Query 013514
Match_columns 441
No_of_seqs 107 out of 140
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 04:37:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1142 Transcription initiati 99.9 9.3E-24 2E-28 201.4 7.9 166 268-440 25-193 (258)
2 PF03847 TFIID_20kDa: Transcri 99.5 3.1E-14 6.6E-19 112.7 3.3 39 403-441 1-39 (68)
3 COG5624 TAF61 Transcription in 99.1 4.7E-11 1E-15 121.6 3.1 57 384-441 367-424 (505)
4 cd07981 TAF12 TATA Binding Pro 99.1 1.8E-10 3.8E-15 90.8 4.6 40 401-440 1-40 (72)
5 PF00808 CBFD_NFYB_HMF: Histon 85.0 1.3 2.8E-05 33.8 3.6 39 402-440 3-41 (65)
6 cd08048 TAF11 TATA Binding Pro 74.4 5.3 0.00011 33.5 4.2 38 402-440 17-54 (85)
7 KOG3489 Mitochondrial import i 69.8 7.4 0.00016 33.6 4.1 36 403-438 23-68 (86)
8 smart00803 TAF TATA box bindin 63.9 15 0.00033 29.2 4.6 39 401-440 2-40 (65)
9 PF00125 Histone: Core histone 62.0 5.9 0.00013 30.5 2.0 40 401-440 5-48 (75)
10 PF10273 WGG: Pre-rRNA-process 60.0 11 0.00025 30.9 3.4 36 402-437 28-68 (82)
11 PF09860 DUF2087: Uncharacteri 58.1 13 0.00027 30.3 3.3 30 407-436 17-47 (71)
12 PRK09281 F0F1 ATP synthase sub 54.4 14 0.00031 39.4 3.9 36 404-439 465-500 (502)
13 cd07979 TAF9 TATA Binding Prot 54.3 21 0.00045 31.2 4.2 34 406-440 6-39 (117)
14 TIGR00962 atpA proton transloc 53.7 15 0.00032 39.2 3.8 36 404-439 464-499 (501)
15 cd03565 VHS_Tom1 VHS domain fa 53.2 18 0.0004 32.0 3.8 37 401-437 78-115 (141)
16 KOG0871 Class 2 transcription 51.4 23 0.0005 33.4 4.3 46 395-440 6-52 (156)
17 COG2036 HHT1 Histones H3 and H 49.4 14 0.00031 31.6 2.4 44 396-440 14-57 (91)
18 TIGR01560 put_DNA_pack unchara 48.4 28 0.0006 28.4 3.9 32 406-440 4-35 (91)
19 TIGR03859 PQQ_PqqD coenzyme PQ 46.4 12 0.00027 30.2 1.5 34 403-436 42-80 (81)
20 PF07524 Bromo_TP: Bromodomain 45.9 41 0.0009 26.5 4.4 37 404-440 5-44 (77)
21 cd03561 VHS VHS domain family; 45.8 36 0.00077 29.4 4.4 37 401-437 76-112 (133)
22 smart00428 H3 Histone H3. 45.5 29 0.00062 30.5 3.7 43 397-439 25-73 (105)
23 PTZ00018 histone H3; Provision 45.4 24 0.00051 32.4 3.3 44 396-439 57-104 (136)
24 PRK10569 NAD(P)H-dependent FMN 43.5 24 0.00051 32.5 3.1 26 414-439 147-172 (191)
25 cd08324 CARD_NOD1_CARD4 Caspas 42.9 26 0.00056 30.2 3.0 31 405-437 49-79 (85)
26 PF08236 SRI: SRI (Set2 Rpb1 i 42.2 25 0.00055 29.1 2.8 39 402-440 28-81 (88)
27 cd03567 VHS_GGA VHS domain fam 41.7 40 0.00087 30.2 4.2 38 400-437 76-116 (139)
28 TIGR03566 FMN_reduc_MsuE FMN r 41.3 28 0.0006 30.7 3.1 26 414-439 146-171 (174)
29 COG4585 Signal transduction hi 41.2 38 0.00081 32.8 4.2 25 416-440 268-292 (365)
30 PRK13343 F0F1 ATP synthase sub 41.0 31 0.00066 37.1 3.9 35 405-439 466-500 (502)
31 PLN00121 histone H3; Provision 40.9 31 0.00067 31.6 3.4 44 396-439 57-104 (136)
32 PRK02079 pyrroloquinoline quin 40.0 14 0.0003 31.0 1.0 33 404-437 48-86 (88)
33 PF12422 Condensin2nSMC: Conde 38.8 32 0.00069 30.8 3.1 38 402-440 91-128 (152)
34 PF02609 Exonuc_VII_S: Exonucl 38.5 37 0.0008 25.6 3.0 35 405-439 6-46 (53)
35 CHL00059 atpA ATP synthase CF1 38.1 35 0.00076 36.6 3.8 33 406-438 446-478 (485)
36 PF07697 7TMR-HDED: 7TM-HD ext 37.5 39 0.00085 29.9 3.4 41 399-439 21-61 (222)
37 PHA02627 hypothetical protein; 37.5 16 0.00035 30.5 0.9 40 400-440 30-69 (73)
38 PF07030 DUF1320: Protein of u 37.3 50 0.0011 28.7 4.0 38 402-440 11-48 (130)
39 PF14357 DUF4404: Domain of un 35.8 60 0.0013 27.0 4.1 32 404-435 3-34 (85)
40 cd00076 H4 Histone H4, one of 35.4 61 0.0013 27.4 4.1 39 401-440 13-51 (85)
41 PF08165 FerA: FerA (NUC095) d 35.4 29 0.00063 27.9 2.1 19 421-439 9-27 (66)
42 PF00616 RasGAP: GTPase-activa 35.2 51 0.0011 29.0 3.7 17 424-440 98-114 (197)
43 PF04719 TAFII28: hTAFII28-lik 34.8 47 0.001 28.4 3.3 39 402-440 24-62 (90)
44 PF06076 Orthopox_F14: Orthopo 34.8 18 0.0004 30.1 0.9 39 401-440 31-69 (73)
45 TIGR03687 pupylate_cterm ubiqu 33.7 39 0.00085 24.9 2.3 25 406-440 4-28 (33)
46 PF07464 ApoLp-III: Apolipopho 33.6 41 0.00088 31.1 3.0 35 405-439 99-141 (155)
47 smart00576 BTP Bromodomain tra 33.3 73 0.0016 25.5 4.0 36 404-440 9-44 (77)
48 KOG2424 Protein involved in tr 33.0 30 0.00064 33.7 2.0 38 396-433 144-182 (195)
49 PHA02780 hypothetical protein; 32.9 20 0.00044 29.9 0.8 39 401-440 31-69 (73)
50 PF12351 Fig1: Ca2+ regulator 32.0 24 0.00052 32.7 1.3 36 404-440 37-73 (182)
51 PF11074 DUF2779: Domain of un 31.8 53 0.0012 29.2 3.3 29 402-437 82-110 (130)
52 PF02291 TFIID-31kDa: Transcri 31.7 59 0.0013 29.3 3.6 35 405-440 16-50 (129)
53 PTZ00015 histone H4; Provision 30.8 78 0.0017 27.8 4.1 39 401-440 30-68 (102)
54 PRK00977 exodeoxyribonuclease 30.6 67 0.0015 26.6 3.5 36 404-439 16-57 (80)
55 PLN00035 histone H4; Provision 30.3 84 0.0018 27.7 4.2 38 402-440 30-67 (103)
56 PRK14070 exodeoxyribonuclease 29.8 71 0.0015 26.2 3.5 35 405-439 2-42 (69)
57 PRK14064 exodeoxyribonuclease 29.5 72 0.0016 26.3 3.5 35 405-439 13-53 (75)
58 cd03568 VHS_STAM VHS domain fa 29.5 80 0.0017 28.3 4.1 34 400-435 75-108 (144)
59 PF05402 PqqD: Coenzyme PQQ sy 29.4 37 0.00081 25.4 1.7 21 403-423 28-48 (68)
60 COG5162 Transcription initiati 29.4 73 0.0016 30.9 4.0 37 404-440 72-126 (197)
61 PRK15380 pathogenicity island 29.2 46 0.00099 34.2 2.7 42 396-437 113-156 (319)
62 PRK14069 exodeoxyribonuclease 28.9 70 0.0015 27.8 3.5 35 405-439 15-55 (95)
63 PF08328 ASL_C: Adenylosuccina 28.4 66 0.0014 29.0 3.3 30 399-432 81-110 (115)
64 cd00043 CYCLIN Cyclin box fold 28.1 63 0.0014 23.3 2.7 33 406-438 4-36 (88)
65 PF10735 DUF2526: Protein of u 27.6 22 0.00047 30.2 0.2 27 406-434 3-33 (77)
66 PRK14067 exodeoxyribonuclease 27.5 79 0.0017 26.4 3.4 35 405-439 14-54 (80)
67 COG5150 Class 2 transcription 26.7 97 0.0021 29.0 4.1 45 396-440 6-51 (148)
68 PF08439 Peptidase_M3_N: Oligo 26.6 47 0.001 25.5 1.8 17 417-433 35-51 (70)
69 PF08479 POTRA_2: POTRA domain 26.5 80 0.0017 24.5 3.1 42 397-438 9-50 (76)
70 smart00417 H4 Histone H4. 26.4 1E+02 0.0023 25.6 3.9 41 399-440 11-51 (74)
71 cd03197 GST_C_mPGES2 GST_C fam 26.4 69 0.0015 29.5 3.2 27 414-440 70-96 (149)
72 TIGR03567 FMN_reduc_SsuE FMN r 25.9 69 0.0015 28.3 3.0 24 414-437 145-170 (171)
73 PF04877 Hairpins: HrpZ; Inte 25.8 60 0.0013 33.5 2.9 37 401-438 139-176 (308)
74 KOG0869 CCAAT-binding factor, 25.7 1E+02 0.0022 29.6 4.1 45 397-441 28-73 (168)
75 cd05392 RasGAP_Neurofibromin_l 25.7 87 0.0019 30.8 3.9 15 426-440 126-140 (323)
76 TIGR01280 xseB exodeoxyribonuc 25.3 98 0.0021 24.9 3.5 35 405-439 8-48 (67)
77 PF07304 SRA1: Steroid recepto 25.3 61 0.0013 29.6 2.6 31 405-436 72-102 (157)
78 PRK14068 exodeoxyribonuclease 25.1 96 0.0021 25.7 3.5 35 405-439 13-53 (76)
79 TIGR01688 dltC D-alanine--poly 25.0 91 0.002 25.7 3.3 32 404-435 1-47 (73)
80 PF14164 YqzH: YqzH-like prote 24.7 81 0.0018 26.0 2.9 38 400-437 24-63 (64)
81 smart00427 H2B Histone H2B. 24.5 1.1E+02 0.0024 26.4 3.9 35 406-440 6-40 (89)
82 cd05128 RasGAP_GAP1_like The G 24.5 78 0.0017 31.9 3.4 16 426-441 132-147 (315)
83 PF08069 Ribosomal_S13_N: Ribo 24.3 37 0.0008 27.5 0.9 13 422-434 31-43 (60)
84 PLN00161 histone H3; Provision 24.3 93 0.002 28.7 3.6 44 396-439 50-98 (135)
85 TIGR03142 cytochro_ccmI cytoch 24.1 1E+02 0.0022 26.4 3.6 43 397-439 35-77 (117)
86 cd05135 RasGAP_RASAL Ras GTPas 24.0 75 0.0016 32.3 3.2 16 426-441 149-164 (333)
87 KOG1924 RhoA GTPase effector D 24.0 3.5E+02 0.0075 32.0 8.5 17 398-414 726-742 (1102)
88 cd05134 RasGAP_RASA3 RASA3 (or 23.7 1.1E+02 0.0023 31.2 4.2 27 414-440 115-145 (310)
89 cd05130 RasGAP_Neurofibromin N 23.7 80 0.0017 32.0 3.3 16 426-441 135-150 (329)
90 cd05391 RasGAP_p120GAP p120GAP 23.0 1E+02 0.0022 31.1 3.9 19 422-440 119-140 (315)
91 cd05136 RasGAP_DAB2IP The DAB2 23.0 1E+02 0.0022 31.0 3.9 27 415-441 113-142 (309)
92 PRK05687 fliH flagellar assemb 22.8 36 0.00079 32.0 0.7 34 407-440 115-149 (246)
93 PF08784 RPA_C: Replication pr 22.8 79 0.0017 25.8 2.6 31 404-434 49-92 (102)
94 cd05022 S-100A13 S-100A13: S-1 22.7 94 0.002 25.8 3.0 34 397-431 21-56 (89)
95 PF01851 PC_rep: Proteasome/cy 22.6 47 0.001 23.4 1.1 20 420-439 14-33 (35)
96 PF08157 NUC129: NUC129 domain 22.2 68 0.0015 26.5 2.1 21 420-440 7-27 (63)
97 PF09862 DUF2089: Protein of u 22.1 91 0.002 27.8 3.0 33 404-436 67-103 (113)
98 cd05127 RasGAP_IQGAP_related T 21.6 1.2E+02 0.0026 29.9 4.0 14 427-440 123-136 (325)
99 cd06845 Bcl-2_like Apoptosis r 21.2 1.4E+02 0.003 25.9 3.9 32 404-438 51-82 (144)
100 COG3900 Predicted periplasmic 21.2 46 0.00099 33.5 1.1 43 399-441 119-162 (262)
101 PF13499 EF-hand_7: EF-hand do 21.0 1.5E+02 0.0033 21.5 3.6 32 395-427 10-41 (66)
102 cd03569 VHS_Hrs_Vps27p VHS dom 20.9 1.4E+02 0.003 26.6 4.0 34 401-436 80-113 (142)
103 PF12646 DUF3783: Domain of un 20.7 1.1E+02 0.0023 23.6 2.8 34 402-435 9-54 (58)
104 PF13833 EF-hand_8: EF-hand do 20.6 1.9E+02 0.004 20.5 3.9 32 400-433 3-35 (54)
