Query 009068
Match_columns 544
No_of_seqs 195 out of 633
Neff 4.6
Searched_HMMs 46136
Date Thu Mar 28 20:01:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009068.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009068hhsearch_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 1.7E-46 3.8E-51 400.9 29.7 205 1-206 65-277 (470)
2 KOG1086 Cytosolic sorting prot 100.0 1.1E-36 2.3E-41 317.5 20.9 224 1-229 72-322 (594)
3 KOG2199 Signal transducing ada 99.9 3.7E-21 8.1E-26 200.2 16.2 203 1-207 72-368 (462)
4 cd03568 VHS_STAM VHS domain fa 99.8 1.9E-20 4.1E-25 173.7 8.7 75 1-76 64-138 (144)
5 cd03569 VHS_Hrs_Vps27p VHS dom 99.8 1.4E-20 3E-25 174.1 7.8 74 1-75 68-141 (142)
6 cd03565 VHS_Tom1 VHS domain fa 99.8 1.1E-20 2.4E-25 174.6 6.9 73 1-74 66-141 (141)
7 PF03127 GAT: GAT domain; Int 99.8 6E-20 1.3E-24 160.0 11.1 88 122-209 9-96 (100)
8 cd03567 VHS_GGA VHS domain fam 99.8 6.5E-19 1.4E-23 162.8 6.7 68 1-72 65-137 (139)
9 smart00288 VHS Domain present 99.7 2.3E-17 5E-22 150.7 7.0 69 1-70 64-133 (133)
10 PF00790 VHS: VHS domain; Int 99.7 6.2E-17 1.3E-21 148.5 6.7 69 1-70 69-140 (140)
11 cd03561 VHS VHS domain family; 99.6 8.8E-16 1.9E-20 139.9 7.1 68 1-68 64-133 (133)
12 KOG1818 Membrane trafficking a 99.1 4.2E-11 9.2E-16 132.5 6.0 82 1-84 72-154 (634)
13 cd00197 VHS_ENTH_ANTH VHS, ENT 98.7 1.9E-08 4.1E-13 89.0 3.9 46 1-46 64-114 (115)
14 PF12210 Hrs_helical: Hepatocy 90.6 2.3 5E-05 38.0 9.2 74 126-201 4-77 (96)
15 cd03562 CID CID (CTD-Interacti 86.4 0.37 8E-06 42.6 1.5 48 1-50 64-111 (114)
16 KOG0307 Vesicle coat complex C 86.0 21 0.00046 43.4 15.8 44 386-432 783-826 (1049)
17 PRK04778 septation ring format 73.1 26 0.00057 39.7 10.8 41 34-77 213-253 (569)
18 PF06160 EzrA: Septation ring 72.9 20 0.00043 40.7 9.8 164 33-204 208-399 (560)
19 KOG0307 Vesicle coat complex C 69.9 69 0.0015 39.2 13.4 26 157-182 559-586 (1049)
20 KOG2199 Signal transducing ada 64.2 26 0.00056 38.7 7.9 15 151-165 124-138 (462)
21 PF14523 Syntaxin_2: Syntaxin- 63.8 59 0.0013 27.9 8.8 79 125-204 4-91 (102)
22 PF07106 TBPIP: Tat binding pr 63.2 95 0.0021 29.5 10.9 90 113-203 76-167 (169)
23 COG4477 EzrA Negative regulato 62.9 58 0.0012 37.3 10.5 44 33-79 211-254 (570)
24 PF03670 UPF0184: Uncharacteri 60.8 26 0.00057 30.7 5.9 54 122-177 24-77 (83)
25 smart00503 SynN Syntaxin N-ter 55.2 1.4E+02 0.003 25.8 10.0 87 117-204 9-109 (117)
26 PF04740 LXG: LXG domain of WX 52.4 1.3E+02 0.0028 29.0 10.0 80 125-204 69-165 (204)
27 PF00618 RasGEF_N: RasGEF N-te 50.6 53 0.0012 28.1 6.3 56 9-67 33-102 (104)
28 cd08779 Death_PIDD Death Domai 48.6 23 0.00051 30.5 3.7 42 26-70 33-74 (86)
29 cd00179 SynN Syntaxin N-termin 47.1 2E+02 0.0043 26.2 9.8 82 123-204 12-108 (151)
30 cd08319 Death_RAIDD Death doma 45.6 26 0.00057 30.3 3.5 37 31-71 38-74 (83)
31 smart00582 RPR domain present 45.2 21 0.00046 31.5 3.1 18 30-47 90-107 (121)
32 PF05400 FliT: Flagellar prote 44.9 73 0.0016 25.9 6.0 51 151-201 8-64 (84)
33 cd08306 Death_FADD Fas-associa 41.0 35 0.00075 29.4 3.6 36 32-71 39-74 (86)
34 PF04818 CTD_bind: RNA polymer 38.4 45 0.00097 26.6 3.7 27 21-47 33-59 (64)
35 PF07531 TAFH: NHR1 homology t 37.7 36 0.00078 30.6 3.2 33 16-48 7-39 (96)
36 KOG1573 Aldehyde reductase [Ge 37.4 1E+02 0.0023 30.5 6.5 59 129-199 75-133 (204)
37 PF12993 DUF3877: Domain of un 37.1 32 0.0007 33.9 3.1 41 7-49 85-125 (175)
38 PF05633 DUF793: Protein of un 37.1 1.1E+02 0.0024 33.8 7.4 55 123-177 314-371 (389)
39 smart00005 DEATH DEATH domain, 36.4 47 0.001 27.6 3.6 35 33-71 44-78 (88)
40 PF09324 DUF1981: Domain of un 35.1 56 0.0012 28.1 3.9 35 16-50 16-50 (86)
41 PF02203 TarH: Tar ligand bind 33.3 3.5E+02 0.0076 24.6 9.2 77 124-201 82-161 (171)
42 smart00549 TAFH TAF homology. 33.3 65 0.0014 28.8 4.0 33 16-48 6-38 (92)
43 PF08899 DUF1844: Domain of un 33.1 69 0.0015 27.5 4.1 41 123-164 31-71 (74)
44 TIGR03752 conj_TIGR03752 integ 32.7 70 0.0015 36.1 5.2 23 153-175 82-104 (472)
45 smart00229 RasGEFN Guanine nuc 32.5 1.7E+02 0.0037 25.9 6.8 40 13-52 40-89 (127)
46 cd08317 Death_ank Death domain 32.2 52 0.0011 27.9 3.3 36 31-70 40-75 (84)
47 TIGR00153 conserved hypothetic 31.9 2.4E+02 0.0051 27.8 8.3 79 123-204 17-101 (216)
48 cd06224 REM Guanine nucleotide 31.4 1.9E+02 0.0042 25.0 6.9 40 13-52 32-84 (122)
49 PF12917 HD_2: HD containing h 31.3 1.2E+02 0.0026 31.0 6.1 44 166-209 112-155 (215)
50 PF08784 RPA_C: Replication pr 31.0 61 0.0013 28.1 3.6 44 33-79 47-102 (102)
51 PRK14148 heat shock protein Gr 30.6 2.5E+02 0.0054 28.1 8.2 43 156-198 63-108 (195)
52 PF09388 SpoOE-like: Spo0E lik 30.6 1.7E+02 0.0037 22.2 5.5 42 158-203 1-44 (45)
53 PF14555 UBA_4: UBA-like domai 30.5 1E+02 0.0022 23.0 4.2 33 169-201 3-37 (43)
54 COG1867 TRM1 N2,N2-dimethylgua 30.3 48 0.0011 36.3 3.4 65 3-72 261-332 (380)
55 cd08805 Death_ank1 Death domai 30.3 60 0.0013 28.2 3.3 36 31-70 40-75 (84)
56 COG5185 HEC1 Protein involved 30.2 3.9E+02 0.0085 30.6 10.2 91 110-204 331-423 (622)
57 PHA03377 EBNA-3C; Provisional 30.2 4.6E+02 0.01 31.5 11.1 14 423-436 831-844 (1000)
58 cd08784 Death_DRs Death Domain 29.9 1.4E+02 0.0029 25.3 5.4 36 33-72 37-72 (79)
59 PRK06863 single-stranded DNA-b 29.7 47 0.001 32.4 2.9 11 423-433 144-154 (168)
60 PRK14141 heat shock protein Gr 29.2 1.6E+02 0.0034 29.9 6.5 18 180-197 81-98 (209)
61 PF08711 Med26: TFIIS helical 28.9 83 0.0018 24.3 3.6 24 26-49 28-52 (53)
62 PRK09458 pspB phage shock prot 28.0 74 0.0016 27.4 3.4 26 148-173 36-61 (75)
63 PRK14161 heat shock protein Gr 27.8 3.8E+02 0.0081 26.4 8.8 43 156-198 42-87 (178)
64 cd01670 Death Death Domain: a 27.6 80 0.0017 25.6 3.5 34 34-71 37-70 (79)
65 PF13324 GCIP: Grap2 and cycli 27.4 4.5E+02 0.0097 27.0 9.7 48 151-198 222-273 (275)
66 PRK14154 heat shock protein Gr 27.3 2.6E+02 0.0057 28.3 7.7 41 158-198 77-120 (208)
67 PRK14143 heat shock protein Gr 26.6 3.1E+02 0.0066 28.3 8.2 41 158-198 92-135 (238)
68 PRK14140 heat shock protein Gr 26.5 3.5E+02 0.0075 27.1 8.3 42 157-198 61-105 (191)
69 PF05397 Med15_fungi: Mediator 26.3 2.3E+02 0.005 25.9 6.6 56 150-208 31-90 (115)
70 PF05769 DUF837: Protein of un 25.8 3.2E+02 0.007 26.9 7.9 49 153-201 33-90 (181)
71 PF02005 TRM: N2,N2-dimethylgu 25.6 1.3E+02 0.0028 32.8 5.6 61 12-72 279-352 (377)
72 PF03273 Baculo_gp64: Baculovi 25.6 2.1E+02 0.0045 32.4 7.2 33 156-188 305-339 (498)
73 PF00531 Death: Death domain; 25.3 91 0.002 25.3 3.5 33 34-70 39-71 (83)
74 PF06667 PspB: Phage shock pro 25.0 91 0.002 26.8 3.5 26 148-173 36-61 (75)
75 PRK14162 heat shock protein Gr 24.9 3.5E+02 0.0076 27.1 8.1 41 158-198 64-107 (194)
76 cd00183 TFIIS_I N-terminal dom 23.8 1.3E+02 0.0029 25.1 4.2 24 26-49 52-75 (76)
77 PRK14139 heat shock protein Gr 23.8 3.7E+02 0.0081 26.7 8.0 40 158-197 57-99 (185)
78 PRK14145 heat shock protein Gr 23.6 4.1E+02 0.0088 26.7 8.2 43 157-199 69-114 (196)
79 PF01865 PhoU_div: Protein of 23.2 4.4E+02 0.0095 25.5 8.4 54 123-176 14-69 (214)
80 KOG3219 Transcription initiati 23.1 1.3E+02 0.0029 30.2 4.7 38 33-73 148-185 (195)
81 cd08777 Death_RIP1 Death Domai 22.6 1.1E+02 0.0023 26.5 3.5 36 32-70 40-75 (86)
82 PF09712 PHA_synth_III_E: Poly 22.4 1.4E+02 0.003 31.4 5.0 61 2-66 221-281 (293)
83 COG3879 Uncharacterized protei 22.3 4.7E+02 0.01 27.4 8.5 81 132-213 27-114 (247)
84 TIGR00606 rad50 rad50. This fa 22.3 5.8E+02 0.013 32.2 11.0 44 5-50 683-726 (1311)
85 cd08318 Death_NMPP84 Death dom 22.2 1.6E+02 0.0034 25.3 4.5 35 33-71 44-78 (86)
86 cd09235 V_Alix Middle V-domain 22.0 2.6E+02 0.0057 29.7 7.0 48 119-166 16-65 (339)
87 PF11867 DUF3387: Domain of un 21.9 6.9E+02 0.015 26.5 10.1 64 126-191 193-258 (335)
88 COG5278 Predicted periplasmic 21.9 5.5E+02 0.012 26.0 8.9 68 126-193 47-116 (207)
89 PRK14155 heat shock protein Gr 21.8 3E+02 0.0066 27.8 7.0 18 180-197 63-80 (208)
90 KOG2003 TPR repeat-containing 21.0 1.3E+02 0.0029 34.2 4.6 29 183-211 207-235 (840)
91 PRK14163 heat shock protein Gr 20.6 4.3E+02 0.0094 26.9 7.8 41 158-198 65-108 (214)
92 KOG3192 Mitochondrial J-type c 20.2 1.9E+02 0.004 28.5 4.9 17 179-195 94-110 (168)
93 PF07106 TBPIP: Tat binding pr 20.1 3.6E+02 0.0078 25.6 6.9 52 156-207 88-139 (169)
94 PF04961 FTCD_C: Formiminotran 20.0 4.2E+02 0.009 26.0 7.4 40 136-175 33-73 (184)
95 PF12729 4HB_MCP_1: Four helix 20.0 6.1E+02 0.013 22.3 8.8 47 130-176 85-131 (181)
No 1
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.7e-46 Score=400.90 Aligned_cols=205 Identities=48% Similarity=0.793 Sum_probs=179.1
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCC-CCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKK-PDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 79 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k-~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~d 79 (544)
||||||+.||.+||+|+||++|||+++++ .+.+||+|||.||++|+++|++..++++.|+.+|++|+++||+||.++++
T Consensus 65 cvkNCG~~fh~~Va~k~fL~emVk~~k~~~~~~~Vr~kiL~LI~~W~~af~~~~~~~~~~~~~y~~l~~~G~~FP~r~~~ 144 (470)
T KOG1087|consen 65 CVKNCGYSFHLQVASKEFLNEMVKRPKNKPRDLKVREKILELIDTWQQAFCGPDGYLPDYYQIYDELRRKGVEFPQRDEE 144 (470)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHhccccCCcchhHHHHHHHHHHHHHHHccCCCCcchhHHHHHHHHHHcCCcCCCCccc
Confidence 89999999999999999999999999999 89999999999999999999996678999999999999999999999998
Q ss_pred CCCCCCCCCCCCCCcccccccCCCCCCcccccchhh------H-HHhhhhHHHHHHHHHHHHHHHHHHHhhCCCCcccch
Q 009068 80 AAPIFTPPVSHPTLGQAQASYGMPSNSSRRLDETMA------T-EVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVK 152 (544)
Q Consensus 80 aaPV~TPp~t~ps~r~aq~~~gsP~qeAnrLiKsM~------~-E~ekls~sELe~V~~nveLLnEML~~~nP~d~~~~d 152 (544)
..++++|+.......+.+...+.|. +++.+++.+. . ++..++++||++|+++++||+|||.++++++++..+
T Consensus 145 sl~~~~pp~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~seLe~~~~~~~ll~emL~~v~p~~~e~~~ 223 (470)
T KOG1087|consen 145 SLAVLTPPAVLRPAPEPQEQSGPPN-EANASMKSMAGYPTEATPEVSTLSLSELESVKGKADLLSEMLNAVDPSDEEAAK 223 (470)
T ss_pred cccccCCCCCCCCCCCchhhcCCcc-ccccccccccccchhhhhhhhhhhHHHHHHHHHHHHHHHHHHhccCCCCcchhH
Confidence 8777776653211111110113333 5555555443 2 455667999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHHHHhcC
Q 009068 153 DEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASG 206 (544)
Q Consensus 153 dElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd~L~sG 206 (544)
+|+|.+|+++||.+|+|||+||+++.||++|+++|+|||+|++||.+||++.+|
T Consensus 224 ~el~~~L~~qcr~~q~rv~~Li~~~~DE~ll~~lL~lND~L~~vL~~ye~~~~g 277 (470)
T KOG1087|consen 224 DELLVDLVEQCRSKQRRVMHLIEETSDEELLCELLKLNDELQRVLERYERIASG 277 (470)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHhHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999999999999999999
No 2
>KOG1086 consensus Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.1e-36 Score=317.50 Aligned_cols=224 Identities=22% Similarity=0.388 Sum_probs=189.1
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCC-----CHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccC--
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKP-----DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQF-- 73 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~-----d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~F-- 73 (544)
||||||++||.||++++|||||+|++++|| ..+||.||++|+..|+.+|+ ..++|+++|++||++||+.
