Query psy7982
Match_columns 72
No_of_seqs 22 out of 24
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 23:48:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7982.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7982hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0193|consensus 92.5 0.074 1.6E-06 45.6 1.9 30 37-66 20-49 (678)
2 PF15188 CCDC-167: Coiled-coil 77.5 17 0.00038 23.8 7.1 56 2-57 4-62 (85)
3 PF10267 Tmemb_cc2: Predicted 76.1 18 0.00039 29.1 7.4 51 2-62 218-268 (395)
4 PF08663 HalX: HalX domain; I 71.4 7.2 0.00016 24.4 3.4 26 38-63 36-61 (71)
5 PRK10636 putative ABC transpor 67.8 45 0.00097 27.2 8.0 56 3-62 563-629 (638)
6 PF14712 Snapin_Pallidin: Snap 63.9 26 0.00057 21.3 4.8 47 17-66 35-85 (92)
7 PF12325 TMF_TATA_bd: TATA ele 62.7 40 0.00087 22.9 5.9 29 36-64 66-94 (120)
8 PF13438 DUF4113: Domain of un 58.9 5.6 0.00012 23.1 1.1 11 18-28 7-17 (52)
9 PF00046 Homeobox: Homeobox do 57.7 17 0.00037 19.9 2.9 32 13-47 6-37 (57)
10 PF08614 ATG16: Autophagy prot 52.1 78 0.0017 22.0 6.6 54 2-62 129-182 (194)
11 cd07666 BAR_SNX7 The Bin/Amphi 51.7 51 0.0011 24.8 5.4 33 17-53 37-69 (243)
12 PRK04270 H/ACA RNA-protein com 50.3 11 0.00023 28.5 1.6 22 14-36 96-119 (300)
13 PF13543 KSR1-SAM: SAM like do 49.5 82 0.0018 21.9 5.8 45 6-53 2-46 (129)
14 TIGR00634 recN DNA repair prot 49.1 76 0.0017 25.5 6.3 46 9-58 136-181 (563)
15 PF08248 Tryp_FSAP: Tryptophyl 48.8 6.3 0.00014 18.2 0.1 6 32-37 6-11 (12)
16 COG2900 SlyX Uncharacterized p 48.4 23 0.0005 23.0 2.7 23 8-30 34-56 (72)
17 PF14257 DUF4349: Domain of un 48.0 36 0.00078 24.3 4.0 51 12-64 100-158 (262)
18 PF10234 Cluap1: Clusterin-ass 46.7 62 0.0013 24.9 5.3 47 6-52 193-239 (267)
19 PF10393 Matrilin_ccoil: Trime 45.4 45 0.00097 19.7 3.5 18 40-57 25-42 (47)
20 PF14767 RPA_interact_M: Repli 41.8 37 0.00081 21.7 3.0 44 1-51 8-53 (83)
21 PF04533 Herpes_U44: Herpes vi 40.1 12 0.00026 28.3 0.5 26 14-43 125-150 (210)
22 PF14278 TetR_C_8: Transcripti 39.5 66 0.0014 17.5 3.7 33 8-40 31-63 (77)
23 PF09036 Bcr-Abl_Oligo: Bcr-Ab 39.4 81 0.0018 20.9 4.3 38 19-57 8-45 (79)
24 PHA00489 scaffolding protein 39.2 39 0.00085 23.3 2.9 23 36-58 39-61 (101)
25 PRK10869 recombination and rep 37.4 1.8E+02 0.0039 23.7 6.8 42 11-56 134-182 (553)
26 COG5278 Predicted periplasmic 37.3 46 0.001 24.5 3.2 24 35-58 77-100 (207)
27 PF03961 DUF342: Protein of un 37.2 2E+02 0.0043 22.4 8.2 62 3-64 334-408 (451)
28 PF07341 DUF1473: Protein of u 37.0 11 0.00024 27.8 -0.1 16 27-42 99-114 (163)
29 cd02896 complement_C3_C4_C5 Pr 37.0 56 0.0012 23.8 3.6 39 5-48 2-40 (297)
30 cd02897 A2M_2 Proteins similar 36.7 63 0.0014 23.1 3.8 39 5-48 2-40 (292)
31 PF11418 Scaffolding_pro: Phi2 35.8 71 0.0015 21.9 3.7 25 35-59 37-61 (97)
32 PF01509 TruB_N: TruB family p 35.5 17 0.00036 25.1 0.6 25 11-36 69-95 (149)
33 KOG3968|consensus 35.5 29 0.00062 28.9 2.1 58 8-66 236-298 (439)
34 PHA02109 hypothetical protein 35.1 1.1E+02 0.0024 23.6 5.0 39 15-64 181-219 (233)
35 COG3102 Uncharacterized protei 34.4 47 0.001 24.9 2.9 25 38-62 8-32 (185)
36 PRK00130 truB tRNA pseudouridi 33.9 26 0.00056 26.9 1.5 23 13-36 93-117 (290)
37 TIGR00425 CBF5 rRNA pseudourid 33.5 28 0.00061 26.9 1.7 22 14-36 108-131 (322)
38 cd00506 PseudoU_synth_TruB_lik 33.3 23 0.00051 25.8 1.1 24 12-36 90-115 (210)
39 PF14304 CSTF_C: Transcription 33.0 17 0.00037 21.6 0.3 17 6-22 9-25 (46)
40 KOG0709|consensus 32.3 82 0.0018 26.6 4.2 45 14-65 269-313 (472)
41 PRK11147 ABC transporter ATPas 32.2 2.8E+02 0.006 22.5 7.3 54 5-62 570-626 (635)
42 PRK01550 truB tRNA pseudouridi 32.1 30 0.00064 26.8 1.6 22 14-36 95-118 (304)
43 KOG3915|consensus 30.7 1.6E+02 0.0035 25.7 5.7 25 4-28 504-528 (641)
44 PRK05561 DNA topoisomerase IV 30.5 1.9E+02 0.0041 24.9 6.1 32 5-37 392-426 (742)
45 PRK04642 truB tRNA pseudouridi 30.1 32 0.0007 26.7 1.5 23 13-36 101-125 (300)
46 PRK03287 truB tRNA pseudouridi 30.1 33 0.00072 26.5 1.5 23 13-36 100-124 (298)
47 PRK00989 truB tRNA pseudouridi 29.9 34 0.00075 25.7 1.6 22 14-36 101-124 (230)
48 KOG3850|consensus 29.8 3.5E+02 0.0075 22.9 7.8 26 2-27 266-291 (455)
49 PF13870 DUF4201: Domain of un 29.7 1.8E+02 0.0039 19.7 7.7 35 19-53 128-167 (177)
50 PRK02755 truB tRNA pseudouridi 29.4 34 0.00074 26.4 1.5 23 13-36 93-117 (295)
51 COG4064 MtrG Tetrahydromethano 28.5 60 0.0013 21.4 2.3 25 32-56 7-33 (75)
52 PF01337 Barstar: Barstar (bar 28.3 28 0.00061 21.0 0.7 43 17-62 30-76 (90)
53 PF04977 DivIC: Septum formati 28.3 1.2E+02 0.0027 17.2 4.2 27 38-64 24-50 (80)
54 PF00957 Synaptobrevin: Synapt 27.9 1.4E+02 0.0031 17.9 6.6 42 7-66 11-52 (89)
55 PF09958 DUF2192: Uncharacteri 27.8 99 0.0021 23.7 3.7 51 13-64 25-101 (231)
56 PRK05389 truB tRNA pseudouridi 27.7 38 0.00083 26.2 1.5 23 13-36 103-127 (305)
57 PF03961 DUF342: Protein of un 27.4 2E+02 0.0044 22.4 5.4 16 38-53 389-404 (451)
58 PRK14124 tRNA pseudouridine sy 27.3 39 0.00085 26.3 1.5 23 13-36 93-117 (308)
59 PF00804 Syntaxin: Syntaxin; 27.2 1.3E+02 0.0029 17.3 7.0 32 3-34 7-38 (103)
60 TIGR01149 mtrG N5-methyltetrah 27.1 63 0.0014 20.9 2.2 23 33-55 5-29 (70)
61 PF07200 Mod_r: Modifier of ru 27.0 1.5E+02 0.0032 19.4 4.0 46 12-57 105-150 (150)
62 PF12896 Apc4: Anaphase-promot 26.9 76 0.0016 21.6 2.7 61 6-67 27-88 (210)
63 PRK00020 truB tRNA pseudouridi 26.6 44 0.00095 25.4 1.6 23 13-36 103-127 (244)
64 COG3461 Uncharacterized conser 26.5 1.4E+02 0.003 20.6 3.9 32 26-64 2-33 (103)
65 cd05140 Barstar_AU1054-like Ba 26.2 1.3E+02 0.0028 19.0 3.5 33 17-49 30-63 (86)
66 PF14823 Sirohm_synth_C: Siroh 26.1 71 0.0015 19.8 2.3 30 4-33 40-69 (70)
67 PRK03830 small acid-soluble sp 26.0 79 0.0017 20.6 2.5 23 5-27 11-33 (73)
68 COG0130 TruB Pseudouridine syn 25.9 46 0.001 25.4 1.7 21 15-36 91-113 (271)
69 PF09025 YopR_core: YopR Core; 25.9 1.6E+02 0.0034 21.4 4.2 48 19-66 54-104 (142)
70 PF00508 PPV_E2_N: E2 (early) 25.9 97 0.0021 23.1 3.3 21 41-61 2-22 (202)
71 PF11553 DUF3231: Protein of u 25.6 80 0.0017 21.1 2.6 30 8-37 52-81 (166)
72 PF09712 PHA_synth_III_E: Poly 25.2 1.6E+02 0.0036 22.3 4.5 43 19-62 221-263 (293)
73 COG0380 OtsA Trehalose-6-phosp 25.1 54 0.0012 27.2 2.0 31 9-39 335-365 (486)
74 PRK04099 truB tRNA pseudouridi 25.0 46 0.001 25.5 1.5 24 12-36 91-116 (273)
75 TIGR02875 spore_0_A sporulatio 25.0 62 0.0013 22.0 2.0 24 6-29 209-234 (262)
76 PRK05033 truB tRNA pseudouridi 24.8 48 0.001 25.9 1.6 23 13-36 100-124 (312)
77 PRK01851 truB tRNA pseudouridi 24.3 50 0.0011 25.7 1.6 22 14-36 107-130 (303)
78 TIGR03090 SASP_tlp small, acid 24.0 1.1E+02 0.0025 19.7 3.0 20 5-24 10-29 (70)
79 PRK01528 truB tRNA pseudouridi 23.9 53 0.0011 25.4 1.7 22 14-36 94-117 (292)
80 PF11488 Lge1: Transcriptional 23.6 58 0.0013 20.2 1.6 15 9-23 64-78 (80)
81 PF11083 Streptin-Immun: Lanti 23.6 61 0.0013 22.1 1.8 34 20-53 55-88 (99)
82 PF09602 PhaP_Bmeg: Polyhydrox 23.6 1.1E+02 0.0024 22.4 3.2 21 38-58 85-105 (165)
83 TIGR01837 PHA_granule_1 poly(h 23.5 1.2E+02 0.0026 20.0 3.1 21 37-57 95-115 (118)
84 PF07369 DUF1488: Protein of u 23.4 1.4E+02 0.0031 17.8 3.2 33 19-51 34-66 (83)
85 PRK02484 truB tRNA pseudouridi 23.4 53 0.0011 25.3 1.6 22 14-36 96-119 (294)
86 KOG3647|consensus 23.4 2.9E+02 0.0062 22.5 5.7 49 4-52 134-182 (338)
87 PRK14122 tRNA pseudouridine sy 22.9 54 0.0012 25.6 1.6 24 12-36 91-116 (312)
88 PF04380 BMFP: Membrane fusoge 22.5 1.7E+02 0.0036 18.2 3.5 23 3-25 50-72 (79)
89 PRK02899 adaptor protein; Prov 22.5 1.8E+02 0.0039 20.9 4.1 37 15-51 153-189 (197)
90 PF08656 DASH_Dad3: DASH compl 22.1 1.3E+02 0.0029 19.4 3.0 30 17-46 17-49 (78)
91 KOG2512|consensus 21.9 1.1E+02 0.0024 24.8 3.1 48 10-57 41-95 (337)
92 TIGR00431 TruB tRNA pseudourid 21.8 58 0.0013 23.9 1.5 22 14-36 93-116 (209)
93 PF07106 TBPIP: Tat binding pr 21.7 2.6E+02 0.0057 18.8 6.6 54 3-61 79-132 (169)
94 PF12579 DUF3755: Protein of u 21.7 1.1E+02 0.0025 16.9 2.3 18 10-27 10-27 (35)
95 KOG0250|consensus 21.5 5.3E+02 0.011 24.1 7.5 58 5-62 705-762 (1074)
96 cd03572 ENTH_epsin_related ENT 21.2 2.5E+02 0.0053 19.1 4.3 37 26-62 10-48 (122)
97 cd02867 PseudoU_synth_TruB_4 P 21.1 46 0.001 26.0 0.9 44 11-66 118-163 (312)
98 KOG4586|consensus 21.0 52 0.0011 24.2 1.1 15 21-35 111-125 (156)
99 cd07667 BAR_SNX30 The Bin/Amph 21.0 2.9E+02 0.0064 20.9 5.1 35 19-58 37-71 (240)
100 PF14728 PHTB1_C: PTHB1 C-term 20.7 4.1E+02 0.009 21.1 6.1 56 9-64 163-226 (377)
101 KOG0964|consensus 20.6 2.3E+02 0.0049 26.7 5.1 56 2-57 396-451 (1200)
102 COG0180 TrpS Tryptophanyl-tRNA 20.5 99 0.0021 24.3 2.6 30 9-38 156-185 (314)
103 smart00389 HOX Homeodomain. DN 20.4 1.5E+02 0.0033 15.6 3.3 32 13-47 6-37 (56)
104 PF05974 DUF892: Domain of unk 20.4 1.3E+02 0.0028 20.4 2.8 27 8-34 40-66 (159)
105 PRK01026 tetrahydromethanopter 20.4 1.2E+02 0.0026 19.9 2.5 23 33-55 8-32 (77)
106 PF08826 DMPK_coil: DMPK coile 20.2 2.2E+02 0.0049 17.4 4.4 29 38-66 25-53 (61)
107 cd02868 PseudoU_synth_hTruB2_l 20.2 56 0.0012 24.1 1.1 26 11-36 96-122 (226)
No 1
>KOG0193|consensus
Probab=92.54 E-value=0.074 Score=45.61 Aligned_cols=30 Identities=57% Similarity=0.646 Sum_probs=28.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy7982 37 LEEYAELTSKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 37 L~EY~ElTsKL~~le~re~~L~E~~~~~~~ 66 (72)
++||+|.|||+++++.++++++|.++.+..
