Query psy10378
Match_columns 62
No_of_seqs 107 out of 447
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 16:19:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10378.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10378hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0196|consensus 99.7 1.2E-16 2.6E-21 116.7 5.1 62 1-62 935-996 (996)
2 PF00536 SAM_1: SAM domain (St 99.6 2.1E-15 4.6E-20 79.7 5.1 48 1-49 17-64 (64)
3 PF07647 SAM_2: SAM domain (St 99.5 2.1E-14 4.6E-19 76.1 5.3 49 1-49 18-66 (66)
4 cd00166 SAM Sterile alpha moti 99.4 1.2E-13 2.7E-18 71.7 4.1 48 1-49 16-63 (63)
5 smart00454 SAM Sterile alpha m 99.4 1.5E-12 3.3E-17 68.1 4.9 49 1-50 18-67 (68)
6 KOG4384|consensus 99.4 6.8E-13 1.5E-17 89.9 4.2 54 1-54 227-280 (361)
7 KOG1170|consensus 98.6 2.9E-08 6.3E-13 73.6 1.9 52 1-53 1012-1063(1099)
8 KOG4374|consensus 98.4 4.3E-08 9.3E-13 63.1 0.4 51 1-52 163-213 (216)
9 KOG4375|consensus 97.9 9.6E-06 2.1E-10 53.7 2.9 47 1-48 224-270 (272)
10 PF09597 IGR: IGR protein moti 97.5 0.0002 4.4E-09 37.7 4.0 43 2-49 13-55 (57)
11 KOG3678|consensus 97.0 0.00068 1.5E-08 49.2 3.3 48 2-50 480-528 (832)
12 KOG3930|consensus 96.5 0.0051 1.1E-07 42.3 4.1 50 3-53 20-69 (389)
13 PF04904 NCD1: NAB conserved r 96.3 0.0095 2.1E-07 33.2 3.8 50 1-50 21-75 (82)
14 KOG1738|consensus 96.1 0.0037 8.1E-08 45.7 1.9 50 1-51 23-72 (638)
15 PF14520 HHH_5: Helix-hairpin- 94.8 0.12 2.6E-06 26.6 4.5 42 4-46 17-59 (60)
16 KOG1899|consensus 94.6 0.035 7.6E-07 41.3 2.9 48 1-49 637-684 (861)
17 KOG1899|consensus 93.9 0.048 1E-06 40.6 2.4 52 2-54 565-617 (861)
18 PRK07758 hypothetical protein; 92.6 0.3 6.4E-06 28.1 3.8 44 6-56 48-91 (95)
19 TIGR01954 nusA_Cterm_rpt trans 92.4 0.67 1.5E-05 22.5 5.3 38 5-43 6-44 (50)
20 PF06568 DUF1127: Domain of un 91.8 0.14 3.1E-06 24.6 1.7 19 15-33 16-34 (40)
21 PF14229 DUF4332: Domain of un 87.6 0.61 1.3E-05 27.4 2.4 28 2-29 63-90 (122)
22 KOG3835|consensus 87.0 0.88 1.9E-05 32.4 3.3 49 1-49 23-76 (495)
23 PF03118 RNA_pol_A_CTD: Bacter 86.7 3.1 6.8E-05 22.0 4.7 26 5-30 24-49 (66)
24 COG2818 Tag 3-methyladenine DN 86.1 1.8 3.9E-05 27.7 4.0 41 4-49 57-101 (188)
25 TIGR02238 recomb_DMC1 meiotic 84.0 3.6 7.8E-05 27.7 5.0 44 4-48 13-57 (313)
26 TIGR02239 recomb_RAD51 DNA rep 82.8 3.6 7.8E-05 27.7 4.6 44 4-48 13-57 (316)
27 PTZ00035 Rad51 protein; Provis 82.8 4.2 9.2E-05 27.7 5.0 44 4-48 35-79 (337)
28 COG5457 Uncharacterized conser 82.4 0.85 1.9E-05 24.4 1.2 18 16-33 32-49 (63)
29 KOG3678|consensus 82.0 2.6 5.6E-05 31.3 3.9 48 1-49 551-599 (832)
30 PF03352 Adenine_glyco: Methyl 80.2 4 8.6E-05 25.8 3.9 43 4-49 51-95 (179)
31 PLN03186 DNA repair protein RA 79.9 6.1 0.00013 27.1 5.0 44 4-48 40-84 (342)
32 KOG3791|consensus 79.5 0.95 2.1E-05 33.3 1.1 42 2-46 488-529 (569)
33 PRK12766 50S ribosomal protein 78.5 4.8 0.0001 26.6 4.0 44 4-48 15-59 (232)
34 KOG4374|consensus 78.0 1.7 3.7E-05 28.4 1.8 47 1-48 130-176 (216)
35 TIGR00624 tag DNA-3-methyladen 77.8 6.2 0.00013 25.0 4.2 43 4-49 55-99 (179)
36 PRK01172 ski2-like helicase; P 75.5 8.5 0.00018 28.2 5.0 43 5-48 625-668 (674)
37 KOG0249|consensus 75.4 5.8 0.00013 30.5 4.1 51 3-54 606-657 (916)
38 PRK10353 3-methyl-adenine DNA 75.3 7.9 0.00017 24.7 4.2 44 3-49 55-100 (187)
39 PLN03187 meiotic recombination 74.8 10 0.00022 26.1 5.0 44 4-48 43-87 (344)
40 KOG4403|consensus 74.0 1.4 3E-05 31.9 0.6 41 1-42 150-194 (575)
41 PRK05182 DNA-directed RNA poly 72.5 8.2 0.00018 26.2 4.0 43 6-55 262-304 (310)
42 TIGR02236 recomb_radA DNA repa 70.1 14 0.00031 24.3 4.7 41 4-45 11-52 (310)
43 PRK04301 radA DNA repair and r 68.4 19 0.00041 23.9 5.1 42 4-46 18-60 (317)
44 PRK00254 ski2-like helicase; P 67.7 13 0.00029 27.5 4.5 42 4-46 657-699 (720)
45 TIGR02027 rpoA DNA-directed RN 63.9 15 0.00033 24.7 4.0 43 6-55 248-290 (297)
46 PF10078 DUF2316: Uncharacteri 61.7 11 0.00025 21.3 2.6 30 4-42 15-44 (89)
47 PF00730 HhH-GPD: HhH-GPD supe 60.5 19 0.00041 19.8 3.4 28 6-33 20-51 (108)
48 PF11372 DUF3173: Domain of un 58.4 21 0.00046 18.7 3.1 27 21-48 3-29 (59)
49 PF13543 KSR1-SAM: SAM like do 57.6 16 0.00036 22.0 2.9 36 13-49 90-129 (129)
50 KOG0507|consensus 56.9 2.1 4.5E-05 32.8 -1.2 51 1-51 309-362 (854)
51 PF02888 CaMBD: Calmodulin bin 55.6 15 0.00033 20.3 2.4 15 35-49 38-52 (77)
52 PHA01516 hypothetical protein 48.0 9 0.0002 21.6 0.7 14 21-34 61-74 (98)
53 PRK02362 ski2-like helicase; P 47.1 33 0.00072 25.5 3.7 39 7-47 667-705 (737)
54 cd08541 SAM_PNT-FLI-1 Sterile 46.9 54 0.0012 18.6 3.8 36 15-52 50-85 (91)
55 PF13099 DUF3944: Domain of un 45.3 15 0.00032 17.4 1.1 16 15-30 6-21 (35)
56 PTZ00096 40S ribosomal protein 44.2 14 0.0003 22.8 1.2 23 7-30 14-36 (143)
57 COG1153 FwdD Formylmethanofura 43.8 5.2 0.00011 24.1 -0.7 21 13-33 26-46 (128)
58 PRK08097 ligB NAD-dependent DN 43.3 73 0.0016 23.6 4.9 45 4-49 437-483 (562)
59 PRK14973 DNA topoisomerase I; 43.1 85 0.0018 24.7 5.4 40 5-44 757-796 (936)
60 PF13735 tRNA_NucTran2_2: tRNA 38.7 34 0.00074 19.9 2.3 26 21-47 104-131 (149)
61 PF11737 DUF3300: Protein of u 37.6 12 0.00026 24.8 0.2 29 28-56 86-114 (237)
62 TIGR00575 dnlj DNA ligase, NAD 37.4 97 0.0021 23.2 4.8 42 7-49 447-490 (652)
63 cd08531 SAM_PNT-ERG_FLI-1 Ster 37.4 70 0.0015 17.3 3.2 34 15-50 38-71 (75)
64 PRK07956 ligA NAD-dependent DN 37.0 1.1E+02 0.0025 23.0 5.1 42 7-49 460-503 (665)
65 KOG0249|consensus 36.4 25 0.00055 27.2 1.7 48 1-49 687-735 (916)
66 PRK04038 rps19p 30S ribosomal 34.8 24 0.00052 21.5 1.2 23 7-30 6-28 (134)
67 PF02889 Sec63: Sec63 Brl doma 34.6 52 0.0011 21.4 2.8 41 5-45 161-201 (314)
68 PRK14351 ligA NAD-dependent DN 34.4 1.1E+02 0.0023 23.3 4.7 43 5-48 475-519 (689)
69 PRK12277 50S ribosomal protein 34.3 55 0.0012 18.4 2.5 45 11-57 32-80 (83)
70 KOG0898|consensus 34.3 29 0.00064 21.4 1.5 24 6-30 20-43 (152)
71 PF13351 DUF4099: Protein of u 32.8 27 0.0006 19.2 1.1 14 20-33 4-17 (85)
72 smart00611 SEC63 Domain of unk 32.7 94 0.002 20.3 3.8 41 5-46 164-205 (312)
73 PRK15363 pathogenicity island 32.0 44 0.00096 20.7 2.1 24 5-29 13-37 (157)
74 CHL00013 rpoA RNA polymerase a 31.9 43 0.00094 23.0 2.2 42 6-54 276-317 (327)
75 PF08620 RPAP1_C: RPAP1-like, 31.5 90 0.002 16.9 3.0 35 10-52 36-70 (73)
76 PRK13482 DNA integrity scannin 30.6 1.6E+02 0.0034 20.7 4.7 38 13-51 307-345 (352)
77 PF09278 MerR-DNA-bind: MerR, 30.1 69 0.0015 15.9 2.3 48 4-54 6-54 (65)
78 PF08861 DUF1828: Domain of un 30.1 55 0.0012 17.8 2.1 24 24-47 31-56 (90)
79 cd08315 Death_TRAILR_DR4_DR5 D 29.8 62 0.0014 18.2 2.3 52 2-53 7-62 (96)
80 COG3743 Uncharacterized conser 29.8 58 0.0013 19.8 2.2 29 3-31 78-106 (133)
81 PF13986 DUF4224: Domain of un 29.8 67 0.0014 15.8 2.2 22 22-43 3-25 (47)
82 PRK09202 nusA transcription el 29.3 1.6E+02 0.0035 21.3 4.8 39 4-42 368-406 (470)
83 PF05105 Phage_holin_4: Holin 28.7 54 0.0012 18.7 1.9 23 25-50 94-116 (118)
84 PF05643 DUF799: Putative bact 28.2 52 0.0011 21.5 2.0 24 6-29 79-102 (215)
85 PF14823 Sirohm_synth_C: Siroh 27.8 25 0.00055 18.8 0.4 15 15-29 43-57 (70)
86 KOG0507|consensus 27.7 19 0.00041 27.8 -0.1 37 7-43 508-544 (854)
87 PF10195 Phospho_p8: DNA-bindi 27.4 54 0.0012 17.3 1.6 15 33-47 41-55 (60)
88 KOG4279|consensus 26.3 78 0.0017 25.2 2.8 49 5-54 1169-1217(1226)
89 PF01698 FLO_LFY: Floricaula / 26.2 22 0.00048 25.2 0.0 42 9-51 69-119 (386)
90 PF10454 DUF2458: Protein of u 26.2 61 0.0013 19.8 1.9 31 7-37 94-124 (150)
91 COG1654 BirA Biotin operon rep 26.1 1.2E+02 0.0027 16.6 3.0 24 23-50 21-45 (79)
92 PF01152 Bac_globin: Bacterial 25.4 1.3E+02 0.0029 16.7 3.5 35 18-53 84-118 (120)
93 COG4380 Uncharacterized protei 25.1 41 0.00088 21.6 1.0 26 5-30 77-102 (216)
94 PRK06288 RNA polymerase sigma 25.0 81 0.0018 20.4 2.5 37 21-57 228-265 (268)
95 cd08538 SAM_PNT-ESE-2-like Ste 24.8 66 0.0014 17.7 1.7 38 8-50 35-73 (78)
96 cd08540 SAM_PNT-ERG Sterile al 24.8 1.3E+02 0.0028 16.3 3.7 34 15-50 38-71 (75)
97 COG5452 Uncharacterized conser 24.6 1.6E+02 0.0036 18.6 3.6 32 17-48 77-108 (180)
98 PF12826 HHH_2: Helix-hairpin- 24.5 61 0.0013 16.6 1.5 24 10-33 20-44 (64)
99 cd00056 ENDO3c endonuclease II 24.3 1.6E+02 0.0034 17.2 3.9 25 8-33 26-50 (158)
100 PF09743 DUF2042: Uncharacteri 24.1 67 0.0014 21.5 2.0 23 5-35 245-267 (272)
101 TIGR01025 rpsS_arch ribosomal 23.6 47 0.001 20.3 1.1 23 7-30 4-26 (135)
102 cd04256 AAK_P5CS_ProBA AAK_P5C 23.4 85 0.0018 20.9 2.4 26 2-29 107-132 (284)
103 PRK14667 uvrC excinuclease ABC 23.4 1.3E+02 0.0028 22.3 3.4 31 13-44 534-564 (567)
104 PRK10308 3-methyl-adenine DNA 22.6 2.2E+02 0.0047 19.0 4.2 21 13-33 155-175 (283)
105 PF03047 ComC: COMC family; I 22.6 29 0.00062 16.0 0.0 17 14-30 6-22 (32)
106 COG4518 Mu-like prophage FluMu 22.4 56 0.0012 19.4 1.2 20 11-30 74-93 (122)