T Consensus 72 cmkncGekfH~evgkfrFLNELIkvvsPKYlG~~tSekvKtkiIelLfsWtv~lp----e~~KikdaYqmLKkqgIik~D 147 (594)
T KOG1086|consen 72 CMKNCGEKFHEEVGKFRFLNELIKVVSPKYLGSRTSEKVKTKIIELLFSWTVSLP----EEPKIKDAYQMLKKQGIIKSD 147 (594)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHhCchhcchhhhHHHHHHHHHHHhhheecCc----ccchHHHHHHHHHhcCcccCC
Confidence 899999999999999999999999999986 47999999999999999998 4689999999999999975
Q ss_pred CCCCCCCCCCCCCCCC--CCCCcccc--------cccCCCC--CCcccccchhhHHHhh----h--hHHHHHHHHHHHHH
Q 009068 74 PKRSPDAAPIFTPPVS--HPTLGQAQ--------ASYGMPS--NSSRRLDETMATEVET----L--SFSSLDSMRDVMEL 135 (544)
Q Consensus 74 P~~~~daaPV~TPp~t--~ps~r~aq--------~~~gsP~--qeAnrLiKsM~~E~ek----l--s~sELe~V~~nveL 135 (544)
|....+..+++.||+. ...+++++ .++.+|+ ++||+|||+|+++.+. + +...|+.|.+++++
T Consensus 148 P~lp~d~~~~p~ppP~pkssvFddEEksklL~rLLkSn~PeDLqaANkLIK~lVkeee~k~eKiskR~~aleev~n~vk~ 227 (594)
T KOG1086|consen 148 PKLPVDETPVPAPPPRPKSSVFDDEEKSKLLARLLKSNHPEDLQAANKLIKTLVKEEEHKLEKISKRVKALEEVNNNVKL 227 (594)
T ss_pred CCCCCCCccCCCCCCCCCccccCcHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777776677766552 22344332 3567888 4899999999986543 2 46889999999999
Q ss_pred HHHHHHhhCCCCcccchhH-HHHHHHHHHHHHHHHHHHHhhhc-CCHHHHHHhhhhhHHHHHHHHHHHHHhcCCCCCCCC
Q 009068 136 LSDMLQAVNPSDREAVKDE-VIVDLVSRCRSNQKKLMQMLTTT-GDEELLGRGLELNDILQNLLAKHDAIASGLPIPTEV 213 (544)
Q Consensus 136 LnEML~~~nP~d~~~~ddE-lI~EL~eqCKsmQprI~rLIeet-dDEElL~eLL~LNDeLn~aL~rYd~L~sG~~~~~e~ 213 (544)
|.|||-.+..++...-++| +++++|+.|.++|+.+++|++++ +||+.|+++|++||.|++++..|+.++.|+..++++
T Consensus 228 l~em~l~~s~eg~a~pd~E~~lq~v~~~ce~lr~tlfrlaset~dnD~aL~eILqanD~ltrvi~~ykt~~~G~~~~g~a 307 (594)
T KOG1086|consen 228 LEEMLLDYSQEGNASPDNELLLQEVYNRCEQLRPTLFRLASETEDNDPALAEILQANDNLTRVINLYKTPKEGNVANGSA 307 (594)
T ss_pred HHHHHHhhccCCCCCCcHHHHHHHHHHHHHHHHHHHHHhhcccccCcHHHHHHHhhhhhHHhhhhhcccccccccccccc
Confidence 9999988876554445555 99999999999999999999997 789999999999999999999999999999998876
Q ss_pred CCCCCCCcchhccccC
Q 009068 214 TNLSPKPNEACAASSL 229 (544)
Q Consensus 214 ~~~s~~~~~~~~l~d~ 229 (544)
. +...|.....|+|.
T Consensus 308 ~-t~slpd~q~~l~~n 322 (594)
T KOG1086|consen 308 R-TQSLPDSQSLLVDN 322 (594)
T ss_pred e-eccCCcchhheeec
Confidence 5 44456666667776
No 3
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=99.86 E-value=3.7e-21 Score=200.15 Aligned_cols=203 Identities=18% Similarity=0.268 Sum_probs=145.8
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDA 80 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~da 80 (544)
||+|||++||+|||+|+|.++|.+|+..+.+.+|++||..|+++|++.|+.++. +..|..+|+.||++||.|+....-.
T Consensus 72 ~~~NCg~~~r~EVsSr~F~~el~al~~~~~h~kV~~k~~~lv~eWsee~K~Dp~-lsLi~~l~~klk~~g~~f~~~~~k~ 150 (462)
T KOG2199|consen 72 CVANCGKRFRLEVSSRDFTTELRALIESKAHPKVCEKMRDLVKEWSEEFKKDPS-LSLISALYKKLKEEGITFLVAGSKP 150 (462)
T ss_pred HHHhcchHHHHHHhhhhHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhccCcc-hhHHHHHHHHHHHcCCCcccCCCch
Confidence 899999999999999999999999999888999999999999999999999986 9999999999999999997544210
Q ss_pred --CCCCC--CCCCCCCCc-----------cc-c---------cccCC-------CC--------------------CCcc
Q 009068 81 --APIFT--PPVSHPTLG-----------QA-Q---------ASYGM-------PS--------------------NSSR 108 (544)
Q Consensus 81 --aPV~T--Pp~t~ps~r-----------~a-q---------~~~gs-------P~--------------------qeAn 108 (544)
..+-+ -.....+.+ .. + ..|.. |. .|.|
T Consensus 151 ~k~a~~~~~v~~k~EeEdiaKAi~lSL~E~~~Q~k~a~~~tst~yPs~qk~nqapa~~l~s~~~~rkVRALYDFeAaE~n 230 (462)
T KOG2199|consen 151 EKHAMSTNTVSSKQEEEDIAKAIELSLKEQEKQKKLAETETSTLYPSHQKQNQAPASQLNSQTVVRKVRALYDFEAAEDN 230 (462)
T ss_pred hHHHhhcccccccccHHHHHHHHHhhHHHHhhchhhccCCccccCccccccccCchhhccCCccchhhhhhhcccccCCC
Confidence 00100 000000000 00 0 00000 11 0112
Q ss_pred cc-------cc-----------------------hhh-HHHhhhhHHH-----------HHHHHHHHHHHHHHHHhhCCC
Q 009068 109 RL-------DE-----------------------TMA-TEVETLSFSS-----------LDSMRDVMELLSDMLQAVNPS 146 (544)
Q Consensus 109 rL-------iK-----------------------sM~-~E~ekls~sE-----------Le~V~~nveLLnEML~~~nP~ 146 (544)
+| |- .++ .+.+.+..++ +.+.+..|+.|..+|++.+|.
T Consensus 231 ELsFkaGdIItVLd~s~~~WWKG~~~~~~GlFPsnfVT~~le~~~~ee~~~~~~~~E~~vfi~e~~iDrlL~~L~~~dPt 310 (462)
T KOG2199|consen 231 ELSFKAGDIITVLDDSDPNWWKGENHRGIGLFPSNFVTADLEEPKIEEQEQKQKNKEAIVFIDEDKIDRLLQVLHEADPT 310 (462)
T ss_pred ccceecCcEEEEcccCCcchhccccCCcccccchhhhhhhhcccchhhhhhhhcCcceeeeccHHHHHHHHHHHhhcCCC
Confidence 21 10 011 0111111111 233467899999999999999
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHHHHhcCC
Q 009068 147 DREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGL 207 (544)
Q Consensus 147 d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd~L~sG~ 207 (544)
++..++++++ +|+..|.+|+++|.++++.++.+ ..+|++||..|..||+.|++|+...
T Consensus 311 d~~~D~~~l~-~le~~~~~mgPlid~~Le~idrk--~~eL~~Ln~~l~~Al~lY~kLm~~~ 368 (462)
T KOG2199|consen 311 DEVQDDDDLL-DLEAAVHQMGPLIDRKLEKIDRK--HEELSQLNVKLLDALRLYNKLMNEA 368 (462)
T ss_pred CccCCCHHHH-HHHHHHHHhhhHHHHHHHHHHhh--HHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 8887666666 99999999999999999999655 4688999999999999999999655
No 4
>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=99.82 E-value=1.9e-20 Score=173.73 Aligned_cols=75 Identities=19% Similarity=0.406 Sum_probs=71.7
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKR 76 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~ 76 (544)
||||||.+||.||++++|+++|++++.++.+..||+|||+||++|+++|+++++ +..|.++|++|+++||.||..
T Consensus 64 ~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~W~~~f~~~~~-l~~i~~~y~~L~~~G~~f~~~ 138 (144)
T cd03568 64 CAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQWADEFKNDPS-LSLMSDLYKKLKNEGPDLVTP 138 (144)
T ss_pred HHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHHHHHHhCCCcc-cHHHHHHHHHHHHcCCCCCCC
Confidence 899999999999999999999999999988999999999999999999998875 999999999999999999943
No 5
>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=99.82 E-value=1.4e-20 Score=174.11 Aligned_cols=74 Identities=31% Similarity=0.567 Sum_probs=71.3
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPK 75 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~ 75 (544)
||||||.+||.||++++||++|++++.++++..||+|||+||+.|+.+|++++ ++..|.++|++|+++||.||+
T Consensus 68 ~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~~f~~~~-~l~~i~~~y~~L~~~G~~FP~ 141 (142)
T cd03569 68 CVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQAWALAFRNKP-QLKYVVDTYQILKAEGHKFPE 141 (142)
T ss_pred HHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHHHhCCCc-ccHHHHHHHHHHHHcCCCCCC
Confidence 89999999999999999999999999988899999999999999999999886 599999999999999999996
No 6
>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=99.82 E-value=1.1e-20 Score=174.62 Aligned_cols=73 Identities=32% Similarity=0.704 Sum_probs=69.0
Q ss_pred CcccchHHHHHHhcChHHHHH-HHHhhcCCC--CHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGE-MVKIVKKKP--DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFP 74 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLne-LvKLv~~k~--d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP 74 (544)
||||||.+||.|||+++|+++ |++++.++. +..||+|||+||++|+++|+++++ ++.|.++|++|+++||.||
T Consensus 66 ~vkNCG~~fh~eiask~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~~f~~~~~-l~~i~~~y~~L~~~G~~FP 141 (141)
T cd03565 66 CVKNCGHRFHVLVAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWADAFRGSPD-LTGVVEVYEELKKKGIEFP 141 (141)
T ss_pred HHHHccHHHHHHHHHHHhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHHHhCCCcc-chHHHHHHHHHHHcCCCCC
Confidence 899999999999999999999 999998764 469999999999999999999874 9999999999999999998
No 7
>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=99.82 E-value=6e-20 Score=159.97 Aligned_cols=88 Identities=28% Similarity=0.518 Sum_probs=82.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHH
Q 009068 122 SFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHD 201 (544)
Q Consensus 122 s~sELe~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd 201 (544)
..++|++|+++++||+|||..++|++....+.|+|+|||++||.||+||++||+.+.||++|++||++||+|++||.+|+
T Consensus 9 ~~~~l~~v~~~~~lL~emL~~~~~~~~~~~~~el~~eL~~~ck~~r~~i~~li~~~~dee~l~~lL~~ND~L~~~l~~Y~ 88 (100)
T PF03127_consen 9 RRSELEKVKNNAKLLNEMLDNYDPGEESSSDNELIQELYESCKSMRPRIQRLIEEVEDEELLGELLQANDELNQALERYD 88 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTTTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTCHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999998887777999999999999999999999999888899999999999999999999
Q ss_pred HHhcCCCC
Q 009068 202 AIASGLPI 209 (544)
Q Consensus 202 ~L~sG~~~ 209 (544)
++++|...
