCChhHHHHHHHHhcCc
Confidence 4899999999999984 6777777765567777777777774
No 32
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=29.36 E-value=52 Score=23.29 Aligned_cols=24 Identities=17% Similarity=0.480 Sum_probs=21.6
Q ss_pred HHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 130 ITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 130 ~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
+.+||+-+|.+..||..+++.+-.
T Consensus 6 ~~~ia~~~~~~~~~v~~vl~~~~~ 29 (87)
T cd00591 6 IEAIAEKTGLSKKDAEAAVDAFLD 29 (87)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHH
Confidence 678999999999999999998863
No 33
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=29.26 E-value=1.2e+02 Score=29.86 Aligned_cols=92 Identities=20% Similarity=0.296 Sum_probs=64.5
Q ss_pred HHHHhcCChhHHhhcCC---------CCCc------ccccccchhhHHHHHHHHHHHHhCCChHhhc-------CCcccc
Q psy4310 64 QNIMKMGPFSQIMGMIP---------GFSQ------DFLSKGSEQESMARLKRLMTIMDSMNDGELD-------NRDGAK 121 (203)
Q Consensus 64 ~~i~kMG~l~~i~~miP---------G~~~------~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~-------~p~~i~ 121 (203)
+.+..-|+++.++.-|| |+-+ ..++.........-+.++....+++|+.||. ||+-
T Consensus 294 ~~f~~kg~~~~~~~~ipv~~i~~~~~~l~Gaa~~~~~~~~~~~~~~~~~l~~~I~~~~~~Lt~~E~~IA~yIl~n~~~-- 371 (638)
T PRK14101 294 ARFEAKGRFEAYLANIPTYLITAEYPAFLGVSAILAEQLSNRTGGASSAVFERIRQMRDALTPAERRVADLALNHPRS-- 371 (638)
T ss_pred HHHHhCCChHHHHhcCCEEEEeCCChhHHHHHHHHHHHhccccCCchHHHHHHHHHHHhhcCHHHHHHHHHHHhCHHH--
Confidence 44566899999999997 3311 1111112223366788899999999999986 4431
Q ss_pred ccccCchhHHHhhccCCCCHHHHHHHHHH-----HHHHHHHHHH
Q psy4310 122 LFSKQTGRITRVAQGAGVTEKEVKDLISQ-----YTKFAAVVKK 160 (203)
Q Consensus 122 l~~~~~SR~~RIA~GSG~~~~eVn~Llkq-----~~~m~km~kk 160 (203)
+ ...-+.-||+=+|||+.-|.+|.+. |..++.-++.
T Consensus 372 v---~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~efK~~L~~ 412 (638)
T PRK14101 372 I---INDPIVDIARKADVSQPTVIRFCRSLGCQGLSDFKLKLAT 412 (638)
T ss_pred H---HhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 1 1234889999999999999999875 7777777654
No 34
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=29.25 E-value=1.3e+02 Score=21.73 Aligned_cols=46 Identities=9% Similarity=0.027 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHhccHhhHHHHHHHH---HcCCCCHHHHHHHHHHHHhcC
Q psy4310 24 MGDIEGLIDKVNELKLDDNEELIEKI---KHGQFTLRDMYEQFQNIMKMG 70 (203)
Q Consensus 24 mGDi~~Liek~~~v~~~~~~~l~~ki---~~G~Ftl~Df~~Ql~~i~kMG 70 (203)
..|+..++... .+..++..++.... ..|.+|+++|+.-+..+.++=
T Consensus 29 ~~el~~~l~~~-~~~~~ev~~i~~~~d~~~~g~I~~~eF~~~~~~~~~~~ 77 (96)
T smart00027 29 GAQAKPILLKS-GLPQTLLAKIWNLADIDNDGELDKDEFALAMHLIYRKL 77 (96)
T ss_pred HHHHHHHHHHc-CCCHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHH
Confidence 33444444432 24445555555544 357899999998888887753
No 35
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=28.79 E-value=55 Score=19.72 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=11.4
Q ss_pred CHHHHHHHHHHHHh
Q psy4310 55 TLRDMYEQFQNIMK 68 (203)
Q Consensus 55 tl~Df~~Ql~~i~k 68 (203)
.|..||+||+.|+.
