Query psy12737
Match_columns 60
No_of_seqs 114 out of 622
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:23:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12737.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12737hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12775 AAA_7: P-loop contain 99.8 5.7E-20 1.2E-24 123.3 2.7 55 6-60 59-113 (272)
2 KOG3595|consensus 99.2 1.8E-11 3.9E-16 95.8 3.8 47 14-60 159-205 (1395)
3 COG5245 DYN1 Dynein, heavy cha 96.2 0.0071 1.5E-07 50.5 4.0 52 9-60 1521-1576(3164)
4 cd03714 RT_DIRS1 RT_DIRS1: Rev 84.3 2.2 4.8E-05 24.7 3.7 44 8-57 28-71 (119)
5 PF07728 AAA_5: AAA domain (dy 84.2 0.4 8.7E-06 28.1 0.5 49 10-58 26-76 (139)
6 PF07693 KAP_NTPase: KAP famil 82.7 1.4 3.1E-05 29.1 2.7 13 45-57 170-182 (325)
7 COG2256 MGS1 ATPase related to 75.5 2.2 4.8E-05 31.3 2.0 41 10-57 73-114 (436)
8 cd01644 RT_pepA17 RT_pepA17: R 73.2 2 4.3E-05 28.0 1.2 50 6-57 96-145 (213)
9 COG2607 Predicted ATPase (AAA+ 66.2 4.1 8.9E-05 28.4 1.6 13 45-57 137-149 (287)
10 cd03715 RT_ZFREV_like RT_ZFREV 61.6 17 0.00036 23.0 3.7 44 9-56 120-163 (210)
11 cd01647 RT_LTR RT_LTR: Reverse 61.1 21 0.00045 20.7 3.8 41 9-57 91-131 (177)
12 KOG2028|consensus 61.1 11 0.00023 28.2 3.0 41 11-57 191-232 (554)
13 PRK11657 dsbG disulfide isomer 60.6 21 0.00045 23.8 4.2 29 31-59 102-130 (251)
14 PF07521 RMMBL: RNA-metabolisi 57.8 9.9 0.00021 18.8 1.8 27 6-32 4-30 (43)
15 KOG1051|consensus 56.3 4 8.7E-05 32.4 0.2 46 11-58 246-291 (898)
16 PF05673 DUF815: Protein of un 56.2 7.7 0.00017 26.5 1.5 11 47-57 106-116 (249)
17 PF09162 Tap-RNA_bind: Tap, RN 54.1 32 0.0007 20.0 3.7 48 8-55 6-53 (88)
18 PLN00020 ribulose bisphosphate 50.8 9 0.0002 28.0 1.2 12 46-57 211-222 (413)
19 TIGR00824 EIIA-man PTS system, 50.3 51 0.0011 19.3 4.6 38 10-54 29-66 (116)
20 cd00006 PTS_IIA_man PTS_IIA, P 49.5 51 0.0011 19.2 4.5 38 10-54 28-65 (122)
21 COG2236 Predicted phosphoribos 48.4 17 0.00037 23.8 2.2 41 11-56 56-96 (192)
22 PRK14958 DNA polymerase III su 47.6 28 0.00061 25.6 3.4 41 11-58 90-130 (509)
23 cd01645 RT_Rtv RT_Rtv: Reverse 47.5 26 0.00056 22.4 2.9 45 8-56 123-167 (213)
24 PRK10877 protein disulfide iso 47.4 22 0.00047 23.4 2.6 22 38-59 99-120 (232)
25 COG0714 MoxR-like ATPases [Gen 47.2 25 0.00054 23.9 2.9 49 10-58 70-123 (329)
26 PF06068 TIP49: TIP49 C-termin 46.4 8.7 0.00019 28.0 0.6 32 22-58 255-289 (398)
27 PF00004 AAA: ATPase family as 43.1 14 0.0003 20.7 1.0 11 47-57 58-68 (132)
28 COG1224 TIP49 DNA helicase TIP 42.2 12 0.00026 27.6 0.8 9 50-58 294-302 (450)
29 PRK00411 cdc6 cell division co 41.7 91 0.002 21.3 5.0 50 8-57 85-148 (394)
30 PRK14951 DNA polymerase III su 41.4 42 0.00091 25.6 3.6 34 18-58 102-135 (618)
31 PRK11331 5-methylcytosine-spec 39.2 17 0.00038 26.8 1.2 14 46-59 271-284 (459)
32 COG1424 BioW Pimeloyl-CoA synt 38.7 25 0.00054 23.8 1.8 15 42-57 204-218 (239)
33 PRK14969 DNA polymerase III su 38.5 83 0.0018 23.3 4.6 39 13-58 92-130 (527)
34 PRK12323 DNA polymerase III su 37.2 34 0.00074 26.7 2.5 41 11-58 95-135 (700)
35 cd01128 rho_factor Transcripti 36.6 20 0.00044 23.9 1.2 13 45-57 101-113 (249)
36 PF00240 ubiquitin: Ubiquitin 35.7 59 0.0013 16.6 2.7 24 11-34 7-30 (69)
37 PRK06645 DNA polymerase III su 35.0 83 0.0018 23.4 4.2 39 13-58 101-139 (507)
38 PRK14960 DNA polymerase III su 33.3 56 0.0012 25.6 3.2 40 12-58 90-129 (702)
39 COG2812 DnaX DNA polymerase II 32.9 45 0.00097 25.0 2.5 20 39-58 111-130 (515)
40 PF07052 Hep_59: Hepatocellula 32.7 27 0.00058 20.3 1.1 26 15-40 2-31 (104)
41 PRK07003 DNA polymerase III su 32.6 78 0.0017 25.3 3.8 39 13-58 92-130 (830)
42 PRK02277 orotate phosphoribosy 32.5 34 0.00074 21.9 1.7 16 41-57 135-150 (200)
43 KOG1942|consensus 32.1 20 0.00043 26.1 0.6 9 50-58 299-307 (456)
44 cd00304 RT_like RT_like: Rever 31.7 36 0.00079 18.3 1.5 12 46-57 40-51 (98)
45 KOG0734|consensus 30.3 28 0.00061 27.1 1.1 12 46-57 395-406 (752)
46 PRK14956 DNA polymerase III su 30.0 63 0.0014 24.1 2.9 18 41-58 115-132 (484)
47 PF01078 Mg_chelatase: Magnesi 29.9 31 0.00067 22.8 1.2 10 49-58 108-117 (206)
48 cd03020 DsbA_DsbC_DsbG DsbA fa 29.9 75 0.0016 19.8 2.9 28 32-59 63-90 (197)
49 PF05496 RuvB_N: Holliday junc 29.4 29 0.00062 23.6 1.0 10 48-57 102-111 (233)
50 smart00042 CUB Domain first fo 28.4 70 0.0015 17.1 2.3 19 41-59 22-40 (102)
51 PF13462 Thioredoxin_4: Thiore 28.3 57 0.0012 19.0 2.1 22 38-59 4-25 (162)
52 PRK14964 DNA polymerase III su 27.0 1.4E+02 0.0031 22.2 4.2 42 10-58 86-127 (491)
53 PF09861 DUF2088: Domain of un 26.9 1.5E+02 0.0033 19.2 4.1 56 4-59 9-67 (204)
54 PF15610 PRTase_3: PRTase ComF 26.3 35 0.00077 23.7 1.0 11 48-58 139-149 (274)
55 PF03610 EIIA-man: PTS system 25.5 1.4E+02 0.0031 17.0 4.6 38 10-54 28-65 (116)
56 PF01644 Chitin_synth_1: Chiti 25.4 1.1E+02 0.0024 19.6 3.1 30 24-53 15-44 (163)
57 KOG4207|consensus 25.3 2.3E+02 0.0051 19.5 4.7 33 9-43 14-46 (256)
58 PRK15483 type III restriction- 25.0 74 0.0016 25.9 2.6 34 24-57 366-403 (986)
59 PF02669 KdpC: K+-transporting 24.9 69 0.0015 21.1 2.1 26 20-45 150-175 (188)
60 PF14909 SPATA6: Spermatogenes 24.2 1.9E+02 0.0042 18.1 4.1 43 14-56 54-96 (140)
61 PF07726 AAA_3: ATPase family 24.0 39 0.00084 21.0 0.8 44 11-58 27-73 (131)
62 PF08002 DUF1697: Protein of u 22.9 70 0.0015 19.5 1.8 28 11-38 42-69 (137)
63 COG1223 Predicted ATPase (AAA+ 22.7 46 0.00099 23.9 1.0 10 47-56 210-219 (368)
64 cd00041 CUB CUB domain; extrac 22.3 1.3E+02 0.0029 16.0 2.8 18 42-59 33-50 (113)
65 TIGR02928 orc1/cdc6 family rep 22.2 2.5E+02 0.0055 18.8 4.9 49 9-57 75-139 (365)
66 PRK09376 rho transcription ter 22.0 53 0.0012 24.1 1.3 14 44-57 253-266 (416)
67 PF04874 Mak16: Mak16 protein 22.0 53 0.0011 19.5 1.1 23 21-43 18-41 (101)
68 PF05098 LEF-4: Late expressio 21.9 66 0.0014 23.9 1.7 11 48-58 255-265 (450)
69 cd00009 AAA The AAA+ (ATPases 21.8 58 0.0012 17.8 1.2 12 47-58 84-95 (151)
70 TIGR00632 vsr DNA mismatch end 21.5 62 0.0013 19.7 1.3 11 45-55 54-64 (117)
71 KOG0733|consensus 21.3 52 0.0011 26.0 1.1 13 45-57 280-292 (802)
72 TIGR00681 kdpC K+-transporting 21.2 92 0.002 20.5 2.2 25 21-45 150-174 (187)
73 PRK14961 DNA polymerase III su 21.1 2.6E+02 0.0057 19.3 4.5 33 19-58 98-130 (363)
74 PF13191 AAA_16: AAA ATPase do 21.1 70 0.0015 18.9 1.5 10 48-57 151-160 (185)
75 PHA02678 hypothetical protein; 20.9 89 0.0019 18.3 1.8 14 42-55 66-79 (89)
76 COG1222 RPT1 ATP-dependent 26S 20.8 50 0.0011 24.3 0.9 13 45-57 242-254 (406)
77 PHA03029 hypothetical protein; 20.8 36 0.00078 19.7 0.2 22 21-42 33-54 (92)
78 KOG2680|consensus 20.6 48 0.001 24.3 0.8 39 15-58 256-299 (454)
79 PLN02709 nudix hydrolase 20.5 1.3E+02 0.0027 20.2 2.7 28 16-43 1-28 (222)
80 smart00213 UBQ Ubiquitin homol 20.5 1.3E+02 0.0027 14.6 3.0 23 11-33 11-33 (64)
81 PHA03118 multifunctional expre 20.3 72 0.0016 23.7 1.6 28 29-57 86-113 (474)
82 PF00647 EF1G: Elongation fact 20.3 1.5E+02 0.0032 17.8 2.7 20 24-43 66-85 (107)
83 PF14847 Ras_bdg_2: Ras-bindin 20.1 2.1E+02 0.0044 16.9 3.9 45 7-57 8-52 (105)
No 1
>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=99.78 E-value=5.7e-20 Score=123.32 Aligned_cols=55 Identities=55% Similarity=0.814 Sum_probs=49.2
Q ss_pred ccCcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCCCC
Q psy12737 6 ACGAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNMPQ 60 (60)
Q Consensus 6 ~~~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNmP~ 60 (60)
++.|.+..++||++|+|..+|+.||++++||+|++||||.||++|+||||+|||+
T Consensus 59 ~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p~ 113 (272)
T PF12775_consen 59 SDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMPQ 113 (272)
T ss_dssp TCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S-
T ss_pred ccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCCC
Confidence 3457788999999999999999999999999999999999999999999999995
No 2
>KOG3595|consensus
Probab=99.17 E-value=1.8e-11 Score=95.84 Aligned_cols=47 Identities=53% Similarity=0.820 Sum_probs=46.0
Q ss_pred EecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCCCC
Q psy12737 14 VNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNMPQ 60 (60)
Q Consensus 14 i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNmP~ 60 (60)
+|||++||++.+|.+++++++|++++.||||.+|.+++||||+|||.