T Consensus 89 ~l~~~~~~ 96 (100)
T PF03127_consen 89 RLVKGQQR 96 (100)
T ss_dssp HHHCCC--
T ss_pred HHHcCccc
Confidence 99999864
No 8
>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=99.76 E-value=6.5e-19 Score=162.80 Aligned_cols=68 Identities=31% Similarity=0.582 Sum_probs=63.3
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCC-----CCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCcc
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKK-----PDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQ 72 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k-----~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~ 72 (544)
||||||.+||.||++++||++|+|+++++ ++..||+|||+||+.|+++|+ +.+.|.++|++||++||+
T Consensus 65 ~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~~f~----~~p~~~~~Y~~Lk~~G~i 137 (139)
T cd03567 65 CMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTLELP----HEPKIKEAYDMLKKQGII 137 (139)
T ss_pred HHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHHhc----ccchHHHHHHHHHHCCCc
Confidence 89999999999999999999999999764 568999999999999999998 367799999999999985
No 9
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=99.70 E-value=2.3e-17 Score=150.67 Aligned_cols=69 Identities=33% Similarity=0.636 Sum_probs=65.5
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHH-HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQ-LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~-VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
||||||.+||.||++++||++|+++++++++.. ||+|||+||+.|+.+|+++++ ++.|.++|++|+++|
T Consensus 64 ~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~W~~~f~~~~~-~~~i~~~y~~L~~~g 133 (133)
T smart00288 64 CVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQEWADAFKNDPD-LSQIVDVYDLLKKKG 133 (133)
T ss_pred HHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCCCC-chHHHHHHHHHHHCc
Confidence 899999999999999999999999999987755 999999999999999999875 999999999999998
No 10
>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=99.67 E-value=6.2e-17 Score=148.51 Aligned_cols=69 Identities=38% Similarity=0.640 Sum_probs=64.2
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHH---HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQ---LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~---VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
||||||.+||.||++++||++|++|+..+.... ||+||++||+.|+++|++++ .+..|.++|++||++|
T Consensus 69 lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~~f~~~~-~~~~i~~~y~~Lk~~G 140 (140)
T PF00790_consen 69 LVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQEWAEAFKSDP-ELSLIQDTYKRLKRKG 140 (140)
T ss_dssp HHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHHHTTTST-TGHHHHHHHHHHHHTT
T ss_pred HHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHHHHCCCC-CchHHHHHHHHHHHCc
Confidence 799999999999999999999999998776543 99999999999999998886 5999999999999998
No 11
>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=99.61 E-value=8.8e-16 Score=139.93 Aligned_cols=68 Identities=44% Similarity=0.716 Sum_probs=63.2
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcC--CCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhh
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKK--KPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRR 68 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~--k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~ 68 (544)
||||||.+||.+|++++||++|++++.+ +.+..||+|||+||+.|+.+|+++..+++.|.++|++||+
T Consensus 64 ~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~~~~~~~~~~~~y~~lk~ 133 (133)
T cd03561 64 LVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAWSESFGGHSEDLPGIEDAYKLLKR 133 (133)
T ss_pred HHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHHhC
Confidence 8999999999999999999999999987 5789999999999999999999873459999999999985
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=99.14 E-value=4.2e-11 Score=132.47 Aligned_cols=82 Identities=30% Similarity=0.552 Sum_probs=75.1
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCC-CCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKK-PDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 79 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k-~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~d 79 (544)
||||||-.||.||++|+||+.|..++... .+..||.|+|.+|+.|+.+|... .++..+.++|+.|+..|+.||+.++.
T Consensus 72 cvkn~G~gv~~ei~tre~m~~~~~~l~~~~~~e~v~~~~l~~~q~wa~af~~~-~~~~~v~~t~~~lk~~g~~Fpe~~e~ 150 (634)
T KOG1818|consen 72 CVKNCGHGVHCEIATREFMDLLKSLLESQRIHEEVKNKILELIQNWAAAFRNS-SKYSYVLDTYQKLKGGGHVFPELDEN 150 (634)
T ss_pred HHhcCCcchhHHHHHHHHHHHHHhhhccccccchHHHHHHHHHHHHHHHccCc-hHHHHHHHHHHHHhcCCccccccccc
Confidence 89999999999999999999999988654 78999999999999999999987 57999999999999999999999876
Q ss_pred CCCCC
Q 009068 80 AAPIF 84 (544)
Q Consensus 80 aaPV~ 84 (544)
.+ +|
T Consensus 151 d~-mf 154 (634)
T KOG1818|consen 151 DA-MF 154 (634)
T ss_pred hh-hh
Confidence 53 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=98.65 E-value=1.9e-08 Score=89.01 Aligned_cols=46 Identities=30% Similarity=0.578 Sum_probs=40.4
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhc-----CCCCHHHHHHHHHHHHHHH
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVK-----KKPDMQLRDKILVLLDSWQ 46 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~-----~k~d~~VKeKILeLIqsWa 46 (544)
||||||++||.+|+++.|+.+|+++.. ...+..||+|+++||+.|+
T Consensus 64 lvkN~g~~f~~~i~~~~~~~~l~~~~~~~~~~~~~~~~Vr~k~~~l~~~w~ 114 (115)
T cd00197 64 CVKNCGERFHQEVASNDFAVELLKFDKSKLLGDDVSTNVREKAIELVQLWA 114 (115)
T ss_pred HHHHccHHHHHHHHHhHHHHHHHHhhccccccCCCChHHHHHHHHHHHHHh
Confidence 799999999999999999999987522 2346899999999999997
No 14
>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=90.60 E-value=2.3 Score=37.95 Aligned_cols=74 Identities=12% Similarity=0.239 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHH
Q 009068 126 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHD 201 (544)
Q Consensus 126 Le~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd 201 (544)
+...+..+++|.+=+....-.......|..|+.|+.++..|+++|+++|.+.++.. ...=.|.|+|.++=+.-.
T Consensus 4 ~~~l~~~v~if~nRmksns~RGrsIanDsaVqsLF~~lt~mH~~LL~~i~~~ee~R--~~~E~lQdkL~qi~eAR~ 77 (96)
T PF12210_consen 4 CNTLRSSVEIFVNRMKSNSSRGRSIANDSAVQSLFQTLTAMHPQLLKYIQEQEEKR--VYYEGLQDKLAQIKEARA 77 (96)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTT--GGG-HHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHhcCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 45667788888886655544455667899999999999999999999999985543 344455677766544433
No 15
>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=86.38 E-value=0.37 Score=42.59 Aligned_cols=48 Identities=29% Similarity=0.387 Sum_probs=33.7
Q ss_pred CcccchHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhC
Q 009068 1 MVKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFG 50 (544)
Q Consensus 1 cVKNCG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~ 50 (544)
++||||.+-...+.. .|.+-+...+. +.+.++|+||..||..|.+.+-
T Consensus 64 Ivkn~~~~~~~~~~~-~~~~~f~~~~~-~~~~~~r~kl~rl~~iW~~~~~ 111 (114)
T cd03562 64 IVKNVGRKYKEFFSE-FLVPLFLDAYE-KVDEKTRKKLERLLNIWEERFV 111 (114)
T ss_pred HHHHcccchHHHHHH-HHHHHHHHHHH-hCCHHHHHHHHHHHHHccCCCC
Confidence 378999887666543 22333333343 5689999999999999987653
No 16
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=86.00 E-value=21 Score=43.38 Aligned_cols=44 Identities=39% Similarity=0.590 Sum_probs=25.4
Q ss_pred CCCcccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009068 386 PYNNYVAPWAQPQSQPLPQSQPQFQPGVQPQYPHYSSAYPPPPWAPT 432 (544)
Q Consensus 386 ~~~~yv~pw~q~~~~~~~~~~~~~~~~~~~q~~~~~~~yp~ppw~~~ 432 (544)
|||.+-+| ++...+.+++-++......+-++ +.+-||+|+|.+-
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 17
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=73.10 E-value=26 Score=39.73 Aligned_cols=41 Identities=17% Similarity=0.240 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCC
Q 009068 34 LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRS 77 (544)
Q Consensus 34 VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~ 77 (544)
.-++|=.|+..-...|+. .+..+...|++|+.+||.|+...
T Consensus 213 ~~~~iP~l~~~~~~~~P~---ql~el~~gy~~m~~~gy~~~~~~ 253 (569)
T PRK04778 213 IMEEIPELLKELQTELPD---QLQELKAGYRELVEEGYHLDHLD 253 (569)
T ss_pred HHHHHHHHHHHHHHHhhH---HHHHHHHHHHHHHHcCCCCCCCC
Confidence 345555667777777863 68889999999999999999764
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=72.89 E-value=20 Score=40.70 Aligned_cols=164 Identities=15% Similarity=0.196 Sum_probs=89.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCCCCCCCCCCCCCCCCcc--cccccCCCCCCcc--
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPDAAPIFTPPVSHPTLGQ--AQASYGMPSNSSR-- 108 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~daaPV~TPp~t~ps~r~--aq~~~gsP~qeAn-- 108 (544)
..-++|=.|+..-...|+. .+..+...|+.|+.+||.|+..+.+.- +-.= ...... .....+.-. ++.
T Consensus 208 ~~~e~IP~l~~~l~~~~P~---ql~eL~~gy~~m~~~gy~l~~~~i~~~-i~~i---~~~l~~~~~~L~~l~l~-~~~~~ 279 (560)
T PF06160_consen 208 EIMEDIPKLYKELQKEFPD---QLEELKEGYREMEEEGYYLEHLDIEEE-IEQI---EEQLEEALALLKNLELD-EVEEE 279 (560)
T ss_pred HHHHHhHHHHHHHHHHhHH---HHHHHHHHHHHHHHCCCCCCCCCHHHH-HHHH---HHHHHHHHHHHHcCCHH-HHHHH
Confidence 4456677777777778864 588899999999999999997553210 0000 000000 000000000 000
Q ss_pred -----c----ccchhhHHHhhh---------hHHHHHHHHHHHHHHHHHHHhhCCC-CcccchhHHHHHHHHHHHHHHHH
Q 009068 109 -----R----LDETMATEVETL---------SFSSLDSMRDVMELLSDMLQAVNPS-DREAVKDEVIVDLVSRCRSNQKK 169 (544)
Q Consensus 109 -----r----LiKsM~~E~ekl---------s~sELe~V~~nveLLnEML~~~nP~-d~~~~ddElI~EL~eqCKsmQpr 169 (544)
. |-..|.+|+... ....|+.++.+.+.|..-|+.++-. .....+.+...+|-.+++.+..+
T Consensus 280 ~~~i~~~Id~lYd~le~E~~Ak~~V~~~~~~l~~~l~~~~~~~~~l~~e~~~v~~sY~L~~~e~~~~~~l~~~l~~l~~~ 359 (560)
T PF06160_consen 280 NEEIEERIDQLYDILEKEVEAKKYVEKNLKELYEYLEHAKEQNKELKEELERVSQSYTLNHNELEIVRELEKQLKELEKR 359 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHHHH
Confidence 0 111222332211 2455777777666666666666432 12223456777888888888888
Q ss_pred HHHHhhhcCC-----HHHHHHhhhhhHHHHHHHHHHHHHh
Q 009068 170 LMQMLTTTGD-----EELLGRGLELNDILQNLLAKHDAIA 204 (544)
Q Consensus 170 I~rLIeetdD-----EElL~eLL~LNDeLn~aL~rYd~L~ 204 (544)
+..+...+.+ -++...+-++.+.|..+-..+..+.