T Consensus 20 ~~~~~~~~s~~~~~~~~~~~~~e~l~~~~~ 49 (678)
T KOG0193|consen 20 LEEYAESTSKLIELEVRERELMERLASGTT 49 (678)
T ss_pred HHHhhhhhhhhhhhhcchhhhhhhhccccc
Confidence 899999999999999999999999997765
No 2
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=77.46 E-value=17 Score=23.80 Aligned_cols=56 Identities=25% Similarity=0.358 Sum_probs=42.8
Q ss_pred hhHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhH---HHHHHHHHhHHHHHHHHHHH
Q psy7982 2 CDELDNIQSVICLTRENIEALNSKFAAYQEPPSIYL---EEYAELTSKLHELEAREAKL 57 (72)
Q Consensus 2 ~eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL---~EY~ElTsKL~~le~re~~L 57 (72)
..||..++.-|.-.+.++++.+.+--+..-||-=.- .|-.++.++|+..+.+.+.|
T Consensus 4 ~~eId~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~~l~~~l~~~E~eL~~L 62 (85)
T PF15188_consen 4 AKEIDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELNELKEKLENNEKELKLL 62 (85)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHhhccHHHHHHH
Confidence 458999999999999999999999999999993333 44455566666666655554
No 3
>PF10267 Tmemb_cc2: Predicted transmembrane and coiled-coil 2 protein; InterPro: IPR019394 This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown.
Probab=76.06 E-value=18 Score=29.13 Aligned_cols=51 Identities=27% Similarity=0.355 Sum_probs=34.6
Q ss_pred hhHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 2 CDELDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 2 ~eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
.+||.-|+.....=.+.|++|.+.| ..+|+-++..|.|-..|.+.|-|+++
T Consensus 218 ~~el~eik~~~~~L~~~~e~Lk~~~----------~~e~~~~~~~LqEEr~R~erLEeqlN 268 (395)
T PF10267_consen 218 LEELREIKESQSRLEESIEKLKEQY----------QREYQFILEALQEERYRYERLEEQLN 268 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence 4788888888888888999999874 45555555555555555555555444
No 4
>PF08663 HalX: HalX domain; InterPro: IPR013971 HalX is a protein of unknown function, previously mis-annotated as HoxA-like transcriptional regulator. It is C-terminal to a CheY-like superfamily domain and suggests a role as a response regulator.
Probab=71.41 E-value=7.2 Score=24.44 Aligned_cols=26 Identities=35% Similarity=0.526 Sum_probs=22.8
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHh
Q psy7982 38 EEYAELTSKLHELEAREAKLIEEREC 63 (72)
Q Consensus 38 ~EY~ElTsKL~~le~re~~L~E~~~~ 63 (72)
++|++|++++.+|..+....++.+..
T Consensus 36 eeY~eL~~ri~~lr~~ld~~~~~~d~ 61 (71)
T PF08663_consen 36 EEYQELEDRIEELRAELDDTLDEFDD 61 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 68999999999999999888887754
No 5
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=67.75 E-value=45 Score=27.18 Aligned_cols=56 Identities=20% Similarity=0.253 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhh-----------HHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 3 DELDNIQSVICLTRENIEALNSKFAAYQEPPSIY-----------LEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 3 eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIY-----------L~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
+++..++.-|.--.+-|.+|.++.++ |..| ..+|.++..+|.++..+-..|-+.++
T Consensus 563 ~~~~~~e~~i~~le~~~~~l~~~l~~----~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~w~~l~~~~~ 629 (638)
T PRK10636 563 KEIARLEKEMEKLNAQLAQAEEKLGD----SELYDQSRKAELTACLQQQASAKSGLEECEMAWLEAQEQLE 629 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC----chhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46677888888888888899988865 3344 23566666666666666655555443
No 6
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=63.93 E-value=26 Score=21.29 Aligned_cols=47 Identities=28% Similarity=0.399 Sum_probs=30.8
Q ss_pred HhHHHHHHHhcccCC---Cchhh-HHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy7982 17 ENIEALNSKFAAYQE---PPSIY-LEEYAELTSKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 17 enIdaLn~kF~~~q~---PPsIY-L~EY~ElTsKL~~le~re~~L~E~~~~~~~ 66 (72)
+.|+.++.+|..... |+.++ +.. +..||..+.+|-..+.+.+...++
T Consensus 35 ~~i~~~~~~L~~~~~~~~~~~~~~~~~---y~~KL~~ikkrm~~l~~~l~~lk~ 85 (92)
T PF14712_consen 35 QQIDRLNEKLKELNEVEQINEPFDLDP---YVKKLVNIKKRMSNLHERLQKLKK 85 (92)
T ss_pred HHHHHHHHHHHHHHHhhhhhhHHHhhH---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457888888866554 55444 444 456777777777777777665544
No 7
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=62.68 E-value=40 Score=22.88 Aligned_cols=29 Identities=31% Similarity=0.298 Sum_probs=23.6
Q ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 36 YLEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 36 YL~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
...+..+|...+.+|+.|+..+++.+|.-
T Consensus 66 ~~~~~~~L~~el~~l~~ry~t~LellGEK 94 (120)
T PF12325_consen 66 LKKEVEELEQELEELQQRYQTLLELLGEK 94 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 34567788899999999999999988753
No 8
>PF13438 DUF4113: Domain of unknown function (DUF4113)
Probab=58.85 E-value=5.6 Score=23.13 Aligned_cols=11 Identities=36% Similarity=0.751 Sum_probs=9.3
Q ss_pred hHHHHHHHhcc
Q psy7982 18 NIEALNSKFAA 28 (72)
Q Consensus 18 nIdaLn~kF~~ 28 (72)
=||++|.+||.
T Consensus 7 ~iD~iN~r~G~ 17 (52)
T PF13438_consen 7 AIDAINRRFGR 17 (52)
T ss_pred HHHHHHHhcCC
Confidence 38999999984
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=57.68 E-value=17 Score=19.87 Aligned_cols=32 Identities=31% Similarity=0.456 Sum_probs=24.7
Q ss_pred HhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhH
Q psy7982 13 CLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKL 47 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL 47 (72)
.+|.+.+..|.+-|..-++|. .++.++|..+|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~---~~~~~~la~~l 37 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPS---KEEREELAKEL 37 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCH---HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhcccc---ccccccccccc
Confidence 478899999999999977777 35666666555
No 10
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=52.06 E-value=78 Score=21.99 Aligned_cols=54 Identities=20% Similarity=0.296 Sum_probs=44.2
Q ss_pred hhHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 2 CDELDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 2 ~eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
..++......|+--...++.|++.....+ .+|--+..|+..|+..-.+|++..=
T Consensus 129 ~~~~~~l~~~l~ek~k~~e~l~DE~~~L~-------l~~~~~e~k~~~l~~En~~Lv~Rwm 182 (194)
T PF08614_consen 129 EEKIKDLEEELKEKNKANEILQDELQALQ-------LQLNMLEEKLRKLEEENRELVERWM 182 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35677788888888888888888887655 5889999999999999999988754
No 11
>cd07666 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=51.69 E-value=51 Score=24.76 Aligned_cols=33 Identities=12% Similarity=0.363 Sum_probs=22.2
Q ss_pred HhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHH
Q psy7982 17 ENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAR 53 (72)
Q Consensus 17 enIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~r 53 (72)
+.+.+++++|.+-++||.. |.|++.+++.|+..
T Consensus 37 d~~~~~~s~~~~v~~~~~e----F~Emkey~d~L~~~ 69 (243)
T cd07666 37 QTVKAVASSVRGVKNRPEE----FTEMNEYVEAFSQK 69 (243)
T ss_pred HHHHHHHHhccccCCCCHH----HHHHHHHHHHHHHH
Confidence 5677888888888999955 55555555554443
No 12
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=50.27 E-value=11 Score=28.54 Aligned_cols=22 Identities=27% Similarity=0.566 Sum_probs=18.8
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 96 ~~~~~~~~~l~~~~g~i~Q~pP-~~ 119 (300)
T PRK04270 96 VPEEDIRKVFKEFTGEIYQKPP-LK 119 (300)
T ss_pred CCHHHHHHHHHHCCCcEEeECC-HH
Confidence 6899999999999886 7777 66
No 13
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=49.54 E-value=82 Score=21.94 Aligned_cols=45 Identities=27% Similarity=0.395 Sum_probs=32.1
Q ss_pred HHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHH
Q psy7982 6 DNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAR 53 (72)
Q Consensus 6 ~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~r 53 (72)
..||+||.++-++++.|-.+-+.- -.+=..|-+.+.+||=.+=++
T Consensus 2 ~~~Q~mIdisa~~L~glRtqc~~s---~eltqqeIr~lE~KLvK~fSk 46 (129)
T PF13543_consen 2 EDIQSMIDISAEQLEGLRTQCATS---SELTQQEIRTLEGKLVKYFSK 46 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccc---hHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999998872 223445666666666554443
No 14
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=49.10 E-value=76 Score=25.46 Aligned_cols=46 Identities=13% Similarity=0.129 Sum_probs=32.0
Q ss_pred HHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHH
Q psy7982 9 QSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLI 58 (72)
Q Consensus 9 ~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~ 58 (72)
.++.-+...+.-.|.+.|||. .| ++.+|+.+-.++.+++.+.+++.
T Consensus 136 ~~~~l~~~~~~~~lLD~~~~~--~~--~~~~~~~~~~~~~~~~~~L~~l~ 181 (563)
T TIGR00634 136 DQQLLFRPDEQRQLLDTFAGA--NE--KVKAYRELYQAWLKARQQLKDRQ 181 (563)
T ss_pred HHHHhcCHHHHHHHHHHhcCc--hH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667888899999999994 22 67777666666666665555443
No 15
>PF08248 Tryp_FSAP: Tryptophyllin-3 skin active peptide; InterPro: IPR013266 PdT-3 or Tryptophyllin-3 peptide is a subfamily of the family Tryptophyllin and of the superfamily FSAP (Frog Skin Active Peptide). Originally identified in skin extracts of Neotropical leaf frogs, Phyllomedusa sp. This subfamily has an average length of 13 amino acids. The pharmacological activity of the tryptophyllins remains to be established [] but it seems that these peptides possess an action on liver protein synthesis and body weight []. It is thought to possesses insulin-releasing activity [].