T Consensus 8 ~f~eFY~rlk~Ike 21 (28)
T PF12108_consen 8 PFSEFYERLKEIKE 21 (28)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHH
Confidence 47789999998864
No 36
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=28.16 E-value=2.7e+02 Score=23.12 Aligned_cols=53 Identities=9% Similarity=0.117 Sum_probs=34.4
Q ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhcC
Q psy4310 43 EELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDN 116 (203)
Q Consensus 43 ~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~ 116 (203)
+++..-|....||=.-+..+++.+.. ...+......+.+..|++-|||++|.-
T Consensus 85 ~~m~~Li~Ad~FDeaAvra~~~kma~---------------------~~~e~~v~~~~~~~qmy~lLTPEQra~ 137 (162)
T PRK12751 85 EAMHKLITADKFDEAAVRAQAEKMSQ---------------------NQIERHVEMAKVRNQMYNLLTPEQKEA 137 (162)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHH---------------------HHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 34444555556666666666555333 112334677889999999999999984
No 37
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=27.64 E-value=1.5e+02 Score=21.56 Aligned_cols=46 Identities=11% Similarity=0.301 Sum_probs=31.5
Q ss_pred cCCCCHHHHHHH-----HHh-ccHhhHHHHHHHHH---cCCCCHHHHHHHHHHHH
Q psy4310 22 CCMGDIEGLIDK-----VNE-LKLDDNEELIEKIK---HGQFTLRDMYEQFQNIM 67 (203)
Q Consensus 22 LGmGDi~~Liek-----~~~-v~~~~~~~l~~ki~---~G~Ftl~Df~~Ql~~i~ 67 (203)
+.--++..++.. +.. .++++..++++.+- .|+++|++|...+..+.
T Consensus 27 I~~~eL~~ll~~~~~~~lg~~~~~~~v~~~i~~~D~n~dG~v~f~eF~~li~~~~ 81 (88)
T cd05027 27 LKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSDGDGECDFQEFMAFVAMVT 81 (88)
T ss_pred ECHHHHHHHHHHHhHHHhcCCCCHHHHHHHHHHhCCCCCCcCcHHHHHHHHHHHH
Confidence 444567777777 544 34566677776663 67899999988776653
No 38
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=27.53 E-value=2.3e+02 Score=21.76 Aligned_cols=48 Identities=15% Similarity=0.232 Sum_probs=36.5
Q ss_pred HHHHHHHHhcc-H---hhHHHHHHHHHcCCCCHHHHHHHHHHHHhcCChhHH
Q psy4310 28 EGLIDKVNELK-L---DDNEELIEKIKHGQFTLRDMYEQFQNIMKMGPFSQI 75 (203)
Q Consensus 28 ~~Liek~~~v~-~---~~~~~l~~ki~~G~Ftl~Df~~Ql~~i~kMG~l~~i 75 (203)
.+|++-.++.+ - +...+++..+..|+.+.++|-.+++...+-.+=-.+
T Consensus 10 ~tLi~ls~~~~qpe~~~~Vr~LV~~L~~~~i~~EeF~~~Lq~~lns~~qP~l 61 (92)
T smart00549 10 TTLIQLSNDISQPEVAERVRTLVLGLVNGTITAEEFTSRLQEALNSPLQPYL 61 (92)
T ss_pred HHHHHHhcCCCcchHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHcCCCCchh
Confidence 46677666654 1 345789999999999999999999999986544333
No 39
>TIGR01597 PYST-B Plasmodium yoelii subtelomeric family PYST-B. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism.
Probab=27.41 E-value=68 Score=28.68 Aligned_cols=48 Identities=17% Similarity=0.308 Sum_probs=32.9
Q ss_pred cCCCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhcCC
Q psy4310 51 HGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNR 117 (203)
Q Consensus 51 ~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p 117 (203)
..+|||+|||+-.-++.. -+ + +-..+.+++..+..||||=-.+-.++-
T Consensus 52 dnqfdLn~FY~Stlsla~---------q~---n-------d~~~ddeEi~~lrniidShikkhkenn 99 (255)
T TIGR01597 52 DNQFDLNEFYQSTLSLAN---------QF---N-------DCNDDDKEIAHLRNIIDSHIKKHKERN 99 (255)
T ss_pred CccccHHHHHHHHHHHHH---------Hh---c-------cccCchHHHHHHHHhHHHHHHhhhccc
Confidence 448999999987655443 11 1 112357889999999999777766654
No 40
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=27.31 E-value=64 Score=22.90 Aligned_cols=24 Identities=25% Similarity=0.556 Sum_probs=21.8
Q ss_pred HHHhhccCCCCHHHHHHHHHHHHH
Q psy4310 130 ITRVAQGAGVTEKEVKDLISQYTK 153 (203)
Q Consensus 130 ~~RIA~GSG~~~~eVn~Llkq~~~ 153 (203)
+.+||.-+|.|..||...|+.|..