105 PF12536 DUF3734: Patatin phos 20.4 52 0.0011 28.2 1.2 35 404-439 21-55 (108)
106 cd05137 RasGAP_CLA2_BUD2 CLA2/ 20.4 1.1E+02 0.0024 31.9 3.6 16 426-441 199-214 (395)
107 COG1710 Uncharacterized protei 20.3 95 0.0021 28.8 2.8 17 402-418 8-24 (139)
108 smart00073 HPT Histidine Phosp 20.0 2E+02 0.0043 21.8 4.1 30 406-435 55-85 (87)
No 1
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.89 E-value=9.3e-24 Score=201.44 Aligned_cols=166 Identities=28% Similarity=0.339 Sum_probs=114.5
Q ss_pred cccCccccccCCCCCCCCCCCCCCCCCCCCcchhccccCcccCCCCcchhhhhhcccccCCCCCCCCCCccccccccCC-
Q 013514 268 QSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSS- 346 (441)
Q Consensus 268 Q~~nQ~WLss~~q~kppl~SP~s~R~Q~n~~slQQR~hipqQh~~~~t~lqqqqlsq~QqqQ~q~~hqqq~H~~QQl~q- 346 (441)
|..++.||+.+..+.++...+ +||+|++.+.+.+|.++.+|+-+..-.. .+. ........+...+|+. ++..
T Consensus 25 q~~qq~~~~~~~~~~s~~~~~-s~~~q~~~~~~~~~~~~~qq~~s~~~~~--~~~---~n~~~~s~~~~~~~~~-~~~~~ 97 (258)
T KOG1142|consen 25 QARQQQWLRQIQGIPSPESYP-SQRQQRFSPTCSIRENPNQQWISTGYPQ--PQV---SNGGPPSQALNQQDSQ-QSAIS 97 (258)
T ss_pred HHHHhhhhccccCCCCCCCCh-hhccccCCCcccccCCCCccccccccCc--ccc---ccCCchHHhhhhhhHH-hhccc
Confidence 456889999999999888886 9999999999999988888875443321 011 0111111111112222 2211
Q ss_pred -CCCCCCCccccccCCCCCCCCCCcccccc-CCCCccccCCcccCCCcccCCCCCcccchhHHHHHHHhcCCCCCCChHH
Q 013514 347 -PRVPQSSPHQQQITRPPGSATQKPSSLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDV 424 (441)
Q Consensus 347 -~q~~q~l~qQqQ~~R~~g~a~qKp~SLtg-sQP~~~~~G~ttk~~~~~~~~~gnrVLtKrKLqELVrQVDP~e~LDpDV 424 (441)
.+.++....+....+++...+++...-.. ++......|++.++.....++++++||+|+||+|||++||.+++||+||
T Consensus 98 ~~q~P~~~~~q~~~~~~~~~~~~~~~~P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId~~~~LD~dV 177 (258)
T KOG1142|consen 98 QQQQPASSPSQGSSMSNQTSSVQKDPAPVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQIDGTTKLDDDV 177 (258)
T ss_pred cCCCCccCCCCCCCccccCcccccCCCCCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhcCcccccHHH
Confidence 34444555566666667777766654433 2233333344455666677889999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhhc
Q 013514 425 EDILVDIAEDFVESVS 440 (441)
Q Consensus 425 EElLLdLADDFVdSVv 440 (441)
|||||||||||||+|+
T Consensus 178 edlLleiADdFV~sii 193 (258)
T KOG1142|consen 178 EDLLLEIADDFVSSII 193 (258)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999999999997
No 2
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=99.46 E-value=3.1e-14 Score=112.65 Aligned_cols=39 Identities=62% Similarity=1.074 Sum_probs=31.9
Q ss_pred chhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhcC
Q 013514 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVSS 441 (441)
Q Consensus 403 tKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVvS 441 (441)
+|+||+|||++|||+++||+||||+||+||||||++|++
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~ 39 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVS 39 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 699999999999999999999999999999999999973
No 3
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.08 E-value=4.7e-11 Score=121.61 Aligned_cols=57 Identities=30% Similarity=0.384 Sum_probs=50.7
Q ss_pred CCcccCCCcccCCCCCcccchhHHHHHHHhc-CCCCCCChHHHHHHHHHHHHHhhhhcC
Q 013514 384 GNQSKIAGTESDEFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESVSS 441 (441)
Q Consensus 384 G~ttk~~~~~~~~~gnrVLtKrKLqELVrQV-DP~e~LDpDVEElLLdLADDFVdSVvS 441 (441)
-.++|++.|+. |+..||++||||+||++.| |..|+||+||||+||++||||||+|+.
T Consensus 367 pg~~k~p~ye~-D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~ 424 (505)
T COG5624 367 PGRDKGPLYER-DDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTE 424 (505)
T ss_pred CcccCCCchhc-chhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccch
Confidence 34567788775 4669999999999999999 999999999999999999999999973
No 4
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.05 E-value=1.8e-10 Score=90.85 Aligned_cols=40 Identities=63% Similarity=1.073 Sum_probs=38.7
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+|+|++|+|||++||+.+.+|+||+|+|+++|||||++|+
T Consensus 1 i~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~ 40 (72)
T cd07981 1 ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVV 40 (72)
T ss_pred CCcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999986
No 5
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=85.04 E-value=1.3 Score=33.83 Aligned_cols=39 Identities=13% Similarity=0.315 Sum_probs=32.8
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|-+.++..|++.......+..|+.++|-+.+.+||+.++
T Consensus 3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~ 41 (65)
T PF00808_consen 3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLA 41 (65)
T ss_dssp S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHH
T ss_pred CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHH
Confidence 567899999999866678999999999999999999875
No 6
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=74.35 E-value=5.3 Score=33.45 Aligned_cols=38 Identities=21% Similarity=0.374 Sum_probs=35.0
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|+|+++..|+..+.. ..+.++|.++|--||-.||-.+|
T Consensus 17 f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeiv 54 (85)
T cd08048 17 FPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIV 54 (85)
T ss_pred ccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHH
Confidence 899999999999876 78999999999999999998876
No 7
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.78 E-value=7.4 Score=33.57 Aligned_cols=36 Identities=31% Similarity=0.552 Sum_probs=32.9
Q ss_pred chhHHHHHHHhc----------CCCCCCChHHHHHHHHHHHHHhhh
Q 013514 403 TKRSIQELVNQI----------DPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 403 tKrKLqELVrQV----------DP~e~LDpDVEElLLdLADDFVdS 438 (441)
.|.|+++.|.++ ++..+||..-|--|-.-+|.|||-
T Consensus 23 qk~k~~~~VHqft~~CWdKCi~~~~sklds~~e~ClsnCV~RfiDt 68 (86)
T KOG3489|consen 23 QKQKFQEQVHQFTEICWDKCIEKPGSKLDSSEETCLSNCVNRFIDT 68 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccccchHHHHHHHHHHHHHHH
Confidence 388999999988 688999999999999999999995
No 8
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=63.86 E-value=15 Score=29.17 Aligned_cols=39 Identities=15% Similarity=0.316 Sum_probs=32.6
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+|.+.-+..|.+.+.-. .|.+|+.+.|.+.+..|+..|+
T Consensus 2 ~~p~~~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~ 40 (65)
T smart00803 2 WLPKETIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIV 40 (65)
T ss_pred CCCHHHHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHH
Confidence 56788889999988655 7899999999999999998875
No 9
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=62.01 E-value=5.9 Score=30.46 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=31.2
Q ss_pred ccchhHHHHHHHhcCCC----CCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPS----ERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~----e~LDpDVEElLLdLADDFVdSVv 440 (441)
.+.|--+.-|+++|..+ ..++.++-++|-.++++|++.++
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il 48 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEIL 48 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhh
Confidence 34455666677777544 79999999999999999998874
No 10
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=59.99 E-value=11 Score=30.94 Aligned_cols=36 Identities=25% Similarity=0.297 Sum_probs=27.0
Q ss_pred cchhHHHHHHHhc-----CCCCCCChHHHHHHHHHHHHHhh
Q 013514 402 LTKRSIQELVNQI-----DPSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 402 LtKrKLqELVrQV-----DP~e~LDpDVEElLLdLADDFVd 437 (441)
-++.|.+.|+..| +.+...-+|+||+|+++-||-.+
T Consensus 28 ~s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~~eF~ 68 (82)
T PF10273_consen 28 DSQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMDDEFN 68 (82)
T ss_pred cHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhHcC
Confidence 4688888888877 44556688999999999854433
No 11
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=58.10 E-value=13 Score=30.29 Aligned_cols=30 Identities=20% Similarity=0.532 Sum_probs=24.6
Q ss_pred HHHHHHhcCCCCCCCh-HHHHHHHHHHHHHh
Q 013514 407 IQELVNQIDPSERLDP-DVEDILVDIAEDFV 436 (441)
Q Consensus 407 LqELVrQVDP~e~LDp-DVEElLLdLADDFV 436 (441)
|..|...++++..++| ||.|+|..+.|||+
T Consensus 17 L~~l~~~f~~g~~y~E~EVN~~L~~~~~D~a 47 (71)
T PF09860_consen 17 LEYLASRFEPGREYSEKEVNEILKRFFDDYA 47 (71)
T ss_pred HHHHHHhCCCCCccCHHHHHHHHHHHcccHH
Confidence 4566777788888865 89999999999986
No 12
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=54.42 E-value=14 Score=39.37 Aligned_cols=36 Identities=19% Similarity=0.402 Sum_probs=30.9
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
|.+..|+++.||.+..||+|+|+.|.++..+|++..
