Query 009098
Match_columns 543
No_of_seqs 166 out of 538
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 20:23:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009098.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009098hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1087 Cytosolic sorting prot 100.0 6.4E-47 1.4E-51 402.8 30.0 200 4-205 68-277 (470)
2 KOG1086 Cytosolic sorting prot 100.0 1.4E-33 3E-38 294.4 17.3 206 4-213 75-308 (594)
3 PF03127 GAT: GAT domain; Int 99.9 4.7E-22 1E-26 172.4 10.5 91 119-209 7-97 (100)
4 cd03569 VHS_Hrs_Vps27p VHS dom 99.7 4E-18 8.6E-23 157.2 9.0 70 4-74 71-141 (142)
5 cd03565 VHS_Tom1 VHS domain fa 99.7 3.4E-18 7.3E-23 157.5 8.2 69 4-73 69-141 (141)
6 cd03568 VHS_STAM VHS domain fa 99.7 1.4E-17 3.1E-22 154.1 9.7 72 4-76 67-139 (144)
7 cd03567 VHS_GGA VHS domain fam 99.7 7.8E-17 1.7E-21 148.6 7.9 64 4-71 68-137 (139)
8 smart00288 VHS Domain present 99.5 1.2E-14 2.7E-19 132.2 8.1 65 4-69 67-133 (133)
9 PF00790 VHS: VHS domain; Int 99.5 8.9E-14 1.9E-18 127.0 8.0 65 4-69 72-140 (140)
10 cd03561 VHS VHS domain family; 99.4 2.8E-13 6E-18 123.0 7.8 64 4-67 67-133 (133)
11 KOG2199 Signal transducing ada 99.4 1.9E-11 4.1E-16 128.5 16.9 199 3-205 74-367 (462)
12 KOG1818 Membrane trafficking a 98.9 1.2E-09 2.6E-14 120.9 6.4 78 4-83 75-154 (634)
13 cd00197 VHS_ENTH_ANTH VHS, ENT 97.8 2.3E-05 5E-10 69.0 5.0 43 4-46 67-115 (115)
14 KOG0307 Vesicle coat complex C 84.2 29 0.00064 42.2 15.8 44 385-431 783-826 (1049)
15 PF12210 Hrs_helical: Hepatocy 83.6 6 0.00013 35.5 7.7 70 125-196 4-73 (96)
16 PRK04778 septation ring format 81.3 11 0.00024 42.6 10.7 41 33-76 213-253 (569)
17 PF07106 TBPIP: Tat binding pr 77.3 27 0.00058 33.2 10.4 89 113-202 77-167 (169)
18 PF06160 EzrA: Septation ring 72.2 27 0.0006 39.5 10.6 42 32-76 208-249 (560)
19 PF14523 Syntaxin_2: Syntaxin- 69.1 31 0.00068 29.5 8.1 81 123-203 3-91 (102)
20 COG4477 EzrA Negative regulato 66.9 33 0.00072 39.1 9.6 44 32-78 211-254 (570)
21 KOG0307 Vesicle coat complex C 66.3 92 0.002 38.2 13.5 12 155-166 558-569 (1049)
22 PF04740 LXG: LXG domain of WX 60.5 65 0.0014 30.9 9.3 82 123-204 68-166 (204)
23 PF03670 UPF0184: Uncharacteri 60.4 24 0.00053 31.0 5.7 55 122-178 25-79 (83)
24 KOG2199 Signal transducing ada 59.6 35 0.00076 37.8 7.9 52 134-189 112-176 (462)
25 cd03562 CID CID (CTD-Interacti 55.5 12 0.00026 32.9 3.1 23 27-49 89-111 (114)
26 COG1867 TRM1 N2,N2-dimethylgua 55.2 23 0.00049 38.8 5.6 48 2-49 260-314 (380)
27 smart00503 SynN Syntaxin N-ter 47.3 1.9E+02 0.004 25.0 9.5 82 122-203 14-109 (117)
28 PF05633 DUF793: Protein of un 45.3 44 0.00096 36.7 6.0 67 109-175 294-370 (389)
29 PF04818 CTD_bind: RNA polymer 44.5 33 0.00071 27.4 3.7 29 18-46 30-59 (64)
30 cd00179 SynN Syntaxin N-termin 44.0 1.8E+02 0.0039 26.4 9.0 82 122-203 12-108 (151)
31 PF05400 FliT: Flagellar prote 43.8 61 0.0013 26.3 5.3 51 150-200 8-64 (84)
32 PF12917 HD_2: HD containing h 41.5 58 0.0013 33.2 5.7 44 165-208 112-155 (215)
33 PF00618 RasGEF_N: RasGEF N-te 41.1 1.1E+02 0.0023 26.2 6.6 42 9-50 33-89 (104)
34 cd08779 Death_PIDD Death Domai 41.0 53 0.0011 28.3 4.7 39 28-69 36-74 (86)
35 KOG3219 Transcription initiati 40.2 38 0.00083 34.0 4.2 37 32-72 148-185 (195)
36 PRK09458 pspB phage shock prot 40.1 36 0.00077 29.5 3.4 25 148-172 37-61 (75)
37 PF02203 TarH: Tar ligand bind 39.8 2.1E+02 0.0046 26.0 8.8 78 122-200 81-161 (171)
38 PF06667 PspB: Phage shock pro 38.9 38 0.00083 29.1 3.4 26 147-172 36-61 (75)
39 PF12993 DUF3877: Domain of un 38.3 22 0.00048 35.1 2.2 40 9-49 87-126 (175)
40 PF08784 RPA_C: Replication pr 38.2 37 0.0008 29.4 3.4 44 32-78 47-102 (102)
41 smart00229 RasGEFN Guanine nuc 38.0 1.2E+02 0.0026 26.8 6.7 40 12-51 39-89 (127)
42 KOG3091 Nuclear pore complex, 34.7 37 0.00081 38.3 3.5 130 14-176 367-500 (508)
43 PF04156 IncA: IncA protein; 33.3 2.5E+02 0.0055 26.7 8.5 17 160-176 151-167 (191)
44 TIGR00308 TRM1 tRNA(guanine-26 32.5 76 0.0016 34.4 5.3 37 13-49 273-309 (374)
45 PF04961 FTCD_C: Formiminotran 31.1 1.6E+02 0.0036 28.7 6.9 41 135-175 33-74 (184)
46 PF01895 PhoU: PhoU domain; I 30.4 2.1E+02 0.0045 22.7 6.4 15 129-143 6-20 (88)
47 PF07200 Mod_r: Modifier of ru 30.1 2.5E+02 0.0054 25.9 7.7 26 119-144 3-28 (150)
48 cd06224 REM Guanine nucleotide 30.0 1E+02 0.0023 26.6 4.9 42 10-51 29-84 (122)
49 PF01544 CorA: CorA-like Mg2+ 29.7 2.5E+02 0.0053 27.7 8.0 77 122-200 157-238 (292)
50 TIGR02976 phageshock_pspB phag 29.3 67 0.0015 27.6 3.4 25 148-172 37-61 (75)
51 cd08319 Death_RAIDD Death doma 28.4 1.2E+02 0.0026 26.3 4.9 39 28-70 36-74 (83)
52 PF10211 Ax_dynein_light: Axon 27.9 2.3E+02 0.0049 27.9 7.3 64 134-207 41-108 (189)
53 PRK06863 single-stranded DNA-b 27.0 56 0.0012 31.9 2.9 11 422-432 144-154 (168)
54 PF00512 HisKA: His Kinase A ( 27.0 3E+02 0.0064 21.3 6.6 48 123-172 11-59 (68)
55 PF09324 DUF1981: Domain of un 26.7 98 0.0021 26.6 4.0 33 15-47 15-48 (86)
56 PHA02334 hypothetical protein 26.5 2.2E+02 0.0048 23.8 5.7 37 149-185 21-57 (64)
57 COG5278 Predicted periplasmic 26.4 3.4E+02 0.0073 27.5 8.3 73 123-195 45-119 (207)
58 PF07531 TAFH: NHR1 homology t 25.9 75 0.0016 28.7 3.2 31 16-46 7-38 (96)
59 PHA03377 EBNA-3C; Provisional 25.8 6.2E+02 0.014 30.6 11.1 14 422-435 831-844 (1000)
60 PF05397 Med15_fungi: Mediator 25.3 1.9E+02 0.0042 26.4 5.9 48 149-196 31-82 (115)
61 TIGR00153 conserved hypothetic 24.9 2.9E+02 0.0064 27.1 7.5 79 122-203 17-101 (216)
62 PF12729 4HB_MCP_1: Four helix 24.5 4E+02 0.0086 23.4 7.7 48 127-174 83-130 (181)
63 COG3879 Uncharacterized protei 24.1 3.4E+02 0.0073 28.4 8.0 67 145-212 43-114 (247)
64 COG5394 Uncharacterized protei 23.9 1.4E+02 0.0031 29.6 4.9 47 126-172 140-193 (193)
65 COG4229 Predicted enolase-phos 23.9 57 0.0012 33.1 2.3 48 20-67 64-114 (229)
66 cd05132 RasGAP_GAPA GAPA is an 23.8 1.5E+02 0.0033 31.4 5.7 51 127-177 203-253 (331)
67 PF10112 Halogen_Hydrol: 5-bro 23.3 3.6E+02 0.0079 26.1 7.8 74 122-206 74-152 (199)
68 PF09388 SpoOE-like: Spo0E lik 23.2 2.2E+02 0.0048 21.6 5.0 42 157-202 1-44 (45)
69 PRK11639 zinc uptake transcrip 23.1 1.5E+02 0.0033 28.3 5.1 50 13-70 4-56 (169)
70 PF07568 HisKA_2: Histidine ki 23.1 2.2E+02 0.0049 23.7 5.4 18 126-143 4-21 (76)
71 PF00015 MCPsignal: Methyl-acc 22.7 78 0.0017 29.8 3.0 20 180-199 191-210 (213)
72 KOG3192 Mitochondrial J-type c 22.4 1.4E+02 0.0031 29.4 4.6 42 153-194 56-110 (168)
73 PRK14139 heat shock protein Gr 22.4 3.5E+02 0.0075 27.0 7.4 40 157-196 57-99 (185)
74 PRK14161 heat shock protein Gr 22.3 4.1E+02 0.009 26.2 7.9 43 155-197 42-87 (178)
75 PRK14143 heat shock protein Gr 22.3 3.4E+02 0.0074 28.0 7.6 42 156-197 91-135 (238)
76 PF07106 TBPIP: Tat binding pr 22.0 2.9E+02 0.0063 26.2 6.6 54 155-208 88-141 (169)
77 KOG4603 TBP-1 interacting prot 21.9 8.4E+02 0.018 24.6 9.9 87 110-204 88-176 (201)
78 PF02403 Seryl_tRNA_N: Seryl-t 21.7 5.4E+02 0.012 22.4 9.5 75 124-201 3-92 (108)
79 PF09789 DUF2353: Uncharacteri 21.5 3.9E+02 0.0085 28.9 8.1 82 114-196 85-181 (319)
80 PF03273 Baculo_gp64: Baculovi 21.4 2.1E+02 0.0047 32.4 6.3 57 119-187 281-339 (498)
81 PF15326 TEX15: Testis express 21.1 1.3E+02 0.0029 31.0 4.3 41 131-175 76-116 (233)
82 PRK14148 heat shock protein Gr 20.8 4E+02 0.0087 26.7 7.6 66 123-197 40-108 (195)
83 PRK09269 chorismate mutase; Pr 20.5 5E+02 0.011 26.0 8.1 60 152-211 90-158 (193)
84 PRK14162 heat shock protein Gr 20.5 4E+02 0.0086 26.7 7.4 41 157-197 64-107 (194)
No 1
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=6.4e-47 Score=402.78 Aligned_cols=200 Identities=43% Similarity=0.702 Sum_probs=171.0
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cC-CCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCCCCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQ-PDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDAAP 81 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK-~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~daaP 81 (543)
=|||.||.|||+|+||+||||++ .+ .+..||+|||.||++|+++|++..+|+++|+++|++|+++||+||.++.++.+
T Consensus 68 NCG~~fh~~Va~k~fL~emVk~~k~~~~~~~Vr~kiL~LI~~W~~af~~~~~~~~~~~~~y~~l~~~G~~FP~r~~~sl~ 147 (470)
T KOG1087|consen 68 NCGYSFHLQVASKEFLNEMVKRPKNKPRDLKVREKILELIDTWQQAFCGPDGYLPDYYQIYDELRRKGVEFPQRDEESLA 147 (470)
T ss_pred hhhHHHHHHHHHHHHHHHHHhccccCCcchhHHHHHHHHHHHHHHHccCCCCcchhHHHHHHHHHHcCCcCCCCcccccc
Confidence 39999999999999999999999 66 77899999999999999999997788999999999999999999999999877
Q ss_pred CCCCCC-CCCccchhhcccCCCCCCcch------hhhhh-hHHHhhhcHHHHHHHHHHHHHHHHHHHhcCCCCCccchhH
Q 009098 82 IFTPPV-SHPTLGQAQASYGMPSNSSRR------LDETM-ATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDE 153 (543)
Q Consensus 82 I~TPp~-S~Pe~~~a~~~~gSP~~~d~~------L~~sm-s~D~ekLS~sELevVrnNvkLLsEML~~~~Pg~~~~~ddE 153 (543)
+++|+. ..+..+..... +.+. +... ....+ ..++..++++||++|++|++||+|||.++++++++..++|
T Consensus 148 ~~~pp~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~seLe~~~~~~~ll~emL~~v~p~~~e~~~~e 225 (470)
T KOG1087|consen 148 VLTPPAVLRPAPEPQEQS-GPPN-EANASMKSMAGYPTEATPEVSTLSLSELESVKGKADLLSEMLNAVDPSDEEAAKDE 225 (470)
T ss_pred ccCCCCCCCCCCCchhhc-CCcc-ccccccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHhccCCCCcchhHHH
Confidence 776654 22221111011 1111 1111 11122 3467788899999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHHHHHHHHHhcC
Q 009098 154 VIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASG 205 (543)
Q Consensus 154 LIqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~VL~RYd~i~sG 205 (543)
+|++|+++||.+|+|||+||++++||++|+++|++||+|++||.|||+|.+|
T Consensus 226 l~~~L~~qcr~~q~rv~~Li~~~~DE~ll~~lL~lND~L~~vL~~ye~~~~g 277 (470)
T KOG1087|consen 226 LLVDLVEQCRSKQRRVMHLIEETSDEELLCELLKLNDELQRVLERYERIASG 277 (470)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHHHHhcc
Confidence 9999999999999999999999999999999999999999999999999999
No 2
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.4e-33 Score=294.44 Aligned_cols=206 Identities=19% Similarity=0.281 Sum_probs=168.1
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCCC-----HHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCC--CCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQPD-----MQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQF--PKR 75 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~~-----~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~F--P~~ 75 (543)
-||-.||.++++|+|||||||+| |||. ..||.||++|+.+|+.+|+. .++|+|+|+|||++||+- |..