T Consensus 7 i~~ia~~~~~s~~~v~~vl~~~~~ 30 (90)
T PF00216_consen 7 IKRIAEKTGLSKKDVEAVLDALFD 30 (90)
T ss_dssp HHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHH
Confidence 678999999999999999999874
No 41
>PF02375 JmjN: jmjN domain; InterPro: IPR003349 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with JmjC (see IPR003347 from INTERPRO).; PDB: 2XML_A 2W2I_C 3DXT_A 3DXU_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=27.07 E-value=27 Score=21.81 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHhcCChhHHhhcCC
Q psy4310 56 LRDMYEQFQNIMKMGPFSQIMGMIP 80 (203)
Q Consensus 56 l~Df~~Ql~~i~kMG~l~~i~~miP 80 (203)
|.|++..+++|.+.|.-..|.+-+|
T Consensus 10 F~dp~~yi~~i~~~g~~~Gi~KIvP 34 (34)
T PF02375_consen 10 FKDPIKYISSIEPEGEKYGICKIVP 34 (34)
T ss_dssp HS-HHHHHHHHHHTTGGGSEEEE--
T ss_pred HhCHHHHHHHHHHHHHHCCEEEecC
Confidence 5688889999888887665555554
No 42
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=26.84 E-value=84 Score=26.98 Aligned_cols=57 Identities=16% Similarity=0.318 Sum_probs=41.9
Q ss_pred HHHHHHHHhCCChHhhc-------CCccccccccCchhHHHhhccCCCCHHHHHHHHHH-----HHHHHHHHHH
Q psy4310 99 LKRLMTIMDSMNDGELD-------NRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQ-----YTKFAAVVKK 160 (203)
Q Consensus 99 lk~~~~IIdSMT~~Er~-------~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq-----~~~m~km~kk 160 (203)
+.++....++||+.|+. ||+- +. ..=++-||+-+|||+.-|.+|.+. |..++.-+.+
T Consensus 4 ~~~i~~~~~~Lt~~e~~Ia~yil~n~~~--v~---~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~k~~l~~ 72 (284)
T PRK11302 4 LEKIQSRLEHLSKSERKVAEVILASPQT--AI---HSSIATLAKMANVSEPTVNRFCRSLDTKGFPDFKLHLAQ 72 (284)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHhCHHH--HH---hcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 45677778889999976 5541 11 123789999999999999999875 6777766554
No 43
>PF12167 DUF3596: Domain of unknown function (DUF3596); InterPro: IPR022000 This N-terminal domain is found in Bacteriophage P27p02, it is functionally uncharacterised, though it is considered to be an integrase. Integrase is necessary for integration of the phage into the host genome by site-specific recombination. In conjunction with excisionase, integrase is also necessary for excision of the prophage from the host genome. This domain is found in related proteins in other bacteriophage, and prophage regions of bacterial genomes. The domain is approximately 90 amino acids in length and is found is associated with the C-terminal domain characterised by PF00589 from PFAM.