T Consensus 465 ~~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~f 500 (502)
T PRK09281 465 RSNHADLLEEIRETKDLSDEIEAKLKAAIEEFKKTF 500 (502)
T ss_pred HHhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHh
Confidence 445667888888889999999999999999999864
No 13
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=54.33 E-value=21 Score=31.21 Aligned_cols=34 Identities=18% Similarity=0.340 Sum_probs=27.1
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-+..|++.. .-+.+|++|...|||+|..++++|+
T Consensus 6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il 39 (117)
T cd07979 6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVL 39 (117)
T ss_pred HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHH
Confidence 345566654 4458999999999999999999885
No 14
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=53.68 E-value=15 Score=39.25 Aligned_cols=36 Identities=17% Similarity=0.439 Sum_probs=30.9
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
|.+..|+++.||.+..||+++|+.|.++..+|++..
T Consensus 464 ~~~~~~~~~~i~~~~~l~~~~~~~L~~~i~~~~~~f 499 (501)
T TIGR00962 464 DANHPDILEEINTKKKLTEELEDKLKEALKNFKKTF 499 (501)
T ss_pred HHhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhh
Confidence 445568888898999999999999999999999863
No 15
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=53.20 E-value=18 Score=32.02 Aligned_cols=37 Identities=19% Similarity=0.399 Sum_probs=27.7
Q ss_pred ccchhHHHH-HHHhcCCCCCCChHHHHHHHHHHHHHhh
Q 013514 401 ILTKRSIQE-LVNQIDPSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 401 VLtKrKLqE-LVrQVDP~e~LDpDVEElLLdLADDFVd 437 (441)
|-+|+-|+| |++-|++....+.+|.+-+|+|.++.-+
T Consensus 78 iask~Fl~e~L~~~i~~~~~~~~~Vk~kil~li~~W~~ 115 (141)
T cd03565 78 VAKKDFIKDVLVKLINPKNNPPTIVQEKVLALIQAWAD 115 (141)
T ss_pred HHHHHhhhHHHHHHHcccCCCcHHHHHHHHHHHHHHHH
Confidence 346888899 9999987777778888777776655443
No 16
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=51.43 E-value=23 Score=33.37 Aligned_cols=46 Identities=15% Similarity=0.434 Sum_probs=40.5
Q ss_pred CCCCCcccchhHHHHHHHhcCC-CCCCChHHHHHHHHHHHHHhhhhc
Q 013514 395 DEFGNRILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 395 ~~~gnrVLtKrKLqELVrQVDP-~e~LDpDVEElLLdLADDFVdSVv 440 (441)
.++++--|-|.-++.+|++|=| +..+-.|..|||++-+-+||.=|.
T Consensus 6 ~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liS 52 (156)
T KOG0871|consen 6 KEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLIS 52 (156)
T ss_pred cccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHH
Confidence 4567777899999999999977 889999999999999999997553
No 17
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=49.44 E-value=14 Score=31.63 Aligned_cols=44 Identities=14% Similarity=0.360 Sum_probs=34.4
Q ss_pred CCCCcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
.+...+|.|.-++.|+|.+... ++..++.|.|-+.+.+|++.+.
T Consensus 14 ~~~~~~Lp~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~ 57 (91)
T COG2036 14 RSTDLLLPKAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIA 57 (91)
T ss_pred hhhhhhcCchHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHH
Confidence 3567788999999999999766 7777777777777777777654
No 18
>TIGR01560 put_DNA_pack uncharacterized phage protein (possible DNA packaging). This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model.
Probab=48.36 E-value=28 Score=28.35 Aligned_cols=32 Identities=19% Similarity=0.479 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+|..-+| ||..+ |+++.+.+++-|.++|++-+
T Consensus 4 ~vK~~Lr-Id~d~--dD~li~~~i~aA~~~i~~~i 35 (91)
T TIGR01560 4 EVKLSLR-IDHDD--DDELIKLMIAAAQDYIQSAI 35 (91)
T ss_pred HHHhHhc-CCCCc--cHHHHHHHHHHHHHHHHHHh
Confidence 3444454 77775 89999999999999998754
No 19
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=46.42 E-value=12 Score=30.18 Aligned_cols=34 Identities=24% Similarity=0.467 Sum_probs=25.7
Q ss_pred chhHHHHHHHhc----CCCCCCChHHHHHHHHHHH-HHh
Q 013514 403 TKRSIQELVNQI----DPSERLDPDVEDILVDIAE-DFV 436 (441)
Q Consensus 403 tKrKLqELVrQV----DP~e~LDpDVEElLLdLAD-DFV 436 (441)
+|+.+.||+..+ |-.+.+..||.++|-+|.+ .||
T Consensus 42 g~~tv~eI~~~L~~~Y~~~e~~~~dV~~fL~~L~~~gli 80 (81)
T TIGR03859 42 GKRSLAEIIQELAQRFPAAEEIEDDVIAFLAVARAKHWL 80 (81)
T ss_pred CCCcHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHCcCc
Confidence 478888888777 4466788888888888876 455
No 20
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=45.89 E-value=41 Score=26.48 Aligned_cols=37 Identities=22% Similarity=0.391 Sum_probs=26.8
Q ss_pred hhHHHHHHHhc---CCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 404 KRSIQELVNQI---DPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 404 KrKLqELVrQV---DP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
++-|+-+|.+| ..-+...+.+-|.|-||+.+||.++.
T Consensus 5 ~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~ 44 (77)
T PF07524_consen 5 RSLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELG 44 (77)
T ss_pred HHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHH
Confidence 34444455555 34467889999999999999998864
No 21
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=45.76 E-value=36 Score=29.39 Aligned_cols=37 Identities=24% Similarity=0.385 Sum_probs=29.3
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhh
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVd 437 (441)
|-+|+.|.||++-+......+.+|.+.+|++..++-+
T Consensus 76 i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W~~ 112 (133)
T cd03561 76 VADKEFLLELVKIAKNSPKYDPKVREKALELILAWSE 112 (133)
T ss_pred HhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 4467999999998877678899999888887766544
No 22
>smart00428 H3 Histone H3.
Probab=45.48 E-value=29 Score=30.47 Aligned_cols=43 Identities=21% Similarity=0.303 Sum_probs=35.0
Q ss_pred CCCcccchhHHHHHHHhcC----C--CCCCChHHHHHHHHHHHHHhhhh
Q 013514 397 FGNRILTKRSIQELVNQID----P--SERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 397 ~gnrVLtKrKLqELVrQVD----P--~e~LDpDVEElLLdLADDFVdSV 439 (441)
+++-++-|--+..|||+|. . +..+..|+.+.|-+.+++|+.++
T Consensus 25 st~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~l 73 (105)
T smart00428 25 STDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGL 73 (105)
T ss_pred CcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHH
Confidence 5566778989999999993 3 56888999999999999988765
No 23
>PTZ00018 histone H3; Provisional
Probab=45.43 E-value=24 Score=32.40 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=37.0
Q ss_pred CCCCcccchhHHHHHHHhcC----CCCCCChHHHHHHHHHHHHHhhhh
Q 013514 396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVD----P~e~LDpDVEElLLdLADDFVdSV 439 (441)
.+++-+|-|--+.-||+||. .+..+..++.+.|=+.|++|+-.+
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~l 104 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGL 104 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHH
Confidence 35677788999999999993 567999999999999999998765
No 24
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=43.48 E-value=24 Score=32.46 Aligned_cols=26 Identities=15% Similarity=0.349 Sum_probs=22.4
Q ss_pred cCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 414 IDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 414 VDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
.|.+..||+++++.|-+++|+||+-+
T Consensus 147 ~d~~~~~d~~~~~rl~~~~~~~~~~~ 172 (191)
T PRK10569 147 YHHQPQFTPNLQTRLDEALETFWQAL 172 (191)
T ss_pred cccccccCHHHHHHHHHHHHHHHHHH
Confidence 45667789999999999999999765
No 25
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=42.89 E-value=26 Score=30.24 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=20.0
Q ss_pred hHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhh
Q 013514 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 405 rKLqELVrQVDP~e~LDpDVEElLLdLADDFVd 437 (441)
|||-|||+.= ++.--+-..++|.+++|+|||
T Consensus 49 RkLld~v~ak--G~~~k~~F~~iL~e~~~~y~~ 79 (85)
T cd08324 49 RKILDLVQSK--GEEVSEYFLYLLQQLADAYVD 79 (85)
T ss_pred HHHHHHHHhc--CchHHHHHHHHHHHHHHhhhh
Confidence 5555665522 223344556889999999998
No 26
>PF08236 SRI: SRI (Set2 Rpb1 interacting) domain; InterPro: IPR013257 The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. ; GO: 0018024 histone-lysine N-methyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0034968 histone lysine methylation, 0005694 chromosome; PDB: 2A7O_A 2C5Z_A.
Probab=42.15 E-value=25 Score=29.14 Aligned_cols=39 Identities=18% Similarity=0.435 Sum_probs=29.3
Q ss_pred cchhHHHHHHHhc---------------CCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQI---------------DPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQV---------------DP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|++..|..|.|+| |+...|+++|+.=+=+++++|+|.++
T Consensus 28 ~~~ddfK~~ar~lt~~l~~KE~K~~~~~~~~~~l~~~~~~Kik~fvk~Ym~K~~ 81 (88)
T PF08236_consen 28 LSKDDFKHLARKLTHKLVEKELKSCRVNDPPLELSDSKRKKIKKFVKDYMDKFG 81 (88)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHTT-GGGSS--HHHHHHHHHHHHHHHCCCH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCCCCccccCHHHHHHHHHHHHHHHHHHH
Confidence 7777777777776 47789999999999999999998764
No 27
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=41.69 E-value=40 Score=30.19 Aligned_cols=38 Identities=16% Similarity=0.334 Sum_probs=28.3
Q ss_pred cccchhHHHHHHHhcCCC---CCCChHHHHHHHHHHHHHhh
Q 013514 400 RILTKRSIQELVNQIDPS---ERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 400 rVLtKrKLqELVrQVDP~---e~LDpDVEElLLdLADDFVd 437 (441)
.|-+|+-|+|||+-|.+. ...+.+|.+-+|+|.+.+-+
T Consensus 76 evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~li~~W~~ 116 (139)
T cd03567 76 EVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIELLYSWTL 116 (139)
T ss_pred HHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHH
Confidence 355788899999999874 45788998877777655443
No 28
>TIGR03566 FMN_reduc_MsuE FMN reductase, MsuE subfamily. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model.
Probab=41.33 E-value=28 Score=30.71 Aligned_cols=26 Identities=0% Similarity=-0.101 Sum_probs=22.0
Q ss_pred cCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 414 IDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 414 VDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
+|.++..|++++|.|-+++|+||+-+
T Consensus 146 ~~~g~l~d~~~~~~l~~~~~~~~~~~ 171 (174)
T TIGR03566 146 FADYRLASEALRARIALAVDRAAPLL 171 (174)
T ss_pred hccccccCHHHHHHHHHHHHHHHHHh
Confidence 35566789999999999999999865
No 29
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=41.17 E-value=38 Score=32.83 Aligned_cols=25 Identities=32% Similarity=0.505 Sum_probs=22.5
Q ss_pred CCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 416 PSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 416 P~e~LDpDVEElLLdLADDFVdSVv 440 (441)
..++|++++|+.|..|+-|+|.||+
T Consensus 268 ~~~~L~~~~e~~l~rivQEaltN~~ 292 (365)
T COG4585 268 ELERLPPEAEDALFRIVQEALTNAI 292 (365)
T ss_pred ccccCChhHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999999985
No 30
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=40.97 E-value=31 Score=37.11 Aligned_cols=35 Identities=17% Similarity=0.163 Sum_probs=30.0
Q ss_pred hHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
.+..|+++.||....|++|.++.|.++..+|.+..