107 KOG0199|consensus 21.8 1.6E+02 0.0036 23.4 3.7 51 2-53 22-73 (1039)
108 COG4367 Uncharacterized protei 21.5 98 0.0021 17.8 2.0 24 19-43 21-45 (97)
109 PF09391 DUF2000: Protein of u 21.3 17 0.00036 21.8 -1.2 28 16-43 97-124 (133)
110 PF02198 SAM_PNT: Sterile alph 21.0 1.6E+02 0.0034 15.9 3.1 39 9-50 44-82 (84)
111 PRK14906 DNA-directed RNA poly 20.7 2E+02 0.0044 24.1 4.2 43 5-54 1326-1368(1460)
112 smart00510 TFS2M Domain in the 20.5 89 0.0019 17.7 1.8 18 11-28 75-92 (102)
No 1
>KOG0196|consensus
Probab=99.66 E-value=1.2e-16 Score=116.67 Aligned_cols=62 Identities=44% Similarity=0.649 Sum_probs=59.7
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhhccCCCCCC
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSANLSEGFLV 62 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~~~~~~~~~ 62 (62)
|++|+++|.++||++++.+.+++.+||.++|||.+||||||+.+|+.++.|+.+.+.+++|+
T Consensus 935 m~rY~~~F~~ag~~s~~~V~q~s~eDl~~~Gitl~GhqkkIl~SIq~m~~q~~~~~~~~~~~ 996 (996)
T KOG0196|consen 935 MGRYKEHFAAAGYTSFEDVAQMSAEDLLRLGITLAGHQKKILSSIQAMRAQMRQTQPVEVPG 996 (996)
T ss_pred hhHHHHHHHhcCcccHHHHHhhhHHHHHhhceeecchhHHHHHHHHHHHHHhccCCCCCCCC
Confidence 78999999999999999999999999999999999999999999999999999999888874
No 2
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=99.60 E-value=2.1e-15 Score=79.71 Aligned_cols=48 Identities=38% Similarity=0.659 Sum_probs=43.7
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~ 49 (62)
|++|.+.| .+++.+++.+..++++||.+|||+.+|||+||+.+|+.||
T Consensus 17 l~~y~~~F-~~~~i~g~~L~~lt~~dL~~lgi~~~ghr~ki~~~i~~Lk 64 (64)
T PF00536_consen 17 LEQYAENF-EKNYIDGEDLLSLTEEDLEELGITKLGHRKKILRAIQKLK 64 (64)
T ss_dssp GGGGHHHH-HHTTSSHHHHTTSCHHHHHHTT-SSHHHHHHHHHHHHHHH
T ss_pred CHHHHHHH-HcCCchHHHHHhcCHHHHHHcCCCCHHHHHHHHHHHHHhC
Confidence 57999999 6667699999999999999999999999999999999886
No 3
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=99.53 E-value=2.1e-14 Score=76.14 Aligned_cols=49 Identities=39% Similarity=0.803 Sum_probs=45.7
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~ 49 (62)
+++|.+.|.++|++.++.+..++++||.++||+.+|||++|+++++.|+
T Consensus 18 l~~y~~~f~~~~i~g~~~L~~l~~~~L~~lGI~~~~~r~kll~~i~~Lk 66 (66)
T PF07647_consen 18 LEQYADNFRENGIDGLEDLLQLTEEDLKELGITNLGHRRKLLSAIQELK 66 (66)
T ss_dssp CGGGHHHHHHTTCSHHHHHTTSCHHHHHHTTTTHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHcCCcHHHHHhhCCHHHHHHcCCCCHHHHHHHHHHHHHcC
Confidence 5789999999999544999999999999999999999999999999886
No 4
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=99.45 E-value=1.2e-13 Score=71.70 Aligned_cols=48 Identities=44% Similarity=0.771 Sum_probs=44.9
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~ 49 (62)
+++|.+.|.++++ +++.+..++.+||.+|||+.+|||++|+.+++.++
T Consensus 16 ~~~y~~~f~~~~i-~g~~L~~l~~~dL~~lgi~~~g~r~~i~~~i~~l~ 63 (63)
T cd00166 16 LGQYADNFRENGI-DGDLLLLLTEEDLKELGITLPGHRKKILKAIQKLK 63 (63)
T ss_pred hHHHHHHHHHcCC-CHHHHhHCCHHHHHHcCCCCHHHHHHHHHHHHHcC
Confidence 4689999999999 89999999999999999999999999999998763
No 5
>smart00454 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.
Probab=99.37 E-value=1.5e-12 Score=68.13 Aligned_cols=49 Identities=41% Similarity=0.732 Sum_probs=44.5
Q ss_pred CcchHHHHhhcCcCcHHHHHcCC-HHHHhcCCCCCchHHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLT-VAELNALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt-~~dL~~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
+++|.+.|.++++ +...+..++ .+||.++||+.+|||++|+.+|+.++.
T Consensus 18 ~~~y~~~f~~~~i-~g~~ll~~~~~~~l~~lgi~~~~~r~~ll~~i~~l~~ 67 (68)
T smart00454 18 LEQYADNFRKNGI-DGALLLLLTSEEDLKELGITKLGHRKKILKAIQKLKD 67 (68)
T ss_pred hHHHHHHHHHCCC-CHHHHHhcChHHHHHHcCCCcHHHHHHHHHHHHHHHh
Confidence 4689999999999 677788887 999999999999999999999999875
No 6
>KOG4384|consensus
Probab=99.36 E-value=6.8e-13 Score=89.93 Aligned_cols=54 Identities=22% Similarity=0.489 Sum_probs=50.9
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
|++|...|..+||++++.|.+++++||.+|||.+|+||||||.+++.++..-+.
T Consensus 227 le~y~~~~L~nGYd~le~~k~i~e~dL~~lgI~nP~Hr~kLL~av~~~~e~d~~ 280 (361)
T KOG4384|consen 227 LEEYIETLLENGYDTLEDLKDITEEDLEELGIDNPDHRKKLLSAVELLKEIDSG 280 (361)
T ss_pred HHHHHHHHHHcchHHHHHHHhccHHHHHHhCCCCHHHHHHHHHHHHHHHhcccc
Confidence 689999999999999999999999999999999999999999999999876554
No 7
>KOG1170|consensus
Probab=98.55 E-value=2.9e-08 Score=73.55 Aligned_cols=52 Identities=33% Similarity=0.613 Sum_probs=48.9
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhh
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLS 53 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~ 53 (62)
|.+|.+.|..+.+ ....++++...||+++||+++||-|+|+.+|.+|+++.+
T Consensus 1012 LsEy~d~f~kndi-rGseLl~L~rrDLkdlgvtkVGhvkril~aIkdl~~~~~ 1063 (1099)
T KOG1170|consen 1012 LSEYKDTFRKNDI-RGSELLHLERRDLKDLGVTKVGHVKRILSAIKDLRAQNQ 1063 (1099)
T ss_pred cchhhhhhhccCc-ccceeeecCcccccccchhhhHHHHHHHHHHHHHHhcch
Confidence 6799999999999 799999999999999999999999999999999976655
No 8
>KOG4374|consensus
Probab=98.45 E-value=4.3e-08 Score=63.15 Aligned_cols=51 Identities=31% Similarity=0.519 Sum_probs=47.0
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHh
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQL 52 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~ 52 (62)
|++|...|....+ +++.+..+|++||++|||+..|.|+||+.|+..++...
T Consensus 163 lg~y~~~f~~~ev-d~~~l~~lte~dlk~~gi~~~GpRkKi~~A~~~~r~~~ 213 (216)
T KOG4374|consen 163 LGAYWKMFEAIEV-DMDNLRLLTEEDLKDMGINSVGPRKKILCAIGKLRRSF 213 (216)
T ss_pred HHHHHHHHHHHHH-HHHHHHhcccchhhhhcccccCcchhhhhhhhcccccc
Confidence 5789999999999 79999999999999999999999999999999887543
No 9
>KOG4375|consensus
Probab=97.90 E-value=9.6e-06 Score=53.72 Aligned_cols=47 Identities=26% Similarity=0.421 Sum_probs=44.0
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l 48 (62)
|.+|.+.|.++.+ +...+-.++.+|..++|||.+|||..|=.|++.|
T Consensus 224 L~E~~~aF~d~eI-dG~hLp~l~k~df~~LGVTRVgHRmnIerALr~l 270 (272)
T KOG4375|consen 224 LIEYDDAFHDIEI-DGKHLPLLRKLDFRGLGVTRVGHRMNIERALRQL 270 (272)
T ss_pred hhhcchhhhhccc-ccchhhhcchhhhhcccchhhhhHHHHHHHHHHh
Confidence 5789999999999 7999999999999999999999999999988765
No 10
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=97.55 E-value=0.0002 Score=37.70 Aligned_cols=43 Identities=23% Similarity=0.356 Sum_probs=35.6
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHH
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~ 49 (62)
++|.+.|.. +++.+..++..+|+++|| ++-+||-||......+
T Consensus 13 ~~~~~kf~~----~w~~lf~~~s~~LK~~GI-p~r~RryiL~~~ek~r 55 (57)
T PF09597_consen 13 EEHAEKFES----DWEKLFTTSSKQLKELGI-PVRQRRYILRWREKYR 55 (57)
T ss_pred HHHHHHHHH----HHHHHHhcCHHHHHHCCC-CHHHHHHHHHHHHHHh
Confidence 456677754 589999999999999999 6999999998766554
No 11
>KOG3678|consensus
Probab=97.04 E-value=0.00068 Score=49.16 Aligned_cols=48 Identities=19% Similarity=0.464 Sum_probs=44.5
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHh-cCCCCCchHHHHHHHHHHHHHH
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELN-ALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~-~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
++|++.|...-+ +.+.++++|+.||+ ++|...-=||||.+..++.|+.
T Consensus 480 eeY~EkFakQ~V-DGDLLLqLTEndLk~DvGM~SGl~RKRFlRELqtLKv 528 (832)
T KOG3678|consen 480 EEYVEKFAKQMV-DGDLLLQLTENDLKHDVGMISGLHRKRFLRELQTLKV 528 (832)
T ss_pred HHHHHHHHHHhc-cchHHHhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHH
Confidence 689999999988 79999999999999 8999888899999999999974
No 12
>KOG3930|consensus
Probab=96.47 E-value=0.0051 Score=42.25 Aligned_cols=50 Identities=28% Similarity=0.525 Sum_probs=43.7
Q ss_pred chHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhh
Q psy10378 3 RYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLS 53 (62)
Q Consensus 3 ~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~ 53 (62)
.|.-.|..|-+ .-+-+++|+.+=|.+||||..|.+--||..+...+.|..
T Consensus 20 ~YA~~Fv~NRI-qk~MLldLnKe~l~ElGvT~iGDiiaILrh~K~v~~q~~ 69 (389)
T KOG3930|consen 20 KYAKSFVTNRI-QKEMLLDLNKETLSELGVTAIGDIIAILRHIKAVKSQIE 69 (389)
T ss_pred hHHHHHHhhhh-hHHHHhhhhHHHHHHhchhhhhhHHHHHHHHHHHHHHHH
Confidence 47777777777 577899999999999999999999999999999987765
No 13
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=96.27 E-value=0.0095 Score=33.24 Aligned_cols=50 Identities=18% Similarity=0.336 Sum_probs=41.9
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcC----CCC-CchHHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNAL----GIT-LVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~l----GIt-~~gh~kkIl~~i~~l~~ 50 (62)
|.+|-+.|.+.|-+++++++...++|..++ |.+ +|=|-+|+.++++++..