T Consensus 75 ncGekfH~evgkfrFLNELIkvvsPKYlG~~tSekvKtkiIelLfsWtv~lpe----~~KikdaYqmLKkqgIik~DP~l 150 (594)
T KOG1086|consen 75 NCGEKFHEEVGKFRFLNELIKVVSPKYLGSRTSEKVKTKIIELLFSWTVSLPE----EPKIKDAYQMLKKQGIIKSDPKL 150 (594)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHhCchhcchhhhHHHHHHHHHHHhhheecCcc----cchHHHHHHHHHhcCcccCCCCC
Confidence 49999999999999999999999 9997 49999999999999999997 689999999999999986 444
Q ss_pred CCCCCCCCCCCC-CC-Cccchhhc------ccCCCCCCcch----hhhhhh-HHH---hhhc--HHHHHHHHHHHHHHHH
Q 009098 76 SPDAAPIFTPPV-SH-PTLGQAQA------SYGMPSNSSRR----LDETMA-TEV---ETLS--FSSLDSMRDVMELLSD 137 (543)
Q Consensus 76 ~~daaPI~TPp~-S~-Pe~~~a~~------~~gSP~~~d~~----L~~sms-~D~---ekLS--~sELevVrnNvkLLsE 137 (543)
..|..+++.|+. .. ...+++.+ -++|.+++|.+ |++.|. +|. +|++ +..||.|+|||+||.|
T Consensus 151 p~d~~~~p~ppP~pkssvFddEEksklL~rLLkSn~PeDLqaANkLIK~lVkeee~k~eKiskR~~aleev~n~vk~l~e 230 (594)
T KOG1086|consen 151 PVDETPVPAPPPRPKSSVFDDEEKSKLLARLLKSNHPEDLQAANKLIKTLVKEEEHKLEKISKRVKALEEVNNNVKLLEE 230 (594)
T ss_pred CCCCccCCCCCCCCCccccCcHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555456665432 22 22222222 25788888754 666664 333 4444 5889999999999999
Q ss_pred HHHhcCCCCC-ccchhHHHHHHHHHHHHhHHHHHHHhhhcCC-HHHHHHhhhcchHHHHHHHHHHHHhcCCCCCCccc
Q 009098 138 MLQAVNPSDR-EAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-EELLGRGLELNDILQNLLAKHDAIASGLPIPTEVT 213 (543)
Q Consensus 138 ML~~~~Pg~~-~~~ddELIqELyetCrsmQpRI~~LIeetsD-EElL~eLL~lNDdLn~VL~RYd~i~sG~~~~~e~~ 213 (543)
||-.+..++. ..+.+.++++||++|+++|+.+++|+++++| |+.|+++|++||.|++|+.-|+.++.|+...+++.
T Consensus 231 m~l~~s~eg~a~pd~E~~lq~v~~~ce~lr~tlfrlaset~dnD~aL~eILqanD~ltrvi~~ykt~~~G~~~~g~a~ 308 (594)
T KOG1086|consen 231 MLLDYSQEGNASPDNELLLQEVYNRCEQLRPTLFRLASETEDNDPALAEILQANDNLTRVINLYKTPKEGNVANGSAR 308 (594)
T ss_pred HHHhhccCCCCCCcHHHHHHHHHHHHHHHHHHHHHhhcccccCcHHHHHHHhhhhhHHhhhhhcccccccccccccce
Confidence 9888765444 4444449999999999999999999999877 99999999999999999999999999999887764
No 3
>PF03127 GAT: GAT domain; InterPro: IPR004152 The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 [] and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins [].; GO: 0006886 intracellular protein transport, 0005622 intracellular; PDB: 1YD8_H 1WR6_C 1WRD_A 1O3X_A 1J2J_B 1NWM_X 1X79_A 1OXZ_A 1NAF_A.
Probab=99.87 E-value=4.7e-22 Score=172.42 Aligned_cols=91 Identities=27% Similarity=0.493 Sum_probs=83.5
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHHHHH
Q 009098 119 TLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAK 198 (543)
Q Consensus 119 kLS~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~VL~R 198 (543)
+..++||++|++|++||+|||++++|++...++.|+|+|||++||+||+||++||+.+.||++|+++|++||+|+++|.|
T Consensus 7 ~k~~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~dee~l~~lL~~ND~L~~~l~~ 86 (100)
T PF03127_consen 7 SKRRSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVEDEELLGELLQANDELNQALER 86 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHH
Confidence 33379999999999999999999999988877789999999999999999999999999988999999999999999999
Q ss_pred HHHHhcCCCCC
Q 009098 199 HDAIASGLPIP 209 (543)
Q Consensus 199 Yd~i~sG~~~~ 209 (543)
|+++++|+...
T Consensus 87 Y~~l~~~~~~~ 97 (100)
T PF03127_consen 87 YDRLVKGQQRG 97 (100)
T ss_dssp HHHHHCCC---
T ss_pred HHHHHcCcccc
Confidence 99999998753
No 4
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=99.74 E-value=4e-18 Score=157.18 Aligned_cols=70 Identities=20% Similarity=0.287 Sum_probs=66.8
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPK 74 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~ 74 (543)
=||+.||.||++++||++|++++ ++++..||+|||+||++|+++|++.++ ++.|+++|++||++||.||+
T Consensus 71 NCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~f~~~~~-l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 71 NCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQAWALAFRNKPQ-LKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred HCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHHHhCCCcc-cHHHHHHHHHHHHcCCCCCC
Confidence 49999999999999999999999 888999999999999999999998755 89999999999999999996
No 5
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=99.74 E-value=3.4e-18 Score=157.50 Aligned_cols=69 Identities=23% Similarity=0.489 Sum_probs=64.9
Q ss_pred CCchhHHHhhhcHHHHHH-HHHhh-cCCC--HHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCC
Q 009098 4 FVSYSVQRLFRPSASTKT-FISLV-LQPD--MQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFP 73 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnE-LVKLI-pK~~--~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP 73 (543)
=||+.||.|||+|+||+| |+|+| ++++ ..||+|||+||++|+++|++.++ ++.|.++|++||++||+||
T Consensus 69 NCG~~fh~eiask~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~~f~~~~~-l~~i~~~y~~L~~~G~~FP 141 (141)
T cd03565 69 NCGHRFHVLVAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADAFRGSPD-LTGVVEVYEELKKKGIEFP 141 (141)
T ss_pred HccHHHHHHHHHHHhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHHHhCCCcc-chHHHHHHHHHHHcCCCCC
Confidence 399999999999999999 99999 7764 59999999999999999999876 8999999999999999998
No 6
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=99.72 E-value=1.4e-17 Score=154.05 Aligned_cols=72 Identities=11% Similarity=0.181 Sum_probs=67.2
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRS 76 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~ 76 (543)
=||..||+||++++||+||+|++ ++.+..||+|||+||+.|+++|++.++ +..|.++|++||++||.||..+
T Consensus 67 NCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~f~~~~~-l~~i~~~y~~L~~~G~~f~~~~ 139 (144)
T cd03568 67 NCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWADEFKNDPS-LSLMSDLYKKLKNEGPDLVTPD 139 (144)
T ss_pred HCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhCCCcc-cHHHHHHHHHHHHcCCCCCCCC
Confidence 49999999999999999999999 779999999999999999999998766 8899999999999999999543
No 7
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=99.68 E-value=7.8e-17 Score=148.61 Aligned_cols=64 Identities=22% Similarity=0.273 Sum_probs=59.5
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCC-----CHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQP-----DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQ 71 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~-----~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~ 71 (543)
=||+.||.||++|+||+||+|+| +|+ +..||+|||+||+.|+++|+. .|+|+++|++||++||+
T Consensus 68 NCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~~----~p~~~~~Y~~Lk~~G~i 137 (139)
T cd03567 68 NCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELPH----EPKIKEAYDMLKKQGII 137 (139)
T ss_pred HcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhcc----cchHHHHHHHHHHCCCc
Confidence 39999999999999999999999 764 579999999999999999995 68999999999999985
No 8
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=99.54 E-value=1.2e-14 Score=132.18 Aligned_cols=65 Identities=17% Similarity=0.301 Sum_probs=60.7
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCCCHH-HHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQPDMQ-LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 69 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~~~~-VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kG 69 (543)
=||.+||.||++++||++|++++ ++++.. ||+|||+||+.|+++|++.++ ++.|.++|++||++|
T Consensus 67 Ncg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~~f~~~~~-~~~i~~~y~~L~~~g 133 (133)
T smart00288 67 NCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQEWADAFKNDPD-LSQIVDVYDLLKKKG 133 (133)
T ss_pred HCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCCCC-chHHHHHHHHHHHCc
Confidence 49999999999999999999999 777754 999999999999999998766 899999999999998
No 9
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=99.47 E-value=8.9e-14 Score=127.03 Aligned_cols=65 Identities=23% Similarity=0.343 Sum_probs=59.4
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-cCCCH-H--HHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-LQPDM-Q--LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 69 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-pK~~~-~--VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kG 69 (543)
=||..||.||++++||++|++|+ .+... . ||+|||+||+.|+++|++.+. +..|+++|++||++|
T Consensus 72 Ncg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~f~~~~~-~~~i~~~y~~Lk~~G 140 (140)
T PF00790_consen 72 NCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQEWAEAFKSDPE-LSLIQDTYKRLKRKG 140 (140)
T ss_dssp HSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHHHTTTSTT-GHHHHHHHHHHHHTT
T ss_pred cCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHHHHCCCCC-chHHHHHHHHHHHCc
Confidence 39999999999999999999999 55554 4 999999999999999988766 899999999999998
No 10
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=99.43 E-value=2.8e-13 Score=122.97 Aligned_cols=64 Identities=23% Similarity=0.334 Sum_probs=58.9
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-c--CCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHH
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-L--QPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRR 67 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-p--K~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~ 67 (543)
=||.+||.+|++++||++|++++ + +.+..||+|||+||+.|+.+|++....+++|+++|++||+
T Consensus 67 Ncg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~~~~~~~~~~~~y~~lk~ 133 (133)
T cd03561 67 NCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAWSESFGGHSEDLPGIEDAYKLLKR 133 (133)
T ss_pred hCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHHhC
Confidence 49999999999999999999999 5 6788999999999999999999873449999999999985
No 11
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=99.36 E-value=1.9e-11 Score=128.46 Aligned_cols=199 Identities=15% Similarity=0.189 Sum_probs=137.5
Q ss_pred CCCchhHHHhhhcHHHHHHHHHhh-cCCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCCC--
Q 009098 3 SFVSYSVQRLFRPSASTKTFISLV-LQPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDA-- 79 (543)
Q Consensus 3 ~~cgYpVH~eIAskeFLnELVKLI-pK~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~da-- 79 (543)
.-||=.||+||++++|.+||-+|| -+.++.|++||-.|+..|++.|+.++. +..|.++|..||+.||.|+....-.
T Consensus 74 ~NCg~~~r~EVsSr~F~~el~al~~~~~h~kV~~k~~~lv~eWsee~K~Dp~-lsLi~~l~~klk~~g~~f~~~~~k~~k 152 (462)
T KOG2199|consen 74 ANCGKRFRLEVSSRDFTTELRALIESKAHPKVCEKMRDLVKEWSEEFKKDPS-LSLISALYKKLKEEGITFLVAGSKPEK 152 (462)
T ss_pred HhcchHHHHHHhhhhHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhccCcc-hhHHHHHHHHHHHcCCCcccCCCchhH
Confidence 459999999999999999999999 699999999999999999999999877 8899999999999999997654321
Q ss_pred CCCCC--CCCCCCccc--hh----------hc---------ccCC-------CC------C--------------Cc---
Q 009098 80 APIFT--PPVSHPTLG--QA----------QA---------SYGM-------PS------N--------------SS--- 106 (543)
Q Consensus 80 aPI~T--Pp~S~Pe~~--~a----------~~---------~~gS-------P~------~--------------~d--- 106 (543)
..+-+ -.....+.+ .+ +. .|.+ |. . ++
T Consensus 153 ~a~~~~~v~~k~EeEdiaKAi~lSL~E~~~Q~k~a~~~tst~yPs~qk~nqapa~~l~s~~~~rkVRALYDFeAaE~nEL 232 (462)
T KOG2199|consen 153 HAMSTNTVSSKQEEEDIAKAIELSLKEQEKQKKLAETETSTLYPSHQKQNQAPASQLNSQTVVRKVRALYDFEAAEDNEL 232 (462)
T ss_pred HHhhcccccccccHHHHHHHHHhhHHHHhhchhhccCCccccCccccccccCchhhccCCccchhhhhhhcccccCCCcc
Confidence 00101 000000000 00 00 0100 00 0 00
Q ss_pred ----chhh----------------hh--------hhHHHhhhcHHH-----------HHHHHHHHHHHHHHHHhcCCCCC
Q 009098 107 ----RRLD----------------ET--------MATEVETLSFSS-----------LDSMRDVMELLSDMLQAVNPSDR 147 (543)
Q Consensus 107 ----~~L~----------------~s--------ms~D~ekLS~sE-----------LevVrnNvkLLsEML~~~~Pg~~ 147 (543)
+.++ .. +..+.+.++.++ ..+-+..|+-|-.||.+.+|.+.