T Consensus 466 ~~~~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~~~ 500 (502)
T PRK13343 466 ARFAALSLALESPRELDEAWLAALEEILREAGERF 500 (502)
T ss_pred hhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhh
Confidence 34557788888899999999999999999999864
No 31
>PLN00121 histone H3; Provisional
Probab=40.88 E-value=31 Score=31.63 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=36.5
Q ss_pred CCCCcccchhHHHHHHHhcC----CCCCCChHHHHHHHHHHHHHhhhh
Q 013514 396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVD----P~e~LDpDVEElLLdLADDFVdSV 439 (441)
.+++-+|-|--++-||+||. .+..+..++.+.|=+.|++|+-++
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~l 104 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGL 104 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHH
Confidence 35677788999999999993 567899999999999999988765
No 32
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=40.04 E-value=14 Score=30.99 Aligned_cols=33 Identities=27% Similarity=0.501 Sum_probs=23.3
Q ss_pred hhHHHHHHHhc-----CCCCCCChHHHHHHHHHHH-HHhh
Q 013514 404 KRSIQELVNQI-----DPSERLDPDVEDILVDIAE-DFVE 437 (441)
Q Consensus 404 KrKLqELVrQV-----DP~e~LDpDVEElLLdLAD-DFVd 437 (441)
++.+.||+..+ |. ..+..||+++|-.+.| .||+
T Consensus 48 ~~tv~eIi~~L~~~y~~~-~~~~~DV~~fl~~L~~~g~i~ 86 (88)
T PRK02079 48 KRTVAAIIAELQQQFPDV-PGLDEDVLEFLEVARAKHWIE 86 (88)
T ss_pred CCCHHHHHHHHHHHccch-hhHHHHHHHHHHHHHHCcCEE
Confidence 56677777666 33 2477899998888877 5775
No 33
>PF12422 Condensin2nSMC: Condensin II non structural maintenance of chromosomes subunit; InterPro: IPR024741 Subunit G2 is a non-SMC subunit of condensin II, which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II [].; GO: 0005634 nucleus
Probab=38.81 E-value=32 Score=30.85 Aligned_cols=38 Identities=11% Similarity=0.184 Sum_probs=28.3
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+.-.|+.++|..+--+. .+.+|++||+++.+-++.+.+
T Consensus 91 ~~~~~~R~~L~~f~~~k-~~~~v~~mL~rl~~PiL~r~L 128 (152)
T PF12422_consen 91 PLHSKFREVLLSFHSQK-KRKGVDEMLLRLYEPILWRAL 128 (152)
T ss_pred HhHHHHHHHHHHHHhcc-cccchHHHHHHHHHHHHHHHH
Confidence 33456666666664444 999999999999999988754
No 34
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=38.48 E-value=37 Score=25.61 Aligned_cols=35 Identities=17% Similarity=0.343 Sum_probs=26.4
Q ss_pred hHHHHHHHhcC-CCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQID-PSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQVD-P~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
.+|.++|++++ ....||+.++. .|++.|.++++.|
T Consensus 6 ~~Le~Iv~~Le~~~~sLdes~~lyeeg~~l~~~c~~~L~~~ 46 (53)
T PF02609_consen 6 ERLEEIVEKLESGELSLDESLKLYEEGMELIKKCQERLEEA 46 (53)
T ss_dssp HHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57999999995 77788887773 4888888888765
No 35
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=38.08 E-value=35 Score=36.63 Aligned_cols=33 Identities=12% Similarity=0.265 Sum_probs=28.0
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhh
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdS 438 (441)
+..|++++||.+..|++|+|+.|.++..+|++.
T Consensus 446 ~~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~ 478 (485)
T CHL00059 446 NKPQFQEIISSTKTFTEEAEALLKEAIQEQLEL 478 (485)
T ss_pred hhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 345777888888999999999999999999875
No 36
>PF07697 7TMR-HDED: 7TM-HD extracellular; InterPro: IPR011624 This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase) protein family []. These proteins are known or predicted, to posses metal-dependent phospohydrolase activity.
Probab=37.50 E-value=39 Score=29.94 Aligned_cols=41 Identities=24% Similarity=0.471 Sum_probs=36.2
Q ss_pred CcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 399 nrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
+...++++-++.+++|.|-..+|++|.+-+++-.++|.+.+
T Consensus 21 D~~~t~~~r~~a~~~v~pvy~~d~~~~~~~~~~~~~~f~~i 61 (222)
T PF07697_consen 21 DEEATEQRRQEAAESVPPVYDFDPEVAEEVINRLEEFFEEI 61 (222)
T ss_pred CHHHHHHHHHHHHhcCCcceecCcHHHHHHHHHHHHHHHHH
Confidence 57789999999999999999999999999888888887654
No 37
>PHA02627 hypothetical protein; Provisional
Probab=37.50 E-value=16 Score=30.47 Aligned_cols=40 Identities=30% Similarity=0.404 Sum_probs=25.1
Q ss_pred cccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 400 rVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
--+..+.|.||++-+.. .--|-|..|-+-+||||.+|+++
T Consensus 30 ~eided~i~ellnilte-lgcdvdfde~fsdiaddilesl~ 69 (73)
T PHA02627 30 IEIDEDDITELLNILTE-LGCDVDFDEDFSDIADDVLESLM 69 (73)
T ss_pred eeeCHHHHHHHHHHHHH-hCCCcccccchHHHHHHHHHHHH
Confidence 33556778888774421 12233444557789999999875
No 38
>PF07030 DUF1320: Protein of unknown function (DUF1320); InterPro: IPR009752 This entry is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.34 E-value=50 Score=28.71 Aligned_cols=38 Identities=16% Similarity=0.301 Sum_probs=27.9
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
++.+.|.+|... +....+|+++.+..|+-|+++||+.+
T Consensus 11 ~~~~el~~ltd~-~~~~~~d~~~v~~Al~dA~~~Id~yL 48 (130)
T PF07030_consen 11 FGEQELIQLTDD-DADGTIDPAVVEAALADASAEIDGYL 48 (130)
T ss_pred cCHHHHHHHhcc-cccCCcCHHHHHHHHHHHHHHHHHHH
Confidence 344445554332 25688999999999999999999854
No 39
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=35.79 E-value=60 Score=27.02 Aligned_cols=32 Identities=16% Similarity=0.391 Sum_probs=20.5
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHH
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDF 435 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDF 435 (441)
|..|+.|=.+++-...||++-.+.|..|.||.
T Consensus 3 ~~~L~~L~~eL~~~~~ld~~~~~~L~~l~~dI 34 (85)
T PF14357_consen 3 QELLEKLHQELEQNPPLDEETRAELSSLDDDI 34 (85)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence 34556666666666667777666666666664
No 40
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=35.37 E-value=61 Score=27.42 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=32.1
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-|+|--|.-|++.- .-+.+..|+.|-|-++.++|.+.|+
T Consensus 13 gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~ 51 (85)
T cd00076 13 GITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVI 51 (85)
T ss_pred cCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHH
Confidence 37888888888865 4778999998888888889988874
No 41
>PF08165 FerA: FerA (NUC095) domain; InterPro: IPR012560 The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease []. This is central domain A in proteins of the Ferlin family [].; GO: 0016021 integral to membrane
Probab=35.36 E-value=29 Score=27.88 Aligned_cols=19 Identities=5% Similarity=0.496 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHHHHhhhh
Q 013514 421 DPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 421 DpDVEElLLdLADDFVdSV 439 (441)
+.+|.++.++|-|++|+++
T Consensus 9 ~~~l~~~~~~lLdqlIeD~ 27 (66)
T PF08165_consen 9 EEELAELWLKLLDQLIEDC 27 (66)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 4688999999999999986
No 42
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=35.17 E-value=51 Score=28.96 Aligned_cols=17 Identities=18% Similarity=0.376 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHhhhhc
Q 013514 424 VEDILVDIAEDFVESVS 440 (441)
Q Consensus 424 VEElLLdLADDFVdSVv 440 (441)
-.+.|.+++++|+|.++
T Consensus 98 n~~~L~~~~~~~~~~i~ 114 (197)
T PF00616_consen 98 NLQNLRELCESFLDAII 114 (197)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34678999999999875
No 43
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=34.84 E-value=47 Score=28.43 Aligned_cols=39 Identities=26% Similarity=0.396 Sum_probs=29.9
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|.|..|..||++|..+..+.+.|.-++--||.=||-.+|
T Consensus 24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiV 62 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIV 62 (90)
T ss_dssp --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHH
Confidence 789999999999998889999999999999999987765
No 44
>PF06076 Orthopox_F14: Orthopoxvirus F14 protein; InterPro: IPR009280 This family consists of several short Orthopoxvirus F14 proteins. The function of this protein is unknown.
Probab=34.81 E-value=18 Score=30.13 Aligned_cols=39 Identities=31% Similarity=0.442 Sum_probs=24.2
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-+..+.|.||++-+.. .--|-|..|-+-+||||.+|+++
T Consensus 31 eided~i~ellnilte-lgcdvdfde~fsdiaddilesl~ 69 (73)
T PF06076_consen 31 EIDEDDIMELLNILTE-LGCDVDFDENFSDIADDILESLM 69 (73)
T ss_pred eeCHHHHHHHHHHHHH-hCCCcccccchhHHHHHHHHHHH
Confidence 3456777787764421 12233444557788999998875
No 45
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=33.66 E-value=39 Score=24.90 Aligned_cols=25 Identities=28% Similarity=0.607 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
.+++||.+| +++|-+=|.+||.+.|
T Consensus 4 ~~D~lLDeI----------d~vLe~NAe~FV~~fV 28 (33)
T TIGR03687 4 GVDDLLDEI----------DGVLESNAEEFVRGFV 28 (33)
T ss_pred hHHHHHHHH----------HHHHHHhHHHHHHHHH
Confidence 466666544 5677788889988754
No 46
>PF07464 ApoLp-III: Apolipophorin-III precursor (apoLp-III); InterPro: IPR010009 This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0005576 extracellular region; PDB: 1EQ1_A.
Probab=33.61 E-value=41 Score=31.11 Aligned_cols=35 Identities=17% Similarity=0.300 Sum_probs=25.0
Q ss_pred hHHHHHHHhc-------CCC-CCCChHHHHHHHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-------DPS-ERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-------DP~-e~LDpDVEElLLdLADDFVdSV 439 (441)
..|+.||+++ ..+ +...++++++|=++.|+||+.+
T Consensus 99 ~~vq~l~~E~qk~~k~v~~~~~~~~e~l~~~~K~~~D~~~k~~ 141 (155)
T PF07464_consen 99 SAVQSLVQESQKLAKEVSENSEGANEKLQPAIKQAYDDAVKAA 141 (155)
T ss_dssp HHHHHHHHHHHHHHHHHHS---SS-GGGHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 3455666555 444 8999999999999999999864
No 47
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=33.31 E-value=73 Score=25.45 Aligned_cols=36 Identities=8% Similarity=0.347 Sum_probs=26.0
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|+.+-.+++.. .-+..++++-|.|.||+.+|+..+.