T Consensus 159 ~~fs~~ts~~~~q~~~~~~~~k~~~~~~~~~~~~~~~~f~ddinmp~ 205 (1395)
T KOG3595|consen 159 LNFSSVTSSELLQEIIESKLDKRRSGNYGPPLGKKLVLFVDDINMPA 205 (1395)
T ss_pred EeeeeeccHHHHHHHHHHHHHHhcccCCCCCCCceeEEEEeccCCch
Confidence 99999999999999999999999999999999999999999999994
No 3
>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]
Probab=96.17 E-value=0.0071 Score=50.48 Aligned_cols=52 Identities=29% Similarity=0.343 Sum_probs=42.7
Q ss_pred cceEEEecCcccCHHHHHHHHhhhceecc--C-CeeeC-CCCcEEEEEEccCCCCC
Q psy12737 9 AVQLLVNFSSRTTSMDVQRNIESVVEKRT--K-DVFGP-PPDKKLILFIDDLNMPQ 60 (60)
Q Consensus 9 ~~~~~i~fSa~Tts~~~q~~ie~kl~kr~--~-~~~gp-p~gk~~v~FvDDlNmP~ 60 (60)
+.++.+|||-.|++...-..+|...++=+ | .++-| |.-|-+|+|+|+||||.
T Consensus 1521 ~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcDeInLp~ 1576 (3164)
T COG5245 1521 TEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCDEINLPY 1576 (3164)
T ss_pred eeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEeeccCCcc
Confidence 56899999999999999999999988744 2 34455 46688999999999994
No 4
>cd03714 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase.
Probab=84.25 E-value=2.2 Score=24.73 Aligned_cols=44 Identities=11% Similarity=0.123 Sum_probs=31.9
Q ss_pred CcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 8 GAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 8 ~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
.|....++|--..++.-.|+.+..-+..-+ ..+..++.|+||+.
T Consensus 28 ~~~~~~mp~Gl~~sp~~f~~~~~~i~~~~~------~~~~~v~~Y~DDil 71 (119)
T cd03714 28 TYQFKALPFGLSLAPRVFTKVVEALLAPLR------LLGVRIFSYLDDLL 71 (119)
T ss_pred cEEEEecCCcccchHHHHHHHHHHHHHHhh------cCCeEEEEEecCeE
Confidence 456677889988999999987776654322 22457889999984
No 5
>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []. The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=84.18 E-value=0.4 Score=28.15 Aligned_cols=49 Identities=22% Similarity=0.168 Sum_probs=28.8
Q ss_pred ceEEEecCcccCHHHHHHHHhhh--ceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 10 VQLLVNFSSRTTSMDVQRNIESV--VEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~~ie~k--l~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
-...+++++.|+...+.....-. ..+...+.+.....+..++++||+|.
T Consensus 26 ~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~ 76 (139)
T PF07728_consen 26 PVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINR 76 (139)
T ss_dssp EEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG
T ss_pred ceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCccc
Confidence 46679999999999887433321 11111222222223678999999985
No 6
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=82.70 E-value=1.4 Score=29.13 Aligned_cols=13 Identities=38% Similarity=0.925 Sum_probs=11.1
Q ss_pred CCcEEEEEEccCC
Q psy12737 45 PDKKLILFIDDLN 57 (60)
Q Consensus 45 ~gk~~v~FvDDlN 57 (60)
.++++|+||||+-
T Consensus 170 ~~~~iViiIDdLD 182 (325)
T PF07693_consen 170 SKKRIVIIIDDLD 182 (325)
T ss_pred CCceEEEEEcchh
Confidence 6789999999973
No 7
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=75.53 E-value=2.2 Score=31.29 Aligned_cols=41 Identities=24% Similarity=0.387 Sum_probs=28.6
Q ss_pred ceEEEecCcccCH-HHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 10 VQLLVNFSSRTTS-MDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 10 ~~~~i~fSa~Tts-~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
...+..|||.|+. ..+++.+|..-..+ + .|++.|+|||++.
T Consensus 73 ~~~f~~~sAv~~gvkdlr~i~e~a~~~~-----~--~gr~tiLflDEIH 114 (436)
T COG2256 73 NAAFEALSAVTSGVKDLREIIEEARKNR-----L--LGRRTILFLDEIH 114 (436)
T ss_pred CCceEEeccccccHHHHHHHHHHHHHHH-----h--cCCceEEEEehhh
Confidence 3557889998865 46777777643222 1 2789999999975
No 8
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=73.21 E-value=2 Score=28.03 Aligned_cols=50 Identities=14% Similarity=0.215 Sum_probs=34.5
Q ss_pred ccCcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 6 ACGAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 6 ~~~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
|..|....++|-...++..+|..+..-++.-... .....-...+||||+-
T Consensus 96 ~~~Y~~~~~pFG~~~AP~~~~~~~~~~~~~~~~~--~~~~~i~~~~YvDDil 145 (213)
T cd01644 96 PIEYRMTVVPFGAASAPFLANRALKQHAEDHPHE--AAAKIIKRNFYVDDIL 145 (213)
T ss_pred ceEEEEEEEccCCccchHHHHHHHHHHHhhcchh--hHHHHHHHeeecccce
Confidence 3678889999999999999999888777543222 0011113468999974
No 9
>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=66.22 E-value=4.1 Score=28.40 Aligned_cols=13 Identities=54% Similarity=0.846 Sum_probs=10.7
Q ss_pred CCcEEEEEEccCC
Q psy12737 45 PDKKLILFIDDLN 57 (60)
Q Consensus 45 ~gk~~v~FvDDlN 57 (60)
..++.|+||||+.
T Consensus 137 ~~~kFIlFcDDLS 149 (287)
T COG2607 137 RPEKFILFCDDLS 149 (287)
T ss_pred CCceEEEEecCCC
Confidence 3568999999985
No 10
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=61.58 E-value=17 Score=23.02 Aligned_cols=44 Identities=9% Similarity=0.087 Sum_probs=31.0
Q ss_pred cceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccC
Q psy12737 9 AVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDL 56 (60)
Q Consensus 9 ~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDl 56 (60)
|....+.|.-..++..+|+.+...++.-.+. ..+..+.+|+||+
T Consensus 120 y~~~~lp~Gl~~sp~~f~~~~~~~l~~~~~~----~~~~~~~~Y~DDi 163 (210)
T cd03715 120 YTFTRLPQGFKNSPTLFHEALARDLAPFPLE----HEGTILLQYVDDL 163 (210)
T ss_pred EEEEEEeccccCcHHHHHHHHHHHHHHHHhh----CCCeEEEEECCcE
Confidence 4556778888889999998887766543221 1345778899997
No 11
>cd01647 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Probab=61.12 E-value=21 Score=20.67 Aligned_cols=41 Identities=12% Similarity=0.194 Sum_probs=28.4
Q ss_pred cceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 9 AVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 9 ~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
+....+.|....++..+|..+..-+... .+..+..|+||+-
T Consensus 91 ~~~~~~p~G~~~s~~~~~~~~~~~l~~~--------~~~~~~~y~DDi~ 131 (177)
T cd01647 91 YEYTRMPFGLKNAPATFQRLMNKILGDL--------LGDFVEVYLDDIL 131 (177)
T ss_pred cEEEEecCCCccHHHHHHHHHHhhhccc--------cccccEEEecCcc
Confidence 4455677888888888887776666543 2345778999974
No 12
>KOG2028|consensus
Probab=61.11 E-value=11 Score=28.17 Aligned_cols=41 Identities=27% Similarity=0.455 Sum_probs=27.8
Q ss_pred eEEEecCccc-CHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 11 QLLVNFSSRT-TSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 11 ~~~i~fSa~T-ts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
..+|..||.+ +.+.+++++|+.-... --.+++-|+|+|++.