Probab=48.78 E-value=6.3 Score=18.18 Aligned_cols=6 Identities=67% Similarity=1.392 Sum_probs=4.2
Q ss_pred CchhhH
Q psy7982 32 PPSIYL 37 (72)
Q Consensus 32 PPsIYL 37 (72)
||+||-
T Consensus 6 ~ppiyp 11 (12)
T PF08248_consen 6 PPPIYP 11 (12)
T ss_pred CCCccc
Confidence 666984
No 16
>COG2900 SlyX Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.41 E-value=23 Score=22.96 Aligned_cols=23 Identities=26% Similarity=0.228 Sum_probs=19.5
Q ss_pred HHHHHHhhHHhHHHHHHHhcccC
Q psy7982 8 IQSVICLTRENIEALNSKFAAYQ 30 (72)
Q Consensus 8 I~~vI~LTrenIdaLn~kF~~~q 30 (72)
-+.+|.-++..+++|-+||.+.+
T Consensus 34 q~~~i~k~q~qlr~L~~kl~~~~ 56 (72)
T COG2900 34 QQLVIDKLQAQLRLLTEKLKDLQ 56 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Confidence 46788889999999999998776
No 17
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=48.05 E-value=36 Score=24.35 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=38.8
Q ss_pred HHhhHHhHHHHHHHhcccCCCchhhH--------HHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 12 ICLTRENIEALNSKFAAYQEPPSIYL--------EEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 12 I~LTrenIdaLn~kF~~~q~PPsIYL--------~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
|++..++.+.+.+..++.. .-.+- ++|.++.++|..++..+..|++.+...
T Consensus 100 iRVP~~~~~~~l~~l~~~g--~v~~~~~~~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka 158 (262)
T PF14257_consen 100 IRVPADKFDSFLDELSELG--KVTSRNISSEDVTEQYVDLEARLKNLEAEEERLLELLEKA 158 (262)
T ss_pred EEECHHHHHHHHHHHhccC--ceeeeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5566777777777777543 22222 679999999999999999999998743
No 18
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=46.69 E-value=62 Score=24.92 Aligned_cols=47 Identities=19% Similarity=0.405 Sum_probs=35.8
Q ss_pred HHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHH
Q psy7982 6 DNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEA 52 (72)
Q Consensus 6 ~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~ 52 (72)
.|+..=|.=-+.-+|..-.++.+.|.-=|-|++||+.+...|+.+=.
T Consensus 193 ~~Le~KIekkk~ELER~qKRL~sLq~vRPAfmdEyEklE~EL~~lY~ 239 (267)
T PF10234_consen 193 ANLEAKIEKKKQELERNQKRLQSLQSVRPAFMDEYEKLEEELQKLYE 239 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHH
Confidence 44444455556677888888999999888999999998887776543
No 19
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=45.38 E-value=45 Score=19.74 Aligned_cols=18 Identities=33% Similarity=0.397 Sum_probs=11.4
Q ss_pred HHHHHHhHHHHHHHHHHH
Q psy7982 40 YAELTSKLHELEAREAKL 57 (72)
Q Consensus 40 Y~ElTsKL~~le~re~~L 57 (72)
-+.||.||+++-+|.+.|
T Consensus 25 lq~Lt~kL~~vs~RLe~L 42 (47)
T PF10393_consen 25 LQSLTQKLDAVSKRLEAL 42 (47)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 355677777776666554
No 20
>PF14767 RPA_interact_M: Replication protein A interacting middle
Probab=41.81 E-value=37 Score=21.72 Aligned_cols=44 Identities=23% Similarity=0.224 Sum_probs=25.7
Q ss_pred ChhHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhH--HHHHHHHHhHHHHH
Q psy7982 1 MCDELDNIQSVICLTRENIEALNSKFAAYQEPPSIYL--EEYAELTSKLHELE 51 (72)
Q Consensus 1 ~~eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL--~EY~ElTsKL~~le 51 (72)
|++|+.++++.=.-+- +-|.+++.+|..|. .+|.++-.-|.+++
T Consensus 8 m~eE~~~L~~~~~~~~-------d~lw~~~~~~~a~~~~~e~~eiL~~mEei~ 53 (83)
T PF14767_consen 8 MEEEWKALQSSSSGLP-------DSLWEYDGLPEASPQEEEPDEILLVMEEIQ 53 (83)
T ss_pred HHHHHHHHHhcCCCch-------hhhhccccchhhccchhhHHHHHHHHHHHH
Confidence 4566666655322211 45667888888777 77777544444433
No 21
>PF04533 Herpes_U44: Herpes virus U44 protein; InterPro: IPR007619 This entry represents proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The entry also includes BSRF1.
Probab=40.14 E-value=12 Score=28.30 Aligned_cols=26 Identities=38% Similarity=0.517 Sum_probs=20.1
Q ss_pred hhHHhHHHHHHHhcccCCCchhhHHHHHHH
Q psy7982 14 LTRENIEALNSKFAAYQEPPSIYLEEYAEL 43 (72)
Q Consensus 14 LTrenIdaLn~kF~~~q~PPsIYL~EY~El 43 (72)
+..+++++|.+|||+.| +=|-|-+.+
T Consensus 125 ~~d~~l~~LLdK~A~Dq----~tL~EmEKl 150 (210)
T PF04533_consen 125 MDDDSLEALLDKFATDQ----VTLCEMEKL 150 (210)
T ss_pred ecHHHHHHHHHHhhhhH----HHHHHHHHH
Confidence 35789999999999987 556665554
No 22
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=39.53 E-value=66 Score=17.52 Aligned_cols=33 Identities=18% Similarity=0.237 Sum_probs=21.4
Q ss_pred HHHHHHhhHHhHHHHHHHhcccCCCchhhHHHH
Q psy7982 8 IQSVICLTRENIEALNSKFAAYQEPPSIYLEEY 40 (72)
Q Consensus 8 I~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY 40 (72)
.+.+..+.++++............+|..|+.+|
T Consensus 31 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~~~f 63 (77)
T PF14278_consen 31 QERLKELIKEWITEYINENSPDNDDPEEYLISF 63 (77)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccHHHHHHHH
Confidence 455666667777777766666666665566555
No 23
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion []. Brc displays serine/threonine protein kinase activity (2.7.11.1 from EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells []. The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein []. ; GO: 0004674 protein serine/threonine kinase activity, 0005096 GTPase activator activity, 0006468 protein phosphorylation, 0007165 signal transduction; PDB: 1K1F_C.
Probab=39.38 E-value=81 Score=20.92 Aligned_cols=38 Identities=26% Similarity=0.467 Sum_probs=20.3
Q ss_pred HHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHH
Q psy7982 19 IEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKL 57 (72)
Q Consensus 19 IdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L 57 (72)
.+|.-++|.+ ++||.+=|.--.++...|..-+.-...|
T Consensus 8 ~~~w~aqfp~-~~~p~m~l~svgd~e~eLerCK~sirrL 45 (79)
T PF09036_consen 8 AEAWRAQFPD-SEPPVMELRSVGDIEQELERCKASIRRL 45 (79)
T ss_dssp HHHHHHHSTT-S-------SSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHCCc-cCCcHHHHHHhccHHHHHHHHHHHHHHH
Confidence 4678899999 8999998877666666665544443333
No 24
>PHA00489 scaffolding protein
Probab=39.17 E-value=39 Score=23.26 Aligned_cols=23 Identities=43% Similarity=0.677 Sum_probs=18.5
Q ss_pred hHHHHHHHHHhHHHHHHHHHHHH
Q psy7982 36 YLEEYAELTSKLHELEAREAKLI 58 (72)
Q Consensus 36 YL~EY~ElTsKL~~le~re~~L~ 58 (72)
|+.||.|+|+-+..+-+.-..|.
T Consensus 39 f~sEy~elT~a~eKl~aek~DLi 61 (101)
T PHA00489 39 FHSEYEELTEALEKLTAEKEDLI 61 (101)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhh
Confidence 57899999999988877666654
No 25
>PRK10869 recombination and repair protein; Provisional
Probab=37.36 E-value=1.8e+02 Score=23.73 Aligned_cols=42 Identities=17% Similarity=0.213 Sum_probs=27.2
Q ss_pred HHHhhHHhHHHHHHHhcccCCCchhhHHHHH-------HHHHhHHHHHHHHHH
Q psy7982 11 VICLTRENIEALNSKFAAYQEPPSIYLEEYA-------ELTSKLHELEAREAK 56 (72)
Q Consensus 11 vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~-------ElTsKL~~le~re~~ 56 (72)
..-+..++.-.|.+.|||.. -++.+|+ ++..+|.+++.+++.
T Consensus 134 ~~ll~~~~~~~lLD~~~~~~----~~~~~~~~~y~~~~~~~~~l~~l~~~~~~ 182 (553)
T PRK10869 134 QLLLKPEHQKTLLDAYANET----SLLQEMRAAYQLWHQSCRDLAQHQQQSQE 182 (553)
T ss_pred HHhcCHHHHHHHHHHhcccH----HHHHHHHHHHHHHHHHHHHHHHHHHhHHH
Confidence 34478889999999999972 3555544 455555555554443
No 26
>COG5278 Predicted periplasmic ligand-binding sensor domain [Signal transduction mechanisms]
Probab=37.32 E-value=46 Score=24.53 Aligned_cols=24 Identities=33% Similarity=0.383 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHhHHHHHHHHHHHH
Q psy7982 35 IYLEEYAELTSKLHELEAREAKLI 58 (72)
Q Consensus 35 IYL~EY~ElTsKL~~le~re~~L~ 58 (72)
-||+.|++.+.-+++...+.+.|.
T Consensus 77 ~yL~py~~a~~~~~~~~~~l~~l~ 100 (207)
T COG5278 77 EYLEPYEEATEELDQKLEELRALT 100 (207)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhc
Confidence 699999999999999888877664
No 27
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=37.17 E-value=2e+02 Score=22.43 Aligned_cols=62 Identities=24% Similarity=0.350 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHhhHHhHHHHHHHhcccCC------Cch-------hhHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 3 DELDNIQSVICLTRENIEALNSKFAAYQE------PPS-------IYLEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 3 eel~NI~~vI~LTrenIdaLn~kF~~~q~------PPs-------IYL~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
+++.++..-++-.++.++.|......... +|+ .+...|.++..++.+++.+...|.+.+...
T Consensus 334 ~~~~~l~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~l~~~ 408 (451)
T PF03961_consen 334 EKLEELEEELEELKEELEKLKKNLKKLKKLKKQGKLPPEKKEQLKKLKEKKKELKEELKELKEELKELKEELERS 408 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44556666666666666666655433332 222 234556666677777777666666666644
No 28
>PF07341 DUF1473: Protein of unknown function (DUF1473); InterPro: IPR009941 This entry represents a family of hypothetical proteins of around 150 residues in length found in Borrelia species. The function of this family is unknown.
Probab=37.01 E-value=11 Score=27.80 Aligned_cols=16 Identities=25% Similarity=0.862 Sum_probs=14.3
Q ss_pred cccCCCchhhHHHHHH
Q psy7982 27 AAYQEPPSIYLEEYAE 42 (72)
Q Consensus 27 ~~~q~PPsIYL~EY~E 42 (72)
.|++.|--||+++|++
T Consensus 99 ~~fkkP~LvYis~y~d 114 (163)
T PF07341_consen 99 EDFKKPSLVYISEYED 114 (163)
T ss_pred ccCCCCcEEEehhhhc
Confidence 6889999999999875
No 29
>cd02896 complement_C3_C4_C5 Proteins similar to C3, C4 and C5 of vertebrate complement. The vertebrate complement system, comprised of a large number of distinct plasma proteins, is an effector of both the acquired and innate immune systems. The point of convergence of the classical, alternative and lectin pathways of the complement system is the proteolytic activation of C3. C4 plays a key role in propagating the classical and lectin pathways. C5 participates in the classical and alternative pathways. The thioester bond located within the structure of C3 and C4 is central to the function of complement. C5 does not contain an active thioester bond.
Probab=36.97 E-value=56 Score=23.80 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHH
Q psy7982 5 LDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLH 48 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~ 48 (72)
..|++++|++--.-.|....+|. |.+|+..|-+-|.++.
T Consensus 2 ~~~l~~L~~~P~GC~EQ~~~~~~-----p~~~~~~yl~~~~~~~ 40 (297)
T cd02896 2 PEGLEKLIRLPTGCGEQTMIKLA-----PTVYALRYLDTTNQWE 40 (297)
T ss_pred chhHHHHHhCCCCcHHHHHHHHH-----HHHHHHHHHHHhcccc
Confidence 46888999999999999999987 8899999999988765
No 30
>cd02897 A2M_2 Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP). Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of proteases. PZP is a trace protein in the plasma of non-pregnant females and males which is elevated in pregnancy. Alpha (2)-M and PZ bind to placental protein-14 and may modulate its activity in T-cell growth and cytokine production contributing to fetal survival. It has been suggested that thioester bond cleavage promotes the binding of PZ and alpha (2)-M to the CD91 receptor clearing them from circulation.