T Consensus 360 ~~~~~~~i~~~~~~yS~i~~~l~~~~~~l~~ie~~q~~~~ 399 (560)
T PF06160_consen 360 YEDLEERIEEQQVPYSEIQEELEEIEEQLEEIEEEQEEIN 399 (560)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8887776633 3344555555555555555555554
No 19
>KOG0307 consensus Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.86 E-value=69 Score=39.24 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=14.3
Q ss_pred HHHHHHHHHHH-HHHHHHhhhc-CCHHH
Q 009068 157 VDLVSRCRSNQ-KKLMQMLTTT-GDEEL 182 (544)
Q Consensus 157 ~EL~eqCKsmQ-prI~rLIeet-dDEEl 182 (544)
.++++.|..++ +.+..+|-++ ++|++
T Consensus 559 ~~~ve~~~~k~Wke~la~i~t~~~~~~~ 586 (1049)
T KOG0307|consen 559 DDYVETCEVKQWKETLAAICTYAQTDEF 586 (1049)
T ss_pred HHHHhhcchhhHHHHHHHHHHhcchhhH
Confidence 37777777776 3344444443 44443
No 20
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=64.18 E-value=26 Score=38.69 Aligned_cols=15 Identities=13% Similarity=0.138 Sum_probs=11.6
Q ss_pred chhHHHHHHHHHHHH
Q 009068 151 VKDEVIVDLVSRCRS 165 (544)
Q Consensus 151 ~ddElI~EL~eqCKs 165 (544)
-...+|.+||+.+|+
T Consensus 124 p~lsLi~~l~~klk~ 138 (462)
T KOG2199|consen 124 PSLSLISALYKKLKE 138 (462)
T ss_pred cchhHHHHHHHHHHH
Confidence 357888888888876
No 21
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=63.80 E-value=59 Score=27.89 Aligned_cols=79 Identities=14% Similarity=0.174 Sum_probs=49.5
Q ss_pred HHHHHHHHHHHHHHHHHhhCC-CCcccchhHHHHHHHHHHHHHHHHHHHHhhhc--C------CHHHHHHhhhhhHHHHH
Q 009068 125 SLDSMRDVMELLSDMLQAVNP-SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT--G------DEELLGRGLELNDILQN 195 (544)
Q Consensus 125 ELe~V~~nveLLnEML~~~nP-~d~~~~ddElI~EL~eqCKsmQprI~rLIeet--d------DEElL~eLL~LNDeLn~ 195 (544)
-|..+.+++..|..|+..+.- .|.. .--+-|.++...|+.+-..|-+.|..+ - +-..-...=.|..++..
T Consensus 4 ~l~~in~~v~~l~k~~~~lGt~~Ds~-~lR~~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~ 82 (102)
T PF14523_consen 4 NLFKINQNVSQLEKLVNQLGTPRDSQ-ELREKIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKE 82 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHH-SSS--H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhCCccccH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHH
Confidence 466778888899999888852 2211 122445677777777777777666543 1 11222455567778888
Q ss_pred HHHHHHHHh
Q 009068 196 LLAKHDAIA 204 (544)
Q Consensus 196 aL~rYd~L~ 204 (544)
+|..|..+.
T Consensus 83 ~l~~fq~~q 91 (102)
T PF14523_consen 83 ALQEFQKAQ 91 (102)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 888888764
No 22
>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=63.24 E-value=95 Score=29.48 Aligned_cols=90 Identities=14% Similarity=0.133 Sum_probs=59.2
Q ss_pred hhhHHHhhhhHHHHHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhc--CCHHHHHHhhhhh
Q 009068 113 TMATEVETLSFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT--GDEELLGRGLELN 190 (544)
Q Consensus 113 sM~~E~ekls~sELe~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeet--dDEElL~eLL~LN 190 (544)
.|..+...+ ..+|..++..+.-|..=|..+.-.-...+=.+.|.+|-..|+.++.||..|-+.. -+++.+..+..-.
T Consensus 76 ~ld~ei~~L-~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~ 154 (169)
T PF07106_consen 76 ELDAEIKEL-REELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEY 154 (169)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 344454554 6788888888888888888886433333335777899999999999999998753 2344445555555
Q ss_pred HHHHHHHHHHHHH
Q 009068 191 DILQNLLAKHDAI 203 (544)
Q Consensus 191 DeLn~aL~rYd~L 203 (544)
..+.+...+..+|
T Consensus 155 ~~~~k~w~kRKri 167 (169)
T PF07106_consen 155 KKWRKEWKKRKRI 167 (169)
T ss_pred HHHHHHHHHHHHH
Confidence 5555544444444
No 23
>COG4477 EzrA Negative regulator of septation ring formation [Cell division and chromosome partitioning]
Probab=62.95 E-value=58 Score=37.26 Aligned_cols=44 Identities=20% Similarity=0.344 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCC
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 79 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~d 79 (544)
...++|=.||..-...++ +.+...+..|+.|+.+||.|+....+
T Consensus 211 ~~~e~IP~L~~e~~~~lP---~ql~~Lk~Gyr~m~~~gY~l~~~~id 254 (570)
T COG4477 211 SIMERIPSLLAELQTELP---GQLQDLKAGYRDMKEEGYHLEHVNID 254 (570)
T ss_pred HHHHHHHHHHHHHHhhch---HHHHHHHHHHHHHHHccCCcccccHH
Confidence 356778888888888887 46899999999999999999987654
No 24
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=60.76 E-value=26 Score=30.66 Aligned_cols=54 Identities=11% Similarity=0.233 Sum_probs=40.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhc
Q 009068 122 SFSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTT 177 (544)
Q Consensus 122 s~sELe~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeet 177 (544)
...|++.+...++-|+-.|+++. ...+.=...+.+|++.+|+.|..+.......
T Consensus 24 ~~~E~~~ins~LD~Lns~LD~LE--~rnD~l~~~L~~LLesnrq~R~e~~~~~~~~ 77 (83)
T PF03670_consen 24 DEEEYAAINSMLDQLNSCLDHLE--QRNDHLHAQLQELLESNRQIRLEFQEQLSKA 77 (83)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHH--HhhhHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 35677888888888888888883 2222234667799999999999998877765
No 25
>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=55.24 E-value=1.4e+02 Score=25.84 Aligned_cols=87 Identities=11% Similarity=0.205 Sum_probs=49.9
Q ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHhhCC-CCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCH-----------H--H
Q 009068 117 EVETLSFSSLDSMRDVMELLSDMLQAVNP-SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDE-----------E--L 182 (544)
Q Consensus 117 E~ekls~sELe~V~~nveLLnEML~~~nP-~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDE-----------E--l 182 (544)
+.+.+ ..+|..++.++.-|..+...+.- .+....-.+-+.++.+.++.+-..|-..|..++.+ + .
T Consensus 9 ~v~~I-~~~I~~i~~~v~~l~~l~~~~l~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~lk~l~~~~~~~~~~~~~~~r~~ 87 (117)
T smart00503 9 KVEEI-RANIQKISQNVAELQKLHEELLTPPDADKELREKLERLIDDIKRLAKEIRAKLKELEKENLENRASGSASDRTR 87 (117)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHhccCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhcccCCHhhhHH
Confidence 44444 56788888888888877776642 11111112445566666666666666655543211 1 1
Q ss_pred HHHhhhhhHHHHHHHHHHHHHh
Q 009068 183 LGRGLELNDILQNLLAKHDAIA 204 (544)
Q Consensus 183 L~eLL~LNDeLn~aL~rYd~L~ 204 (544)
....=.|-.++..+|.+|..+-
T Consensus 88 ~~q~~~L~~~f~~~m~~fq~~Q 109 (117)
T smart00503 88 KAQTEKLRKKFKEVMNEFQRLQ 109 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 2234446777888999997663
No 26
>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=52.37 E-value=1.3e+02 Score=28.97 Aligned_cols=80 Identities=13% Similarity=0.266 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCcccchhHHHH-HHHHHHHHHHHHHHHHhhhc----------------CCHHHHHHhh
Q 009068 125 SLDSMRDVMELLSDMLQAVNPSDREAVKDEVIV-DLVSRCRSNQKKLMQMLTTT----------------GDEELLGRGL 187 (544)
Q Consensus 125 ELe~V~~nveLLnEML~~~nP~d~~~~ddElI~-EL~eqCKsmQprI~rLIeet----------------dDEElL~eLL 187 (544)
-++.+...++.+.+-+..+++......+.+.++ ||...++.+...+..+...+ +...+...+.
T Consensus 69 ~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~~~~~~~~~~~~~~~~vsdiv~~~~~~~~~~~~~~~ 148 (204)
T PF04740_consen 69 LLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKEQIEDLQDEINSILSSVSDIVSLPKPSSSSFIDSLE 148 (204)
T ss_pred HHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccchHHHHhhccchHHHHHHHHH
Confidence 345555555666666666654333334456665 66666666666555544321 2244455555
Q ss_pred hhhHHHHHHHHHHHHHh
Q 009068 188 ELNDILQNLLAKHDAIA 204 (544)
Q Consensus 188 ~LNDeLn~aL~rYd~L~ 204 (544)
.+...|+..|++.+.+.
T Consensus 149 ~~~~~l~~~lekL~~fd 165 (204)
T PF04740_consen 149 KAKKKLQETLEKLRAFD 165 (204)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66666777777776665
No 27
>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=50.63 E-value=53 Score=28.12 Aligned_cols=56 Identities=14% Similarity=0.178 Sum_probs=35.6
Q ss_pred HHHHhcChHHHHHHHHhhcCC---CC-----------HHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHh
Q 009068 9 VHFQIAERNVLGEMVKIVKKK---PD-----------MQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLR 67 (544)
Q Consensus 9 FH~EIaskeFLneLvKLv~~k---~d-----------~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK 67 (544)
++.=+...++|+.|+..+... .. ..+|.||+.+|..|-+.+..+ +..=..+++.|+
T Consensus 33 yr~F~tp~~Ll~~L~~ry~~~~~~~~~~~~~~~~~~~~~i~~rv~~~l~~Wi~~~~~d---f~~~~~l~~~l~ 102 (104)
T PF00618_consen 33 YRSFTTPEELLDKLIQRYNIPPPNGLSQDESWDQDSQEPIRLRVLNVLKYWIENYPDD---FRDDPELLEKLK 102 (104)
T ss_dssp HHHCS-HHHHHHHHHHHHT---SSS-HHHHT-HHHHHHHHHHHHHHHHHHHHHHHCCC---CHH-HHHHHHHH
T ss_pred hHhhCCHHHHHHHHHHHhcccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHChHh---hCCCHHHHHHHH
Confidence 334456788999998887421 11 148889999999999999853 333333455544
No 28
>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=48.58 E-value=23 Score=30.48 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=29.7
Q ss_pred hcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 26 VKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 26 v~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
|...+...++++|++||+.|.+..++++ ..+..+.+-|++-|
T Consensus 33 Ie~~~~~dl~eq~~~mL~~W~~~~~~~~---atv~~L~~AL~~~g 74 (86)
T cd08779 33 IKYNNRDDLDEQIFDMLFSWAQRQAGDP---DAVGKLVTALEESG 74 (86)
T ss_pred HHHHCccCHHHHHHHHHHHHHHhcCCCc---hHHHHHHHHHHHcC
Confidence 3333345699999999999999887542 34666777777655
No 29
>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=47.11 E-value=2e+02 Score=26.22 Aligned_cols=82 Identities=12% Similarity=0.182 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCC-CCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCC--H----------H--HHHHhh
Q 009068 123 FSSLDSMRDVMELLSDMLQAVNP-SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD--E----------E--LLGRGL 187 (544)
Q Consensus 123 ~sELe~V~~nveLLnEML~~~nP-~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdD--E----------E--lL~eLL 187 (544)
...|..++.+++-|..+...+-- .+....-.+-|.++.+.++.+...|-..|..+.. + . .-...=
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 45677777777766666655531 1111112345556666666666666666655411 1 1 113444
Q ss_pred hhhHHHHHHHHHHHHHh
Q 009068 188 ELNDILQNLLAKHDAIA 204 (544)
Q Consensus 188 ~LNDeLn~aL~rYd~L~ 204 (544)
.|..++..+|..|..+-
T Consensus 92 ~L~~~f~~~m~~fq~~Q 108 (151)
T cd00179 92 GLSKKFVEVMTEFNKAQ 108 (151)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57888999999997663
No 30
>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=45.64 E-value=26 Score=30.30 Aligned_cols=37 Identities=19% Similarity=0.361 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCc
Q 009068 31 DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 71 (544)
Q Consensus 31 d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv 71 (544)
...+.++|.++|..|.+..+. -.-+..+...|++-|+
T Consensus 38 p~~l~eQv~~mL~~W~~r~G~----~ATv~~L~~aL~~~~~ 74 (83)
T cd08319 38 PHNVQSQIVEALVKWRQRFGK----KATVQSLIQSLKAVEV 74 (83)
T ss_pred CCCHHHHHHHHHHHHHHhcCC----CCcHHHHHHHHHHcCC
Confidence 446999999999999998863 4567888888888875
No 31
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=45.24 E-value=21 Score=31.53 Aligned_cols=18 Identities=33% Similarity=0.630 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHHHHHHHH
Q 009068 30 PDMQLRDKILVLLDSWQE 47 (544)
Q Consensus 30 ~d~~VKeKILeLIqsWae 47 (544)
.+..+|+||+.||..|.+
T Consensus 90 ~~~~~~~ki~kll~iW~~ 107 (121)
T smart00582 90 ANDETKKKIRRLLNIWEE 107 (121)
T ss_pred CCHHHHHHHHHHHHHHhc
Confidence 347899999999999987
No 32
>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=44.87 E-value=73 Score=25.90 Aligned_cols=51 Identities=25% Similarity=0.297 Sum_probs=34.0
Q ss_pred chhHHHHHHHHHHHHHHHHHHH---Hhhhc---CCHHHHHHhhhhhHHHHHHHHHHH
Q 009068 151 VKDEVIVDLVSRCRSNQKKLMQ---MLTTT---GDEELLGRGLELNDILQNLLAKHD 201 (544)
Q Consensus 151 ~ddElI~EL~eqCKsmQprI~r---LIeet---dDEElL~eLL~LNDeLn~aL~rYd 201 (544)
.+.|.+.+|.+.|..+-.+|.. .+..- ...+.|.++|+++..|...+..-.