T Consensus 191 yrfvelSAt~a~t~dvR~ife~aq~~~------~l~krkTilFiDEiH 232 (554)
T KOG2028|consen 191 YRFVELSATNAKTNDVRDIFEQAQNEK------SLTKRKTILFIDEIH 232 (554)
T ss_pred eEEEEEeccccchHHHHHHHHHHHHHH------hhhcceeEEEeHHhh
Confidence 5578888876 4567888888743221 123578899999974
No 13
>PRK11657 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional
Probab=60.61 E-value=21 Score=23.77 Aligned_cols=29 Identities=17% Similarity=0.250 Sum_probs=21.0
Q ss_pred hhceeccCCeeeCCCCcEEEEEEccCCCC
Q psy12737 31 SVVEKRTKDVFGPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 31 ~kl~kr~~~~~gpp~gk~~v~FvDDlNmP 59 (60)
..|+....-.||++.+++.|+-.-|.|+|
T Consensus 102 ~~l~~~~~i~~g~~~ak~~I~vFtDp~Cp 130 (251)
T PRK11657 102 QRLEQSHWILDGKADAPRIVYVFADPNCP 130 (251)
T ss_pred HHhhccCCccccCCCCCeEEEEEECCCCh
Confidence 35656667889999888866555577876
No 14
>PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [].; PDB: 3ZQ4_D 2I7T_A 2I7V_A 2YCB_B 3BK1_A 3T3N_A 3BK2_A 3T3O_A 3AF5_A 3AF6_A ....
Probab=57.85 E-value=9.9 Score=18.76 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=19.9
Q ss_pred ccCcceEEEecCcccCHHHHHHHHhhh
Q psy12737 6 ACGAVQLLVNFSSRTTSMDVQRNIESV 32 (60)
Q Consensus 6 ~~~~~~~~i~fSa~Tts~~~q~~ie~k 32 (60)
+-+..+..+.||+-.+...+.+.|+.-
T Consensus 4 ~v~a~v~~~~fSgHad~~~L~~~i~~~ 30 (43)
T PF07521_consen 4 PVRARVEQIDFSGHADREELLEFIEQL 30 (43)
T ss_dssp E--SEEEESGCSSS-BHHHHHHHHHHH
T ss_pred EeEEEEEEEeecCCCCHHHHHHHHHhc
Confidence 334456788999999999999988874
No 15
>KOG1051|consensus
Probab=56.26 E-value=4 Score=32.39 Aligned_cols=46 Identities=20% Similarity=0.319 Sum_probs=29.9
Q ss_pred eEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
...+.|.+...-+.-..-+|.+++...+.+-. .|..+|+|+||+++
T Consensus 246 l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~--~~~gvILfigelh~ 291 (898)
T KOG1051|consen 246 LIALDFGSLVAGAKRRGEFEERLKELLKEVES--GGGGVILFLGELHW 291 (898)
T ss_pred eEEEEhhhcccCcccchHHHHHHHHHHHHHhc--CCCcEEEEecceee
Confidence 45566766555555455566666655544333 56789999999975
No 16
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=56.24 E-value=7.7 Score=26.50 Aligned_cols=11 Identities=64% Similarity=0.948 Sum_probs=9.5
Q ss_pred cEEEEEEccCC
Q psy12737 47 KKLILFIDDLN 57 (60)
Q Consensus 47 k~~v~FvDDlN 57 (60)
.+.|+||||+.
T Consensus 106 ~kFIlf~DDLs 116 (249)
T PF05673_consen 106 YKFILFCDDLS 116 (249)
T ss_pred CCEEEEecCCC
Confidence 58899999985
No 17
>PF09162 Tap-RNA_bind: Tap, RNA-binding; InterPro: IPR015245 This domain adopts a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. It is mainly found in mRNA export factors, which mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element []. ; GO: 0003723 RNA binding, 0006406 mRNA export from nucleus, 0005634 nucleus, 0005737 cytoplasm; PDB: 1FT8_A 1KOH_C 1KOO_C 3RW6_B 3RW7_C 1FO1_A.
Probab=54.06 E-value=32 Score=19.95 Aligned_cols=48 Identities=10% Similarity=0.078 Sum_probs=20.3
Q ss_pred CcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEcc
Q psy12737 8 GAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDD 55 (60)
Q Consensus 8 ~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDD 55 (60)
.|.-++|.+-..=.-.-|.+.|++.+.---.-++---.+.+..+||||
T Consensus 6 ~WfKVtIp~G~KYdK~wLl~~iq~~c~v~F~Pv~fh~~~~~a~FfV~D 53 (88)
T PF09162_consen 6 SWFKVTIPYGKKYDKDWLLNSIQSHCSVPFTPVDFHYEKNRAQFFVED 53 (88)
T ss_dssp -EEEEEETTGGGS-HHHHHHHHHHHSSS----EEEEEETTEEEEEESS
T ss_pred cEEEEEecCCcccCHHHHHHHHHHHCCCCeeeeeeeeeCCEEEEEeCC
Confidence 344445555555555555566666443111111111123355666665
No 18
>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional
Probab=50.80 E-value=9 Score=28.05 Aligned_cols=12 Identities=50% Similarity=0.744 Sum_probs=10.1
Q ss_pred CcEEEEEEccCC
Q psy12737 46 DKKLILFIDDLN 57 (60)
Q Consensus 46 gk~~v~FvDDlN 57 (60)
++.||+|||||-
T Consensus 211 ~aPcVLFIDEID 222 (413)
T PLN00020 211 GKMSCLFINDLD 222 (413)
T ss_pred CCCeEEEEehhh
Confidence 578999999974
No 19
>TIGR00824 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components.
Probab=50.34 E-value=51 Score=19.32 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=28.6
Q ss_pred ceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEc
Q psy12737 10 VQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFID 54 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvD 54 (60)
.+..++|....+...+++.++..++.- +.+..+++|.|
T Consensus 29 ~i~~i~~~~~~~~~~~~~~l~~~i~~~-------~~~~~vivltD 66 (116)
T TIGR00824 29 NVGAVPFVPGENAETLQEKYNAALADL-------DTEEEVLFLVD 66 (116)
T ss_pred CeEEEEcCCCcCHHHHHHHHHHHHHhc-------CCCCCEEEEEe
Confidence 477889999999999999998888643 22455666665
No 20
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=49.53 E-value=51 Score=19.17 Aligned_cols=38 Identities=11% Similarity=0.264 Sum_probs=28.4
Q ss_pred ceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEc
Q psy12737 10 VQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFID 54 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvD 54 (60)
....+.|....+...+.+.++..+++- +.++.+++|+|
T Consensus 28 ~i~~~~~~~~~~~~~~~~~i~~~i~~~-------~~~~~viil~D 65 (122)
T cd00006 28 NVEAIDFPPGESPDDLLEKIKAALAEL-------DSGEGVLILTD 65 (122)
T ss_pred CeEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCCcEEEEEe
Confidence 567788999999999998888888652 22455677776
No 21
>COG2236 Predicted phosphoribosyltransferases [General function prediction only]
Probab=48.39 E-value=17 Score=23.79 Aligned_cols=41 Identities=15% Similarity=0.262 Sum_probs=24.5
Q ss_pred eEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDL 56 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDl 56 (60)
...|.-+.++..+..+ ....=++.-.+.|-.||+ |+.|||+
T Consensus 56 l~~i~v~~y~~~~~~~----~~~~v~~~~~~d~l~Gkk-VLIVDDI 96 (192)
T COG2236 56 LYSIKVEHYDETAERD----GEAKVKYPITIDPLSGKK-VLIVDDI 96 (192)
T ss_pred eEEEEEEEehhhcccC----CcceeecCccccccCCCe-EEEEecc
Confidence 3455566666555443 223333455566678888 6789997
No 22
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=47.59 E-value=28 Score=25.64 Aligned_cols=41 Identities=22% Similarity=0.438 Sum_probs=27.8
Q ss_pred eEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
...++-++.+....++++++.- .|.|..|+.-|++||++.|
T Consensus 90 ~~eidaas~~~v~~iR~l~~~~-------~~~p~~~~~kV~iIDE~~~ 130 (509)
T PRK14958 90 LFEVDAASRTKVEDTRELLDNI-------PYAPTKGRFKVYLIDEVHM 130 (509)
T ss_pred EEEEcccccCCHHHHHHHHHHH-------hhccccCCcEEEEEEChHh
Confidence 4445555667777777766642 2346677888999999876
No 23
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=47.49 E-value=26 Score=22.38 Aligned_cols=45 Identities=16% Similarity=0.240 Sum_probs=30.9
Q ss_pred CcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccC
Q psy12737 8 GAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDL 56 (60)
Q Consensus 8 ~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDl 56 (60)
.|....+.|.-..++..+|..+..-+..-.+. + .+..++.|+||+
T Consensus 123 ~~~~~~lP~Gl~~SP~~f~~~m~~~l~~~~~~-~---~~~~~~~Y~DDi 167 (213)
T cd01645 123 RYQWKVLPQGMKNSPTICQSFVAQALEPFRKQ-Y---PDIVIYHYMDDI 167 (213)
T ss_pred eEEEEEeCCCCcChHHHHHHHHHHHHHHHHHH-C---CCeEEEEEcCCE
Confidence 45567788888888888888777666543321 1 134678899997
No 24
>PRK10877 protein disulfide isomerase II DsbC; Provisional
Probab=47.44 E-value=22 Score=23.42 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=16.3
Q ss_pred CCeeeCCCCcEEEEEEccCCCC
Q psy12737 38 KDVFGPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 38 ~~~~gpp~gk~~v~FvDDlNmP 59 (60)
.-+||++.|++.|+-+-|.|+|
T Consensus 99 ~i~~g~~~~k~~I~vFtDp~Cp 120 (232)
T PRK10877 99 MIVYKAPQEKHVITVFTDITCG 120 (232)
T ss_pred cEEecCCCCCEEEEEEECCCCh
Confidence 5688999888766555567776
No 25
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=47.25 E-value=25 Score=23.86 Aligned_cols=49 Identities=14% Similarity=0.245 Sum_probs=28.1
Q ss_pred ceEEEecCcccCHHHHHH--HHhhhce-eccCCee-eCC-CCcEEEEEEccCCC
Q psy12737 10 VQLLVNFSSRTTSMDVQR--NIESVVE-KRTKDVF-GPP-PDKKLILFIDDLNM 58 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~--~ie~kl~-kr~~~~~-gpp-~gk~~v~FvDDlNm 58 (60)
-...|+|...+++.++-- .+..+.. .+...+. ||- .+-+.|+|+|+||.