Probab=36.67 E-value=63 Score=23.06 Aligned_cols=39 Identities=28% Similarity=0.461 Sum_probs=33.2
Q ss_pred HHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHH
Q psy7982 5 LDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLH 48 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~ 48 (72)
+.||.++|++--...|....+|. |.+|+-.|-+-|.++.
T Consensus 2 ~~~l~~L~~~P~gc~Eq~~~~~~-----p~~~~~~yl~~~~~~~ 40 (292)
T cd02897 2 LQNLDNLLRMPYGCGEQNMVNFA-----PNIYVLDYLKATGQLT 40 (292)
T ss_pred hhhHHHHHhCCCCcHHHHHHHHH-----HHHHHHHHHHHhcCCC
Confidence 46888899999999999888886 8899999999877665
No 31
>PF11418 Scaffolding_pro: Phi29 scaffolding protein; InterPro: IPR024374 This protein is also referred to as Gp7. The protein contains a DNA-binding function and may have a role in mediating the structural transition from prohead to mature virus and also scaffold release [].Gp7 is arranged within the capsid as a series of concentric shells [].; PDB: 1NOH_C 1NO4_C 3MTU_E 3OA7_A.
Probab=35.75 E-value=71 Score=21.87 Aligned_cols=25 Identities=36% Similarity=0.562 Sum_probs=19.7
Q ss_pred hhHHHHHHHHHhHHHHHHHHHHHHH
Q psy7982 35 IYLEEYAELTSKLHELEAREAKLIE 59 (72)
Q Consensus 35 IYL~EY~ElTsKL~~le~re~~L~E 59 (72)
-|+-||.++|+-+..+-+.-..|.-
T Consensus 37 sf~sEy~dlT~~~eKl~aek~DL~v 61 (97)
T PF11418_consen 37 SFHSEYEDLTEALEKLTAEKEDLIV 61 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 4678999999998888777666653
No 32
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=35.52 E-value=17 Score=25.14 Aligned_cols=25 Identities=36% Similarity=0.604 Sum_probs=16.3
Q ss_pred HHHhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 11 VICLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 11 vI~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.-.+|.+.|++..++|-|. |-|| +|
T Consensus 69 ~~~it~e~l~~~l~~f~G~~~Q~pP-~y 95 (149)
T PF01509_consen 69 YDHITEEDLEKVLAKFQGEIEQVPP-MY 95 (149)
T ss_dssp -TT--HHHHHHHHHHTSEEEEES-S-SS
T ss_pred cccCCHHHHHHHHHhCcCCEeeeCc-hh
Confidence 4467999999999999764 4455 55
No 33
>KOG3968|consensus
Probab=35.51 E-value=29 Score=28.91 Aligned_cols=58 Identities=28% Similarity=0.353 Sum_probs=46.4
Q ss_pred HHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHH-----HhHHHHHHHHHHHHHHHHhhhh
Q psy7982 8 IQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELT-----SKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 8 I~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElT-----sKL~~le~re~~L~E~~~~~~~ 66 (72)
|+..|-=-.+-|++--+=|+..++|+..|.. |..|| +-+-.|...+-.++.++++.-.
T Consensus 236 ~q~hIsen~~EI~~~~~ff~~~~~y~~~yd~-~~lL~~ktvlaH~~hl~d~ei~~l~k~g~svs 298 (439)
T KOG3968|consen 236 IQIHISENGKEIEAVKNFFPEKLSYTDVYDK-GGLLTEKTVLAHLEHLSDEEIELLAKRGCSVS 298 (439)
T ss_pred hhhhhhhcHHHHHHHHHhhhhcccchHHHHH-hcccchHhHhhhheecCchhHHHHHhcCCceE
Confidence 4556666678899999999999999999987 88888 3456778888888888876543
No 34
>PHA02109 hypothetical protein
Probab=35.11 E-value=1.1e+02 Score=23.62 Aligned_cols=39 Identities=33% Similarity=0.425 Sum_probs=25.6
Q ss_pred hHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 15 TRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 15 TrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
|-+|++-|-+| |++--+||+||+.|-...-++-+.+.+.
T Consensus 181 t~~~L~~~~~~-----------L~~I~~L~~ki~~LS~E~~Q~~~Ki~N~ 219 (233)
T PHA02109 181 TGENLEGLTDK-----------LKQISELTIKLEALSDEACQVKHKILNL 219 (233)
T ss_pred chhhhhhhhHH-----------HHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555554 6777899999988876655555544443
No 35
>COG3102 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.38 E-value=47 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.311 Sum_probs=22.9
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 38 EEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 38 ~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
.++++|+.||..++.+-++|.++++
T Consensus 8 ~qLqqL~adL~~Fe~~ieqLa~~L~ 32 (185)
T COG3102 8 DELQQLLADLPRFEHKIEQLANRLG 32 (185)
T ss_pred hhHHHHHHhccHHHHHHHHHHHHhc
Confidence 6899999999999999999998776
No 36
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=33.92 E-value=26 Score=26.88 Aligned_cols=23 Identities=39% Similarity=0.572 Sum_probs=18.8
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 93 ~~t~~~l~~~l~~f~G~i~Q~PP-~y 117 (290)
T PRK00130 93 HLTEEEIREAILSFQGEIDQVPP-MY 117 (290)
T ss_pred CCCHHHHHHHHHHccCeEEEECC-hH
Confidence 48999999999999885 6676 55
No 37
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=33.48 E-value=28 Score=26.85 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=17.2
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 108 ~~~~~l~~~l~~f~g~i~Q~pP-~~ 131 (322)
T TIGR00425 108 AKEEDILRVLKEFTGRIFQRPP-LK 131 (322)
T ss_pred CCHHHHHHHHHHcCCcEEeeCC-hh
Confidence 6888898888999775 7777 55
No 38
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=33.29 E-value=23 Score=25.85 Aligned_cols=24 Identities=29% Similarity=0.472 Sum_probs=18.8
Q ss_pred HHhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 12 ICLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 12 I~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.++|.+.|++..++|-|. |-|| +|
T Consensus 90 ~~it~e~l~~~l~~f~G~i~Q~pP-~y 115 (210)
T cd00506 90 DHITHEQLERALETLTGDIQQVPP-LY 115 (210)
T ss_pred CCCCHHHHHHHHHHCCCeEEEeCC-ch
Confidence 458999999999999875 5555 66
No 39
>PF14304 CSTF_C: Transcription termination and cleavage factor C-terminal; PDB: 2J8P_A.
Probab=32.98 E-value=17 Score=21.65 Aligned_cols=17 Identities=41% Similarity=0.466 Sum_probs=13.7
Q ss_pred HHHHHHHHhhHHhHHHH
Q psy7982 6 DNIQSVICLTRENIEAL 22 (72)
Q Consensus 6 ~NI~~vI~LTrenIdaL 22 (72)
.=|.+|+.||.+-|++|
T Consensus 9 aLl~QVL~Lt~eQI~~L 25 (46)
T PF14304_consen 9 ALLMQVLQLTPEQINAL 25 (46)
T ss_dssp HHHHHHHTS-HHHHHTS
T ss_pred HHHHHHHcCCHHHHHhC
Confidence 34789999999999987
No 40
>KOG0709|consensus
Probab=32.32 E-value=82 Score=26.55 Aligned_cols=45 Identities=29% Similarity=0.460 Sum_probs=37.5
Q ss_pred hhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhhh
Q psy7982 14 LTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERECVK 65 (72)
Q Consensus 14 LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~~ 65 (72)
=.++-||.|-.+.+.+-- +=+||..|.++|+..-++|+++|..-+
T Consensus 269 kKkeYid~LE~rv~~~ta-------eNqeL~kkV~~Le~~N~sLl~qL~klQ 313 (472)
T KOG0709|consen 269 KKKEYIDGLESRVSAFTA-------ENQELQKKVEELELSNRSLLAQLKKLQ 313 (472)
T ss_pred hHhhHHHHHhhhhhhccc-------CcHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 357889999999875554 459999999999999999999998544
No 41
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=32.18 E-value=2.8e+02 Score=22.54 Aligned_cols=54 Identities=20% Similarity=0.300 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhHHhHHHHHHHhcccCCCchhhH---HHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 5 LDNIQSVICLTRENIEALNSKFAAYQEPPSIYL---EEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL---~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
+..++.-|.--.+-+.+|.++.++ |.+|= .+.+++..++++++.....+++...
T Consensus 570 ~~~~e~~i~~le~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~ 626 (635)
T PRK11147 570 LEQLPQLLEDLEAEIEALQAQVAD----ADFFSQPHEQTQKVLADLADAEQELEVAFERWE 626 (635)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC----chhhcccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555566666666667777777753 34552 2566666666666666666665544
No 42
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=32.12 E-value=30 Score=26.76 Aligned_cols=22 Identities=45% Similarity=0.730 Sum_probs=18.3
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 95 ~~~~~i~~~l~~f~G~i~Q~PP-~y 118 (304)
T PRK01550 95 ITREEIEAALASLTGTIEQIPP-MY 118 (304)
T ss_pred CCHHHHHHHHHhccceEEEeCC-hh
Confidence 7999999999999885 6676 55
No 43
>KOG3915|consensus
Probab=30.73 E-value=1.6e+02 Score=25.72 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhhHHhHHHHHHHhcc
Q psy7982 4 ELDNIQSVICLTRENIEALNSKFAA 28 (72)
Q Consensus 4 el~NI~~vI~LTrenIdaLn~kF~~ 28 (72)
=+.|||.++++--.|+.+--.+|.-
T Consensus 504 ll~niq~llkva~dnar~qekQiq~ 528 (641)
T KOG3915|consen 504 LLTNIQGLLKVAIDNARAQEKQIQL 528 (641)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3789999999999999887777653
No 44
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=30.45 E-value=1.9e+02 Score=24.88 Aligned_cols=32 Identities=28% Similarity=0.331 Sum_probs=20.6
Q ss_pred HHHHHHHHHhhHH---hHHHHHHHhcccCCCchhhH
Q psy7982 5 LDNIQSVICLTRE---NIEALNSKFAAYQEPPSIYL 37 (72)
Q Consensus 5 l~NI~~vI~LTre---nIdaLn~kF~~~q~PPsIYL 37 (72)
+.+|..||.+.|. -...|.++| ++...=.=||
T Consensus 392 ~~~id~vI~iir~s~~ak~~l~~~f-~~~~~qa~~I 426 (742)
T PRK05561 392 FLNIDEVIRIIRESDEPKANLMARF-DLSEIQAEAI 426 (742)
T ss_pred HhhHHHHHHHHhcCccHHHHHHHHh-CCCHHHHHHH
Confidence 5677888877666 577788887 4544444444
No 45
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=30.12 E-value=32 Score=26.70 Aligned_cols=23 Identities=26% Similarity=0.397 Sum_probs=18.4
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 101 ~~~~~~l~~~l~~f~G~i~Q~PP-~y 125 (300)
T PRK04642 101 DLSAAALQAALAPLIGRIRQRAP-IY 125 (300)
T ss_pred CCCHHHHHHHHHHCCCcEEEeCC-ch
Confidence 47999999999999884 5566 55
No 46
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=30.11 E-value=33 Score=26.54 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=18.6
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 100 ~it~~~i~~~l~~f~G~i~Q~PP-~y 124 (298)
T PRK03287 100 AVTDEAIAAAVAALTGEIMQVPS-AV 124 (298)
T ss_pred CCCHHHHHHHHHhCcCeEEEeCC-hh
Confidence 58999999999999775 5566 55
No 47
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=29.91 E-value=34 Score=25.66 Aligned_cols=22 Identities=32% Similarity=0.466 Sum_probs=17.3
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|++-|++..++|-|. |-|| +|
T Consensus 101 ~~~~~i~~~l~~f~G~~~Q~PP-~y 124 (230)
T PRK00989 101 PTLEEVLSAASYFQGEIQQVPP-MF 124 (230)
T ss_pred CCHHHHHHHHHhCcceEEeeCC-hh
Confidence 6899999999999774 4565 66
No 48
>KOG3850|consensus
Probab=29.77 E-value=3.5e+02 Score=22.94 Aligned_cols=26 Identities=27% Similarity=0.395 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHHhhHHhHHHHHHHhc
Q psy7982 2 CDELDNIQSVICLTRENIEALNSKFA 27 (72)
Q Consensus 2 ~eel~NI~~vI~LTrenIdaLn~kF~ 27 (72)
-+||+-|+..--+=.+.+|+|-+.|-
T Consensus 266 leeL~eIk~~q~~Leesye~Lke~~k 291 (455)
T KOG3850|consen 266 LEELREIKETQALLEESYERLKEQIK 291 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899998888888899999998864
No 49
>PF13870 DUF4201: Domain of unknown function (DUF4201)
Probab=29.71 E-value=1.8e+02 Score=19.68 Aligned_cols=35 Identities=26% Similarity=0.320 Sum_probs=19.5
Q ss_pred HHHHHHHhcccCCCchhh-H----HHHHHHHHhHHHHHHH
Q psy7982 19 IEALNSKFAAYQEPPSIY-L----EEYAELTSKLHELEAR 53 (72)
Q Consensus 19 IdaLn~kF~~~q~PPsIY-L----~EY~ElTsKL~~le~r 53 (72)
+..|..+-|.+..|+-++ . ++..++...+..++.+
T Consensus 128 ~~~l~~~~~~~~~P~ll~Dy~~~~~~~~~l~~~i~~l~rk 167 (177)
T PF13870_consen 128 NKKLRQQGGLLGVPALLRDYDKTKEEVEELRKEIKELERK 167 (177)
T ss_pred HHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344677778888888663 1 3334444444444443
No 50
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=29.36 E-value=34 Score=26.36 Aligned_cols=23 Identities=35% Similarity=0.548 Sum_probs=18.1
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 93 ~~~~~~l~~~l~~f~G~i~Q~PP-~y 117 (295)
T PRK02755 93 HLSLAEIETALPQFRGKIEQRPP-QY 117 (295)
T ss_pred CCCHHHHHHHHHhccCeEEEeCC-hh
Confidence 47899999999999874 4566 65
No 51
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=28.48 E-value=60 Score=21.35 Aligned_cols=25 Identities=20% Similarity=0.543 Sum_probs=20.1
Q ss_pred CchhhH--HHHHHHHHhHHHHHHHHHH
Q psy7982 32 PPSIYL--EEYAELTSKLHELEAREAK 56 (72)
Q Consensus 32 PPsIYL--~EY~ElTsKL~~le~re~~ 56 (72)
-|.+|. .+|.++.++|++++.|-.-
T Consensus 7 ~P~v~v~~~dfne~~kRLdeieekvef 33 (75)
T COG4064 7 VPKVVVDPDDFNEIHKRLDEIEEKVEF 33 (75)
T ss_pred CCccccCHHHHHHHHHHHHHHHHHHHh
Confidence 455665 6899999999999988763
No 52
>PF01337 Barstar: Barstar (barnase inhibitor); InterPro: IPR000468 Barstar is a small single chain protein. Barnase is the extracellular ribonuclease IPR001887 from INTERPRO of Bacillus amyloliquefaciens, and barstar its specific intracellular inhibitor [, ]. Expression of barstar is necessary to counter the lethal effect of expressed active barnase. The structure of the barnase-barstar complex is known [].; PDB: 2CX6_A 1B2U_F 1A19_A 1X1U_F 1B27_E 1X1W_F 1BGS_E 1X1Y_D 1B3S_D 1B2S_D ....