T Consensus 233 sFkaGdIItVLd~s~~~WWKG~~~~~~GlFPsnfVT~~le~~~~ee~~~~~~~~E~~vfi~e~~iDrlL~~L~~~dPtd~ 312 (462)
T KOG2199|consen 233 SFKAGDIITVLDDSDPNWWKGENHRGIGLFPSNFVTADLEEPKIEEQEQKQKNKEAIVFIDEDKIDRLLQVLHEADPTDE 312 (462)
T ss_pred ceecCcEEEEcccCCcchhccccCCcccccchhhhhhhhcccchhhhhhhhcCcceeeeccHHHHHHHHHHHhhcCCCCc
Confidence 0000 00 011222222222 23456678888899999999765
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHHHHHHHHHhcC
Q 009098 148 EAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASG 205 (543)
Q Consensus 148 ~~~ddELIqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~VL~RYd~i~sG 205 (543)
. .|++-|.+|+..|..|++.|-++++.+.-+- ++|++||-.|-.++.-|+.++.-
T Consensus 313 ~-~D~~~l~~le~~~~~mgPlid~~Le~idrk~--~eL~~Ln~~l~~Al~lY~kLm~~ 367 (462)
T KOG2199|consen 313 V-QDDDDLLDLEAAVHQMGPLIDRKLEKIDRKH--EELSQLNVKLLDALRLYNKLMNE 367 (462)
T ss_pred c-CCCHHHHHHHHHHHHhhhHHHHHHHHHHhhH--HHHHHHHHHHHHHHHHHHHHHhh
Confidence 4 4566688999999999999999999986532 46789999999999999999843
No 12
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=98.92 E-value=1.2e-09 Score=120.91 Aligned_cols=78 Identities=23% Similarity=0.345 Sum_probs=71.0
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-c-CCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCCCCC
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-L-QPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDAAP 81 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-p-K~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~daaP 81 (543)
-||-+||.+|++|+||+.|..++ . +.+..||.|||++|+.|+.+|+.. .++..+.++|+.||.+|+.||..++..+
T Consensus 75 n~G~gv~~ei~tre~m~~~~~~l~~~~~~e~v~~~~l~~~q~wa~af~~~-~~~~~v~~t~~~lk~~g~~Fpe~~e~d~- 152 (634)
T KOG1818|consen 75 NCGHGVHCEIATREFMDLLKSLLESQRIHEEVKNKILELIQNWAAAFRNS-SKYSYVLDTYQKLKGGGHVFPELDENDA- 152 (634)
T ss_pred cCCcchhHHHHHHHHHHHHHhhhccccccchHHHHHHHHHHHHHHHccCc-hHHHHHHHHHHHHhcCCccccccccchh-
Confidence 48999999999999999999999 4 478899999999999999999997 5688899999999999999999988654
Q ss_pred CC
Q 009098 82 IF 83 (543)
Q Consensus 82 I~ 83 (543)
+|
T Consensus 153 mf 154 (634)
T KOG1818|consen 153 MF 154 (634)
T ss_pred hh
Confidence 44
No 13
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=97.83 E-value=2.3e-05 Score=69.04 Aligned_cols=43 Identities=9% Similarity=0.186 Sum_probs=37.6
Q ss_pred CCchhHHHhhhcHHHHHHHHHhh-c-----CCCHHHHHHHHHHHHHHHH
Q 009098 4 FVSYSVQRLFRPSASTKTFISLV-L-----QPDMQLRDKILVLLDSWQE 46 (543)
Q Consensus 4 ~cgYpVH~eIAskeFLnELVKLI-p-----K~~~~VreKILeLIQsWae 46 (543)
.||..||.+|+++.|+++|+|+. . ..+..||+|+++||+.|+.
T Consensus 67 N~g~~f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w~~ 115 (115)
T cd00197 67 NCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLWAS 115 (115)
T ss_pred HccHHHHHHHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHHHHHhC
Confidence 59999999999999999998864 2 3457999999999999973
No 14
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=84.19 E-value=29 Score=42.21 Aligned_cols=44 Identities=39% Similarity=0.590 Sum_probs=25.4
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009098 385 PYNNYVAPWAQPQSQPLPQSQPQFQPGVQPQYPHYSSAYPPPPWAPT 431 (543)
Q Consensus 385 ~~n~yv~pwaq~~~~~q~~~~~~~~~~~~~q~~~~~~~yp~ppwa~~ 431 (543)
|||.+-+| ++...+.+++-++......+-++ +.+-||+|+|.+-
T Consensus 783 p~~p~p~p--~~~~~p~~~s~~~p~~~stP~~~-~~~~~P~~~~~~~ 826 (1049)
T KOG0307|consen 783 PYNPSPAP--QPSYTPAPQSNARPNSASTPTPP-AFSFTPPPSSGAA 826 (1049)
T ss_pred CCCCCCCC--CCCCCCCCcCCCCCCCCCCCCCC-CcCCCCCCccccc
Confidence 66666666 44444444444444443444444 7778888889873
No 15
>PF12210 Hrs_helical: Hepatocyte growth factor-regulated tyrosine kinase substrate; InterPro: IPR024641 This domain comprises the helical region of hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). It is approximately 100 amino acids in length. Hrs, together with signal transducing adaptor molecule (STAM), forms the ESCRT-0 complex, which sorts ubiquitinated cell surface receptors to lysosomes for degradation []. ; PDB: 3F1I_H.
Probab=83.60 E-value=6 Score=35.51 Aligned_cols=70 Identities=13% Similarity=0.301 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHHH
Q 009098 125 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLL 196 (543)
Q Consensus 125 LevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~VL 196 (543)
++..+..|++|.+=+......+.....|..|+.|+.+.-.|+++|++.|.+..|.-.=.+ .+.|.|..+=
T Consensus 4 ~~~l~~~v~if~nRmksns~RGrsIanDsaVqsLF~~lt~mH~~LL~~i~~~ee~R~~~E--~lQdkL~qi~ 73 (96)
T PF12210_consen 4 CNTLRSSVEIFVNRMKSNSSRGRSIANDSAVQSLFQTLTAMHPQLLKYIQEQEEKRVYYE--GLQDKLAQIK 73 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--GGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHhcCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Confidence 566778888887766655445567888999999999999999999999998776332222 2345554443
No 16
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=81.29 E-value=11 Score=42.56 Aligned_cols=41 Identities=17% Similarity=0.226 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCC
Q 009098 33 LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRS 76 (543)
Q Consensus 33 VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~ 76 (543)
..++|=.|+..-...|+.. +..+.+.|+.|+.+||.|+...
T Consensus 213 ~~~~iP~l~~~~~~~~P~q---l~el~~gy~~m~~~gy~~~~~~ 253 (569)
T PRK04778 213 IMEEIPELLKELQTELPDQ---LQELKAGYRELVEEGYHLDHLD 253 (569)
T ss_pred HHHHHHHHHHHHHHHhhHH---HHHHHHHHHHHHHcCCCCCCCC
Confidence 3444556666667777653 6679999999999999998653
No 17
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=77.32 E-value=27 Score=33.15 Aligned_cols=89 Identities=15% Similarity=0.138 Sum_probs=61.0
Q ss_pred hhHHHhhhcHHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCC--HHHHHHhhhcch
Q 009098 113 MATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD--EELLGRGLELND 190 (543)
Q Consensus 113 ms~D~ekLS~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsD--EElL~eLL~lND 190 (543)
|..+...| ..+|..++.-++-|..=|..+...-...+=.+.|.+|-..|+.++.||..|-+.... ++.+.++..-..
T Consensus 77 ld~ei~~L-~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~ 155 (169)
T PF07106_consen 77 LDAEIKEL-REELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYK 155 (169)
T ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 33444555 788999999999999999988654333334566789999999999999999985433 555555555555
Q ss_pred HHHHHHHHHHHH
Q 009098 191 ILQNLLAKHDAI 202 (543)
Q Consensus 191 dLn~VL~RYd~i 202 (543)
.+.+...+..+|
T Consensus 156 ~~~k~w~kRKri 167 (169)
T PF07106_consen 156 KWRKEWKKRKRI 167 (169)
T ss_pred HHHHHHHHHHHH
Confidence 555554444444
No 18
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=72.15 E-value=27 Score=39.49 Aligned_cols=42 Identities=14% Similarity=0.229 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCC
Q 009098 32 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRS 76 (543)
Q Consensus 32 ~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~ 76 (543)
..-++|=.|+..-...|+.. +..+.+.|+.|+.+||.|+..+
T Consensus 208 ~~~e~IP~l~~~l~~~~P~q---l~eL~~gy~~m~~~gy~l~~~~ 249 (560)
T PF06160_consen 208 EIMEDIPKLYKELQKEFPDQ---LEELKEGYREMEEEGYYLEHLD 249 (560)
T ss_pred HHHHHhHHHHHHHHHHhHHH---HHHHHHHHHHHHHCCCCCCCCC
Confidence 44555666677777777753 6678999999999999998644
No 19
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=69.09 E-value=31 Score=29.51 Aligned_cols=81 Identities=12% Similarity=0.150 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhc------CC--HHHHHHhhhcchHHHH
Q 009098 123 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT------GD--EELLGRGLELNDILQN 194 (543)
Q Consensus 123 sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeet------sD--EElL~eLL~lNDdLn~ 194 (543)
.-|..+.+++.-|.-|+..+....-...--+-|.++...|+.+-..+-++|... .+ -..-...=.|..++..
T Consensus 3 ~~l~~in~~v~~l~k~~~~lGt~~Ds~~lR~~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~ 82 (102)
T PF14523_consen 3 SNLFKINQNVSQLEKLVNQLGTPRDSQELREKIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKE 82 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHH-SSS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHhCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 357889999999999999984211111122334566666666655555544331 11 1222344566777788
Q ss_pred HHHHHHHHh
Q 009098 195 LLAKHDAIA 203 (543)
Q Consensus 195 VL~RYd~i~ 203 (543)
+|.+|.++.
T Consensus 83 ~l~~fq~~q 91 (102)
T PF14523_consen 83 ALQEFQKAQ 91 (102)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 888887654
No 20
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=66.87 E-value=33 Score=39.11 Aligned_cols=44 Identities=20% Similarity=0.331 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCC
Q 009098 32 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 78 (543)
Q Consensus 32 ~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~d 78 (543)
.+.++|=.||..-...+++. +...+..|+.|+.+||.|+....+
T Consensus 211 ~~~e~IP~L~~e~~~~lP~q---l~~Lk~Gyr~m~~~gY~l~~~~id 254 (570)
T COG4477 211 SIMERIPSLLAELQTELPGQ---LQDLKAGYRDMKEEGYHLEHVNID 254 (570)
T ss_pred HHHHHHHHHHHHHHhhchHH---HHHHHHHHHHHHHccCCcccccHH
Confidence 56778888999999888874 778999999999999999976544
No 21
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=66.31 E-value=92 Score=38.24 Aligned_cols=12 Identities=33% Similarity=0.623 Sum_probs=8.5
Q ss_pred HHHHHHHHHHhH
Q 009098 155 IVDLVSRCRSNQ 166 (543)
Q Consensus 155 IqELyetCrsmQ 166 (543)
+++++++|..++
T Consensus 558 ~~~~ve~~~~k~ 569 (1049)
T KOG0307|consen 558 LDDYVETCEVKQ 569 (1049)
T ss_pred HHHHHhhcchhh
Confidence 456777777776
No 22
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=60.46 E-value=65 Score=30.91 Aligned_cols=82 Identities=12% Similarity=0.252 Sum_probs=49.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHH-HHHHHHHHhHHHHHHHhhhc----------------CCHHHHHHh
Q 009098 123 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIV-DLVSRCRSNQKKLMQMLTTT----------------GDEELLGRG 185 (543)
Q Consensus 123 sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIq-ELyetCrsmQpRI~~LIeet----------------sDEElL~eL 185 (543)
.=++.+...++.+.+-+..+++......+.+.++ ||...+++....+..+...+ ....+...+
T Consensus 68 ~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~~~~~~~~~~~~~~~~vsdiv~~~~~~~~~~~~~~ 147 (204)
T PF04740_consen 68 LLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKEQIEDLQDEINSILSSVSDIVSLPKPSSSSFIDSL 147 (204)
T ss_pred HHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccchHHHHhhccchHHHHHHHH
Confidence 3445566666777777777765333345566666 77666666666665554442 124455556
Q ss_pred hhcchHHHHHHHHHHHHhc
Q 009098 186 LELNDILQNLLAKHDAIAS 204 (543)
Q Consensus 186 L~lNDdLn~VL~RYd~i~s 204 (543)
..+.+.|+.++++...|-.