T Consensus 21 Ll~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~sKPLHVrRlqKAL~ew~~ 75 (82)
T PF04904_consen 21 LLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWST 75 (82)
T ss_pred HHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccCccHHHHHHHHHHHHHhc
Confidence 458999999999999999999999887653 443 48899999999988754
No 14
>KOG1738|consensus
Probab=96.06 E-value=0.0037 Score=45.73 Aligned_cols=50 Identities=30% Similarity=0.525 Sum_probs=45.7
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQ 51 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~ 51 (62)
|.+|...|.++-. .+.++..++.++|..+|+...||+..|+.++..|.+-
T Consensus 23 m~~Y~~~~e~~~~-~g~ql~~~~pq~le~lg~rrig~qeli~~av~~L~~l 72 (638)
T KOG1738|consen 23 MQSYLAIFEDALI-PGRQLLRLKPQSLETLGVRRIGHQELILEAVEQLWAL 72 (638)
T ss_pred hhHHHHHHHHhhc-ccccccccChHHHHHHhhhhhhhHHHHHHHHHHHHHH
Confidence 5789999999988 7999999999999999999999999999988887653
No 15
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=94.78 E-value=0.12 Score=26.56 Aligned_cols=42 Identities=21% Similarity=0.381 Sum_probs=32.4
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQ 46 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~ 46 (62)
....+.++||.|++++...+.++|.++ ||. +-.-++|..+++
T Consensus 17 ~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig-~~~a~~i~~~~~ 59 (60)
T PF14520_consen 17 RAEKLYEAGIKTLEDLANADPEELAEIPGIG-EKTAEKIIEAAR 59 (60)
T ss_dssp HHHHHHHTTCSSHHHHHTSHHHHHHTSTTSS-HHHHHHHHHHHH
T ss_pred HHHHHHhcCCCcHHHHHcCCHHHHhcCCCCC-HHHHHHHHHHHh
Confidence 346677889999999999999999987 664 555666665543
No 16
>KOG1899|consensus
Probab=94.62 E-value=0.035 Score=41.32 Aligned_cols=48 Identities=25% Similarity=0.398 Sum_probs=45.3
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~ 49 (62)
|.||++.|.++-+ +..-+..||-.||..|-|+..=|--.|-.+|+-|+
T Consensus 637 LPQYKdqF~E~rV-DgrmL~ylTvnDll~lkVvs~lHhaSlkraIqvLr 684 (861)
T KOG1899|consen 637 LPQYKDQFAENRV-DGRMLHYLTVNDLLELKVVSALHHASLKRAIQVLR 684 (861)
T ss_pred ChhhHHHHhhhcc-chhhHhhhhHhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 6899999999999 79999999999999999999999999999999886
No 17
>KOG1899|consensus
Probab=93.94 E-value=0.048 Score=40.65 Aligned_cols=52 Identities=17% Similarity=0.296 Sum_probs=40.3
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHh-cCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELN-ALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~-~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
.+|....... +.+...+++++.+|++ ++||..|=||||+.-+++.|..+..+
T Consensus 565 ~qY~n~~r~w-v~Sg~tfltaS~qd~EkeLnIKhplHRKkl~lal~ai~~keee 617 (861)
T KOG1899|consen 565 GQYMNEVRRW-VRSGRTFLTASPQDYEKELNIKHPLHRKKLALALRAIEEKEEE 617 (861)
T ss_pred HHHHHHHHHH-HhcCchhhcCCHHHHHHHhccCCchHHHHHHHHHHHhcccccc
Confidence 4565544433 3355679999999998 89999999999999999999765543
No 18
>PRK07758 hypothetical protein; Provisional
Probab=92.57 E-value=0.3 Score=28.14 Aligned_cols=44 Identities=23% Similarity=0.347 Sum_probs=32.9
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhhcc
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSANL 56 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~~~ 56 (62)
..+.++||.+++++..++++||.++ ...|. +++++|++.+.+.+
T Consensus 48 N~Lk~AGI~TL~dLv~~te~ELl~i--knlGk-----KSL~EIkekL~E~G 91 (95)
T PRK07758 48 RALEHHGIHTVEELSKYSEKEILKL--HGMGP-----ASLPKLRKALEESG 91 (95)
T ss_pred HHHHHcCCCcHHHHHcCCHHHHHHc--cCCCH-----HHHHHHHHHHHHcC
Confidence 4567899999999999999998753 33343 47777777777543
No 19
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=92.42 E-value=0.67 Score=22.48 Aligned_cols=38 Identities=18% Similarity=0.379 Sum_probs=28.9
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHH
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNAL-GITLVGHQKKIMN 43 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~ 43 (62)
...+..+||.+++.+...+.++|..+ |++ ..-..+|..
T Consensus 6 ~~~L~~~G~~s~e~la~~~~~eL~~i~g~~-~e~a~~ii~ 44 (50)
T TIGR01954 6 AQLLVEEGFTTVEDLAYVPIDELLSIEGFD-EETAKELIN 44 (50)
T ss_pred HHHHHHcCCCCHHHHHccCHHHHhcCCCCC-HHHHHHHHH
Confidence 46788999999999999999999986 544 444444443
No 20
>PF06568 DUF1127: Domain of unknown function (DUF1127); InterPro: IPR009506 This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence.
Probab=91.76 E-value=0.14 Score=24.65 Aligned_cols=19 Identities=21% Similarity=0.427 Sum_probs=17.4
Q ss_pred cHHHHHcCCHHHHhcCCCC
Q psy10378 15 SMEAVVRLTVAELNALGIT 33 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~lGIt 33 (62)
+...+..|++..|.++|++
T Consensus 16 tr~~L~~Lsd~~L~DIGl~ 34 (40)
T PF06568_consen 16 TRRELAELSDRQLADIGLT 34 (40)
T ss_pred HHHHHccCCHHHHHHcCCC
Confidence 5678999999999999998
No 21
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=87.63 E-value=0.61 Score=27.42 Aligned_cols=28 Identities=18% Similarity=0.445 Sum_probs=25.1
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHhc
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELNA 29 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~~ 29 (62)
.+|+..+..+||+|++++...+.++|..
T Consensus 63 ~~~a~LL~~AGv~Tv~~LA~~~p~~L~~ 90 (122)
T PF14229_consen 63 PQYAELLEHAGVDTVEELAQRNPQNLHQ 90 (122)
T ss_pred HHHHHHHHHhCcCcHHHHHhCCHHHHHH
Confidence 4799999999999999999999998864
No 22
>KOG3835|consensus
Probab=87.05 E-value=0.88 Score=32.37 Aligned_cols=49 Identities=14% Similarity=0.299 Sum_probs=40.6
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcC----CC-CCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNAL----GI-TLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~l----GI-t~~gh~kkIl~~i~~l~ 49 (62)
|-+|.+.|.+.|-+++.++|.--+++..+| |. ++|=|.+|+.+++.++-
T Consensus 23 LlsYyd~FIqQGGDDvqQlceagEeEFLEIMaLVGMa~KPLHVRRlQkALrew~ 76 (495)
T KOG3835|consen 23 LLSYYDVFIQQGGDDVQQLCEAGEEEFLEIMALVGMAPKPLHVRRLQKALREWS 76 (495)
T ss_pred HHHHHHHHHHhcchHHHHHHHhhHHHHHHHHHHhccCCcchhHHHHHHHHHHHh
Confidence 357999999999999999998888876553 43 45889999999988874
No 23
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=86.73 E-value=3.1 Score=21.95 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=19.6
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
...+..+|+.++.++..++.+||..+
T Consensus 24 ~n~L~~~~I~tv~dL~~~s~~~L~~i 49 (66)
T PF03118_consen 24 YNCLKRAGIHTVGDLVKYSEEDLLKI 49 (66)
T ss_dssp HHHHHCTT--BHHHHHCS-HHHHHTS
T ss_pred HHHHHHhCCcCHHHHHhCCHHHHHhC
Confidence 35678899999999999999999874
No 24
>COG2818 Tag 3-methyladenine DNA glycosylase [DNA replication, recombination, and repair]
Probab=86.05 E-value=1.8 Score=27.72 Aligned_cols=41 Identities=27% Similarity=0.498 Sum_probs=31.8
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc----CCCCCchHHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA----LGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~----lGIt~~gh~kkIl~~i~~l~ 49 (62)
|...|. || +.+.++.++++|+.+ .|| .-||.||-..|..-+
T Consensus 57 freaF~--~F-d~~kVA~~~~~dverLl~d~gI--IR~r~KI~A~i~NA~ 101 (188)
T COG2818 57 FREAFH--GF-DPEKVAAMTEEDVERLLADAGI--IRNRGKIKATINNAR 101 (188)
T ss_pred HHHHHh--cC-CHHHHHcCCHHHHHHHHhCcch--hhhHHHHHHHHHHHH
Confidence 555554 57 799999999999875 466 589999998777665
No 25
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=83.95 E-value=3.6 Score=27.75 Aligned_cols=44 Identities=18% Similarity=0.316 Sum_probs=36.2
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
-...+.++||.|++.+...+..+|.+ .|++ ..--.+|++++..+
T Consensus 13 ~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls-~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 13 DIKKLKSAGICTVNGVIMTTRRALCKIKGLS-EAKVDKIKEAASKI 57 (313)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC-HHHHHHHHHHHHhh
Confidence 35688999999999999999999976 6776 67777888766665
No 26
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=82.76 E-value=3.6 Score=27.73 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=34.6
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
....+.++||.|++.+...+..||.+ .||+ ....++++..+..+
T Consensus 13 ~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls-~~~~~~~~~~~~~~ 57 (316)
T TIGR02239 13 DIKKLQEAGLHTVESVAYAPKKQLLEIKGIS-EAKADKILAEAAKL 57 (316)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHHhCCC-HHHHHHHHHHHHHh
Confidence 46789999999999999999999987 5665 55556677666544
No 27
>PTZ00035 Rad51 protein; Provisional
Probab=82.75 E-value=4.2 Score=27.67 Aligned_cols=44 Identities=23% Similarity=0.364 Sum_probs=34.9
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
-...+.++||.|++.+...+..+|.+ .||+ ..--.+|+.....+
T Consensus 35 ~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis-~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 35 DIKKLKEAGICTVESVAYATKKDLCNIKGIS-EAKVEKIKEAASKL 79 (337)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHhhCCC-HHHHHHHHHHHHHh
Confidence 35678999999999999999999976 6776 55666777665554
No 28
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=82.41 E-value=0.85 Score=24.37 Aligned_cols=18 Identities=28% Similarity=0.473 Sum_probs=15.7
Q ss_pred HHHHHcCCHHHHhcCCCC
Q psy10378 16 MEAVVRLTVAELNALGIT 33 (62)
Q Consensus 16 ~~~~~~lt~~dL~~lGIt 33 (62)
--.+..|++..|.++||+
T Consensus 32 r~eL~~lsd~~L~DiGis 49 (63)
T COG5457 32 RRELLRLSDHLLSDIGIS 49 (63)
T ss_pred HHHHHHHhHHHHHHcCCC
Confidence 346789999999999999
No 29
>KOG3678|consensus
Probab=81.95 E-value=2.6 Score=31.25 Aligned_cols=48 Identities=21% Similarity=0.290 Sum_probs=39.4
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHh-cCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELN-ALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~-~lGIt~~gh~kkIl~~i~~l~ 49 (62)
+.+|.=....+|+ +-..+..+|++-+. +.||+++=||-||+.+....+
T Consensus 551 ls~YTY~mlt~Gv-nRSLLssltde~m~naCGI~~~iHR~kl~qA~eta~ 599 (832)
T KOG3678|consen 551 LSVYTYQMLTNGV-NRSLLSSLTDEMMQNACGITNPIHRLKLTQAFETAK 599 (832)
T ss_pred HHHHhHHHhhccc-cHHHHHHhhHHHHHHhcCccchHHHHHHHHHHHhhc
Confidence 3567777888998 68888899998876 789999999999998766543
No 30
>PF03352 Adenine_glyco: Methyladenine glycosylase; InterPro: IPR005019 This family of methyladenine glycosylases includes DNA-3-methyladenine glycosylase I (3.2.2.20 from EC) which acts as a base excision repair enzyme by severing the glycosylic bond of numerous damaged bases. The enzyme is constitutively expressed and is specific for the alkylated 3-methyladenine DNA.; GO: 0008725 DNA-3-methyladenine glycosylase I activity, 0006284 base-excision repair; PDB: 2OFI_A 2OFK_A 2JG6_A 4AIA_E 4AI5_C 4AI4_A 1LMZ_A 1P7M_A 1NKU_A.
Probab=80.25 E-value=4 Score=25.81 Aligned_cols=43 Identities=21% Similarity=0.393 Sum_probs=28.9
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcCCCCC--chHHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNALGITL--VGHQKKIMNSIQAMR 49 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~--~gh~kkIl~~i~~l~ 49 (62)
|...|. || +.+.++.++++|+.++-... .-|++||-..+..-+
T Consensus 51 ~r~aF~--~F-d~~~vA~~~e~~ie~l~~d~~iIRnr~KI~Avi~NA~ 95 (179)
T PF03352_consen 51 FREAFA--GF-DPEKVAKMDEEDIERLMQDPGIIRNRRKIRAVINNAR 95 (179)
T ss_dssp HHHHTG--GG-HHHHHHT--HHHHHHHTTSTTSS--HHHHHHHHHHHH
T ss_pred HHHHHH--CC-CHHHHHcCCHHHHHHHhcCcchhhhHHHHHHHHHHHH
Confidence 445554 57 78999999999999886553 459999997766654
No 31
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=79.91 E-value=6.1 Score=27.11 Aligned_cols=44 Identities=18% Similarity=0.350 Sum_probs=34.1
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
....+.++||.|++.+...+..+|.+ .||+ ..-..+++..+..+
T Consensus 40 ~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is-~~~~~~~~~~~~~~ 84 (342)
T PLN03186 40 DIKKLKDAGIHTVESLAYAPKKDLLQIKGIS-EAKVEKILEAASKL 84 (342)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC-HHHHHHHHHHHHHh
Confidence 35678899999999999999999976 5666 55566677666544
No 32
>KOG3791|consensus
Probab=79.55 E-value=0.95 Score=33.25 Aligned_cols=42 Identities=14% Similarity=0.400 Sum_probs=36.3
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHH
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQ 46 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~ 46 (62)
-+|.+.|.. + +++.+.-+++.+|...||...|-+++.|++-.
