Query psy16186
Match_columns 111
No_of_seqs 75 out of 77
Neff 3.8
Searched_HMMs 46136
Date Fri Aug 16 22:57:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16186.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16186hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2373|consensus 100.0 3.5E-44 7.5E-49 303.8 4.1 107 2-110 303-415 (514)
2 cd00984 DnaB_C DnaB helicase C 98.6 1.8E-07 4E-12 70.0 7.2 107 2-110 44-163 (242)
3 cd01122 GP4d_helicase GP4d_hel 98.5 5.6E-07 1.2E-11 68.8 7.8 107 2-110 61-181 (271)
4 TIGR03600 phage_DnaB phage rep 98.4 7.3E-07 1.6E-11 73.5 6.9 106 2-110 225-344 (421)
5 TIGR00665 DnaB replicative DNA 98.3 2E-06 4.4E-11 70.9 7.6 107 2-110 226-345 (434)
6 PF13481 AAA_25: AAA domain; P 98.2 1.2E-06 2.7E-11 63.2 3.3 104 2-110 72-179 (193)
7 PF03796 DnaB_C: DnaB-like hel 98.1 4.7E-06 1E-10 64.1 5.3 106 3-110 51-170 (259)
8 PRK07004 replicative DNA helic 97.9 3.4E-05 7.4E-10 65.7 6.8 106 3-110 245-364 (460)
9 PRK05748 replicative DNA helic 97.7 0.00013 2.7E-09 61.1 7.0 107 3-110 235-355 (448)
10 PRK06749 replicative DNA helic 97.7 0.00017 3.7E-09 61.0 7.6 108 2-110 216-340 (428)
11 PRK08840 replicative DNA helic 97.7 0.00015 3.4E-09 62.0 7.1 106 3-110 249-369 (464)
12 PRK08506 replicative DNA helic 97.6 0.00019 4.2E-09 61.2 7.1 106 3-110 223-342 (472)
13 PRK06321 replicative DNA helic 97.6 0.00023 5E-09 61.1 7.0 107 3-110 258-379 (472)
14 PRK05595 replicative DNA helic 97.5 0.00029 6.4E-09 59.1 6.9 106 3-110 233-351 (444)
15 PRK06904 replicative DNA helic 97.1 0.0017 3.7E-08 55.7 7.1 107 2-110 252-374 (472)
16 PRK08760 replicative DNA helic 96.8 0.004 8.6E-08 53.5 7.0 106 3-110 261-379 (476)
17 PRK09165 replicative DNA helic 96.7 0.0058 1.2E-07 52.7 7.3 106 4-110 264-383 (497)
18 PRK05636 replicative DNA helic 96.7 0.0056 1.2E-07 53.2 7.3 105 4-110 298-415 (505)
19 PHA02542 41 41 helicase; Provi 96.3 0.014 3E-07 50.4 6.9 108 2-110 220-344 (473)
20 PRK07773 replicative DNA helic 96.2 0.014 3.1E-07 53.4 6.8 106 3-110 249-367 (886)
21 PRK08006 replicative DNA helic 95.9 0.034 7.4E-07 47.9 7.3 106 3-110 256-376 (471)
22 cd01121 Sms Sms (bacterial rad 90.9 0.55 1.2E-05 39.4 5.4 59 48-110 141-200 (372)
23 TIGR03877 thermo_KaiC_1 KaiC d 89.4 1.2 2.6E-05 34.1 5.8 54 51-110 108-161 (237)
24 PRK11823 DNA repair protein Ra 88.3 1.2 2.5E-05 38.1 5.5 58 49-110 140-198 (446)
25 cd01123 Rad51_DMC1_radA Rad51_ 85.9 1.6 3.4E-05 32.5 4.4 59 52-110 97-160 (235)
26 cd01393 recA_like RecA is a b 85.6 2.3 5E-05 31.4 5.1 60 51-110 93-159 (226)
27 TIGR00416 sms DNA repair prote 84.7 2.3 5.1E-05 36.5 5.5 61 46-110 151-212 (454)
28 COG0305 DnaB Replicative DNA h 80.9 4.9 0.00011 35.1 6.0 83 4-87 229-324 (435)
29 cd01120 RecA-like_NTPases RecA 77.6 6.8 0.00015 26.2 4.8 61 46-108 62-125 (165)
30 PF06745 KaiC: KaiC; InterPro 76.4 18 0.00038 27.0 7.2 31 51-81 97-127 (226)
31 PRK09361 radB DNA repair and r 74.6 8.6 0.00019 28.7 5.1 58 53-110 89-152 (225)
32 COG0288 CynT Carbonic anhydras 71.6 3.4 7.3E-05 32.4 2.4 26 55-86 76-101 (207)
33 PF09722 DUF2384: Protein of u 68.7 1.3 2.8E-05 27.1 -0.4 40 26-65 9-54 (54)
34 PF08423 Rad51: Rad51; InterP 68.1 15 0.00033 29.0 5.4 60 51-110 112-178 (256)
35 PRK04328 hypothetical protein; 66.7 18 0.00038 28.2 5.5 54 51-110 110-163 (249)
36 PF00484 Pro_CA: Carbonic anhy 66.7 6.4 0.00014 28.1 2.8 29 54-88 38-66 (153)
37 PF13401 AAA_22: AAA domain; P 66.0 24 0.00052 23.3 5.3 45 51-107 69-113 (131)
38 cd01124 KaiC KaiC is a circadi 64.8 25 0.00054 24.8 5.5 30 55-84 81-110 (187)
39 cd03379 beta_CA_cladeD Carboni 62.7 8.5 0.00018 27.9 2.8 35 46-86 31-65 (142)
40 cd00382 beta_CA Carbonic anhyd 61.2 26 0.00056 24.7 5.0 54 46-105 31-87 (119)
41 TIGR03881 KaiC_arch_4 KaiC dom 59.7 31 0.00067 25.7 5.4 33 51-83 101-135 (229)
42 TIGR00288 conserved hypothetic 59.1 9.5 0.00021 29.2 2.6 27 48-75 85-111 (160)
43 COG2355 Zn-dependent dipeptida 57.8 11 0.00024 31.7 3.1 25 51-75 234-258 (313)
44 cd00883 beta_CA_cladeA Carboni 57.7 9.2 0.0002 28.9 2.4 25 56-86 66-90 (182)
45 PLN03006 carbonate dehydratase 57.6 8.4 0.00018 32.3 2.3 19 57-75 158-176 (301)
46 PRK04296 thymidine kinase; Pro 56.9 10 0.00022 28.3 2.4 28 52-81 63-90 (190)
47 cd01394 radB RadB. The archaea 55.8 53 0.0011 24.2 6.1 42 69-110 103-148 (218)
48 TIGR03878 thermo_KaiC_2 KaiC d 55.5 39 0.00085 26.4 5.6 30 52-81 114-143 (259)
49 cd01125 repA Hexameric Replica 55.3 39 0.00084 25.7 5.4 53 54-109 96-148 (239)
50 PRK15219 carbonic anhydrase; P 52.6 11 0.00025 30.3 2.2 26 55-86 127-152 (245)
51 cd03378 beta_CA_cladeC Carboni 52.5 15 0.00032 27.6 2.7 37 46-88 67-103 (154)
52 PRK09302 circadian clock prote 52.4 50 0.0011 28.2 6.2 74 3-83 63-144 (509)
53 cd00884 beta_CA_cladeB Carboni 51.8 13 0.00028 28.6 2.4 25 56-86 72-96 (190)
54 cd01301 rDP_like renal dipepti 51.4 19 0.00042 29.5 3.4 26 50-75 236-261 (309)
55 PF00265 TK: Thymidine kinase; 50.2 9.5 0.00021 28.8 1.4 15 68-82 75-89 (176)
56 PF05621 TniB: Bacterial TniB 48.8 63 0.0014 27.1 6.1 55 48-108 124-178 (302)
57 TIGR02238 recomb_DMC1 meiotic 48.1 43 0.00093 27.5 5.0 61 50-110 169-236 (313)
58 TIGR02293 TAS_TIGR02293 putati 48.0 3.8 8.2E-05 29.6 -1.1 31 37-67 101-133 (133)
59 PF00580 UvrD-helicase: UvrD/R 47.2 26 0.00056 26.3 3.3 18 65-82 252-269 (315)
60 PF01244 Peptidase_M19: Membra 47.0 22 0.00048 29.2 3.2 26 50-75 244-269 (320)
61 PLN02154 carbonic anhydrase 47.0 17 0.00037 30.4 2.5 20 56-75 151-170 (290)
62 PLN03014 carbonic anhydrase 46.7 16 0.00034 31.4 2.3 25 56-86 205-229 (347)
63 PLN03186 DNA repair protein RA 46.6 48 0.001 27.7 5.1 61 50-110 196-263 (342)
64 PLN00416 carbonate dehydratase 46.4 17 0.00036 29.6 2.3 25 56-86 125-149 (258)
65 TIGR02239 recomb_RAD51 DNA rep 45.9 57 0.0012 26.7 5.3 61 50-110 169-236 (316)
66 PTZ00293 thymidine kinase; Pro 44.0 20 0.00044 28.3 2.4 14 68-81 76-89 (211)
67 PRK10437 carbonic anhydrase; P 43.9 22 0.00047 28.3 2.5 26 55-86 75-100 (220)
68 PF02244 Propep_M14: Carboxype 43.8 33 0.00071 21.5 3.0 25 59-83 46-71 (74)
69 KOG3601|consensus 41.7 12 0.00026 30.4 0.9 42 63-104 2-43 (222)
70 TIGR03880 KaiC_arch_3 KaiC dom 41.1 1E+02 0.0022 22.9 5.7 30 52-81 90-119 (224)
71 PLN03019 carbonic anhydrase 40.7 20 0.00043 30.6 2.0 20 56-75 200-219 (330)
72 PF01407 Gemini_AL3: Geminivir 40.6 9.5 0.00021 28.3 0.1 35 33-67 80-114 (120)
73 TIGR02237 recomb_radB DNA repa 40.5 1E+02 0.0022 22.5 5.5 54 57-110 85-140 (209)
74 PLN03187 meiotic recombination 39.7 82 0.0018 26.5 5.5 65 46-110 195-266 (344)
75 PF09288 UBA_3: Fungal ubiquit 39.4 21 0.00047 23.2 1.6 27 83-109 7-37 (55)
76 PRK05973 replicative DNA helic 39.0 83 0.0018 25.1 5.2 50 53-110 134-183 (237)
77 TIGR01618 phage_P_loop phage n 38.1 53 0.0011 25.9 3.9 38 46-83 57-95 (220)
78 PF00535 Glycos_transf_2: Glyc 37.8 36 0.00079 22.1 2.6 29 48-77 7-35 (169)
79 cd06442 DPM1_like DPM1_like re 37.4 29 0.00062 24.7 2.1 30 48-77 6-35 (224)
80 PRK04301 radA DNA repair and r 34.4 1.1E+02 0.0023 24.6 5.2 56 55-110 183-243 (317)
81 KOG1578|consensus 33.0 26 0.00057 29.3 1.5 23 53-75 136-158 (276)
82 PF00270 DEAD: DEAD/DEAH box h 32.8 37 0.0008 23.2 2.0 31 54-84 103-134 (169)
83 PF13479 AAA_24: AAA domain 31.3 69 0.0015 24.1 3.5 30 52-81 50-80 (213)
84 cd06913 beta3GnTL1_like Beta 1 29.3 31 0.00067 24.9 1.2 30 48-77 6-35 (219)
85 PF00101 RuBisCO_small: Ribulo 28.0 99 0.0021 21.9 3.6 35 44-78 47-85 (99)
86 cd04187 DPM1_like_bac Bacteria 27.3 71 0.0015 22.1 2.7 30 48-77 6-37 (181)
87 COG1435 Tdk Thymidine kinase [ 27.0 47 0.001 26.6 2.0 12 70-81 83-94 (201)
88 TIGR02012 tigrfam_recA protein 26.8 2.1E+02 0.0046 23.9 5.9 50 32-83 97-147 (321)
89 PRK09302 circadian clock prote 26.5 2E+02 0.0043 24.6 5.8 32 52-83 346-377 (509)
90 PF13173 AAA_14: AAA domain 25.9 38 0.00082 23.2 1.1 14 69-82 61-74 (128)
91 PF11328 DUF3130: Protein of u 25.6 71 0.0015 22.8 2.4 53 41-100 27-86 (90)
92 cd07019 S49_SppA_1 Signal pept 25.1 1.3E+02 0.0027 22.9 3.9 29 48-76 17-45 (211)
93 PRK11054 helD DNA helicase IV; 25.0 60 0.0013 29.7 2.5 27 56-82 417-443 (684)
94 cd04188 DPG_synthase DPG_synth 24.5 65 0.0014 23.0 2.2 30 48-77 6-38 (211)
95 PTZ00035 Rad51 protein; Provis 23.7 1.9E+02 0.0042 23.9 5.0 63 48-110 189-258 (337)
96 PRK14464 ribosomal RNA large s 23.0 1.6E+02 0.0035 24.9 4.6 45 51-105 123-167 (344)
97 cd00983 recA RecA is a bacter 22.7 4E+02 0.0087 22.3 6.8 51 32-84 97-148 (325)
98 cd03527 RuBisCO_small Ribulose 21.7 1.4E+02 0.0029 21.3 3.3 33 46-78 51-86 (99)
99 PRK06067 flagellar accessory p 21.7 1.2E+02 0.0027 22.7 3.3 31 52-82 103-133 (234)
100 PLN02726 dolichyl-phosphate be 21.3 83 0.0018 23.4 2.3 32 46-77 16-48 (243)
101 PRK12726 flagellar biosynthesi 20.5 1E+02 0.0023 27.0 3.0 28 51-78 267-294 (407)
102 KOG2884|consensus 20.1 1.7E+02 0.0037 24.4 4.0 32 71-103 6-37 (259)
No 1
>KOG2373|consensus
Probab=100.00 E-value=3.5e-44 Score=303.78 Aligned_cols=107 Identities=31% Similarity=0.467 Sum_probs=98.4
Q ss_pred CCcceecccCCccccchhhHHHhhcCcCc-----hHHHHHHhccCCCee-eccccCCchHHHHHHHHHHHHHhccceEEe
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTTHI-----SSEWEMVLQSSQPLW-LGLRCLSSMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~~~-----~~e~e~~f~~~lPl~-m~f~g~~~i~~V~dam~~avyv~dI~HVii 75 (111)
.||||||||+|+||++||+ .||+|-+.. ..-|++.| +.+|+| |.|||+++++.||++|+||+|||||+||||
T Consensus 303 nTLwgSFEi~n~rla~~mL-~Qyagyrl~drl~~y~HWadrF-Erlplyfmtfhgqq~~~~vi~~i~ha~yV~di~HViI 380 (514)
T KOG2373|consen 303 NTLWGSFEIPNKRLAHWML-VQYAGYRLLDRLNSYKHWADRF-ERLPLYFMTFHGQQFMEKVINEIAHAIYVEDIQHVII 380 (514)
T ss_pred hheeeeeecchHHHHHHHH-HHHccCchHhhhhhhhHHHHHH-hccchHhhhhcccchHHHHHHHHHHHHHHHhhhhhhh
Confidence 5999999999999999996 999998432 25566666 359999 999999999999999999999999999999
Q ss_pred cchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 76 DNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 76 DNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
||||||||++.-+.|||..||+||+.||+|||++|
T Consensus 381 DNLQFmmg~~~~~~Drf~~QD~iig~fR~fAT~nn 415 (514)
T KOG2373|consen 381 DNLQFMMGQGMMALDRFHLQDRIIGYFRQFATQNN 415 (514)
T ss_pred hhHHHHhccchhccchhhhHHHHHHHHHHHhhccc
Confidence 99999999999999999999999999999999998
No 2
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=98.59 E-value=1.8e-07 Score=70.03 Aligned_cols=107 Identities=15% Similarity=0.123 Sum_probs=82.1
Q ss_pred CCcceecccCCccccchhhHHHhhcCcC-------ch-HHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHh
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTTH-------IS-SEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~~-------~~-~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~ 68 (111)
+.||-|+|++.+.+++.++ .+..+.+. .. .+|+.. .-...|+|....++-++++|.+.+++++..+
T Consensus 44 ~vly~s~E~~~~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~i~~~~~~~ 122 (242)