Probab=28.35 E-value=28 Score=21.01 Aligned_cols=43 Identities=30% Similarity=0.319 Sum_probs=29.9
Q ss_pred HhHHHHHHHhccc----CCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 17 ENIEALNSKFAAY----QEPPSIYLEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 17 enIdaLn~kF~~~----q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
.|+|||.+-..+. ..|-.|.+..+..+...+.+- -..+++.+.
T Consensus 30 ~NlDAl~D~L~d~~~~~~~~~~i~~~~~~~~~~~~~~~---~~~l~~vl~ 76 (90)
T PF01337_consen 30 RNLDALWDCLTDLSWIPEEPIVIIWENADKLKKRLPED---FEILLEVLE 76 (90)
T ss_dssp SSHHHHHHHHHCT---S-SSEEEEEETHHHHHHTTTCH---CHHHHHHHH
T ss_pred CCHHHHHHHhcCcccCCCCCEEEEEcCcHHHHHHhHHH---HHHHHHHHH
Confidence 5999999999999 777778888888877665422 223455544
No 53
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=28.26 E-value=1.2e+02 Score=17.23 Aligned_cols=27 Identities=37% Similarity=0.493 Sum_probs=20.2
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 38 EEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 38 ~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
.++.+++.++.+++.+-..|-..+...
T Consensus 24 ~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 24 QEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 467778888888888877777777665
No 54
>PF00957 Synaptobrevin: Synaptobrevin; InterPro: IPR001388 Synaptobrevin is an intrinsic membrane protein of small synaptic vesicles [], specialised secretory organelles of neurons that actively accumulate neurotransmitters and participate in their calcium-dependent release by exocytosis. Vesicle function is mediated by proteins in their membranes, although the precise nature of the protein-protein interactions underlying this are still uncertain []. Synaptobrevin may play a role in the molecular events underlying neurotransmitter release and vesicle recycling and may be involved in the regulation of membrane flow in the nerve terminal, a process mediated by interaction with low molecular weight GTP-binding proteins []. Synaptic vesicle-associated membrane proteins (VAMPs) from Torpedo californica (Pacific electric ray) and SNC1 from yeast are related to synaptobrevin.; GO: 0016192 vesicle-mediated transport, 0016021 integral to membrane; PDB: 3EGX_C 2NUP_C 3EGD_C 2NUT_C 1IOU_A 1H8M_A 3B5N_A 3ZYM_A 2NPS_A 1SFC_E ....
Probab=27.88 E-value=1.4e+02 Score=17.92 Aligned_cols=42 Identities=33% Similarity=0.490 Sum_probs=28.7
Q ss_pred HHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy7982 7 NIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 7 NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~~~ 66 (72)
++..+-....+||+.+.++ -.+|++|+.+=.+|-+.-..-+.
T Consensus 11 ~v~~v~~im~~Ni~~ll~R------------------ge~L~~L~~kt~~L~~~a~~F~k 52 (89)
T PF00957_consen 11 QVEEVKNIMRENIDKLLER------------------GEKLEELEDKTEELSDNAKQFKK 52 (89)
T ss_dssp HHHHHHHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHc------------------CchHHHHHHHHHHHHHHhHHHHH
Confidence 4556667778999998765 45777777777777665554443
No 55
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=27.78 E-value=99 Score=23.70 Aligned_cols=51 Identities=33% Similarity=0.421 Sum_probs=38.7
Q ss_pred HhhHHhHHHHHHH---------hcccCCCchhh-----------------HHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 13 CLTRENIEALNSK---------FAAYQEPPSIY-----------------LEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 13 ~LTrenIdaLn~k---------F~~~q~PPsIY-----------------L~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
.+||+.+-.+..+ |-|+. ||.|| .++|.+.=++|=..|.+...-++..-++
T Consensus 25 ~~~R~~lv~~L~~~Y~~~gIeP~RG~s-~~diYDKElatlYVVGkyGlGl~~e~p~~f~~lF~~E~~~eea~~~i~~~ 101 (231)
T PF09958_consen 25 VLDREELVELLREVYEENGIEPFRGLS-PPDIYDKELATLYVVGKYGLGLDEEYPEDFDKLFYIEEKYEEALEIILEE 101 (231)
T ss_pred cCCHHHHHHHHHHHHHHcCCCcCCCCC-ccchhhhhHhheeeeeccccccchhhhHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3567776666654 78999 99999 3778888888888888888777776533
No 56
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=27.73 E-value=38 Score=26.21 Aligned_cols=23 Identities=35% Similarity=0.427 Sum_probs=18.4
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 103 ~~~~~~i~~~l~~f~G~i~Q~PP-~y 127 (305)
T PRK05389 103 RPTDEEIRAALPAFTGEIMQVPP-QF 127 (305)
T ss_pred CCCHHHHHHHHHhccceEEEeCC-ch
Confidence 37999999999999874 5666 55
No 57
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=27.37 E-value=2e+02 Score=22.42 Aligned_cols=16 Identities=44% Similarity=0.619 Sum_probs=6.7
Q ss_pred HHHHHHHHhHHHHHHH
Q psy7982 38 EEYAELTSKLHELEAR 53 (72)
Q Consensus 38 ~EY~ElTsKL~~le~r 53 (72)
.+..++..++.+|+..
T Consensus 389 ~~~~~l~~~~~~l~~~ 404 (451)
T PF03961_consen 389 EELKELKEELKELKEE 404 (451)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444333
No 58
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=27.32 E-value=39 Score=26.25 Aligned_cols=23 Identities=35% Similarity=0.479 Sum_probs=18.7
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 93 ~~~~~~i~~~l~~f~G~i~Q~PP-~y 117 (308)
T PRK14124 93 NVTEEEIREAIFSFVGEYKQVPP-AY 117 (308)
T ss_pred CCCHHHHHHHHHhCcCeEEEeCC-ch
Confidence 48999999999999884 6666 55
No 59
>PF00804 Syntaxin: Syntaxin; InterPro: IPR006011 Syntaxins A and B are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane. Syntaxins are a family of receptors for intracellular transport vesicles. Each target membrane may be identified by a specific member of the syntaxin family []. Members of the syntaxin family [, ] have a size ranging from 30 Kd to 40 Kd; a C-terminal extremity which is highly hydrophobic and anchors the protein on the cytoplasmic surface of cellular membranes; a central, well conserved region, which seems to be in a coiled-coil conformation. ; GO: 0016020 membrane; PDB: 1S94_B 1EZ3_A 3C98_B 1BR0_A 1FIO_A 2XHE_B.
Probab=27.23 E-value=1.3e+02 Score=17.35 Aligned_cols=32 Identities=22% Similarity=0.329 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHhhHHhHHHHHHHhcccCCCch
Q psy7982 3 DELDNIQSVICLTRENIEALNSKFAAYQEPPS 34 (72)
Q Consensus 3 eel~NI~~vI~LTrenIdaLn~kF~~~q~PPs 34 (72)
+++..|+.-|.-.+.+++.|...-...-.+|.
T Consensus 7 ~~v~~i~~~i~~i~~~~~~l~~l~~~~l~~~~ 38 (103)
T PF00804_consen 7 DEVQEIREDIDKIKEKLNELRKLHKKILSSPD 38 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 57788899999999999999888887777775
No 60
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=27.06 E-value=63 Score=20.93 Aligned_cols=23 Identities=26% Similarity=0.762 Sum_probs=18.9
Q ss_pred chhhH--HHHHHHHHhHHHHHHHHH
Q psy7982 33 PSIYL--EEYAELTSKLHELEAREA 55 (72)
Q Consensus 33 PsIYL--~EY~ElTsKL~~le~re~ 55 (72)
|+++. -+|.++-.||++++.+-.
T Consensus 5 P~v~v~~~d~~~i~~rLd~iEeKVE 29 (70)
T TIGR01149 5 PAVFVEPDEFNEVMKRLDEIEEKVE 29 (70)
T ss_pred CeeecCHHHHHHHHHHHHHHHHHHH
Confidence 55555 589999999999998866
No 61
>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.
Probab=27.01 E-value=1.5e+02 Score=19.43 Aligned_cols=46 Identities=24% Similarity=0.269 Sum_probs=30.2
Q ss_pred HHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHH
Q psy7982 12 ICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKL 57 (72)
Q Consensus 12 I~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L 57 (72)
+.=.-+-=++|-.+|-+..-+---||..|.+.-...|.-..|...|
T Consensus 105 ~~e~eeeSe~lae~fl~g~~d~~~Fl~~f~~~R~~yH~R~~K~EkL 150 (150)
T PF07200_consen 105 ASEAEEESEELAEEFLDGEIDVDDFLKQFKEKRKLYHLRRAKEEKL 150 (150)
T ss_dssp HHHHHHHHHHHC-S-SSSHHHHHHHHHHHHHHHHHHHHHH---HHH
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhhhccC
Confidence 3334444567777888777788889999999999888877666554
No 62
>PF12896 Apc4: Anaphase-promoting complex, cyclosome, subunit 4; InterPro: IPR024790 Apc4 is one of the larger of the subunits of the anaphase-promoting complex (APC) or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes [, ]. Results in Caenorhabditis elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle. The APC is likely to be required for all metaphase-to-anaphase transitions in a multicellular organism []. This entry represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits.