T Consensus 9 ~~~Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~ 44 (77)
T smart00576 9 RIAVAQILESA-GFDSFQESALETLTDILQSYIQELG 44 (77)
T ss_pred HHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHH
Confidence 44444444433 4578899999999999999988764
No 48
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=32.96 E-value=30 Score=33.67 Aligned_cols=38 Identities=24% Similarity=0.426 Sum_probs=31.7
Q ss_pred CCCCcccchhHHHHHHHhcC-CCCCCChHHHHHHHHHHH
Q 013514 396 EFGNRILTKRSIQELVNQID-PSERLDPDVEDILVDIAE 433 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVD-P~e~LDpDVEElLLdLAD 433 (441)
...+..|+-.-|-||+..|. -.+.||++++|||+++-+
T Consensus 144 n~EdA~~Gaf~I~elcq~l~~~s~d~Ed~ideil~~~ee 182 (195)
T KOG2424|consen 144 NHEDATLGAFLILELCQCLQAQSDDLEDNIDEILLEFEE 182 (195)
T ss_pred CHHhhhhhHHHHHHHHHHHHhccccHHHHHHHHHHHHHH
Confidence 34567788888999999997 888999999999998754
No 49
>PHA02780 hypothetical protein; Provisional
Probab=32.94 E-value=20 Score=29.87 Aligned_cols=39 Identities=31% Similarity=0.436 Sum_probs=24.1
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-+..+.|.||++-+.. .--|-|..|-+-+||||.+|+++
T Consensus 31 eided~i~ellnilte-lgcdvdfde~fsdiaddilesl~ 69 (73)
T PHA02780 31 EIDEDEIMELLNILTE-LGCDVDFDENFSDIADDILESLI 69 (73)
T ss_pred eechHHHHHHHHHHHH-hCCCcccccchhHHHHHHHHHHH
Confidence 3456777787764421 12233444557788999998875
No 50
>PF12351 Fig1: Ca2+ regulator and membrane fusion protein Fig1
Probab=32.00 E-value=24 Score=32.68 Aligned_cols=36 Identities=19% Similarity=0.348 Sum_probs=23.3
Q ss_pred hhHHHHHHHhcC-CCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 404 KRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 404 KrKLqELVrQVD-P~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+..+++|-+.++ .....|.|-.+ |+++|++|-|+|+
T Consensus 37 ~~~~~~l~~~~~~~~~~~~~~~ln-Li~~A~~f~~~iv 73 (182)
T PF12351_consen 37 NSSATSLADDLSSNNSSSDQDPLN-LIWLAQTFQDNIV 73 (182)
T ss_pred CCCchhHHHHhhhccCCCCCCccc-HHHHHHHHHHhHh
Confidence 344444444444 55566666444 6999999999975
No 51
>PF11074 DUF2779: Domain of unknown function(DUF2779); InterPro: IPR021301 This domain is conserved in bacteria. The function is not known.
Probab=31.85 E-value=53 Score=29.18 Aligned_cols=29 Identities=31% Similarity=0.415 Sum_probs=19.1
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhh
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVd 437 (441)
+.|.+|.||.+- .+|.+|.|..|.+.+||
T Consensus 82 fE~~rL~ela~~-------~p~~~~~l~~I~~r~vD 110 (130)
T PF11074_consen 82 FEKTRLKELAEL-------FPDYAEKLNSIIERTVD 110 (130)
T ss_pred HHHHHHHHHHHH-------hHHHHHHHHHHHHHHHH
Confidence 456677776664 66666666666666665
No 52
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=31.68 E-value=59 Score=29.30 Aligned_cols=35 Identities=20% Similarity=0.403 Sum_probs=26.8
Q ss_pred hHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 405 rKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+-|..|+++..=+ ..|+.|--.|||+|-.|+.+|+
T Consensus 16 ~~i~~iL~~~Gv~-~yeprVv~qLLEfayRYt~~vL 50 (129)
T PF02291_consen 16 RVIHLILKSMGVT-EYEPRVVNQLLEFAYRYTSDVL 50 (129)
T ss_dssp HHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCc-ccCHHHHHHHHHHHHHHHHHHH
Confidence 4567888888543 4799999999999999999885
No 53
>PTZ00015 histone H4; Provisional
Probab=30.85 E-value=78 Score=27.79 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=30.5
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-|+|--|.-|++. ..-+.+.+|+.|.|-++.++|++.|+
T Consensus 30 gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~ 68 (102)
T PTZ00015 30 GITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVV 68 (102)
T ss_pred CCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHH
Confidence 4677777777774 46678888898888888888888875
No 54
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=30.55 E-value=67 Score=26.60 Aligned_cols=36 Identities=11% Similarity=0.252 Sum_probs=28.2
Q ss_pred hhHHHHHHHhcC-CCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 404 KRSIQELVNQID-PSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 404 KrKLqELVrQVD-P~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
-++|.++|+.++ ....||+.++. -|+..|.++++.+
T Consensus 16 ~~~LEeIv~~LE~~~l~Lees~~lyeeg~~L~k~C~~~L~~a 57 (80)
T PRK00977 16 LAELEEIVTRLESGDLPLEESLAAFERGVALARQCQKKLQQA 57 (80)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367999999995 77788888873 3888888887754
No 55
>PLN00035 histone H4; Provisional
Probab=30.28 E-value=84 Score=27.71 Aligned_cols=38 Identities=21% Similarity=0.266 Sum_probs=28.6
Q ss_pred cchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|+|--|.-|++.-. -+.|.+|+.|.|-++.++|.+.|+
T Consensus 30 ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~ 67 (103)
T PLN00035 30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVI 67 (103)
T ss_pred CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHH
Confidence 55556666666544 778999998888888888888775
No 56
>PRK14070 exodeoxyribonuclease VII small subunit; Provisional
Probab=29.82 E-value=71 Score=26.22 Aligned_cols=35 Identities=14% Similarity=0.344 Sum_probs=26.9
Q ss_pred hHHHHHHHhcC-CCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQID-PSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQVD-P~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
++|.++|++++ ....||+.++- -|+..|+++++.+
T Consensus 2 ~~LEeIV~~LE~gel~Leesl~lyeeG~~L~k~C~~~L~~a 42 (69)
T PRK14070 2 KELEEIVNRLENEDLPLEESIKLFERGVELYRKCKEILQQN 42 (69)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47999999994 66688888773 3788888887754
No 57
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=29.53 E-value=72 Score=26.30 Aligned_cols=35 Identities=17% Similarity=0.385 Sum_probs=27.5
Q ss_pred hHHHHHHHhc-CCCCCCChHHHHH-----HHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-DPSERLDPDVEDI-----LVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-DP~e~LDpDVEEl-----LLdLADDFVdSV 439 (441)
.+|.++|+.+ +....||+.++.. |+..|.++++.+
T Consensus 13 ~~LE~IV~~LE~~~l~Leesl~~ye~G~~L~k~c~~~L~~a 53 (75)
T PRK14064 13 AELETIVEALENGSASLEDSLDMYQKGIELTKLCQDKLQSA 53 (75)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999 5777899888743 788888887754
No 58
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=29.52 E-value=80 Score=28.28 Aligned_cols=34 Identities=21% Similarity=0.437 Sum_probs=25.9
Q ss_pred cccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHH
Q 013514 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDF 435 (441)
Q Consensus 400 rVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDF 435 (441)
.|-+|+=|+||++=|+.. .+.+|.+.+|+|.++.
T Consensus 75 evask~Fl~eL~kl~~~~--~~~~Vk~kil~li~~W 108 (144)
T cd03568 75 EVASRDFTQELKKLINDR--VHPTVKEKLREVVKQW 108 (144)
T ss_pred HHhhHHHHHHHHHHhccc--CCHHHHHHHHHHHHHH
Confidence 355788899999988876 8888887777665544
No 59
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=29.41 E-value=37 Score=25.42 Aligned_cols=21 Identities=24% Similarity=0.589 Sum_probs=12.7
Q ss_pred chhHHHHHHHhcCCCCCCChH
Q 013514 403 TKRSIQELVNQIDPSERLDPD 423 (441)
Q Consensus 403 tKrKLqELVrQVDP~e~LDpD 423 (441)
+++.+.|||+.|.....+|++
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~ 48 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPE 48 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HH
T ss_pred CCCCHHHHHHHHHHHcCCCHH
Confidence 467788888888655555544
No 60
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=29.39 E-value=73 Score=30.86 Aligned_cols=37 Identities=24% Similarity=0.515 Sum_probs=28.4
Q ss_pred hhHHHHHHHhcCCCC------------------CCChHHHHHHHHHHHHHhhhhc
Q 013514 404 KRSIQELVNQIDPSE------------------RLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 404 KrKLqELVrQVDP~e------------------~LDpDVEElLLdLADDFVdSVv 440 (441)
.+.|.||+..+|-.. +.|.-|+.||-=+|..||.+|.
T Consensus 72 dktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA 126 (197)
T COG5162 72 DKTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIA 126 (197)
T ss_pred HHHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHH
Confidence 456999999998554 4466677888888999998774
No 61
>PRK15380 pathogenicity island 1 protein SopD2; Provisional
Probab=29.16 E-value=46 Score=34.17 Aligned_cols=42 Identities=19% Similarity=0.398 Sum_probs=33.1
Q ss_pred CCCCcccchhHHHHHHHhcC--CCCCCChHHHHHHHHHHHHHhh
Q 013514 396 EFGNRILTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVD--P~e~LDpDVEElLLdLADDFVd 437 (441)
.-++.|++|-+|+++++--| --+.++.|-|||+|+|+.-.=+
T Consensus 113 ~i~~~vI~q~~i~~iLN~sdn~i~k~M~~~E~eLFlkiC~~~G~ 156 (319)
T PRK15380 113 EIDGKVIDKCNLHRLLNVSENCIFKVMEEDEEELFFKICIKYGE 156 (319)
T ss_pred EeCCEEeehhhHHHHhccchhheeeccchhHHHHHHHHHHHhcc
Confidence 45789999999999998333 3357889999999999875433
No 62
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=28.88 E-value=70 Score=27.83 Aligned_cols=35 Identities=11% Similarity=0.340 Sum_probs=27.7
Q ss_pred hHHHHHHHhc-CCCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-DPSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-DP~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
++|.++|+.| +....||+.++- -|+..|.++++.+
T Consensus 15 ~~LEeIV~~LEsgdl~LEesl~lyeeGv~L~k~C~~~L~~A 55 (95)
T PRK14069 15 RELEQIAEKLERQDFSLEESLKAYERGMELKKICSGILDDA 55 (95)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999 577788888873 3888888888764
No 63
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=28.38 E-value=66 Score=29.02 Aligned_cols=30 Identities=17% Similarity=0.488 Sum_probs=21.5
Q ss_pred CcccchhHHHHHHHhcCCCCCCChHHHHHHHHHH
Q 013514 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIA 432 (441)
Q Consensus 399 nrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLA 432 (441)
++-++|..|+++|.++| |.+|+++-|+.|-
T Consensus 81 g~~it~~~l~~fI~~L~----ip~~~k~~L~~lt 110 (115)
T PF08328_consen 81 GKKITKEDLREFIESLD----IPEEAKARLLALT 110 (115)
T ss_dssp TS---HHHHHHHHHTSS----S-HHHHHHHHH--
T ss_pred CCCCCHHHHHHHHHhCC----CCHHHHHHHHhcC
Confidence 44789999999999998 9999999998873
No 64
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=28.08 E-value=63 Score=23.29 Aligned_cols=33 Identities=12% Similarity=0.353 Sum_probs=24.6
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhh
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdS 438 (441)
.+-+.++++.-...++.+|.++=..|+|.|++.
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~ 36 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLD 36 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence 344445555555589999999999999999874
No 65
>PF10735 DUF2526: Protein of unknown function (DUF2526) ; InterPro: IPR019671 This entry represents proteins with unknown function and is a highly conserved sequence, it is restricted to Enterobacteriaceae.