T cd00984 44 PVLFFSLEMSKEQLLQRLL-ASESGISLSKLRTGSLSDEDWERLAEAIGELKELPIYIDDSSSLTVSDIRSRARRLKKEH 122 (242)
T ss_pred ceEEEeCCCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEeCCCCCCHHHHHHHHHHHHHhc
Confidence 4689999999999997653 55565521 11 233321 1135788877778889999999999999999
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++..||||++|-+.... ...++...++.++..||+||.+.|
T Consensus 123 ~~~~vvID~l~~l~~~~-~~~~~~~~~~~~~~~L~~la~~~~ 163 (242)
T cd00984 123 GLGLIVIDYLQLMSGSK-KKGNRQQEVAEISRSLKLLAKELN 163 (242)
T ss_pred CCCEEEEcCchhcCCCC-CCCCHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999875433 346888999999999999998776
No 3
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=98.50 E-value=5.6e-07 Score=68.80 Aligned_cols=107 Identities=17% Similarity=0.071 Sum_probs=78.8
Q ss_pred CCcceecccCCccccchhhHHHhhcCcCc--------h-HHHH---HHhccCCC-eeecc-ccCCchHHHHHHHHHHHHH
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTTHI--------S-SEWE---MVLQSSQP-LWLGL-RCLSSMIHLDLAVEHAMYV 67 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~~~--------~-~e~e---~~f~~~lP-l~m~f-~g~~~i~~V~dam~~avyv 67 (111)
+.+|-|+|++.+.+++.++ .+.++.+.. . .+++ +.+.+ .| +++.. .+..+++++++.+++++.-
T Consensus 61 ~vl~iS~E~~~~~~~~r~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~i~d~~~~~~~~~i~~~i~~~~~~ 138 (271)
T cd01122 61 RVGTISLEEPVVRTARRLL-GQYAGKRLHLPDTVFIYTLEEFDAAFDEFEG-TGRLFMYDSFGEYSMDSVLEKVRYMAVS 138 (271)
T ss_pred eEEEEEcccCHHHHHHHHH-HHHhCCCcccCCccccccHHHHHHHHHHhcC-CCcEEEEcCCCccCHHHHHHHHHHHHhc
Confidence 4689999999999987653 666665321 1 2332 33322 34 44333 3445899999999999999
Q ss_pred hccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 68 YDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 68 ~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
|++..||||++|.|........++...++.++..|+++|.+.|
T Consensus 139 ~~~~~vvID~l~~l~~~~~~~~~~~~~~~~~~~~L~~la~~~~ 181 (271)
T cd01122 139 HGIQHIIIDNLSIMVSDERASGDERKALDEIMTKLRGFATEHG 181 (271)
T ss_pred CCceEEEECCHHHHhccCCCchhHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999999986654456778889999999999998765
No 4
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=98.41 E-value=7.3e-07 Score=73.50 Aligned_cols=106 Identities=12% Similarity=0.030 Sum_probs=83.2
Q ss_pred CCcceecccCCccccchhhHHHhhcCcC--------chHHHHHHh-----ccCCCeeeccccCCchHHHHHHHHHHHHHh
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMVL-----QSSQPLWLGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~f-----~~~lPl~m~f~g~~~i~~V~dam~~avyv~ 68 (111)
..+|.|+||+.+.|+.-++ .+.+|.+. ...+|++.. -...|+|..-.+.-+++++...++....-+
T Consensus 225 ~v~~fSlEm~~~~l~~Rl~-~~~~~v~~~~~~~~~l~~~~~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~~~ 303 (421)
T TIGR03600 225 PVLFFSLEMSAEQLGERLL-ASKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDTGGLTVAQIRSIARRIKRKK 303 (421)
T ss_pred cEEEEECCCCHHHHHHHHH-HHHcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 3689999999999997553 66676631 225565321 135799987788889999999999888777
Q ss_pred -ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 -DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 -dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.-||||.||.|-+. .+.+|......+...++++|.+.|
T Consensus 304 ~~~~lvvIDyLql~~~~--~~~~~~~~~~~i~~~Lk~lAke~~ 344 (421)
T TIGR03600 304 GGLDLIVVDYIQLMAPT--RGRDRNEELGGISRGLKALAKELD 344 (421)
T ss_pred CCCCEEEEecccccCCC--CCCCHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999998753 346788889999999999999876
No 5
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=98.33 E-value=2e-06 Score=70.85 Aligned_cols=107 Identities=17% Similarity=0.130 Sum_probs=81.0
Q ss_pred CCcceecccCCccccchhhHHHhhcCc--------CchHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHh
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~ 68 (111)
+.||-|+||+.+.+..-++ ..-++.+ .-..+|++. .-...|+|..-.+..+++++...++..+.-|
T Consensus 226 ~vl~~SlEm~~~~i~~R~~-~~~~~v~~~~~~~g~l~~~~~~~~~~a~~~l~~~~l~i~d~~~~~~~~i~~~i~~~~~~~ 304 (434)
T TIGR00665 226 PVAFFSLEMSAEQLAMRML-SSESRVDSQKLRTGKLSDEDWEKLTSAAGKLSEAPLYIDDTPGLTITELRAKARRLKREH 304 (434)
T ss_pred eEEEEeCcCCHHHHHHHHH-HHhcCCCHHHhccCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 3578999999999987543 5555553 122556432 1145899977778889999999999999999
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.-||||.||.|-+... +.+|...-..+...|++||.+.|
T Consensus 305 ~~~~vvID~l~~i~~~~~-~~~r~~~i~~i~~~Lk~lA~e~~ 345 (434)
T TIGR00665 305 GLGLIVIDYLQLMSGSGR-SENRQQEVSEISRSLKALAKELN 345 (434)
T ss_pred CCCEEEEcchHhcCCCCC-CCCHHHHHHHHHHHHHHHHHHhC
Confidence 999999999999864432 34666666788999999998765
No 6
>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.
Probab=98.20 E-value=1.2e-06 Score=63.16 Aligned_cols=104 Identities=13% Similarity=-0.018 Sum_probs=57.5
Q ss_pred CCcceecccCCccccchhhHHHhhcC-cCchHHHHHHhc--cCCCeeeccccCCchHHHHHHHHHHHHH-hccceEEecc
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENT-THISSEWEMVLQ--SSQPLWLGLRCLSSMIHLDLAVEHAMYV-YDTGHVIIDN 77 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~-~~~~~e~e~~f~--~~lPl~m~f~g~~~i~~V~dam~~avyv-~dI~HViiDN 77 (111)
.+||-++|.+...+.+.+ .+..+. +.....+..... +.+|++...++...++.+++.++.++.. +++..||||+
T Consensus 72 ~Vl~i~~E~~~~~~~~rl--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~ 149 (193)
T PF13481_consen 72 RVLYISLEDSESQIARRL--RALLQDYDDDANLFFVDLSNWGCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDP 149 (193)
T ss_dssp -EEEEESSS-HHHHHHHH--HHHHTTS-HHHHHHHHHH--E-EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-
T ss_pred eEEEEeccCCHHHHHHHH--HHHhcccCCccceEEeeccccccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcC
Confidence 468999999987888653 333333 222222221111 3566764334444478889999888887 9999999999
Q ss_pred hhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 78 VQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 78 LQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
|+.+.+... +.-.....++..+++||.+.|
T Consensus 150 l~~~~~~~~---~~~~~~~~~~~~l~~la~~~~ 179 (193)
T PF13481_consen 150 LQSLHDGDE---NSNSAVAQLMQELKRLAKEYG 179 (193)
T ss_dssp GGGG--S-T---T-HHHHHHHHHHHHHHHHHH-
T ss_pred HHHHhcCCC---CCHHHHHHHHHHHHHHHHHcC
Confidence 999998832 222223899999999997654
No 7
>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....
Probab=98.13 E-value=4.7e-06 Score=64.10 Aligned_cols=106 Identities=15% Similarity=0.099 Sum_probs=83.8
Q ss_pred CcceecccCCccccchhhHHHhhcCcC-------c-hHHHHHHh-----ccCCCeeeccccCCchHHHHHHHHHHHHH-h
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTH-------I-SSEWEMVL-----QSSQPLWLGLRCLSSMIHLDLAVEHAMYV-Y 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~-------~-~~e~e~~f-----~~~lPl~m~f~g~~~i~~V~dam~~avyv-~ 68 (111)
.|+-|+||+.+++...+ +...++.+. + .++|++.. -+..|+|..-.++.++++|.+.++..... +
T Consensus 51 vly~SlEm~~~~l~~R~-la~~s~v~~~~i~~g~l~~~e~~~~~~~~~~l~~~~l~i~~~~~~~~~~i~~~i~~~~~~~~ 129 (259)
T PF03796_consen 51 VLYFSLEMSEEELAARL-LARLSGVPYNKIRSGDLSDEEFERLQAAAEKLSDLPLYIEDTPSLTIDDIESKIRRLKREGK 129 (259)
T ss_dssp EEEEESSS-HHHHHHHH-HHHHHTSTHHHHHCCGCHHHHHHHHHHHHHHHHTSEEEEEESSS-BHHHHHHHHHHHHHHST
T ss_pred EEEEcCCCCHHHHHHHH-HHHhhcchhhhhhccccCHHHHHHHHHHHHHHhhCcEEEECCCCCCHHHHHHHHHHHHhhcc
Confidence 57899999999999755 488888832 2 26666431 14678887777888999999999988888 9
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.-||||.||-|-... .+.++....+.+...+|++|.+.|
T Consensus 130 ~~~~v~IDyl~ll~~~~-~~~~~~~~~~~i~~~Lk~lA~~~~ 170 (259)
T PF03796_consen 130 KVDVVFIDYLQLLKSED-SSDNRRQEIGEISRELKALAKELN 170 (259)
T ss_dssp TEEEEEEEEGGGSBTSC-SSSCCHHHHHHHHHHHHHHHHHHT
T ss_pred CCCEEEechHHHhcCCC-CCCCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999776655 567788999999999999998765
No 8
>PRK07004 replicative DNA helicase; Provisional
Probab=97.89 E-value=3.4e-05 Score=65.66 Aligned_cols=106 Identities=15% Similarity=0.066 Sum_probs=80.1
Q ss_pred CcceecccCCccccchhhHHHhhcCc--------CchHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHh-
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVY- 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~- 68 (111)
.++-|+||+.+.|+.-++ ...++.+ .-.++|++. .-+..|+|..-.++-++.++...++..+.-+
T Consensus 245 v~~fSlEM~~~ql~~R~l-a~~~~v~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d~~~~~~~~i~~~~r~l~~~~~ 323 (460)
T PRK07004 245 VAVFSMEMPGTQLAMRML-GSVGRLDQHRMRTGRLTDEDWPKLTHAVQKMSEAQLFIDETGGLNPMELRSRARRLARQCG 323 (460)
T ss_pred EEEEeCCCCHHHHHHHHH-HhhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence 578899999999997664 5555542 223677642 1146899987788889999888877665545
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++..||||.||.|.+.. .+.+|...-..|...++.||.+.|
T Consensus 324 ~~~lviIDYLql~~~~~-~~~~r~~ei~~Isr~LK~lAkel~ 364 (460)
T PRK07004 324 KLGLIIIDYLQLMSGSS-QGENRATEISEISRSLKSLAKELD 364 (460)
T ss_pred CCCEEEEChhhhccCCC-CCCcHHHHHHHHHHHHHHHHHHhC
Confidence 59999999999997643 245688888999999999998765
No 9
>PRK05748 replicative DNA helicase; Provisional
Probab=97.69 E-value=0.00013 Score=61.12 Aligned_cols=107 Identities=14% Similarity=0.085 Sum_probs=81.1
Q ss_pred CcceecccCCccccchhhHHHhhcCcC--------chHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHh-
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVY- 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~- 68 (111)
.++-|+||+.+.|+..++ ...++.+. -..+|++. .-...|+|..-.+.-+++++...++..+..+
T Consensus 235 v~~fSlEms~~~l~~R~l-~~~~~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~~i~d~~~~ti~~i~~~~r~~~~~~~ 313 (448)
T PRK05748 235 VAIFSLEMGAESLVMRML-CAEGNIDAQRLRTGQLTDDDWPKLTIAMGSLSDAPIYIDDTPGIKVTEIRARCRRLAQEHG 313 (448)
T ss_pred EEEEeCCCCHHHHHHHHH-HHhcCCCHHHhhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence 467899999999997654 56665532 22566532 1145899988788889999999999998888
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.=||||.||-|-+....+.+|...=..+...|+++|-+.|
T Consensus 314 ~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~LK~lAke~~ 355 (448)
T PRK05748 314 GLGLILIDYLQLIQGSGRSGENRQQEVSEISRSLKALAKELK 355 (448)
T ss_pred CCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHHHHHHHHhC
Confidence 899999999998854433335677667889999999998765
No 10
>PRK06749 replicative DNA helicase; Provisional
Probab=97.67 E-value=0.00017 Score=60.99 Aligned_cols=108 Identities=16% Similarity=0.099 Sum_probs=80.5
Q ss_pred CCcceecccCCccccchhhHHHhhcCc---------Cc-hHHHHHH---h--ccCCCeeeccccCCchHHHHHHHHHHHH
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTT---------HI-SSEWEMV---L--QSSQPLWLGLRCLSSMIHLDLAVEHAMY 66 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~---------~~-~~e~e~~---f--~~~lPl~m~f~g~~~i~~V~dam~~avy 66 (111)
+.+|-|.||+.+.|..-++ ..-++.+ .+ .++|++. + -+.+|+|..-.+.-++.+|...++.-..