T Consensus 488 hKyt~~~~~--t-~~~e~l~ls~~~l~~~Gv~a~g~~~~~L~~~~ 529 (569)
T KOG3791|consen 488 HKYTNALKS--T-TWFELLILSDMKLQHVGVLALGARRKLLKAFS 529 (569)
T ss_pred hhhhccccC--c-cHHHhhccchhhcccchhhhhhHHHhhhcccc
Confidence 467888777 5 79999999999999999999999999997543
No 33
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=78.51 E-value=4.8 Score=26.58 Aligned_cols=44 Identities=20% Similarity=0.318 Sum_probs=35.3
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l 48 (62)
....+..+||.|++.+...+.++|..+ ||+ ..--.+|...+..+
T Consensus 15 rakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg-~k~AekI~e~l~~~ 59 (232)
T PRK12766 15 KAEALREAGFESVEDVRAADQSELAEVDGIG-NALAARIKADVGGL 59 (232)
T ss_pred HHHHHHHcCCCCHHHHHhCCHHHHHHccCCC-HHHHHHHHHHhccc
Confidence 345677889999999999999999998 887 66677777766543
No 34
>KOG4374|consensus
Probab=77.95 E-value=1.7 Score=28.36 Aligned_cols=47 Identities=26% Similarity=0.378 Sum_probs=39.8
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l 48 (62)
++.|...|..+-. ++.++.++++++|..||+.-.|-..+++.++.-.
T Consensus 130 l~s~~~~~~~~~~-~l~~~~t~~~~vl~~L~~lglg~y~~~f~~~evd 176 (216)
T KOG4374|consen 130 LESYIKEFNLQEI-DLQTFGTLTEGVLMELGILGLGAYWKMFEAIEVD 176 (216)
T ss_pred ccccchhhhcchH-hhhhcccccchHHHHHHHHhHHHHHHHHHHHHHH
Confidence 4567778888766 6888999999999999999999999999877654
No 35
>TIGR00624 tag DNA-3-methyladenine glycosylase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.78 E-value=6.2 Score=24.98 Aligned_cols=43 Identities=28% Similarity=0.387 Sum_probs=31.3
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcCCCCC--chHHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNALGITL--VGHQKKIMNSIQAMR 49 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~--~gh~kkIl~~i~~l~ 49 (62)
|...| .|| +.+.++.++++|+.+|=-.. .-|++||-..|..-+
T Consensus 55 fr~aF--~~F-d~~~VA~~~e~~ie~L~~d~~IIRnr~KI~Avi~NA~ 99 (179)
T TIGR00624 55 YRRAF--SGF-DIVKVARMTDADVERLLQDDGIIRNRGKIEATIANAR 99 (179)
T ss_pred HHHHH--cCC-CHHHHhCCCHHHHHHHhcCccchhhHHHHHHHHHHHH
Confidence 44555 457 78999999999997664332 578999987776554
No 36
>PRK01172 ski2-like helicase; Provisional
Probab=75.49 E-value=8.5 Score=28.15 Aligned_cols=43 Identities=12% Similarity=0.261 Sum_probs=33.4
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
...+.++||.|..+++.++.++|.+ +|++ ...-++|+.+.+.+
T Consensus 625 a~~l~~~g~~~~~di~~~~~~~~~~i~~~~-~~~~~~i~~~~~~~ 668 (674)
T PRK01172 625 ARRLYDAGFKTVDDIARSSPERIKKIYGFS-DTLANAIVNRAMKI 668 (674)
T ss_pred HHHHHHcCCCCHHHHHhCCHHHHHHHhccC-HHHHHHHHHHHHHH
Confidence 4567889999999999999999998 4655 56667777665443
No 37
>KOG0249|consensus
Probab=75.43 E-value=5.8 Score=30.45 Aligned_cols=51 Identities=24% Similarity=0.219 Sum_probs=43.2
Q ss_pred chHHHHhhcCcCcHHHHHcCCHHHHh-cCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 3 RYLDNFERGGISSMEAVVRLTVAELN-ALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 3 ~Y~~~f~~~g~~~~~~~~~lt~~dL~-~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
.|...|..+-- +...++.+++.++. ++||..|=|+.|+--+|++++.-.+.
T Consensus 606 ~yva~c~~nVk-sg~im~~lsd~eiq~~igisnplhrlklrLaiqe~~sltsp 657 (916)
T KOG0249|consen 606 WYVAACRANVK-SGAIMSALSDTEIQREIGISNPLHRLKLRLAIQEMVSLTSP 657 (916)
T ss_pred HHHHHHHHHhh-hhHHHHhhhhHHHHhhhcccchhhhhhhHHHHHHHHHhcCC
Confidence 68888887755 78888999999887 89999999999999999999865553
No 38
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=75.30 E-value=7.9 Score=24.66 Aligned_cols=44 Identities=20% Similarity=0.248 Sum_probs=31.8
Q ss_pred chHHHHhhcCcCcHHHHHcCCHHHHhcCCCCC--chHHHHHHHHHHHHH
Q psy10378 3 RYLDNFERGGISSMEAVVRLTVAELNALGITL--VGHQKKIMNSIQAMR 49 (62)
Q Consensus 3 ~Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~--~gh~kkIl~~i~~l~ 49 (62)
.|...|. || +.+.++.++++|+.+|=... .-|++||-..|..-+
T Consensus 55 ~fr~aF~--~F-d~~~VA~~~e~die~Ll~d~~IIRnr~KI~Avi~NA~ 100 (187)
T PRK10353 55 NYRACFH--QF-DPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNAR 100 (187)
T ss_pred HHHHHHc--CC-CHHHHhCCCHHHHHHHhcCchhHHhHHHHHHHHHHHH
Confidence 3555554 57 68999999999998764432 468999987766544
No 39
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=74.80 E-value=10 Score=26.09 Aligned_cols=44 Identities=16% Similarity=0.302 Sum_probs=34.8
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~~l 48 (62)
-...+.++||.|++.++..+..+|.+ .|++ ..-..||+.....+
T Consensus 43 ~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s-~~~~~ki~~~a~~~ 87 (344)
T PLN03187 43 DVKKLQDAGIYTCNGLMMHTKKNLTGIKGLS-EAKVDKICEAAEKL 87 (344)
T ss_pred HHHHHHHcCCCcHHHHHhCCHHHHHHhcCCC-HHHHHHHHHHHHHh
Confidence 35678999999999999999999975 6776 66677777655554
No 40
>KOG4403|consensus
Probab=73.99 E-value=1.4 Score=31.90 Aligned_cols=41 Identities=27% Similarity=0.471 Sum_probs=29.3
Q ss_pred CcchHHHHhhcCcCcHHHHHcCC---HHHH-hcCCCCCchHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLT---VAEL-NALGITLVGHQKKIM 42 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt---~~dL-~~lGIt~~gh~kkIl 42 (62)
|.+|.+.|..+-+ +...+-++- .+=+ ..+||+.+.||+||-
T Consensus 150 LPqyve~fk~~kv-~G~alPRlAv~n~~f~~~~Lgikd~~hrQKlq 194 (575)
T KOG4403|consen 150 LPQYVEAFKAKKV-DGKALPRLAVPNSDFLGKVLGIKDRSHRQKLQ 194 (575)
T ss_pred cHHHHHHHHhccC-CcccccccccCchHHhhhhhccCchHHHHhhh
Confidence 6799999999987 455444332 2211 478999999999974
No 41
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=72.52 E-value=8.2 Score=26.18 Aligned_cols=43 Identities=26% Similarity=0.434 Sum_probs=29.7
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhhc
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSAN 55 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~~ 55 (62)
..+.++|+.++.+++.++.+||..+ ...| + +|+++++.++..+
T Consensus 262 n~Lk~~~I~ti~dL~~~~~~~l~~~--~n~G--~---ksl~ei~~~L~~~ 304 (310)
T PRK05182 262 NCLKRAGINTIGDLVQRTEEELLKT--RNLG--K---KSLEEIKEKLAEL 304 (310)
T ss_pred HHHHHcCCcCHHHHHhCCHHHHhcC--CCCC--h---hhHHHHHHHHHHc
Confidence 4567899999999999999997642 1222 1 2666666666643
No 42
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=70.10 E-value=14 Score=24.28 Aligned_cols=41 Identities=24% Similarity=0.427 Sum_probs=30.6
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSI 45 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i 45 (62)
....+.++||.+++++...+.++|.+ .|++ ...-.+|+..+
T Consensus 11 ~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~-~~~a~~l~~~~ 52 (310)
T TIGR02236 11 TAEKLREAGYDTFEAIAVASPKELSEIAGIS-EGTAAKIIQAA 52 (310)
T ss_pred HHHHHHHcCCCCHHHHHcCCHHHHHhccCCC-HHHHHHHHHHH
Confidence 45788999999999999999999975 4765 33344454443
No 43
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=68.43 E-value=19 Score=23.94 Aligned_cols=42 Identities=21% Similarity=0.361 Sum_probs=31.2
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhc-CCCCCchHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNA-LGITLVGHQKKIMNSIQ 46 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~-lGIt~~gh~kkIl~~i~ 46 (62)
..+.+.++|+.+++++..++.++|.+ .|++ ...-.+|+..+.
T Consensus 18 ~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~-~~~a~~l~~~a~ 60 (317)
T PRK04301 18 TAEKLREAGYDTVEAIAVASPKELSEAAGIG-ESTAAKIIEAAR 60 (317)
T ss_pred HHHHHHHcCCCCHHHHHcCCHHHHHHhcCCC-HHHHHHHHHHHH
Confidence 35788999999999999999999965 5776 344455554443
No 44
>PRK00254 ski2-like helicase; Provisional
Probab=67.70 E-value=13 Score=27.48 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=33.6
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQ 46 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~ 46 (62)
....+.++||.+++.+...+.++|..+ ||. ..--++|.+.+.
T Consensus 657 ~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~-~~~a~~i~~~~~ 699 (720)
T PRK00254 657 RARALYNAGFRSIEDIVNAKPSELLKVEGIG-AKIVEGIFKHLG 699 (720)
T ss_pred HHHHHHHccCCCHHHHHhCCHHHHhcCCCCC-HHHHHHHHHHhc
Confidence 345678899999999999999999998 887 666666665543
No 45
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=63.87 E-value=15 Score=24.69 Aligned_cols=43 Identities=23% Similarity=0.407 Sum_probs=30.2
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhhc
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSAN 55 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~~ 55 (62)
....++|+.++.+++..+.+||.+ |...|- +|+++++.++..+
T Consensus 248 n~Lk~~~I~ti~dL~~~~~~~l~~--~~n~G~-----ksl~ei~~~l~~~ 290 (297)
T TIGR02027 248 NCLKRAGIHTLGELVSKSEEELLK--IKNFGK-----KSLTEIKEKLAEL 290 (297)
T ss_pred hHHHHcCCcCHHHHHhCCHHHHhh--CCCCCh-----hhHHHHHHHHHHc
Confidence 455689999999999999999764 223332 3666676666653
No 46
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=61.73 E-value=11 Score=21.32 Aligned_cols=30 Identities=30% Similarity=0.589 Sum_probs=20.6
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIM 42 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl 42 (62)
-..+|...|+ +.+.++ .+||++ ++|-.++|
T Consensus 15 Lq~nf~~~~l-s~~~ia-------~dL~~s-~~~le~vL 44 (89)
T PF10078_consen 15 LQANFELSGL-SLEQIA-------ADLGTS-PEHLEQVL 44 (89)
T ss_pred HHHHHHHcCC-CHHHHH-------HHhCCC-HHHHHHHH
Confidence 4578888888 677765 355666 66666666
No 47
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=60.47 E-value=19 Score=19.82 Aligned_cols=28 Identities=36% Similarity=0.510 Sum_probs=22.0
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcC----CCC
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNAL----GIT 33 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~l----GIt 33 (62)
..+..-|+-+.+.+...+.++|.++ |..
T Consensus 20 ~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~ 51 (108)
T PF00730_consen 20 RLFERYGFPTPEALAEASEEELRELIRPLGFS 51 (108)
T ss_dssp HHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSH
T ss_pred HHHHHhcCCCHHHHHhCCHHHHHHHhhccCCC
Confidence 3444446669999999999999998 765
No 48
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=58.43 E-value=21 Score=18.74 Aligned_cols=27 Identities=22% Similarity=0.410 Sum_probs=19.8
Q ss_pred cCCHHHHhcCCCCCchHHHHHHHHHHHH
Q psy10378 21 RLTVAELNALGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 21 ~lt~~dL~~lGIt~~gh~kkIl~~i~~l 48 (62)
.+|-.||.+||.. ++--++|+.....+
T Consensus 3 tv~k~dLi~lGf~-~~tA~~IIrqAK~~ 29 (59)
T PF11372_consen 3 TVTKKDLIELGFS-ESTARDIIRQAKAL 29 (59)
T ss_pred ccCHHHHHHcCCC-HHHHHHHHHHHHHH
Confidence 5788999999997 66667776544433
No 49
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=57.57 E-value=16 Score=21.99 Aligned_cols=36 Identities=17% Similarity=0.397 Sum_probs=29.3
Q ss_pred cCcHHHHHcCCHHHHh----cCCCCCchHHHHHHHHHHHHH
Q psy10378 13 ISSMEAVVRLTVAELN----ALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 13 ~~~~~~~~~lt~~dL~----~lGIt~~gh~kkIl~~i~~l~ 49 (62)
..|++.+..|++++++ +.|.+ ....+|+..|++.||
T Consensus 90 ~~tLe~Llemsd~el~~~l~~~g~~-~EE~rRL~~Al~~LR 129 (129)
T PF13543_consen 90 VLTLEALLEMSDEELKEILNRCGAR-EEECRRLCRALSNLR 129 (129)
T ss_pred hcCHHHHHhCCHHHHHHHHHHhCCC-HHHHHHHHHHHHhcC
Confidence 4589999999999986 56887 788899888887664
No 50
>KOG0507|consensus
Probab=56.91 E-value=2.1 Score=32.76 Aligned_cols=51 Identities=12% Similarity=0.311 Sum_probs=41.0
Q ss_pred CcchHHHHhhcCcCcH-HHHH--cCCHHHHhcCCCCCchHHHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSM-EAVV--RLTVAELNALGITLVGHQKKIMNSIQAMRTQ 51 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~-~~~~--~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~ 51 (62)
+.+|.++-..||++.. ..+. .|-.+++.++|+-.+.|+++++.++..++..