Probab=26.89 E-value=76 Score=21.59 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=37.7
Q ss_pred HHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHH-HHHhHHHHHHHHHHHHHHHHhhhhh
Q psy7982 6 DNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAE-LTSKLHELEAREAKLIEERECVKKS 67 (72)
Q Consensus 6 ~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~E-lTsKL~~le~re~~L~E~~~~~~~~ 67 (72)
-.|+.+++-.+++++++.....+....|.-++..|.+ +.++ ..-..-..+|++.+-.|..|
T Consensus 27 ~~i~~ll~yi~~~l~~i~~~w~~~~~~~~~~l~~~~~~l~~~-~~~~~~~~el~~lLltG~~s 88 (210)
T PF12896_consen 27 SQIQSLLRYIKDTLDAIQEEWEEALQEFDRKLTNLADELQEK-GGEGSLQDELLDLLLTGHAS 88 (210)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCcHHHHHHHHHHhcCCC
Confidence 4577888888999999999987776666666666653 2222 10001124566666655543
No 63
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=26.62 E-value=44 Score=25.38 Aligned_cols=23 Identities=26% Similarity=0.546 Sum_probs=18.5
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
++|.+.|++...+|-|. |-|| +|
T Consensus 103 ~it~e~l~~~l~~f~G~i~Q~PP-~y 127 (244)
T PRK00020 103 GVEEAALRDVLSRFVGTIEQIPP-MY 127 (244)
T ss_pred CCCHHHHHHHHHhccCeEEEeCC-hh
Confidence 57999999999999885 5666 55
No 64
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=26.48 E-value=1.4e+02 Score=20.65 Aligned_cols=32 Identities=41% Similarity=0.757 Sum_probs=25.8
Q ss_pred hcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 26 FAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 26 F~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
|-.++.|| .||+.|..++-.--+.|+|..+..
T Consensus 2 ~dqyhEp~-------eeLs~kirdf~Ra~~SLiEEiEA~ 33 (103)
T COG3461 2 FDQYHEPP-------EELSEKIRDFSRARQSLIEEIEAM 33 (103)
T ss_pred CccccCCH-------HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55667777 689999999999999998877643
No 65
>cd05140 Barstar_AU1054-like Barstar_AU1054-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor AU1054 found in Burkholderia cenocepacia. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase.
Probab=26.24 E-value=1.3e+02 Score=19.01 Aligned_cols=33 Identities=15% Similarity=0.332 Sum_probs=23.8
Q ss_pred HhHHHHHHHhcccCC-CchhhHHHHHHHHHhHHH
Q psy7982 17 ENIEALNSKFAAYQE-PPSIYLEEYAELTSKLHE 49 (72)
Q Consensus 17 enIdaLn~kF~~~q~-PPsIYL~EY~ElTsKL~~ 49 (72)
.|.|||.+-..|... |+.|-+.-+..+..++-+
T Consensus 30 ~N~DAl~D~lt~~~~lP~~i~~~~~~~~~~~~~~ 63 (86)
T cd05140 30 CNWDAFWDAITGLVSMPPVLRFVGWSQFKRRLPR 63 (86)
T ss_pred CCHHHHHHHHcCCccCCCEEEEeChHHHHHHCHH
Confidence 599999999988876 556666666665554444
No 66
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=26.14 E-value=71 Score=19.78 Aligned_cols=30 Identities=17% Similarity=0.258 Sum_probs=25.0
Q ss_pred HHHHHHHHHHhhHHhHHHHHHHhcccCCCc
Q psy7982 4 ELDNIQSVICLTRENIEALNSKFAAYQEPP 33 (72)
Q Consensus 4 el~NI~~vI~LTrenIdaLn~kF~~~q~PP 33 (72)
|.|-++++-.+|-+-++.|.+.|...+-|.
T Consensus 40 d~w~l~~l~~l~~~d~~~Ll~~y~~~~~~~ 69 (70)
T PF14823_consen 40 DYWSLEELAELDDEDMENLLDFYWSNKVPT 69 (70)
T ss_dssp HHHHHHHGGGB-HHHHHHHHHHHHTTTTS-
T ss_pred cccCHHHHHHCCHHHHHHHHHHhhccCCCC
Confidence 678899999999999999999998887764
No 67
>PRK03830 small acid-soluble spore protein Tlp; Provisional
Probab=25.96 E-value=79 Score=20.56 Aligned_cols=23 Identities=35% Similarity=0.432 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhHHhHHHHHHHhc
Q psy7982 5 LDNIQSVICLTRENIEALNSKFA 27 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~kF~ 27 (72)
+.-||.||.=|-+||++-.+-.+
T Consensus 11 VEkLQ~mi~nTieNi~eAee~l~ 33 (73)
T PRK03830 11 VEKLQEMIQNTIENIEEAEETIA 33 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 55789999999999998776554
No 68
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=25.94 E-value=46 Score=25.41 Aligned_cols=21 Identities=29% Similarity=0.574 Sum_probs=16.9
Q ss_pred hHHhHHHHHHHhccc--CCCchhh
Q psy7982 15 TRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 15 TrenIdaLn~kF~~~--q~PPsIY 36 (72)
|.++|++...+|-|. |-|| +|
T Consensus 91 ~~e~i~~~l~~F~G~I~Q~PP-~~ 113 (271)
T COG0130 91 SEEEVRAALEAFTGEIYQIPP-MF 113 (271)
T ss_pred CHHHHHHHHHhcceeeEecCC-ch
Confidence 689999999999874 6676 65
No 69
>PF09025 YopR_core: YopR Core; InterPro: IPR013349 Proteins in this entry are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yop protein is unusual in that it is released to the extracellular environment rather than injected directly into the target cell as are most Yop proteins.; GO: 0009405 pathogenesis, 0030254 protein secretion by the type III secretion system, 0030257 type III protein secretion system complex; PDB: 1Z21_A.
Probab=25.87 E-value=1.6e+02 Score=21.35 Aligned_cols=48 Identities=23% Similarity=0.306 Sum_probs=29.0
Q ss_pred HHHHHHHhcccCCC--chhhHHHHHHHHHhHHHH-HHHHHHHHHHHHhhhh
Q psy7982 19 IEALNSKFAAYQEP--PSIYLEEYAELTSKLHEL-EAREAKLIEERECVKK 66 (72)
Q Consensus 19 IdaLn~kF~~~q~P--PsIYL~EY~ElTsKL~~l-e~re~~L~E~~~~~~~ 66 (72)
=++|.+.|||.+-| |+|=..|-+.+-+.-.-| ..+|+-|+.+++.-+.
T Consensus 54 ~~~L~~~F~g~~~~~~pp~D~~ELrall~e~~plg~qkE~~Ll~~l~~lK~ 104 (142)
T PF09025_consen 54 KQELLGRFGGRLLPAVPPIDRPELRALLREFFPLGAQKEQALLHSLAELKP 104 (142)
T ss_dssp HHHHHHHHTT--S---HHHHHHHHHHHHHHHS-SSHHHHHHHHHHHHT---
T ss_pred HHHHHHHHhhhccCCCCCcchHHHHHHHHHhCcchhHHHHHHHHHHHHhcc
Confidence 46899999999984 557666655554443333 4678888888876654
No 70
>PF00508 PPV_E2_N: E2 (early) protein, N terminal; InterPro: IPR001866 E2 is an early regulatory protein found in the dsDNA papillomaviruses. E2 regulates viral transcription and DNA replication. It binds to the E2RE response element (5'-ACCNNNNNNGGT-3') present in multiple copies in the regulatory region. It can either activate or repress transcription, depending on E2RE's posiiton with regard to proximal promoter elements. Repression occurs by sterically hindering the assembly of the transcription initiation complex. The E1-E2 dimer complex binds to the origin of DNA replication [].; GO: 0006275 regulation of DNA replication, 0006355 regulation of transcription, DNA-dependent, 0016032 viral reproduction; PDB: 1R6K_A 1R6N_A 2JEX_A 2JEU_A 1TUE_E 1QQH_A 1DTO_A 2NNU_A.
Probab=25.87 E-value=97 Score=23.13 Aligned_cols=21 Identities=24% Similarity=0.396 Sum_probs=17.5
Q ss_pred HHHHHhHHHHHHHHHHHHHHH
Q psy7982 41 AELTSKLHELEAREAKLIEER 61 (72)
Q Consensus 41 ~ElTsKL~~le~re~~L~E~~ 61 (72)
+.|+.+|+.+|.+.-+|+|.=
T Consensus 2 E~L~~RLdalQe~~l~lyE~d 22 (202)
T PF00508_consen 2 ETLSQRLDALQEQLLELYEKD 22 (202)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT
T ss_pred hhHHHHHHHHHHHHHHHHhCC
Confidence 468999999999988888753
No 71
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=25.58 E-value=80 Score=21.09 Aligned_cols=30 Identities=17% Similarity=0.187 Sum_probs=20.2
Q ss_pred HHHHHHhhHHhHHHHHHHhcccCCCchhhH
Q psy7982 8 IQSVICLTRENIEALNSKFAAYQEPPSIYL 37 (72)
Q Consensus 8 I~~vI~LTrenIdaLn~kF~~~q~PPsIYL 37 (72)
++..+.+++++|+.|.+-|-.+.-|-+.-.
T Consensus 52 l~~~~~~~~~~i~~l~~ll~~e~ip~P~~~ 81 (166)
T PF11553_consen 52 LKKGLDLSQKQIEQLEKLLKEEGIPVPPGF 81 (166)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT-------
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 567789999999999999988876655444
No 72
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=25.18 E-value=1.6e+02 Score=22.27 Aligned_cols=43 Identities=19% Similarity=0.388 Sum_probs=28.6
Q ss_pred HHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 19 IEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 19 IdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
|++.++-|...-.-| =|...|..+...+-+++++-++++|..-
T Consensus 221 i~~ae~~~~~~~~S~-ef~~~~g~~~~a~m~~r~~~~~~~e~~L 263 (293)
T PF09712_consen 221 IDAAEEAYEELFRSE-EFAQAYGQLVNALMDLRKQQQEVVEEYL 263 (293)
T ss_pred HHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444 4667788888888888888888877643
No 73
>COG0380 OtsA Trehalose-6-phosphate synthase [Carbohydrate transport and metabolism]
Probab=25.14 E-value=54 Score=27.20 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=25.3
Q ss_pred HHHHHhhHHhHHHHHHHhcccCCCchhhHHH
Q psy7982 9 QSVICLTRENIEALNSKFAAYQEPPSIYLEE 39 (72)
Q Consensus 9 ~~vI~LTrenIdaLn~kF~~~q~PPsIYL~E 39 (72)
+.+-+-..+...+.|.+||....+|-+|+..
T Consensus 335 ~~~~~~i~~~V~rIN~~fG~~~~~Pv~~l~~ 365 (486)
T COG0380 335 QALRLQIEELVGRINGEFGSLSWTPVHYLHR 365 (486)
T ss_pred HHHHHHHHHHHHHHHhhcCCCCcceeEEEec
Confidence 4455556778899999999999999999843
No 74
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=24.97 E-value=46 Score=25.54 Aligned_cols=24 Identities=17% Similarity=0.312 Sum_probs=19.1
Q ss_pred HHhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 12 ICLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 12 I~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
..+|.+.|++..++|-|. |-|| +|
T Consensus 91 ~~~~~~~i~~~l~~f~G~i~Q~PP-~y 116 (273)
T PRK04099 91 KPFDKDLIEKILKSLQGEISYTPP-KF 116 (273)
T ss_pred CCCCHHHHHHHHHhCcceEEEeCC-hh
Confidence 358999999999999885 6676 55
No 75
>TIGR02875 spore_0_A sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species.
Probab=24.97 E-value=62 Score=21.98 Aligned_cols=24 Identities=33% Similarity=0.443 Sum_probs=20.6
Q ss_pred HHHHHHHHhh--HHhHHHHHHHhccc
Q psy7982 6 DNIQSVICLT--RENIEALNSKFAAY 29 (72)
Q Consensus 6 ~NI~~vI~LT--renIdaLn~kF~~~ 29 (72)
++|+++|++. +.|++.|+.=||-.