T Consensus 216 ~v~~fSlEMs~~ql~~R~l-s~~~~i~~~~l~~~~~~l~~~e~~~~~~a~~~l~~~~i~i~d~~~~t~~~I~~~~r~~~~ 294 (428)
T PRK06749 216 AVGLFSLEMSSKQLLKRMA-SCVGEVSGGRLKNPKHRFAMEDWEKVSKAFAEIGELPLEIYDNAGVTVQDIWMQTRKLKR 294 (428)
T ss_pred CEEEEEeeCCHHHHHHHHH-HhccCCCHHHHhcCcccCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH
Confidence 3578899999999987553 5544432 12 2677632 1 1568999887888899999999988887
Q ss_pred Hhc--cceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 67 VYD--TGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 67 v~d--I~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
.|+ ..-||||.||.|.+....+.+|+..-..|...|+.+|.+.|
T Consensus 295 ~~~~~~~lvvIDyLqli~~~~~~~~~r~~ei~~isr~LK~lAkel~ 340 (428)
T PRK06749 295 KHGDKKILIIVDYLQLITGDPKHKGNRFQEISEISRKLKLLARELN 340 (428)
T ss_pred hcCCCCcEEEEeChhhcCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 887 45999999999876433335688888899999999998765
No 11
>PRK08840 replicative DNA helicase; Provisional
Probab=97.65 E-value=0.00015 Score=62.01 Aligned_cols=106 Identities=9% Similarity=-0.001 Sum_probs=79.0
Q ss_pred CcceecccCCccccchhhHHHhhcCc--------CchHHHHHHh------ccCCCeeeccccCCchHHHHHHHHHHHHHh
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMVL------QSSQPLWLGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~f------~~~lPl~m~f~g~~~i~~V~dam~~avyv~ 68 (111)
.++-|+||+.+.|+.-++ .+.++.+ .-..+|++.. .++.|+|..-.+.-++.++...++..+.-|
T Consensus 249 v~~fSlEMs~~ql~~Rll-a~~s~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~~~ 327 (464)
T PRK08840 249 VLIFSLEMPAEQLMMRML-ASLSRVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAREH 327 (464)
T ss_pred EEEEeccCCHHHHHHHHH-HhhCCCCHHHHhcCCCCHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 578899999999997654 6766652 2237887632 146899987778888999998887766666
Q ss_pred -ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 -DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 -dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++..||||-||.|-+.+. ...|...=..|...|+.+|.+.|
T Consensus 328 ~~~~lvvIDYLql~~~~~~-~~~r~~ei~~isr~LK~lAkel~ 369 (464)
T PRK08840 328 GGLSMIMVDYLQLMRVPAL-SDNRTLEIAEISRSLKALAKELN 369 (464)
T ss_pred CCCCEEEEccHHhcCCCCC-CCchHHHHHHHHHHHHHHHHHhC
Confidence 599999999998853332 23455555789999999998876
No 12
>PRK08506 replicative DNA helicase; Provisional
Probab=97.61 E-value=0.00019 Score=61.18 Aligned_cols=106 Identities=16% Similarity=0.116 Sum_probs=79.8
Q ss_pred CcceecccCCccccchhhHHHhhcCcC--------chHHHHHHh-----ccCCCeeeccccCCchHHHHHHHHHHHHHh-
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMVL-----QSSQPLWLGLRCLSSMIHLDLAVEHAMYVY- 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~f-----~~~lPl~m~f~g~~~i~~V~dam~~avyv~- 68 (111)
.++-|+||+.+.|+..++ .+.++.+. -.++|++.. -...|+|..-.+..++.+|...++....-+
T Consensus 223 V~~fSlEMs~~ql~~Rll-a~~s~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~l~~~~~ 301 (472)
T PRK08506 223 VAFFSLEMPAEQLMLRML-SAKTSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYDSGYVNIHQVRAQLRKLKSQHP 301 (472)
T ss_pred EEEEeCcCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHHcCCeEEECCCCCCHHHHHHHHHHHHHhCC
Confidence 467799999999997654 67676632 225676321 145899987778889999999999876655
Q ss_pred ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.-||||.||-|-+.+. .-+|...-..|...++.+|.+.|
T Consensus 302 ~~~lvvIDyLql~~~~~~-~~~r~~ev~~isr~LK~lAkel~ 342 (472)
T PRK08506 302 EIGLAVIDYLQLMSGSGN-FKDRHLQISEISRGLKLLARELD 342 (472)
T ss_pred CCCEEEEcChhhccCCCC-CCCHHHHHHHHHHHHHHHHHHhC
Confidence 799999999998764332 24677777788999999998765
No 13
>PRK06321 replicative DNA helicase; Provisional
Probab=97.57 E-value=0.00023 Score=61.13 Aligned_cols=107 Identities=14% Similarity=0.101 Sum_probs=78.9
Q ss_pred CcceecccCCccccchhhHHHhhcCcC--------chHHHHHHhc-----cCCCeeeccccCCchHHHHHHHHHHHHHhc
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMVLQ-----SSQPLWLGLRCLSSMIHLDLAVEHAMYVYD 69 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~f~-----~~lPl~m~f~g~~~i~~V~dam~~avyv~d 69 (111)
.+|-|.||+.+.|+.-++ ...++.+. -.++|.+... ...|+|.+-.++-+++++...++..+.-++
T Consensus 258 v~~fSLEMs~~ql~~Rll-a~~s~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~~idd~~~~ti~~i~~~~r~~~~~~~ 336 (472)
T PRK06321 258 VGIFSLEMTVDQLIHRII-CSRSEVESKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKITDLRARARRMKESYD 336 (472)
T ss_pred EEEEeccCCHHHHHHHHH-HhhcCCCHHHhhcCCCCHHHHHHHHHHHHHHHcCCEEEeCCCCCCHHHHHHHHHHHHHhcC
Confidence 468899999999997653 55555531 2367774211 468999777788899999999999999999
Q ss_pred cceEEecchhhhhcCCC--cchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 70 TGHVIIDNVQFMLGLSD--SALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 70 I~HViiDNLQFmmg~~~--~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.-||||-||.|-+.+. ...+|-..=..|...|+.||.+.|
T Consensus 337 ~~lvvIDyLql~~~~~~~~~~~~r~~ei~~Isr~LK~lAkel~ 379 (472)
T PRK06321 337 IQFLIIDYLQLLSGSGNLRNSESRQTEISEISRMLKNLARELN 379 (472)
T ss_pred CCEEEEcchHHcCCCCccCCcchHHHHHHHHHHHHHHHHHHhC
Confidence 99999999999865331 223443333568888999998765
No 14
>PRK05595 replicative DNA helicase; Provisional
Probab=97.52 E-value=0.00029 Score=59.10 Aligned_cols=106 Identities=12% Similarity=0.079 Sum_probs=80.1
Q ss_pred CcceecccCCccccchhhHHHhhcCcC--------chHHHHHHhc-----cCCCeeeccccCCchHHHHHHHHHHHHHhc
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMVLQ-----SSQPLWLGLRCLSSMIHLDLAVEHAMYVYD 69 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~f~-----~~lPl~m~f~g~~~i~~V~dam~~avyv~d 69 (111)
.|+-|+||+.+.++.-++ ..-++.+. -..+|.+... ...|+|..-.+..+++++...++..+..++
T Consensus 233 vl~fSlEms~~~l~~R~~-a~~~~v~~~~~~~~~l~~~e~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~~~~~ 311 (444)
T PRK05595 233 VAIFSLEMSKEQLAYKLL-CSEANVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLKIEHG 311 (444)
T ss_pred EEEEecCCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence 578899999999997653 55555531 1256653211 458999888888999999999999888899
Q ss_pred cceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 70 TGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 70 I~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.=||||-||-|-+.. .+.+|...=..|-..++.+|.+.|
T Consensus 312 ~~~vvIDylql~~~~~-~~~~r~~~v~~is~~LK~lAke~~ 351 (444)
T PRK05595 312 IDMILIDYLQLMSGGK-GSESRQQEVSEISRSIKALAKEME 351 (444)
T ss_pred CCEEEEeHHHhccCCC-CCccHHHHHHHHHHHHHHHHHHhC
Confidence 9999999999885433 234566555788999999998765
No 15
>PRK06904 replicative DNA helicase; Validated
Probab=97.11 E-value=0.0017 Score=55.72 Aligned_cols=107 Identities=10% Similarity=0.023 Sum_probs=76.1
Q ss_pred CCcceecccCCccccchhhHHHhhcCc---------CchHHHHHH------hccCCCeeeccccCCchHHHHHHHHHHHH
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTT---------HISSEWEMV------LQSSQPLWLGLRCLSSMIHLDLAVEHAMY 66 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~---------~~~~e~e~~------f~~~lPl~m~f~g~~~i~~V~dam~~avy 66 (111)
+.|+-|.||+.+.|+.-++ .+.++.+ .-.++|++. ..+..|+|..-.++-++.+|...+.....
T Consensus 252 ~Vl~fSlEMs~~ql~~Rll-a~~s~v~~~~i~~g~~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~ 330 (472)
T PRK06904 252 PVLVFSLEMPAEQIMMRML-ASLSRVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYR 330 (472)
T ss_pred eEEEEeccCCHHHHHHHHH-HhhCCCCHHHhccCCCCCHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHH
Confidence 3578899999999997654 6666642 223677642 22345699777777888998877765554
Q ss_pred Hh-ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 67 VY-DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 67 v~-dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
-+ ++..||||-||.|-+.+. +.+|-..=..|...|+.+|.+.|
T Consensus 331 ~~~~~~lvvIDYLqli~~~~~-~~~r~~ei~~isr~LK~lAkel~ 374 (472)
T PRK06904 331 ENGGLSLIMVDYLQLMRAPGF-EDNRTLEIAEISRSLKALAKELK 374 (472)
T ss_pred hCCCCCEEEEecHHhcCCCCC-CCcHHHHHHHHHHHHHHHHHHhC
Confidence 44 799999999998865432 23455444788999999998876
No 16
>PRK08760 replicative DNA helicase; Provisional
Probab=96.84 E-value=0.004 Score=53.47 Aligned_cols=106 Identities=14% Similarity=0.023 Sum_probs=76.4
Q ss_pred CcceecccCCccccchhhHHHhhcCc--------CchHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHhc
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVYD 69 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~d 69 (111)
.+.-|+||+.+.|+.-++ ..-++.+ .-..+|++. .-.++|+|..-..+-+++++...++..+.-++
T Consensus 261 V~~fSlEMs~~ql~~Rl~-a~~s~i~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d~~~~t~~~I~~~~r~l~~~~~ 339 (476)
T PRK08760 261 VAVFSMEMSASQLAMRLI-SSNGRINAQRLRTGALEDEDWARVTGAIKMLKETKIFIDDTPGVSPEVLRSKCRRLKREHD 339 (476)
T ss_pred eEEEeccCCHHHHHHHHH-HhhCCCcHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEeCCCCCCHHHHHHHHHHHHHhcC
Confidence 356699999998886543 4444332 122566532 11458999777777889999999999988899
Q ss_pred cceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 70 TGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 70 I~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.=||||-||-|-..+ .+..|...=..|...++.+|.+.|
T Consensus 340 ~~lVvIDyLql~~~~~-~~~~r~~ei~~Isr~LK~lAkel~ 379 (476)
T PRK08760 340 LGLIVIDYLQLMSVPG-NSENRATEISEISRSLKGLAKELN 379 (476)
T ss_pred CCEEEEecHHhcCCCC-CCcccHHHHHHHHHHHHHHHHHhC
Confidence 9999999999775332 234566666788899999998765
No 17
>PRK09165 replicative DNA helicase; Provisional
Probab=96.74 E-value=0.0058 Score=52.68 Aligned_cols=106 Identities=17% Similarity=0.129 Sum_probs=79.4
Q ss_pred cceecccCCccccchhhHHHhhcCcC--------chHHHHHHh-----ccCCCeeeccccCCchHHHHHHHHHHHHHhcc
Q psy16186 4 PWDELESKLKKPCPTKSMLEFENTTH--------ISSEWEMVL-----QSSQPLWLGLRCLSSMIHLDLAVEHAMYVYDT 70 (111)
Q Consensus 4 LWgSFE~~~~rl~~~~~m~Qfa~~~~--------~~~e~e~~f-----~~~lPl~m~f~g~~~i~~V~dam~~avyv~dI 70 (111)
|.=|+||+.+.|+.-++ ..-++.+. -.++|++.. -...|+|....+.-++.++...++..+.-+++
T Consensus 264 l~fSlEMs~~ql~~R~l-a~~s~v~~~~i~~~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~~~~~~ 342 (497)
T PRK09165 264 GFFSLEMSAEQLATRIL-SEQSEISSSKIRRGKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLKRQHGL 342 (497)
T ss_pred EEEeCcCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHHHhcCC
Confidence 44599999999987543 55555531 236776422 14689998888888999999999988888999
Q ss_pred ceEEecchhhhhcCCC-cchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 71 GHVIIDNVQFMLGLSD-SALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 71 ~HViiDNLQFmmg~~~-~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
.=||||=||-|-+... .+..|...-..|...++.+|.+.|
T Consensus 343 ~lvvIDyLqli~~~~~~~~~~r~~ev~~is~~LK~lAkel~ 383 (497)
T PRK09165 343 DLLVVDYLQLIRGSSKRSSDNRVQEISEITQGLKALAKELN 383 (497)
T ss_pred CEEEEcchHhccCCCCCCCCchHHHHHHHHHHHHHHHHHhC
Confidence 9999999998865443 235566667888899999998765
No 18
>PRK05636 replicative DNA helicase; Provisional
Probab=96.74 E-value=0.0056 Score=53.21 Aligned_cols=105 Identities=11% Similarity=0.065 Sum_probs=76.3
Q ss_pred cceecccCCccccchhhHHHhhcCc--------CchHHHHHHh-----ccCCCeeeccccCCchHHHHHHHHHHHHHhcc
Q psy16186 4 PWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMVL-----QSSQPLWLGLRCLSSMIHLDLAVEHAMYVYDT 70 (111)
Q Consensus 4 LWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~f-----~~~lPl~m~f~g~~~i~~V~dam~~avyv~dI 70 (111)
+.=|.||+.+.|+.-++ ..-++.+ .-.++|++.. -.+.|+|..-.+.-+++++...++..+.-+++
T Consensus 298 ~~fSlEMs~~ql~~R~l-s~~s~v~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~~~~~ 376 (505)
T PRK05636 298 VIFSLEMSKSEIVMRLL-SAEAEVRLSDMRGGKMDEDAWEKLVQRLGKIAQAPIFIDDSANLTMMEIRSKARRLKQKHDL 376 (505)
T ss_pred EEEEeeCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcCC
Confidence 34599999998886543 5545442 2237776421 14689998878888999999999998888999
Q ss_pred ceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 71 GHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 71 ~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
.=||||-||-|-.. ....+|-..=..|...|+.+|.+.|
T Consensus 377 ~lvvIDYLql~~~~-~~~~~r~~ei~~isr~LK~lAkel~ 415 (505)
T PRK05636 377 KLIVVDYLQLMSSG-KRVESRQQEVSEFSRQLKLLAKELD 415 (505)
T ss_pred CEEEEcchHhcCCC-CCCCcHHHHHHHHHHHHHHHHHHhC
Confidence 99999999987432 2223455445678889999998765
No 19
>PHA02542 41 41 helicase; Provisional
Probab=96.29 E-value=0.014 Score=50.41 Aligned_cols=108 Identities=9% Similarity=0.027 Sum_probs=74.3
Q ss_pred CCcceecccCCccccchhhHHHhhcCcC--c----hHHHHHHhc-----cCCCee--eccccCCchHHHHHHHHHHHHHh
Q psy16186 2 SGPWDELESKLKKPCPTKSMLEFENTTH--I----SSEWEMVLQ-----SSQPLW--LGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 2 sTLWgSFE~~~~rl~~~~~m~Qfa~~~~--~----~~e~e~~f~-----~~lPl~--m~f~g~~~i~~V~dam~~avyv~ 68 (111)
+.|+=|+||+...|...++ ...++.+. + .++|++... ...||| -..-+.-++.++-..++....-+
T Consensus 220 ~Vl~fSLEM~~~ql~~Rl~-a~~~~i~~~~l~~l~~~~~~~~~~~~~~~~~~~l~I~~~d~~~lt~~~ir~~~rrlk~~~ 298 (473)