Probab=27.57 E-value=22 Score=30.23 Aligned_cols=27 Identities=19% Similarity=0.623 Sum_probs=20.5
Q ss_pred HHHHHHHhcCCCCCCChHHH----HHHHHHHHH
Q 013514 406 SIQELVNQIDPSERLDPDVE----DILVDIAED 434 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVE----ElLLdLADD 434 (441)
-++|+|+.||.. |++.|. |||++|.||
T Consensus 3 H~devi~rVd~~--iae~vI~~MNELLi~LS~D 33 (77)
T PF10735_consen 3 HYDEVIARVDAA--IAENVIAHMNELLIELSDD 33 (77)
T ss_pred cHHHHHHHHHHH--HHHhHHHHHHHHHHHHcch
Confidence 378888888754 556554 899999887
No 66
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=27.54 E-value=79 Score=26.44 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=27.8
Q ss_pred hHHHHHHHhc-CCCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-DPSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-DP~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
.+|.++|+++ ++...||+.++. .|+..|.++++.+
T Consensus 14 ~~LEeIV~~LE~~~l~Lees~~lyeeG~~L~k~C~~~L~~a 54 (80)
T PRK14067 14 ARLQEIVDALEGGDLPLEESVALYKEGLGLARACREQLAKA 54 (80)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999 577789988874 3788888877654
No 67
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=26.74 E-value=97 Score=28.99 Aligned_cols=45 Identities=18% Similarity=0.362 Sum_probs=38.4
Q ss_pred CCCCcccchhHHHHHHHhc-CCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 396 EFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQV-DP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
.+++--|-|.-.+.+|.+| +-+..+..|..|+|.+-+=+||.=|.
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~ls 51 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLS 51 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHH
Confidence 4566678999999999998 56678999999999999999997553
No 68
>PF08439 Peptidase_M3_N: Oligopeptidase F; InterPro: IPR013647 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found towards the N terminus of metallopeptidases belonging to MEROPS peptidase subfamily M3B (oligopeptidase F, clan MA). An example protein is Lactococcus lactisPepF []. The function of this N-terminal domain is unknown.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2QR4_B 3CE2_A.
Probab=26.63 E-value=47 Score=25.51 Aligned_cols=17 Identities=18% Similarity=0.393 Sum_probs=11.3
Q ss_pred CCCCChHHHHHHHHHHH
Q 013514 417 SERLDPDVEDILVDIAE 433 (441)
Q Consensus 417 ~e~LDpDVEElLLdLAD 433 (441)
.-.|++++|++|..+++
T Consensus 35 ~H~Ls~~~E~lLa~~~~ 51 (70)
T PF08439_consen 35 KHTLSEEEEKLLAKLSP 51 (70)
T ss_dssp GG---HHHHHHHHHCCC
T ss_pred CcCCCHHHHHHHHHhhh
Confidence 44799999999998844
No 69
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=26.54 E-value=80 Score=24.54 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=31.3
Q ss_pred CCCcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhh
Q 013514 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 397 ~gnrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdS 438 (441)
+|+.+|+..+|.++++..-..+.=..|+++++-+|.+-++++
T Consensus 9 ~G~~~~~~~~l~~~~~~~~g~~l~~~~l~~~~~~l~~~y~~~ 50 (76)
T PF08479_consen 9 EGNTLLPEEELQAILAPYIGRCLTLADLQQLADALTNYYREK 50 (76)
T ss_dssp ES-TSSSCCHHHHHHGGGTTSBB-HHHHHHHHHHHHHHHHHT
T ss_pred ECCCcCCHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHc
Confidence 567799999999999998777666677888777777766653
No 70
>smart00417 H4 Histone H4.
Probab=26.42 E-value=1e+02 Score=25.56 Aligned_cols=41 Identities=22% Similarity=0.297 Sum_probs=32.6
Q ss_pred CcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 399 nrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
.+-|+|--|.-|++. ..-+.+.+|+.|-|-++.++|.+.|+
T Consensus 11 i~gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~ 51 (74)
T smart00417 11 IQGITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVV 51 (74)
T ss_pred hcCCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHH
Confidence 345788889999884 46678888888888888888888875
No 71
>cd03197 GST_C_mPGES2 GST_C family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminus contains two structural domains a N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between t
Probab=26.39 E-value=69 Score=29.51 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=21.9
Q ss_pred cCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 414 IDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 414 VDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
+.-...|++||.+-|.+-+|+||+.|.
T Consensus 70 lkk~~~i~~D~r~~L~~a~~~w~~~~~ 96 (149)
T cd03197 70 LKKPRLLQDDVREWLYDALNTWVAALG 96 (149)
T ss_pred hccccCCCchHHHHHHHHHHHHHHHhc
Confidence 344456789999999999999998763
No 72
>TIGR03567 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566).
Probab=25.86 E-value=69 Score=28.34 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=19.2
Q ss_pred cCCCCC--CChHHHHHHHHHHHHHhh
Q 013514 414 IDPSER--LDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 414 VDP~e~--LDpDVEElLLdLADDFVd 437 (441)
+|.+.. .|+|+.+.|-+++|+|+.
T Consensus 145 ~d~~g~~~~d~~~~~~l~~~~~~~~~ 170 (171)
T TIGR03567 145 RDEDGTLQLDEEIKERLDEALEDLVQ 170 (171)
T ss_pred cccCCccccCHHHHHHHHHHHHHHHh
Confidence 355554 489999999999999985
No 73
>PF04877 Hairpins: HrpZ; InterPro: IPR006961 HrpZ (harpin elicitor) from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants []. The entry also represents hairpinN which is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis [].
Probab=25.77 E-value=60 Score=33.50 Aligned_cols=37 Identities=19% Similarity=0.335 Sum_probs=28.2
Q ss_pred ccchhHHHHHHHhc-CCCCCCChHHHHHHHHHHHHHhhh
Q 013514 401 ILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 401 VLtKrKLqELVrQV-DP~e~LDpDVEElLLdLADDFVdS 438 (441)
.|.|++|.+|+... +....+++|=.++|-+||+ |.|.
T Consensus 139 glg~~~L~~ll~~~~g~g~~F~~~D~~lL~eIaq-FMD~ 176 (308)
T PF04877_consen 139 GLGKSKLDDLLTPKDGGGATFSKEDMPLLKEIAQ-FMDQ 176 (308)
T ss_pred hHHHHHHHHHhccccCCCcccCcccHHHHHHHHH-HHhc
Confidence 35689999999955 5667888888888888775 7663
No 74
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=25.74 E-value=1e+02 Score=29.59 Aligned_cols=45 Identities=11% Similarity=0.347 Sum_probs=35.4
Q ss_pred CCCcccchhHHHHHHHhc-CCCCCCChHHHHHHHHHHHHHhhhhcC
Q 013514 397 FGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESVSS 441 (441)
Q Consensus 397 ~gnrVLtKrKLqELVrQV-DP~e~LDpDVEElLLdLADDFVdSVvS 441 (441)
+-+|.|-=..+--|++.+ .++.+|..|..|.+-|-+-|||.=|++
T Consensus 28 eqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~ 73 (168)
T KOG0869|consen 28 EQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTG 73 (168)
T ss_pred hhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhh
Confidence 456666655555666554 889999999999999999999987763
No 75
>cd05392 RasGAP_Neurofibromin_like Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin prote
Probab=25.68 E-value=87 Score=30.75 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=12.6
Q ss_pred HHHHHHHHHHhhhhc
Q 013514 426 DILVDIAEDFVESVS 440 (441)
Q Consensus 426 ElLLdLADDFVdSVv 440 (441)
+.|.+++++|++.++
T Consensus 126 ~~L~~~~~~~l~~I~ 140 (323)
T cd05392 126 DLLEKYCQKFIDAII 140 (323)
T ss_pred HHHHHHHHHHHHHHH
Confidence 568999999999875
No 76
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=25.33 E-value=98 Score=24.86 Aligned_cols=35 Identities=11% Similarity=0.211 Sum_probs=27.4
Q ss_pred hHHHHHHHhc-CCCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-DPSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-DP~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
.+|.++|+++ ++...||+.++- -|+..|.++++.+
T Consensus 8 ~~Le~Iv~~LE~~~l~Leesl~lyeeG~~L~k~c~~~L~~a 48 (67)
T TIGR01280 8 SELEQIVQKLESGDLALEEALNLFERGMALARRCEKKLAQA 48 (67)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6899999999 677788888873 3778888777654
No 77
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=25.32 E-value=61 Score=29.56 Aligned_cols=31 Identities=19% Similarity=0.387 Sum_probs=19.7
Q ss_pred hHHHHHHHhcCCCCCCChHHHHHHHHHHHHHh
Q 013514 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFV 436 (441)
Q Consensus 405 rKLqELVrQVDP~e~LDpDVEElLLdLADDFV 436 (441)
|||.-|...+. ++.|...|.+-|.+||..+-
T Consensus 72 KRL~iLfd~ln-~g~Ls~~v~~~L~~L~~aL~ 102 (157)
T PF07304_consen 72 KRLNILFDHLN-NGKLSKPVVDKLHQLAQALQ 102 (157)
T ss_dssp HHHHHHHHHHH-HT-S-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHh-cCCCCHHHHHHHHHHHHHHH
Confidence 44444444443 45799999999999987653
No 78
>PRK14068 exodeoxyribonuclease VII small subunit; Provisional
Probab=25.06 E-value=96 Score=25.73 Aligned_cols=35 Identities=9% Similarity=0.308 Sum_probs=27.3
Q ss_pred hHHHHHHHhc-CCCCCCChHHHH-----HHHHHHHHHhhhh
Q 013514 405 RSIQELVNQI-DPSERLDPDVED-----ILVDIAEDFVESV 439 (441)
Q Consensus 405 rKLqELVrQV-DP~e~LDpDVEE-----lLLdLADDFVdSV 439 (441)
++|.++|+++ +....||+.++- -|+..|.++++.+
T Consensus 13 ~~Le~IV~~LE~gdl~Leesl~lyeeG~~L~k~C~~~L~~a 53 (76)
T PRK14068 13 QELEQIVQKLDNETVSLEESLDLYQRGMKLSAACDTTLKNA 53 (76)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999 577788888873 3888888887764
No 79
>TIGR01688 dltC D-alanine--poly(phosphoribitol) ligase, subunit 2. This protein is part of the teichoic acid operon in gram-positive organisms. Gram positive organisms incorporate teichoic acid in their cell walls, and in the fatty acid residues of the glycolipid component of the outer layer of the cytoplasmic membrane. This gene, dltC, encodes the alanyl carrier protein.
Probab=24.99 E-value=91 Score=25.66 Aligned_cols=32 Identities=16% Similarity=0.454 Sum_probs=20.1
Q ss_pred hhHHHHHHHhc--CCCCCC--ChH-----------HHHHHHHHHHHH
Q 013514 404 KRSIQELVNQI--DPSERL--DPD-----------VEDILVDIAEDF 435 (441)
Q Consensus 404 KrKLqELVrQV--DP~e~L--DpD-----------VEElLLdLADDF 435 (441)
|.+|.|++++| .+...+ |.+ +-+||+.|-|+|
T Consensus 1 ~e~i~eIL~~i~~~~~~~~~~d~~L~~~GllDS~~~v~Li~~lE~ef 47 (73)
T TIGR01688 1 KNGVLDILAEVTGSDDVKENPDLELFEEGLLDSFGTVQLLLEIQNQF 47 (73)
T ss_pred ChHHHHHHHHHhcCcccccCccHHHHHccchhHHHHHHHHHHHHHHh
Confidence 56788888888 333222 222 236788888877
No 80
>PF14164 YqzH: YqzH-like protein
Probab=24.73 E-value=81 Score=26.01 Aligned_cols=38 Identities=26% Similarity=0.478 Sum_probs=25.6
Q ss_pred cccchhHHHHHHHhcC--CCCCCChHHHHHHHHHHHHHhh
Q 013514 400 RILTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVE 437 (441)
Q Consensus 400 rVLtKrKLqELVrQVD--P~e~LDpDVEElLLdLADDFVd 437 (441)
--|+++...+|++.|. -++.-|.|+-|++-|++=|||.
T Consensus 24 ~pls~~E~~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~yiT 63 (64)
T PF14164_consen 24 MPLSDEEWEELCKHIQERKNEEPDEDLHEIVEDVVYDYIT 63 (64)
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhc
Confidence 3478889999999883 3344455666666666666663
No 81
>smart00427 H2B Histone H2B.