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 4567788888888888777776 11111 234577788888888888776553
No 33
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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 (Caspase activation and recruitment domain),
Probab=41.00 E-value=35 Score=29.39 Aligned_cols=36 Identities=17% Similarity=0.234 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCc
Q 009068 32 MQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 71 (544)
Q Consensus 32 ~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv 71 (544)
..++++|.+||..|.+..+. ..-+..+...|++-|.
T Consensus 39 ~~~~eq~~~mL~~W~~~~g~----~At~~~L~~aL~~~~l 74 (86)
T cd08306 39 RNLREQVRQSLREWKKIKKK----EAKVADLIKALRDCQL 74 (86)
T ss_pred CCHHHHHHHHHHHHHHhHCc----chHHHHHHHHHHHcCc
Confidence 46999999999999998763 3456667777777654
No 34
>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=38.37 E-value=45 Score=26.60 Aligned_cols=27 Identities=30% Similarity=0.511 Sum_probs=18.9
Q ss_pred HHHHhhcCCCCHHHHHHHHHHHHHHHH
Q 009068 21 EMVKIVKKKPDMQLRDKILVLLDSWQE 47 (544)
Q Consensus 21 eLvKLv~~k~d~~VKeKILeLIqsWae 47 (544)
.+..-+....+.++++||..||.-|.+
T Consensus 33 ~~~~~~~~~~~~~~~~kv~rll~iW~~ 59 (64)
T PF04818_consen 33 DAFAHAYKNVDPEVRKKVQRLLNIWEE 59 (64)
T ss_dssp HHHHHHCCCS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhcCCHHHHHHHHHHHHHhhC
Confidence 333333334489999999999999975
No 35
>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=37.68 E-value=36 Score=30.56 Aligned_cols=33 Identities=12% Similarity=0.370 Sum_probs=26.6
Q ss_pred hHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 009068 16 RNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEA 48 (544)
Q Consensus 16 keFLneLvKLv~~k~d~~VKeKILeLIqsWaea 48 (544)
+.||..|+++.+++..++|.+++.+||+..-++
T Consensus 7 k~FL~tLi~las~~~spev~~~Vr~LV~~L~~~ 39 (96)
T PF07531_consen 7 KNFLNTLIQLASDKQSPEVGENVRELVQNLVDG 39 (96)
T ss_dssp HHHHHHHHHHHCCSC-CCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhcCCCChHHHHHHHHHHHHHHcC
Confidence 789999999999866778888888888877543
No 36
>KOG1573 consensus Aldehyde reductase [General function prediction only]
Probab=37.35 E-value=1e+02 Score=30.46 Aligned_cols=59 Identities=22% Similarity=0.316 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHH
Q 009068 129 MRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAK 199 (544)
Q Consensus 129 V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~r 199 (544)
+.++++||++++++.+| + .+..-|.-++.+.+..|+ ..-||++| -|-.|--+|-++|.-
T Consensus 75 i~ec~ell~~~vDESDP---D-lDepni~Ha~QtAE~iR~-------~~Pd~dWl-HLtaLiHDLGKvl~f 133 (204)
T KOG1573|consen 75 IWECCELLNEVVDESDP---D-LDEPNIQHALQTAEAIRK-------DYPDEDWL-HLTALIHDLGKVLAF 133 (204)
T ss_pred HHHHHHHHHhhhcccCC---C-CchHHHHHHHHHHHHHHH-------hCCCccHH-HHHHHHHHHHHHHHh
Confidence 56899999999988766 2 345556677777776654 34677775 566667788888843
No 37
>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=37.13 E-value=32 Score=33.87 Aligned_cols=41 Identities=22% Similarity=0.447 Sum_probs=35.1
Q ss_pred HHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHh
Q 009068 7 DFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAF 49 (544)
Q Consensus 7 ~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF 49 (544)
..+|.++...+||.+|+.+|.++. --.+.|++|+..|.+..
T Consensus 85 ~YVhe~~~~~eFik~lIe~v~~hg--cT~e~I~~~F~~ys~~~ 125 (175)
T PF12993_consen 85 EYVHEHTKENEFIKELIELVGKHG--CTLEDILELFHKYSDNV 125 (175)
T ss_pred HHHHhcCCCCHHHHHHHHHHhcCC--cCHHHHHHHHHHhcCCe
Confidence 568999999999999999998853 45788999999998644
No 38
>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=37.09 E-value=1.1e+02 Score=33.78 Aligned_cols=55 Identities=13% Similarity=0.219 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCcccc---hhHHHHHHHHHHHHHHHHHHHHhhhc
Q 009068 123 FSSLDSMRDVMELLSDMLQAVNPSDREAV---KDEVIVDLVSRCRSNQKKLMQMLTTT 177 (544)
Q Consensus 123 ~sELe~V~~nveLLnEML~~~nP~d~~~~---ddElI~EL~eqCKsmQprI~rLIeet 177 (544)
+.||+.+.-.++.|.|+++.+.-..+.+. =.+.+.||...|+.|+.=|.-|..++
T Consensus 314 LkEl~~ve~~vr~L~el~d~~~~p~~~e~~~ev~~~V~EL~~~~~~L~~GLdpLerqV 371 (389)
T PF05633_consen 314 LKELQQVEASVRELHELIDSFQFPLEEEKEEEVREAVEELARVCEALSQGLDPLERQV 371 (389)
T ss_pred HHHHHHHHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHHHHHHHHHcccHHHHHHH
Confidence 79999999999999999998752221111 13455677777777766555555544
No 39
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=36.40 E-value=47 Score=27.57 Aligned_cols=35 Identities=26% Similarity=0.412 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCc
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 71 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv 71 (544)
.+++++.+||..|....+. ...+..+...|++-|.
T Consensus 44 ~~~~~~~~lL~~W~~~~g~----~at~~~L~~aL~~~~~ 78 (88)
T smart00005 44 DLAEQSVQLLRLWEQREGK----NATLGTLLEALRKMGR 78 (88)
T ss_pred CHHHHHHHHHHHHHHccch----hhHHHHHHHHHHHcCh
Confidence 5889999999999988763 3457778888877663
No 40
>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=35.08 E-value=56 Score=28.07 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=28.4
Q ss_pred hHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhC
Q 009068 16 RNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFG 50 (544)
Q Consensus 16 keFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~ 50 (544)
++||.-+..|+....+.+||++||+.|..--....
T Consensus 16 ~~fL~Pf~~i~~~~~~~~vre~il~ci~qil~~~~ 50 (86)
T PF09324_consen 16 KDFLKPFEYIMSNNPSIDVRELILECILQILQSRG 50 (86)
T ss_pred HHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhH
Confidence 78888888888777889999999999877655443
No 41
>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=33.30 E-value=3.5e+02 Score=24.62 Aligned_cols=77 Identities=14% Similarity=0.181 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCccc-chhHHHHHHHHHHHH-HHHHHHHHhhhcCCHHHHHHhhhh-hHHHHHHHHHH
Q 009068 124 SSLDSMRDVMELLSDMLQAVNPSDREA-VKDEVIVDLVSRCRS-NQKKLMQMLTTTGDEELLGRGLEL-NDILQNLLAKH 200 (544)
Q Consensus 124 sELe~V~~nveLLnEML~~~nP~d~~~-~ddElI~EL~eqCKs-mQprI~rLIeetdDEElL~eLL~L-NDeLn~aL~rY 200 (544)
..++.++..++-..+.+..+....... .+.+++.++.+.-+. ++.-|..++..+...+ +.+...+ +..++..+..|
T Consensus 82 ~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~al~~~d-~~~~~~~~~~~~~~~~~~~ 160 (171)
T PF02203_consen 82 ELLARAEQNLEQAEQAFDAFKALPHASPEERALADELEASFDAYLQQALDPLLAALRAGD-IAAFMQLPNEKIQPLFDAF 160 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCS---GTGGHHHHHHHHHHHHH-HHHHHHHHHHHHHTT--HHHHHHSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHCCC-HHHHHHHHHHhcchhHHHH
Confidence 445555555655555555554222222 455677777777777 5566666666552221 2334444 45555555555
Q ss_pred H
Q 009068 201 D 201 (544)
Q Consensus 201 d 201 (544)
.
T Consensus 161 ~ 161 (171)
T PF02203_consen 161 T 161 (171)
T ss_dssp H
T ss_pred H
Confidence 4
No 42
>smart00549 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1).
Probab=33.30 E-value=65 Score=28.81 Aligned_cols=33 Identities=6% Similarity=0.242 Sum_probs=25.8
Q ss_pred hHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHH
Q 009068 16 RNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEA 48 (544)
Q Consensus 16 keFLneLvKLv~~k~d~~VKeKILeLIqsWaea 48 (544)
++||..|+++-++...++|-+++.+||+..-++
T Consensus 6 k~FL~tLi~ls~~~~qpe~~~~Vr~LV~~L~~~ 38 (92)
T smart00549 6 KRFLTTLIQLSNDISQPEVAERVRTLVLGLVNG 38 (92)
T ss_pred HHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhC
Confidence 689999999988765477777777777777543
No 43
>PF08899 DUF1844: Domain of unknown function (DUF1844); InterPro: IPR014995 This group of proteins are functionally uncharacterised.
Probab=33.14 E-value=69 Score=27.49 Aligned_cols=41 Identities=17% Similarity=0.307 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHH
Q 009068 123 FSSLDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCR 164 (544)
Q Consensus 123 ~sELe~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCK 164 (544)
..+|..++..|++|. ||..=..++.+.++.+++.+++-.+|
T Consensus 31 ~~dl~~Ak~tID~L~-mL~eKTkGNL~~~E~~lL~~~L~eLR 71 (74)
T PF08899_consen 31 EVDLELAKQTIDLLA-MLQEKTKGNLDEEEERLLESALYELR 71 (74)
T ss_pred cCCHHHHHHHHHHHH-HHHHHHccCCCHHHHHHHHHHHHHHh
Confidence 457888999999997 88887788888788888888777665
No 44
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=32.66 E-value=70 Score=36.05 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=10.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhh
Q 009068 153 DEVIVDLVSRCRSNQKKLMQMLT 175 (544)
Q Consensus 153 dElI~EL~eqCKsmQprI~rLIe 175 (544)
++.+.+=.+.+|+.+..|-.-|+
T Consensus 82 N~~l~~eN~~L~~r~~~id~~i~ 104 (472)
T TIGR03752 82 NEALKAENERLQKREQSIDQQIQ 104 (472)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHH
Confidence 33344444455554444444444
No 45
>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=32.47 E-value=1.7e+02 Score=25.85 Aligned_cols=40 Identities=18% Similarity=0.446 Sum_probs=28.7
Q ss_pred hcChHHHHHHHHhhcCCCC----------HHHHHHHHHHHHHHHHHhCCC
Q 009068 13 IAERNVLGEMVKIVKKKPD----------MQLRDKILVLLDSWQEAFGGP 52 (544)
Q Consensus 13 IaskeFLneLvKLv~~k~d----------~~VKeKILeLIqsWaeaF~~~ 52 (544)
+...++++.|+..+..... ..+|.||+.+|+.|-+.+..+
T Consensus 40 ~tp~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~~d 89 (127)
T smart00229 40 ITTQELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYWQD 89 (127)
T ss_pred CCHHHHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCCcc
Confidence 3456777777776553221 358999999999999988754
No 46
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. 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-associati
Probab=32.19 E-value=52 Score=27.90 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 31 DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 31 d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
...+.+++.+||..|.+..+. ...+..+...|++-|
T Consensus 40 ~~~~~eq~~~mL~~W~~r~g~----~at~~~L~~AL~~i~ 75 (84)
T cd08317 40 PNSLAQQAQAMLKLWLEREGK----KATGNSLEKALKKIG 75 (84)
T ss_pred CCCHHHHHHHHHHHHHHhcCC----cchHHHHHHHHHHcC
Confidence 345779999999999998763 344566677776655
No 47
>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=31.85 E-value=2.4e+02 Score=27.80 Aligned_cols=79 Identities=15% Similarity=0.284 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCccc--chhHHHHHHHHHHHHHHHHHHHHhhhc----CCHHHHHHhhhhhHHHHHH
Q 009068 123 FSSLDSMRDVMELLSDMLQAVNPSDREA--VKDEVIVDLVSRCRSNQKKLMQMLTTT----GDEELLGRGLELNDILQNL 196 (544)
Q Consensus 123 ~sELe~V~~nveLLnEML~~~nP~d~~~--~ddElI~EL~eqCKsmQprI~rLIeet----dDEElL~eLL~LNDeLn~a 196 (544)
.+-.+.+...+.+|.+++..+..++-.. ..-..|.+|...|..++.+|...+... -|-+ .++.+.+.+.++
T Consensus 17 ~~~~~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~I~~lE~eaD~i~~~i~~~L~~~fitP~dRe---Di~~L~~~lD~I 93 (216)
T TIGR00153 17 RQHIEKVGECVQLLIKSFELLKSGNNEKDEELRKEIIEIEHEADEIKREIRLNLEKGAFLPNDRR---DLLELAELLDEI 93 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcccccCcCcHH---HHHHHHHHHHHH
Confidence 3456778899999999998885333211 234667789999999999999988763 2322 456666666666
Q ss_pred HHHHHHHh
Q 009068 197 LAKHDAIA 204 (544)
Q Consensus 197 L~rYd~L~ 204 (544)
++.=+...