T PHA02542 220 NVLYISMEMAEEVIAKRID-ANLLDVSLDDIDDLSKAEYKAKMEKLRSKTQGKLIIKQYPTGGAHAGHFRALLNELKLKK 298 (473)
T ss_pred cEEEEeccCCHHHHHHHHH-HHHcCCCHHHHhhcCHHHHHHHHHHHHHHhCCCceeecCCCCCCCHHHHHHHHHHHHHhc
Confidence 3567799999999887654 55565532 1 256764221 246775 34456677777766666555445
Q ss_pred c--cceEEecchhhhhcCC--CcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 D--TGHVIIDNVQFMLGLS--DSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 d--I~HViiDNLQFmmg~~--~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+ +.=||||-||.|-+.. ..+-+|......|-..++.+|-+.|
T Consensus 299 g~~~dlVvIDYLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~ 344 (473)
T PHA02542 299 NFKPDVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHD 344 (473)
T ss_pred CCCCCEEEEechhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhC
Confidence 5 7889999999996331 1236788889999999999998766
No 20
>PRK07773 replicative DNA helicase; Validated
Probab=96.20 E-value=0.014 Score=53.41 Aligned_cols=106 Identities=11% Similarity=0.060 Sum_probs=79.5
Q ss_pred CcceecccCCccccchhhHHHhhcCc--------CchHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHhc
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVYD 69 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~d 69 (111)
.++-|+||+.+.|+.-++ ..-++.+ .-..+|.+. .-...|+|..-.++-+++++...+...+.-++
T Consensus 249 V~~fSlEms~~ql~~R~~-s~~~~i~~~~i~~g~l~~~~~~~~~~a~~~l~~~~i~i~d~~~~~i~~i~~~~r~~~~~~~ 327 (886)
T PRK07773 249 VAIFSLEMSKEQLVMRLL-SAEAKIKLSDMRSGRMSDDDWTRLARAMGEISEAPIFIDDTPNLTVMEIRAKARRLRQEAN 327 (886)
T ss_pred EEEEecCCCHHHHHHHHH-HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence 467899999999987553 4444442 122566532 11468999888888899999999998888899
Q ss_pred cceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 70 TGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 70 I~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.=||||-||-|-+. ....+|...=..|...++.+|-+.|
T Consensus 328 ~~lvvIDyLql~~~~-~~~~~r~~ei~~isr~LK~lAkel~ 367 (886)
T PRK07773 328 LGLIVVDYLQLMTSG-KKYENRQQEVSEISRHLKLLAKELE 367 (886)
T ss_pred CCEEEEcchhhcCCC-CCCCCHHHHHHHHHHHHHHHHHHHC
Confidence 999999999987643 2345677667889999999998765
No 21
>PRK08006 replicative DNA helicase; Provisional
Probab=95.88 E-value=0.034 Score=47.88 Aligned_cols=106 Identities=11% Similarity=0.007 Sum_probs=77.9
Q ss_pred CcceecccCCccccchhhHHHhhcCc--------CchHHHHHH------hccCCCeeeccccCCchHHHHHHHHHHHHHh
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV------LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVY 68 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~------f~~~lPl~m~f~g~~~i~~V~dam~~avyv~ 68 (111)
.+.-|.||+.+.|+.-++ .+.++.+ .-.++|.+. .-++.|+|..-.+.-++.++...++..+--|
T Consensus 256 V~~fSlEM~~~ql~~Rll-a~~~~v~~~~i~~~~l~~~e~~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~~~ 334 (471)
T PRK08006 256 VLIFSLEMPGEQIMMRML-ASLSRVDQTRIRTGQLDDEDWARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFREH 334 (471)
T ss_pred EEEEeccCCHHHHHHHHH-HHhcCCCHHHhhcCCCCHHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHhc
Confidence 356799999999997654 5656553 223677652 2146899988888889999999997777667
Q ss_pred -ccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 -DTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 -dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.=||||=||-|-+.+. +.+|...=..|...|+.+|.+.|
T Consensus 335 ~~~~lvvIDYLqli~~~~~-~~~r~~ei~~isr~LK~lAkel~ 376 (471)
T PRK08006 335 GGLSLIMIDYLQLMRVPSL-SDNRTLEIAEISRSLKALAKELQ 376 (471)
T ss_pred CCCCEEEEccHHHccCCCC-CCCcHHHHHHHHHHHHHHHHHhC
Confidence 799999999998754432 24455444778899999998765
No 22
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=90.92 E-value=0.55 Score=39.44 Aligned_cols=59 Identities=19% Similarity=0.146 Sum_probs=41.0
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCc-chhhhHHHHHHHHHHHhhhcCCC
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDS-ALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~-~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+...+++++++++++ .+++.-||||.+|+|...... +-++...-..++..|+++|.++|
T Consensus 141 l~~e~~le~I~~~i~----~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~lak~~~ 200 (372)
T cd01121 141 LLAETNLEDILASIE----ELKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMRFAKERN 200 (372)
T ss_pred EEccCcHHHHHHHHH----hcCCcEEEEcchHHhhccccccCCCCHHHHHHHHHHHHHHHHHcC
Confidence 345667777777664 478999999999999754432 23344445567788999987765
No 23
>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.
Probab=89.41 E-value=1.2 Score=34.12 Aligned_cols=54 Identities=22% Similarity=0.196 Sum_probs=40.0
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+++++++.+..++--++...||||.|+=+.-.. ....| +++..|.+++++.|
T Consensus 108 ~~~~~~~~~~i~~~i~~~~~~~vVIDSls~l~~~~-~~~~r-----~~l~~l~~~lk~~~ 161 (237)
T TIGR03877 108 PTDVRELIDVLRQAIRDINAKRVVIDSVTTLYITK-PAMAR-----SIVMQLKRVLSGLG 161 (237)
T ss_pred cccHHHHHHHHHHHHHHhCCCEEEEcChhHhhcCC-hHHHH-----HHHHHHHHHHHhCC
Confidence 46899999999999999999999999997543221 11122 56777888776655
No 24
>PRK11823 DNA repair protein RadA; Provisional
Probab=88.31 E-value=1.2 Score=38.14 Aligned_cols=58 Identities=12% Similarity=0.052 Sum_probs=40.7
Q ss_pred ccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcc-hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 49 RCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSA-LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 49 ~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~-~drf~~QD~~I~~fR~fAT~~n 110 (111)
...++++++++.++ -+++.-||||.+|.+......+ .++....-.++..|+++|.++|
T Consensus 140 ~~e~~l~~i~~~i~----~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~ 198 (446)
T PRK11823 140 LAETNLEAILATIE----EEKPDLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRG 198 (446)
T ss_pred eCCCCHHHHHHHHH----hhCCCEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 35567777777664 4788999999999987643222 3444555667788999987765
No 25
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=85.92 E-value=1.6 Score=32.53 Aligned_cols=59 Identities=15% Similarity=0.126 Sum_probs=41.4
Q ss_pred CchHHHHHHHHHHHHHh-ccceEEecchhhhhcCC--Cc--chhhhHHHHHHHHHHHhhhcCCC
Q psy16186 52 SSMIHLDLAVEHAMYVY-DTGHVIIDNVQFMLGLS--DS--ALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~-dI~HViiDNLQFmmg~~--~~--~~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+.++++.++..+--+ ++.-||||.+..+.... .. ..+|...=-+++..++++|.+.|
T Consensus 97 ~~l~~~l~~l~~~l~~~~~~~liVIDSis~~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 160 (235)
T cd01123 97 DHQLQLLEELEAILIESSRIKLVIVDSVTALFRAEFDGRGELAERQQHLAKLLRTLKRLADEFN 160 (235)
T ss_pred HHHHHHHHHHHHHHhhcCCeeEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 34555667777777777 99999999999875422 11 24555555678899999997665
No 26
>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.
Probab=85.56 E-value=2.3 Score=31.44 Aligned_cols=60 Identities=15% Similarity=0.007 Sum_probs=39.7
Q ss_pred CCchHHHHHHHHHHHH---HhccceEEecchhhhhcCCC--c--chhhhHHHHHHHHHHHhhhcCCC
Q psy16186 51 LSSMIHLDLAVEHAMY---VYDTGHVIIDNVQFMLGLSD--S--ALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 51 ~~~i~~V~dam~~avy---v~dI~HViiDNLQFmmg~~~--~--~~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+.+++++.++.... -+++.=||||.++.+..... . ..+|-..=.+++..++++|.++|
T Consensus 93 ~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~ 159 (226)
T cd01393 93 PYNGEQQLEIVEELERIMSSGRVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFN 159 (226)
T ss_pred CCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3456666666665544 67899999999988765321 1 13444444567888999998765
No 27
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=84.65 E-value=2.3 Score=36.53 Aligned_cols=61 Identities=11% Similarity=0.046 Sum_probs=40.1
Q ss_pred eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcc-hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSA-LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~-~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.+...+++++++++++ -++..-||||.+|.|.-....+ -......-..+..|.++|.+.|
T Consensus 151 l~~~~e~~~~~I~~~i~----~~~~~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~~ak~~g 212 (454)
T TIGR00416 151 LYVLSETNWEQICANIE----EENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRG 212 (454)
T ss_pred eEEcCCCCHHHHHHHHH----hcCCcEEEEecchhhcccccccCCCCHHHHHHHHHHHHHHHHHhC
Confidence 33445667777776664 4688899999999986543221 2233344566778888887765
No 28
>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]
Probab=80.89 E-value=4.9 Score=35.13 Aligned_cols=83 Identities=17% Similarity=0.151 Sum_probs=65.9
Q ss_pred cceecccCCccccchhhHHHhhcCc--------CchHHHHHH-----hccCCCeeeccccCCchHHHHHHHHHHHHHhcc
Q psy16186 4 PWDELESKLKKPCPTKSMLEFENTT--------HISSEWEMV-----LQSSQPLWLGLRCLSSMIHLDLAVEHAMYVYDT 70 (111)
Q Consensus 4 LWgSFE~~~~rl~~~~~m~Qfa~~~--------~~~~e~e~~-----f~~~lPl~m~f~g~~~i~~V~dam~~avyv~dI 70 (111)
++-|.||+.+-|+.-++ ..-++.+ ....+|++. .-...|+|..=.+.-++.++-...+--.--|+|
T Consensus 229 ~iFSLEM~~eql~~R~L-s~~s~v~~~kirtg~l~~~d~~~l~~a~~~l~~~~i~IdD~~~~si~eir~~aRrlk~~~~l 307 (435)
T COG0305 229 AIFSLEMSEEQLVMRLL-SSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDTPGLTITEIRSKARRLKLKHNL 307 (435)
T ss_pred EEEEccCCHHHHHHHhh-ccccccchhccccccccHHHHHHHHHHHHHHhhCCeeecCCCcCCHHHHHHHHHHHHHhcCc
Confidence 57799999999986554 3444442 133888853 225689998888999999999999999999999
Q ss_pred ceEEecchhhhhcCCCc
Q psy16186 71 GHVIIDNVQFMLGLSDS 87 (111)
Q Consensus 71 ~HViiDNLQFmmg~~~~ 87 (111)
.-|+||=||.|-|....
T Consensus 308 ~~i~iDYLqLm~~~~~~ 324 (435)
T COG0305 308 GLIVIDYLQLMTGGKKS 324 (435)
T ss_pred cEEEEEEEEeecccccc
Confidence 99999999999998854
No 29
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=77.60 E-value=6.8 Score=26.16 Aligned_cols=61 Identities=11% Similarity=-0.036 Sum_probs=37.7
Q ss_pred eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCc---chhhhHHHHHHHHHHHhhhcC
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDS---ALDRFYMQDTIIQVLLYFLSL 108 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~---~~drf~~QD~~I~~fR~fAT~ 108 (111)
....+...+..+.....+....++..-||||+++.+...... +.++. -.+.+..+..++.+
T Consensus 62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~--~~~~l~~l~~~~~~ 125 (165)
T cd01120 62 FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGE--LDEELRELLERARK 125 (165)
T ss_pred EcCCCCCcHHHHHHHHHHHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChH--HHHHHHHHHHHHhc
Confidence 334444555666667778888899999999999988754321 12222 23445555555543
No 30
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=76.39 E-value=18 Score=27.00 Aligned_cols=31 Identities=16% Similarity=0.230 Sum_probs=29.2
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecchhhh
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNVQFM 81 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNLQFm 81 (111)
..+++++++.+..++--+....||||.|..+
T Consensus 97 ~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l 127 (226)
T PF06745_consen 97 PNDLEELLSKIREAIEELKPDRVVIDSLSAL 127 (226)
T ss_dssp SCCHHHHHHHHHHHHHHHTSSEEEEETHHHH
T ss_pred ccCHHHHHHHHHHHHHhcCCCEEEEECHHHH
Confidence 5789999999999999999999999999888
No 31
>PRK09361 radB DNA repair and recombination protein RadB; Provisional
Probab=74.58 E-value=8.6 Score=28.67 Aligned_cols=58 Identities=14% Similarity=0.124 Sum_probs=33.4
Q ss_pred chHHHHHHHHHHHHH--hccceEEecchhhhhcCC----CcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 53 SMIHLDLAVEHAMYV--YDTGHVIIDNVQFMLGLS----DSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 53 ~i~~V~dam~~avyv--~dI~HViiDNLQFmmg~~----~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.+..+.++..... +.+.-||||.+.-+.... ....+|-..--+++..|+++|.++|
T Consensus 89 ~~~~~~~~i~~~~~~~~~~~~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L~~~a~~~~ 152 (225)
T PRK09361 89 SFEEQSEAIRKAEKLAKENVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHD 152 (225)
T ss_pred CHHHHHHHHHHHHHHHHhcccEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 444444444433322 899999999998665432 1223333333455566888887655
No 32
>COG0288 CynT Carbonic anhydrase [Inorganic ion transport and metabolism]
Probab=71.64 E-value=3.4 Score=32.37 Aligned_cols=26 Identities=27% Similarity=0.359 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 55 IHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 55 ~~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
..++.+++|||++-+|.||| .+|...
T Consensus 76 ~~~l~sleyAv~~L~v~~Ii------V~GH~~ 101 (207)
T COG0288 76 GSVLRSLEYAVYVLGVKEII------VCGHTD 101 (207)
T ss_pred cchhHHHHHHHHHcCCCEEE------EecCCC
Confidence 58999999999999999999 477664
No 33
>PF09722 DUF2384: Protein of unknown function (DUF2384); InterPro: IPR024467 This domain is found predominantly in proteobacterial proteins. Its function in unknown.