T Consensus 148 ~~~~~~l~~~lekL~~fd~ 166 (204)
T PF04740_consen 148 EKAKKKLQETLEKLRAFDQ 166 (204)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6666777777777777653
No 23
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=60.43 E-value=24 Score=30.97 Aligned_cols=55 Identities=11% Similarity=0.219 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD 178 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsD 178 (543)
..|+..|...++-|+--|+++. ++.+.=..-+++|.+.||+.|..+++.......
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE--~rnD~l~~~L~~LLesnrq~R~e~~~~~~~~~~ 79 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLE--QRNDHLHAQLQELLESNRQIRLEFQEQLSKAPS 79 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH--HhhhHHHHHHHHHHHHHHHHHHHHHHHhccCCc
Confidence 5678888888888888888883 344444556889999999999999887776543
No 24
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=59.63 E-value=35 Score=37.77 Aligned_cols=52 Identities=17% Similarity=0.334 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCccchhHHHHHHHHHHHHh-----------HHHHHHH--hhhcCCHHHHHHhhhcc
Q 009098 134 LLSDMLQAVNPSDREAVKDEVIVDLVSRCRSN-----------QKKLMQM--LTTTGDEELLGRGLELN 189 (543)
Q Consensus 134 LLsEML~~~~Pg~~~~~ddELIqELyetCrsm-----------QpRI~~L--IeetsDEElL~eLL~lN 189 (543)
|+.|.-++++ ++-...||.+||+..|+- ....+.- ++.-.+||.|.++|++.
T Consensus 112 lv~eWsee~K----~Dp~lsLi~~l~~klk~~g~~f~~~~~k~~k~a~~~~~v~~k~EeEdiaKAi~lS 176 (462)
T KOG2199|consen 112 LVKEWSEEFK----KDPSLSLISALYKKLKEEGITFLVAGSKPEKHAMSTNTVSSKQEEEDIAKAIELS 176 (462)
T ss_pred HHHHHHHHhc----cCcchhHHHHHHHHHHHcCCCcccCCCchhHHHhhcccccccccHHHHHHHHHhh
Confidence 3444445563 234588999998888862 2223322 33344688888888764
No 25
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=55.51 E-value=12 Score=32.90 Aligned_cols=23 Identities=35% Similarity=0.540 Sum_probs=20.0
Q ss_pred cCCCHHHHHHHHHHHHHHHHHhC
Q 009098 27 LQPDMQLRDKILVLLDSWQEAFG 49 (543)
Q Consensus 27 pK~~~~VreKILeLIQsWaeAF~ 49 (543)
.+.++.+|+||..|+..|.+.+-
T Consensus 89 ~~~~~~~r~kl~rl~~iW~~~~~ 111 (114)
T cd03562 89 EKVDEKTRKKLERLLNIWEERFV 111 (114)
T ss_pred HhCCHHHHHHHHHHHHHccCCCC
Confidence 67889999999999999986543
No 26
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=55.21 E-value=23 Score=38.78 Aligned_cols=48 Identities=8% Similarity=0.139 Sum_probs=33.8
Q ss_pred CCCCchhHHHh-------hhcHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHhC
Q 009098 2 ASFVSYSVQRL-------FRPSASTKTFISLVLQPDMQLRDKILVLLDSWQEAFG 49 (543)
Q Consensus 2 ~~~cgYpVH~e-------IAskeFLnELVKLIpK~~~~VreKILeLIQsWaeAF~ 49 (543)
+..||+.||.- +-.++|+++|..+..+.-...++|++.||..-.+...
T Consensus 260 c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~~~~~l~~~~~~~klL~~i~~E~~ 314 (380)
T COG1867 260 CPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIAEGLELGTKKRALKLLKLIKKELD 314 (380)
T ss_pred CCcccccceeccCcccCcccCHHHHHHHHHHhhccccccHHHHHHHHHHHHhhcC
Confidence 56899877753 6789999999998833344566777777765554444
No 27
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=47.32 E-value=1.9e+02 Score=24.98 Aligned_cols=82 Identities=7% Similarity=0.127 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCc-cchhHHHHHHHHHHHHhHHHHHHHhhhcCC------------H-HHHHHhhh
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDRE-AVKDEVIVDLVSRCRSNQKKLMQMLTTTGD------------E-ELLGRGLE 187 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~~-~~ddELIqELyetCrsmQpRI~~LIeetsD------------E-ElL~eLL~ 187 (543)
..+|..+++|+.-|..+...+...... ..-.+-+.++...+...-..|..+|..+.. + -.....=.
T Consensus 14 ~~~I~~i~~~v~~l~~l~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~~~~~~~r~~~~q~~~ 93 (117)
T smart00503 14 RANIQKISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRASGSASDRTRKAQTEK 93 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccCCHhhhHHHHHHHH
Confidence 578888888888888888876421110 111123344444444443333333332211 1 11223344
Q ss_pred cchHHHHHHHHHHHHh
Q 009098 188 LNDILQNLLAKHDAIA 203 (543)
Q Consensus 188 lNDdLn~VL~RYd~i~ 203 (543)
|-.++..++.+|..+-
T Consensus 94 L~~~f~~~m~~fq~~Q 109 (117)
T smart00503 94 LRKKFKEVMNEFQRLQ 109 (117)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5677788888887653
No 28
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=45.25 E-value=44 Score=36.71 Aligned_cols=67 Identities=16% Similarity=0.286 Sum_probs=41.4
Q ss_pred hhhhhhHHHhhh----c---HHHHHHHHHHHHHHHHHHHhcCCCCCccch---hHHHHHHHHHHHHhHHHHHHHhhh
Q 009098 109 LDETMATEVETL----S---FSSLDSMRDVMELLSDMLQAVNPSDREAVK---DEVIVDLVSRCRSNQKKLMQMLTT 175 (543)
Q Consensus 109 L~~sms~D~ekL----S---~sELevVrnNvkLLsEML~~~~Pg~~~~~d---dELIqELyetCrsmQpRI~~LIee 175 (543)
|++.+.+|..+. + +.||+.|.-.++-|.|+++...-....... .+.+.||-..|+.|..=|--|..+
T Consensus 294 LQ~rI~eEikkk~~kgs~gLLkEl~~ve~~vr~L~el~d~~~~p~~~e~~~ev~~~V~EL~~~~~~L~~GLdpLerq 370 (389)
T PF05633_consen 294 LQERINEEIKKKERKGSCGLLKELQQVEASVRELHELIDSFQFPLEEEKEEEVREAVEELARVCEALSQGLDPLERQ 370 (389)
T ss_pred HHHHHHHHHhhccccCcchHHHHHHHHHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHHHHHHHHHcccHHHHHH
Confidence 455555554332 1 689999999999999999987422221111 234567777777766555444433
No 29
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=44.47 E-value=33 Score=27.38 Aligned_cols=29 Identities=24% Similarity=0.386 Sum_probs=20.4
Q ss_pred HHHHHHHhh-cCCCHHHHHHHHHHHHHHHH
Q 009098 18 STKTFISLV-LQPDMQLRDKILVLLDSWQE 46 (543)
Q Consensus 18 FLnELVKLI-pK~~~~VreKILeLIQsWae 46 (543)
+|.+++..+ ...+++++.||..+|..|.+
T Consensus 30 ~l~~~~~~~~~~~~~~~~~kv~rll~iW~~ 59 (64)
T PF04818_consen 30 VLPDAFAHAYKNVDPEVRKKVQRLLNIWEE 59 (64)
T ss_dssp CHHHHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHhhC
Confidence 344444444 44488999999999999975
No 30
>cd00179 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain
Probab=43.97 E-value=1.8e+02 Score=26.37 Aligned_cols=82 Identities=10% Similarity=0.142 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCC-ccchhHHHHHHHHHHHHhHHHHHHHhhhcCC------------HH--HHHHhh
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDR-EAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD------------EE--LLGRGL 186 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~-~~~ddELIqELyetCrsmQpRI~~LIeetsD------------EE--lL~eLL 186 (543)
..+|..++.+++-|..+...+..... ...-.+-|.+|...+..+-..|-..|..+.. +. --...=
T Consensus 12 ~~~i~~i~~~v~~l~~l~~~~~t~~~~~~~~~~~l~~~~~~~~~~~~~ik~~lk~l~~~~~~~~~~~~s~~~r~~~~q~~ 91 (151)
T cd00179 12 RGNIDKISEDVEELQKLHSQLLTAPDADPELKQELESLVQEIKKLAKEIKGKLKELEESNEQNEALNGSSVDRIRKTQHS 91 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHH
Confidence 56788888888888877776532111 1111223344444444444444444433221 01 113344
Q ss_pred hcchHHHHHHHHHHHHh
Q 009098 187 ELNDILQNLLAKHDAIA 203 (543)
Q Consensus 187 ~lNDdLn~VL~RYd~i~ 203 (543)
.|..++..++.+|..+-
T Consensus 92 ~L~~~f~~~m~~fq~~Q 108 (151)
T cd00179 92 GLSKKFVEVMTEFNKAQ 108 (151)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57788899999997554
No 31
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=43.84 E-value=61 Score=26.31 Aligned_cols=51 Identities=25% Similarity=0.294 Sum_probs=36.7
Q ss_pred chhHHHHHHHHHHHHhHHHHHH---Hhh-hcC--CHHHHHHhhhcchHHHHHHHHHH
Q 009098 150 VKDEVIVDLVSRCRSNQKKLMQ---MLT-TTG--DEELLGRGLELNDILQNLLAKHD 200 (543)
Q Consensus 150 ~ddELIqELyetCrsmQpRI~~---LIe-ets--DEElL~eLL~lNDdLn~VL~RYd 200 (543)
.+.|-+.+|...|...-.+|+. .+. ... ..++|.++|.++..|...+....
T Consensus 8 ~dWe~l~~l~~~R~~ll~~l~~~~~~~~~~~~~~~~~~l~~Il~~d~~i~~ll~~~~ 64 (84)
T PF05400_consen 8 GDWEELEELLDERQELLERLFEEQAALSPPEQEELRELLRRILELDQEIRALLQARR 64 (84)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHCHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHHhhccccCChhhHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 4688999999999888877777 111 111 15788889999999988887654
No 32
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=41.55 E-value=58 Score=33.19 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=34.3
Q ss_pred hHHHHHHHhhhcCCHHHHHHhhhcchHHHHHHHHHHHHhcCCCC
Q 009098 165 NQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLPI 208 (543)
Q Consensus 165 mQpRI~~LIeetsDEElL~eLL~lNDdLn~VL~RYd~i~sG~~~ 208 (543)
+|+.-.+++.+.-||.+-+++|.+-|.|..+++-+..+.+|..-
T Consensus 112 ~q~~Y~~~l~E~KDdt~EG~Iv~~ADkidal~e~~~Ei~~GN~E 155 (215)
T PF12917_consen 112 FQEAYRRRLKEGKDDTLEGQIVKAADKIDALYECFGEIQKGNPE 155 (215)
T ss_dssp GHHHHHHHHS---SSSHHHHHHHHHHHHHHHHHHHHHHHTT-S-
T ss_pred HHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHcCCCc
Confidence 56666677777777888899999999999999999999999975
No 33
>PF00618 RasGEF_N: RasGEF N-terminal motif; InterPro: IPR000651 The crystal structure of the guanine nucleotide exchange factor (GEF) region of human Sos1 complexes with Ras has been solved []. The structure consists of two distinct alpha helical structural domains: the N-terminal domain which seems to have a purely structural role and the C-terminal domain which is sufficient for catalytic activity and contains all residues that interact with Ras. A main feature of the catalytic domain is the protrusion of a helical hairpin important for the nucleotide-exchange mechanism. The N-terminal domain is likely to be important for the stability and correct placement of the hairpin structure. This entry represents a domain found in several GEF for Ras-like small GTPases which lies N-terminal to the RasGef (Cdc25-like) domain. ; GO: 0005085 guanyl-nucleotide exchange factor activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3CF6_E 2BYV_E 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=41.14 E-value=1.1e+02 Score=26.21 Aligned_cols=42 Identities=19% Similarity=0.396 Sum_probs=30.9
Q ss_pred HHHhhhcHHHHHHHHHhh-cCCC--------------HHHHHHHHHHHHHHHHHhCC
Q 009098 9 VQRLFRPSASTKTFISLV-LQPD--------------MQLRDKILVLLDSWQEAFGG 50 (543)
Q Consensus 9 VH~eIAskeFLnELVKLI-pK~~--------------~~VreKILeLIQsWaeAF~~ 50 (543)
++.-+...++|+.|+.++ -... ..+|.||+.+|..|-+.+..