T Consensus 94 ~D~i~~~a 101 (216)
T TIGR00153 94 LDSLEHAA 101 (216)
T ss_pred HHHHHHHH
Confidence 66555544
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=31.39 E-value=1.9e+02 Score=24.99 Aligned_cols=40 Identities=18% Similarity=0.402 Sum_probs=30.5
Q ss_pred hcChHHHHHHHHhhcCCC-------------CHHHHHHHHHHHHHHHHHhCCC
Q 009068 13 IAERNVLGEMVKIVKKKP-------------DMQLRDKILVLLDSWQEAFGGP 52 (544)
Q Consensus 13 IaskeFLneLvKLv~~k~-------------d~~VKeKILeLIqsWaeaF~~~ 52 (544)
+...++++.|+..+.... ...+|.||+.+|..|-+.+..+
T Consensus 32 ~s~~~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~~~~d 84 (122)
T cd06224 32 TTPTELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENYPYD 84 (122)
T ss_pred CCHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 456778888888765432 2468999999999999988865
No 49
>PF12917 HD_2: HD containing hydrolase-like enzyme ; PDB: 3MZO_B.
Probab=31.35 E-value=1.2e+02 Score=30.99 Aligned_cols=44 Identities=23% Similarity=0.256 Sum_probs=32.5
Q ss_pred HHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHHHHhcCCCC
Q 009068 166 NQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGLPI 209 (544)
Q Consensus 166 mQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd~L~sG~~~ 209 (544)
+|+.-.+++.+--||.+-+++|.+-|.|...++-+..+.+|++-
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 46666667777666667789999999999999999999998864
No 50
>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=31.00 E-value=61 Score=28.08 Aligned_cols=44 Identities=20% Similarity=0.279 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHH------------HHHHhCCCCCCchHHHHHHHHHhhcCccCCCCCCC
Q 009068 33 QLRDKILVLLDS------------WQEAFGGPGGKHPQYYWAYEDLRRYGVQFPKRSPD 79 (544)
Q Consensus 33 ~VKeKILeLIqs------------WaeaF~~~p~klp~i~~aY~~LK~eGv~FP~~~~d 79 (544)
.++++||.+|+. -+..| +- ....|+++.+.|-.+|+.|...|++
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l-~~--~~~~v~~al~~L~~eG~IYsTiDd~ 102 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQL-GM--SENEVRKALDFLSNEGHIYSTIDDD 102 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHS-TS---HHHHHHHHHHHHHTTSEEESSSTT
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHh-Cc--CHHHHHHHHHHHHhCCeEecccCCC
Confidence 567777777776 12233 11 2567899999999999999888754
No 51
>PRK14148 heat shock protein GrpE; Provisional
Probab=30.59 E-value=2.5e+02 Score=28.14 Aligned_cols=43 Identities=14% Similarity=0.159 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 156 IVDLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 156 I~EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
+..+...+..+|+|+.+=++.. ..+.++.+||.+=|+|.++|.
T Consensus 63 ~lR~~Ae~eN~rKR~~rE~e~~~~~a~~~~~~~LLpV~DnlerAl~ 108 (195)
T PRK14148 63 ALRAKAEMENIRKRAERDVSNARKFGIEKFAKELLPVIDSIEQALK 108 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 3467777788888888777664 567888889999999888886
No 52
>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=30.58 E-value=1.7e+02 Score=22.16 Aligned_cols=42 Identities=19% Similarity=0.322 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHhhhc--CCHHHHHHhhhhhHHHHHHHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT--GDEELLGRGLELNDILQNLLAKHDAI 203 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet--dDEElL~eLL~LNDeLn~aL~rYd~L 203 (544)
+|....+.+|.++..++..- .|+ +.|++.-+|...|..|-++
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 46677788899999999874 566 4578888888888888754
No 53
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=30.49 E-value=1e+02 Score=23.04 Aligned_cols=33 Identities=27% Similarity=0.285 Sum_probs=22.0
Q ss_pred HHHHHhhhc-CCHHHHHHhhhhhH-HHHHHHHHHH
Q 009068 169 KLMQMLTTT-GDEELLGRGLELND-ILQNLLAKHD 201 (544)
Q Consensus 169 rI~rLIeet-dDEElL~eLL~LND-eLn~aL~rYd 201 (544)
+|.++++-+ -+++.-..+|+.|+ +|..++..|=
T Consensus 3 ~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~ 37 (43)
T PF14555_consen 3 KIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYF 37 (43)
T ss_dssp HHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHH
T ss_pred HHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHH
Confidence 444554443 25565668888888 9999999884
No 54
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=30.29 E-value=48 Score=36.29 Aligned_cols=65 Identities=20% Similarity=0.414 Sum_probs=39.0
Q ss_pred ccchHHHHH-------HhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCcc
Q 009068 3 KNCGDFVHF-------QIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQ 72 (544)
Q Consensus 3 KNCG~~FH~-------EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~ 72 (544)
.+||..||. -+-+++|+++|..+.... ...-+++++.||+.-.+...-. +.|+++.+..++-|+.
T Consensus 261 ~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~~~~-~l~~~~~~~klL~~i~~E~~~~----p~fydl~~ias~l~~s 332 (380)
T COG1867 261 PHCGGKVHLAGPLWLGPLHDEEFIEEMLEIAEGL-ELGTKKRALKLLKLIKKELDIS----PLFYDLHRIASKLGLS 332 (380)
T ss_pred CcccccceeccCcccCcccCHHHHHHHHHHhhcc-ccccHHHHHHHHHHHHhhcCCC----ceEEEHHHHHHHhCCC
Confidence 467776665 356999999999988765 3344666666666555544321 3344444444444433
No 55
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=30.25 E-value=60 Score=28.20 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 31 DMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 31 d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
...+.+++..+|..|.+..+ +...+..++..|++-|
T Consensus 40 p~~l~~Q~~~~L~~W~~r~g----~~At~~~L~~AL~~i~ 75 (84)
T cd08805 40 PNSLLEQSTALLNLWVDREG----ENAKMSPLYPALYSID 75 (84)
T ss_pred CCCHHHHHHHHHHHHHHhcC----ccchHHHHHHHHHHCC
Confidence 34599999999999998887 3466777888888765
No 56
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=30.22 E-value=3.9e+02 Score=30.62 Aligned_cols=91 Identities=13% Similarity=0.144 Sum_probs=61.0
Q ss_pred ccchhhHHHhhhhHHHHHHHHHHHHHHHHHHHhhCC--CCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhh
Q 009068 110 LDETMATEVETLSFSSLDSMRDVMELLSDMLQAVNP--SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGL 187 (544)
Q Consensus 110 LiKsM~~E~ekls~sELe~V~~nveLLnEML~~~nP--~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL 187 (544)
+++.|..+.+.+ .++|+..+.+.+=|.-.|....- ++-+....|-. +|...+..+.+++-.|-..+.+-+++++
T Consensus 331 ~l~kl~~eie~k-Eeei~~L~~~~d~L~~q~~kq~Is~e~fe~mn~Ere-~L~reL~~i~~~~~~L~k~V~~~~leaq-- 406 (622)
T COG5185 331 KLEKLKSEIELK-EEEIKALQSNIDELHKQLRKQGISTEQFELMNQERE-KLTRELDKINIQSDKLTKSVKSRKLEAQ-- 406 (622)
T ss_pred HHHHHHHHHHHH-HHHHHHHHhhHHHHHHHHHhcCCCHHHHHHHHHHHH-HHHHHHHHhcchHHHHHHHHHhHHHHHH--
Confidence 345566666665 67788888888877777765432 11111112222 6777888888888888888877666443
Q ss_pred hhhHHHHHHHHHHHHHh
Q 009068 188 ELNDILQNLLAKHDAIA 204 (544)
Q Consensus 188 ~LNDeLn~aL~rYd~L~ 204 (544)
..=|+|-+.|.+|+-+.
T Consensus 407 ~~~~slek~~~~~~sl~ 423 (622)
T COG5185 407 GIFKSLEKTLRQYDSLI 423 (622)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45688999999998775
No 57
>PHA03377 EBNA-3C; Provisional
Probab=30.21 E-value=4.6e+02 Score=31.52 Aligned_cols=14 Identities=29% Similarity=0.574 Sum_probs=9.0
Q ss_pred CCCCCCCCCCCCCC
Q 009068 423 AYPPPPWAPTPGYF 436 (544)
Q Consensus 423 ~yp~ppw~~~~~~~ 436 (544)
+|.+|+|+.-+++.
T Consensus 831 ~h~~p~Wdp~a~h~ 844 (1000)
T PHA03377 831 PHLPPQWDGSAGHG 844 (1000)
T ss_pred CCCCCCCCCCCCCC
Confidence 45568888766544
No 58
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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 (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=29.93 E-value=1.4e+02 Score=25.29 Aligned_cols=36 Identities=22% Similarity=0.366 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCcc
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQ 72 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~ 72 (544)
..++++.+||..|.+.-+. -.-+..+.+.|++.|..
T Consensus 37 ~~~eq~~~mL~~W~~k~G~----~At~~~L~~aL~~~~~~ 72 (79)
T cd08784 37 QHRDRVYELLRIWRNKEGR----KATLNTLIKALKDLDQR 72 (79)
T ss_pred chHHHHHHHHHHHHhccCc----CcHHHHHHHHHHHcccH
Confidence 3899999999999987763 34577777788877643
No 59
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=29.70 E-value=47 Score=32.39 Aligned_cols=11 Identities=27% Similarity=0.440 Sum_probs=7.9
Q ss_pred CCCCCCCCCCC
Q 009068 423 AYPPPPWAPTP 433 (544)
Q Consensus 423 ~yp~ppw~~~~ 433 (544)
.||+|.|+++.
T Consensus 144 ~~~~~~~~~~~ 154 (168)
T PRK06863 144 SRPAPQQAAPQ 154 (168)
T ss_pred cccCccccccc
Confidence 47888888663
No 60
>PRK14141 heat shock protein GrpE; Provisional
Probab=29.20 E-value=1.6e+02 Score=29.90 Aligned_cols=18 Identities=22% Similarity=0.235 Sum_probs=8.1
Q ss_pred HHHHHHhhhhhHHHHHHH
Q 009068 180 EELLGRGLELNDILQNLL 197 (544)
Q Consensus 180 EElL~eLL~LNDeLn~aL 197 (544)
+.++..||.+=|.|.++|
T Consensus 81 ~~~~~dLLpViDnLerAl 98 (209)
T PRK14141 81 AGFARDMLSVSDNLRRAL 98 (209)
T ss_pred HHHHHHHhhhHhHHHHHH
Confidence 444444444444444444
No 61
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=28.91 E-value=83 Score=24.26 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=18.6
Q ss_pred hcCC-CCHHHHHHHHHHHHHHHHHh
Q 009068 26 VKKK-PDMQLRDKILVLLDSWQEAF 49 (544)
Q Consensus 26 v~~k-~d~~VKeKILeLIqsWaeaF 49 (544)
+.++ .+.+|++++..||..|...+
T Consensus 28 l~k~~~~~~i~~~A~~Li~~Wk~~v 52 (53)
T PF08711_consen 28 LRKHSENPEIRKLAKELIKKWKRIV 52 (53)
T ss_dssp HHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHHHHHHHhHhc
Confidence 3444 68899999999999998654
No 62
>PRK09458 pspB phage shock protein B; Provisional
Probab=28.04 E-value=74 Score=27.45 Aligned_cols=26 Identities=4% Similarity=0.216 Sum_probs=21.5
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHH
Q 009068 148 REAVKDEVIVDLVSRCRSNQKKLMQM 173 (544)
Q Consensus 148 ~~~~ddElI~EL~eqCKsmQprI~rL 173 (544)
.+.++...+++|++..++|+.||..|
T Consensus 36 Ls~~d~~~L~~L~~~A~rm~~RI~tL 61 (75)
T PRK09458 36 LSQEEQQRLAQLTEKAERMRERIQAL 61 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456788999999999999999765
No 63
>PRK14161 heat shock protein GrpE; Provisional
Probab=27.76 E-value=3.8e+02 Score=26.45 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 156 IVDLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 156 I~EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
+..+...+..+|+|..+=.+.. .-+.++..||.+=|+|.++|.
T Consensus 42 ~lR~~AefeN~rkR~~ke~~~~~~~a~~~~~~~LLpv~DnlerAl~ 87 (178)
T PRK14161 42 LIRTTAEIDNTRKRLEKARDEAKDYAIATFAKELLNVSDNLSRALA 87 (178)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 3466777777777777766654 457777888888888887775
No 64
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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 (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=27.57 E-value=80 Score=25.56 Aligned_cols=34 Identities=29% Similarity=0.407 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCc
Q 009068 34 LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 71 (544)
Q Consensus 34 VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv 71 (544)
+.+++.+||..|....+. ...+..++..|++-|.
T Consensus 37 ~~~~~~~mL~~W~~~~~~----~at~~~L~~aL~~~~~ 70 (79)
T cd01670 37 VREQAYQLLLKWEEREGD----NATVGNLIEALREIGR 70 (79)
T ss_pred HHHHHHHHHHHHHhccCc----CcHHHHHHHHHHHcCH
Confidence 899999999999988873 3557778888887764
No 65
>PF13324 GCIP: Grap2 and cyclin-D-interacting; PDB: 3AY5_A.