Probab=68.73 E-value=1.3 Score=27.09 Aligned_cols=40 Identities=15% Similarity=0.164 Sum_probs=30.5
Q ss_pred cCcCchHHHHH----HhccCCCee-ec-cccCCchHHHHHHHHHHH
Q psy16186 26 NTTHISSEWEM----VLQSSQPLW-LG-LRCLSSMIHLDLAVEHAM 65 (111)
Q Consensus 26 ~~~~~~~e~e~----~f~~~lPl~-m~-f~g~~~i~~V~dam~~av 65 (111)
|.+....+|-. .|++..|+- +. ..|..-|.+++++++|.|
T Consensus 9 gd~~~a~~Wl~~p~~~l~g~~Plel~~t~~G~~~V~~~L~~~~~Gv 54 (54)
T PF09722_consen 9 GDEDKARRWLRTPNPALGGRTPLELLRTEAGAERVLDYLDRIEYGV 54 (54)
T ss_pred CCHHHHHHHHHChHHHhCCCCHHHHHcChHHHHHHHHHHHHHHcCC
Confidence 66666667764 477889985 44 888889999999999865
No 34
>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....
Probab=68.13 E-value=15 Score=28.99 Aligned_cols=60 Identities=13% Similarity=0.127 Sum_probs=42.4
Q ss_pred CCchHHHHHHHH---HHHHHhccceEEecchhhhhcCC----CcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 51 LSSMIHLDLAVE---HAMYVYDTGHVIIDNVQFMLGLS----DSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 51 ~~~i~~V~dam~---~avyv~dI~HViiDNLQFmmg~~----~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
-.+.+++++.++ ....-..|.=||||.+-.+.-.. ....+|-..-.++...+|++|.++|
T Consensus 112 ~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalfr~e~~~~~~~~~R~~~L~~~~~~L~~lA~~~~ 178 (256)
T PF08423_consen 112 VFDLEELLELLEQLPKLLSESKIKLIVIDSIAALFRSEFSGRGDLAERQRMLARLARILKRLARKYN 178 (256)
T ss_dssp -SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHHHHHSGSTTTHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred cCCHHHHHHHHHHHHhhccccceEEEEecchHHHHHHHHccchhhHHHHHHHHHHHHHHHHHHHhCC
Confidence 334445444444 44556789999999998776432 1236788888899999999999876
No 35
>PRK04328 hypothetical protein; Provisional
Probab=66.69 E-value=18 Score=28.16 Aligned_cols=54 Identities=20% Similarity=0.146 Sum_probs=37.6
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+++++++.+..++-.++...||||.+.-+.-.. .... .+++..|.+++.+.|
T Consensus 110 ~~~~~~~~~~i~~~i~~~~~~~vVIDSlt~l~~~~-~~~~-----r~~~~~l~~~lk~~g 163 (249)
T PRK04328 110 PDDVRELIDVLRQAIKDIGAKRVVIDSVSTLYLTK-PAMA-----RSIVMQLKRVLSGLG 163 (249)
T ss_pred cccHHHHHHHHHHHHHhhCCCEEEEeChhHhhcCC-hHHH-----HHHHHHHHHHHHhCC
Confidence 45789999999999999999999999997543211 1111 245666666665443
No 36
>PF00484 Pro_CA: Carbonic anhydrase; InterPro: IPR001765 Carbonic anhydrases (4.2.1.1 from EC) (CA) are zinc metalloenzymes which catalyze the reversible hydration of carbon dioxide. In Escherichia coli, CA (gene cynT) is involved in recycling carbon dioxide formed in the bicarbonate-dependent decomposition of cyanate by cyanase (gene cynS). By this action, it prevents the depletion of cellular bicarbonate []. In photosynthetic bacteria and plant chloroplast, CA is essential to inorganic carbon fixation []. Prokaryotic and plant chloroplast CA are structurally and evolutionary related and form a family distinct from the one which groups the many different forms of eukaryotic CA's (see IPR001148 from INTERPRO). Hypothetical proteins yadF from Escherichia coli and HI1301 from Haemophilus influenzae also belong to this family. This family also includes, YbcF and related proteins, which are inactive homologues of bacterial carbonic anhydrase.; GO: 0004089 carbonate dehydratase activity, 0008270 zinc ion binding; PDB: 1DDZ_B 3LAS_A 2W3N_A 2W3Q_A 1G5C_F 3E2A_A 3E2X_B 2A8C_A 2A8D_D 3E3F_A ....
Probab=66.68 E-value=6.4 Score=28.05 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHHHHhccceEEecchhhhhcCCCcc
Q psy16186 54 MIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSA 88 (111)
Q Consensus 54 i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~ 88 (111)
-..++.+++||++..+|.+|| .+|...-+
T Consensus 38 ~~~~~~sle~av~~l~v~~Ii------V~gHt~CG 66 (153)
T PF00484_consen 38 DDSALASLEYAVYHLGVKEII------VCGHTDCG 66 (153)
T ss_dssp -HHHHHHHHHHHHTST-SEEE------EEEETT-H
T ss_pred ccchhhheeeeeecCCCCEEE------EEcCCCch
Confidence 378899999999999999999 58877644
No 37
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=65.99 E-value=24 Score=23.32 Aligned_cols=45 Identities=16% Similarity=0.188 Sum_probs=34.7
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhc
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLS 107 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT 107 (111)
..+.+++.+.+..+.--+...=|||||+|.+- .+..++.+|.++-
T Consensus 69 ~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~------------~~~~l~~l~~l~~ 113 (131)
T PF13401_consen 69 RQTSDELRSLLIDALDRRRVVLLVIDEADHLF------------SDEFLEFLRSLLN 113 (131)
T ss_dssp TS-HHHHHHHHHHHHHHCTEEEEEEETTHHHH------------THHHHHHHHHHTC
T ss_pred cCCHHHHHHHHHHHHHhcCCeEEEEeChHhcC------------CHHHHHHHHHHHh
Confidence 45778888888888888888899999999965 1666777777654
No 38
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=64.83 E-value=25 Score=24.79 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhccceEEecchhhhhcC
Q psy16186 55 IHLDLAVEHAMYVYDTGHVIIDNVQFMLGL 84 (111)
Q Consensus 55 ~~V~dam~~avyv~dI~HViiDNLQFmmg~ 84 (111)
++++..+..++..++..-||||+++-++..
T Consensus 81 ~~~~~~i~~~~~~~~~~~lviD~~~~~~~~ 110 (187)
T cd01124 81 LELIQRLKDAIEEFKAKRVVIDSVSGLLLM 110 (187)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeCcHHHhhc
Confidence 378889999999999999999999877654
No 39
>cd03379 beta_CA_cladeD Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=62.68 E-value=8.5 Score=27.88 Aligned_cols=35 Identities=11% Similarity=0.084 Sum_probs=26.2
Q ss_pred eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
.+=-|..=...++.+++||++..++++||+ +|...
T Consensus 31 iRnaGn~V~~~~~~sl~~av~~l~~~~IiV------~gHt~ 65 (142)
T cd03379 31 IRNAGGRVTDDAIRSLVVSVYLLGTREIIV------IHHTD 65 (142)
T ss_pred EeccCCccCHhHHHHHHHHHHHhCCCEEEE------EeecC
Confidence 444455433579999999999999999994 66653
No 40
>cd00382 beta_CA Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=61.22 E-value=26 Score=24.75 Aligned_cols=54 Identities=13% Similarity=0.108 Sum_probs=35.6
Q ss_pred eccccCCchH---HHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhh
Q psy16186 46 LGLRCLSSMI---HLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYF 105 (111)
Q Consensus 46 m~f~g~~~i~---~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~f 105 (111)
.+=-|..=.. .++.+++||++..+|.||| .+|..+=+.=+......+..-.+++
T Consensus 31 ~Rn~Gn~v~~~~~~~~~sl~~av~~l~v~~iv------V~gHt~CG~v~a~~~~nV~~~v~~L 87 (119)
T cd00382 31 VRNAGNLVPPYDLDVLASLEYAVEVLGVKHII------VCGHTDCGAVKALVEENVREQVENL 87 (119)
T ss_pred EeccCCcCCCCcccHHHHHHHHHHhhCCCEEE------EEccCCCcHHHHHHHHHHHHHHHHH
Confidence 3444444333 7999999999999999999 5888764443334445554444443
No 41
>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.
Probab=59.69 E-value=31 Score=25.68 Aligned_cols=33 Identities=21% Similarity=0.092 Sum_probs=26.8
Q ss_pred CCchHHHHHHHHHHHHHhccc--eEEecchhhhhc
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTG--HVIIDNVQFMLG 83 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~--HViiDNLQFmmg 83 (111)
..+++++.++++.++-.++.. -||||.++-++-
T Consensus 101 ~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~ 135 (229)
T TIGR03881 101 ELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWL 135 (229)
T ss_pred cCCHHHHHHHHHHHHHhhccCceEEEecCchhhhc
Confidence 457899999999998887644 599999987753
No 42
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=59.14 E-value=9.5 Score=29.19 Aligned_cols=27 Identities=15% Similarity=-0.005 Sum_probs=23.7
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEe
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HVii 75 (111)
-.|++++.-++|||+.+ |..+|.++||
T Consensus 85 ~kG~~Dv~laIDame~~-~~~~iD~~vL 111 (160)
T TIGR00288 85 VAGDVDVRMAVEAMELI-YNPNIDAVAL 111 (160)
T ss_pred ecCcccHHHHHHHHHHh-ccCCCCEEEE
Confidence 35899999999999996 7889999994
No 43
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=57.77 E-value=11 Score=31.66 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=23.1
Q ss_pred CCchHHHHHHHHHHHHHhccceEEe
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HVii 75 (111)
..+++++++.|+|.|-+.++.||.|
T Consensus 234 ~atldd~v~hI~h~v~~~G~dhVgl 258 (313)
T COG2355 234 RATLDDLVRHIDHFVELVGIDHVGL 258 (313)
T ss_pred CCCHHHHHHHHHHHHHhcCcceeEe
Confidence 4589999999999999999999984
No 44
>cd00883 beta_CA_cladeA Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=57.72 E-value=9.2 Score=28.94 Aligned_cols=25 Identities=20% Similarity=0.203 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 56 HLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
.++-++||||+.-+|.||| .+|.+.
T Consensus 66 ~~~asleyAv~~L~v~~Iv------V~GHs~ 90 (182)
T cd00883 66 NCLSVLQYAVDVLKVKHII------VCGHYG 90 (182)
T ss_pred chhhhHHHHHHhcCCCEEE------EecCCC
Confidence 4889999999999999999 477765
No 45
>PLN03006 carbonate dehydratase
Probab=57.58 E-value=8.4 Score=32.33 Aligned_cols=19 Identities=11% Similarity=0.328 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHhccceEEe
Q psy16186 57 LDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 57 V~dam~~avyv~dI~HVii 75 (111)
++.++||||+.-+|.|||+
T Consensus 158 ~~aSLEYAV~~L~V~~IVV 176 (301)
T PLN03006 158 TKAALEFSVNTLNVENILV 176 (301)
T ss_pred hhhhHHHHHHHhCCCEEEE
Confidence 6789999999999999994
No 46
>PRK04296 thymidine kinase; Provisional
Probab=56.93 E-value=10 Score=28.28 Aligned_cols=28 Identities=29% Similarity=0.252 Sum_probs=19.1
Q ss_pred CchHHHHHHHHHHHHHhccceEEecchhhh
Q psy16186 52 SSMIHLDLAVEHAMYVYDTGHVIIDNVQFM 81 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~dI~HViiDNLQFm 81 (111)
.+.+++++.++. -..++.-||||++||+
T Consensus 63 ~~~~~~~~~~~~--~~~~~dvviIDEaq~l 90 (190)
T PRK04296 63 SSDTDIFELIEE--EGEKIDCVLIDEAQFL 90 (190)
T ss_pred CChHHHHHHHHh--hCCCCCEEEEEccccC
Confidence 445666666554 3346677999999985
No 47
>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=55.78 E-value=53 Score=24.21 Aligned_cols=42 Identities=12% Similarity=0.252 Sum_probs=25.8
Q ss_pred ccceEEecchhhhhcCCC----cchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 69 DTGHVIIDNVQFMLGLSD----SALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 69 dI~HViiDNLQFmmg~~~----~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
++.=||||.++.+..... ...++...--+++..++++|.++|
T Consensus 103 ~~~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~~a~~~~ 148 (218)
T cd01394 103 KVDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHD 148 (218)
T ss_pred CCcEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHHHHHHhC
Confidence 478899999998742111 112333333445667888887665
No 48
>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.
Probab=55.48 E-value=39 Score=26.44 Aligned_cols=30 Identities=17% Similarity=0.257 Sum_probs=26.7
Q ss_pred CchHHHHHHHHHHHHHhccceEEecchhhh
Q psy16186 52 SSMIHLDLAVEHAMYVYDTGHVIIDNVQFM 81 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~dI~HViiDNLQFm 81 (111)
.+++++++.+..++--+++.-||||-++.+
T Consensus 114 ~~~~~l~~~l~~~i~~~~~~~vVIDSls~l 143 (259)
T TIGR03878 114 ENVPNLLATLAYAIKEYKVKNTVIDSITGL 143 (259)
T ss_pred hhHHHHHHHHHHHHHhhCCCEEEEcCchHh
Confidence 468889999999999999999999999654
No 49
>cd01125 repA Hexameric Replicative Helicase RepA. RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.
Probab=55.26 E-value=39 Score=25.65 Aligned_cols=53 Identities=17% Similarity=0.170 Sum_probs=35.8
Q ss_pred hHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCC
Q psy16186 54 MIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLP 109 (111)
Q Consensus 54 i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~ 109 (111)
....++++...+-..++.=||||.+.-.-+. ...|. ..++.++..++++|.+.
T Consensus 96 ~~~~~~~l~~~~~~~~~~lvviDpl~~~~~~--~~~d~-~~~~~~~~~L~~~a~~~ 148 (239)
T cd01125 96 VVPEFERIIEQLLIRRIDLVVIDPLVSFHGV--SENDN-GAMDAVIKALRRIAAQT 148 (239)
T ss_pred ccHHHHHHHHHHHhcCCCEEEECChHHhCCC--CcCCH-HHHHHHHHHHHHHHHHh
Confidence 3455666666666789999999999766222 22333 45677899999988653
No 50
>PRK15219 carbonic anhydrase; Provisional
Probab=52.57 E-value=11 Score=30.28 Aligned_cols=26 Identities=23% Similarity=0.188 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 55 IHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 55 ~~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
+.++.++||||++-+|.|||+ +|.+.