T Consensus 33 yr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi~~~~~ 89 (104)
T PF00618_consen 33 YRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWIENYPD 89 (104)
T ss_dssp HHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred hHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHChH
Confidence 344567889999999888 2211 13888999999999999886
No 34
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=40.99 E-value=53 Score=28.32 Aligned_cols=39 Identities=21% Similarity=0.237 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcC
Q 009098 28 QPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 69 (543)
Q Consensus 28 K~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kG 69 (543)
+|.-.++++|++||+.|.+..++.. ..+....+-|+.-|
T Consensus 36 ~~~~dl~eq~~~mL~~W~~~~~~~~---atv~~L~~AL~~~g 74 (86)
T cd08779 36 NNRDDLDEQIFDMLFSWAQRQAGDP---DAVGKLVTALEESG 74 (86)
T ss_pred HCccCHHHHHHHHHHHHHHhcCCCc---hHHHHHHHHHHHcC
Confidence 3444799999999999999887642 23555566665554
No 35
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=40.22 E-value=38 Score=33.99 Aligned_cols=37 Identities=22% Similarity=0.304 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCCc-hHHHHHHHHHHcCCCC
Q 009098 32 QLRDKILVLLDSWQEAFGGPGGKHP-QYYWAYEDLRRYGVQF 72 (543)
Q Consensus 32 ~VreKILeLIQsWaeAF~~~~~klp-~i~eaY~~LK~kGV~F 72 (543)
+|-+-+|.+-..|.+ ..+- .| .|++||+.||.+|-.+
T Consensus 148 EvVEeAl~V~~~~~e---~~PL-qP~HIREA~rrL~~qgk~~ 185 (195)
T KOG3219|consen 148 EVVEEALDVREEWGE---SGPL-QPKHIREAYRRLKLQGKLP 185 (195)
T ss_pred HHHHHHHHHHHHhcc---CCCC-CcHHHHHHHHHHHhcCCCC
Confidence 889999999999998 2222 45 5999999999999766
No 36
>PRK09458 pspB phage shock protein B; Provisional
Probab=40.10 E-value=36 Score=29.48 Aligned_cols=25 Identities=4% Similarity=0.254 Sum_probs=21.6
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHH
Q 009098 148 EAVKDEVIVDLVSRCRSNQKKLMQM 172 (543)
Q Consensus 148 ~~~ddELIqELyetCrsmQpRI~~L 172 (543)
+.+|...+++|+++.++|+.||..|
T Consensus 37 s~~d~~~L~~L~~~A~rm~~RI~tL 61 (75)
T PRK09458 37 SQEEQQRLAQLTEKAERMRERIQAL 61 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557788999999999999999765
No 37
>PF02203 TarH: Tar ligand binding domain homologue; InterPro: IPR003122 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 ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.; GO: 0004888 transmembrane signaling receptor activity, 0006935 chemotaxis, 0007165 signal transduction, 0016020 membrane; PDB: 2ASR_A 3ATP_A 2D4U_A 2LIG_A 1VLS_A 1LIH_A 1WAT_B 1VLT_B 1WAS_A 1JMW_A.
Probab=39.80 E-value=2.1e+02 Score=25.97 Aligned_cols=78 Identities=14% Similarity=0.140 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCcc-chhHHHHHHHHHHHH-hHHHHHHHhhhcCCHHHHHHhhhc-chHHHHHHHH
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDREA-VKDEVIVDLVSRCRS-NQKKLMQMLTTTGDEELLGRGLEL-NDILQNLLAK 198 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~~~-~ddELIqELyetCrs-mQpRI~~LIeetsDEElL~eLL~l-NDdLn~VL~R 198 (543)
...|+.++..++-..+.+..+....... .+.+++.+|.+.-+. .+..|..++...... .+.+.+.+ +..++..+..
T Consensus 81 ~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~al~~~-d~~~~~~~~~~~~~~~~~~ 159 (171)
T PF02203_consen 81 AELLARAEQNLEQAEQAFDAFKALPHASPEERALADELEASFDAYLQQALDPLLAALRAG-DIAAFMQLPNEKIQPLFDA 159 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCS---GTGGHHHHHHHHHHHHH-HHHHHHHHHHHHHTT--HHHHHHSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHCC-CHHHHHHHHHHhcchhHHH
Confidence 4567777777777777777765333333 567788888888877 667777777654331 12223333 5555555555
Q ss_pred HH
Q 009098 199 HD 200 (543)
Q Consensus 199 Yd 200 (543)
|.
T Consensus 160 ~~ 161 (171)
T PF02203_consen 160 FT 161 (171)
T ss_dssp HH
T ss_pred HH
Confidence 54
No 38
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=38.90 E-value=38 Score=29.15 Aligned_cols=26 Identities=4% Similarity=0.198 Sum_probs=22.2
Q ss_pred CccchhHHHHHHHHHHHHhHHHHHHH
Q 009098 147 REAVKDEVIVDLVSRCRSNQKKLMQM 172 (543)
Q Consensus 147 ~~~~ddELIqELyetCrsmQpRI~~L 172 (543)
-+.+|.+.++||+++.++|+.||..|
T Consensus 36 Ls~~d~~~L~~L~~~a~rm~eRI~tL 61 (75)
T PF06667_consen 36 LSEEDEQRLQELYEQAERMEERIETL 61 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999999999865
No 39
>PF12993 DUF3877: Domain of unknown function, E. rectale Gene description (DUF3877); InterPro: IPR024539 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=38.34 E-value=22 Score=35.07 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=33.6
Q ss_pred HHHhhhcHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHhC
Q 009098 9 VQRLFRPSASTKTFISLVLQPDMQLRDKILVLLDSWQEAFG 49 (543)
Q Consensus 9 VH~eIAskeFLnELVKLIpK~~~~VreKILeLIQsWaeAF~ 49 (543)
||..+...+||.+||.+|-+ +---.+.|+++...|++...
T Consensus 87 Vhe~~~~~eFik~lIe~v~~-hgcT~e~I~~~F~~ys~~~~ 126 (175)
T PF12993_consen 87 VHEHTKENEFIKELIELVGK-HGCTLEDILELFHKYSDNVH 126 (175)
T ss_pred HHhcCCCCHHHHHHHHHHhc-CCcCHHHHHHHHHHhcCCeE
Confidence 89999999999999999954 33467889999999986543
No 40
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=38.18 E-value=37 Score=29.41 Aligned_cols=44 Identities=20% Similarity=0.273 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHH------------HHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCC
Q 009098 32 QLRDKILVLLDS------------WQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 78 (543)
Q Consensus 32 ~VreKILeLIQs------------WaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~d 78 (543)
.+++|||.+|+. -+..| + .. ...++++-+.|-.+|+.|...|++
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l-~-~~-~~~v~~al~~L~~eG~IYsTiDd~ 102 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQL-G-MS-ENEVRKALDFLSNEGHIYSTIDDD 102 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHS-T-S--HHHHHHHHHHHHHTTSEEESSSTT
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHh-C-cC-HHHHHHHHHHHHhCCeEecccCCC
Confidence 678888888887 11122 1 01 346899999999999999887764
No 41
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=38.01 E-value=1.2e+02 Score=26.75 Aligned_cols=40 Identities=13% Similarity=0.393 Sum_probs=30.1
Q ss_pred hhhcHHHHHHHHHhh-cC-CC---------HHHHHHHHHHHHHHHHHhCCC
Q 009098 12 LFRPSASTKTFISLV-LQ-PD---------MQLRDKILVLLDSWQEAFGGP 51 (543)
Q Consensus 12 eIAskeFLnELVKLI-pK-~~---------~~VreKILeLIQsWaeAF~~~ 51 (543)
=+...++|+.|+.++ .. .. ..+|.||+.+|+.|-+.+..+
T Consensus 39 F~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~d 89 (127)
T smart00229 39 FITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQD 89 (127)
T ss_pred hCCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcc
Confidence 345678888888888 21 11 248999999999999998863
No 42
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.74 E-value=37 Score=38.34 Aligned_cols=130 Identities=17% Similarity=0.213 Sum_probs=0.0
Q ss_pred hcHHHHHHHHHhh--cCCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCCCCCCCCCCCCCCCCCCCCCCc
Q 009098 14 RPSASTKTFISLV--LQPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDAAPIFTPPVSHPT 91 (543)
Q Consensus 14 AskeFLnELVKLI--pK~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV~FP~~~~daaPI~TPp~S~Pe 91 (543)
..|+=++-.+||. +..+.++..|||.++-.-. -||++|+.--.-++.. ...
T Consensus 367 Lqk~~ad~~~KI~~~k~r~~~Ls~RiLRv~ikqe------------------ilr~~G~~L~~~EE~L---------r~K 419 (508)
T KOG3091|consen 367 LQKHHADAVAKIEEAKNRHVELSHRILRVMIKQE------------------ILRKRGYALTPDEEEL---------RAK 419 (508)
T ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH------------------HHhccCCcCCccHHHH---------HHH
Q ss_pred cchhhcccCCCCCCcchhhhhhhHHHhhhc-HHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHH-
Q 009098 92 LGQAQASYGMPSNSSRRLDETMATEVETLS-FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKL- 169 (543)
Q Consensus 92 ~~~a~~~~gSP~~~d~~L~~sms~D~ekLS-~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI- 169 (543)
++.-.+....|....++|++.+...-.+-+ +.-.+++..--+++.||+.++ ..+.|.|.-|++.|+.+++-|
T Consensus 420 ldtll~~ln~Pnq~k~Rl~~L~e~~r~q~~~~~~~~~~~iD~~~~~e~~e~l------t~~~e~l~~Lv~Ilk~d~edi~ 493 (508)
T KOG3091|consen 420 LDTLLAQLNAPNQLKARLDELYEILRMQNSQLKLQESYWIDFDKLIEMKEHL------TQEQEALTKLVNILKGDQEDIK 493 (508)
T ss_pred HHHHHHHhcChHHHHHHHHHHHHHHHhhcchhccccceeechhhhHHHHHHH------HHHHHHHHHHHHHHHhHHHHHH
Q ss_pred HHHhhhc
Q 009098 170 MQMLTTT 176 (543)
Q Consensus 170 ~~LIeet 176 (543)
..|++.+
T Consensus 494 ~~l~E~~ 500 (508)
T KOG3091|consen 494 HQLIEDL 500 (508)
T ss_pred HHHHhhH
No 43
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=33.27 E-value=2.5e+02 Score=26.73 Aligned_cols=17 Identities=0% Similarity=0.180 Sum_probs=6.8
Q ss_pred HHHHHhHHHHHHHhhhc
Q 009098 160 SRCRSNQKKLMQMLTTT 176 (543)
Q Consensus 160 etCrsmQpRI~~LIeet 176 (543)
..|+..+.++..+....
T Consensus 151 ~~~~~~~~~~~~~~~~~ 167 (191)
T PF04156_consen 151 KELQDSREEVQELRSQL 167 (191)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333334444444433
No 44
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=32.45 E-value=76 Score=34.44 Aligned_cols=37 Identities=8% Similarity=0.230 Sum_probs=25.5
Q ss_pred hhcHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHhC
Q 009098 13 FRPSASTKTFISLVLQPDMQLRDKILVLLDSWQEAFG 49 (543)
Q Consensus 13 IAskeFLnELVKLIpK~~~~VreKILeLIQsWaeAF~ 49 (543)
|-.++||++|..+.......-+.|++.||....+.+.
T Consensus 273 l~d~~fl~~m~~~~~~~~~~~~~~~~~lL~~~~~E~~ 309 (374)
T TIGR00308 273 LHDKEFIEEVLRIAEEKEYGTRKRVLKMLSLIKNELS 309 (374)
T ss_pred cCCHHHHHHHHHhhhhccccchHHHHHHHHHHHhccC
Confidence 4468999999888732222356678888887776654
No 45
>PF04961 FTCD_C: Formiminotransferase-cyclodeaminase; InterPro: IPR007044 Enzymes containing the cyclodeaminase domain function in channeling one-carbon units to the folate pool. In most cases, this domain catalyses the cyclisation of formimidoyltetrahydrofolate to methenyltetrahydrofolate as shown in reaction (1). In the methylotrophic bacterium Methylobacterium extorquens, however, it catalyses the interconversion of formyltetrahydrofolate and methylenetetrahydrofolate [],as shown in reaction (2) (1) 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH(3) (2) 10- formyltetrahydrofolate = 5,10-methenyltetrahydrofolate + H(2)O In prokaryotes, this domain mostly occurs on its own, while in eukaryotes it is fused to a glutamate formiminotransferase domain (which catalyses the previous step in the pathway) to form the bifunctional enzyme formiminotransferase-cyclodeaminase []. The eukaryotic enzyme is a circular tetramer of homodimers [], while the prokaryotic enzyme is a dimer [, ]. The crystal structure of the cyclodeaminase enzyme (Q9X1P6 from SWISSPROT) from Thermaotogoa maritima has been studied []. It is a homodimer, where each monomer is composed of six alpha helices arranged in an up and down helical bundle, forming a novel fold. The location of the active site is not known, but sequence alignments revealed two clusters of conserved residues located in a deep pocket within the dimmer interface. This pocket was large enough to accommodate the reaction product and it was postulated that this is the active site.; GO: 0003824 catalytic activity, 0044237 cellular metabolic process; PDB: 2PFD_C 1O5H_B.
Probab=31.10 E-value=1.6e+02 Score=28.74 Aligned_cols=41 Identities=10% Similarity=0.302 Sum_probs=32.2
Q ss_pred HHHHHHhcCCCCCc-cchhHHHHHHHHHHHHhHHHHHHHhhh
Q 009098 135 LSDMLQAVNPSDRE-AVKDEVIVDLVSRCRSNQKKLMQMLTT 175 (543)
Q Consensus 135 LsEML~~~~Pg~~~-~~ddELIqELyetCrsmQpRI~~LIee 175 (543)
|..|.-++.-+.+. .+-.+.++++.+.|+..+.++.+|+.+
T Consensus 33 L~~Mv~~lT~gkk~~~~~~~~~~~~~~~~~~~~~~ll~l~d~ 74 (184)
T PF04961_consen 33 LGSMVANLTLGKKKYEDVEEELKEIIEKLEELREELLDLADE 74 (184)
T ss_dssp HHHHHHHCTTTSTTSGGGHHHHHHHHHHHHHHHHHHHCHHHH
T ss_pred HHHHHHHHhCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66788887765543 345678999999999999999999976
No 46
>PF01895 PhoU: PhoU domain; InterPro: IPR008170 This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle []. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect; suggesting that the protein has some secondary function []. ; PDB: 2I0M_A 1T72_B 1T8B_A 1SUM_B 1VCT_A 2BKN_A 2BKP_A 2BKO_A.