T Consensus 70 ~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInr 123 (329)
T COG0714 70 PFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINR 123 (329)
T ss_pred CeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEecccc
Confidence 467899999999998863 2332211 1111111 221 12125999999996
No 26
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=46.38 E-value=8.7 Score=27.99 Aligned_cols=32 Identities=31% Similarity=0.523 Sum_probs=20.0
Q ss_pred HHHHHHHHhhhceecc---CCeeeCCCCcEEEEEEccCCC
Q psy12737 22 SMDVQRNIESVVEKRT---KDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 22 s~~~q~~ie~kl~kr~---~~~~gpp~gk~~v~FvDDlNm 58 (60)
+..+++.|..++.+.. +.-.-| =|+||||++|
T Consensus 255 ~~elR~eInk~V~~wieegkAelvp-----GVLFIDEvHm 289 (398)
T PF06068_consen 255 TDELREEINKKVNKWIEEGKAELVP-----GVLFIDEVHM 289 (398)
T ss_dssp -HHHHHHHHHHHHHHHHCTSEEEEE------EEEEESGGG
T ss_pred hHHHHHHHhHHHHHHHhcCceEEec-----ceEEecchhh
Confidence 4567777777776653 222222 2899999988
No 27
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=43.09 E-value=14 Score=20.69 Aligned_cols=11 Identities=45% Similarity=0.957 Sum_probs=9.2
Q ss_pred cEEEEEEccCC
Q psy12737 47 KKLILFIDDLN 57 (60)
Q Consensus 47 k~~v~FvDDlN 57 (60)
+.+|+|+||+.
T Consensus 58 ~~~vl~iDe~d 68 (132)
T PF00004_consen 58 KPCVLFIDEID 68 (132)
T ss_dssp TSEEEEEETGG
T ss_pred cceeeeeccch
Confidence 56899999974
No 28
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=42.19 E-value=12 Score=27.59 Aligned_cols=9 Identities=56% Similarity=1.213 Sum_probs=8.1
Q ss_pred EEEEccCCC
Q psy12737 50 ILFIDDLNM 58 (60)
Q Consensus 50 v~FvDDlNm 58 (60)
|+||||++|
T Consensus 294 VLFIDEvHm 302 (450)
T COG1224 294 VLFIDEVHM 302 (450)
T ss_pred eEEEechhh
Confidence 789999988
No 29
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=41.65 E-value=91 Score=21.25 Aligned_cols=50 Identities=22% Similarity=0.249 Sum_probs=28.7
Q ss_pred CcceEEEecCcccCHHHHHHHHhhhceec----cCCee----------eCCCCcEEEEEEccCC
Q psy12737 8 GAVQLLVNFSSRTTSMDVQRNIESVVEKR----TKDVF----------GPPPDKKLILFIDDLN 57 (60)
Q Consensus 8 ~~~~~~i~fSa~Tts~~~q~~ie~kl~kr----~~~~~----------gpp~gk~~v~FvDDlN 57 (60)
.+....+++...++...+...|-..+... ++..+ --..++.+|+++||+.
T Consensus 85 ~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d 148 (394)
T PRK00411 85 KVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDIN 148 (394)
T ss_pred CcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHh
Confidence 45677888887777766655444444320 01000 0123567899999974
No 30
>PRK14951 DNA polymerase III subunits gamma and tau; Provisional
Probab=41.38 E-value=42 Score=25.58 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=23.5
Q ss_pred cccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 18 SRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 18 a~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
..+.-..++++++.- .|.|..|+.-|++|||+.|
T Consensus 102 s~~~Vd~iReli~~~-------~~~p~~g~~KV~IIDEvh~ 135 (618)
T PRK14951 102 SNRGVDEVQQLLEQA-------VYKPVQGRFKVFMIDEVHM 135 (618)
T ss_pred cccCHHHHHHHHHHH-------HhCcccCCceEEEEEChhh
Confidence 345666777777642 3556667777999999875
No 31
>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional
Probab=39.21 E-value=17 Score=26.83 Aligned_cols=14 Identities=36% Similarity=0.757 Sum_probs=11.7
Q ss_pred CcEEEEEEccCCCC
Q psy12737 46 DKKLILFIDDLNMP 59 (60)
Q Consensus 46 gk~~v~FvDDlNmP 59 (60)
++..|++|||+|++
T Consensus 271 ~~~~vliIDEINRa 284 (459)
T PRK11331 271 EKKYVFIIDEINRA 284 (459)
T ss_pred cCCcEEEEehhhcc
Confidence 35689999999986
No 32
>COG1424 BioW Pimeloyl-CoA synthetase [Coenzyme metabolism]
Probab=38.68 E-value=25 Score=23.84 Aligned_cols=15 Identities=27% Similarity=0.549 Sum_probs=9.8
Q ss_pred eCCCCcEEEEEEccCC
Q psy12737 42 GPPPDKKLILFIDDLN 57 (60)
Q Consensus 42 gpp~gk~~v~FvDDlN 57 (60)
|-+-|-+ |+||||.+
T Consensus 204 gt~~GgR-VfFVd~~~ 218 (239)
T COG1424 204 GTRYGGR-VFFVDDCI 218 (239)
T ss_pred CCccCcE-EEEEcCcc
Confidence 4454555 78999864
No 33
>PRK14969 DNA polymerase III subunits gamma and tau; Provisional
Probab=38.52 E-value=83 Score=23.28 Aligned_cols=39 Identities=18% Similarity=0.347 Sum_probs=25.7
Q ss_pred EEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 13 LVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 13 ~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.++-+..+....++++++.-. |.|-.|++-|++|||+.+
T Consensus 92 ei~~~~~~~vd~ir~l~~~~~-------~~p~~~~~kVvIIDEad~ 130 (527)
T PRK14969 92 EVDAASNTQVDAMRELLDNAQ-------YAPTRGRFKVYIIDEVHM 130 (527)
T ss_pred EeeccccCCHHHHHHHHHHHh-------hCcccCCceEEEEcCccc
Confidence 344455667777777766522 345567778999999754
No 34
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.16 E-value=34 Score=26.71 Aligned_cols=41 Identities=15% Similarity=0.361 Sum_probs=26.3
Q ss_pred eEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.+.++-+..+....++++++... |.|-.|++-|++||++.|
T Consensus 95 viEIdAas~~gVDdIReLie~~~-------~~P~~gr~KViIIDEah~ 135 (700)
T PRK12323 95 YIEMDAASNRGVDEMAQLLDKAV-------YAPTAGRFKVYMIDEVHM 135 (700)
T ss_pred ceEecccccCCHHHHHHHHHHHH-------hchhcCCceEEEEEChHh
Confidence 33455455566777777766432 335567777999999865
No 35
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=36.57 E-value=20 Score=23.94 Aligned_cols=13 Identities=15% Similarity=0.608 Sum_probs=11.0
Q ss_pred CCcEEEEEEccCC
Q psy12737 45 PDKKLILFIDDLN 57 (60)
Q Consensus 45 ~gk~~v~FvDDlN 57 (60)
.|++.++|+||+.
T Consensus 101 ~G~~vll~iDei~ 113 (249)
T cd01128 101 HGKDVVILLDSIT 113 (249)
T ss_pred CCCCEEEEEECHH
Confidence 4789999999974
No 36
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=35.72 E-value=59 Score=16.61 Aligned_cols=24 Identities=13% Similarity=0.234 Sum_probs=20.6
Q ss_pred eEEEecCcccCHHHHHHHHhhhce
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVE 34 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~ 34 (60)
...+.++..+|-..+.+.|+....