T Consensus 127 ~~~~~slEyAv~~L~v~~IvV------lGHt~ 152 (245)
T PRK15219 127 DDLLGSMEFACAVAGAKVVLV------MGHTA 152 (245)
T ss_pred cchhhHHHHHHHHcCCCEEEE------ecCCc
Confidence 458899999999999999994 66654
No 51
>cd03378 beta_CA_cladeC Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=52.50 E-value=15 Score=27.63 Aligned_cols=37 Identities=16% Similarity=0.047 Sum_probs=28.2
Q ss_pred eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcc
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSA 88 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~ 88 (111)
.+=-|..=...++.+++|||+.-+|.||| .+|...-+
T Consensus 67 iRn~gn~v~~~~~~sl~yav~~l~v~~Iv------V~GHt~CG 103 (154)
T cd03378 67 VRVAGNIVDDDVLGSLEYAVEVLGVPLVV------VLGHESCG 103 (154)
T ss_pred EeccccccChhHHHHHHHHHHHhCCCEEE------EEcCCCcc
Confidence 44444443356899999999999999999 58888644
No 52
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=52.36 E-value=50 Score=28.22 Aligned_cols=74 Identities=12% Similarity=0.082 Sum_probs=47.1
Q ss_pred CcceecccCCccccchhhHHHhhcCcCchHHHHHHhccCC------Ce-e-eccccCCchHHHHHHHHHHHHHhccceEE
Q psy16186 3 GPWDELESKLKKPCPTKSMLEFENTTHISSEWEMVLQSSQ------PL-W-LGLRCLSSMIHLDLAVEHAMYVYDTGHVI 74 (111)
Q Consensus 3 TLWgSFE~~~~rl~~~~~m~Qfa~~~~~~~e~e~~f~~~l------Pl-~-m~f~g~~~i~~V~dam~~avyv~dI~HVi 74 (111)
.||-|+|.+.+.+...+ ..| |-+ .+++.. ++.+ |. . -.-.+..+++.+++.+..++..++..+||
T Consensus 63 ~lyis~ee~~~~i~~~~--~~~-g~d--~~~~~~--~g~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vV 135 (509)
T PRK09302 63 GVFVTFEESPEDIIRNV--ASF-GWD--LQKLID--EGKLFILDASPDPSEQEEAGEYDLEALFIRIEYAIDKIGAKRVV 135 (509)
T ss_pred EEEEEccCCHHHHHHHH--HHc-CCC--HHHHhh--CCeEEEEecCcccccccccccccHHHHHHHHHHHHHhhCCCEEE
Confidence 47888888888877653 344 221 123321 0111 11 0 01134567899999999999999999999
Q ss_pred ecchhhhhc
Q psy16186 75 IDNVQFMLG 83 (111)
Q Consensus 75 iDNLQFmmg 83 (111)
||.+.-+..
T Consensus 136 IDSls~l~~ 144 (509)
T PRK09302 136 LDSIEALFS 144 (509)
T ss_pred ECCHHHHHh
Confidence 999986543
No 53
>cd00884 beta_CA_cladeB Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=51.80 E-value=13 Score=28.58 Aligned_cols=25 Identities=32% Similarity=0.452 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 56 HLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
.++-++||||+.-+|.|||| +|...
T Consensus 72 ~~~asleyav~~l~v~~ivV------~GH~~ 96 (190)
T cd00884 72 GTSAAIEYAVAVLKVEHIVV------CGHSD 96 (190)
T ss_pred chhhhHHHHHHHhCCCEEEE------eCCCc
Confidence 48899999999999999994 66653
No 54
>cd01301 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
Probab=51.37 E-value=19 Score=29.48 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=24.0
Q ss_pred cCCchHHHHHHHHHHHHHhccceEEe
Q psy16186 50 CLSSMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 50 g~~~i~~V~dam~~avyv~dI~HVii 75 (111)
+..+++++++.++|.+.+.+++||-|
T Consensus 236 ~~~~~~~~~~hi~~i~~l~G~dhVgi 261 (309)
T cd01301 236 ADATLDDVVRHIDYIVDLIGIDHVGL 261 (309)
T ss_pred CCCCHHHHHHHHHHHHHhcCCCeEEE
Confidence 46889999999999999999999975
No 55
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=50.21 E-value=9.5 Score=28.77 Aligned_cols=15 Identities=33% Similarity=0.337 Sum_probs=12.7
Q ss_pred hccceEEecchhhhh
Q psy16186 68 YDTGHVIIDNVQFML 82 (111)
Q Consensus 68 ~dI~HViiDNLQFmm 82 (111)
.++..|+|||.||+-
T Consensus 75 ~~~dvI~IDEaQFf~ 89 (176)
T PF00265_consen 75 NDYDVIGIDEAQFFD 89 (176)
T ss_dssp TTCSEEEESSGGGST
T ss_pred cCCCEEEEechHhhH
Confidence 348899999999974
No 56
>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].
Probab=48.85 E-value=63 Score=27.14 Aligned_cols=55 Identities=18% Similarity=0.154 Sum_probs=41.5
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcC
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSL 108 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~ 108 (111)
+....++.+.-....+-.-..++.=+||||++.++-++. ..|=.+...+|.++.+
T Consensus 124 ~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~------~~qr~~Ln~LK~L~Ne 178 (302)
T PF05621_consen 124 YRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSY------RKQREFLNALKFLGNE 178 (302)
T ss_pred cCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccH------HHHHHHHHHHHHHhhc
Confidence 445556666555566777788999999999999876653 4588888899888654
No 57
>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=48.12 E-value=43 Score=27.49 Aligned_cols=61 Identities=11% Similarity=-0.030 Sum_probs=38.0
Q ss_pred cCCchHHHHHHHHH---HHHHhccceEEecchhhhhcCCCc----chhhhHHHHHHHHHHHhhhcCCC
Q psy16186 50 CLSSMIHLDLAVEH---AMYVYDTGHVIIDNVQFMLGLSDS----ALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 50 g~~~i~~V~dam~~---avyv~dI~HViiDNLQFmmg~~~~----~~drf~~QD~~I~~fR~fAT~~n 110 (111)
...+.++.++.++. .+.-.++.=||||-++.+.-.... ..+|-..=.+++.+++++|.++|
T Consensus 169 ~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSisal~r~~~~~~g~~~~r~~~l~~~~~~L~~la~~~~ 236 (313)
T TIGR02238 169 RAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKISEEFN 236 (313)
T ss_pred cCCCHHHHHHHHHHHHHHhhccCCCEEEEEcchHhhhhhccCccchHHHHHHHHHHHHHHHHHHHHcC
Confidence 33445555544443 445568999999999987643221 13332223467788999998776
No 58
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=47.98 E-value=3.8 Score=29.56 Aligned_cols=31 Identities=19% Similarity=0.102 Sum_probs=26.0
Q ss_pred HhccCCCee-e-ccccCCchHHHHHHHHHHHHH
Q psy16186 37 VLQSSQPLW-L-GLRCLSSMIHLDLAVEHAMYV 67 (111)
Q Consensus 37 ~f~~~lPl~-m-~f~g~~~i~~V~dam~~avyv 67 (111)
.|++..|+- + ...|.+.|.++++.|+|.||.
T Consensus 101 ~lgg~~Pldll~t~~G~~~V~~~L~rie~G~~s 133 (133)
T TIGR02293 101 GLGNRRPIDLLLTEAGAEIVEDLLGRLEYGVYA 133 (133)
T ss_pred hhCCCCHHHHHcCHHHHHHHHHHHHHHHcCCCC
Confidence 377889985 4 788899999999999999883
No 59
>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....
Probab=47.17 E-value=26 Score=26.32 Aligned_cols=18 Identities=22% Similarity=0.172 Sum_probs=13.4
Q ss_pred HHHhccceEEecchhhhh
Q psy16186 65 MYVYDTGHVIIDNVQFML 82 (111)
Q Consensus 65 vyv~dI~HViiDNLQFmm 82 (111)
.+..-+.||+|||.|-.-
T Consensus 252 ~~~~~~~~i~IDE~QD~s 269 (315)
T PF00580_consen 252 KIRQRYDHILIDEFQDTS 269 (315)
T ss_dssp HHHHHSSEEEESSGGG-B
T ss_pred HHHhhCCeEEeEccccCC
Confidence 344678999999999753
No 60
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=46.99 E-value=22 Score=29.17 Aligned_cols=26 Identities=19% Similarity=0.060 Sum_probs=21.9
Q ss_pred cCCchHHHHHHHHHHHHHhccceEEe
Q psy16186 50 CLSSMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 50 g~~~i~~V~dam~~avyv~dI~HVii 75 (111)
+..+++++++.++|.+.+-++.||-|
T Consensus 244 ~~~~~~~~~~Hi~y~~~l~G~dhVgi 269 (320)
T PF01244_consen 244 PRASLDDLVDHIDYIVDLVGIDHVGI 269 (320)
T ss_dssp SG-BHHHHHHHHHHHHHHH-GGGEEE
T ss_pred ccccHHHHHHHHHHHHHhcCCCeEEE
Confidence 44589999999999999999999974
No 61
>PLN02154 carbonic anhydrase
Probab=46.95 E-value=17 Score=30.39 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhccceEEe
Q psy16186 56 HLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HVii 75 (111)
.++.++||||+.-+|.|||+
T Consensus 151 ~~~aslEyAv~~L~v~~IvV 170 (290)
T PLN02154 151 ETNSALEFAVTTLQVENIIV 170 (290)
T ss_pred chhhHHHHHHHHhCCCEEEE
Confidence 47789999999999999994
No 62
>PLN03014 carbonic anhydrase
Probab=46.66 E-value=16 Score=31.42 Aligned_cols=25 Identities=20% Similarity=0.352 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 56 HLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
.++.++||||++-+|.||| .+|+..
T Consensus 205 ~v~asLEYAV~~L~V~~IV------V~GHs~ 229 (347)
T PLN03014 205 GVGAAIEYAVLHLKVENIV------VIGHSA 229 (347)
T ss_pred cchhHHHHHHHHhCCCEEE------EeCCCC
Confidence 3788999999999999999 466653
No 63
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=46.58 E-value=48 Score=27.75 Aligned_cols=61 Identities=13% Similarity=-0.043 Sum_probs=38.0
Q ss_pred cCCchHHHHHHHHHH---HHHhccceEEecchhhhhcCCCcc-hhhhHHH---HHHHHHHHhhhcCCC
Q psy16186 50 CLSSMIHLDLAVEHA---MYVYDTGHVIIDNVQFMLGLSDSA-LDRFYMQ---DTIIQVLLYFLSLPN 110 (111)
Q Consensus 50 g~~~i~~V~dam~~a---vyv~dI~HViiDNLQFmmg~~~~~-~drf~~Q---D~~I~~fR~fAT~~n 110 (111)
...+.++.++.+..+ +.-+++.-||||-++.+.-....+ .+-..+| -+++..++++|.++|
T Consensus 196 ~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA~~~~ 263 (342)
T PLN03186 196 RAYNTDHQSELLLEAASMMAETRFALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLADEFG 263 (342)
T ss_pred ecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHHHcC
Confidence 344566665555443 556789999999999875432111 1112333 467788889998776
No 64
>PLN00416 carbonate dehydratase
Probab=46.40 E-value=17 Score=29.59 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 56 HLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
.++-++||||.+-+|.|||+ +|.+.
T Consensus 125 ~~~asLEyAv~~L~V~~IVV------~GHs~ 149 (258)
T PLN00416 125 GVGAAVEYAVVHLKVENILV------IGHSC 149 (258)
T ss_pred cchhHHHHHHHHhCCCEEEE------ecCCC
Confidence 47789999999999999994 66653
No 65
>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=45.88 E-value=57 Score=26.70 Aligned_cols=61 Identities=13% Similarity=-0.007 Sum_probs=38.6
Q ss_pred cCCchHHHHHHHHHH---HHHhccceEEecchhhhhcCCCc--c--hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 50 CLSSMIHLDLAVEHA---MYVYDTGHVIIDNVQFMLGLSDS--A--LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 50 g~~~i~~V~dam~~a---vyv~dI~HViiDNLQFmmg~~~~--~--~drf~~QD~~I~~fR~fAT~~n 110 (111)
...+.+++++.++.+ +.-..+.=||||-++.+.-.... + ..|-..=.+++..++++|.++|
T Consensus 169 ~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la~~~~ 236 (316)
T TIGR02239 169 RAYNTDHQLQLLQQAAAMMSESRFALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLADEFG 236 (316)
T ss_pred ecCChHHHHHHHHHHHHhhccCCccEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHHHHhC
Confidence 344566666666554 44567889999999988543211 1 1333222577889999998765
No 66
>PTZ00293 thymidine kinase; Provisional
Probab=44.03 E-value=20 Score=28.31 Aligned_cols=14 Identities=29% Similarity=0.387 Sum_probs=12.2
Q ss_pred hccceEEecchhhh
Q psy16186 68 YDTGHVIIDNVQFM 81 (111)
Q Consensus 68 ~dI~HViiDNLQFm 81 (111)
.++.-|+||+.||+
T Consensus 76 ~~~dvI~IDEaQFf 89 (211)
T PTZ00293 76 KNYDVIAIDEGQFF 89 (211)
T ss_pred cCCCEEEEEchHhh
Confidence 56778999999997
No 67
>PRK10437 carbonic anhydrase; Provisional
Probab=43.86 E-value=22 Score=28.32 Aligned_cols=26 Identities=23% Similarity=0.295 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHhccceEEecchhhhhcCCC
Q psy16186 55 IHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSD 86 (111)
Q Consensus 55 ~~V~dam~~avyv~dI~HViiDNLQFmmg~~~ 86 (111)
..++-+++|||.+-+|.||| .+|...
T Consensus 75 ~~~~~~leyAV~~L~v~~Iv------V~GHt~ 100 (220)
T PRK10437 75 LNCLSVVQYAVDVLEVEHII------ICGHYG 100 (220)
T ss_pred cchHHHHHHHHHHcCCCEEE------EeCCCC
Confidence 35789999999999999999 476654
No 68
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=43.84 E-value=33 Score=21.49 Aligned_cols=25 Identities=20% Similarity=0.226 Sum_probs=15.0
Q ss_pred HHHHHHHHHhccce-EEecchhhhhc
Q psy16186 59 LAVEHAMYVYDTGH-VIIDNVQFMLG 83 (111)
Q Consensus 59 dam~~avyv~dI~H-ViiDNLQFmmg 83 (111)
+..+.-.-.++|.| |+|||+|-++-
T Consensus 46 ~~f~~~L~~~~i~~~v~i~dvq~~Id 71 (74)
T PF02244_consen 46 EEFEELLKEHGIEYEVLIEDVQKLID 71 (74)
T ss_dssp HHHHHHHHHTT-EEEEEES-HHHHHH
T ss_pred HHHHHHHHHCCCcEEEEeHHHHHHHH
Confidence 34444445677776 67999998764
No 69
>KOG3601|consensus
Probab=41.69 E-value=12 Score=30.41 Aligned_cols=42 Identities=19% Similarity=-0.065 Sum_probs=36.9
Q ss_pred HHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHh
Q psy16186 63 HAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLY 104 (111)
Q Consensus 63 ~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~ 104 (111)
+|++.||..-=|=|+|+|+-|-.-...+.++.++.-+.+++-
T Consensus 2 ea~a~n~f~a~i~dELsFlkg~~lk~l~~~d~~nw~~ael~g 43 (222)
T KOG3601|consen 2 EAVAKNDFLAGIRDELSFLKGDNLKILNMEDDINWYKAELDG 43 (222)
T ss_pred chhhhhhhhhcCcccceeecCCceEecchHHhhhhhhHhhcC
Confidence 689999999999999999999988888999888887777653
No 70
>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.