Probab=24.50 E-value=1.1e+02 Score=26.43 Aligned_cols=35 Identities=17% Similarity=0.406 Sum_probs=28.9
Q ss_pred HHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 406 KLqELVrQVDP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
-|.-+++||.|+..|..+...++--+++|+.|.+.
T Consensus 6 Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa 40 (89)
T smart00427 6 YIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIA 40 (89)
T ss_pred HHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHH
Confidence 36678999999999999988888888888877654
No 82
>cd05128 RasGAP_GAP1_like The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin homology domain that is associated with a Bruton's tyrosine kinase motif. While this domain structure is conserved, a small change in the function of each individual domain and the interaction between domains has a marked effect on the regulation of each protein.
Probab=24.47 E-value=78 Score=31.85 Aligned_cols=16 Identities=13% Similarity=0.233 Sum_probs=13.4
Q ss_pred HHHHHHHHHHhhhhcC
Q 013514 426 DILVDIAEDFVESVSS 441 (441)
Q Consensus 426 ElLLdLADDFVdSVvS 441 (441)
+.|.+++|+|++.+++
T Consensus 132 ~~L~~~~~~~~~~I~~ 147 (315)
T cd05128 132 ENLRYYLDRLFEAITK 147 (315)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5789999999998763
No 83
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=24.34 E-value=37 Score=27.48 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=11.5
Q ss_pred hHHHHHHHHHHHH
Q 013514 422 PDVEDILVDIAED 434 (441)
Q Consensus 422 pDVEElLLdLADD 434 (441)
+||||++++||.+
T Consensus 31 ~eVe~~I~klakk 43 (60)
T PF08069_consen 31 EEVEELIVKLAKK 43 (60)
T ss_dssp HHHHHHHHHHCCT
T ss_pred HHHHHHHHHHHHc
Confidence 8999999999864
No 84
>PLN00161 histone H3; Provisional
Probab=24.32 E-value=93 Score=28.74 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=34.6
Q ss_pred CCCCcccchhHHHHHHHhcC-----CCCCCChHHHHHHHHHHHHHhhhh
Q 013514 396 EFGNRILTKRSIQELVNQID-----PSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 396 ~~gnrVLtKrKLqELVrQVD-----P~e~LDpDVEElLLdLADDFVdSV 439 (441)
.+++-++-|--++-|||||- .+..+..++.+.|=|.+++|+..+
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~l 98 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHL 98 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHH
Confidence 35666778999999999992 346788888888888888887654
No 85
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=24.10 E-value=1e+02 Score=26.45 Aligned_cols=43 Identities=9% Similarity=0.130 Sum_probs=33.9
Q ss_pred CCCcccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 397 ~gnrVLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
..|.-+=|++|.||=++.+-+..=++|-|++-.||...+++++
T Consensus 35 ~~n~~iyr~qL~ELe~d~~~G~l~~~e~~~~~~El~rrLL~d~ 77 (117)
T TIGR03142 35 ELNLAVYRDRLAELERDLAEGLLDEAEAEAARAELQRRLLADI 77 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHCc
Confidence 4566778999999999998876667777888888887777653
No 86
>cd05135 RasGAP_RASAL Ras GTPase activating-like protein (RASAL) or RASAL1 is a member of the GAP1 family, and a Ca2+ sensor responding in-phase to repetitive Ca2+ signals by associating with the plasma membrane and deactivating Ras. It contains a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. However, unlike RASAL4, RASAL undergoes an oscillatory translocation to the plasma membrane that occurs in synchrony with repetitive Ca2+ spikes.
Probab=24.01 E-value=75 Score=32.30 Aligned_cols=16 Identities=6% Similarity=0.291 Sum_probs=12.4
Q ss_pred HHHHHHHHHHhhhhcC
Q 013514 426 DILVDIAEDFVESVSS 441 (441)
Q Consensus 426 ElLLdLADDFVdSVvS 441 (441)
+.|.+++++|+|.+++
T Consensus 149 ~~L~~~~~~~~~~I~~ 164 (333)
T cd05135 149 EMLQGYLSSITDAIVG 164 (333)
T ss_pred HHHHHHHHHHHHHHHh
Confidence 4677889999988763
No 87
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=23.99 E-value=3.5e+02 Score=31.99 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=7.7
Q ss_pred CCcccchhHHHHHHHhc
Q 013514 398 GNRILTKRSIQELVNQI 414 (441)
Q Consensus 398 gnrVLtKrKLqELVrQV 414 (441)
+..||+-.-|+.||+.+
T Consensus 726 ne~vLse~~iqnLik~l 742 (1102)
T KOG1924|consen 726 NEDVLSESMIQNLIKHL 742 (1102)
T ss_pred cHHHHHHHHHHHHHHhC
Confidence 33444444444444444
No 88
>cd05134 RasGAP_RASA3 RASA3 (or GAP1_IP4BP) is a member of the GAP1 family and has been shown to specifically bind 1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may function as an IP4 receptor. The members of GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. Purified RASA3 stimulates GAP activity on Ras with about a five-fold lower potency than p120RasGAP, but shows no GAP-stimulating activity at all against Rac or Rab3A.
Probab=23.75 E-value=1.1e+02 Score=31.20 Aligned_cols=27 Identities=22% Similarity=0.404 Sum_probs=18.8
Q ss_pred cCCCCCCCh-HHH---HHHHHHHHHHhhhhc
Q 013514 414 IDPSERLDP-DVE---DILVDIAEDFVESVS 440 (441)
Q Consensus 414 VDP~e~LDp-DVE---ElLLdLADDFVdSVv 440 (441)
|||...-++ +|| +.|..++|.|+++|+
T Consensus 115 vDP~k~~~~e~le~n~~~L~~~~~~i~~~I~ 145 (310)
T cd05134 115 IDPVKLKDGENLENNRENLRQYVDRIFRVIT 145 (310)
T ss_pred cCcccCCchhhHHHHHHHHHHHHHHHHHHHH
Confidence 366555443 466 578999999998875
No 89
>cd05130 RasGAP_Neurofibromin Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low molecular weight G proteins such as Ras by stimulating their intrinsic GTPase activity. NF1 is a common genetic disorder characterized by various symptoms ranging from predisposition for the development of tumors to learning disability or mental retardation. Loss of neurofibromin activity can be correlated to the increase in Ras-GTP concentration in neurofibromas of NF1 of patients, supporting the notion that unregulated Ras signaling may contribute to their development.
Probab=23.75 E-value=80 Score=32.04 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhhhhcC
Q 013514 426 DILVDIAEDFVESVSS 441 (441)
Q Consensus 426 ElLLdLADDFVdSVvS 441 (441)
+.|.+++|+|++.+++
T Consensus 135 ~~L~~~~~~fl~~I~~ 150 (329)
T cd05130 135 RNLLQLTEKFFHAIIN 150 (329)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5689999999998763
No 90
>cd05391 RasGAP_p120GAP p120GAP is a negative regulator of Ras that stimulates hydrolysis of bound GTP to GDP. Once the Ras regulator p120GAP, a member of the GAP protein family, is recruited to the membrane, it is transiently immobilized to interact with Ras-GTP. The down regulation of Ras by p120GAP is a critical step in the regulation of many cellular processes, which is disrupted in approximately 30% of human cancers. p120GAP contains SH2, SH3, PH, calcium- and lipid-binding domains, suggesting its involvement in a complex network of cellular interactions in vivo.
Probab=22.99 E-value=1e+02 Score=31.13 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=14.9
Q ss_pred hHHH---HHHHHHHHHHhhhhc
Q 013514 422 PDVE---DILVDIAEDFVESVS 440 (441)
Q Consensus 422 pDVE---ElLLdLADDFVdSVv 440 (441)
+|+| +.|+.++++|++.++
T Consensus 119 e~~~~n~~~L~~~~~~~~~~I~ 140 (315)
T cd05391 119 EDVNTNLEHLLNILSELVEKIF 140 (315)
T ss_pred hhHHHHHHHHHHHHHHHHHHHH
Confidence 4454 568999999999875
No 91
>cd05136 RasGAP_DAB2IP The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism by which TNF signaling is coupled to DAB2IP is not known.
Probab=22.99 E-value=1e+02 Score=31.01 Aligned_cols=27 Identities=19% Similarity=0.042 Sum_probs=19.1
Q ss_pred CCCCCCChH---HHHHHHHHHHHHhhhhcC
Q 013514 415 DPSERLDPD---VEDILVDIAEDFVESVSS 441 (441)
Q Consensus 415 DP~e~LDpD---VEElLLdLADDFVdSVvS 441 (441)
||...-.+| +.+.|..++|.|++.+++
T Consensus 113 DP~k~~~~~l~~n~~~L~~~~~~~~~~I~~ 142 (309)
T cd05136 113 DPSKCSASELPDHQANLRMCCELAWCKIIN 142 (309)
T ss_pred CccccCchhHHHHHHHHHHHHHHHHHHHHH
Confidence 555544444 347899999999998763
No 92
>PRK05687 fliH flagellar assembly protein H; Validated
Probab=22.83 E-value=36 Score=31.99 Aligned_cols=34 Identities=32% Similarity=0.469 Sum_probs=22.5
Q ss_pred HHHHHHhc-CCCCCCChHHHHHHHHHHHHHhhhhc
Q 013514 407 IQELVNQI-DPSERLDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 407 LqELVrQV-DP~e~LDpDVEElLLdLADDFVdSVv 440 (441)
|..|+.++ .+...|+.++|+.|++||-+.++.|+
T Consensus 115 l~~l~~~l~~~l~~l~~~ie~~Lv~Lal~ia~~vi 149 (246)
T PRK05687 115 LQALAAQFQEPLALLDSVIESRLVQLALELARQVI 149 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455544 36667788888877777777766664
No 93
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=22.82 E-value=79 Score=25.80 Aligned_cols=31 Identities=10% Similarity=0.193 Sum_probs=17.5
Q ss_pred hhHHHHHHHhcC-CC------------CCCChHHHHHHHHHHHH
Q 013514 404 KRSIQELVNQID-PS------------ERLDPDVEDILVDIAED 434 (441)
Q Consensus 404 KrKLqELVrQVD-P~------------e~LDpDVEElLLdLADD 434 (441)
+++|-++|++-+ -. ..-+.||++.|-+|+||
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 667777777721 11 12256777777777765
No 94
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=22.66 E-value=94 Score=25.80 Aligned_cols=34 Identities=26% Similarity=0.378 Sum_probs=24.4
Q ss_pred CCCcccchhHHHHHHHh-cCCCCCCC-hHHHHHHHHH
Q 013514 397 FGNRILTKRSIQELVNQ-IDPSERLD-PDVEDILVDI 431 (441)
Q Consensus 397 ~gnrVLtKrKLqELVrQ-VDP~e~LD-pDVEElLLdL 431 (441)
+++-.|++..|..|+++ +..... + +||+++|-++
T Consensus 21 ~~~g~i~~~ELk~ll~~elg~~ls-~~~~v~~mi~~~ 56 (89)
T cd05022 21 GGKESLTASEFQELLTQQLPHLLK-DVEGLEEKMKNL 56 (89)
T ss_pred CCCCeECHHHHHHHHHHHhhhhcc-CHHHHHHHHHHh
Confidence 56678999999999998 753311 3 6888887544
No 95
>PF01851 PC_rep: Proteasome/cyclosome repeat; InterPro: IPR002015 A weakly conserved repeat module of unknown function, which occurs in two regulatory subunits of the 26S-proteasome and in one subunit of the APC-complex (cyclosome) [].; PDB: 4ADY_A.