Probab=27.36 E-value=4.5e+02 Score=27.01 Aligned_cols=48 Identities=13% Similarity=0.283 Sum_probs=35.2
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHhhhc----CCHHHHHHhhhhhHHHHHHHH
Q 009068 151 VKDEVIVDLVSRCRSNQKKLMQMLTTT----GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 151 ~ddElI~EL~eqCKsmQprI~rLIeet----dDEElL~eLL~LNDeLn~aL~ 198 (544)
..-+.+.+|++.|++..+.|..++..+ +-+++-..+-.|+.-|.++|.
T Consensus 222 ~~v~~Ld~L~~~~~~i~~~VDel~~slYpP~d~~~v~~~~~~L~~~l~~~l~ 273 (275)
T PF13324_consen 222 EQVAQLDKLLDLCQEISPSVDELASSLYPPQDPDEVRAAAAKLSSVLKKMLK 273 (275)
T ss_dssp T-HHHHHHHHHHHHHHHHHHHHHHHHHSSS--HHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHhhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 345778999999999999999999986 334455566666666666654
No 66
>PRK14154 heat shock protein GrpE; Provisional
Probab=27.27 E-value=2.6e+02 Score=28.33 Aligned_cols=41 Identities=17% Similarity=0.186 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
-+...+..+|+|+.+-++.+ .-+.++..||.+=|+|.++|.
T Consensus 77 Rl~ADfeNyRKR~~kE~e~~~~~a~e~~~~~LLpVlDnLeRAL~ 120 (208)
T PRK14154 77 RAQAEMDNLRKRIEREKADIIKFGSKQLITDLLPVADSLIHGLE 120 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 44444445555555544443 345555555555555555554
No 67
>PRK14143 heat shock protein GrpE; Provisional
Probab=26.60 E-value=3.1e+02 Score=28.32 Aligned_cols=41 Identities=10% Similarity=0.000 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
.+...+..+|+|..+-++.. ..+.++..||.+-|.|.++|.
T Consensus 92 R~~AdfeN~RKR~~kE~e~~~~~a~~~~~~~lLpV~DnLerAl~ 135 (238)
T PRK14143 92 RIAADFDNFRKRTSREQEDLRLQLKCNTLSEILPVVDNFERARQ 135 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHh
Confidence 55556666666666555443 456667777777777777764
No 68
>PRK14140 heat shock protein GrpE; Provisional
Probab=26.45 E-value=3.5e+02 Score=27.05 Aligned_cols=42 Identities=12% Similarity=0.138 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 157 VDLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 157 ~EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
..+...+..+|+|..+=++.. .-+.++..||.+-|+|.++|.
T Consensus 61 lR~~Ae~eN~rkR~~rE~~~~~~~a~~~~~~~LLpvlDnLerAl~ 105 (191)
T PRK14140 61 LRLQADFENYKRRIQKENEAAEKYRAQSLASDLLPALDNFERALQ 105 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 355566667777766665543 567788888888888888875
No 69
>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=26.32 E-value=2.3e+02 Score=25.93 Aligned_cols=56 Identities=14% Similarity=0.169 Sum_probs=39.8
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHhhh----cCCHHHHHHhhhhhHHHHHHHHHHHHHhcCCC
Q 009068 150 AVKDEVIVDLVSRCRSNQKKLMQMLTT----TGDEELLGRGLELNDILQNLLAKHDAIASGLP 208 (544)
Q Consensus 150 ~~ddElI~EL~eqCKsmQprI~rLIee----tdDEElL~eLL~LNDeLn~aL~rYd~L~sG~~ 208 (544)
.++...|.+....|..|-.++-.||.- +.+|+.+.+||++.--+-+.| |.+..|.-
T Consensus 31 ~eeK~~i~~~l~~~~~m~~~vd~li~~f~~lt~ne~~~k~LlqMr~~~~~q~---e~~~~~~f 90 (115)
T PF05397_consen 31 PEEKAAIRQQLQEIQDMLARVDSLIPWFYKLTKNEENTKRLLQMRIMLKEQF---EWLPQGQF 90 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHH---hhhhcCce
Confidence 345667777778888888887777764 378888888888887777776 55555543
No 70
>PF05769 DUF837: Protein of unknown function (DUF837); InterPro: IPR008555 This family consists of several eukaryotic proteins of unknown function. One of the family members (O02197 from SWISSPROT) is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke) [].
Probab=25.79 E-value=3.2e+02 Score=26.91 Aligned_cols=49 Identities=14% Similarity=0.218 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhhc---------CCHHHHHHhhhhhHHHHHHHHHHH
Q 009068 153 DEVIVDLVSRCRSNQKKLMQMLTTT---------GDEELLGRGLELNDILQNLLAKHD 201 (544)
Q Consensus 153 dElI~EL~eqCKsmQprI~rLIeet---------dDEElL~eLL~LNDeLn~aL~rYd 201 (544)
-+.+...+..|++++.-|..|=+.. .....+.+|+.=|.+|..+|+.|.
T Consensus 33 a~~l~~~i~sm~~y~eei~~l~~~~~~~~~~~l~~En~qi~~Lq~EN~eL~~~leEhq 90 (181)
T PF05769_consen 33 AEALNKQIESMRQYQEEIQELNELSKNRPRAGLQQENRQIRQLQQENRELRQSLEEHQ 90 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666666655442211 123346788888988888888875
No 71
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=25.65 E-value=1.3e+02 Score=32.79 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=39.4
Q ss_pred HhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCC-------------CchHHHHHHHHHhhcCcc
Q 009068 12 QIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGG-------------KHPQYYWAYEDLRRYGVQ 72 (544)
Q Consensus 12 EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~-------------klp~i~~aY~~LK~eGv~ 72 (544)
.|-+++|++.|...+.+......++|+..||....+.....|- ..|.+..+...|++.||.
T Consensus 279 pL~d~~fl~~ml~~~~~~~~~~~~~ri~~lL~~i~eE~~~~P~yY~l~~ias~lk~~~P~~~~ii~aL~~~Gy~ 352 (377)
T PF02005_consen 279 PLHDKEFLEKMLEEAEEMPELNTSKRIEKLLETIKEELIDPPFYYDLHEIASRLKCNPPPLDKIISALRNAGYR 352 (377)
T ss_dssp -SB-HHHHHHHHHHHCT-S-TTTHHHHHHHHHHHHHCHS-SSS-EEHHHHHHHHT-SC--HHHHHHHHHHTTTT
T ss_pred ccCCHHHHHHHHhhhhccchhhhHHHHhhhcchhhhhcccceeEEeHHHHHHhcCCCCCCHHHHHHHHhhcceE
Confidence 4668999999999887754444589999999999887543332 123445666677777765
No 72
>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=25.57 E-value=2.1e+02 Score=32.44 Aligned_cols=33 Identities=21% Similarity=0.297 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc--CCHHHHHHhhh
Q 009068 156 IVDLVSRCRSNQKKLMQMLTTT--GDEELLGRGLE 188 (544)
Q Consensus 156 I~EL~eqCKsmQprI~rLIeet--dDEElL~eLL~ 188 (544)
+..|+...++|..++-++|..+ -||++++.||.
T Consensus 305 l~~L~~~~~~l~~~l~~vI~SvaKiDeRLIG~L~~ 339 (498)
T PF03273_consen 305 LEQLHAHFNKLSNMLNTVIQSVAKIDERLIGRLMG 339 (498)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTT-TTHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhc
Confidence 5678888888999999999887 58899999986
No 73
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=25.30 E-value=91 Score=25.26 Aligned_cols=33 Identities=24% Similarity=0.451 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 34 LRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 34 VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
+++++.+||..|....+. ...+..+...|++-|
T Consensus 39 ~~~~~~~~L~~W~~~~~~----~at~~~L~~aL~~~~ 71 (83)
T PF00531_consen 39 LREQTYEMLQRWRQREGP----NATVDQLIQALRDIG 71 (83)
T ss_dssp HHHHHHHHHHHHHHHHGS----TSSHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHHHhcCC----CCcHHHHHHHHHHCC
Confidence 999999999999999543 344556666666544
No 74
>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=25.02 E-value=91 Score=26.79 Aligned_cols=26 Identities=4% Similarity=0.198 Sum_probs=21.7
Q ss_pred cccchhHHHHHHHHHHHHHHHHHHHH
Q 009068 148 REAVKDEVIVDLVSRCRSNQKKLMQM 173 (544)
Q Consensus 148 ~~~~ddElI~EL~eqCKsmQprI~rL 173 (544)
.+.++.+.+++|+++.+.|+.||.-|
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 44556788999999999999998765
No 75
>PRK14162 heat shock protein GrpE; Provisional
Probab=24.92 E-value=3.5e+02 Score=27.07 Aligned_cols=41 Identities=17% Similarity=0.097 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
.+...+..+|+|..+=++.. .-+.++..||.+=|+|.+||.
T Consensus 64 R~~AEfeN~rkR~~kE~e~~~~~a~~~~~~~LLpV~DnLerAl~ 107 (194)
T PRK14162 64 RSQAEIQNMQNRYAKERAQLIKYESQSLAKDVLPAMDNLERALA 107 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHHh
Confidence 55555666666666655543 456667777777777777764
No 76
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=23.80 E-value=1.3e+02 Score=25.10 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=19.4
Q ss_pred hcCCCCHHHHHHHHHHHHHHHHHh
Q 009068 26 VKKKPDMQLRDKILVLLDSWQEAF 49 (544)
Q Consensus 26 v~~k~d~~VKeKILeLIqsWaeaF 49 (544)
+.++.+++|+..+..||..|...+
T Consensus 52 Lrkh~~~~i~~~A~~Lv~~Wk~~v 75 (76)
T cd00183 52 LRKHSNEKIRKLAKALIKSWKKLV 75 (76)
T ss_pred HHcCCcHHHHHHHHHHHHHHHHhc
Confidence 344556899999999999998754
No 77
>PRK14139 heat shock protein GrpE; Provisional
Probab=23.77 E-value=3.7e+02 Score=26.71 Aligned_cols=40 Identities=13% Similarity=0.140 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLL 197 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL 197 (544)
.+...+..+|+|+.+=.+.. .-+.++.+||.+-|+|.++|
T Consensus 57 R~~AefeN~rKR~~kE~e~~~~~a~~~~~~~LLpv~DnLerAl 99 (185)
T PRK14139 57 RAKAETENVRRRAQEDVAKAHKFAIESFAESLLPVKDSLEAAL 99 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhHHHHHH
Confidence 55555566666666655543 34566667777777776666
No 78
>PRK14145 heat shock protein GrpE; Provisional
Probab=23.57 E-value=4.1e+02 Score=26.74 Aligned_cols=43 Identities=19% Similarity=0.206 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHHH
Q 009068 157 VDLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLAK 199 (544)
Q Consensus 157 ~EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~r 199 (544)
..+...+..+|+|+.+=++.. .-+.++..||.+-|+|.++|..
T Consensus 69 lR~~AEfeN~rkR~~kE~e~~~~~a~e~~~~~LLpV~DnLerAl~~ 114 (196)
T PRK14145 69 QRLKAEFENYRKRTEKEKSEMVEYGKEQVILELLPVMDNFERALAS 114 (196)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHhc
Confidence 356666667777776666553 4577777888888888877743
No 79
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=23.21 E-value=4.4e+02 Score=25.53 Aligned_cols=54 Identities=22% Similarity=0.308 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCcccc--hhHHHHHHHHHHHHHHHHHHHHhhh
Q 009068 123 FSSLDSMRDVMELLSDMLQAVNPSDREAV--KDEVIVDLVSRCRSNQKKLMQMLTT 176 (544)
Q Consensus 123 ~sELe~V~~nveLLnEML~~~nP~d~~~~--ddElI~EL~eqCKsmQprI~rLIee 176 (544)
..-++.+..++..+.++|..+-.++.... --+-|.++-..|..++.+|+..+..
T Consensus 14 ~~~~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~i~~lE~~aD~i~~~i~~~L~~ 69 (214)
T PF01865_consen 14 FDHFEEVAEASVLLAELLEAYLEGDYEDVEELLEEIKELEHEADEIKREIREELYK 69 (214)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHCTT-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677788888888888888865442222 2366778889999999999998877
No 80
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=23.10 E-value=1.3e+02 Score=30.18 Aligned_cols=38 Identities=18% Similarity=0.218 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCccC
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGVQF 73 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv~F 73 (544)
+|-+-.|.+-..|.+ ..|=.-..|+++|+.|+.+|-.+
T Consensus 148 EvVEeAl~V~~~~~e---~~PLqP~HIREA~rrL~~qgk~~ 185 (195)
T KOG3219|consen 148 EVVEEALDVREEWGE---SGPLQPKHIREAYRRLKLQGKLP 185 (195)
T ss_pred HHHHHHHHHHHHhcc---CCCCCcHHHHHHHHHHHhcCCCC
Confidence 678899999999998 22322345999999999999766
No 81
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=22.56 E-value=1.1e+02 Score=26.53 Aligned_cols=36 Identities=17% Similarity=0.170 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcC
Q 009068 32 MQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYG 70 (544)
Q Consensus 32 ~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eG 70 (544)
..+++++.+||..|....+.. ...+..+...|++-|
T Consensus 40 ~~~~eq~~~mL~~W~~r~g~~---~ATv~~L~~aL~~~~ 75 (86)
T cd08777 40 DGLKEKVHQMLHKWKMKEGSK---GATVGKLAQALEGCI 75 (86)
T ss_pred CCHHHHHHHHHHHHHHccCCC---CcHHHHHHHHHHHcc
Confidence 358999999999999887632 244566666666544
No 82
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=22.40 E-value=1.4e+02 Score=31.45 Aligned_cols=61 Identities=11% Similarity=0.171 Sum_probs=46.8
Q ss_pred cccchHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHH
Q 009068 2 VKNCGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDL 66 (544)
Q Consensus 2 VKNCG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~L 66 (544)
++.|.+.|-..+++.+|...+.++++.- ..+|.+.=+++..|-..+.-. . -..|.++|++|
T Consensus 221 i~~ae~~~~~~~~S~ef~~~~g~~~~a~--m~~r~~~~~~~e~~L~~l~lP-T-r~evd~l~k~l 281 (293)
T PF09712_consen 221 IDAAEEAYEELFRSEEFAQAYGQLVNAL--MDLRKQQQEVVEEYLRSLNLP-T-RSEVDELYKRL 281 (293)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCCCC-C-HHHHHHHHHHH
Confidence 4678888999999999999999998764 478888999999998887632 2 34566666643
No 83
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.32 E-value=4.7e+02 Score=27.36 Aligned_cols=81 Identities=28% Similarity=0.313 Sum_probs=50.1
Q ss_pred HHHHHHHHHHhh--CCCCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCC-HHHHHHh----hhhhHHHHHHHHHHHHHh
Q 009068 132 VMELLSDMLQAV--NPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGD-EELLGRG----LELNDILQNLLAKHDAIA 204 (544)
Q Consensus 132 nveLLnEML~~~--nP~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdD-EElL~eL----L~LNDeLn~aL~rYd~L~ 204 (544)
++.+..-|+... +-+.+.....+.+ +|....++.|+++.+|..++.+ |..+... +..+-.|++-|+++..+.