Probab=41.14 E-value=1e+02 Score=22.90 Aligned_cols=30 Identities=13% Similarity=0.280 Sum_probs=25.8
Q ss_pred CchHHHHHHHHHHHHHhccceEEecchhhh
Q psy16186 52 SSMIHLDLAVEHAMYVYDTGHVIIDNVQFM 81 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~dI~HViiDNLQFm 81 (111)
..++++.+.+...+.-+++..||||-++.+
T Consensus 90 ~~~~~l~~~~~~~i~~~~~~~vVIDsls~l 119 (224)
T TIGR03880 90 TSLNRIKNELPILIKELGASRVVIDPISLL 119 (224)
T ss_pred hhHHHHHHHHHHHHHHhCCCEEEEcChHHH
Confidence 347788888888888899999999999986
No 71
>PLN03019 carbonic anhydrase
Probab=40.72 E-value=20 Score=30.59 Aligned_cols=20 Identities=15% Similarity=0.308 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhccceEEe
Q psy16186 56 HLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HVii 75 (111)
.++-++||||.+-+|.|||+
T Consensus 200 ~v~aSIEYAV~~L~V~~IVV 219 (330)
T PLN03019 200 GVGAAIEYAVLHLKVENIVV 219 (330)
T ss_pred ccchhHHHHHHHhCCCEEEE
Confidence 47889999999999999994
No 72
>PF01407 Gemini_AL3: Geminivirus AL3 protein; InterPro: IPR000657 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL3 protein comprises approximately 0.05% of the cellular proteins and is present in the soluble and organelle fractions []. AL3 may form oligomers []. Immunoprecipitation of AL3 in a baculovirus expression system extracts expressing both AL1 and AL3 showed that the two proteins also complex with each other. The AL3 protein is involved in viral replication. ; GO: 0016032 viral reproduction
Probab=40.57 E-value=9.5 Score=28.35 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=31.1
Q ss_pred HHHHHhccCCCeeeccccCCchHHHHHHHHHHHHH
Q psy16186 33 EWEMVLQSSQPLWLGLRCLSSMIHLDLAVEHAMYV 67 (111)
Q Consensus 33 e~e~~f~~~lPl~m~f~g~~~i~~V~dam~~avyv 67 (111)
.|-++|..++-.|++=-|-=||..|+.|++|+.|-
T Consensus 80 ~fLrvFk~qv~~yL~nLGvISINnVIrav~hvl~~ 114 (120)
T PF01407_consen 80 RFLRVFKTQVLKYLDNLGVISINNVIRAVNHVLYN 114 (120)
T ss_pred hHHHHHHHHHHHHHHhcCceeehhHHHHHHhhhHh
Confidence 38888888888889999999999999999999874
No 73
>TIGR02237 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).
Probab=40.52 E-value=1e+02 Score=22.48 Aligned_cols=54 Identities=13% Similarity=0.067 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhccceEEecchhhhhcCCC--cchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 57 LDLAVEHAMYVYDTGHVIIDNVQFMLGLSD--SALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 57 V~dam~~avyv~dI~HViiDNLQFmmg~~~--~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
.++.+...+--+++.=||||.+..+..... ...+|-..--+.+..++++|.++|
T Consensus 85 ~~~~l~~~~~~~~~~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~ 140 (209)
T TIGR02237 85 AIQKTSKFIDRDSASLVVVDSFTALYRLELSDDRISRNRELARQLTLLLSLARKKN 140 (209)
T ss_pred HHHHHHHHHhhcCccEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHHHHHHHHHcC
Confidence 355554445556889999999987653221 111222111234566888886654
No 74
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=39.71 E-value=82 Score=26.48 Aligned_cols=65 Identities=12% Similarity=-0.034 Sum_probs=40.9
Q ss_pred eccccCCchHHHHHHHHH---HHHHhccceEEecchhhhhcCCC--cc--hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 46 LGLRCLSSMIHLDLAVEH---AMYVYDTGHVIIDNVQFMLGLSD--SA--LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~---avyv~dI~HViiDNLQFmmg~~~--~~--~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+....++++.++.+.. .+.-+++.=||||-+..+.-... ++ .+|-..=-+.+..++++|.++|
T Consensus 195 I~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSital~r~~~~~rg~l~~rq~~L~~~~~~L~~lA~~~~ 266 (344)
T PLN03187 195 IIYARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGELAERQQKLAQMLSRLTKIAEEFN 266 (344)
T ss_pred EEEecCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHhhhccccCccchHHHHHHHHHHHHHHHHHHHHcC
Confidence 345555677766555443 45567899999999998765422 11 2332222356778888888765
No 75
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=39.36 E-value=21 Score=23.19 Aligned_cols=27 Identities=22% Similarity=0.359 Sum_probs=16.1
Q ss_pred cCCCcchhhhHHH----HHHHHHHHhhhcCC
Q psy16186 83 GLSDSALDRFYMQ----DTIIQVLLYFLSLP 109 (111)
Q Consensus 83 g~~~~~~drf~~Q----D~~I~~fR~fAT~~ 109 (111)
|....-+|+|..| |++|++||+.-=++
T Consensus 7 Gi~~~lVd~F~~mGF~~dkVvevlrrlgik~ 37 (55)
T PF09288_consen 7 GIDKDLVDQFENMGFERDKVVEVLRRLGIKS 37 (55)
T ss_dssp --SHHHHHHHHHHT--HHHHHHHHHHS--SS
T ss_pred CCCHHHHHHHHHcCCcHHHHHHHHHHhCCCC
Confidence 4443336666654 89999999976554
No 76
>PRK05973 replicative DNA helicase; Provisional
Probab=38.95 E-value=83 Score=25.06 Aligned_cols=50 Identities=12% Similarity=0.054 Sum_probs=31.3
Q ss_pred chHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhhhcCCC
Q psy16186 53 SMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 53 ~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~fAT~~n 110 (111)
+.+++++.+.. .+++.=||||-||.+-.... .+.+ ..++..++++|.+.|
T Consensus 134 ~~~~ii~~l~~---~~~~~lVVIDsLq~l~~~~~--~~el---~~~~~~Lk~~Ak~~g 183 (237)
T PRK05973 134 CADYIIARLAS---APRGTLVVIDYLQLLDQRRE--KPDL---SVQVRALKSFARERG 183 (237)
T ss_pred CHHHHHHHHHH---hhCCCEEEEEcHHHHhhccc--chhH---HHHHHHHHHHHHhCC
Confidence 44555554443 57889999999999853321 1223 233566888887765
No 77
>TIGR01618 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.
Probab=38.15 E-value=53 Score=25.90 Aligned_cols=38 Identities=8% Similarity=0.042 Sum_probs=23.6
Q ss_pred eccccCCchHHHHHHHHHHHH-HhccceEEecchhhhhc
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMY-VYDTGHVIIDNVQFMLG 83 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avy-v~dI~HViiDNLQFmmg 83 (111)
..+-...++..++|.++++-. ..+..-|||||+.-|-.
T Consensus 57 ~~~d~~~~~~~~~d~l~~~~~~~~~ydtVVIDsI~~l~~ 95 (220)
T TIGR01618 57 ADHDDMPPIQAMVEFYVMQNIQAVKYDNIVIDNISALQN 95 (220)
T ss_pred eecCCCCCHHHHHHHHHHHHhccccCCEEEEecHHHHHH
Confidence 444455566677777664421 34456699999976543
No 78
>PF00535 Glycos_transf_2: Glycosyl transferase family 2; InterPro: IPR001173 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. This domain is found in a diverse family of glycosyl transferases that transfer the sugar from UDP-glucose, UDP-N-acetyl-galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids.; PDB: 2Z87_A 2Z86_B 2D7R_A 2D7I_A 3CKN_A 3CKQ_A 3CKJ_A 3CKV_A 3CKO_A 2FFU_A ....
Probab=37.78 E-value=36 Score=22.06 Aligned_cols=29 Identities=7% Similarity=-0.051 Sum_probs=22.7
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEecc
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIIDN 77 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiDN 77 (111)
|.+...+.+.++.+... ...+++-||+||
T Consensus 7 ~n~~~~l~~~l~sl~~q-~~~~~eiivvdd 35 (169)
T PF00535_consen 7 YNEAEYLERTLESLLKQ-TDPDFEIIVVDD 35 (169)
T ss_dssp SS-TTTHHHHHHHHHHH-SGCEEEEEEEEC
T ss_pred eCCHHHHHHHHHHHhhc-cCCCEEEEEecc
Confidence 45567788888888888 777888888887
No 79
>cd06442 DPM1_like DPM1_like represents putative enzymes similar to eukaryotic DPM1. Proteins similar to eukaryotic DPM1, including enzymes from bacteria and archaea; DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. In lower eukaryotes, such as Saccharomyces cerevisiae and Trypanosoma brucei, DPM synthase consists of a single component (Dpm1p and TbDpm1, respectively) that possesses one predicted transmembrane region near the C terminus for anchoring to the ER membrane. In contrast, the Dpm1 homologues of higher eukaryotes, namely fission yeast, fungi,
Probab=37.42 E-value=29 Score=24.67 Aligned_cols=30 Identities=13% Similarity=0.137 Sum_probs=23.8
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEecc
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIIDN 77 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiDN 77 (111)
|+....+...++.+....+-.+++-||+||
T Consensus 6 yn~~~~l~~~l~sl~~q~~~~~~eiiiVDd 35 (224)
T cd06442 6 YNERENIPELIERLDAALKGIDYEIIVVDD 35 (224)
T ss_pred cchhhhHHHHHHHHHHhhcCCCeEEEEEeC
Confidence 555667888888888877756888999998
No 80
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=34.41 E-value=1.1e+02 Score=24.60 Aligned_cols=56 Identities=18% Similarity=0.131 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHH-hccceEEecchhhhhcCCCcc----hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 55 IHLDLAVEHAMYV-YDTGHVIIDNVQFMLGLSDSA----LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 55 ~~V~dam~~avyv-~dI~HViiDNLQFmmg~~~~~----~drf~~QD~~I~~fR~fAT~~n 110 (111)
..+++.++..+-- +++.=||||-+..+.-..-.+ .+|-..=.+.+..++++|.++|
T Consensus 183 ~~~~~~l~~~i~~~~~~~lvVIDSisa~~~~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 243 (317)
T PRK04301 183 MLLAEKAEELIKEGENIKLVIVDSLTAHFRAEYVGRGNLAERQQKLNKHLHDLLRLADLYN 243 (317)
T ss_pred HHHHHHHHHHHhccCceeEEEEECchHHhhhhccCCccHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4556666666655 789999999999875432111 2232212345677888887765
No 81
>KOG1578|consensus
Probab=33.05 E-value=26 Score=29.34 Aligned_cols=23 Identities=17% Similarity=0.260 Sum_probs=20.0
Q ss_pred chHHHHHHHHHHHHHhccceEEe
Q psy16186 53 SMIHLDLAVEHAMYVYDTGHVII 75 (111)
Q Consensus 53 ~i~~V~dam~~avyv~dI~HVii 75 (111)
....+..||||||-.+.|++||+
T Consensus 136 ~~~~~~AalE~aV~~lkvenIiv 158 (276)
T KOG1578|consen 136 KPTNVGAALEYAVTTLKVENIIV 158 (276)
T ss_pred CcccccchHHHHHHHhccceEEE
Confidence 34567799999999999999996
No 82
>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....
Probab=32.77 E-value=37 Score=23.20 Aligned_cols=31 Identities=10% Similarity=0.111 Sum_probs=21.7
Q ss_pred hHHHHHHHHHH-HHHhccceEEecchhhhhcC
Q psy16186 54 MIHLDLAVEHA-MYVYDTGHVIIDNVQFMLGL 84 (111)
Q Consensus 54 i~~V~dam~~a-vyv~dI~HViiDNLQFmmg~ 84 (111)
.+.+.+.+.+. .....+..|||||++-+...
T Consensus 103 ~~~l~~~~~~~~~~~~~~~~iViDE~h~l~~~ 134 (169)
T PF00270_consen 103 PEQLLDLISNGKINISRLSLIVIDEAHHLSDE 134 (169)
T ss_dssp HHHHHHHHHTTSSTGTTESEEEEETHHHHHHT
T ss_pred cchhhccccccccccccceeeccCcccccccc
Confidence 34556666651 24566999999999988775
No 83
>PF13479 AAA_24: AAA domain
Probab=31.33 E-value=69 Score=24.14 Aligned_cols=30 Identities=17% Similarity=0.234 Sum_probs=23.4
Q ss_pred CchHHHHHHHHHH-HHHhccceEEecchhhh
Q psy16186 52 SSMIHLDLAVEHA-MYVYDTGHVIIDNVQFM 81 (111)
Q Consensus 52 ~~i~~V~dam~~a-vyv~dI~HViiDNLQFm 81 (111)
.++.+++++++.. -...+.+-||||++-.|
T Consensus 50 ~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~ 80 (213)
T PF13479_consen 50 TSWEDFLEALDELEEDEADYDTIVIDSISWL 80 (213)
T ss_pred CCHHHHHHHHHHHHhccCCCCEEEEECHHHH
Confidence 3788888888764 33589999999999765
No 84
>cd06913 beta3GnTL1_like Beta 1, 3-N-acetylglucosaminyltransferase is essential for the formation of poly-N-acetyllactosamine . This family includes human Beta3GnTL1 and related eukaryotic proteins. Human Beta3GnTL1 is a putative beta-1,3-N-acetylglucosaminyltransferase. Beta3GnTL1 is expressed at various levels in most of tissues examined. Beta 1, 3-N-acetylglucosaminyltransferase has been found to be essential for the formation of poly-N-acetyllactosamine. Poly-N-acetyllactosamine is a unique carbohydrate composed of N-acetyllactosamine repeats. It is often an important part of cell-type-specific oligosaccharide structures and some functional oligosaccharides. It has been shown that the structure and biosynthesis of poly-N-acetyllactosamine display a dramatic change during development and oncogenesis. Several members of beta-1, 3-N-acetylglucosaminyltransferase have been identified.
Probab=29.26 E-value=31 Score=24.90 Aligned_cols=30 Identities=3% Similarity=-0.175 Sum_probs=18.7
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEecc
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIIDN 77 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiDN 77 (111)
|++...+.+.++.+....|-.+++-||+||
T Consensus 6 yn~~~~l~~~l~sl~~q~~~~~~eiiVvDd 35 (219)
T cd06913 6 HNGEQWLDECLESVLQQDFEGTLELSVFND 35 (219)
T ss_pred cCcHHHHHHHHHHHHhCCCCCCEEEEEEeC
Confidence 344555666777665555544577777776
No 85
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=28.03 E-value=99 Score=21.87 Aligned_cols=35 Identities=17% Similarity=0.170 Sum_probs=29.2
Q ss_pred ee-eccccCCchHHHHHHHHHHHHHhccceEE---ecch
Q psy16186 44 LW-LGLRCLSSMIHLDLAVEHAMYVYDTGHVI---IDNV 78 (111)
Q Consensus 44 l~-m~f~g~~~i~~V~dam~~avyv~dI~HVi---iDNL 78 (111)
|| +..+|.++..+|+.+++.+.-.|-=++|= |||.
T Consensus 47 mW~~p~~~~~~~~~Vl~el~~c~~~~p~~yVRlig~D~~ 85 (99)
T PF00101_consen 47 MWKLPMFGCTDPAQVLAELEACLAEHPGEYVRLIGFDNK 85 (99)
T ss_dssp EESSEBTTBSSHHHHHHHHHHHHHHSTTSEEEEEEEETT
T ss_pred cCCCCCcCCCCHHHHHHHHHHHHHhCCCceEEEEEEcCc
Confidence 55 67799999999999999999999877774 3654
No 86
>cd04187 DPM1_like_bac Bacterial DPM1_like enzymes are related to eukaryotic DPM1. A family of bacterial enzymes related to eukaryotic DPM1; Although the mechanism of eukaryotic enzyme is well studied, the mechanism of the bacterial enzymes is not well understood. The eukaryotic DPM1 is the catalytic subunit of eukaryotic Dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. The enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. This protein family belongs to Glycosyltransferase 2 superfamily.