T Consensus 209 ~~~r~~i~~~~~~~~~~~~~~~~~~~ 234 (262)
T TIGR02875 209 RAIRHAIEVAWSRGNIEPINKLFGYT 234 (262)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHhCcc
Confidence 6789999985 88999999999855
No 76
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=24.81 E-value=48 Score=25.87 Aligned_cols=23 Identities=39% Similarity=0.579 Sum_probs=18.7
Q ss_pred HhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 13 CLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+|.+.|++..++|-|. |-|| +|
T Consensus 100 ~~t~~~l~~~l~~f~G~i~Q~PP-~y 124 (312)
T PRK05033 100 TLSAEQLEAALEKFRGDIEQVPS-MY 124 (312)
T ss_pred CCCHHHHHHHHHHCcCcEEEeCC-hh
Confidence 48999999999999885 5666 55
No 77
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=24.31 E-value=50 Score=25.68 Aligned_cols=22 Identities=32% Similarity=0.567 Sum_probs=17.7
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 107 ~t~~~i~~~l~~f~G~i~Q~PP-~y 130 (303)
T PRK01851 107 CDPAALEAALARFTGEIRQVPP-MY 130 (303)
T ss_pred CCHHHHHHHHHhccCeeeeeCC-ch
Confidence 7999999999999774 5566 55
No 78
>TIGR03090 SASP_tlp small, acid-soluble spore protein tlp. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C-terminus probably represents at a germination protease cleavage site.
Probab=24.00 E-value=1.1e+02 Score=19.67 Aligned_cols=20 Identities=35% Similarity=0.448 Sum_probs=17.2
Q ss_pred HHHHHHHHHhhHHhHHHHHH
Q psy7982 5 LDNIQSVICLTRENIEALNS 24 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~ 24 (72)
+.-||.||.=|.+||++-.+
T Consensus 10 VEkLQ~mi~nTieN~~eAee 29 (70)
T TIGR03090 10 VEKLQQMIDNTIENMEEANE 29 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999998765
No 79
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=23.90 E-value=53 Score=25.38 Aligned_cols=22 Identities=36% Similarity=0.539 Sum_probs=17.5
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 94 ~~~e~l~~~l~~f~G~i~Q~PP-~y 117 (292)
T PRK01528 94 PSKEEAYAVCSKFIGNITQIPP-AF 117 (292)
T ss_pred CCHHHHHHHHHhccceEEeeCC-hh
Confidence 5899999999999875 5666 55
No 80
>PF11488 Lge1: Transcriptional regulatory protein LGE1
Probab=23.64 E-value=58 Score=20.16 Aligned_cols=15 Identities=27% Similarity=0.379 Sum_probs=9.6
Q ss_pred HHHHHhhHHhHHHHH
Q psy7982 9 QSVICLTRENIEALN 23 (72)
Q Consensus 9 ~~vI~LTrenIdaLn 23 (72)
.--|.||++|+|.|.
T Consensus 64 ~l~vQlt~EkLdel~ 78 (80)
T PF11488_consen 64 ELNVQLTQEKLDELL 78 (80)
T ss_pred HHhHHHHHHhHHHHh
Confidence 334667777777663
No 81
>PF11083 Streptin-Immun: Lantibiotic streptin immunity protein; InterPro: IPR021112 Streptococcal species produce a lantibiotic, streptin, in a similar manner to the production of nisin and subtilin by other lactic acid bacteria, in order to compete against competing bacteria within the environment []. The immunity protein protects the bacterium from destruction by its own lantibiotic. In general, there is little homology between the immunity proteins of different genera of bacteria.
Probab=23.62 E-value=61 Score=22.08 Aligned_cols=34 Identities=24% Similarity=0.481 Sum_probs=22.5
Q ss_pred HHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHH
Q psy7982 20 EALNSKFAAYQEPPSIYLEEYAELTSKLHELEAR 53 (72)
Q Consensus 20 daLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~r 53 (72)
+.++......|.-=+.|+.+|+.+-.||..+=+.
T Consensus 55 e~ve~Ei~~lQ~qL~~~ldeYE~~VrrLE~fvkv 88 (99)
T PF11083_consen 55 EQVEKEIRELQNQLGLYLDEYEKLVRRLEKFVKV 88 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444445555567888999998888876543
No 82
>PF09602 PhaP_Bmeg: Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg); InterPro: IPR011728 This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage [].
Probab=23.62 E-value=1.1e+02 Score=22.40 Aligned_cols=21 Identities=38% Similarity=0.544 Sum_probs=17.3
Q ss_pred HHHHHHHHhHHHHHHHHHHHH
Q psy7982 38 EEYAELTSKLHELEAREAKLI 58 (72)
Q Consensus 38 ~EY~ElTsKL~~le~re~~L~ 58 (72)
..+.|+|+|++++..+-+.|+
T Consensus 85 d~inE~t~k~~El~~~i~el~ 105 (165)
T PF09602_consen 85 DSINEWTDKLNELSAKIQELL 105 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999887764
No 83
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=23.51 E-value=1.2e+02 Score=20.02 Aligned_cols=21 Identities=29% Similarity=0.444 Sum_probs=17.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHH
Q psy7982 37 LEEYAELTSKLHELEAREAKL 57 (72)
Q Consensus 37 L~EY~ElTsKL~~le~re~~L 57 (72)
=+++.+|..|++.|+.+.+.|
T Consensus 95 k~ev~~L~~RI~~Le~~l~~l 115 (118)
T TIGR01837 95 REEIEALSAKIEQLAVQVEEL 115 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 378999999999999887766
No 84
>PF07369 DUF1488: Protein of unknown function (DUF1488); InterPro: IPR009962 This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown.; PDB: 2GPI_A.
Probab=23.44 E-value=1.4e+02 Score=17.77 Aligned_cols=33 Identities=21% Similarity=0.227 Sum_probs=25.4
Q ss_pred HHHHHHHhcccCCCchhhHHHHHHHHHhHHHHH
Q psy7982 19 IEALNSKFAAYQEPPSIYLEEYAELTSKLHELE 51 (72)
Q Consensus 19 IdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le 51 (72)
.+||-+.||.-...++=+|..|+..-..+.+.=
T Consensus 34 ~~aL~~~~~~~~~~~~~~l~~F~~~R~~Ie~~A 66 (83)
T PF07369_consen 34 AEALEDLFGARGASEEDLLAAFDRHRFDIEEAA 66 (83)
T ss_dssp HHHHHHHHTS---SHHHHHHHHHHTHHHHHHHH
T ss_pred HHHHHhhhCcCCCCHHHHHHHHHHCHHHHHHHH
Confidence 478999999888889999999999988876653
No 85
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=23.41 E-value=53 Score=25.30 Aligned_cols=22 Identities=36% Similarity=0.708 Sum_probs=17.6
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
+|.+.|++..++|-|. |-|| +|
T Consensus 96 ~~~~~l~~~l~~f~G~i~Q~PP-~y 119 (294)
T PRK02484 96 LTEEEVDQAMTSFTGKITQIPP-MY 119 (294)
T ss_pred CCHHHHHHHHHhccCeEEEeCC-hh
Confidence 7899999999999875 4566 65
No 86
>KOG3647|consensus
Probab=23.38 E-value=2.9e+02 Score=22.55 Aligned_cols=49 Identities=18% Similarity=0.270 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHH
Q psy7982 4 ELDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEA 52 (72)
Q Consensus 4 el~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~ 52 (72)
+..|+.+-|.=-+.-++.+-.+|+..|.--+-|..||+.-...|.+|=.
T Consensus 134 dea~L~~Kierrk~ElEr~rkRle~LqsiRP~~MdEyE~~EeeLqkly~ 182 (338)
T KOG3647|consen 134 DEAALGSKIERRKAELERTRKRLEALQSIRPAHMDEYEDCEEELQKLYQ 182 (338)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHH
Confidence 4455666777788889999999999999888999999887766655443
No 87
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=22.86 E-value=54 Score=25.63 Aligned_cols=24 Identities=33% Similarity=0.487 Sum_probs=18.8
Q ss_pred HHhhHHhHHHHHHHhccc--CCCchhh
Q psy7982 12 ICLTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 12 I~LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
..+|.+-|++..++|-|. |-|| +|
T Consensus 91 ~~~~~~~l~~~l~~f~G~i~Q~PP-~y 116 (312)
T PRK14122 91 SPLDEKDLEAALPGFLGLTEQVPP-QY 116 (312)
T ss_pred CCCCHHHHHHHHHhCcCeEEEeCC-hH
Confidence 357999999999999874 5666 65
No 88
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=22.55 E-value=1.7e+02 Score=18.17 Aligned_cols=23 Identities=39% Similarity=0.681 Sum_probs=11.7
Q ss_pred hHHHHHHHHHHhhHHhHHHHHHH
Q psy7982 3 DELDNIQSVICLTRENIEALNSK 25 (72)
Q Consensus 3 eel~NI~~vI~LTrenIdaLn~k 25 (72)
||....+.|+.=|++-|++|-++
T Consensus 50 EEFd~q~~~L~~~r~kl~~LEar 72 (79)
T PF04380_consen 50 EEFDAQKAVLARTREKLEALEAR 72 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445555555555555555444
No 89
>PRK02899 adaptor protein; Provisional
Probab=22.49 E-value=1.8e+02 Score=20.86 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=29.1
Q ss_pred hHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHH
Q psy7982 15 TRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELE 51 (72)
Q Consensus 15 TrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le 51 (72)
.-.++-|+...||....-..-||.||.+.=-.=++++
T Consensus 153 ~~~~~~ail~EYg~~s~~t~~~l~EhGk~I~~~~Al~ 189 (197)
T PRK02899 153 LKADFIAILAEYGNPSTVTIYRLEEYGKELMASQAVE 189 (197)
T ss_pred hHHHHHHHHHhhCCCCcccHHHHHHhhHHHhHhhHHH
Confidence 3467788999999998888889999998765555554
No 90
>PF08656 DASH_Dad3: DASH complex subunit Dad3; InterPro: IPR013965 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ].
Probab=22.11 E-value=1.3e+02 Score=19.38 Aligned_cols=30 Identities=23% Similarity=0.447 Sum_probs=15.0
Q ss_pred HhHHHHHHHhccc---CCCchhhHHHHHHHHHh
Q psy7982 17 ENIEALNSKFAAY---QEPPSIYLEEYAELTSK 46 (72)
Q Consensus 17 enIdaLn~kF~~~---q~PPsIYL~EY~ElTsK 46 (72)
.|+..|++..... ..||+--|+.-++|..|
T Consensus 17 ~~L~~L~~~l~~L~~~~~~~~~lL~~LR~LE~K 49 (78)
T PF08656_consen 17 DNLKTLSDTLKDLNSSNSPSEELLDGLRELERK 49 (78)
T ss_pred HHHHHHHHHHHHHHccCCChHHHHHHHHHHHHH
Confidence 3555566665555 44555444444444433
No 91
>KOG2512|consensus
Probab=21.88 E-value=1.1e+02 Score=24.83 Aligned_cols=48 Identities=25% Similarity=0.304 Sum_probs=36.2
Q ss_pred HHHHhhHHhHHHHHHHhcccCCCc------hhhHH-HHHHHHHhHHHHHHHHHHH
Q psy7982 10 SVICLTRENIEALNSKFAAYQEPP------SIYLE-EYAELTSKLHELEAREAKL 57 (72)
Q Consensus 10 ~vI~LTrenIdaLn~kF~~~q~PP------sIYL~-EY~ElTsKL~~le~re~~L 57 (72)
+.=.|++|+-+.+-++|++.+--= ++||+ -|+|.|+.+++++.-.-.+
T Consensus 41 ~~s~~k~Es~~~f~~tf~~~t~~ie~~l~~~~~l~~~l~e~tv~Iddl~~~l~~~ 95 (337)
T KOG2512|consen 41 SNSTLKKESVDRFPATFAGSTADIEERLNENEYLERFLEEATVTIDDLTRCLIEL 95 (337)
T ss_pred hhhhhhhhhhhhhhHhHhccchhHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHhc
Confidence 556789999999999999987633 44544 3889999999988654443
No 92
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=21.75 E-value=58 Score=23.95 Aligned_cols=22 Identities=41% Similarity=0.620 Sum_probs=16.7
Q ss_pred hhHHhHHHHHHHhccc--CCCchhh
Q psy7982 14 LTRENIEALNSKFAAY--QEPPSIY 36 (72)
Q Consensus 14 LTrenIdaLn~kF~~~--q~PPsIY 36 (72)
.+.+.|++..++|-|. |-|| +|
T Consensus 93 ~~~~~l~~~l~~f~G~~~Q~PP-~y 116 (209)
T TIGR00431 93 PTTEDVEAALPTFRGEIEQIPP-MY 116 (209)
T ss_pred CCHHHHHHHHHHccCcEEEECC-hh
Confidence 5678999999999774 4566 55
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=21.72 E-value=2.6e+02 Score=18.76 Aligned_cols=54 Identities=20% Similarity=0.399 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHH
Q psy7982 3 DELDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEER 61 (72)
Q Consensus 3 eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~ 61 (72)
.+|..++.=+.--+..+-.|.+.+++...-||. .+|...+.+|+..-..|-+.+
T Consensus 79 ~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~-----~el~~~i~~l~~e~~~l~~kL 132 (169)
T PF07106_consen 79 AEIKELREELAELKKEVKSLEAELASLSSEPTN-----EELREEIEELEEEIEELEEKL 132 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCH-----HHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666667777888888887777754 334444444444444333333
No 94
>PF12579 DUF3755: Protein of unknown function (DUF3755); InterPro: IPR022228 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Probab=21.67 E-value=1.1e+02 Score=16.93 Aligned_cols=18 Identities=33% Similarity=0.612 Sum_probs=14.1
Q ss_pred HHHHhhHHhHHHHHHHhc
Q psy7982 10 SVICLTRENIEALNSKFA 27 (72)
Q Consensus 10 ~vI~LTrenIdaLn~kF~ 27 (72)
++..=||.||.++.++-.