T Consensus 309 ~~~~q~~~~~n~~~gy~~sl~sn~i~~qpps~~g~~~~l~~~ks~~a~ss~p~e 362 (854)
T KOG0507|consen 309 LPQYQPKLSQNGFDGYPHSLGSNVIEYQPPSIIGILRSLHRQKSLQALSSLPKE 362 (854)
T ss_pred ccccccccccccccccCccccccchhhCCHHHhccCCCCCcchhhhhhhccccc
Confidence 3578888888888666 3333 6788899999999999999999998887643
No 51
>PF02888 CaMBD: Calmodulin binding domain; InterPro: IPR004178 Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM) []. CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known []. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.; GO: 0005516 calmodulin binding, 0015269 calcium-activated potassium channel activity, 0006813 potassium ion transport, 0016021 integral to membrane; PDB: 1G4Y_B 1QX7_D 3SJQ_D 2PNV_A 1KKD_A.
Probab=55.56 E-value=15 Score=20.32 Aligned_cols=15 Identities=33% Similarity=0.649 Sum_probs=13.2
Q ss_pred chHHHHHHHHHHHHH
Q psy10378 35 VGHQKKIMNSIQAMR 49 (62)
Q Consensus 35 ~gh~kkIl~~i~~l~ 49 (62)
.-||++.|.+|..++
T Consensus 38 R~HQRkfL~AI~~lR 52 (77)
T PF02888_consen 38 RKHQRKFLQAIHRLR 52 (77)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 569999999999986
No 52
>PHA01516 hypothetical protein
Probab=47.99 E-value=9 Score=21.64 Aligned_cols=14 Identities=29% Similarity=0.337 Sum_probs=12.6
Q ss_pred cCCHHHHhcCCCCC
Q psy10378 21 RLTVAELNALGITL 34 (62)
Q Consensus 21 ~lt~~dL~~lGIt~ 34 (62)
.+|++||.+||.|.
T Consensus 61 ~ltd~dleem~ltd 74 (98)
T PHA01516 61 SLTDQDLEEMELTD 74 (98)
T ss_pred hcchhHHHHccchh
Confidence 78999999999984
No 53
>PRK02362 ski2-like helicase; Provisional
Probab=47.14 E-value=33 Score=25.52 Aligned_cols=39 Identities=13% Similarity=0.128 Sum_probs=32.3
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHH
Q psy10378 7 NFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQA 47 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~ 47 (62)
.+.++|+.|++++..++.++|..+ +. ..-.++|+.++..
T Consensus 667 ~l~~~gi~s~~dl~~~~~~~l~~~-~g-~~~~~~i~~~~~~ 705 (737)
T PRK02362 667 RLYNAGIESRADLRAADKSVVLAI-LG-EKIAENILEQAGR 705 (737)
T ss_pred HHHHcCCCCHHHHHhCCHHHHHHH-HC-HHHHHHHHHHhCc
Confidence 445699999999999999999998 54 6678888888763
No 54
>cd08541 SAM_PNT-FLI-1 Sterile alpha motif (SAM)/Pointed domain of friend leukemia integration 1 transcription activator. SAM Pointed domain of FLI-1 (Friend Leukemia Integration) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The FLI-1 protein participates in regulation of cellular differentiation, proliferation, and survival. The Fli-1 gene was initially described in Friend virus-induced erythroleukemias as a site for virus integration. It is highly expressed in hematopoietic tissues and at lower level in lungs, heart, and ovaries. Fli-1 is a proto-oncogene implicated in Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=46.86 E-value=54 Score=18.60 Aligned_cols=36 Identities=3% Similarity=0.084 Sum_probs=27.1
Q ss_pred cHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHh
Q psy10378 15 SMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQL 52 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~ 52 (62)
++..+|.|+.+|..++.-...| .-+.+.++.||.-.
T Consensus 50 ~Gk~LC~LskedF~~~~p~~~g--diLw~HL~~Lr~~~ 85 (91)
T cd08541 50 DGKELCKMNKEDFLRATSLYNT--EVLLSHLSYLRESS 85 (91)
T ss_pred CHHHHHhCCHHHHHHHcCCCcc--HHHHHHHHHHHhCc
Confidence 7889999999999987655566 45567777777543
No 55
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=45.33 E-value=15 Score=17.42 Aligned_cols=16 Identities=19% Similarity=0.333 Sum_probs=13.2
Q ss_pred cHHHHHcCCHHHHhcC
Q psy10378 15 SMEAVVRLTVAELNAL 30 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~l 30 (62)
+++.+...+.+||..+
T Consensus 6 DLeFL~~cs~edL~~L 21 (35)
T PF13099_consen 6 DLEFLAECSNEDLKDL 21 (35)
T ss_pred chHHHHHCCHHHHHHH
Confidence 6788889999998764
No 56
>PTZ00096 40S ribosomal protein S15; Provisional
Probab=44.20 E-value=14 Score=22.77 Aligned_cols=23 Identities=30% Similarity=0.514 Sum_probs=19.6
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 7 NFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
.|.--|+ ++|++..|+.+||.+|
T Consensus 14 ~f~yRG~-~l~~L~~m~~~e~~~L 36 (143)
T PTZ00096 14 KFTYRGV-ELEKLLALPEEELVEL 36 (143)
T ss_pred eeeeecC-CHHHHHcCCHHHHHHH
Confidence 5667789 7999999999999764
No 57
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=43.83 E-value=5.2 Score=24.12 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=17.6
Q ss_pred cCcHHHHHcCCHHHHhcCCCC
Q psy10378 13 ISSMEAVVRLTVAELNALGIT 33 (62)
Q Consensus 13 ~~~~~~~~~lt~~dL~~lGIt 33 (62)
|.++-..|.|+++|++.||+.
T Consensus 26 Y~~a~a~~~inp~D~~~Lgv~ 46 (128)
T COG1153 26 YFNACAVCEINPEDMKQLGVS 46 (128)
T ss_pred hhhheeEEEECHHHHHHhCCC
Confidence 445566789999999999997
No 58
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=43.26 E-value=73 Score=23.62 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=32.6
Q ss_pred hHHHHhhcCc-CcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHHH
Q psy10378 4 YLDNFERGGI-SSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 4 Y~~~f~~~g~-~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l~ 49 (62)
-...|.++|+ .+..++..|+.+||..+ |.. .---++|+++|+.-|
T Consensus 437 ~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfg-eks~~nll~aIe~sk 483 (562)
T PRK08097 437 TWRALHQTGLFEHLFSWLALTPEQLANTPGIG-KARAEQLWHQFNLAR 483 (562)
T ss_pred HHHHHHHcCCcCCHHHHhcCCHHHHhcCcCcc-HHHHHHHHHHHHHHc
Confidence 3566788885 88999999999999988 333 334557777776544
No 59
>PRK14973 DNA topoisomerase I; Provisional
Probab=43.08 E-value=85 Score=24.69 Aligned_cols=40 Identities=18% Similarity=0.333 Sum_probs=33.2
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHH
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNS 44 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~ 44 (62)
-.+|...|+.++..++..+..+|+..|++-.-++.-+-.+
T Consensus 757 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~sE~~~~~~~~~a 796 (936)
T PRK14973 757 MKALISSGINDIAALARADPADLKKAGLSEAEAASLLAEA 796 (936)
T ss_pred HHHHHhcCcchHHHHhhCCHHHHHHcCCCHHHHHHHHHHH
Confidence 3578899999999999999999999999976665554444
No 60
>PF13735 tRNA_NucTran2_2: tRNA nucleotidyltransferase domain 2 putative; PDB: 1MIY_A 1MIV_B 1MIW_B.
Probab=38.69 E-value=34 Score=19.90 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=16.9
Q ss_pred cCCHHHHhc-CCCCCchH-HHHHHHHHHH
Q psy10378 21 RLTVAELNA-LGITLVGH-QKKIMNSIQA 47 (62)
Q Consensus 21 ~lt~~dL~~-lGIt~~gh-~kkIl~~i~~ 47 (62)
.+|+.||.+ +|+. ||. -.+||+.+..
T Consensus 104 aI~G~DLi~~lg~~-pGp~iG~iL~~l~~ 131 (149)
T PF13735_consen 104 AINGNDLIEALGIK-PGPWIGEILERLLE 131 (149)
T ss_dssp SS-HHHHHHHHT---SSCHHHHHHHHHHH
T ss_pred CcCHHHHHHHcCCC-CCcHHHHHHHHHHH
Confidence 689999999 6997 565 5677766544
No 61
>PF11737 DUF3300: Protein of unknown function (DUF3300); InterPro: IPR021728 This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein.
Probab=37.56 E-value=12 Score=24.78 Aligned_cols=29 Identities=24% Similarity=0.434 Sum_probs=25.0
Q ss_pred hcCCCCCchHHHHHHHHHHHHHHHhhhcc
Q psy10378 28 NALGITLVGHQKKIMNSIQAMRTQLSANL 56 (62)
Q Consensus 28 ~~lGIt~~gh~kkIl~~i~~l~~~~~~~~ 56 (62)
..||=.....++.++++||.||.+...-+
T Consensus 86 q~LGdAfl~q~~dVm~aIQ~LR~~A~~~G 114 (237)
T PF11737_consen 86 QQLGDAFLAQPQDVMDAIQRLRQRAQAAG 114 (237)
T ss_pred HHHHHHHHhCHHHHHHHHHHHHHHHHHcC
Confidence 47888888999999999999998887543
No 62
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=37.38 E-value=97 Score=23.24 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=31.4
Q ss_pred HHhhcC-cCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHHH
Q psy10378 7 NFERGG-ISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 7 ~f~~~g-~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l~ 49 (62)
.|.++| +.+++++..++.++|..+ |+. ..-..+|+++|+.-+
T Consensus 447 ~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG-~Ksa~nIl~~Ie~sk 490 (652)
T TIGR00575 447 QLFEKKLVRSVADLYALKKEDLLELEGFG-EKSAQNLLNAIEKSK 490 (652)
T ss_pred HHHHcCCcCCHHHHHhcCHHHHhhccCcc-HHHHHHHHHHHHHhc
Confidence 344444 578999999999999988 554 556778998888654
No 63
>cd08531 SAM_PNT-ERG_FLI-1 Sterile alpha motif (SAM)/Pointed domain of ERG (Ets related gene) and FLI-1 (Friend leukemia integration 1) transcription factors. SAM Pointed domain of ERG/FLI-1 subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The ERG and FLI regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. They are proto-oncogenes implicated in cancer development such as myeloid leukemia, Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=37.37 E-value=70 Score=17.33 Aligned_cols=34 Identities=9% Similarity=0.205 Sum_probs=22.5
Q ss_pred cHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHH
Q psy10378 15 SMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
++..+|.||.+|..+..-...| .-+.+.++.||.