Probab=27.26 E-value=71 Score=22.10 Aligned_cols=30 Identities=13% Similarity=0.166 Sum_probs=15.8
Q ss_pred cccCCchHHHHHHHHHHHH--HhccceEEecc
Q psy16186 48 LRCLSSMIHLDLAVEHAMY--VYDTGHVIIDN 77 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avy--v~dI~HViiDN 77 (111)
|.++..+..+++++....+ ...++-||+||
T Consensus 6 ~n~~~~l~~~l~sl~~~~~~~~~~~eiivvdd 37 (181)
T cd04187 6 YNEEENLPELYERLKAVLESLGYDYEIIFVDD 37 (181)
T ss_pred cCchhhHHHHHHHHHHHHHhcCCCeEEEEEeC
Confidence 3444556666666655554 23455555554
No 87
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=26.98 E-value=47 Score=26.56 Aligned_cols=12 Identities=42% Similarity=0.722 Sum_probs=11.1
Q ss_pred cceEEecchhhh
Q psy16186 70 TGHVIIDNVQFM 81 (111)
Q Consensus 70 I~HViiDNLQFm 81 (111)
+.=|.|||.||+
T Consensus 83 ~~~v~IDEaQF~ 94 (201)
T COG1435 83 VDCVLIDEAQFF 94 (201)
T ss_pred cCEEEEehhHhC
Confidence 888999999996
No 88
>TIGR02012 tigrfam_recA protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.
Probab=26.78 E-value=2.1e+02 Score=23.86 Aligned_cols=50 Identities=10% Similarity=-0.026 Sum_probs=35.2
Q ss_pred HHHHHHhccCCCee-eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhc
Q psy16186 32 SEWEMVLQSSQPLW-LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLG 83 (111)
Q Consensus 32 ~e~e~~f~~~lPl~-m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg 83 (111)
.+++..+. +.+- +-.....+.++.++.++..+--.++.-||||-+.-+..
T Consensus 97 ~~~a~~lG--vd~~~l~v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~al~~ 147 (321)
T TIGR02012 97 PVYARKLG--VDIDNLLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVAALVP 147 (321)
T ss_pred HHHHHHcC--CCHHHeEEecCCCHHHHHHHHHHHhhccCCcEEEEcchhhhcc
Confidence 44555443 3332 33444567888888888888778999999999998765
No 89
>PRK09302 circadian clock protein KaiC; Reviewed
Probab=26.47 E-value=2e+02 Score=24.63 Aligned_cols=32 Identities=9% Similarity=0.161 Sum_probs=27.3
Q ss_pred CchHHHHHHHHHHHHHhccceEEecchhhhhc
Q psy16186 52 SSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLG 83 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~dI~HViiDNLQFmmg 83 (111)
.++++.++.+..++.-++...||||.|.-+.-
T Consensus 346 ~~~~~~~~~i~~~i~~~~~~~vVIDslt~l~~ 377 (509)
T PRK09302 346 YGLEDHLIIIKREIEEFKPSRVAIDPLSALAR 377 (509)
T ss_pred CCHHHHHHHHHHHHHHcCCCEEEEcCHHHHHH
Confidence 35688889999999999999999999987653
No 90
>PF13173 AAA_14: AAA domain
Probab=25.87 E-value=38 Score=23.18 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=12.2
Q ss_pred ccceEEecchhhhh
Q psy16186 69 DTGHVIIDNVQFML 82 (111)
Q Consensus 69 dI~HViiDNLQFmm 82 (111)
+-.+|+|||+|.+=
T Consensus 61 ~~~~i~iDEiq~~~ 74 (128)
T PF13173_consen 61 GKKYIFIDEIQYLP 74 (128)
T ss_pred CCcEEEEehhhhhc
Confidence 77899999999883
No 91
>PF11328 DUF3130: Protein of unknown function (DUF3130; InterPro: IPR021477 This bacterial family of proteins has no known function.
Probab=25.63 E-value=71 Score=22.78 Aligned_cols=53 Identities=23% Similarity=0.201 Sum_probs=42.3
Q ss_pred CCCee---eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcc----hhhhHHHHHHHH
Q psy16186 41 SQPLW---LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSA----LDRFYMQDTIIQ 100 (111)
Q Consensus 41 ~lPl~---m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~----~drf~~QD~~I~ 100 (111)
-+||. |.|+..-||++.-+||.--|.+ +|+.|=........ ...|..||+-++
T Consensus 27 y~plK~gnMaysraNsin~~r~Al~dLv~~-------Ve~fq~v~~~DA~RlkkmG~a~~kqD~~lg 86 (90)
T PF11328_consen 27 YLPLKNGNMAYSRANSINQLRTALIDLVDV-------VENFQQVVKKDASRLKKMGKAFTKQDQKLG 86 (90)
T ss_pred cccccCCCeehhhhhhHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47886 9999999999999999988875 57888777766532 467899998765
No 92
>cd07019 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-te
Probab=25.08 E-value=1.3e+02 Score=22.87 Aligned_cols=29 Identities=3% Similarity=-0.113 Sum_probs=26.3
Q ss_pred cccCCchHHHHHHHHHHHHHhccceEEec
Q psy16186 48 LRCLSSMIHLDLAVEHAMYVYDTGHVIID 76 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv~dI~HViiD 76 (111)
..|.++..++.++++.|-.--+|.-|||+
T Consensus 17 ~~~~~~~~~l~~~l~~a~~d~~v~~ivL~ 45 (211)
T cd07019 17 TQGNVGGDTTAAQIRDARLDPKVKAIVLR 45 (211)
T ss_pred CCCccCHHHHHHHHHHHhhCCCceEEEEE
Confidence 44678899999999999999999999997
No 93
>PRK11054 helD DNA helicase IV; Provisional
Probab=25.00 E-value=60 Score=29.66 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHhccceEEecchhhhh
Q psy16186 56 HLDLAVEHAMYVYDTGHVIIDNVQFML 82 (111)
Q Consensus 56 ~V~dam~~avyv~dI~HViiDNLQFmm 82 (111)
..++.++..-+.....||+||+.|..-
T Consensus 417 ~A~~lL~~~~~~~~~~~IlVDE~QD~s 443 (684)
T PRK11054 417 QAVNYLEKGRFISPWKHILVDEFQDIS 443 (684)
T ss_pred HHHHHHhhhhhhhcccEEEEEccccCC
Confidence 334445555566678999999998753
No 94
>cd04188 DPG_synthase DPG_synthase is involved in protein N-linked glycosylation. UDP-glucose:dolichyl-phosphate glucosyltransferase (DPG_synthase) is a transmembrane-bound enzyme of the endoplasmic reticulum involved in protein N-linked glycosylation. This enzyme catalyzes the transfer of glucose from UDP-glucose to dolichyl phosphate.
Probab=24.55 E-value=65 Score=23.04 Aligned_cols=30 Identities=3% Similarity=-0.032 Sum_probs=19.0
Q ss_pred cccCCchHHHHHHHHHHHHH---hccceEEecc
Q psy16186 48 LRCLSSMIHLDLAVEHAMYV---YDTGHVIIDN 77 (111)
Q Consensus 48 f~g~~~i~~V~dam~~avyv---~dI~HViiDN 77 (111)
|+....+.++++.+....+- .+.+-||+||
T Consensus 6 yN~~~~l~~~l~~l~~~~~~~~~~~~eiivvdd 38 (211)
T cd04188 6 YNEEKRLPPTLEEAVEYLEERPSFSYEIIVVDD 38 (211)
T ss_pred cChHHHHHHHHHHHHHHHhccCCCCEEEEEEeC
Confidence 34445567777777665553 5677777775
No 95
>PTZ00035 Rad51 protein; Provisional
Probab=23.69 E-value=1.9e+02 Score=23.90 Aligned_cols=63 Identities=14% Similarity=0.058 Sum_probs=37.6
Q ss_pred cccCCchHHHHHHHHHH---HHHhccceEEecchhhhhcCCCc--c--hhhhHHHHHHHHHHHhhhcCCC
Q psy16186 48 LRCLSSMIHLDLAVEHA---MYVYDTGHVIIDNVQFMLGLSDS--A--LDRFYMQDTIIQVLLYFLSLPN 110 (111)
Q Consensus 48 f~g~~~i~~V~dam~~a---vyv~dI~HViiDNLQFmmg~~~~--~--~drf~~QD~~I~~fR~fAT~~n 110 (111)
+....+.++.++.+..+ +....+.=||||-+..+.-.... + .+|-..=-+++..++++|.++|
T Consensus 189 ~~~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la~~~~ 258 (337)
T PTZ00035 189 YARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLADEFN 258 (337)
T ss_pred EEccCCHHHHHHHHHHHHHHhhccCccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHHHHcC
Confidence 33444555555554332 23478999999999987654221 1 2232222457788899988765
No 96
>PRK14464 ribosomal RNA large subunit methyltransferase N; Provisional
Probab=23.03 E-value=1.6e+02 Score=24.88 Aligned_cols=45 Identities=11% Similarity=0.196 Sum_probs=27.6
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecchhhhhcCCCcchhhhHHHHHHHHHHHhh
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLLYF 105 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR~f 105 (111)
.-+..++++.+.++.--..|.+|| .||.+. .++.+ |.++.++|.+
T Consensus 123 nLs~~EI~~Qv~~~~~~~~i~nIV------fmGmGE-Pl~N~---d~vl~ai~~l 167 (344)
T PRK14464 123 QLGSAEIVAQVVLARRRRAVKKVV------FMGMGE-PAHNL---DNVLEAIDLL 167 (344)
T ss_pred CCCHHHHHHHHHHHHhcCCCCEEE------EeccCc-ccCCH---HHHHHHHHHh
Confidence 336688888888776544455555 456553 34444 6777776654
No 97
>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange.
Probab=22.74 E-value=4e+02 Score=22.34 Aligned_cols=51 Identities=10% Similarity=-0.026 Sum_probs=36.6
Q ss_pred HHHHHHhccCCCee-eccccCCchHHHHHHHHHHHHHhccceEEecchhhhhcC
Q psy16186 32 SEWEMVLQSSQPLW-LGLRCLSSMIHLDLAVEHAMYVYDTGHVIIDNVQFMLGL 84 (111)
Q Consensus 32 ~e~e~~f~~~lPl~-m~f~g~~~i~~V~dam~~avyv~dI~HViiDNLQFmmg~ 84 (111)
.+++..++ +++- +-+.-..+.++.++.++..+--.++.-||||-+..+...
T Consensus 97 ~~~a~~lG--vd~~~l~v~~p~~~eq~l~i~~~li~s~~~~lIVIDSvaal~~~ 148 (325)
T cd00983 97 PVYAKKLG--VDLDNLLISQPDTGEQALEIADSLVRSGAVDLIVVDSVAALVPK 148 (325)
T ss_pred HHHHHHcC--CCHHHheecCCCCHHHHHHHHHHHHhccCCCEEEEcchHhhccc
Confidence 44555443 3332 334445578889999988888889999999999988753
No 98
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=21.72 E-value=1.4e+02 Score=21.29 Aligned_cols=33 Identities=18% Similarity=0.079 Sum_probs=26.9
Q ss_pred eccccCCchHHHHHHHHHHHHHhccceE---Eecch
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVYDTGHV---IIDNV 78 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~dI~HV---iiDNL 78 (111)
+-.+|.++..+|+.+++.+.-.|-=.+| =+||.
T Consensus 51 lP~f~~~d~~~Vl~ei~~C~~~~p~~YVRliG~D~~ 86 (99)
T cd03527 51 LPMFGCTDPAQVLREIEACRKAYPDHYVRVVGFDNY 86 (99)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCeEEEEEEeCC
Confidence 5668999999999999999999986665 45553
No 99
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=21.67 E-value=1.2e+02 Score=22.68 Aligned_cols=31 Identities=13% Similarity=0.066 Sum_probs=26.0
Q ss_pred CchHHHHHHHHHHHHHhccceEEecchhhhh
Q psy16186 52 SSMIHLDLAVEHAMYVYDTGHVIIDNVQFML 82 (111)
Q Consensus 52 ~~i~~V~dam~~avyv~dI~HViiDNLQFmm 82 (111)
...+++++.+..++.-++..-||||++-.+.
T Consensus 103 ~~~~~ll~~l~~~i~~~~~~~iviDs~t~~~ 133 (234)
T PRK06067 103 TLANKLLELIIEFIKSKREDVIIIDSLTIFA 133 (234)
T ss_pred chHHHHHHHHHHHHHhcCCCEEEEecHHHHH
Confidence 4567889999998888999999999997553
No 100
>PLN02726 dolichyl-phosphate beta-D-mannosyltransferase
Probab=21.35 E-value=83 Score=23.37 Aligned_cols=32 Identities=9% Similarity=0.044 Sum_probs=19.1
Q ss_pred eccccCCchHHHHHHHHHHHHHh-ccceEEecc
Q psy16186 46 LGLRCLSSMIHLDLAVEHAMYVY-DTGHVIIDN 77 (111)
Q Consensus 46 m~f~g~~~i~~V~dam~~avyv~-dI~HViiDN 77 (111)
-.|+....|..+++.+.....-+ +++-||+||
T Consensus 16 p~yne~~~l~~~l~~l~~~~~~~~~~eiivvDd 48 (243)
T PLN02726 16 PTYNERLNIALIVYLIFKALQDVKDFEIIVVDD 48 (243)
T ss_pred ccCCchhhHHHHHHHHHHHhccCCCeEEEEEeC
Confidence 34555666666666665544333 667777775
No 101
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=20.50 E-value=1e+02 Score=27.01 Aligned_cols=28 Identities=36% Similarity=0.463 Sum_probs=24.0
Q ss_pred CCchHHHHHHHHHHHHHhccceEEecch
Q psy16186 51 LSSMIHLDLAVEHAMYVYDTGHVIIDNV 78 (111)
Q Consensus 51 ~~~i~~V~dam~~avyv~dI~HViiDNL 78 (111)
..+..++.++++++.+..+..+|+||--
T Consensus 267 ~~dp~dL~~al~~l~~~~~~D~VLIDTA 294 (407)
T PRK12726 267 ATSPAELEEAVQYMTYVNCVDHILIDTV 294 (407)
T ss_pred cCCHHHHHHHHHHHHhcCCCCEEEEECC
Confidence 4577889999999988888999999964
No 102
>KOG2884|consensus
Probab=20.12 E-value=1.7e+02 Score=24.38 Aligned_cols=32 Identities=22% Similarity=0.300 Sum_probs=25.8
Q ss_pred ceEEecchhhhhcCCCcchhhhHHHHHHHHHHH
Q psy16186 71 GHVIIDNVQFMLGLSDSALDRFYMQDTIIQVLL 103 (111)
Q Consensus 71 ~HViiDNLQFmmg~~~~~~drf~~QD~~I~~fR 103 (111)
.-|+|||=-+|-.+. ..=-||.+|-.+|..+=
T Consensus 6 tmi~iDNse~mrNgD-y~PtRf~aQ~daVn~v~ 37 (259)
T KOG2884|consen 6 TMICIDNSEYMRNGD-YLPTRFQAQKDAVNLVC 37 (259)
T ss_pred EEEEEeChHHhhcCC-CChHHHHHHHHHHHHHH
Confidence 458999999998876 45689999998887653
Done!