Probab=26.50 E-value=1.4e+02 Score=20.77 Aligned_cols=34 Identities=18% Similarity=0.175 Sum_probs=22.8
Q ss_pred cCCCCHHHHHHHHHhccHhhHHHHHHHHHcCCCCHHHH
Q psy4310 22 CCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFTLRDM 59 (203)
Q Consensus 22 LGmGDi~~Liek~~~v~~~~~~~l~~ki~~G~Ftl~Df 59 (203)
||+-|-..=+..|+. -..++..+|..|.||+.++
T Consensus 26 l~l~dT~~N~k~a~~----~~~~I~~~I~~G~Fdy~~~ 59 (64)
T PF12167_consen 26 LGLPDTPANRKKAER----LRAEIEAEIALGTFDYAKY 59 (64)
T ss_pred CCCCCCHHHHHHHHH----HHHHHHHHHHhCCCcHHHh
Confidence 356665555555543 2345778999999998775
No 44
>PRK00153 hypothetical protein; Validated
Probab=25.64 E-value=74 Score=24.08 Aligned_cols=32 Identities=13% Similarity=0.443 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHHhccHhhHHHHHHHHHcCCCC
Q psy4310 23 CMGDIEGLIDKVNELKLDDNEELIEKIKHGQFT 55 (203)
Q Consensus 23 GmGDi~~Liek~~~v~~~~~~~l~~ki~~G~Ft 55 (203)
++||+..++.+++++- ++.+++.+.+..-+||
T Consensus 1 ~~~~~~~m~~qaq~~q-~~~~~~q~~l~~~~~~ 32 (104)
T PRK00153 1 GMGNMQNLMKQAQQMQ-EKMQKMQEELAQMEVE 32 (104)
T ss_pred CcccHHHHHHHHHHHH-HHHHHHHHHHhccEEE
Confidence 5789999999998853 4445566666655555
No 45
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=25.21 E-value=1.1e+02 Score=23.39 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhCCChHhhcCCccccccccCchhHHHhhccCCCCHHHHHHHHHHHHHHHH
Q psy4310 96 MARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRITRVAQGAGVTEKEVKDLISQYTKFAA 156 (203)
Q Consensus 96 ~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~~RIA~GSG~~~~eVn~Llkq~~~m~k 156 (203)
..++.....-..+|||+|++.- ..|..+ =+..|+++-..+-..|..+++
T Consensus 28 r~k~l~~a~r~~~mspeqq~r~---------~~rm~~---W~~LspeqR~~~R~~~~~~~~ 76 (107)
T PF11304_consen 28 RRKWLQIAERWPSMSPEQQQRL---------RERMRR---WAALSPEQRQQARENYQRFKQ 76 (107)
T ss_pred HHHHHHHHHHHhcCCHHHHHHH---------HHHHHH---HHhCCHHHHHHHHHHHHHHHc
Confidence 4466666677789999998854 144444 456889998888888886654
No 46
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=25.01 E-value=1e+02 Score=19.95 Aligned_cols=29 Identities=7% Similarity=0.078 Sum_probs=18.4
Q ss_pred cHhhHHHHHHHHH---cCCCCHHHHHHHHHHH
Q psy4310 38 KLDDNEELIEKIK---HGQFTLRDMYEQFQNI 66 (203)
Q Consensus 38 ~~~~~~~l~~ki~---~G~Ftl~Df~~Ql~~i 66 (203)
..++..++.+.+- .|.+++++|+.-+..+
T Consensus 31 ~~~~~~~i~~~~d~~~~g~i~~~ef~~~~~~~ 62 (67)
T cd00052 31 PRSVLAQIWDLADTDKDGKLDKEEFAIAMHLI 62 (67)
T ss_pred CHHHHHHHHHHhcCCCCCcCCHHHHHHHHHHH
Confidence 3344555555553 5789999988776654
No 47
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.02 E-value=1.9e+02 Score=23.82 Aligned_cols=13 Identities=15% Similarity=0.002 Sum_probs=11.8
Q ss_pred ccccCCchhHHhh
Q psy4310 9 LCHYLNFPLYCGI 21 (203)
Q Consensus 9 lE~F~P~rf~sRi 21 (203)
.++|+++++..-|
T Consensus 58 ~v~Fd~~KI~~AI 70 (154)
T PRK00464 58 REPFDREKLRRGL 70 (154)
T ss_pred CCCcCHHHHHHHH
Confidence 5899999999988
No 48
>smart00417 H4 Histone H4.