T Consensus 38 ~Gk~LC~lt~edF~~~~~~~~G--diL~~hL~~Lr~ 71 (75)
T cd08531 38 DGKELCKMTKEDFLRLTSAYNA--DVLLSHLSYLRE 71 (75)
T ss_pred ChHHHHcCCHHHHHHHcCCCcc--hHHHHHHHHHHh
Confidence 6788999999999876322233 334466666664
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=37.05 E-value=1.1e+02 Score=22.98 Aligned_cols=42 Identities=19% Similarity=0.345 Sum_probs=30.5
Q ss_pred HHhh-cCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHHH
Q psy10378 7 NFER-GGISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 7 ~f~~-~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l~ 49 (62)
.|.+ .++.+++++..++.++|..+ |+. .--..+|+++|+..+
T Consensus 460 ~L~~~g~I~~i~DL~~L~~~~L~~l~gfG-~Ksa~~ll~~Ie~sk 503 (665)
T PRK07956 460 QLFEKGLIHDPADLFKLTAEDLLGLEGFG-EKSAQNLLDAIEKSK 503 (665)
T ss_pred HHHHcCCCCCHHHHHhcCHHHHhcCcCcc-hHHHHHHHHHHHHhh
Confidence 3444 44678999999999999887 443 344568999988665
No 65
>KOG0249|consensus
Probab=36.41 E-value=25 Score=27.20 Aligned_cols=48 Identities=15% Similarity=0.229 Sum_probs=41.4
Q ss_pred CcchHHHHhhcCcCcHHHHHcCCHHHHh-cCCCCCchHHHHHHHHHHHHH
Q psy10378 1 MARYLDNFERGGISSMEAVVRLTVAELN-ALGITLVGHQKKIMNSIQAMR 49 (62)
Q Consensus 1 L~~Y~~~f~~~g~~~~~~~~~lt~~dL~-~lGIt~~gh~kkIl~~i~~l~ 49 (62)
|.||..-|++.=+ +..-+=+++..||. .+++...=||.-|..+|--|+
T Consensus 687 LpQYrsyFme~Lv-DARMLdhLsKkdLr~~LkmvdsFHr~Sl~yGImcLk 735 (916)
T KOG0249|consen 687 LPQYRSYFMECLV-DARMLDHLSKKDLRGHLKMVDSFHRTSLQYGIMCLK 735 (916)
T ss_pred chHHHHHHHHHHH-HHHHHHhhhHHHHHHHHHHHHHHHHHHHHhhhhhhh
Confidence 6799999999755 67888899999998 799999999999988887664
No 66
>PRK04038 rps19p 30S ribosomal protein S19P; Provisional
Probab=34.84 E-value=24 Score=21.46 Aligned_cols=23 Identities=22% Similarity=0.507 Sum_probs=19.7
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 7 NFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
.|.-.|+ ++|++..|+.++|..|
T Consensus 6 ~f~yrG~-~l~~L~~m~~~~~~~l 28 (134)
T PRK04038 6 EFTYRGY-TLEELQEMSLEEFAEL 28 (134)
T ss_pred eeeeccc-CHHHHHcCCHHHHHHH
Confidence 5667789 7999999999999875
No 67
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=34.57 E-value=52 Score=21.41 Aligned_cols=41 Identities=24% Similarity=0.327 Sum_probs=26.4
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHH
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSI 45 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i 45 (62)
...+...|+.+++++..++.+++..+--..+..-+.|.+.+
T Consensus 161 ~~~l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~ 201 (314)
T PF02889_consen 161 LKKLEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVA 201 (314)
T ss_dssp HHHHHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHH
T ss_pred HHHHhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHH
Confidence 45677888889999999999999987654455555555444
No 68
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=34.43 E-value=1.1e+02 Score=23.26 Aligned_cols=43 Identities=23% Similarity=0.423 Sum_probs=29.6
Q ss_pred HHHHhhcCc-CcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHH
Q psy10378 5 LDNFERGGI-SSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 5 ~~~f~~~g~-~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l 48 (62)
...|.++|+ .++.++..++.+||..+ |+. .---++|+++|+.-
T Consensus 475 i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g-~Ksa~~Ll~~Ie~s 519 (689)
T PRK14351 475 VQQLVDAGLVESLADLYDLTVADLAELEGWG-ETSAENLLAELEAS 519 (689)
T ss_pred HHHHHHcCCCCCHHHHHHcCHHHHhcCcCcc-hhHHHHHHHHHHHH
Confidence 455666664 68999999999999877 333 22334777777644
No 69
>PRK12277 50S ribosomal protein L13e; Provisional
Probab=34.32 E-value=55 Score=18.38 Aligned_cols=45 Identities=22% Similarity=0.402 Sum_probs=29.9
Q ss_pred cCcCcHHHH--HcCCHHHHhcCCCCCchHHHHHH--HHHHHHHHHhhhccC
Q psy10378 11 GGISSMEAV--VRLTVAELNALGITLVGHQKKIM--NSIQAMRTQLSANLS 57 (62)
Q Consensus 11 ~g~~~~~~~--~~lt~~dL~~lGIt~~gh~kkIl--~~i~~l~~~~~~~~~ 57 (62)
-|| |++.+ +.|+...=.-+||. .-||++=. ..++.|+.-.+..++
T Consensus 32 RGF-sl~ELkaaGi~~~~ArtiGI~-VD~RRrn~~~eNVerLk~y~skL~~ 80 (83)
T PRK12277 32 RGF-SIGELEAAGLDIKNARKLGIR-VDKRRKTVHEENVEALKKFLEQLGN 80 (83)
T ss_pred CCc-CHHHHHHcCCCHHHhcccCee-ecccccCCCHHHHHHHHHHHHHhcc
Confidence 467 56654 36788877888887 77766533 467777766555543
No 70
>KOG0898|consensus
Probab=34.29 E-value=29 Score=21.42 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=19.8
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
..|.--|+ ++|++++|+-+||.++
T Consensus 20 rkftyrGV-dld~Lldms~~~~~~l 43 (152)
T KOG0898|consen 20 RKFTYRGV-DLDQLLDMSTEQLVKL 43 (152)
T ss_pred hhccccCC-CHHHHhcCCHHHHHHH
Confidence 35667788 7999999999999765
No 71
>PF13351 DUF4099: Protein of unknown function (DUF4099)
Probab=32.81 E-value=27 Score=19.19 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=12.1
Q ss_pred HcCCHHHHhcCCCC
Q psy10378 20 VRLTVAELNALGIT 33 (62)
Q Consensus 20 ~~lt~~dL~~lGIt 33 (62)
..+.++.|..+||+
T Consensus 4 ~~i~w~~L~~~Gi~ 17 (85)
T PF13351_consen 4 EEIPWEELEKFGIS 17 (85)
T ss_pred hHCCHHHHHHcCCC
Confidence 35789999999999
No 72
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=32.73 E-value=94 Score=20.26 Aligned_cols=41 Identities=20% Similarity=0.373 Sum_probs=27.9
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHH
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQ 46 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~ 46 (62)
...+...|+.+++++..++.+++..+ |.. ...-+.|.+.++
T Consensus 164 ~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~-~~~~~~i~~~~~ 205 (312)
T smart00611 164 LKRLEKKKVLSLEDLLELEDEERGELLGLL-DAEGERVYKVLS 205 (312)
T ss_pred HHHHHhCCCCCHHHHHhcCHHHHHHHHcCC-HHHHHHHHHHHH
Confidence 45566778889999999999888866 443 344555555443
No 73
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=32.02 E-value=44 Score=20.70 Aligned_cols=24 Identities=25% Similarity=0.232 Sum_probs=20.0
Q ss_pred HHHHhhcCcCcHHHHHcCC-HHHHhc
Q psy10378 5 LDNFERGGISSMEAVVRLT-VAELNA 29 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt-~~dL~~ 29 (62)
..+|.+.|- |+..+.+++ .++|..
T Consensus 13 ~~~f~~~Gg-sl~~l~~~~~~~~l~~ 37 (157)
T PRK15363 13 TMRFFRRGG-SLRMLLDDDVTQPLNT 37 (157)
T ss_pred HHHHHHcCC-cHHHHHCCChHHHHHH
Confidence 457888888 899999999 888875
No 74
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=31.92 E-value=43 Score=23.01 Aligned_cols=42 Identities=14% Similarity=0.288 Sum_probs=29.8
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
....++++.++.++...|.+||.++ ...| | +|+.+++.++..
T Consensus 276 NcLk~a~I~ti~dL~~~s~~dLl~i--kN~G--k---KSl~EI~~~L~~ 317 (327)
T CHL00013 276 NCLKRANIHTLLDLLNYSQEDLLKI--KNFG--Q---KSAKEVLEALQK 317 (327)
T ss_pred hhhhhcCccCHHHHHhcCHHHHhhh--hccC--H---hHHHHHHHHHHH
Confidence 3567789999999999999998764 3333 2 366666666643
No 75
>PF08620 RPAP1_C: RPAP1-like, C-terminal; InterPro: IPR013929 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.
Probab=31.50 E-value=90 Score=16.92 Aligned_cols=35 Identities=6% Similarity=0.215 Sum_probs=22.4
Q ss_pred hcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHh
Q psy10378 10 RGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQL 52 (62)
Q Consensus 10 ~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~ 52 (62)
.+|| |+.+++.++.+ +.++.|--.+.-+..+-.+.
T Consensus 36 ~aGY-Ti~El~~L~RS-------sv~~QR~~al~~L~~Il~~~ 70 (73)
T PF08620_consen 36 AAGY-TIQELFHLSRS-------SVPSQRCIALQTLGRILYRA 70 (73)
T ss_pred cCCc-CHHHHHHHHhc-------CcHHHHHHHHHHHHHHHHHH
Confidence 5689 79999988865 34555555555555554443
No 76
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=30.58 E-value=1.6e+02 Score=20.72 Aligned_cols=38 Identities=16% Similarity=0.383 Sum_probs=27.3
Q ss_pred cCcHHHHHcCCHHHHhcC-CCCCchHHHHHHHHHHHHHHH
Q psy10378 13 ISSMEAVVRLTVAELNAL-GITLVGHQKKIMNSIQAMRTQ 51 (62)
Q Consensus 13 ~~~~~~~~~lt~~dL~~l-GIt~~gh~kkIl~~i~~l~~~ 51 (62)
|.++..++..+.+||.++ ||. +.--+.|.+.+.++..+
T Consensus 307 FGSL~~Il~As~eeL~~VeGIG-e~rA~~I~e~l~Rl~e~ 345 (352)
T PRK13482 307 FGSLQGLLAASIEDLDEVEGIG-EVRARAIREGLSRLAEQ 345 (352)
T ss_pred cCCHHHHHcCCHHHHhhCCCcC-HHHHHHHHHHHHHHHHH
Confidence 458999999999999876 666 44444466666666544
No 77
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=30.14 E-value=69 Score=15.93 Aligned_cols=48 Identities=17% Similarity=0.396 Sum_probs=23.9
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHH-HHHHHHHHHhhh
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIM-NSIQAMRTQLSA 54 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl-~~i~~l~~~~~~ 54 (62)
+.-.+...|+ |++.+..+- ++.+-|-........++ .-+..+..++.+
T Consensus 6 ~I~~~r~lGf-sL~eI~~~l--~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~ 54 (65)
T PF09278_consen 6 FIRRLRELGF-SLEEIRELL--ELYDQGDPPCADRRALLEEKLEEIEEQIAE 54 (65)
T ss_dssp HHHHHHHTT---HHHHHHHH--HHCCSHCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCC-CHHHHHHHH--hccCCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3456777888 788777665 44333333333333333 445555555544
No 78
>PF08861 DUF1828: Domain of unknown function DUF1828; InterPro: IPR014960 These proteins are functionally uncharacterised.
Probab=30.07 E-value=55 Score=17.83 Aligned_cols=24 Identities=38% Similarity=0.565 Sum_probs=16.9
Q ss_pred HHHHhcCCCCC--chHHHHHHHHHHH
Q psy10378 24 VAELNALGITL--VGHQKKIMNSIQA 47 (62)
Q Consensus 24 ~~dL~~lGIt~--~gh~kkIl~~i~~ 47 (62)
-.+|...|+.. .+.|+++++++..
T Consensus 31 l~~L~~~G~~~~~s~~R~~~l~~il~ 56 (90)
T PF08861_consen 31 LMNLSSSGIDIDRSKKRKKILNSILN 56 (90)
T ss_pred HHhHhHcCCccccchHHHHHHHHHHH
Confidence 34566678876 5889998887643
No 79
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=29.84 E-value=62 Score=18.15 Aligned_cols=52 Identities=12% Similarity=0.177 Sum_probs=35.5
Q ss_pred cchHHHHhhc-CcCcHHHH---HcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhh
Q psy10378 2 ARYLDNFERG-GISSMEAV---VRLTVAELNALGITLVGHQKKIMNSIQAMRTQLS 53 (62)
Q Consensus 2 ~~Y~~~f~~~-g~~~~~~~---~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~ 53 (62)
.+|.+.|..+ ++..+..+ +.+|+.++..+-...++.+.++..-+..++.+..
T Consensus 7 ~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i~~~~~~~~eq~~qmL~~W~~~~G 62 (96)
T cd08315 7 RRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVAKANERVTREQLYQMLLTWVNKTG 62 (96)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHhhC
Confidence 4566666443 34456655 4799999999888888877777777666665554
No 80
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=29.83 E-value=58 Score=19.84 Aligned_cols=29 Identities=14% Similarity=0.198 Sum_probs=23.1
Q ss_pred chHHHHhhcCcCcHHHHHcCCHHHHhcCC
Q psy10378 3 RYLDNFERGGISSMEAVVRLTVAELNALG 31 (62)
Q Consensus 3 ~Y~~~f~~~g~~~~~~~~~lt~~dL~~lG 31 (62)
.|...+...|+.+..++..+|..|+..+-
T Consensus 78 k~e~~Ln~~GI~tfaQIAAwt~~di~~id 106 (133)
T COG3743 78 KLEKVLNELGIFTFAQIAAWTRADIAWID 106 (133)
T ss_pred HHHHHHHHcCCccHHHHHhcCHHHHHHHH
Confidence 35667888898899999999999887543
No 81
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=29.83 E-value=67 Score=15.77 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=13.4
Q ss_pred CCHHHHhcC-CCCCchHHHHHHH
Q psy10378 22 LTVAELNAL-GITLVGHQKKIMN 43 (62)
Q Consensus 22 lt~~dL~~l-GIt~~gh~kkIl~ 43 (62)
||.+||.+| |-..+..|.+.|.
T Consensus 3 LT~~El~elTG~k~~~~Q~~~L~ 25 (47)
T PF13986_consen 3 LTDEELQELTGYKRPSKQIRWLR 25 (47)
T ss_pred CCHHHHHHHHCCCCHHHHHHHHH
Confidence 567777765 4445666666554
No 82
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=29.30 E-value=1.6e+02 Score=21.27 Aligned_cols=39 Identities=18% Similarity=0.125 Sum_probs=28.8
Q ss_pred hHHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHH
Q psy10378 4 YLDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIM 42 (62)
Q Consensus 4 Y~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl 42 (62)
..+.+..+|+++++.+...+.++|..+.--.......+.