T Consensus 7 ~~~~~v~~~~tV~~lK~~i~~~~~ 30 (69)
T PF00240_consen 7 TFTLEVDPDDTVADLKQKIAEETG 30 (69)
T ss_dssp EEEEEEETTSBHHHHHHHHHHHHT
T ss_pred EEEEEECCCCCHHHhhhhcccccc
Confidence 567888999999999999988764
No 37
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=35.00 E-value=83 Score=23.37 Aligned_cols=39 Identities=33% Similarity=0.531 Sum_probs=26.2
Q ss_pred EEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 13 LVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 13 ~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.++=++.+....++++++..- +.|-.|++-|++|||+.|
T Consensus 101 eidaas~~~vd~Ir~iie~a~-------~~P~~~~~KVvIIDEa~~ 139 (507)
T PRK06645 101 EIDAASKTSVDDIRRIIESAE-------YKPLQGKHKIFIIDEVHM 139 (507)
T ss_pred EeeccCCCCHHHHHHHHHHHH-------hccccCCcEEEEEEChhh
Confidence 333345677788888887632 335566777899999765
No 38
>PRK14960 DNA polymerase III subunits gamma and tau; Provisional
Probab=33.30 E-value=56 Score=25.58 Aligned_cols=40 Identities=23% Similarity=0.472 Sum_probs=25.4
Q ss_pred EEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 12 LLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 12 ~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
..++-+..+....++++++.- .|.|..|++-|++||++.|
T Consensus 90 iEIDAAs~~~VddIReli~~~-------~y~P~~gk~KV~IIDEVh~ 129 (702)
T PRK14960 90 IEIDAASRTKVEDTRELLDNV-------PYAPTQGRFKVYLIDEVHM 129 (702)
T ss_pred EEecccccCCHHHHHHHHHHH-------hhhhhcCCcEEEEEechHh
Confidence 344444456666677666532 3456667777999999865
No 39
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=32.91 E-value=45 Score=25.02 Aligned_cols=20 Identities=20% Similarity=0.491 Sum_probs=17.0
Q ss_pred CeeeCCCCcEEEEEEccCCC
Q psy12737 39 DVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 39 ~~~gpp~gk~~v~FvDDlNm 58 (60)
-.|-|-.||.=|+-||++.|
T Consensus 111 v~y~P~~~ryKVyiIDEvHM 130 (515)
T COG2812 111 VNYAPSEGRYKVYIIDEVHM 130 (515)
T ss_pred hccCCccccceEEEEecHHh
Confidence 45778888888999999988
No 40
>PF07052 Hep_59: Hepatocellular carcinoma-associated antigen 59; InterPro: IPR010756 This family represents a conserved region approximately 100 residues long within mammalian hepatocellular carcinoma-associated antigen 59 and similar proteins. Family members are found in a variety of eukaryotes, mainly as hypothetical proteins.
Probab=32.72 E-value=27 Score=20.34 Aligned_cols=26 Identities=27% Similarity=0.415 Sum_probs=18.6
Q ss_pred ecCcccCHHH----HHHHHhhhceeccCCe
Q psy12737 15 NFSSRTTSMD----VQRNIESVVEKRTKDV 40 (60)
Q Consensus 15 ~fSa~Tts~~----~q~~ie~kl~kr~~~~ 40 (60)
+|+++|.-.. ..+.||+.|.+|++..
T Consensus 2 ~F~~qT~~~d~DkhM~~YIE~eL~kr~~~~ 31 (104)
T PF07052_consen 2 RFTAQTGQRDVDKHMMKYIEEELAKRKGRA 31 (104)
T ss_pred cccccccchhHHHHHHHHHHHHHHHhhccC
Confidence 4777776544 3567999999888754
No 41
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=32.61 E-value=78 Score=25.33 Aligned_cols=39 Identities=18% Similarity=0.329 Sum_probs=24.0
Q ss_pred EEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 13 LVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 13 ~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.|+=+..+....+.++++.- .|.|..++.-|++|||+.|
T Consensus 92 EIDAas~rgVDdIReLIe~a-------~~~P~~gr~KVIIIDEah~ 130 (830)
T PRK07003 92 EMDAASNRGVDEMAALLERA-------VYAPVDARFKVYMIDEVHM 130 (830)
T ss_pred EecccccccHHHHHHHHHHH-------HhccccCCceEEEEeChhh
Confidence 34334445556666666543 2445566777899999865
No 42
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=32.54 E-value=34 Score=21.94 Aligned_cols=16 Identities=25% Similarity=0.517 Sum_probs=10.9
Q ss_pred eeCCCCcEEEEEEccCC
Q psy12737 41 FGPPPDKKLILFIDDLN 57 (60)
Q Consensus 41 ~gpp~gk~~v~FvDDlN 57 (60)
|+...|++ |+.|||+-
T Consensus 135 ~~~~~gk~-VlIVDDVi 150 (200)
T PRK02277 135 FASVEGKR-CVIVDDVI 150 (200)
T ss_pred cccCCcCE-EEEEeecc
Confidence 34456777 57889973
No 43
>KOG1942|consensus
Probab=32.08 E-value=20 Score=26.11 Aligned_cols=9 Identities=56% Similarity=1.213 Sum_probs=7.8
Q ss_pred EEEEccCCC
Q psy12737 50 ILFIDDLNM 58 (60)
Q Consensus 50 v~FvDDlNm 58 (60)
|+|||+++|
T Consensus 299 VLFIDEVhM 307 (456)
T KOG1942|consen 299 VLFIDEVHM 307 (456)
T ss_pred ceEeeehhh
Confidence 789999887
No 44
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=31.70 E-value=36 Score=18.32 Aligned_cols=12 Identities=50% Similarity=0.775 Sum_probs=8.9
Q ss_pred CcEEEEEEccCC
Q psy12737 46 DKKLILFIDDLN 57 (60)
Q Consensus 46 gk~~v~FvDDlN 57 (60)
+...+.|+||+-
T Consensus 40 ~~~~~~Y~DD~~ 51 (98)
T cd00304 40 DITLIRYVDDLV 51 (98)
T ss_pred CceEEEeeCcEE
Confidence 456788999963
No 45
>KOG0734|consensus
Probab=30.27 E-value=28 Score=27.11 Aligned_cols=12 Identities=33% Similarity=0.761 Sum_probs=9.1
Q ss_pred CcEEEEEEccCC
Q psy12737 46 DKKLILFIDDLN 57 (60)
Q Consensus 46 gk~~v~FvDDlN 57 (60)
...||+|||+|-
T Consensus 395 ~APcIIFIDEiD 406 (752)
T KOG0734|consen 395 RAPCIIFIDEID 406 (752)
T ss_pred cCCeEEEEechh
Confidence 346899999873
No 46
>PRK14956 DNA polymerase III subunits gamma and tau; Provisional
Probab=30.02 E-value=63 Score=24.06 Aligned_cols=18 Identities=33% Similarity=0.611 Sum_probs=13.8
Q ss_pred eeCCCCcEEEEEEccCCC
Q psy12737 41 FGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 41 ~gpp~gk~~v~FvDDlNm 58 (60)
|.|..|++-|++||++.|
T Consensus 115 ~~p~~g~~KV~IIDEah~ 132 (484)
T PRK14956 115 FAPMGGKYKVYIIDEVHM 132 (484)
T ss_pred hhhhcCCCEEEEEechhh
Confidence 455567778999999875
No 47
>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.
Probab=29.94 E-value=31 Score=22.82 Aligned_cols=10 Identities=50% Similarity=0.856 Sum_probs=8.3
Q ss_pred EEEEEccCCC
Q psy12737 49 LILFIDDLNM 58 (60)
Q Consensus 49 ~v~FvDDlNm 58 (60)
=|+|+||+|.
T Consensus 108 GVLflDE~~e 117 (206)
T PF01078_consen 108 GVLFLDELNE 117 (206)
T ss_dssp SEEEECETTT
T ss_pred CEEEechhhh
Confidence 4889999984
No 48
>cd03020 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer.
Probab=29.93 E-value=75 Score=19.78 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=18.3
Q ss_pred hceeccCCeeeCCCCcEEEEEEccCCCC
Q psy12737 32 VVEKRTKDVFGPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 32 kl~kr~~~~~gpp~gk~~v~FvDDlNmP 59 (60)
.+.....-.||.+.++.-|+..-|.+.|
T Consensus 63 ~l~~~~~i~~g~~~~~~~i~~f~D~~Cp 90 (197)
T cd03020 63 ALPLDDAIVYGKGNGKRVVYVFTDPDCP 90 (197)
T ss_pred hCCcccCeEEcCCCCCEEEEEEECCCCc
Confidence 4444456788988777665544457776
No 49
>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.
Probab=29.44 E-value=29 Score=23.57 Aligned_cols=10 Identities=50% Similarity=0.843 Sum_probs=7.6
Q ss_pred EEEEEEccCC
Q psy12737 48 KLILFIDDLN 57 (60)
Q Consensus 48 ~~v~FvDDlN 57 (60)
.-|+||||++
T Consensus 102 ~~ILFIDEIH 111 (233)
T PF05496_consen 102 GDILFIDEIH 111 (233)
T ss_dssp T-EEEECTCC
T ss_pred CcEEEEechh
Confidence 4489999986
No 50
>smart00042 CUB Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain.