Probab=23.21 E-value=82 Score=22.99 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=18.8
Q ss_pred hhHHHhhccCCCC------HHHHHHHHHHHH
Q psy4310 128 GRITRVAQGAGVT------EKEVKDLISQYT 152 (203)
Q Consensus 128 SR~~RIA~GSG~~------~~eVn~Llkq~~ 152 (203)
.=++|||+.+|+. ..|+.+.|++|-
T Consensus 17 ~~IrRLaRr~GvkRIS~~~y~elr~vle~~l 47 (74)
T smart00417 17 PAIRRLARRGGVKRISGLIYDETRNVLKSFL 47 (74)
T ss_pred HHHHHHHHHcCcchhhHHHHHHHHHHHHHHH
Confidence 4589999999986 466777776663
No 49
>PRK14621 hypothetical protein; Provisional
Probab=23.08 E-value=82 Score=24.63 Aligned_cols=29 Identities=3% Similarity=0.343 Sum_probs=19.5
Q ss_pred cCCCCHHHHHHHHHhccHhhHHHHHHHHHc
Q psy4310 22 CCMGDIEGLIDKVNELKLDDNEELIEKIKH 51 (203)
Q Consensus 22 LGmGDi~~Liek~~~v~~~~~~~l~~ki~~ 51 (203)
+||||+..++.+++++- ++.+++.+.+.+
T Consensus 1 ~~~~nm~~mmkqaq~mQ-~km~~~Q~eL~~ 29 (111)
T PRK14621 1 MAMPNLGDMMKQIQQAG-EKMQDVQKQLEK 29 (111)
T ss_pred CCchhHHHHHHHHHHHH-HHHHHHHHHHHc
Confidence 48999999999999852 333444444443
No 50
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=22.80 E-value=80 Score=24.04 Aligned_cols=33 Identities=18% Similarity=0.358 Sum_probs=22.1
Q ss_pred cCCCCHHHHHHHHHhccHhhHHHHHHHHHcCCCC
Q psy4310 22 CCMGDIEGLIDKVNELKLDDNEELIEKIKHGQFT 55 (203)
Q Consensus 22 LGmGDi~~Liek~~~v~~~~~~~l~~ki~~G~Ft 55 (203)
+|+||+..++.+++++- ++.+++.+++..=+||
T Consensus 2 ~~~~n~~~m~kqaq~mQ-~k~~~~q~eL~~~~v~ 34 (102)
T TIGR00103 2 FGKGNLGELMKQAQQMQ-EKMKKLQEEIAQFEVT 34 (102)
T ss_pred CChhhHHHHHHHHHHHH-HHHHHHHHHHhccEEE
Confidence 37899999999998853 3444555555544444
No 51
>KOG0512|consensus
Probab=22.14 E-value=2.7e+02 Score=24.31 Aligned_cols=71 Identities=24% Similarity=0.301 Sum_probs=41.9
Q ss_pred cCCCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhcCCccccccccCchhH
Q psy4310 51 HGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNRDGAKLFSKQTGRI 130 (203)
Q Consensus 51 ~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p~~i~l~~~~~SR~ 130 (203)
.+.+|+.|-.+|++.+..-| ..+|||--..-.+..++. +++= .||. ++++|+
T Consensus 15 e~~~d~~d~k~q~e~lr~h~------~~~pgmfvS~W~ddsdel-eE~d---------------k~me------~dp~rl 66 (228)
T KOG0512|consen 15 ENQLDFSDHKNQLEELRTHG------HLIPGMFVSLWVDDSEEL-EEQD---------------KNME------KDPIRL 66 (228)
T ss_pred hhccchHHHHHHHHHHHhcC------cCCCcceeeeecCCcHHH-Hhhc---------------cCcc------cCHHHH
Confidence 46899999999999998655 467998422222222222 1111 2343 245666
Q ss_pred HHhhccCCCCHHHHHHHHHH
Q psy4310 131 TRVAQGAGVTEKEVKDLISQ 150 (203)
Q Consensus 131 ~RIA~GSG~~~~eVn~Llkq 150 (203)
.--|.--++ ..+|..||+.
T Consensus 67 ~lwaae~nr-l~eV~~lL~e 85 (228)
T KOG0512|consen 67 LLWAAEKNR-LTEVQRLLSE 85 (228)
T ss_pred HHHHHhhcc-HHHHHHHHHh
Confidence 655555543 4677787764
No 52
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=21.92 E-value=58 Score=23.42 Aligned_cols=23 Identities=17% Similarity=0.419 Sum_probs=16.9
Q ss_pred hcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhc
Q psy4310 77 GMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELD 115 (203)
Q Consensus 77 ~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~ 115 (203)
.+|||+|- + |++|-+.+++.|++
T Consensus 33 ~~LPGLGV-l---------------FE~~W~~~~~~ek~ 55 (65)
T PF14098_consen 33 KALPGLGV-L---------------FEVIWKNSDESEKQ 55 (65)
T ss_pred hcCCchHH-H---------------HHHHHHhCCHHHHH
Confidence 58999983 2 66777777777765
No 53
>PF00390 malic: Malic enzyme, N-terminal domain; InterPro: IPR012301 Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate [], a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis []. There are 3 forms of the enzyme []: an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form []. Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase []; and the hypothetical Saccharomyces cerevisiae protein YKL029c. Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity []. The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate-or divalent metal ion-binding in the active site []. Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme [], although it is absent in the sequences from some species. There are three well conserved regions in the enzyme sequences. Two of them seem to be involved in the binding NAD or NADP. The significance of the third one, located in the central part of the enzymes, is not yet known.; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process; PDB: 2DVM_B 1WW8_A 2HAE_B 1VL6_A 1PJ2_A 1PJL_B 1GZ3_A 1PJ4_A 1PJ3_C 1EFL_A ....