T Consensus 10 dLf~~~R~NI~~il~~m~ 27 (35)
T PF12579_consen 10 DLFCQTRDNILAILNDMN 27 (35)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 345668999999988765
No 95
>KOG0250|consensus
Probab=21.48 E-value=5.3e+02 Score=24.09 Aligned_cols=58 Identities=24% Similarity=0.245 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy7982 5 LDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLIEERE 62 (72)
Q Consensus 5 l~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~ 62 (72)
+.-++.+|+.++.-+..|-..-.+.+-|-+++=++++++.++.++++..+..+-++-+
T Consensus 705 ~~q~~~~~~~~~~em~el~n~~e~~~~~~~~~~~l~~ei~~~~~eIe~~~~~~e~l~~ 762 (1074)
T KOG0250|consen 705 IEQIKRRIRKKRAEMTELKNTAEEKQVDISKLEDLAREIKKKEKEIEEKEAPLEKLKE 762 (1074)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhcchhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566665566555421566678889999999999999999888766554433
No 96
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. 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. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=21.16 E-value=2.5e+02 Score=19.09 Aligned_cols=37 Identities=30% Similarity=0.329 Sum_probs=21.7
Q ss_pred hcccCCCchhhH-HHHHHHHHh-HHHHHHHHHHHHHHHH
Q psy7982 26 FAAYQEPPSIYL-EEYAELTSK-LHELEAREAKLIEERE 62 (72)
Q Consensus 26 F~~~q~PPsIYL-~EY~ElTsK-L~~le~re~~L~E~~~ 62 (72)
=++-..|||.|+ +|-.++|-+ ..++..-..-|+..++
T Consensus 10 Tsdd~~p~pgy~~~Eia~~t~~s~~~~~ei~d~L~kRL~ 48 (122)
T cd03572 10 TSDDDEPTPGYLYEEIAKLTRKSVGSCQELLEYLLKRLK 48 (122)
T ss_pred hcCCCCCCchHHHHHHHHHHHcCHHHHHHHHHHHHHHhc
Confidence 356678888998 455555555 2444444445555554
No 97
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=21.08 E-value=46 Score=26.01 Aligned_cols=44 Identities=34% Similarity=0.446 Sum_probs=29.0
Q ss_pred HHHhhHHhHHHHHHHhccc--CCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy7982 11 VICLTRENIEALNSKFAAY--QEPPSIYLEEYAELTSKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 11 vI~LTrenIdaLn~kF~~~--q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~~~ 66 (72)
+.++|++.|++..++|-|. |-|| +| ..++..-+.|+|.--.|..
T Consensus 118 ~~~it~e~i~~~l~~F~G~i~Q~PP-~y-----------SAvKv~GkrlYeyAR~G~~ 163 (312)
T cd02867 118 YSHITREDIEEVLAKFRGDIKQVPP-LY-----------SALKMDGKRLYEYAREGKP 163 (312)
T ss_pred CCCCCHHHHHHHHHhcceeeeeeCc-ch-----------heeeeCCHHHHHHHhCCcc
Confidence 4468999999999999774 4555 66 3444455555555554444
No 98
>KOG4586|consensus
Probab=21.05 E-value=52 Score=24.15 Aligned_cols=15 Identities=33% Similarity=0.718 Sum_probs=13.1
Q ss_pred HHHHHhcccCCCchh
Q psy7982 21 ALNSKFAAYQEPPSI 35 (72)
Q Consensus 21 aLn~kF~~~q~PPsI 35 (72)
-|.++|-|-++||-|
T Consensus 111 PlI~rfCG~~nPp~I 125 (156)
T KOG4586|consen 111 PLIARFCGDRNPPEI 125 (156)
T ss_pred HHHHHHhccCCChhh
Confidence 478999999999965
No 99
>cd07667 BAR_SNX30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX30 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=20.97 E-value=2.9e+02 Score=20.87 Aligned_cols=35 Identities=11% Similarity=0.285 Sum_probs=24.1
Q ss_pred HHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHHH
Q psy7982 19 IEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKLI 58 (72)
Q Consensus 19 IdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L~ 58 (72)
..++|+-|. -++|| .+|.|+..+.+.|....-++.
T Consensus 37 ~~~lna~~k-v~~~d----~eF~e~~ey~d~l~~~l~~ie 71 (240)
T cd07667 37 VKYVTGGYK-LRSRP----LEFAAIGDYLDTFALKLGTID 71 (240)
T ss_pred HHHHHHHhc-cCCCC----hHHHHHHHHHHHHHHhhhhHH
Confidence 788999886 78888 566777666666665544443
No 100
>PF14728 PHTB1_C: PTHB1 C-terminus
Probab=20.73 E-value=4.1e+02 Score=21.05 Aligned_cols=56 Identities=23% Similarity=0.266 Sum_probs=38.4
Q ss_pred HHHHHhhHHhHHHHHHHhcc--------cCCCchhhHHHHHHHHHhHHHHHHHHHHHHHHHHhh
Q psy7982 9 QSVICLTRENIEALNSKFAA--------YQEPPSIYLEEYAELTSKLHELEAREAKLIEERECV 64 (72)
Q Consensus 9 ~~vI~LTrenIdaLn~kF~~--------~q~PPsIYL~EY~ElTsKL~~le~re~~L~E~~~~~ 64 (72)
..+-=+++|=|.+|.++|++ ..-+++|=|.+|-+.=+.-++++.+..++-+.++..
T Consensus 163 e~l~lv~~eLi~Rl~~~~~~~~~~~~~~~~~~~~lPl~~~~~~id~H~~lr~~~~~~~~~L~~~ 226 (377)
T PF14728_consen 163 EALWLVLEELIRRLKEHFPKQGVKDRFKISFSGPLPLQEYFEIIDQHFELRQELKELEEELDER 226 (377)
T ss_pred hHHHHHHHHHHHHHHHhccccCcccceEEecCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445678888999999988 222334448888888777777777777666666543
No 101
>KOG0964|consensus
Probab=20.62 E-value=2.3e+02 Score=26.72 Aligned_cols=56 Identities=23% Similarity=0.293 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHHhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhHHHHHHHHHHH
Q psy7982 2 CDELDNIQSVICLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKLHELEAREAKL 57 (72)
Q Consensus 2 ~eel~NI~~vI~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL~~le~re~~L 57 (72)
+.||.-|...|+=|+++.+.|-....+.-.--+=-+++|+++.+-+++...|-.++
T Consensus 396 r~ei~~l~~~i~~~ke~e~~lq~e~~~~e~~l~~~~e~i~~l~~si~e~~~r~~~~ 451 (1200)
T KOG0964|consen 396 RSEIEKLKRGINDTKEQENILQKEIEDLESELKEKLEEIKELESSINETKGRMEEF 451 (1200)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHhhhhhHHHHH
Confidence 45778888888888888887776666554444444566666655555444444433
No 102
>COG0180 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.48 E-value=99 Score=24.28 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=25.7
Q ss_pred HHHHHhhHHhHHHHHHHhcccCCCchhhHH
Q psy7982 9 QSVICLTRENIEALNSKFAAYQEPPSIYLE 38 (72)
Q Consensus 9 ~~vI~LTrenIdaLn~kF~~~q~PPsIYL~ 38 (72)
.++++|||+=-+++|..|+..=.+|+..+.
T Consensus 156 ~qHleLtRDiA~rfn~~y~~~f~~P~~~~~ 185 (314)
T COG0180 156 DQHLELTRDIARRFNHLYGEVFPLPEALIS 185 (314)
T ss_pred hHHHHHHHHHHHHHHhhcCCccCCcccccc
Confidence 468999999999999999998888876653
No 103
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=20.41 E-value=1.5e+02 Score=15.61 Aligned_cols=32 Identities=38% Similarity=0.547 Sum_probs=23.3
Q ss_pred HhhHHhHHHHHHHhcccCCCchhhHHHHHHHHHhH
Q psy7982 13 CLTRENIEALNSKFAAYQEPPSIYLEEYAELTSKL 47 (72)
Q Consensus 13 ~LTrenIdaLn~kF~~~q~PPsIYL~EY~ElTsKL 47 (72)
.+|.+.++.|-+-|..-+.|.. .+.++|...+
T Consensus 6 ~~~~~~~~~L~~~f~~~~~P~~---~~~~~la~~~ 37 (56)
T smart00389 6 SFTPEQLEELEKEFQKNPYPSR---EEREELAAKL 37 (56)
T ss_pred cCCHHHHHHHHHHHHhCCCCCH---HHHHHHHHHH
Confidence 3788999999999998887763 4455555544
No 104
>PF05974 DUF892: Domain of unknown function (DUF892); InterPro: IPR010287 This domain is found in several hypothetical bacterial proteins of unknown function.; PDB: 4ERU_B 3OGH_A 2GS4_B 2GYQ_B 3HIU_A.
Probab=20.36 E-value=1.3e+02 Score=20.43 Aligned_cols=27 Identities=30% Similarity=0.402 Sum_probs=23.0
Q ss_pred HHHHHHhhHHhHHHHHHHhcccCCCch
Q psy7982 8 IQSVICLTRENIEALNSKFAAYQEPPS 34 (72)
Q Consensus 8 I~~vI~LTrenIdaLn~kF~~~q~PPs 34 (72)
++..+.-|+.+++.|-.-|.....+|+
T Consensus 40 l~~h~~eT~~q~~rLe~~~~~lg~~p~ 66 (159)
T PF05974_consen 40 LEEHLEETEQQIERLEQIFEALGADPS 66 (159)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTTS-S-
T ss_pred HHHHHHHHHHHHHHHHHHHHHccCCCc
Confidence 678889999999999999999999996
No 105
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=20.35 E-value=1.2e+02 Score=19.90 Aligned_cols=23 Identities=22% Similarity=0.647 Sum_probs=18.4
Q ss_pred chhhH--HHHHHHHHhHHHHHHHHH
Q psy7982 33 PSIYL--EEYAELTSKLHELEAREA 55 (72)
Q Consensus 33 PsIYL--~EY~ElTsKL~~le~re~ 55 (72)
|.++. .+|.++-.||++++.+-.
T Consensus 8 P~viv~~~d~~~i~~rLD~iEeKVE 32 (77)
T PRK01026 8 PQVVVDPKDFKEIQKRLDEIEEKVE 32 (77)
T ss_pred CeeecCHHHHHHHHHHHHHHHHHHH
Confidence 44444 679999999999998865
No 106
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=20.24 E-value=2.2e+02 Score=17.41 Aligned_cols=29 Identities=38% Similarity=0.412 Sum_probs=22.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy7982 38 EEYAELTSKLHELEAREAKLIEERECVKK 66 (72)
Q Consensus 38 ~EY~ElTsKL~~le~re~~L~E~~~~~~~ 66 (72)
..|....+||.+-+.|-+.|...+...+.
T Consensus 25 ~~n~~~e~kLqeaE~rn~eL~~ei~~L~~ 53 (61)
T PF08826_consen 25 SANLAFESKLQEAEKRNRELEQEIERLKK 53 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35777889999999999888877765443
No 107
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=20.20 E-value=56 Score=24.07 Aligned_cols=26 Identities=27% Similarity=0.172 Sum_probs=18.7
Q ss_pred HHHhhHHhHHHHHHHhc-ccCCCchhh
Q psy7982 11 VICLTRENIEALNSKFA-AYQEPPSIY 36 (72)
Q Consensus 11 vI~LTrenIdaLn~kF~-~~q~PPsIY 36 (72)
+.++|++.|++...+|- +.+..|+.|
T Consensus 96 ~~~it~~~i~~~l~~f~g~~~q~~p~~ 122 (226)
T cd02868 96 YDHITREKIERLLAVIQSGHQQKAFEL 122 (226)
T ss_pred CCCCCHHHHHHHHHHhhCCceEECCce
Confidence 44689999999999997 554444344
Done!