Probab=30.42 E-value=2.1e+02 Score=22.72 Aligned_cols=15 Identities=33% Similarity=0.459 Sum_probs=7.5
Q ss_pred HHHHHHHHHHHHhcC
Q 009098 129 RDVMELLSDMLQAVN 143 (543)
Q Consensus 129 rnNvkLLsEML~~~~ 143 (543)
+...++|.+++..+.
T Consensus 6 ~~~~~~l~~~~~~~~ 20 (88)
T PF01895_consen 6 ELVEEMLDDAIEAFE 20 (88)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 334445555555553
No 47
>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=30.15 E-value=2.5e+02 Score=25.93 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=19.4
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhcCC
Q 009098 119 TLSFSSLDSMRDVMELLSDMLQAVNP 144 (543)
Q Consensus 119 kLS~sELevVrnNvkLLsEML~~~~P 144 (543)
.+|.+||+..-++=+.|.+++..++.
T Consensus 3 ~lS~~eL~~Ll~d~~~l~~~v~~l~~ 28 (150)
T PF07200_consen 3 DLSTEELQELLSDEEKLDAFVKSLPQ 28 (150)
T ss_dssp S-TTHHHHHHHHH-HHHHHHGGGGS-
T ss_pred cCCHHHHHHHHcCHHHHHHHHHcCHH
Confidence 56778898888899999998888753
No 48
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=30.02 E-value=1e+02 Score=26.60 Aligned_cols=42 Identities=19% Similarity=0.388 Sum_probs=32.1
Q ss_pred HHhhhcHHHHHHHHHhh--cCC------------CHHHHHHHHHHHHHHHHHhCCC
Q 009098 10 QRLFRPSASTKTFISLV--LQP------------DMQLRDKILVLLDSWQEAFGGP 51 (543)
Q Consensus 10 H~eIAskeFLnELVKLI--pK~------------~~~VreKILeLIQsWaeAF~~~ 51 (543)
+.-+...++|+.|+.++ +.. ...+|.||+.+|..|-+.+...
T Consensus 29 rsF~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~~~~d 84 (122)
T cd06224 29 RSFTTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYD 84 (122)
T ss_pred hhhCCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 33455778899999988 322 1368999999999999998864
No 49
>PF01544 CorA: CorA-like Mg2+ transporter protein; InterPro: IPR002523 The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli [, ]. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. Transporter ZntB mediates efflux of zinc ions [].; GO: 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0055085 transmembrane transport, 0016020 membrane; PDB: 2HN1_A 3NWI_D 3NVO_B 3CK6_A 2IUB_E 2BBJ_E 2HN2_A 2BBH_A.
Probab=29.69 E-value=2.5e+02 Score=27.72 Aligned_cols=77 Identities=14% Similarity=0.190 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHHHHHHHHh-cC---CCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCC-HHHHHHhhhcchHHHHHH
Q 009098 122 FSSLDSMRDVMELLSDMLQA-VN---PSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-EELLGRGLELNDILQNLL 196 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~-~~---Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsD-EElL~eLL~lNDdLn~VL 196 (543)
+.+|...+..+.-+.++|.. +. .........+.+.+++..|+.+..++..+.+.+.. .+.... .+|.++|+++
T Consensus 157 ~~~l~~l~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~n~~m 234 (292)
T PF01544_consen 157 RRELSRLRRSLSPLREVLQRLLRRDDSPFISDEDKEYLRDLLDRIERLLERAESLRERLESLQDLYQS--KLSNRQNRVM 234 (292)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCCSTTSHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHTCHHHHHH
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHH
Confidence 34555555555555555522 21 11122233456889999999888888888777666 333333 2455577777
Q ss_pred HHHH
Q 009098 197 AKHD 200 (543)
Q Consensus 197 ~RYd 200 (543)
.+.-
T Consensus 235 ~~LT 238 (292)
T PF01544_consen 235 KVLT 238 (292)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6643
No 50
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=29.33 E-value=67 Score=27.61 Aligned_cols=25 Identities=4% Similarity=0.228 Sum_probs=21.9
Q ss_pred ccchhHHHHHHHHHHHHhHHHHHHH
Q 009098 148 EAVKDEVIVDLVSRCRSNQKKLMQM 172 (543)
Q Consensus 148 ~~~ddELIqELyetCrsmQpRI~~L 172 (543)
+.+|.+.++||+++.++|+.||.-|
T Consensus 37 s~~d~~~L~~L~~~a~rm~eRI~tL 61 (75)
T TIGR02976 37 STDDQALLQELYAKADRLEERIDTL 61 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999999765
No 51
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=28.37 E-value=1.2e+02 Score=26.31 Aligned_cols=39 Identities=18% Similarity=0.339 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCC
Q 009098 28 QPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 70 (543)
Q Consensus 28 K~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV 70 (543)
++...++++|.+|+..|.+..+. ..-+.....-|++-|+
T Consensus 36 ~~p~~l~eQv~~mL~~W~~r~G~----~ATv~~L~~aL~~~~~ 74 (83)
T cd08319 36 NHPHNVQSQIVEALVKWRQRFGK----KATVQSLIQSLKAVEV 74 (83)
T ss_pred hCCCCHHHHHHHHHHHHHHhcCC----CCcHHHHHHHHHHcCC
Confidence 34447999999999999999875 3456667777777775
No 52
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=27.90 E-value=2.3e+02 Score=27.93 Aligned_cols=64 Identities=22% Similarity=0.275 Sum_probs=41.9
Q ss_pred HHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcC-C---HHHHHHhhhcchHHHHHHHHHHHHhcCCC
Q 009098 134 LLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG-D---EELLGRGLELNDILQNLLAKHDAIASGLP 207 (543)
Q Consensus 134 LLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeets-D---EElL~eLL~lNDdLn~VL~RYd~i~sG~~ 207 (543)
.|..||...... .... -.+..+||.+| +-+||-+++ | -++| |+.|=|++..+|.+|..+.....
T Consensus 41 ~Ld~~L~~~~ar-~~gI-cpvr~~ly~~~------F~ELIRQVTi~C~ERGlL--L~rvrde~~~~l~~y~~l~~s~~ 108 (189)
T PF10211_consen 41 WLDKMLQQRQAR-ETGI-CPVREELYSQC------FDELIRQVTIDCPERGLL--LLRVRDEYRMTLDAYQTLYESSI 108 (189)
T ss_pred HHHHHHHHhcCC-cccc-cHHHHHHHHHH------HHHHHHHHHhCcHHHhHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 555666665332 2222 56778899999 456777654 2 3333 67888999999999987775543
No 53
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=26.96 E-value=56 Score=31.86 Aligned_cols=11 Identities=27% Similarity=0.440 Sum_probs=7.8
Q ss_pred CCCCCCCCCCC
Q 009098 422 AYPPPPWAPTP 432 (543)
Q Consensus 422 ~yp~ppwa~~~ 432 (543)
.||+|.|+++.
T Consensus 144 ~~~~~~~~~~~ 154 (168)
T PRK06863 144 SRPAPQQAAPQ 154 (168)
T ss_pred cccCccccccc
Confidence 37788888663
No 54
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=26.96 E-value=3e+02 Score=21.27 Aligned_cols=48 Identities=13% Similarity=0.119 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCccch-hHHHHHHHHHHHHhHHHHHHH
Q 009098 123 SSLDSMRDVMELLSDMLQAVNPSDREAVK-DEVIVDLVSRCRSNQKKLMQM 172 (543)
Q Consensus 123 sELevVrnNvkLLsEML~~~~Pg~~~~~d-dELIqELyetCrsmQpRI~~L 172 (543)
+||..--+.+..+.++|... ......+ .+.+..+...|+.|...|-+|
T Consensus 11 Helr~PL~~i~~~~~~l~~~--~~~~~~~~~~~l~~i~~~~~~l~~li~~l 59 (68)
T PF00512_consen 11 HELRNPLTAIRGYLELLERD--SDLDPEQLREYLDRIRSAADRLNELINDL 59 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHCS--SCC-HHHCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56665556666666666662 1122222 344555555555444444443
No 55
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=26.67 E-value=98 Score=26.59 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=25.9
Q ss_pred cHHHHHHHHHhh-cCCCHHHHHHHHHHHHHHHHH
Q 009098 15 PSASTKTFISLV-LQPDMQLRDKILVLLDSWQEA 47 (543)
Q Consensus 15 skeFLnELVKLI-pK~~~~VreKILeLIQsWaeA 47 (543)
.++||.=+..++ ...+.+||++||+.|..=-.+
T Consensus 15 Q~~fL~Pf~~i~~~~~~~~vre~il~ci~qil~~ 48 (86)
T PF09324_consen 15 QKDFLKPFEYIMSNNPSIDVRELILECILQILQS 48 (86)
T ss_pred HHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHH
Confidence 468888899998 677889999999886655443
No 56
>PHA02334 hypothetical protein
Probab=26.48 E-value=2.2e+02 Score=23.81 Aligned_cols=37 Identities=24% Similarity=0.230 Sum_probs=31.1
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHh
Q 009098 149 AVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRG 185 (543)
Q Consensus 149 ~~ddELIqELyetCrsmQpRI~~LIeetsDEElL~eL 185 (543)
.++.|+-..|++-|--.-.+.++|-....||++|+.+
T Consensus 21 Pd~~elgeklieici~il~kaVklT~TdmDD~ll~~v 57 (64)
T PHA02334 21 PDDEELGEKLIEICLLILGKAVKLTKTDMDDELLEVV 57 (64)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHhccCcchHHHHHHH
Confidence 5678999999999999999999998888888877643
No 57
>COG5278 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=26.41 E-value=3.4e+02 Score=27.50 Aligned_cols=73 Identities=18% Similarity=0.151 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCC--ccchhHHHHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHH
Q 009098 123 SSLDSMRDVMELLSDMLQAVNPSDR--EAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNL 195 (543)
Q Consensus 123 sELevVrnNvkLLsEML~~~~Pg~~--~~~ddELIqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~V 195 (543)
+--+......+|++.|++.-+-... -..+++.+...++.-+.+.+++-+|-.-+.||+.+.+.|..+..++..
T Consensus 45 ~t~~~~~a~~~l~s~~~~~esgqRGYLLTG~~~yL~py~~a~~~~~~~~~~l~~l~~d~p~~~~~l~~l~~~i~~ 119 (207)
T COG5278 45 ETQQVLAAALDLLSAVSDAESGQRGYLLTGNDEYLEPYEEATEELDQKLEELRALTADDPELLESLDDLEPLIQW 119 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCcceeecCCHhhhhHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 3446667777888999887653221 235789999999999999999999998888866666777766665443
No 58
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=25.90 E-value=75 Score=28.68 Aligned_cols=31 Identities=13% Similarity=0.193 Sum_probs=22.2
Q ss_pred HHHHHHHHHhh-cCCCHHHHHHHHHHHHHHHH
Q 009098 16 SASTKTFISLV-LQPDMQLRDKILVLLDSWQE 46 (543)
Q Consensus 16 keFLnELVKLI-pK~~~~VreKILeLIQsWae 46 (543)
+.||+.|+++- .+..++|.++|.+||+.--+
T Consensus 7 k~FL~tLi~las~~~spev~~~Vr~LV~~L~~ 38 (96)
T PF07531_consen 7 KNFLNTLIQLASDKQSPEVGENVRELVQNLVD 38 (96)
T ss_dssp HHHHHHHHHHHCCSC-CCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHc
Confidence 68999999999 64566666666666666543
No 59
>PHA03377 EBNA-3C; Provisional
Probab=25.81 E-value=6.2e+02 Score=30.60 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCCCC
Q 009098 422 AYPPPPWAPTPGYF 435 (543)
Q Consensus 422 ~yp~ppwa~~~~~~ 435 (543)
+|.+|+|+.-+++.
T Consensus 831 ~h~~p~Wdp~a~h~ 844 (1000)
T PHA03377 831 PHLPPQWDGSAGHG 844 (1000)
T ss_pred CCCCCCCCCCCCCC
Confidence 45568888766544
No 60
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 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. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=25.31 E-value=1.9e+02 Score=26.42 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=30.5
Q ss_pred cchhHHHHHHHHHHHHhHHHHHHHhhh----cCCHHHHHHhhhcchHHHHHH
Q 009098 149 AVKDEVIVDLVSRCRSNQKKLMQMLTT----TGDEELLGRGLELNDILQNLL 196 (543)
Q Consensus 149 ~~ddELIqELyetCrsmQpRI~~LIee----tsDEElL~eLL~lNDdLn~VL 196 (543)
.++...|.+....|..|-.|+=.||.. +.+|+.+.+||++.--+-+.|
T Consensus 31 ~eeK~~i~~~l~~~~~m~~~vd~li~~f~~lt~ne~~~k~LlqMr~~~~~q~ 82 (115)
T PF05397_consen 31 PEEKAAIRQQLQEIQDMLARVDSLIPWFYKLTKNEENTKRLLQMRIMLKEQF 82 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH
Confidence 344555666666666666666666665 455777777777666665555
No 61
>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=24.90 E-value=2.9e+02 Score=27.09 Aligned_cols=79 Identities=15% Similarity=0.279 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCcc--chhHHHHHHHHHHHHhHHHHHHHhhhcC----CHHHHHHhhhcchHHHHH
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDREA--VKDEVIVDLVSRCRSNQKKLMQMLTTTG----DEELLGRGLELNDILQNL 195 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~~~--~ddELIqELyetCrsmQpRI~~LIeets----DEElL~eLL~lNDdLn~V 195 (543)
.+-.+.+..-+.+|.+|+..+..++... ....-|.+|-..|...+.+|...+..+- |- ++++.+.+.+.++
T Consensus 17 ~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~~~fitP~dR---eDi~~L~~~lD~I 93 (216)
T TIGR00153 17 RQHIEKVGECVQLLIKSFELLKSGNNEKDEELRKEIIEIEHEADEIKREIRLNLEKGAFLPNDR---RDLLELAELLDEI 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccCcCcH---HHHHHHHHHHHHH
Confidence 3467888999999999999885333211 2334577888899999999999887632 31 3345555666666
Q ss_pred HHHHHHHh
Q 009098 196 LAKHDAIA 203 (543)
Q Consensus 196 L~RYd~i~ 203 (543)
+..=+...