T Consensus 368 ~~~~l~~~g~~~~e~~~~~~~~el~~i~~~~ee~~~~l~ 406 (470)
T PRK09202 368 IAQLLVEEGFSSLEELAYVPVEELLEIEGFDEETVEELR 406 (470)
T ss_pred HHHHHHHcCcccHHHHhcCCHHHHhhccCCCHHHHHHHH
Confidence 356788999999999999999999876533344443333
No 83
>PF05105 Phage_holin_4: Holin family ; InterPro: IPR006480 This group of sequences describe one of the many mutually dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species []. This entry is represented by the Bacteriophage phi-29, Gp14 (holin). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.65 E-value=54 Score=18.74 Aligned_cols=23 Identities=9% Similarity=0.329 Sum_probs=14.9
Q ss_pred HHHhcCCCCCchHHHHHHHHHHHHHH
Q psy10378 25 AELNALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 25 ~dL~~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
|.+.++|+..|. .+.+.++.+++
T Consensus 94 EN~~~~G~~iP~---~l~~~l~~l~~ 116 (118)
T PF05105_consen 94 ENLAEMGVPIPK---WLKKFLKQLKD 116 (118)
T ss_pred HHHHHhCCCchH---HHHHHHHHHhc
Confidence 677889998884 44444455543
No 84
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=28.23 E-value=52 Score=21.53 Aligned_cols=24 Identities=21% Similarity=0.498 Sum_probs=15.4
Q ss_pred HHHhhcCcCcHHHHHcCCHHHHhc
Q psy10378 6 DNFERGGISSMEAVVRLTVAELNA 29 (62)
Q Consensus 6 ~~f~~~g~~~~~~~~~lt~~dL~~ 29 (62)
+.|.++|+.+.+++...+.+-|.+
T Consensus 79 e~fkqnGlt~~~~i~~v~~~kL~e 102 (215)
T PF05643_consen 79 ETFKQNGLTDAEDIHAVPPAKLRE 102 (215)
T ss_pred HHHHHcCCCCHHHhccCCHHHHHH
Confidence 456677776666666666665554
No 85
>PF14823 Sirohm_synth_C: Sirohaem biosynthesis protein C-terminal; PDB: 1KYQ_B.
Probab=27.80 E-value=25 Score=18.85 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=11.6
Q ss_pred cHHHHHcCCHHHHhc
Q psy10378 15 SMEAVVRLTVAELNA 29 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~ 29 (62)
++++++.|+++|+.+
T Consensus 43 ~l~~l~~l~~~d~~~ 57 (70)
T PF14823_consen 43 SLEELAELDDEDMEN 57 (70)
T ss_dssp HHHHGGGB-HHHHHH
T ss_pred CHHHHHHCCHHHHHH
Confidence 688899999998865
No 86
>KOG0507|consensus
Probab=27.74 E-value=19 Score=27.84 Aligned_cols=37 Identities=11% Similarity=0.013 Sum_probs=29.8
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHH
Q psy10378 7 NFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMN 43 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~ 43 (62)
...+++|.....+.++++++|.+.++++.||+++-..
T Consensus 508 ~~~d~ty~nsm~i~dlr~t~ltedaeaklg~n~~~sl 544 (854)
T KOG0507|consen 508 QYPDKTYLNSMLIKDLRGTELTEDAEAKLGLNQSKSL 544 (854)
T ss_pred ccchhhhhcchhhhhcccccccchhhhhccccccchH
Confidence 3455677778889999999999999999998776443
No 87
>PF10195 Phospho_p8: DNA-binding nuclear phosphoprotein p8; InterPro: IPR018792 P8 is a short 80-82 amino acid protein that is conserved from nematodes to humans. It carries at least one protein kinase C domain suggesting a possible role in signal transduction and it is thought to be a phosphoprotein, but the sites of phosphorylation and the kinases involved remain to be determined [].
Probab=27.36 E-value=54 Score=17.26 Aligned_cols=15 Identities=33% Similarity=0.612 Sum_probs=11.4
Q ss_pred CCchHHHHHHHHHHH
Q psy10378 33 TLVGHQKKIMNSIQA 47 (62)
Q Consensus 33 t~~gh~kkIl~~i~~ 47 (62)
.+.||-+||+.-++.
T Consensus 41 ~P~Gh~RKiv~kl~N 55 (60)
T PF10195_consen 41 SPGGHERKIVTKLQN 55 (60)
T ss_pred CCCchHHHHHHHHHh
Confidence 357999999976654
No 88
>KOG4279|consensus
Probab=26.29 E-value=78 Score=25.18 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=39.8
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
...|..++|+-.+.+--+|.+||..+|+. .|--=||.++|-..|.+-..
T Consensus 1169 i~lilne~fT~~d~l~yvtrddL~~l~lr-gGm~criwraIi~~R~~qtp 1217 (1226)
T KOG4279|consen 1169 IALILNEAFTLSDMLYYVTRDDLLSLGLR-GGMSCRIWRAIIEVRERQTP 1217 (1226)
T ss_pred HHHHHhccccHHHHHHHhhHhhHhhhccc-CceeehHHHHHHHHHccCCc
Confidence 45678889955555668999999999998 89999999999888876543
No 89
>PF01698 FLO_LFY: Floricaula / Leafy protein; InterPro: IPR002910 This family consists of various plant development proteins which are homologues of Floricaula (FLO) and leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2VY1_A 2VY2_A.
Probab=26.24 E-value=22 Score=25.20 Aligned_cols=42 Identities=24% Similarity=0.385 Sum_probs=0.0
Q ss_pred hhcCcCcHHHHHcCCHHHHhcCCCCC---------chHHHHHHHHHHHHHHH
Q psy10378 9 ERGGISSMEAVVRLTVAELNALGITL---------VGHQKKIMNSIQAMRTQ 51 (62)
Q Consensus 9 ~~~g~~~~~~~~~lt~~dL~~lGIt~---------~gh~kkIl~~i~~l~~~ 51 (62)
.+-|| |+..+.+|++++|.+|=-++ +|.|--|-.+|..=|..
T Consensus 69 aElGF-TvsTLl~M~deELDdmM~sL~~ifRwdLLVGERYGIKAAvRAERRR 119 (386)
T PF01698_consen 69 AELGF-TVSTLLNMTDEELDDMMNSLSQIFRWDLLVGERYGIKAAVRAERRR 119 (386)
T ss_dssp ----------------------------------------------------
T ss_pred HHhcc-cHHHHhcccHHHHHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHHHH
Confidence 45577 78889999999999874432 45555555565544433
No 90
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=26.17 E-value=61 Score=19.82 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=21.7
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcCCCCCchH
Q psy10378 7 NFERGGISSMEAVVRLTVAELNALGITLVGH 37 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh 37 (62)
.|.+.-|..+..+..-....|.+|||..-+.
T Consensus 94 ~fD~kV~~a~~~m~~~~~~~L~~LgVPfF~~ 124 (150)
T PF10454_consen 94 KFDEKVYKASKQMSKEQQAELKELGVPFFYI 124 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCeeeC
Confidence 4555555566677777888999999976443
No 91
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=26.09 E-value=1.2e+02 Score=16.55 Aligned_cols=24 Identities=29% Similarity=0.515 Sum_probs=16.6
Q ss_pred CHHHHh-cCCCCCchHHHHHHHHHHHHHH
Q psy10378 23 TVAELN-ALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 23 t~~dL~-~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
|.++|. .+|++ |..|-+.|+.||+
T Consensus 21 SGe~La~~LgiS----RtaVwK~Iq~Lr~ 45 (79)
T COG1654 21 SGEKLAEELGIS----RTAVWKHIQQLRE 45 (79)
T ss_pred cHHHHHHHHCcc----HHHHHHHHHHHHH
Confidence 444443 67887 6777888888874
No 92
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=25.44 E-value=1.3e+02 Score=16.70 Aligned_cols=35 Identities=14% Similarity=0.343 Sum_probs=24.6
Q ss_pred HHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhh
Q psy10378 18 AVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLS 53 (62)
Q Consensus 18 ~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~ 53 (62)
.++..-.+-|.++|+. ...++.++..++.++..+.
T Consensus 84 ~~~~~~~~al~~~~v~-~~~~~~~~~~~~~~~~~i~ 118 (120)
T PF01152_consen 84 RWLELLKQALDELGVP-EELIDELLARLESLRDDIV 118 (120)
T ss_dssp HHHHHHHHHHHHTTCT-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCC-HHHHHHHHHHHHHHHHHhc
Confidence 3445555667888886 6678888888888777664
No 93
>COG4380 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.12 E-value=41 Score=21.63 Aligned_cols=26 Identities=15% Similarity=0.414 Sum_probs=20.7
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
.+.|.++|.++..++.......|.++
T Consensus 77 eETFkQNGlT~AgDih~v~paKL~qI 102 (216)
T COG4380 77 EETFKQNGLTNAGDIHAVRPAKLHQI 102 (216)
T ss_pred HHHHHHcCCCcccccccCCHHHHHHH
Confidence 46889999988888888888777654
No 94
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=25.04 E-value=81 Score=20.36 Aligned_cols=37 Identities=22% Similarity=0.308 Sum_probs=26.4
Q ss_pred cCCHHHH-hcCCCCCchHHHHHHHHHHHHHHHhhhccC
Q psy10378 21 RLTVAEL-NALGITLVGHQKKIMNSIQAMRTQLSANLS 57 (62)
Q Consensus 21 ~lt~~dL-~~lGIt~~gh~kkIl~~i~~l~~~~~~~~~ 57 (62)
.+|..++ ..+||+...-++++-.+++.|+..+...++
T Consensus 228 ~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~~ 265 (268)
T PRK06288 228 DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEIKK 265 (268)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4444444 367998666666666899999999887765
No 95
>cd08538 SAM_PNT-ESE-2-like Sterile alpha motif (SAM)/Pointed domain of ESE-2 like ETS transcriptional regulators. SAM Pointed domain of ESE-2-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ESE-2 factors are involved in regulation of gene expression in a variety of epithelial (glandular and secretory) cells. ESE-2 mRNA was found in skin keratinocytes, salivary gland, mammary gland, stomach, prostate, and kidneys. The DNA binding consensus motif for ESE-2 consists of a GGA core and AT-rich flanks. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy.
Probab=24.81 E-value=66 Score=17.70 Aligned_cols=38 Identities=24% Similarity=0.186 Sum_probs=23.7
Q ss_pred HhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHH-HHHHHHHH
Q psy10378 8 FERGGISSMEAVVRLTVAELNALGITLVGHQKKIM-NSIQAMRT 50 (62)
Q Consensus 8 f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl-~~i~~l~~ 50 (62)
|..-.. +...+|.|+.+|..+.=-. .|+ || ..++.++-
T Consensus 35 ~~~f~m-~Gk~LC~ms~eeF~~~~p~-~Gd---vLy~~lq~~~~ 73 (78)
T cd08538 35 FCHFNI-SGLQLCSMTQEEFIEAAGI-CGE---YLYFILQNIRT 73 (78)
T ss_pred hhhcCC-CHHHHHcCCHHHHHHHccc-chH---HHHHHHHHHHh
Confidence 344456 6889999999998863211 343 34 55666653
No 96
>cd08540 SAM_PNT-ERG Sterile alpha motif (SAM)/Pointed domain of ERG transcription factor. SAM Pointed domain of ERG subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It may participate in formation of homodimers or heterodimers with ETS-2, Fli-1, ER81, and Pu-1. However, dimeric forms are inactive and SAM Pointed domain is not essential for dimerization, since ER81 and Pu-1 do not have it. In mouse, a regulator of this type binds the ESET histone H3-specific methyltransferase (human homolog is SETDB1), followed by modification of local chromatin structure through histone methylation. ERG regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. The Erg gene is a proto-oncogene. It is a target of chromosomal translocations resulting in fusions with new neighboring genes. Chimeric proteins were found in solid tumors such as myeloid leukemia or Ewing's sarcoma. Members of this subfamily are po
Probab=24.80 E-value=1.3e+02 Score=16.31 Aligned_cols=34 Identities=9% Similarity=0.245 Sum_probs=22.9
Q ss_pred cHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHH
Q psy10378 15 SMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 15 ~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
++..+|.||.+|..++--...| .-+.+.++.||.
T Consensus 38 ~Gk~LC~LskedF~~~ap~~~G--diL~~HL~~Lr~ 71 (75)
T cd08540 38 DGKELCKMTKDDFQRLTPSYNA--DILLSHLHYLRE 71 (75)
T ss_pred CHHHHHhCCHHHHHHHcCCCCc--hHHHHHHHHHHh
Confidence 7889999999999775433345 344466666654
No 97
>COG5452 Uncharacterized conserved protein [Function unknown]
Probab=24.57 E-value=1.6e+02 Score=18.63 Aligned_cols=32 Identities=22% Similarity=0.231 Sum_probs=22.7
Q ss_pred HHHHcCCHHHHhcCCCCCchHHHHHHHHHHHH
Q psy10378 17 EAVVRLTVAELNALGITLVGHQKKIMNSIQAM 48 (62)
Q Consensus 17 ~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l 48 (62)
+.+..--+..|.++||...|=-||+-+-....
T Consensus 77 Daff~dvDhs~RElGigD~gVpKrMKKlAgmF 108 (180)
T COG5452 77 DAFFKDVDHSLRELGIGDQGVPKRMKKLAGMF 108 (180)
T ss_pred HHHHhhhhHHHHHhCCCcccchHHHHHHHHHH
Confidence 33444456679999999999999887644433
No 98
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=24.54 E-value=61 Score=16.60 Aligned_cols=24 Identities=38% Similarity=0.555 Sum_probs=16.2
Q ss_pred hcCcCcHHHHHcCCHHHHhcC-CCC
Q psy10378 10 RGGISSMEAVVRLTVAELNAL-GIT 33 (62)
Q Consensus 10 ~~g~~~~~~~~~lt~~dL~~l-GIt 33 (62)
..-|.+++.+...+.+||..+ ||.
T Consensus 20 ~~~f~sl~~l~~a~~e~L~~i~gIG 44 (64)
T PF12826_consen 20 AKHFGSLEALMNASVEELSAIPGIG 44 (64)
T ss_dssp HHCCSCHHHHCC--HHHHCTSTT--
T ss_pred HHHcCCHHHHHHcCHHHHhccCCcC
Confidence 345778999999999999876 444
No 99
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=24.29 E-value=1.6e+02 Score=17.17 Aligned_cols=25 Identities=36% Similarity=0.336 Sum_probs=19.9
Q ss_pred HhhcCcCcHHHHHcCCHHHHhcCCCC
Q psy10378 8 FERGGISSMEAVVRLTVAELNALGIT 33 (62)
Q Consensus 8 f~~~g~~~~~~~~~lt~~dL~~lGIt 33 (62)
+...|. |.+.+..++.++|.++|..