Probab=28.42 E-value=70 Score=17.07 Aligned_cols=19 Identities=21% Similarity=0.525 Sum_probs=13.1
Q ss_pred eeCCCCcEEEEEEccCCCC
Q psy12737 41 FGPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 41 ~gpp~gk~~v~FvDDlNmP 59 (60)
+.+|.|+++.+-+++++++
T Consensus 22 i~~~~g~~i~l~f~~~~l~ 40 (102)
T smart00042 22 IRAPPGYRIELQFTDFDLE 40 (102)
T ss_pred EECCCCeEEEEEEEEEecc
Confidence 3456678887877777664
No 51
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=28.34 E-value=57 Score=19.00 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=14.9
Q ss_pred CCeeeCCCCcEEEEEEccCCCC
Q psy12737 38 KDVFGPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 38 ~~~~gpp~gk~~v~FvDDlNmP 59 (60)
.-++|.|..+..|...-|..+|
T Consensus 4 ~~~~G~~~a~~~v~~f~d~~Cp 25 (162)
T PF13462_consen 4 DPTIGNPDAPITVTEFFDFQCP 25 (162)
T ss_dssp SEEES-TTTSEEEEEEE-TTSH
T ss_pred CCeecCCCCCeEEEEEECCCCH
Confidence 4578999998877766676665
No 52
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.01 E-value=1.4e+02 Score=22.17 Aligned_cols=42 Identities=21% Similarity=0.320 Sum_probs=28.6
Q ss_pred ceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 10 VQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.+..++=++.+....++++++.-- |-|-.+++-|++|||+.|
T Consensus 86 Dv~eidaas~~~vddIR~Iie~~~-------~~P~~~~~KVvIIDEah~ 127 (491)
T PRK14964 86 DVIEIDAASNTSVDDIKVILENSC-------YLPISSKFKVYIIDEVHM 127 (491)
T ss_pred CEEEEecccCCCHHHHHHHHHHHH-------hccccCCceEEEEeChHh
Confidence 345566566778888888776532 335556777899999765
No 53
>PF09861 DUF2088: Domain of unknown function (DUF2088); InterPro: IPR018657 This domain, found in various hypothetical proteins, has no known function. ; PDB: 2YJG_B.
Probab=26.88 E-value=1.5e+02 Score=19.24 Aligned_cols=56 Identities=13% Similarity=0.230 Sum_probs=24.2
Q ss_pred ccccCcceEEEecCcccCHHHHHHHHhhhceeccCC-eee--CCCCcEEEEEEccCCCC
Q psy12737 4 NFACGAVQLLVNFSSRTTSMDVQRNIESVVEKRTKD-VFG--PPPDKKLILFIDDLNMP 59 (60)
Q Consensus 4 ~~~~~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~-~~g--pp~gk~~v~FvDDlNmP 59 (60)
++|+.+....+............+.|+..|+.--+. .+. ...++++++-|||..-|
T Consensus 9 ~lP~~~~~~v~~~~~~~~~~~~~~~i~~aL~~Pig~~~L~~~~~~~~~V~Ivv~D~TRp 67 (204)
T PF09861_consen 9 ELPDEWLVDVLEPPEPPPLADPEEAIREALDNPIGSPPLRELVKPGKRVAIVVDDITRP 67 (204)
T ss_dssp E--CCCEEEE-----------HHHHHHHHHHS-BSS--HHHHCTT-SEEEEEEE-TTS-
T ss_pred EcCCCceEEEECCCCCCCCCCHHHHHHHHHHchhcCccHHHHhCCCCeEEEEeCCCCCC
Confidence 578888777777777666666666666666542221 010 13468999999998654
No 54
>PF15610 PRTase_3: PRTase ComF-like
Probab=26.25 E-value=35 Score=23.73 Aligned_cols=11 Identities=36% Similarity=0.975 Sum_probs=8.5
Q ss_pred EEEEEEccCCC
Q psy12737 48 KLILFIDDLNM 58 (60)
Q Consensus 48 ~~v~FvDDlNm 58 (60)
++++|+||+-+
T Consensus 139 k~lIflDDIkI 149 (274)
T PF15610_consen 139 KHLIFLDDIKI 149 (274)
T ss_pred cEEEEeccEEe
Confidence 56789999853
No 55
>PF03610 EIIA-man: PTS system fructose IIA component; InterPro: IPR004701 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of Escherichia coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for IIA and IIB components.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane; PDB: 3GDW_B 2JZN_A 1VSQ_A 2JZO_B 1VRC_A 1PDO_A 3GX1_A 3B48_B 3BED_B 3IPR_C ....
Probab=25.52 E-value=1.4e+02 Score=17.02 Aligned_cols=38 Identities=13% Similarity=0.240 Sum_probs=28.4
Q ss_pred ceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEc
Q psy12737 10 VQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFID 54 (60)
Q Consensus 10 ~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvD 54 (60)
....+.|....+...+.+.++..+++- ..+..+++|+|
T Consensus 28 ~i~~~~~~~~~~~~~~~~~l~~~i~~~-------~~~~~vlil~D 65 (116)
T PF03610_consen 28 NIEAVDLYPDESIEDFEEKLEEAIEEL-------DEGDGVLILTD 65 (116)
T ss_dssp SEEEEEETTTSCHHHHHHHHHHHHHHC-------CTTSEEEEEES
T ss_pred cEEEEECcCCCCHHHHHHHHHHHHHhc-------cCCCcEEEEee
Confidence 466788999999999988888888543 22456777776
No 56
>PF01644 Chitin_synth_1: Chitin synthase; InterPro: IPR004834 This region is found commonly in chitin synthases classes I, II and III 2.4.1.16 from EC. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases []. ; GO: 0004100 chitin synthase activity, 0006031 chitin biosynthetic process
Probab=25.43 E-value=1.1e+02 Score=19.61 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=18.9
Q ss_pred HHHHHHhhhceeccCCeeeCCCCcEEEEEE
Q psy12737 24 DVQRNIESVVEKRTKDVFGPPPDKKLILFI 53 (60)
Q Consensus 24 ~~q~~ie~kl~kr~~~~~gpp~gk~~v~Fv 53 (60)
.+.+.|+--+.+++....|+..-|++|+-|
T Consensus 15 gv~~Ni~~l~~r~~s~~wG~d~WkkiVVcI 44 (163)
T PF01644_consen 15 GVMKNIAHLCSRKRSKTWGKDAWKKIVVCI 44 (163)
T ss_pred HHHHHHHHHHhCCcCCcCCCCCCcEEEEEE
Confidence 344555555555556677888778876543
No 57
>KOG4207|consensus
Probab=25.29 E-value=2.3e+02 Score=19.47 Aligned_cols=33 Identities=30% Similarity=0.375 Sum_probs=26.5
Q ss_pred cceEEEecCcccCHHHHHHHHhhhceeccCCeeeC
Q psy12737 9 AVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGP 43 (60)
Q Consensus 9 ~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gp 43 (60)
+..+.-|+++.||+..|...+|..= +-+++|-|
T Consensus 14 ~SLkVdNLTyRTspd~LrrvFekYG--~vgDVyIP 46 (256)
T KOG4207|consen 14 TSLKVDNLTYRTSPDDLRRVFEKYG--RVGDVYIP 46 (256)
T ss_pred eeEEecceeccCCHHHHHHHHHHhC--cccceecc
Confidence 4567889999999999999888753 34788876
No 58
>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional
Probab=25.04 E-value=74 Score=25.88 Aligned_cols=34 Identities=29% Similarity=0.494 Sum_probs=20.0
Q ss_pred HHHHHHhhhceeccCC---eeeCCCCcEE-EEEEccCC
Q psy12737 24 DVQRNIESVVEKRTKD---VFGPPPDKKL-ILFIDDLN 57 (60)
Q Consensus 24 ~~q~~ie~kl~kr~~~---~~gpp~gk~~-v~FvDDlN 57 (60)
++++.|++.++|-+.- .+.+|+=|-+ ++|||++.
T Consensus 366 qIR~tI~~HfekE~~L~~r~~~~~gIKvLSLFFID~Va 403 (986)
T PRK15483 366 MIQQAIDKHFETERANFLRRNEPPKIKTLSLFFIDSIA 403 (986)
T ss_pred HHHHHHHHHHHHHHHHhhccCCCCCceEEEEEEEcccc
Confidence 3556788888876432 1122233433 68999983
No 59
>PF02669 KdpC: K+-transporting ATPase, c chain; InterPro: IPR003820 Kdp, the high affinity ATP-driven K+-transport system of Escherichia coli, is a complex of the membrane-bound subunits KdpA, KdpB, KdpC and the small peptide KdpF. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilise the Kdp complex []. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+- transporting subunit KdpA []. The K+ transport system actively transports K+ ions via ATP hydrolysis.; GO: 0008556 potassium-transporting ATPase activity, 0006813 potassium ion transport, 0016020 membrane
Probab=24.87 E-value=69 Score=21.05 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=22.3
Q ss_pred cCHHHHHHHHhhhceeccCCeeeCCC
Q psy12737 20 TTSMDVQRNIESVVEKRTKDVFGPPP 45 (60)
Q Consensus 20 Tts~~~q~~ie~kl~kr~~~~~gpp~ 45 (60)
.+...++++|+...+.+.-+.||.|.