T Consensus 94 ~D~i~~~a 101 (216)
T TIGR00153 94 LDSLEHAA 101 (216)
T ss_pred HHHHHHHH
Confidence 65554443
No 62
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=24.53 E-value=4e+02 Score=23.41 Aligned_cols=48 Identities=6% Similarity=0.113 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhh
Q 009098 127 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLT 174 (543)
Q Consensus 127 vVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIe 174 (543)
.+.....-+.+.|..+........+.+++.++.+..+..+....+++.
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~ 130 (181)
T PF12729_consen 83 EIDEARAEIDEALEEYEKLILSPEEKQLLEEFKEAWKAYRKLRDQVIE 130 (181)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444555555433223334556666666666555544444443
No 63
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.12 E-value=3.4e+02 Score=28.40 Aligned_cols=67 Identities=24% Similarity=0.264 Sum_probs=46.6
Q ss_pred CCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCC-HHHHHHhh----hcchHHHHHHHHHHHHhcCCCCCCcc
Q 009098 145 SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-EELLGRGL----ELNDILQNLLAKHDAIASGLPIPTEV 212 (543)
Q Consensus 145 g~~~~~ddELIqELyetCrsmQpRI~~LIeetsD-EElL~eLL----~lNDdLn~VL~RYd~i~sG~~~~~e~ 212 (543)
+.+...+.+.+ +|....++.|+++.+|..++.+ |..+...= ..+-.|++-|+++.....--.+.+++
T Consensus 43 k~~~~~~~r~~-~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v~V~G~G 114 (247)
T COG3879 43 KGESVRRARDL-DLVKELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSVPVTGPG 114 (247)
T ss_pred cCcchhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHhccCCCcCCc
Confidence 34444555555 8999999999999999999877 66555444 56666666666776666655555554
No 64
>COG5394 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.90 E-value=1.4e+02 Score=29.65 Aligned_cols=47 Identities=21% Similarity=0.355 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCc-------cchhHHHHHHHHHHHHhHHHHHHH
Q 009098 126 DSMRDVMELLSDMLQAVNPSDRE-------AVKDEVIVDLVSRCRSNQKKLMQM 172 (543)
Q Consensus 126 evVrnNvkLLsEML~~~~Pg~~~-------~~ddELIqELyetCrsmQpRI~~L 172 (543)
|-+|.|+++|..|+..+.|-... ....+-++||..+.+.||+++-+|
T Consensus 140 eq~rrn~~mf~~aM~~f~pf~~~pa~~~~~~~~~~d~~~lk~ql~a~Q~kldkl 193 (193)
T COG5394 140 EQIRRNMEMFQQAMQMFSPFAKAPAPKEAPKPMSDDLDELKGQLRAMQPKLDKL 193 (193)
T ss_pred HHHHHhHHHHHHHHHhcCcccCCCCccccCccchhHHHHHHHHHHHhhhhhccC
Confidence 56899999999999877652211 112233999999999999998653
No 65
>COG4229 Predicted enolase-phosphatase [Energy production and conversion]
Probab=23.89 E-value=57 Score=33.06 Aligned_cols=48 Identities=19% Similarity=0.253 Sum_probs=26.3
Q ss_pred HHHHHhh-cCCCHHHHHHHHHHHH--HHHHHhCCCCCCCchHHHHHHHHHH
Q 009098 20 KTFISLV-LQPDMQLRDKILVLLD--SWQEAFGGPGGKHPQYYWAYEDLRR 67 (543)
Q Consensus 20 nELVKLI-pK~~~~VreKILeLIQ--sWaeAF~~~~~klp~i~eaY~~LK~ 67 (543)
++||.++ .=-+..+|+.+|..+| -|+..|.+..-+-+.|-|+|+.||+
T Consensus 64 E~lva~~~~wiaed~K~t~lK~lQG~iWa~Gy~sgelkahlypDav~~ik~ 114 (229)
T COG4229 64 EALVALLLEWIAEDSKDTPLKALQGMIWAHGYESGELKAHLYPDAVQAIKR 114 (229)
T ss_pred HHHHHHHHHHHhcccccchHHHHHhHHHHhccccCccccccCHhHHHHHHH
Confidence 3344444 3233455666666665 4888887643333446666666654
No 66
>cd05132 RasGAP_GAPA GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function.
Probab=23.83 E-value=1.5e+02 Score=31.36 Aligned_cols=51 Identities=22% Similarity=0.271 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcC
Q 009098 127 SMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG 177 (543)
Q Consensus 127 vVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeets 177 (543)
.++.|+.++.-+|.++-.+.....++..++-|+.-+++...++.+++.++.
T Consensus 203 ~~rrnL~lIaKvLQ~lan~~~f~~ke~~m~pLn~fi~~~~~~~~~fl~~l~ 253 (331)
T cd05132 203 TARKNLTLIAKMLQNLANKPSFGDKEKWMVPLNPWIDENKEKVNNFLEELT 253 (331)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467888999999998865555555677788888777777888888777643
No 67
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=23.29 E-value=3.6e+02 Score=26.14 Aligned_cols=74 Identities=12% Similarity=0.165 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhc----CC-HHHHHHhhhcchHHHHHH
Q 009098 122 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT----GD-EELLGRGLELNDILQNLL 196 (543)
Q Consensus 122 ~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeet----sD-EElL~eLL~lNDdLn~VL 196 (543)
++.|+.++..++-|.+.+.... +.++...+++.|+-.+ +|++.|++- .+ +..+.--| |.+.+++
T Consensus 74 ~~~l~ea~~~i~~i~~~~~~i~-------~~~~~~~~~~~~~~~~-~I~~~v~~~P~~l~~a~~Fl~~yL---p~~~~l~ 142 (199)
T PF10112_consen 74 REILEEAKEKIRRIEKAIKRIR-------DLEMIEKVSRIEKIAR-RIFKYVEKDPERLTQARKFLYYYL---PTAVKLL 142 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC-------CHHHHHHHHHHHHHHH-HHHHHHHHCHHhHHHHHHHHHHHh---hHHHHHH
Confidence 5567777777777777766652 2333444444443333 344444432 22 33333333 5667777
Q ss_pred HHHHHHhcCC
Q 009098 197 AKHDAIASGL 206 (543)
Q Consensus 197 ~RYd~i~sG~ 206 (543)
++|..+.+..
T Consensus 143 ~kY~~l~~~~ 152 (199)
T PF10112_consen 143 EKYAELESQP 152 (199)
T ss_pred HHHHHHHhcc
Confidence 8887777543
No 68
>PF09388 SpoOE-like: Spo0E like sporulation regulatory protein; InterPro: IPR018540 Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure []. ; PDB: 2BZB_B 2C0S_A.
Probab=23.20 E-value=2.2e+02 Score=21.58 Aligned_cols=42 Identities=19% Similarity=0.322 Sum_probs=31.8
Q ss_pred HHHHHHHHhHHHHHHHhhhc--CCHHHHHHhhhcchHHHHHHHHHHHH
Q 009098 157 DLVSRCRSNQKKLMQMLTTT--GDEELLGRGLELNDILQNLLAKHDAI 202 (543)
Q Consensus 157 ELyetCrsmQpRI~~LIeet--sDEElL~eLL~lNDdLn~VL~RYd~i 202 (543)
+|...-+.+|.+|.+++..- .|+ +.|++.-+|..++..|.++
T Consensus 1 ~L~~~Ie~~R~~L~~~~~~~~l~~~----~vl~~Sq~LD~lI~~y~~~ 44 (45)
T PF09388_consen 1 ELLEEIEELRQELNELAEKKGLTDP----EVLELSQELDKLINEYQKL 44 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHCCTTCH----HHHHHHHHHHHHHHHHHCH
T ss_pred CHHHHHHHHHHHHHHHHHHcCCCCH----HHHHHHHHHHHHHHHHhhh
Confidence 45667778888999999864 454 4567888888998888764
No 69
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=23.10 E-value=1.5e+02 Score=28.33 Aligned_cols=50 Identities=16% Similarity=-0.002 Sum_probs=37.4
Q ss_pred hhcHHHHHHHHHhh-cC--CCHHHHHHHHHHHHHHHHHhCCCCCCCchHHHHHHHHHHcCC
Q 009098 13 FRPSASTKTFISLV-LQ--PDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 70 (543)
Q Consensus 13 IAskeFLnELVKLI-pK--~~~~VreKILeLIQsWaeAF~~~~~klp~i~eaY~~LK~kGV 70 (543)
++..++++.+.+++ .+ ....-|..||++|..= .+ +....+.|+.|+.+|.
T Consensus 4 ~~~~~~~~~~~~~L~~~GlR~T~qR~~IL~~l~~~----~~----hlSa~eI~~~L~~~~~ 56 (169)
T PRK11639 4 TTTQELLAQAEKLCAQRNVRLTPQRLEVLRLMSLQ----PG----AISAYDLLDLLREAEP 56 (169)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHhc----CC----CCCHHHHHHHHHhhCC
Confidence 45788999999998 33 3457889999999851 21 5677888999988883
No 70
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=23.06 E-value=2.2e+02 Score=23.72 Aligned_cols=18 Identities=11% Similarity=0.420 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHhcC
Q 009098 126 DSMRDVMELLSDMLQAVN 143 (543)
Q Consensus 126 evVrnNvkLLsEML~~~~ 143 (543)
-.||||+.++..||.-..
T Consensus 4 HRVkNnLq~i~sll~lq~ 21 (76)
T PF07568_consen 4 HRVKNNLQIISSLLRLQA 21 (76)
T ss_pred HhHHhHHHHHHHHHHHHH
Confidence 368999999999998653
No 71
>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=22.75 E-value=78 Score=29.75 Aligned_cols=20 Identities=25% Similarity=0.189 Sum_probs=9.5
Q ss_pred HHHHHhhhcchHHHHHHHHH
Q 009098 180 ELLGRGLELNDILQNLLAKH 199 (543)
Q Consensus 180 ElL~eLL~lNDdLn~VL~RY 199 (543)
+.+.++..+-++|+..+.||
T Consensus 191 ~~~~~l~~~a~~L~~~v~~F 210 (213)
T PF00015_consen 191 EAAEELSESAEELQELVDRF 210 (213)
T ss_dssp HHHHHHHHHHCCCCHHCHHH
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 33444444444555555444
No 72
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=22.39 E-value=1.4e+02 Score=29.36 Aligned_cols=42 Identities=19% Similarity=0.232 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhHHHHHH------Hhh-------hcCCHHHHHHhhhcchHHHH
Q 009098 153 EVIVDLVSRCRSNQKKLMQ------MLT-------TTGDEELLGRGLELNDILQN 194 (543)
Q Consensus 153 ELIqELyetCrsmQpRI~~------LIe-------etsDEElL~eLL~lNDdLn~ 194 (543)
|-..+|.+.|+.+...|-| |-. .+.|.++|.++|+++++|.+
T Consensus 56 eqSa~lnkAY~TLk~pL~RA~Yilkl~g~e~~sne~stDpe~Lmevle~~E~IS~ 110 (168)
T KOG3192|consen 56 EQSAELNKAYDTLKDPLARARYLLKLKGQEQTSNELSTDPEFLMEVLEYHEAISE 110 (168)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHhCCCCchhhhccCHHHHHHHHHHHHHHHh
Confidence 3455666666655444333 222 12366777777777777654
No 73
>PRK14139 heat shock protein GrpE; Provisional
Probab=22.37 E-value=3.5e+02 Score=26.97 Aligned_cols=40 Identities=13% Similarity=0.159 Sum_probs=22.5
Q ss_pred HHHHHHHHhHHHHHHHhhhcCC---HHHHHHhhhcchHHHHHH
Q 009098 157 DLVSRCRSNQKKLMQMLTTTGD---EELLGRGLELNDILQNLL 196 (543)
Q Consensus 157 ELyetCrsmQpRI~~LIeetsD---EElL~eLL~lNDdLn~VL 196 (543)
-+..-|+.+++|+.+=.++.-+ +.++.++|.+-|+|.+++
T Consensus 57 R~~AefeN~rKR~~kE~e~~~~~a~~~~~~~LLpv~DnLerAl 99 (185)
T PRK14139 57 RAKAETENVRRRAQEDVAKAHKFAIESFAESLLPVKDSLEAAL 99 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHH
Confidence 3444455555555555444322 566666666666666665
No 74
>PRK14161 heat shock protein GrpE; Provisional
Probab=22.35 E-value=4.1e+02 Score=26.19 Aligned_cols=43 Identities=19% Similarity=0.255 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCC---HHHHHHhhhcchHHHHHHH
Q 009098 155 IVDLVSRCRSNQKKLMQMLTTTGD---EELLGRGLELNDILQNLLA 197 (543)
Q Consensus 155 IqELyetCrsmQpRI~~LIeetsD---EElL~eLL~lNDdLn~VL~ 197 (543)
+.-+..-+..+++|..+=.+...+ +.++.++|.+=|+|.++|.