T Consensus 27 ~~~l~~~~~a~~~q~~k~~~~~~~r~~-~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~a 105 (247)
T COG3879 27 AMLLAGVMLAAVFQTSKGESVRRARDL-DLVKELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLA 105 (247)
T ss_pred HHHHHHHHHHHHHhhccCcchhhhhhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHh
Confidence 444555555443 2234444555666 9999999999999999887733 3333333 355666666677777766
Q ss_pred cCCCCCCCC
Q 009068 205 SGLPIPTEV 213 (544)
Q Consensus 205 sG~~~~~e~ 213 (544)
...++.++.
T Consensus 106 G~v~V~G~G 114 (247)
T COG3879 106 GSVPVTGPG 114 (247)
T ss_pred ccCCCcCCc
Confidence 555554443
No 84
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.32 E-value=5.8e+02 Score=32.22 Aligned_cols=44 Identities=7% Similarity=0.117 Sum_probs=24.2
Q ss_pred chHHHHHHhcChHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhC
Q 009068 5 CGDFVHFQIAERNVLGEMVKIVKKKPDMQLRDKILVLLDSWQEAFG 50 (544)
Q Consensus 5 CG~~FH~EIaskeFLneLvKLv~~k~d~~VKeKILeLIqsWaeaF~ 50 (544)
|...|..+=...+|++.|...+...+ ...+.+-..+..|...+.
T Consensus 683 C~R~f~~eee~~~f~~~L~~~~~~~p--~~~~~~~~~~~~~~~~~e 726 (1311)
T TIGR00606 683 CQRVFQTEAELQEFISDLQSKLRLAP--DKLKSTESELKKKEKRRD 726 (1311)
T ss_pred CCCCCCChhHHHHHHHHHHHHHhcch--hhHHHHHHHHHHHHHHHH
Confidence 55555544333577777766665532 344444555556666554
No 85
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. 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 (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.20 E-value=1.6e+02 Score=25.29 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCCchHHHHHHHHHhhcCc
Q 009068 33 QLRDKILVLLDSWQEAFGGPGGKHPQYYWAYEDLRRYGV 71 (544)
Q Consensus 33 ~VKeKILeLIqsWaeaF~~~p~klp~i~~aY~~LK~eGv 71 (544)
.+++++.+||..|.+..+.. .-+..+...|++-|.
T Consensus 44 ~~~eq~~~mL~~W~~r~g~~----AT~~~L~~aL~~~~~ 78 (86)
T cd08318 44 DIKMQAKQLLVAWQDREGSQ----ATPETLITALNAAGL 78 (86)
T ss_pred CHHHHHHHHHHHHHHhcCcc----ccHHHHHHHHHHcCc
Confidence 57999999999999888743 446667777777664
No 86
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=22.05 E-value=2.6e+02 Score=29.74 Aligned_cols=48 Identities=27% Similarity=0.455 Sum_probs=29.7
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHhhC-CCCcccch-hHHHHHHHHHHHHH
Q 009068 119 ETLSFSSLDSMRDVMELLSDMLQAVN-PSDREAVK-DEVIVDLVSRCRSN 166 (544)
Q Consensus 119 ekls~sELe~V~~nveLLnEML~~~n-P~d~~~~d-dElI~EL~eqCKsm 166 (544)
.++...+++.++...+.|+.+|..+| |+.-...+ ..+=..|.+.|..+
T Consensus 16 ~~lv~~~~~~l~~~~~~l~~~L~slnLP~sl~~l~~~~lP~sl~~~~~~i 65 (339)
T cd09235 16 AELVNREIGKLREATQLLNGVLASLNLPAAIEDVSGDTVPQSLLEKSRTV 65 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHhcCCCCCHHHHHHHHHH
Confidence 34446778899999999999998887 43311111 12444555555555
No 87
>PF11867 DUF3387: Domain of unknown function (DUF3387); InterPro: IPR021810 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with PF04851 from PFAM, PF04313 from PFAM.
Probab=21.91 E-value=6.9e+02 Score=26.46 Aligned_cols=64 Identities=16% Similarity=0.179 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhh-c-CCHHHHHHhhhhhH
Q 009068 126 LDSMRDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT-T-GDEELLGRGLELND 191 (544)
Q Consensus 126 Le~V~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIee-t-dDEElL~eLL~LND 191 (544)
...-+.=.+.|.++|..++-+. ....+++.+|++-.+.++..-.+-... + ++|-.+..+|.-|+
T Consensus 193 ~~~~~~fsErLe~iI~~Y~~~~--i~~~e~~~eLi~la~el~~~~~r~~~~gLseeE~AFyd~L~~~~ 258 (335)
T PF11867_consen 193 PVRYKKFSERLEEIIEKYNNRS--ISSEEVIEELIKLAKELREEEERAEELGLSEEELAFYDALAKNE 258 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHccc--chHHHHHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHccc
Confidence 3333456678888888887543 346788888888877777654444332 2 23334445565443
No 88
>COG5278 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=21.89 E-value=5.5e+02 Score=25.97 Aligned_cols=68 Identities=19% Similarity=0.146 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHHhhCC--CCcccchhHHHHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHH
Q 009068 126 LDSMRDVMELLSDMLQAVNP--SDREAVKDEVIVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDIL 193 (544)
Q Consensus 126 Le~V~~nveLLnEML~~~nP--~d~~~~ddElI~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeL 193 (544)
-+......+|+..|++..+- +=.--.+++.+...++.-+.+..++-++-..+.|++...+.|..+..+
T Consensus 47 ~~~~~a~~~l~s~~~~~esgqRGYLLTG~~~yL~py~~a~~~~~~~~~~l~~l~~d~p~~~~~l~~l~~~ 116 (207)
T COG5278 47 QQVLAAALDLLSAVSDAESGQRGYLLTGNDEYLEPYEEATEELDQKLEELRALTADDPELLESLDDLEPL 116 (207)
T ss_pred HHHHHHHHHHHHHHHHHHhcCcceeecCCHhhhhHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 34445677788888877653 323445789999999999999998888887775544445666655553
No 89
>PRK14155 heat shock protein GrpE; Provisional
Probab=21.81 E-value=3e+02 Score=27.79 Aligned_cols=18 Identities=17% Similarity=0.047 Sum_probs=7.7
Q ss_pred HHHHHHhhhhhHHHHHHH
Q 009068 180 EELLGRGLELNDILQNLL 197 (544)
Q Consensus 180 EElL~eLL~LNDeLn~aL 197 (544)
+.++..||.+=|+|.++|
T Consensus 63 ~~~~~~LLpV~DnLerAl 80 (208)
T PRK14155 63 QKFARDLLGAADNLGRAT 80 (208)
T ss_pred HHHHHHHhhHHhhHHHHH
Confidence 334444444444444444
No 90
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=21.02 E-value=1.3e+02 Score=34.24 Aligned_cols=29 Identities=24% Similarity=0.338 Sum_probs=24.6
Q ss_pred HHHhhhhhHHHHHHHHHHHHHhcCCCCCC
Q 009068 183 LGRGLELNDILQNLLAKHDAIASGLPIPT 211 (544)
Q Consensus 183 L~eLL~LNDeLn~aL~rYd~L~sG~~~~~ 211 (544)
|++--++||.-..+|..|+.+++.+..+.
T Consensus 207 laqqy~~ndm~~ealntyeiivknkmf~n 235 (840)
T KOG2003|consen 207 LAQQYEANDMTAEALNTYEIIVKNKMFPN 235 (840)
T ss_pred HHHHhhhhHHHHHHhhhhhhhhcccccCC
Confidence 45556899999999999999999888763
No 91
>PRK14163 heat shock protein GrpE; Provisional
Probab=20.64 E-value=4.3e+02 Score=26.94 Aligned_cols=41 Identities=15% Similarity=0.112 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHhhhc---CCHHHHHHhhhhhHHHHHHHH
Q 009068 158 DLVSRCRSNQKKLMQMLTTT---GDEELLGRGLELNDILQNLLA 198 (544)
Q Consensus 158 EL~eqCKsmQprI~rLIeet---dDEElL~eLL~LNDeLn~aL~ 198 (544)
.+...+..+|+|+.+=++.. ..+.++..||.+=|+|.++|.
T Consensus 65 R~~AEfeN~rkR~~kE~e~~~~~a~~~~~~~LLpVlDnLerAl~ 108 (214)
T PRK14163 65 RLQAEYQNYRRRVERDRVTVKEIAVANLLSELLPVLDDVGRARE 108 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHhHHHHHHh
Confidence 55555666666666655543 456677777777777777764
No 92
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=20.18 E-value=1.9e+02 Score=28.48 Aligned_cols=17 Identities=29% Similarity=0.432 Sum_probs=10.1
Q ss_pred CHHHHHHhhhhhHHHHH
Q 009068 179 DEELLGRGLELNDILQN 195 (544)
Q Consensus 179 DEElL~eLL~LNDeLn~ 195 (544)
|.++|+++|+++++|.+
T Consensus 94 Dpe~Lmevle~~E~IS~ 110 (168)
T KOG3192|consen 94 DPEFLMEVLEYHEAISE 110 (168)
T ss_pred CHHHHHHHHHHHHHHHh
Confidence 55666666666665543
No 93
>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=20.10 E-value=3.6e+02 Score=25.58 Aligned_cols=52 Identities=23% Similarity=0.312 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCHHHHHHhhhhhHHHHHHHHHHHHHhcCC
Q 009068 156 IVDLVSRCRSNQKKLMQMLTTTGDEELLGRGLELNDILQNLLAKHDAIASGL 207 (544)
Q Consensus 156 I~EL~eqCKsmQprI~rLIeetdDEElL~eLL~LNDeLn~aL~rYd~L~sG~ 207 (544)
+.+|-..|+.++..|..|.....++++...+-++-.++...-.+-+.|..+.
T Consensus 88 l~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~ 139 (169)
T PF07106_consen 88 LAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRSGS 139 (169)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4578888899999999999988899998898899999999888888888644
No 94
>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=20.05 E-value=4.2e+02 Score=25.98 Aligned_cols=40 Identities=10% Similarity=0.277 Sum_probs=29.0
Q ss_pred HHHHHHhhCCCCc-ccchhHHHHHHHHHHHHHHHHHHHHhh
Q 009068 136 LSDMLQAVNPSDR-EAVKDEVIVDLVSRCRSNQKKLMQMLT 175 (544)
Q Consensus 136 LnEML~~~nP~d~-~~~ddElI~EL~eqCKsmQprI~rLIe 175 (544)
|..|.-++.-+++ ..+-.+.+.++.+.|+.++.++..|+.
T Consensus 33 L~~Mv~~lT~gkk~~~~~~~~~~~~~~~~~~~~~~ll~l~d 73 (184)
T PF04961_consen 33 LGSMVANLTLGKKKYEDVEEELKEIIEKLEELREELLDLAD 73 (184)
T ss_dssp HHHHHHHCTTTSTTSGGGHHHHHHHHHHHHHHHHHHHCHHH
T ss_pred HHHHHHHHhCCCccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4457777765443 223457888999999999999988885
No 95
>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=20.02 E-value=6.1e+02 Score=22.33 Aligned_cols=47 Identities=6% Similarity=0.087 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhhCCCCcccchhHHHHHHHHHHHHHHHHHHHHhhh
Q 009068 130 RDVMELLSDMLQAVNPSDREAVKDEVIVDLVSRCRSNQKKLMQMLTT 176 (544)
Q Consensus 130 ~~nveLLnEML~~~nP~d~~~~ddElI~EL~eqCKsmQprI~rLIee 176 (544)
.....-+.+.|..+........+.+++.++.+..+.++....+++..
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~ 131 (181)
T PF12729_consen 85 DEARAEIDEALEEYEKLILSPEEKQLLEEFKEAWKAYRKLRDQVIEL 131 (181)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444444444322222234556666666666665555555443
Done!