T Consensus 26 ~~~~gp-t~~~l~~~~~~~l~~~~~~ 50 (158)
T cd00056 26 FERYGP-TPEALAAADEEELRELIRS 50 (158)
T ss_pred HHHhCC-CHHHHHCCCHHHHHHHHHh
Confidence 333344 8999999999999998876
No 100
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=24.06 E-value=67 Score=21.46 Aligned_cols=23 Identities=26% Similarity=0.325 Sum_probs=15.9
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcCCCCCc
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNALGITLV 35 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~ 35 (62)
..-|.+|||. +.+-|.++||+.|
T Consensus 245 ~~f~~qNgyI--------e~~~l~~lgI~~p 267 (272)
T PF09743_consen 245 DNFFKQNGYI--------EYDALKRLGISDP 267 (272)
T ss_pred HHHHHHcCcE--------eHHHHHhcCCCCh
Confidence 3567888884 5555677888765
No 101
>TIGR01025 rpsS_arch ribosomal protein S19(archaeal)/S15(eukaryotic). This model represents eukaryotic ribosomal protein S15 and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15.
Probab=23.65 E-value=47 Score=20.25 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=19.0
Q ss_pred HHhhcCcCcHHHHHcCCHHHHhcC
Q psy10378 7 NFERGGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 7 ~f~~~g~~~~~~~~~lt~~dL~~l 30 (62)
.|.--|+ ++|.+..|+.+|+..|
T Consensus 4 ~f~yrG~-~l~~L~~m~~~e~~~l 26 (135)
T TIGR01025 4 EFRYRGY-TLEELQDMSLEELAKL 26 (135)
T ss_pred eEeeccc-CHHHHHcCCHHHHHHH
Confidence 4556788 7999999999999875
No 102
>cd04256 AAK_P5CS_ProBA AAK_P5CS_ProBA: Glutamate-5-kinase (G5K) domain of the bifunctional delta 1-pyrroline-5-carboxylate synthetase (P5CS), composed of an N-terminal G5K (ProB) and a C-terminal glutamyl 5- phosphate reductase (G5PR, ProA), the first and second enzyme catalyzing proline (and, in mammals, ornithine) biosynthesis. G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, and is subject to feedback allosteric inhibition by proline or ornithine. In plants, proline plays an important role as an osmoprotectant and, in mammals, ornithine biosynthesis is crucial for proper ammonia detoxification, since a G5K mutation has been shown to cause human hyperammonaemia.
Probab=23.44 E-value=85 Score=20.88 Aligned_cols=26 Identities=27% Similarity=0.356 Sum_probs=19.4
Q ss_pred cchHHHHhhcCcCcHHHHHcCCHHHHhc
Q psy10378 2 ARYLDNFERGGISSMEAVVRLTVAELNA 29 (62)
Q Consensus 2 ~~Y~~~f~~~g~~~~~~~~~lt~~dL~~ 29 (62)
.-|.+.|...++ ...++ -+|.+|+.+
T Consensus 107 ~~y~~~f~~~~~-~~~q~-llt~~d~~~ 132 (284)
T cd04256 107 ALYEAMFTQYGI-TVAQV-LVTKPDFYD 132 (284)
T ss_pred HHHHHHHHHcCC-cHHHe-eeecccccc
Confidence 458999999999 45565 477777765
No 103
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=23.42 E-value=1.3e+02 Score=22.32 Aligned_cols=31 Identities=16% Similarity=0.292 Sum_probs=23.7
Q ss_pred cCcHHHHHcCCHHHHhcCCCCCchHHHHHHHH
Q psy10378 13 ISSMEAVVRLTVAELNALGITLVGHQKKIMNS 44 (62)
Q Consensus 13 ~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~ 44 (62)
|.|++.+...|.++|..+||+ ..--++|.+.
T Consensus 534 Fgs~~~ik~As~eeL~~vgi~-~~~A~~I~~~ 564 (567)
T PRK14667 534 FKTLYDFLKADDEELKKLGIP-PSVKQEVKKY 564 (567)
T ss_pred hCCHHHHHhCCHHHHHHcCCC-HHHHHHHHHH
Confidence 557899999999999998887 5555555544
No 104
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=22.60 E-value=2.2e+02 Score=18.98 Aligned_cols=21 Identities=24% Similarity=0.350 Sum_probs=18.5
Q ss_pred cCcHHHHHcCCHHHHhcCCCC
Q psy10378 13 ISSMEAVVRLTVAELNALGIT 33 (62)
Q Consensus 13 ~~~~~~~~~lt~~dL~~lGIt 33 (62)
|-+.+.++..+.++|..+|++
T Consensus 155 FPtpe~La~~~~~eL~~~Gl~ 175 (283)
T PRK10308 155 FPTPERLAAADPQALKALGMP 175 (283)
T ss_pred CCCHHHHHcCCHHHHHHCCCC
Confidence 457899999999999999886
No 105
>PF03047 ComC: COMC family; InterPro: IPR004288 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. This family consists of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type []. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine []. Some COMC proteins and their precursors (not included in this family) do not fully follow the above description. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus []. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognised by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organism may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species []. This entry also includes proteins that form bacteriocin-like propetides with a glycine-glycine cleavage site. The bacteriocin is initially formed as a pre-propeptide and upon cleavage at the glycine-glycine cleavage site, a leader peptide and the propeptide would be formed. The propeptide then undergoes posttranslational modification before becoming functional [].; GO: 0005186 pheromone activity; PDB: 2I2J_A 2I2H_A 2A1C_A.
Probab=22.59 E-value=29 Score=16.01 Aligned_cols=17 Identities=29% Similarity=0.434 Sum_probs=0.0
Q ss_pred CcHHHHHcCCHHHHhcC
Q psy10378 14 SSMEAVVRLTVAELNAL 30 (62)
Q Consensus 14 ~~~~~~~~lt~~dL~~l 30 (62)
.+++++-.+++++|..+
T Consensus 6 ~~L~~F~~lt~~eL~~I 22 (32)
T PF03047_consen 6 KTLEQFEELTEEELQEI 22 (32)
T ss_dssp -----------------
T ss_pred hhHHHHhcCCHHHHhhc
Confidence 46788889999999875
No 106
>COG4518 Mu-like prophage FluMu protein gp41 [Function unknown]
Probab=22.36 E-value=56 Score=19.43 Aligned_cols=20 Identities=25% Similarity=0.426 Sum_probs=16.0
Q ss_pred cCcCcHHHHHcCCHHHHhcC
Q psy10378 11 GGISSMEAVVRLTVAELNAL 30 (62)
Q Consensus 11 ~g~~~~~~~~~lt~~dL~~l 30 (62)
+|--|+.++..+|..||.++
T Consensus 74 ~GP~S~rqi~~Ls~rDl~rl 93 (122)
T COG4518 74 QGPFSVRQILKLSSRDLARL 93 (122)
T ss_pred CCCcCHHHHHhhhHHHHHHH
Confidence 35448999999999999764
No 107
>KOG0199|consensus
Probab=21.76 E-value=1.6e+02 Score=23.35 Aligned_cols=51 Identities=10% Similarity=0.278 Sum_probs=35.6
Q ss_pred cchHHHHhh-cCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhh
Q psy10378 2 ARYLDNFER-GGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLS 53 (62)
Q Consensus 2 ~~Y~~~f~~-~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~ 53 (62)
.+|...|.+ -.+...+.|...-++||.++|...++ |||+-+++..++..+.
T Consensus 22 ~qf~s~lr~~lnvrr~~hf~yVk~eDLl~IGMgRp~-qRRLrea~kkm~~~~k 73 (1039)
T KOG0199|consen 22 DQFISQLRFLLNVRRFDHFSYVKDEDLLEIGMGRPQ-QRRLREAIKKMSREMK 73 (1039)
T ss_pred HHHHHHHHHHhccCchhhhhhcchhhhhhhccCcHH-HHHHHHHHHHhhhhcc
Confidence 344443332 33556778888999999999999665 6677788887766544
No 108
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.52 E-value=98 Score=17.76 Aligned_cols=24 Identities=29% Similarity=0.318 Sum_probs=17.0
Q ss_pred HHcCCHHHHh-cCCCCCchHHHHHHH
Q psy10378 19 VVRLTVAELN-ALGITLVGHQKKIMN 43 (62)
Q Consensus 19 ~~~lt~~dL~-~lGIt~~gh~kkIl~ 43 (62)
++.+|.+.+. +++++ ++|-.|||.
T Consensus 21 l~~LS~~~iA~~Ln~t-~~~lekil~ 45 (97)
T COG4367 21 LCPLSDEEIATALNWT-EVKLEKILQ 45 (97)
T ss_pred hccccHHHHHHHhCCC-HHHHHHHHH
Confidence 4555655554 78888 888888883
No 109
>PF09391 DUF2000: Protein of unknown function (DUF2000); InterPro: IPR018988 This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold. ; PDB: 2GAX_A.
Probab=21.28 E-value=17 Score=21.84 Aligned_cols=28 Identities=29% Similarity=0.402 Sum_probs=20.3
Q ss_pred HHHHHcCCHHHHhcCCCCCchHHHHHHH
Q psy10378 16 MEAVVRLTVAELNALGITLVGHQKKIMN 43 (62)
Q Consensus 16 ~~~~~~lt~~dL~~lGIt~~gh~kkIl~ 43 (62)
.+.+...+.+||.=+||...|.+|.|=+
T Consensus 97 ~~~~~~~~~~~l~y~Gi~L~G~kk~V~k 124 (133)
T PF09391_consen 97 RAAVAATPEEDLEYVGIALFGPKKAVDK 124 (133)
T ss_dssp HHHHTT--TTT--EEEEEEEEEHHHHHH
T ss_pred HHHHhcCChhhccEEEEEEECCHHHHHH
Confidence 3568899999999999999999998753
No 110
>PF02198 SAM_PNT: Sterile alpha motif (SAM)/Pointed domain; InterPro: IPR003118 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain IPR000418 from INTERPRO has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. This entry describes the highly conserved PNT (or Pointed) domain which is found within a subset of the ETs domain (IPR000418 from INTERPRO ), including mammalian Ets-1, Ets-2, Erg, Fli-1, GABPalpha, and Tel, as well as Drosophila Pnt-P2 and Yan. The PNT domain (IPR001660 from INTERPRO ) through a common tertiary arrangement of four alpha-helices. A role in protein-protein association has been established for the PNT domain [, ].; GO: 0043565 sequence-specific DNA binding, 0005634 nucleus; PDB: 1SXE_A 1SXD_A 2KMD_A 2JV3_A 2E8P_A 1SV4_B 1SV0_B 1LKY_F 1JI7_B 2DKX_A ....
Probab=20.97 E-value=1.6e+02 Score=15.86 Aligned_cols=39 Identities=13% Similarity=0.134 Sum_probs=24.8
Q ss_pred hhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHH
Q psy10378 9 ERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRT 50 (62)
Q Consensus 9 ~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~ 50 (62)
..-.. ++..++.||.+|..+..-+..| ..+...++.|+.
T Consensus 44 ~~f~~-~G~~Lc~lt~e~F~~~~~~~~G--~~Ly~~L~~Lk~ 82 (84)
T PF02198_consen 44 SRFNM-NGRELCSLTKEDFRRRFPSGYG--DILYSHLQLLKK 82 (84)
T ss_dssp GGGTS--HHHHHHSHHHHHHHHSTHTTH--HHHHHHHHHHHH
T ss_pred hccCC-CHHHHHHcCHHHHHHHcCCCcH--HHHHHHHHHHHH
Confidence 33345 6889999999999886543233 345566666654
No 111
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=20.67 E-value=2e+02 Score=24.06 Aligned_cols=43 Identities=23% Similarity=0.430 Sum_probs=29.2
Q ss_pred HHHHhhcCcCcHHHHHcCCHHHHhcCCCCCchHHHHHHHHHHHHHHHhhh
Q psy10378 5 LDNFERGGISSMEAVVRLTVAELNALGITLVGHQKKIMNSIQAMRTQLSA 54 (62)
Q Consensus 5 ~~~f~~~g~~~~~~~~~lt~~dL~~lGIt~~gh~kkIl~~i~~l~~~~~~ 54 (62)
...+.++|+.++.++...+++||.. |...|. +|+.++++++.+
T Consensus 1326 ~NcLk~agI~tvgdLv~~se~eLlk--ikN~Gk-----KSl~EIkekL~e 1368 (1460)
T PRK14906 1326 ANKFSEAGIETVGDLIGKTEEDLLR--IEGIGA-----KAIEELKDGLEA 1368 (1460)
T ss_pred HHHHHHcCCCcHHHHhhCCHHHHhh--ccCCCc-----chHHHHHHHHHH
Confidence 3566789999999999999999874 222221 255555555554
No 112
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=20.52 E-value=89 Score=17.70 Aligned_cols=18 Identities=28% Similarity=0.357 Sum_probs=13.9
Q ss_pred cCcCcHHHHHcCCHHHHh
Q psy10378 11 GGISSMEAVVRLTVAELN 28 (62)
Q Consensus 11 ~g~~~~~~~~~lt~~dL~ 28 (62)
.|-.+.+.++.||.+||.
T Consensus 75 ~G~i~p~~lv~Ms~~ElA 92 (102)
T smart00510 75 NGEITPEKLATMTAEELA 92 (102)
T ss_pred cCCCCHHHHhcCCHHHcC
Confidence 344578899999998884
Done!