T Consensus 42 ~lR~~AefeN~rkR~~ke~~~~~~~a~~~~~~~LLpv~DnlerAl~ 87 (178)
T PRK14161 42 LIRTTAEIDNTRKRLEKARDEAKDYAIATFAKELLNVSDNLSRALA 87 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 344555666666666665555432 6677777777777777664
No 75
>PRK14143 heat shock protein GrpE; Provisional
Probab=22.32 E-value=3.4e+02 Score=28.02 Aligned_cols=42 Identities=10% Similarity=0.040 Sum_probs=24.6
Q ss_pred HHHHHHHHHhHHHHHHHhhhcC---CHHHHHHhhhcchHHHHHHH
Q 009098 156 VDLVSRCRSNQKKLMQMLTTTG---DEELLGRGLELNDILQNLLA 197 (543)
Q Consensus 156 qELyetCrsmQpRI~~LIeets---DEElL~eLL~lNDdLn~VL~ 197 (543)
.-|..-++.+|+|+.+=++..- -+.++.++|.+-|+|.++|.
T Consensus 91 lR~~AdfeN~RKR~~kE~e~~~~~a~~~~~~~lLpV~DnLerAl~ 135 (238)
T PRK14143 91 MRIAADFDNFRKRTSREQEDLRLQLKCNTLSEILPVVDNFERARQ 135 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHh
Confidence 3445555556666655444432 36667777777777776664
No 76
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=21.98 E-value=2.9e+02 Score=26.17 Aligned_cols=54 Identities=22% Similarity=0.281 Sum_probs=46.6
Q ss_pred HHHHHHHHHHhHHHHHHHhhhcCCHHHHHHhhhcchHHHHHHHHHHHHhcCCCC
Q 009098 155 IVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLPI 208 (543)
Q Consensus 155 IqELyetCrsmQpRI~~LIeetsDEElL~eLL~lNDdLn~VL~RYd~i~sG~~~ 208 (543)
+.+|-..|+.++..|..|....+++++...+-++-.++..+-.|-+.+.++...
T Consensus 88 l~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~ 141 (169)
T PF07106_consen 88 LAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKP 141 (169)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 567778889999999999999999999999999999999999999988875543
No 77
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=21.86 E-value=8.4e+02 Score=24.64 Aligned_cols=87 Identities=14% Similarity=0.088 Sum_probs=0.0
Q ss_pred hhhhhHHHhhhcHHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcCC--HHHHHHhhh
Q 009098 110 DETMATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD--EELLGRGLE 187 (543)
Q Consensus 110 ~~sms~D~ekLS~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeetsD--EElL~eLL~ 187 (543)
+-........| ..++.-|..-++.|+.||+. ..=.|-|++|-..|+.|+.||..+=+-+.+ .+.....-.
T Consensus 88 i~~l~ek~q~l-~~t~s~veaEik~L~s~Lt~-------eemQe~i~~L~kev~~~~erl~~~k~g~~~vtpedk~~v~~ 159 (201)
T KOG4603|consen 88 IVALTEKVQSL-QQTCSYVEAEIKELSSALTT-------EEMQEEIQELKKEVAGYRERLKNIKAGTNHVTPEDKEQVYR 159 (201)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHhcCh-------HHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHH
Q ss_pred cchHHHHHHHHHHHHhc
Q 009098 188 LNDILQNLLAKHDAIAS 204 (543)
Q Consensus 188 lNDdLn~VL~RYd~i~s 204 (543)
--.+-.+-..+-+++.+
T Consensus 160 ~y~~~~~~wrk~krmf~ 176 (201)
T KOG4603|consen 160 EYQKYCKEWRKRKRMFR 176 (201)
T ss_pred HHHHHHHHHHHHHHHHH
No 78
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=21.68 E-value=5.4e+02 Score=22.38 Aligned_cols=75 Identities=20% Similarity=0.255 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhh-------------c-CC-HHHHHHhhhc
Q 009098 124 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT-------------T-GD-EELLGRGLEL 188 (543)
Q Consensus 124 ELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIee-------------t-sD-EElL~eLL~l 188 (543)
||.-++.|.+++.+.|..=. ....+-+-|.+|+...|..+.++-.|-.+ . .+ +++..++-.+
T Consensus 3 Dik~ir~n~e~v~~~l~~R~---~~~~~vd~i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~l 79 (108)
T PF02403_consen 3 DIKLIRENPEEVRENLKKRG---GDEEDVDEIIELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKEL 79 (108)
T ss_dssp SHHHHHHHHHHHHHHHHHTT---CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHH
T ss_pred CHHHHHhCHHHHHHHHHHcC---CCHhhHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHH
Confidence 57788889999999988753 23455677888888888887777666543 1 24 7888888888
Q ss_pred chHHHHHHHHHHH
Q 009098 189 NDILQNLLAKHDA 201 (543)
Q Consensus 189 NDdLn~VL~RYd~ 201 (543)
.++|..+=...+.
T Consensus 80 k~~i~~le~~~~~ 92 (108)
T PF02403_consen 80 KEEIKELEEQLKE 92 (108)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 8877666554443
No 79
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=21.49 E-value=3.9e+02 Score=28.87 Aligned_cols=82 Identities=20% Similarity=0.308 Sum_probs=52.5
Q ss_pred hHHHhhhcHHHHHHHHHHHHHHHHHHHhcCCCCCc-------cchhHHHHH---HHHHHHHhHHHHHHHhhhcC----C-
Q 009098 114 ATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDRE-------AVKDEVIVD---LVSRCRSNQKKLMQMLTTTG----D- 178 (543)
Q Consensus 114 s~D~ekLS~sELevVrnNvkLLsEML~~~~Pg~~~-------~~ddELIqE---LyetCrsmQpRI~~LIeets----D- 178 (543)
..|...| +..|..+++=++||++=|..+..+... ....++|.+ +-.+|+.++.-|+.++.+.. +
T Consensus 85 ~~Ev~~L-rqkl~E~qGD~KlLR~~la~~r~~~~~~~~~~~~~ere~lV~qLEk~~~q~~qLe~d~qs~lDEkeEl~~ER 163 (319)
T PF09789_consen 85 KEEVEEL-RQKLNEAQGDIKLLREKLARQRVGDEGIGARHFPHEREDLVEQLEKLREQIEQLERDLQSLLDEKEELVTER 163 (319)
T ss_pred HHHHHHH-HHHHHHHhchHHHHHHHHHhhhhhhccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555 778899999999999988765432211 233445443 35566666666666665533 2
Q ss_pred HHHHHHhhhcchHHHHHH
Q 009098 179 EELLGRGLELNDILQNLL 196 (543)
Q Consensus 179 EElL~eLL~lNDdLn~VL 196 (543)
|..=.++=.+|-+|+-+|
T Consensus 164 D~yk~K~~RLN~ELn~~L 181 (319)
T PF09789_consen 164 DAYKCKAHRLNHELNYIL 181 (319)
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 445557778888888887
No 80
>PF03273 Baculo_gp64: Baculovirus gp64 envelope glycoprotein family; InterPro: IPR004955 Gp64 is the major envelope fusion glycoprotein in some, though not all, baculoviruses [, ]. It is found on the surface of both infected cells and budded virions as a homotrimer, and by determining the viral receptor preferences it defines the host range and infection efficiency. Baculovirus enters its host cells by endocytosis followed by a low-pH-induced fusion of the viral envelope with the endosomal membrane, allowing viral entrance into the cell cytoplasm. This membrane fusion, and also the efficient budding of virions from the infected cell, is dependent on Gp64. Gp75 is a homologous envelope glycoprotein from Thogotoviruses that, like Gp64, forms homotrimers and is involved in both binding and entering the host cell [].; GO: 0019048 virus-host interaction, 0019031 viral envelope; PDB: 3DUZ_A.
Probab=21.38 E-value=2.1e+02 Score=32.40 Aligned_cols=57 Identities=19% Similarity=0.247 Sum_probs=37.3
Q ss_pred hhcHHHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcC--CHHHHHHhhh
Q 009098 119 TLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG--DEELLGRGLE 187 (543)
Q Consensus 119 kLS~sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeets--DEElL~eLL~ 187 (543)
+.|+.||..+.+...-=+|+|-. -+..|+..-++|..++-+||..++ ||+|++.||.
T Consensus 281 ~AS~~Dl~~i~~~lmyE~~~Lr~------------nl~~L~~~~~~l~~~l~~vI~SvaKiDeRLIG~L~~ 339 (498)
T PF03273_consen 281 TASKEDLMNIQESLMYENEGLRY------------NLEQLHAHFNKLSNMLNTVIQSVAKIDERLIGRLMG 339 (498)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHHHHHHHTT-TTHHHHHTT
T ss_pred ccCHHHHHHHHHHHHHhchhhHh------------hHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhc
Confidence 34466666665554333444433 266788888888888888888876 6899999886
No 81
>PF15326 TEX15: Testis expressed sequence 15
Probab=21.09 E-value=1.3e+02 Score=30.96 Aligned_cols=41 Identities=20% Similarity=0.328 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhh
Q 009098 131 VMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT 175 (543)
Q Consensus 131 NvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIee 175 (543)
.+--++|+|+..+ ..++.+.++||-.+|..+-+.+.+..+.
T Consensus 76 ~I~~lseIL~qAd----e~asL~~LQelt~~C~~~L~~f~k~Fe~ 116 (233)
T PF15326_consen 76 DICCLSEILDQAD----EAASLKKLQELTLRCQNHLPIFKKYFER 116 (233)
T ss_pred hHHHHHHHHHHHH----hhccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556889999873 2467899999999999999988887765
No 82
>PRK14148 heat shock protein GrpE; Provisional
Probab=20.82 E-value=4e+02 Score=26.72 Aligned_cols=66 Identities=14% Similarity=0.180 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCccchhHHHHHHHHHHHHhHHHHHHHhhhcC---CHHHHHHhhhcchHHHHHHH
Q 009098 123 SSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTG---DEELLGRGLELNDILQNLLA 197 (543)
Q Consensus 123 sELevVrnNvkLLsEML~~~~Pg~~~~~ddELIqELyetCrsmQpRI~~LIeets---DEElL~eLL~lNDdLn~VL~ 197 (543)
.+++.++.-++-|.+=+..+ .+-+.-+..-+..+++|+.+=++... -+.++.++|.+=|+|.++|.
T Consensus 40 ~e~~~l~~~l~~l~~e~~el---------kd~~lR~~Ae~eN~rKR~~rE~e~~~~~a~~~~~~~LLpV~DnlerAl~ 108 (195)
T PRK14148 40 EQLERAKDTIKELEDSCDQF---------KDEALRAKAEMENIRKRAERDVSNARKFGIEKFAKELLPVIDSIEQALK 108 (195)
T ss_pred hHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 34455555444444444443 23344566667777777777666543 37888888888888888875
No 83
>PRK09269 chorismate mutase; Provisional
Probab=20.52 E-value=5e+02 Score=25.98 Aligned_cols=60 Identities=18% Similarity=0.139 Sum_probs=47.2
Q ss_pred hHHHHHHHHHHHHhHHHHHHHhhhc--------CC-HHHHHHhhhcchHHHHHHHHHHHHhcCCCCCCc
Q 009098 152 DEVIVDLVSRCRSNQKKLMQMLTTT--------GD-EELLGRGLELNDILQNLLAKHDAIASGLPIPTE 211 (543)
Q Consensus 152 dELIqELyetCrsmQpRI~~LIeet--------sD-EElL~eLL~lNDdLn~VL~RYd~i~sG~~~~~e 211 (543)
..+..++++.||..|.+++..=... .| .++=-+|.++|++|...|.++..+..+..+..+
T Consensus 90 ~~iF~~~I~aSk~iQ~~~~a~W~~~~~~~~~~~~dL~~~Rp~l~~L~~~il~~l~~~~~~r~~~~C~~~ 158 (193)
T PRK09269 90 RRFFRDQIEANKLVQYALLARWRLAGAAPPGPRPDLASIRPRLDRLQQELLDALADVAPLRSAPDCPAR 158 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcHHH
Confidence 5778899999999999988743221 24 455668999999999999999999888777644
No 84
>PRK14162 heat shock protein GrpE; Provisional
Probab=20.50 E-value=4e+02 Score=26.74 Aligned_cols=41 Identities=17% Similarity=0.067 Sum_probs=21.5
Q ss_pred HHHHHHHHhHHHHHHHhhhcC---CHHHHHHhhhcchHHHHHHH
Q 009098 157 DLVSRCRSNQKKLMQMLTTTG---DEELLGRGLELNDILQNLLA 197 (543)
Q Consensus 157 ELyetCrsmQpRI~~LIeets---DEElL~eLL~lNDdLn~VL~ 197 (543)
-+..-+..+|+|..+=++... -+.++.++|.+=|+|.++|.
T Consensus 64 R~~AEfeN~rkR~~kE~e~~~~~a~~~~~~~LLpV~DnLerAl~ 107 (194)
T PRK14162 64 RSQAEIQNMQNRYAKERAQLIKYESQSLAKDVLPAMDNLERALA 107 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 333444555555555444332 25566666666666666653
Done!