T Consensus 150 l~~~~v~~li~~~t~~~~lG~~Ge~~ 175 (188)
T PF02669_consen 150 LSEEEVEALIDKHTEGPLLGFFGEPR 175 (188)
T ss_pred cCHHHHHHHHHHHhcCCCcccCCCCc
Confidence 36678999999999999999999874
No 60
>PF14909 SPATA6: Spermatogenesis-assoc protein 6
Probab=24.23 E-value=1.9e+02 Score=18.15 Aligned_cols=43 Identities=12% Similarity=0.129 Sum_probs=31.1
Q ss_pred EecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccC
Q psy12737 14 VNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDL 56 (60)
Q Consensus 14 i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDl 56 (60)
=.|....+++++++.+|...-+--=-...+|.|..+-.|-.+.
T Consensus 54 K~F~~~~dp~~l~~~Le~e~~~iELiQl~~~~g~iLA~ye~n~ 96 (140)
T PF14909_consen 54 KVFPNAVDPAQLADLLEDETVYIELIQLVPPAGEILAYYEENT 96 (140)
T ss_pred EEecCCCCHHHHHHHhhcCcEEEEEEEEeCCCCcEEEEEeccc
Confidence 3578889999999999987665544455677777776665543
No 61
>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model. AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.
Probab=23.97 E-value=39 Score=20.99 Aligned_cols=44 Identities=20% Similarity=0.230 Sum_probs=20.4
Q ss_pred eEEEecCcccCHHHHHHHHhhhceec---cCCeeeCCCCcEEEEEEccCCC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKR---TKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr---~~~~~gpp~gk~~v~FvDDlNm 58 (60)
...|.|+....+..+--. .-.+.. -.-..||-.. . |+++||+|.
T Consensus 27 f~RIq~tpdllPsDi~G~--~v~~~~~~~f~~~~GPif~-~-ill~DEiNr 73 (131)
T PF07726_consen 27 FKRIQFTPDLLPSDILGF--PVYDQETGEFEFRPGPIFT-N-ILLADEINR 73 (131)
T ss_dssp EEEEE--TT--HHHHHEE--EEEETTTTEEEEEE-TT-S-S-EEEEETGGG
T ss_pred eeEEEecCCCCcccceee--eeeccCCCeeEeecChhhh-c-eeeeccccc
Confidence 466888888887776532 111111 1112244332 2 789999995
No 62
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=22.94 E-value=70 Score=19.45 Aligned_cols=28 Identities=25% Similarity=0.274 Sum_probs=21.4
Q ss_pred eEEEecCcccCHHHHHHHHhhhceeccC
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVVEKRTK 38 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl~kr~~ 38 (60)
+-++-|++..+...++..||..++++-+
T Consensus 42 SGNvvf~~~~~~~~l~~~ie~~l~~~fG 69 (137)
T PF08002_consen 42 SGNVVFESDRDPAELAAKIEKALEERFG 69 (137)
T ss_dssp TTEEEEEESS-HHHHHHHHHHHHHHH-T
T ss_pred eCCEEEecCCChHHHHHHHHHHHHHhcC
Confidence 4467788999999999999999987543
No 63
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=22.73 E-value=46 Score=23.87 Aligned_cols=10 Identities=50% Similarity=0.856 Sum_probs=7.3
Q ss_pred cEEEEEEccC
Q psy12737 47 KKLILFIDDL 56 (60)
Q Consensus 47 k~~v~FvDDl 56 (60)
..||+|||++
T Consensus 210 aPcivFiDE~ 219 (368)
T COG1223 210 APCIVFIDEL 219 (368)
T ss_pred CCeEEEehhh
Confidence 3588888875
No 64
>cd00041 CUB CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
Probab=22.30 E-value=1.3e+02 Score=15.98 Aligned_cols=18 Identities=22% Similarity=0.602 Sum_probs=12.8
Q ss_pred eCCCCcEEEEEEccCCCC
Q psy12737 42 GPPPDKKLILFIDDLNMP 59 (60)
Q Consensus 42 gpp~gk~~v~FvDDlNmP 59 (60)
-+|.|+++.+-+++++++
T Consensus 33 ~~~~g~~i~l~f~~~~l~ 50 (113)
T cd00041 33 EAPPGYRIRLTFEDFDLE 50 (113)
T ss_pred EcCCCCEEEEEEeCcccc
Confidence 345578888888888775
No 65
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=22.16 E-value=2.5e+02 Score=18.79 Aligned_cols=49 Identities=18% Similarity=0.284 Sum_probs=26.1
Q ss_pred cceEEEecCcccCHHHHHHHHhhhcee---c---cC--------Cee--eCCCCcEEEEEEccCC
Q psy12737 9 AVQLLVNFSSRTTSMDVQRNIESVVEK---R---TK--------DVF--GPPPDKKLILFIDDLN 57 (60)
Q Consensus 9 ~~~~~i~fSa~Tts~~~q~~ie~kl~k---r---~~--------~~~--gpp~gk~~v~FvDDlN 57 (60)
+....+++....+...+...|-..+.. . ++ ..+ -...++.+|+++||+.
T Consensus 75 ~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d 139 (365)
T TIGR02928 75 VVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEID 139 (365)
T ss_pred eEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchh
Confidence 456677877766665554434444421 0 00 000 0124667899999974
No 66
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=22.03 E-value=53 Score=24.13 Aligned_cols=14 Identities=14% Similarity=0.553 Sum_probs=11.6
Q ss_pred CCCcEEEEEEccCC
Q psy12737 44 PPDKKLILFIDDLN 57 (60)
Q Consensus 44 p~gk~~v~FvDDlN 57 (60)
..|+.+++|+|++.
T Consensus 253 e~G~dVlL~iDsIt 266 (416)
T PRK09376 253 EHGKDVVILLDSIT 266 (416)
T ss_pred HcCCCEEEEEEChH
Confidence 45789999999974
No 67
>PF04874 Mak16: Mak16 protein C-terminal region; InterPro: IPR006958 The function of these proteins is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni (Blood fluke) Mak16 has been shown to target protein transport to the nucleolus [].
Probab=22.00 E-value=53 Score=19.51 Aligned_cols=23 Identities=17% Similarity=0.427 Sum_probs=16.2
Q ss_pred CHHHHHHHHhhhceec-cCCeeeC
Q psy12737 21 TSMDVQRNIESVVEKR-TKDVFGP 43 (60)
Q Consensus 21 ts~~~q~~ie~kl~kr-~~~~~gp 43 (60)
.++++.+.|+.-|-.| +.|+||-
T Consensus 18 ~AA~le~~IEkELLeRLk~G~Ygd 41 (101)
T PF04874_consen 18 IAAKLEKSIEKELLERLKSGTYGD 41 (101)
T ss_pred HHHHHHHHHHHHHHHHHHcCCccc
Confidence 4677778887766554 6788983
No 68
>PF05098 LEF-4: Late expression factor 4 (LEF-4); InterPro: IPR007790 The baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) virus encodes a DNA-dependent RNA polymerase that is required for transcription of viral late genes. This polymerase is composed of four equimolar subunits, LEF-8, LEF-4, LEF-9, and p47. LEF-4 carries out all the enzymatic functions related to mRNA capping []. ; GO: 0006355 regulation of transcription, DNA-dependent
Probab=21.92 E-value=66 Score=23.94 Aligned_cols=11 Identities=36% Similarity=0.709 Sum_probs=9.9
Q ss_pred EEEEEEccCCC
Q psy12737 48 KLILFIDDLNM 58 (60)
Q Consensus 48 ~~v~FvDDlNm 58 (60)
.+++|.||+.|
T Consensus 255 ~~~i~~DDMq~ 265 (450)
T PF05098_consen 255 FIIIQMDDMQM 265 (450)
T ss_pred EEEEEEchhhh
Confidence 78999999876
No 69
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=21.76 E-value=58 Score=17.75 Aligned_cols=12 Identities=42% Similarity=0.758 Sum_probs=9.4
Q ss_pred cEEEEEEccCCC
Q psy12737 47 KKLILFIDDLNM 58 (60)
Q Consensus 47 k~~v~FvDDlNm 58 (60)
+..++++||++.
T Consensus 84 ~~~~lilDe~~~ 95 (151)
T cd00009 84 KPGVLFIDEIDS 95 (151)
T ss_pred CCeEEEEeChhh
Confidence 456899999874
No 70
>TIGR00632 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase.
Probab=21.47 E-value=62 Score=19.65 Aligned_cols=11 Identities=18% Similarity=0.561 Sum_probs=8.9
Q ss_pred CCcEEEEEEcc
Q psy12737 45 PDKKLILFIDD 55 (60)
Q Consensus 45 ~gk~~v~FvDD 55 (60)
.+.+++||||=
T Consensus 54 ~~~klaIfVDG 64 (117)
T TIGR00632 54 DEYRCVIFIHG 64 (117)
T ss_pred cCCCEEEEEcc
Confidence 46789999985
No 71
>KOG0733|consensus
Probab=21.33 E-value=52 Score=26.02 Aligned_cols=13 Identities=31% Similarity=0.751 Sum_probs=10.0
Q ss_pred CCcEEEEEEccCC
Q psy12737 45 PDKKLILFIDDLN 57 (60)
Q Consensus 45 ~gk~~v~FvDDlN 57 (60)
....||+|||||-
T Consensus 280 ~~aPcivFiDeID 292 (802)
T KOG0733|consen 280 SNAPCIVFIDEID 292 (802)
T ss_pred ccCCeEEEeeccc
Confidence 3457999999974
No 72
>TIGR00681 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [PubMed:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [PubMed:9858692].
Probab=21.20 E-value=92 Score=20.47 Aligned_cols=25 Identities=28% Similarity=0.405 Sum_probs=21.7
Q ss_pred CHHHHHHHHhhhceeccCCeeeCCC
Q psy12737 21 TSMDVQRNIESVVEKRTKDVFGPPP 45 (60)
Q Consensus 21 ts~~~q~~ie~kl~kr~~~~~gpp~ 45 (60)
+...++++|....+.|.-+.||.|.