Probab=21.83 E-value=27 Score=29.72 Aligned_cols=10 Identities=30% Similarity=0.421 Sum_probs=7.9
Q ss_pred HhhcCCCCHH
Q psy4310 19 CGICCMGDIE 28 (203)
Q Consensus 19 sRiLGmGDi~ 28 (203)
+||||+||+-
T Consensus 76 ~rILGlGD~G 85 (182)
T PF00390_consen 76 ERILGLGDLG 85 (182)
T ss_dssp SSBTTTBS-G
T ss_pred hhhccccCcC
Confidence 6899999985
No 54
>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional
Probab=21.77 E-value=36 Score=32.34 Aligned_cols=20 Identities=15% Similarity=-0.222 Sum_probs=18.3
Q ss_pred ccccccCCchhHHhhcCCCC
Q psy4310 7 LMLCHYLNFPLYCGICCMGD 26 (203)
Q Consensus 7 ~~lE~F~P~rf~sRiLGmGD 26 (203)
|||++|+|+.||.++|+.++
T Consensus 367 ~Dl~~a~~~~lv~~ll~~~~ 386 (420)
T PRK14721 367 EDLHEANSRYLLHRIFKPSR 386 (420)
T ss_pred hhhhhCCHHHHHHHHhcCcc
Confidence 89999999999999999653
No 55
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=21.68 E-value=1.7e+02 Score=21.59 Aligned_cols=47 Identities=15% Similarity=0.381 Sum_probs=30.7
Q ss_pred cCCCCHHHHHHH-HHh-ccH-hhHHHHHHHH---HcCCCCHHHHHHHHHHHHh
Q psy4310 22 CCMGDIEGLIDK-VNE-LKL-DDNEELIEKI---KHGQFTLRDMYEQFQNIMK 68 (203)
Q Consensus 22 LGmGDi~~Liek-~~~-v~~-~~~~~l~~ki---~~G~Ftl~Df~~Ql~~i~k 68 (203)
|.-.++..++.+ +-+ +.. ++..++++.+ ..|+.+|++|..-+..+..
T Consensus 26 i~~~ELk~ll~~elg~~ls~~~~v~~mi~~~D~d~DG~I~F~EF~~l~~~l~~ 78 (89)
T cd05022 26 LTASEFQELLTQQLPHLLKDVEGLEEKMKNLDVNQDSKLSFEEFWELIGELAK 78 (89)
T ss_pred ECHHHHHHHHHHHhhhhccCHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHH
Confidence 445567777766 544 444 5666666655 4568999999887766543
No 56
>PF09592 DUF2031: Protein of unknown function (DUF2031); InterPro: IPR006484 The sequences in this group represent a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism.
Probab=21.13 E-value=1e+02 Score=27.30 Aligned_cols=48 Identities=25% Similarity=0.380 Sum_probs=33.4
Q ss_pred cCCCCHHHHHHHHHHHHhcCChhHHhhcCCCCCcccccccchhhHHHHHHHHHHHHhCCChHhhcCC
Q psy4310 51 HGQFTLRDMYEQFQNIMKMGPFSQIMGMIPGFSQDFLSKGSEQESMARLKRLMTIMDSMNDGELDNR 117 (203)
Q Consensus 51 ~G~Ftl~Df~~Ql~~i~kMG~l~~i~~miPG~~~~~~~~~~~~~~~~~lk~~~~IIdSMT~~Er~~p 117 (203)
..+|||+|||+---++.. .++. -..+.+++..+..||||=..+-.++-
T Consensus 51 dn~fdlN~Fy~Stlsl~n------------q~nd-------~~~ddeei~~lrn~i~shikkhkenn 98 (228)
T PF09592_consen 51 DNQFDLNDFYESTLSLAN------------QFND-------YNDDDEEIIYLRNIIDSHIKKHKENN 98 (228)
T ss_pred CccccHHHHHHHHHHHHh------------hccc-------ccCCcHHHHHHHhhhHHHhhhhhccc
Confidence 348999999986555443 2221 12257899999999999887766654
Done!