Probab=22.55 E-value=47 Score=23.40 Aligned_cols=20 Identities=20% Similarity=0.200 Sum_probs=15.1
Q ss_pred CChHHHHHHHHHHHHHhhhh
Q 013514 420 LDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 420 LDpDVEElLLdLADDFVdSV 439 (441)
-++||.|+|+.++.|+-+.+
T Consensus 14 ~~~~~~~~L~~~l~~~~~~~ 33 (35)
T PF01851_consen 14 GNEEVLDLLRPYLSDTSNEM 33 (35)
T ss_dssp --HHHHHHHHHHHCTSSHHH
T ss_pred CCHHHHHHHHHHHHhccccc
Confidence 35689999999999887665
No 96
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=22.22 E-value=68 Score=26.53 Aligned_cols=21 Identities=29% Similarity=0.370 Sum_probs=18.1
Q ss_pred CChHHHHHHHHHHHHHhhhhc
Q 013514 420 LDPDVEDILVDIAEDFVESVS 440 (441)
Q Consensus 420 LDpDVEElLLdLADDFVdSVv 440 (441)
-|.|+.++..+.|.|||.+.+
T Consensus 7 Kd~~l~~~~QqaAk~Fi~~~L 27 (63)
T PF08157_consen 7 KDQSLRDSQQQAAKDFIQSRL 27 (63)
T ss_pred ccchhhhHHHHHHHHHHHHhc
Confidence 378899999999999998753
No 97
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.11 E-value=91 Score=27.83 Aligned_cols=33 Identities=9% Similarity=0.332 Sum_probs=25.7
Q ss_pred hhHHHHHHHhcCC----CCCCChHHHHHHHHHHHHHh
Q 013514 404 KRSIQELVNQIDP----SERLDPDVEDILVDIAEDFV 436 (441)
Q Consensus 404 KrKLqELVrQVDP----~e~LDpDVEElLLdLADDFV 436 (441)
|.||++||+.|.= ...-+.+.+|+|-.|++.-|
T Consensus 67 R~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeI 103 (113)
T PF09862_consen 67 RNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEI 103 (113)
T ss_pred HHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCC
Confidence 7899999999954 55666778888888877554
No 98
>cd05127 RasGAP_IQGAP_related This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% indentity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGA
Probab=21.60 E-value=1.2e+02 Score=29.87 Aligned_cols=14 Identities=21% Similarity=0.589 Sum_probs=11.9
Q ss_pred HHHHHHHHHhhhhc
Q 013514 427 ILVDIAEDFVESVS 440 (441)
Q Consensus 427 lLLdLADDFVdSVv 440 (441)
.|.+++|.|++.++
T Consensus 123 ~L~~~~~~fl~~I~ 136 (325)
T cd05127 123 SLRELTEQFLDAII 136 (325)
T ss_pred HHHHHHHHHHHHHH
Confidence 58999999999775
No 99
>cd06845 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting
Probab=21.23 E-value=1.4e+02 Score=25.94 Aligned_cols=32 Identities=13% Similarity=0.389 Sum_probs=22.9
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhh
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdS 438 (441)
++.+++++++++ .-++++.+.+.++|++..++
T Consensus 51 ~~~f~~~~~~l~---~~~~~~~~~f~~v~~~lf~d 82 (144)
T cd06845 51 RRLFENMCRQLN---ISPDNAYEVFQEVARELFED 82 (144)
T ss_pred HHHHHHHHHHhC---CCcchHHHHHHHHHHHHhcc
Confidence 344556666666 34677888999999998876
No 100
>COG3900 Predicted periplasmic protein [Function unknown]
Probab=21.20 E-value=46 Score=33.52 Aligned_cols=43 Identities=30% Similarity=0.410 Sum_probs=33.0
Q ss_pred CcccchhHHHHHHHhcCCCCCCChHHHHHHH-HHHHHHhhhhcC
Q 013514 399 NRILTKRSIQELVNQIDPSERLDPDVEDILV-DIAEDFVESVSS 441 (441)
Q Consensus 399 nrVLtKrKLqELVrQVDP~e~LDpDVEElLL-dLADDFVdSVvS 441 (441)
++|=.+..|+|||.+||.+.-|+-.-.|||+ +..||.|+-|.+
T Consensus 119 aqieapgTiD~lvdei~~kyG~~lp~adllsadpyd~L~~gv~s 162 (262)
T COG3900 119 AQIEAPGTIDELVDEIDDKYGITLPGADLLSADPYDDLIAGVES 162 (262)
T ss_pred eeccCCCcHHHHHHHHHhhcCCCccchhhhccChHHHHHhhhhh
Confidence 3444456799999999998888888888765 677888877653
No 101
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=20.97 E-value=1.5e+02 Score=21.51 Aligned_cols=32 Identities=13% Similarity=0.397 Sum_probs=22.5
Q ss_pred CCCCCcccchhHHHHHHHhcCCCCCCChHHHHH
Q 013514 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDI 427 (441)
Q Consensus 395 ~~~gnrVLtKrKLqELVrQVDP~e~LDpDVEEl 427 (441)
+.+++-.|++..|..+++.+..... +.+++++
T Consensus 10 D~d~~G~i~~~el~~~~~~~~~~~~-~~~~~~~ 41 (66)
T PF13499_consen 10 DKDGDGYISKEELRRALKHLGRDMS-DEESDEM 41 (66)
T ss_dssp STTSSSEEEHHHHHHHHHHTTSHST-HHHHHHH
T ss_pred cCCccCCCCHHHHHHHHHHhccccc-HHHHHHH
Confidence 4577888999999999998864332 4444444
No 102
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=20.94 E-value=1.4e+02 Score=26.58 Aligned_cols=34 Identities=12% Similarity=0.367 Sum_probs=25.5
Q ss_pred ccchhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHh
Q 013514 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFV 436 (441)
Q Consensus 401 VLtKrKLqELVrQVDP~e~LDpDVEElLLdLADDFV 436 (441)
|-+|+=|+||++=|.. ..+.+|.+-+|+|.++.-
T Consensus 80 vas~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~ 113 (142)
T cd03569 80 VASREFMDELKDLIKT--TKNEEVRQKILELIQAWA 113 (142)
T ss_pred HhhHHHHHHHHHHHcc--cCCHHHHHHHHHHHHHHH
Confidence 5578888899998876 788888877777655443
No 103
>PF12646 DUF3783: Domain of unknown function (DUF3783); InterPro: IPR016621 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=20.72 E-value=1.1e+02 Score=23.64 Aligned_cols=34 Identities=9% Similarity=0.401 Sum_probs=25.8
Q ss_pred cchhHHHHHHHhcC------------CCCCCChHHHHHHHHHHHHH
Q 013514 402 LTKRSIQELVNQID------------PSERLDPDVEDILVDIAEDF 435 (441)
Q Consensus 402 LtKrKLqELVrQVD------------P~e~LDpDVEElLLdLADDF 435 (441)
++++.|+++|..+- -...+++.+++||-+|++|-
T Consensus 9 ~~~~el~~~l~~~r~~~~~~~~kAvlT~tN~~Wt~~~L~~El~~Eh 54 (58)
T PF12646_consen 9 FSGEELDKFLDALRKAGIPIPLKAVLTPTNINWTLKDLLEELKEEH 54 (58)
T ss_pred CCHHHHHHHHHHHHHcCCCcceEEEECCCcccCcHHHHHHHHHHHH
Confidence 46677887777662 23468999999999999984
No 104
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=20.60 E-value=1.9e+02 Score=20.51 Aligned_cols=32 Identities=13% Similarity=0.224 Sum_probs=20.3
Q ss_pred cccchhHHHHHHHhcCCCCC-CChHHHHHHHHHHH
Q 013514 400 RILTKRSIQELVNQIDPSER-LDPDVEDILVDIAE 433 (441)
Q Consensus 400 rVLtKrKLqELVrQVDP~e~-LDpDVEElLLdLAD 433 (441)
..|++..|..+++.+ ... ++++..+.|+..+|
T Consensus 3 G~i~~~~~~~~l~~~--g~~~~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 3 GKITREEFRRALSKL--GIKDLSEEEVDRLFREFD 35 (54)
T ss_dssp SEEEHHHHHHHHHHT--TSSSSCHHHHHHHHHHHT
T ss_pred CEECHHHHHHHHHHh--CCCCCCHHHHHHHHHhcc
Confidence 356777777777655 223 66666666666665
No 105
>PF12536 DUF3734: Patatin phospholipase ; InterPro: IPR021095 This entry represents bacterial proteins of approximately 110 amino acids in length. These proteins are found in association with PF01734 from PFAM. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Probab=20.44 E-value=52 Score=28.18 Aligned_cols=35 Identities=26% Similarity=0.467 Sum_probs=24.4
Q ss_pred hhHHHHHHHhcCCCCCCChHHHHHHHHHHHHHhhhh
Q 013514 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESV 439 (441)
Q Consensus 404 KrKLqELVrQVDP~e~LDpDVEElLLdLADDFVdSV 439 (441)
|+-|.+|+..|++.++-|++|.+ |.+++++..-+|
T Consensus 21 r~~i~~Ll~~lP~~~r~dp~~~~-l~~~~~~~~~~I 55 (108)
T PF12536_consen 21 RHAIRELLERLPEELRDDPDVRE-LAELGCGKRVNI 55 (108)
T ss_pred HHHHHHHHHcCCHHHhCCHHHHH-HHHhcCCCceEE
Confidence 56677888888888888888865 455555544444
No 106
>cd05137 RasGAP_CLA2_BUD2 CLA2/BUD2 functions as a GTPase-activating protein (GAP) for BUD1/RSR1 and is necessary for proper bud-site selection in yeast. BUD2 has sequence similarity to the catalytic domain of RasGAPs, and stimulates the hydrolysis of BUD1-GTP to BUD1-GDP. Elimination of Bud2p activity by mutation causes a random budding pattern with no growth defect. Overproduction of Bud2p also alters the budding pattern.
Probab=20.42 E-value=1.1e+02 Score=31.89 Aligned_cols=16 Identities=13% Similarity=0.461 Sum_probs=13.3
Q ss_pred HHHHHHHHHHhhhhcC
Q 013514 426 DILVDIAEDFVESVSS 441 (441)
Q Consensus 426 ElLLdLADDFVdSVvS 441 (441)
+.|.+++++|++.+++
T Consensus 199 ~~L~~~~~~~~~~I~~ 214 (395)
T cd05137 199 ERLISLTEEIWKRIAN 214 (395)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5699999999998763
No 107
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.25 E-value=95 Score=28.85 Aligned_cols=17 Identities=47% Similarity=0.685 Sum_probs=13.8
Q ss_pred cchhHHHHHHHhcCCCC
Q 013514 402 LTKRSIQELVNQIDPSE 418 (441)
Q Consensus 402 LtKrKLqELVrQVDP~e 418 (441)
|+-|.+.||++.||+.+
T Consensus 8 l~ar~i~ELleki~e~l 24 (139)
T COG1710 8 LTARNIRELLEKIDEDL 24 (139)
T ss_pred hhhhhHHHHHHHcchhh
Confidence 56688999999998764
No 108
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=20.04 E-value=2e+02 Score=21.84 Aligned_cols=30 Identities=20% Similarity=0.505 Sum_probs=19.8
Q ss_pred HHHHHHHhcC-CCCCCChHHHHHHHHHHHHH
Q 013514 406 SIQELVNQID-PSERLDPDVEDILVDIAEDF 435 (441)
Q Consensus 406 KLqELVrQVD-P~e~LDpDVEElLLdLADDF 435 (441)
+|.++++.++ ....+.++++|+|+++.|..
T Consensus 55 ~lE~~~~~~~~~~~~~~~~l~~~~~~~~~~l 85 (87)
T smart00073 55 QLENLLDAARSGEVELTPDLLDLLLELVDVL 85 (87)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence 3444455443 44578899999998887753
Done!