T Consensus 150 ~~~~v~~LI~~~t~~~~lG~~Ge~~ 174 (187)
T TIGR00681 150 SPQQLQSLITKHTEGRFLGIFGEPG 174 (187)
T ss_pred CHHHHHHHHHHHhcCCCCCcCCCCc
Confidence 5678899999999999999999874
No 73
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=21.12 E-value=2.6e+02 Score=19.32 Aligned_cols=33 Identities=18% Similarity=0.496 Sum_probs=20.9
Q ss_pred ccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCCC
Q psy12737 19 RTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 19 ~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlNm 58 (60)
.+....++++++. ++ +.|..+++-|++|||+.+
T Consensus 98 ~~~v~~ir~i~~~-~~------~~p~~~~~kviIIDEa~~ 130 (363)
T PRK14961 98 RTKVEEMREILDN-IY------YSPSKSRFKVYLIDEVHM 130 (363)
T ss_pred cCCHHHHHHHHHH-Hh------cCcccCCceEEEEEChhh
Confidence 3566666666553 22 345566777899999754
No 74
>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A.
Probab=21.12 E-value=70 Score=18.88 Aligned_cols=10 Identities=60% Similarity=1.006 Sum_probs=8.0
Q ss_pred EEEEEEccCC
Q psy12737 48 KLILFIDDLN 57 (60)
Q Consensus 48 ~~v~FvDDlN 57 (60)
.+|+++||+.
T Consensus 151 ~~vlviDd~d 160 (185)
T PF13191_consen 151 PLVLVIDDLD 160 (185)
T ss_dssp -EEEEEETTT
T ss_pred eEEEEEeCCC
Confidence 4899999985
No 75
>PHA02678 hypothetical protein; Provisional
Probab=20.93 E-value=89 Score=18.30 Aligned_cols=14 Identities=21% Similarity=0.695 Sum_probs=11.6
Q ss_pred eCCCCcEEEEEEcc
Q psy12737 42 GPPPDKKLILFIDD 55 (60)
Q Consensus 42 gpp~gk~~v~FvDD 55 (60)
|+|.|-+.++.||-
T Consensus 66 ~~~~~~~~~~~~~~ 79 (89)
T PHA02678 66 GAPAGVRVLVLVDV 79 (89)
T ss_pred CCCCCcEEEEEEEe
Confidence 78999998888874
No 76
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=20.85 E-value=50 Score=24.26 Aligned_cols=13 Identities=31% Similarity=0.695 Sum_probs=10.0
Q ss_pred CCcEEEEEEccCC
Q psy12737 45 PDKKLILFIDDLN 57 (60)
Q Consensus 45 ~gk~~v~FvDDlN 57 (60)
..+.+|+|||++-
T Consensus 242 ekaPsIIFiDEID 254 (406)
T COG1222 242 EKAPSIIFIDEID 254 (406)
T ss_pred hcCCeEEEEechh
Confidence 3457899999873
No 77
>PHA03029 hypothetical protein; Provisional
Probab=20.82 E-value=36 Score=19.70 Aligned_cols=22 Identities=14% Similarity=0.315 Sum_probs=16.7
Q ss_pred CHHHHHHHHhhhceeccCCeee
Q psy12737 21 TSMDVQRNIESVVEKRTKDVFG 42 (60)
Q Consensus 21 ts~~~q~~ie~kl~kr~~~~~g 42 (60)
+-+.++..|.+.+..|||+.|.
T Consensus 33 si~k~raai~qnirsrrkg~yw 54 (92)
T PHA03029 33 SINKIRAAIDQNIRSRRKGLYW 54 (92)
T ss_pred HHHHHHHHHHHHHHHHhhhHHH
Confidence 3456677888889889998773
No 78
>KOG2680|consensus
Probab=20.61 E-value=48 Score=24.27 Aligned_cols=39 Identities=31% Similarity=0.412 Sum_probs=23.7
Q ss_pred ecCcccC--HHHHHHHHhhhceecc---CCeeeCCCCcEEEEEEccCCC
Q psy12737 15 NFSSRTT--SMDVQRNIESVVEKRT---KDVFGPPPDKKLILFIDDLNM 58 (60)
Q Consensus 15 ~fSa~Tt--s~~~q~~ie~kl~kr~---~~~~gpp~gk~~v~FvDDlNm 58 (60)
-||+.|- -+.++++|..|+-..+ |--+- .-|+|||++.|
T Consensus 256 LFsGdTGEIr~EvRdqin~KV~eWreEGKAeiv-----pGVLFIDEvHM 299 (454)
T KOG2680|consen 256 LFSGDTGEIRSEVRDQINTKVAEWREEGKAEIV-----PGVLFIDEVHM 299 (454)
T ss_pred EEeCCcccccHHHHHHHHHHHHHHHhcCCeeec-----cceEEEeeehh
Confidence 4777763 2456677777765443 11221 23789999988
No 79
>PLN02709 nudix hydrolase
Probab=20.53 E-value=1.3e+02 Score=20.18 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=17.8
Q ss_pred cCcccCHHHHHHHHhhhceeccCCeeeC
Q psy12737 16 FSSRTTSMDVQRNIESVVEKRTKDVFGP 43 (60)
Q Consensus 16 fSa~Tts~~~q~~ie~kl~kr~~~~~gp 43 (60)
+|+.||-...|+.|-+++..++....|-
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 28 (222)
T PLN02709 1 MSSTTTDSTELQNLIKLFQNCETHLRQH 28 (222)
T ss_pred CCCccccHHHHHHHHHHHHhccccccCC
Confidence 4667776677766777776555555544
No 80
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=20.48 E-value=1.3e+02 Score=14.65 Aligned_cols=23 Identities=9% Similarity=0.261 Sum_probs=19.2
Q ss_pred eEEEecCcccCHHHHHHHHhhhc
Q psy12737 11 QLLVNFSSRTTSMDVQRNIESVV 33 (60)
Q Consensus 11 ~~~i~fSa~Tts~~~q~~ie~kl 33 (60)
...+.+++.+|...+.+.|+.+.
T Consensus 11 ~~~~~v~~~~tv~~lk~~i~~~~ 33 (64)
T smart00213 11 TITLEVKPSDTVSELKEKIAELT 33 (64)
T ss_pred eEEEEECCCCcHHHHHHHHHHHH
Confidence 45678899999999999998765
No 81
>PHA03118 multifunctional expression regulator; Provisional
Probab=20.33 E-value=72 Score=23.69 Aligned_cols=28 Identities=29% Similarity=0.503 Sum_probs=18.6
Q ss_pred HhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 29 IESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 29 ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
+|+|-.-|| .-|.--..|-+|.|.||+|
T Consensus 86 ~~~~~~~~~-~~yh~~~~k~lv~~~~~~~ 113 (474)
T PHA03118 86 FEKKAHGRR-EGYHHDDEKCLVTFLDDIN 113 (474)
T ss_pred hhhhhhccc-cccccCCCceEEEecCCCC
Confidence 444444333 3466566788999999998
No 82
>PF00647 EF1G: Elongation factor 1 gamma, conserved domain; InterPro: IPR001662 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents a conserved domain usually found near the C terminus of EF1B-gamma chains, a peptide of 410-440 residues. The gamma chain appears to play a role in anchoring the EF1B complex to the beta and delta chains and to other cellular components. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 1PBU_A.
Probab=20.30 E-value=1.5e+02 Score=17.81 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=13.9
Q ss_pred HHHHHHhhhceeccCCeeeC
Q psy12737 24 DVQRNIESVVEKRTKDVFGP 43 (60)
Q Consensus 24 ~~q~~ie~kl~kr~~~~~gp 43 (60)
++-.=..+++|+-||..||-
T Consensus 66 Nli~Gf~QRle~~rK~aFg~ 85 (107)
T PF00647_consen 66 NLIGGFFQRLEKLRKYAFGS 85 (107)
T ss_dssp HHHHHHHHHGGGTGGGEEE-
T ss_pred hHHHHHHHHHHHHhhhheeE
Confidence 33333458999999999983
No 83
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=20.15 E-value=2.1e+02 Score=16.93 Aligned_cols=45 Identities=13% Similarity=0.126 Sum_probs=24.7
Q ss_pred cCcceEEEecCcccCHHHHHHHHhhhceeccCCeeeCCCCcEEEEEEccCC
Q psy12737 7 CGAVQLLVNFSSRTTSMDVQRNIESVVEKRTKDVFGPPPDKKLILFIDDLN 57 (60)
Q Consensus 7 ~~~~~~~i~fSa~Tts~~~q~~ie~kl~kr~~~~~gpp~gk~~v~FvDDlN 57 (60)
+.-....+|-+..+++..+-+.+..|+-++- -....+++++|+..
T Consensus 8 ~dG~tk~VNV~~c~~a~eI~~rvLKKfg~~~------~~~~~~~~v~d~~~ 52 (105)
T PF14847_consen 8 EDGSTKTVNVSGCFNAQEIKRRVLKKFGLPE------HPRNYCFYVLDGES 52 (105)
T ss_dssp TTTEEEEEE--S--HHHHHHHHHHHHHTSS--------CCCEEEEEE-S--
T ss_pred CCCcEEEEEECCCCCHHHHHHHHHHHcCCcc------ccccceEEEecccc
Confidence 4456788999999988887777776665443 22346777777733
Done!